[med-svn] [gdcm] 01/07: Imported Upstream version 2.6.2
Gert Wollny
gert-guest at moszumanska.debian.org
Fri Jan 8 21:08:31 UTC 2016
This is an automated email from the git hooks/post-receive script.
gert-guest pushed a commit to branch master
in repository gdcm.
commit 60a3cd553da9934c95d8c09fec74619e7e9efe86
Author: Gert Wollny <gw.fossdev at gmail.com>
Date: Fri Jan 8 17:17:32 2016 +0100
Imported Upstream version 2.6.2
---
.gitattributes | 1 +
.travis.yml | 4 +-
Applications/Cxx/gdcmimg.cxx | 2 +-
CMakeLists.txt | 6 +-
Source/Common/gdcmBoxRegion.cxx | 22 +-
Source/Common/gdcmFilename.h | 2 +-
Source/Common/gdcmTrace.h | 2 +-
Source/DataDictionary/gdcmPrivateDefaultDicts.cxx | 15 +-
.../gdcmCP246ExplicitDataElement.txx | 2 +-
.../gdcmDataElement.h | 2 +-
.../gdcmDataSet.cxx | 2 +-
.../gdcmDataSet.h | 7 +-
.../gdcmElement.h | 2 +-
.../gdcmExplicitDataElement.txx | 2 +-
.../gdcmExplicitImplicitDataElement.txx | 2 +-
.../gdcmFileMetaInformation.cxx | 2 +-
.../gdcmMediaStorage.cxx | 6 +-
.../gdcmUNExplicitDataElement.txx | 2 +-
.../DataStructureAndEncodingDefinition/gdcmVR.cxx | 9 +-
.../gdcmVR16ExplicitDataElement.txx | 2 +-
.../gdcmFileChangeTransferSyntax.h | 2 +-
Source/MediaStorageAndFileFormat/gdcmIPPSorter.h | 2 +-
.../gdcmIconImageFilter.cxx | 6 +-
Source/MediaStorageAndFileFormat/gdcmImage.cxx | 4 +-
.../MediaStorageAndFileFormat/gdcmImageCodec.cxx | 4 +-
Source/MediaStorageAndFileFormat/gdcmImageCodec.h | 2 +-
.../MediaStorageAndFileFormat/gdcmImageHelper.cxx | 27 +-
Source/MediaStorageAndFileFormat/gdcmImageHelper.h | 9 +
.../gdcmImageRegionReader.cxx | 43 +-
.../MediaStorageAndFileFormat/gdcmImageWriter.cxx | 15 +-
Source/MediaStorageAndFileFormat/gdcmImageWriter.h | 3 +
.../gdcmJPEG2000Codec.cxx | 22 +-
.../gdcmJPEGBITSCodec.cxx | 4 +-
.../MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx | 14 +-
Source/MediaStorageAndFileFormat/gdcmOverlay.cxx | 2 +
Source/MediaStorageAndFileFormat/gdcmOverlay.h | 2 +-
.../gdcmPhotometricInterpretation.cxx | 6 +-
.../gdcmPhotometricInterpretation.h | 4 +-
.../MediaStorageAndFileFormat/gdcmPixmapReader.cxx | 31 +-
.../MediaStorageAndFileFormat/gdcmPixmapWriter.cxx | 2 +-
.../gdcmStreamImageReader.cxx | 6 +-
.../gdcmSurfaceHelper.cxx | 84 +-
.../MediaStorageAndFileFormat/gdcmSurfaceHelper.h | 24 +-
.../MediaStorageAndFileFormat/gdcmUIDGenerator.cxx | 1 +
Source/MediaStorageAndFileFormat/gdcmXMLPrinter.h | 4 +-
.../Cxx/TestAttribute1.cxx | 4 +-
.../Cxx/TestSurfaceWriter2.cxx | 2 +-
Utilities/VTK/VTK4/vtkMedicalImageProperties.h | 2 +-
Utilities/VTK/vtkGDCMImageReader.cxx | 2 +-
Utilities/VTK/vtkGDCMImageReader2.cxx | 2 +-
Utilities/VTK/vtkGDCMMedicalImageProperties.h | 2 +-
Utilities/VTK/vtkRTStructSetProperties.h | 2 +-
Utilities/doxygen/CMakeLists.txt | 86 +-
Utilities/doxygen/doxyfile.in | 2434 ++++++++++++--------
Utilities/doxygen/man/gdcm2pnm.dox | 71 -
Utilities/doxygen/man/gdcm2pnm.xml | 82 +
Utilities/doxygen/man/gdcm2vtk.dox | 187 --
Utilities/doxygen/man/gdcm2vtk.xml | 184 ++
Utilities/doxygen/man/gdcmanon.dox | 288 ---
Utilities/doxygen/man/gdcmanon.xml | 278 +++
Utilities/doxygen/man/gdcmconv.dox | 396 ----
Utilities/doxygen/man/gdcmconv.xml | 404 ++++
Utilities/doxygen/man/gdcmdiff.dox | 68 -
Utilities/doxygen/man/gdcmdiff.xml | 82 +
.../doxygen/man/{gdcmdump.dox => gdcmdump.xml} | 389 ++--
Utilities/doxygen/man/gdcmgendir.dox | 92 -
Utilities/doxygen/man/gdcmgendir.xml | 107 +
Utilities/doxygen/man/gdcmimg.dox | 290 ---
Utilities/doxygen/man/gdcmimg.xml | 271 +++
Utilities/doxygen/man/gdcminfo.dox | 164 --
Utilities/doxygen/man/gdcminfo.xml | 170 ++
Utilities/doxygen/man/gdcmpap3.dox | 93 -
Utilities/doxygen/man/gdcmpap3.xml | 99 +
Utilities/doxygen/man/{gdcmpdf.dox => gdcmpdf.xml} | 154 +-
Utilities/doxygen/man/gdcmraw.dox | 213 --
Utilities/doxygen/man/gdcmraw.xml | 221 ++
Utilities/doxygen/man/gdcmscanner.dox | 79 -
Utilities/doxygen/man/gdcmscanner.xml | 91 +
Utilities/doxygen/man/gdcmscu.dox | 341 ---
Utilities/doxygen/man/gdcmscu.xml | 318 +++
Utilities/doxygen/man/gdcmtar.dox | 137 --
Utilities/doxygen/man/gdcmtar.xml | 147 ++
Utilities/doxygen/man/gdcmviewer.dox | 88 -
Utilities/doxygen/man/gdcmviewer.xml | 109 +
Utilities/doxygen/man/gdcmxml.dox | 77 -
Utilities/doxygen/man/gdcmxml.xml | 86 +
Utilities/gdcmrle/info.h | 2 +-
Utilities/gdcmrle/rle.cxx | 4 +-
Wrapping/Python/docstrings.i | 742 ++++--
appveyor.yml | 149 +-
90 files changed, 5485 insertions(+), 4141 deletions(-)
diff --git a/.gitattributes b/.gitattributes
index 325b352..049993f 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,3 +1,4 @@
+appveyor.yml merge=ours
* -whitespace
/Source/DataDictionary/gdcmDefaultDicts.cxx hooks.MaxObjectKiB=2048
diff --git a/.travis.yml b/.travis.yml
index 05a60d5..9c3b659 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -23,8 +23,8 @@ matrix:
- compiler: clang
os: linux
env:
- - CFLAGS="-Wall -Wextra -m64 -fsanitize=address,undefined"
- - CXXFLAGS="-Wall -Wextra -m64 -fsanitize=address,undefined"
+ - CFLAGS="-Wall -Wextra -m64 -fsanitize=address,undefined,shift"
+ - CXXFLAGS="-g -Wall -Wextra -m64 -fsanitize=address,undefined,shift"
- B_NAME=fsanitize
- compiler: clang
os: osx
diff --git a/Applications/Cxx/gdcmimg.cxx b/Applications/Cxx/gdcmimg.cxx
index 636c433..345b1ce 100644
--- a/Applications/Cxx/gdcmimg.cxx
+++ b/Applications/Cxx/gdcmimg.cxx
@@ -818,7 +818,7 @@ int main (int argc, char *argv[])
if( pinter )
{
refpi = gdcm::PhotometricInterpretation::GetPIType( pinterstr.c_str() );
- if( refpi == gdcm::PhotometricInterpretation::UNKNOW
+ if( refpi == gdcm::PhotometricInterpretation::UNKNOWN
|| refpi == gdcm::PhotometricInterpretation::PI_END )
{
std::cerr << "Invalid PI: " << pinterstr << std::endl;
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6b88677..e33645a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,7 +32,7 @@ set(GDCM_PACKAGE_CONTACT "GDCM Developers <gdcm-developers at lists.sourceforge.net
#----------------------------------------------------------------------------
set(GDCM_MAJOR_VERSION 2)
set(GDCM_MINOR_VERSION 6)
-set(GDCM_BUILD_VERSION 1)
+set(GDCM_BUILD_VERSION 2)
set(GDCM_VERSION
"${GDCM_MAJOR_VERSION}.${GDCM_MINOR_VERSION}.${GDCM_BUILD_VERSION}")
# let advanced user the option to define GDCM_API_VERSION:
@@ -524,8 +524,8 @@ if(GDCM_STANDALONE)
option(GDCM_USE_JPEGLS "Build GDCM with JPEG-LS support" ON)
mark_as_advanced(GDCM_USE_JPEGLS)
if(GDCM_WRAP_JAVA)
- set(GDCM_JAVA_SOURCE_VERSION "1.5" CACHE STRING "javac source version")
- set(GDCM_JAVA_TARGET_VERSION "1.5" CACHE STRING "javac target version")
+ set(GDCM_JAVA_SOURCE_VERSION "1.7" CACHE STRING "javac source version")
+ set(GDCM_JAVA_TARGET_VERSION "1.7" CACHE STRING "javac target version")
mark_as_advanced(GDCM_JAVA_SOURCE_VERSION GDCM_JAVA_TARGET_VERSION)
endif()
if(GDCM_WRAP_CSHARP)
diff --git a/Source/Common/gdcmBoxRegion.cxx b/Source/Common/gdcmBoxRegion.cxx
index 98c274b..f0d4960 100644
--- a/Source/Common/gdcmBoxRegion.cxx
+++ b/Source/Common/gdcmBoxRegion.cxx
@@ -79,14 +79,30 @@ bool BoxRegion::IsValid() const
{
return false;
}
+ // Some properly crafted DICOM could have bigger values, reject them:
+ // technically there is no such restrictions for Z direction
+ if (Internals->XMax >= std::numeric_limits<uint16_t>::max() ||
+ Internals->YMax >= std::numeric_limits<uint16_t>::max() ||
+ Internals->ZMax == std::numeric_limits<uint32_t>::max() )
+ {
+ return false;
+ }
return true;
}
size_t BoxRegion::Area() const
{
- return (Internals->YMax - Internals->YMin + 1)*
- (Internals->XMax - Internals->XMin + 1)*
- (Internals->ZMax - Internals->ZMin + 1);
+ // on some system size_t is too small:
+ const uint64_t A = Internals->XMax - Internals->XMin + 1;
+ const uint64_t B = Internals->YMax - Internals->YMin + 1;
+ const uint64_t C = Internals->ZMax - Internals->ZMin + 1;
+ const uint64_t tmp = A * B;
+ if (tmp != 0 && (std::numeric_limits<size_t>::max() / tmp) < C)
+ {
+ // multiplication exceed range of unsigned
+ return 0;
+ }
+ return tmp * C;
}
unsigned int BoxRegion::GetXMin() const
diff --git a/Source/Common/gdcmFilename.h b/Source/Common/gdcmFilename.h
index d380371..f90a067 100644
--- a/Source/Common/gdcmFilename.h
+++ b/Source/Common/gdcmFilename.h
@@ -39,7 +39,7 @@ public:
const char *GetExtension();
/// Convert backslash (windows style) to UNIX style slash.
const char *ToUnixSlashes();
- /// Convert foward slash (UNIX style) to windows style slash.
+ /// Convert forward slash (UNIX style) to windows style slash.
const char *ToWindowsSlashes();
/// Join two paths
diff --git a/Source/Common/gdcmTrace.h b/Source/Common/gdcmTrace.h
index fb8e209..41e48ce 100644
--- a/Source/Common/gdcmTrace.h
+++ b/Source/Common/gdcmTrace.h
@@ -106,7 +106,7 @@ private:
# define GDCM_FUNCTION __FUNCTION__
#endif //__GNUC__
#else
-# define GDCM_FUNCTION "<unknow>"
+# define GDCM_FUNCTION "<unknown>"
#endif //GDCM_CXX_HAS_FUNCTION
/**
diff --git a/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx b/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
index cb2c144..fd5b719 100644
--- a/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
+++ b/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
@@ -37,9 +37,10 @@ typedef struct
} DICT_ENTRY;
static const DICT_ENTRY DICOMV3DataDict [] = {
+ {0x0029,0x0004,"TELEMIS",VR::US,VM::VM1,"?",false },
{0x3129,0x0010,"RamSoft Race Identifier",VR::LO,VM::VM1,"?",false },
{0x7501,0x0001,"CoActiv_PvtTags",VR::LO,VM::VM1,"?",false },
- {0x7501,0x0002,"CoActiv_PvtTags",VR::LO,VM::VM1,"?IP Adress?",false },
+ {0x7501,0x0002,"CoActiv_PvtTags",VR::LO,VM::VM1,"?IP Address?",false },
{0x7501,0x0003,"CoActiv_PvtTags",VR::UI,VM::VM1,"?Transfer Syntax UID?",false },
{0x7501,0x0004,"CoActiv_PvtTags",VR::LO,VM::VM1,"?Transfer Syntax Name?",false },
{0x0009,0x0002,"PMTF INFORMATION DATA^10",VR::SH,VM::VM1,"?",false },
@@ -3150,7 +3151,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
{0x0043,0x0036,"GEMS_PARM_01",VR::UL,VM::VM1,"User_fill_map_MSW",false },
{0x0043,0x0037,"GEMS_PARM_01",VR::UL,VM::VM1,"User_fill_map_LSW",false },
{0x0043,0x0038,"GEMS_PARM_01",VR::FL,VM::VM24,"User data 25...User data 48 {User48=Effective Resolution for spiral}",false },
- {0x0043,0x0039,"GEMS_PARM_01",VR::IS,VM::VM4,"Slop_int_6... slop_int_9",false },
+ {0x0043,0x0039,"GEMS_PARM_01",VR::IS,VM::VM4,"Slop_int_6... slop_int_9 (B_value/?/?/?)",false },
{0x0043,0x0040,"GEMS_PARM_01",VR::FL,VM::VM4,"Trigger on position",false },
{0x0043,0x0041,"GEMS_PARM_01",VR::FL,VM::VM4,"Degree of rotation",false },
{0x0043,0x0042,"GEMS_PARM_01",VR::SL,VM::VM4,"DAS trigger source",false },
@@ -5249,7 +5250,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
{0x2001,0x003e,"Philips Imaging DD 002",VR::SS,VM::VM1,"?",false },
{0x2001,0x003f,"Philips Imaging DD 002",VR::SS,VM::VM1,"?",false },
{0x2001,0x0040,"Philips Imaging DD 002",VR::SS,VM::VM1,"?",false },
- {0x2001,0x006b,"Philips Imaging DD 002",VR::OB,VM::VM1,"?",false },
+ {0x2001,0x006b,"Philips Imaging DD 002",VR::LO,VM::VM1,"?",false },
{0x4007,0x0000,"Philips Imaging DD 065",VR::CS,VM::VM1,"?",false },
{0x4001,0x0000,"Philips Imaging DD 067",VR::SQ,VM::VM1,"?",false },
{0x4001,0x0001,"Philips Imaging DD 067",VR::CS,VM::VM1,"?",false },
@@ -5264,7 +5265,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
{0x4001,0x001d,"Philips Imaging DD 070",VR::LT,VM::VM1,"?",false },
{0x4007,0x0048,"Philips Imaging DD 073",VR::FL,VM::VM1,"?",false },
{0x1001,0x0003,"Philips Imaging DD 124",VR::LO,VM::VM1,"?",false }, /* MR Import Filter 3/21/2014 1:57:35 PM */
- {0x2001,0x0000,"Philips Imaging DD 129",VR::SQ,VM::VM1,"?",false },
+ {0x2001,0x0000,"Philips Imaging DD 129",VR::SQ,VM::VM1,"PresentationStateSequence",false },
{0x2001,0x0001,"Philips Imaging DD 129",VR::SQ,VM::VM1,"?",false },
{0x2005,0x0000,"PHILIPS MR IMAGING DD 001",VR::FL,VM::VM1,"?AngulationAP?",false },
{0x2005,0x0001,"PHILIPS MR IMAGING DD 001",VR::FL,VM::VM1,"?AngulationFH?",false },
@@ -5458,7 +5459,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
{0x2005,0x002d,"Philips MR Imaging DD 001",VR::IS,VM::VM1,"PlanScanSurveyNumberOfImages", false },
{0x2005,0x002e,"Philips MR Imaging DD 001",VR::CS,VM::VM1,"PPGPPUGating", false },
{0x2005,0x002f,"Philips MR Imaging DD 001",VR::CS,VM::VM1,"SpatialPresaturation", false },
- {0x2005,0x0030,"Philips MR Imaging DD 001",VR::FL,VM::VM1,"Repetition Time",false },
+ {0x2005,0x0030,"Philips MR Imaging DD 001",VR::FL,VM::VM1_n,"Repetition Time",false },
{0x2005,0x0031,"Philips MR Imaging DD 001",VR::CS,VM::VM1,"RespiratoryGating", false },
{0x2005,0x0032,"Philips MR Imaging DD 001",VR::CS,VM::VM1,"?SampleRepresentation",false },
{0x2005,0x0033,"Philips MR Imaging DD 001",VR::FL,VM::VM1,"Scan Duration",false },
@@ -5711,7 +5712,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
{0x2005,0x0026,"Philips MR Imaging DD 005",VR::CS,VM::VM1,"ViewingHardcopyOnly", false },
{0x2005,0x0027,"Philips MR Imaging DD 005",VR::CS,VM::VM1,"?PrivateEMR",false },
{0x2005,0x0028,"Philips MR Imaging DD 005",VR::SL,VM::VM1,"MRSeriesNrOfLabelTypes", false },
- {0x2005,0x0029,"Philips MR Imaging DD 005",VR::OB,VM::VM1,"?MRImageLabelType",false },
+ {0x2005,0x0029,"Philips MR Imaging DD 005",VR::CS,VM::VM1,"?MRImageLabelType",false },
{0x2005,0x002a,"Philips MR Imaging DD 005",VR::CS,VM::VM1,"ExamPrintStatus", false },
{0x2005,0x002b,"Philips MR Imaging DD 005",VR::CS,VM::VM1,"ExamExportStatus", false },
{0x2005,0x002c,"Philips MR Imaging DD 005",VR::CS,VM::VM1,"ExamStorageCommitStatus", false },
@@ -5750,7 +5751,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
{0x2005,0x004f,"Philips MR Imaging DD 005",VR::CS,VM::VM1,"VolumeSelect", false },
{0x2005,0x0050,"Philips MR Imaging DD 005",VR::SS,VM::VM1,"MRNrOfPatientOtherIDs", false },
{0x2005,0x0055,"Philips MR Imaging DD 005",VR::FD,VM::VM3,"ImageVelocityEncodingDirection", false },
- {0x2005,0x0092,"Philips MR Imaging DD 005",VR::OB,VM::VM1,"?",false },
+ {0x2005,0x0092,"Philips MR Imaging DD 005",VR::FL,VM::VM1,"Specific Energy Dose",false },
/* new group */
{0x7043,0x0000,"Philips NM Private Group",VR::SH,VM::VM1,"?",false },
{0x0511,0x0000,"Philips PET Private Group",VR::US,VM::VM1,"?",false },
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmCP246ExplicitDataElement.txx b/Source/DataStructureAndEncodingDefinition/gdcmCP246ExplicitDataElement.txx
index faaae5a..355081c 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmCP246ExplicitDataElement.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmCP246ExplicitDataElement.txx
@@ -131,7 +131,7 @@ std::istream &CP246ExplicitDataElement::ReadValue(std::istream &is, bool readval
//assert( ValueField == 0 );
if( VRField == VR::SQ )
{
- // Check wether or not this is an undefined length sequence
+ // Check whether or not this is an undefined length sequence
assert( TagField != Tag(0x7fe0,0x0010) );
ValueField = new SequenceOfItems;
}
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmDataElement.h b/Source/DataStructureAndEncodingDefinition/gdcmDataElement.h
index f7292ca..ceedc25 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmDataElement.h
+++ b/Source/DataStructureAndEncodingDefinition/gdcmDataElement.h
@@ -91,7 +91,7 @@ public:
}
/// Set/Get Value (bytes array, SQ of items, SQ of fragments):
- Value const &GetValue() const { assert(ValueField); return *ValueField; }
+ Value const &GetValue() const { gdcmAssertAlwaysMacro(ValueField); return *ValueField; }
Value &GetValue() { return *ValueField; }
/// \warning you need to set the ValueLengthField explicitly
void SetValue(Value const & vl) {
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.cxx b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.cxx
index b63ed72..1d6cc3d 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.cxx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.cxx
@@ -148,7 +148,7 @@ MediaStorage DataSet::GetMediaStorage() const
MediaStorage ms = MediaStorage::GetMSType(ts.c_str());
if( ms == MediaStorage::MS_END )
{
- gdcmWarningMacro( "Media Storage Class UID: " << ts << " is unknow" );
+ gdcmWarningMacro( "Media Storage Class UID: " << ts << " is unknown" );
}
return ms;
}
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h
index 442e231..82745a2 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h
+++ b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h
@@ -148,12 +148,17 @@ public:
}
/// Replace a dataelement with another one
void Replace(const DataElement& de) {
- if( DES.find(de) != DES.end() ) DES.erase(de);
+ ConstIterator it = DES.find(de);
+ // detect loop:
+ gdcmAssertAlwaysMacro( &*it != &de );
+ if( it != DES.end() ) DES.erase(de);
DES.insert(de);
}
/// Only replace a DICOM attribute when it is missing or empty
void ReplaceEmpty(const DataElement& de) {
ConstIterator it = DES.find(de);
+ // detect loop:
+ gdcmAssertAlwaysMacro( &*it != &de );
if( it != DES.end() && it->IsEmpty() )
DES.erase(de);
DES.insert(de);
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmElement.h b/Source/DataStructureAndEncodingDefinition/gdcmElement.h
index 2edd8f9..d4ace85 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmElement.h
+++ b/Source/DataStructureAndEncodingDefinition/gdcmElement.h
@@ -273,7 +273,7 @@ std::string to_string ( Float data ) {
int const digits =
static_cast< int >(
- std::log( std::numeric_limits<Float>::epsilon() )
- / std::log( 10.0 ) );
+ / static_cast< Float >( std::log( 10.0 ) ) );
if ( in << std::dec << std::setprecision(/*2+*/digits) << data ) {
return ( in.str() );
} else {
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx b/Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx
index 1adc0c0..b5d32d2 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx
@@ -191,7 +191,7 @@ std::istream &ExplicitDataElement::ReadValue(std::istream &is, bool readvalues)
//assert( ValueField == 0 );
if( VRField == VR::SQ )
{
- // Check wether or not this is an undefined length sequence
+ // Check whether or not this is an undefined length sequence
assert( TagField != Tag(0x7fe0,0x0010) );
ValueField = new SequenceOfItems;
}
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmExplicitImplicitDataElement.txx b/Source/DataStructureAndEncodingDefinition/gdcmExplicitImplicitDataElement.txx
index 2cdc1a1..fafff32 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmExplicitImplicitDataElement.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmExplicitImplicitDataElement.txx
@@ -352,7 +352,7 @@ std::istream &ExplicitImplicitDataElement::ReadValue(std::istream &is, bool read
//assert( ValueField == 0 );
if( VRField == VR::SQ )
{
- // Check wether or not this is an undefined length sequence
+ // Check whether or not this is an undefined length sequence
assert( TagField != Tag(0x7fe0,0x0010) );
ValueField = new SequenceOfItems;
}
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmFileMetaInformation.cxx b/Source/DataStructureAndEncodingDefinition/gdcmFileMetaInformation.cxx
index 1d29b9c..b2687ad 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmFileMetaInformation.cxx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmFileMetaInformation.cxx
@@ -844,7 +844,7 @@ MediaStorage FileMetaInformation::GetMediaStorage() const
MediaStorage ms = MediaStorage::GetMSType(ts.c_str());
if( ms == MediaStorage::MS_END )
{
- gdcmWarningMacro( "Media Storage Class UID: " << ts << " is unknow" );
+ gdcmWarningMacro( "Media Storage Class UID: " << ts << " is unknown" );
}
return ms;
}
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmMediaStorage.cxx b/Source/DataStructureAndEncodingDefinition/gdcmMediaStorage.cxx
index 48ca00c..5a30639 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmMediaStorage.cxx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmMediaStorage.cxx
@@ -484,7 +484,9 @@ void MediaStorage::SetFromSourceImageSequence(DataSet const &ds)
bool MediaStorage::SetFromModality(DataSet const &ds)
{
// Ok let's try againg with little luck it contains a pixel data...
- if( ds.FindDataElement( Tag(0x7fe0,0x0010) ) )
+ // technically GDCM is called with a template DataSet before Pixel Data
+ // is even set, so do not check for presence of this attribute at this point
+ //if( ds.FindDataElement( Tag(0x7fe0,0x0010) ) )
{
// Pixel Data found !
// Attempt to recover from the modality (0008,0060):
@@ -512,7 +514,7 @@ bool MediaStorage::SetFromModality(DataSet const &ds)
}
return true;
}
- return false;
+ //return false;
}
bool MediaStorage::SetFromFile(File const &file)
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmUNExplicitDataElement.txx b/Source/DataStructureAndEncodingDefinition/gdcmUNExplicitDataElement.txx
index 88cde8d..7d1a962 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmUNExplicitDataElement.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmUNExplicitDataElement.txx
@@ -149,7 +149,7 @@ std::istream &UNExplicitDataElement::ReadValue(std::istream &is, bool readvalues
//assert( ValueField == 0 );
if( VRField == VR::SQ )
{
- // Check wether or not this is an undefined length sequence
+ // Check whether or not this is an undefined length sequence
assert( TagField != Tag(0x7fe0,0x0010) );
ValueField = new SequenceOfItems;
}
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmVR.cxx b/Source/DataStructureAndEncodingDefinition/gdcmVR.cxx
index 7432f77..e0ea954 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmVR.cxx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmVR.cxx
@@ -223,8 +223,9 @@ unsigned int VR::GetSizeof() const
int VR::GetIndex(VRType vr)
{
- assert( vr <= VR_END );
+ if( vr == VR::VL32 ) return 0;
int l;
+ assert( vr <= VR_END );
switch(vr)
{
case INVALID:
@@ -306,6 +307,12 @@ VR::VRType VR::GetVRTypeFromFile(const char *vr)
std::lower_bound(start, end, vr, MySort());
if( (*p)[0] != vr[0] || (*p)[1] != vr[1] )
{
+ if( vr[0] >= 'A' && vr[0] <= 'Z'
+ && vr[1] >= 'A' && vr[1] <= 'Z' )
+ {
+ // newly added VR ?
+ return VR::VL32;
+ }
return VR::INVALID;
}
assert( (*p)[0] == vr[0] && (*p)[1] == vr[1] );
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmVR16ExplicitDataElement.txx b/Source/DataStructureAndEncodingDefinition/gdcmVR16ExplicitDataElement.txx
index c06c308..57fa386 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmVR16ExplicitDataElement.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmVR16ExplicitDataElement.txx
@@ -188,7 +188,7 @@ std::istream &VR16ExplicitDataElement::ReadValue(std::istream &is, bool readvalu
//assert( ValueField == 0 );
if( VRField == VR::SQ )
{
- // Check wether or not this is an undefined length sequence
+ // Check whether or not this is an undefined length sequence
assert( TagField != Tag(0x7fe0,0x0010) );
ValueField = new SequenceOfItems;
}
diff --git a/Source/MediaStorageAndFileFormat/gdcmFileChangeTransferSyntax.h b/Source/MediaStorageAndFileFormat/gdcmFileChangeTransferSyntax.h
index e4c8686..ccae18e 100644
--- a/Source/MediaStorageAndFileFormat/gdcmFileChangeTransferSyntax.h
+++ b/Source/MediaStorageAndFileFormat/gdcmFileChangeTransferSyntax.h
@@ -29,7 +29,7 @@ class TransferSyntax;
* This class is a file-based (limited) replacement of the in-memory
* ImageChangeTransferSyntax.
*
- * This class provide a file-based compression-only mecanism. It will take in
+ * This class provide a file-based compression-only mechanism. It will take in
* an uncompressed DICOM image file (Pixel Data element). Then produced as
* output a compressed DICOM file (Transfer Syntax will be updated).
*
diff --git a/Source/MediaStorageAndFileFormat/gdcmIPPSorter.h b/Source/MediaStorageAndFileFormat/gdcmIPPSorter.h
index 00133e8..a3cc8b5 100644
--- a/Source/MediaStorageAndFileFormat/gdcmIPPSorter.h
+++ b/Source/MediaStorageAndFileFormat/gdcmIPPSorter.h
@@ -81,7 +81,7 @@ public:
double GetDirectionCosinesTolerance() const { return DirCosTolerance; }
/// Makes the IPPSorter ignore multiple images located at the same position.
- /// Only the first occurence will be kept.
+ /// Only the first occurrence will be kept.
/// DropDuplicatePositions defaults to false.
void SetDropDuplicatePositions(bool b) { DropDuplicatePositions = b; }
diff --git a/Source/MediaStorageAndFileFormat/gdcmIconImageFilter.cxx b/Source/MediaStorageAndFileFormat/gdcmIconImageFilter.cxx
index 4b42769..444256f 100644
--- a/Source/MediaStorageAndFileFormat/gdcmIconImageFilter.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmIconImageFilter.cxx
@@ -109,7 +109,7 @@ void IconImageFilter::ExtractIconImages()
PhotometricInterpretation pi(
PhotometricInterpretation::GetPIType(
photometricinterpretation_str.c_str()));
- assert( pi != PhotometricInterpretation::UNKNOW);
+ assert( pi != PhotometricInterpretation::UNKNOWN);
pixeldata.SetPhotometricInterpretation( pi );
//
@@ -287,7 +287,7 @@ void IconImageFilter::ExtractIconImages()
PhotometricInterpretation pi(
PhotometricInterpretation::GetPIType(
photometricinterpretation_str.c_str()));
- assert( pi != PhotometricInterpretation::UNKNOW);
+ assert( pi != PhotometricInterpretation::UNKNOWN);
pixeldata.SetPhotometricInterpretation( pi );
const Tag tpixeldata = Tag(0x7fe0, 0x0010);
assert( ds.FindDataElement( tpixeldata ) );
@@ -425,7 +425,7 @@ void IconImageFilter::ExtractIconImages()
PhotometricInterpretation pi(
PhotometricInterpretation::GetPIType(
photometricinterpretation_str.c_str()));
- assert( pi != PhotometricInterpretation::UNKNOW);
+ assert( pi != PhotometricInterpretation::UNKNOWN);
pixeldata.SetPhotometricInterpretation( pi );
//const Tag tpixeldata = Tag(0x7fe0, 0x0010);
const PrivateTag tpixeldata(0x6003,0x0011,"GEMS_Ultrasound_ImageGroup_001");
diff --git a/Source/MediaStorageAndFileFormat/gdcmImage.cxx b/Source/MediaStorageAndFileFormat/gdcmImage.cxx
index 17530a8..67bc631 100644
--- a/Source/MediaStorageAndFileFormat/gdcmImage.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmImage.cxx
@@ -79,7 +79,7 @@ void Image::SetOrigin(const float *ori)
Origin.resize( NumberOfDimensions );
for(unsigned int i = 0; i < NumberOfDimensions; ++i)
{
- Origin[i] = ori[i];
+ Origin[i] = static_cast<double>(ori[i]);
}
}
@@ -119,7 +119,7 @@ void Image::SetDirectionCosines(const float *dircos)
DirectionCosines.resize( 6 );
for(int i = 0; i < 6; ++i)
{
- DirectionCosines[i] = dircos[i];
+ DirectionCosines[i] = static_cast<double>(dircos[i]);
}
}
diff --git a/Source/MediaStorageAndFileFormat/gdcmImageCodec.cxx b/Source/MediaStorageAndFileFormat/gdcmImageCodec.cxx
index 1773be9..3dad3d1 100644
--- a/Source/MediaStorageAndFileFormat/gdcmImageCodec.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmImageCodec.cxx
@@ -36,7 +36,7 @@ ImageCodec::ImageCodec()
PlanarConfiguration = 0;
RequestPlanarConfiguration = false;
RequestPaddedCompositePixelCode = false;
- PI = PhotometricInterpretation::UNKNOW;
+ PI = PhotometricInterpretation::UNKNOWN;
//LUT = LookupTable(LookupTable::UNKNOWN);
LUT = new LookupTable;
NeedByteSwap = false;
@@ -466,7 +466,7 @@ bool ImageCodec::Decode(DataElement const &, DataElement &)
bool ImageCodec::DecodeByStreams(std::istream &is, std::ostream &os)
{
assert( PlanarConfiguration == 0 || PlanarConfiguration == 1);
- assert( PI != PhotometricInterpretation::UNKNOW );
+ assert( PI != PhotometricInterpretation::UNKNOWN );
std::stringstream bs_os; // ByteSwap
std::stringstream pcpc_os; // Padded Composite Pixel Code
std::stringstream pi_os; // PhotometricInterpretation
diff --git a/Source/MediaStorageAndFileFormat/gdcmImageCodec.h b/Source/MediaStorageAndFileFormat/gdcmImageCodec.h
index d1bbfda..72a0a2a 100644
--- a/Source/MediaStorageAndFileFormat/gdcmImageCodec.h
+++ b/Source/MediaStorageAndFileFormat/gdcmImageCodec.h
@@ -105,7 +105,7 @@ public:
protected:
// Streaming (write) API:
/// This is a high level API to encode in a streaming fashion. Each plugin
- /// will handle differently the caching mecanism so that a limited memory is
+ /// will handle differently the caching mechanism so that a limited memory is
/// used when compressing dataset.
/// Codec will fall into two categories:
/// - Full row encoder: only a single scanline (row) of data is needed to be loaded at a time;
diff --git a/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx b/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx
index 0b1aaa0..e7bfd00 100644
--- a/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx
@@ -46,6 +46,7 @@ namespace gdcm
{
bool ImageHelper::ForceRescaleInterceptSlope = false;
+bool ImageHelper::PMSRescaleInterceptSlope = true;
bool ImageHelper::ForcePixelSpacing = false;
bool GetOriginValueFromSequence(const DataSet& ds, const Tag& tfgs, std::vector<double> &ori)
@@ -628,6 +629,16 @@ bool ImageHelper::GetForceRescaleInterceptSlope()
return ForceRescaleInterceptSlope;
}
+void ImageHelper::SetPMSRescaleInterceptSlope(bool b)
+{
+ PMSRescaleInterceptSlope = b;
+}
+
+bool ImageHelper::GetPMSRescaleInterceptSlope()
+{
+ return PMSRescaleInterceptSlope;
+}
+
void ImageHelper::SetForcePixelSpacing(bool b)
{
ForcePixelSpacing = b;
@@ -946,8 +957,12 @@ std::vector<double> ImageHelper::GetRescaleInterceptSlopeValue(File const & f)
el_ri.SetFromDataElement( priv_rescaleintercept );
Element<VR::DS,VM::VM1> el_rs = {{ 0 }};
el_rs.SetFromDataElement( priv_rescaleslope );
- interceptslope[0] = el_ri.GetValue();
- interceptslope[1] = el_rs.GetValue();
+ if( PMSRescaleInterceptSlope )
+ {
+ interceptslope[0] = el_ri.GetValue();
+ interceptslope[1] = el_rs.GetValue();
+ gdcmWarningMacro( "PMS Modality LUT found for MR Image Storage: [" << interceptslope[0] << "," << interceptslope[1] << "]" );
+ }
}
else
{
@@ -1650,7 +1665,7 @@ void ImageHelper::SetSpacingValue(DataSet & ds, const std::vector<double> & spac
}
-void SetDataElementInSQAsItemNumber(DataSet & ds, DataElement const & de, Tag const & sqtag, unsigned int itemidx)
+static void SetDataElementInSQAsItemNumber(DataSet & ds, DataElement const & de, Tag const & sqtag, unsigned int itemidx)
{
const Tag tfgs = sqtag; //(0x5200,0x9230);
SmartPointer<SequenceOfItems> sqi;
@@ -2271,7 +2286,7 @@ PhotometricInterpretation ImageHelper::GetPhotometricInterpretationValue(File co
const Tag tphotometricinterpretation(0x0028, 0x0004);
const ByteValue *photometricinterpretation =
ImageHelper::GetPointerFromElement(tphotometricinterpretation, f);
- PhotometricInterpretation pi = PhotometricInterpretation::UNKNOW;
+ PhotometricInterpretation pi = PhotometricInterpretation::UNKNOWN;
if( photometricinterpretation )
{
std::string photometricinterpretation_str(
@@ -2310,14 +2325,14 @@ PhotometricInterpretation ImageHelper::GetPhotometricInterpretationValue(File co
}
if( !pf.GetSamplesPerPixel() || (pi.GetSamplesPerPixel() != pf.GetSamplesPerPixel()) )
{
- if( pi != PhotometricInterpretation::UNKNOW )
+ if( pi != PhotometricInterpretation::UNKNOWN )
{
pf.SetSamplesPerPixel( pi.GetSamplesPerPixel() );
}
else if ( isacrnema )
{
assert ( pf.GetSamplesPerPixel() == 0 );
- assert ( pi == PhotometricInterpretation::UNKNOW );
+ assert ( pi == PhotometricInterpretation::UNKNOWN );
pf.SetSamplesPerPixel( 1 );
pi = PhotometricInterpretation::MONOCHROME2;
}
diff --git a/Source/MediaStorageAndFileFormat/gdcmImageHelper.h b/Source/MediaStorageAndFileFormat/gdcmImageHelper.h
index 00a1f1f..2f70231 100644
--- a/Source/MediaStorageAndFileFormat/gdcmImageHelper.h
+++ b/Source/MediaStorageAndFileFormat/gdcmImageHelper.h
@@ -68,6 +68,14 @@ public:
static void SetForceRescaleInterceptSlope(bool);
static bool GetForceRescaleInterceptSlope();
+ /// Since GDCM 2.6.1 Philips Medical System are read using the Private Field
+ /// For Rescale Slope/Intercept by default. This mechanism can be deactivated
+ /// using the following API:
+ /// This option has no effect when ForceRescaleInterceptSlope is set to true
+ /// GDCM will only read those private attribute but never write them out.
+ static void SetPMSRescaleInterceptSlope(bool);
+ static bool GetPMSRescaleInterceptSlope();
+
/// GDCM 1.x compatibility issue:
/// When using ReWrite an MR Image Storage would be rewritten as Secondary Capture Object while
/// still having a Pixel Spacing tag (0028,0030). If you have deal with those files, use this
@@ -146,6 +154,7 @@ protected:
private:
static bool ForceRescaleInterceptSlope;
+ static bool PMSRescaleInterceptSlope;
static bool ForcePixelSpacing;
};
diff --git a/Source/MediaStorageAndFileFormat/gdcmImageRegionReader.cxx b/Source/MediaStorageAndFileFormat/gdcmImageRegionReader.cxx
index 1efab3b..8db02ed 100644
--- a/Source/MediaStorageAndFileFormat/gdcmImageRegionReader.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmImageRegionReader.cxx
@@ -85,6 +85,7 @@ Region const &ImageRegionReader::GetRegion() const
size_t ImageRegionReader::ComputeBufferLength() const
{
// Is this a legal extent:
+ size_t npixels = 0;
if( Internals->GetRegion() )
{
if( !Internals->GetRegion()->IsValid() )
@@ -92,10 +93,26 @@ size_t ImageRegionReader::ComputeBufferLength() const
gdcmDebugMacro( "Sorry not a valid extent. Giving up" );
return 0;
}
+ npixels = this->Internals->GetRegion()->Area();
}
- PixelFormat pixelInfo = ImageHelper::GetPixelFormatValue(GetFile());
- size_t bytesPerPixel = pixelInfo.GetPixelSize();
- return this->Internals->GetRegion()->Area()*bytesPerPixel;
+ else
+ {
+ std::vector<unsigned int> dims = ImageHelper::GetDimensionsValue(GetFile());
+ BoxRegion full;
+ // Use BoxRegion to do robust computation
+ full.SetDomain(0, dims[0] - 1,
+ 0, dims[1] - 1,
+ 0, dims[2] - 1 );
+ if( full.IsValid() )
+ {
+ gdcmDebugMacro( "Sorry not a valid extent. Giving up" );
+ return 0;
+ }
+ npixels = full.Area();
+ }
+ const PixelFormat pixelInfo = ImageHelper::GetPixelFormatValue(GetFile());
+ const size_t bytesPerPixel = pixelInfo.GetPixelSize();
+ return npixels*bytesPerPixel;
}
bool ImageRegionReader::ReadInformation()
@@ -371,7 +388,17 @@ bool ImageRegionReader::ReadJPEGIntoBuffer(char *buffer, size_t buflen)
theCodec.SetPixelFormat( ImageHelper::GetPixelFormatValue(GetFile()) );
std::istream* theStream = GetStreamPtr();
- const BoxRegion &boundingbox = this->Internals->GetRegion()->ComputeBoundingBox();
+ BoxRegion boundingbox;
+ if( Internals->GetRegion() )
+ boundingbox = this->Internals->GetRegion()->ComputeBoundingBox();
+ else
+ {
+ std::vector<unsigned int> dims = ImageHelper::GetDimensionsValue(GetFile());
+ boundingbox.SetDomain(
+ 0, dims[0] - 1,
+ 0, dims[1] - 1,
+ 0, dims[2] - 1 );
+ }
unsigned int xmin = boundingbox.GetXMin();
unsigned int xmax = boundingbox.GetXMax();
unsigned int ymin = boundingbox.GetYMin();
@@ -445,7 +472,13 @@ bool ImageRegionReader::ReadJPEGLSIntoBuffer(char *buffer, size_t buflen)
bool ImageRegionReader::ReadIntoBuffer(char *buffer, size_t buflen)
{
size_t thelen = ComputeBufferLength();
- if( buflen < thelen )
+ if( thelen == 0 )
+ {
+ // does not sound right, something seems odd.
+ gdcmDebugMacro( "Cannot load an image of 0 bytes" );
+ return false;
+ }
+ if( buflen < thelen )
{
gdcmDebugMacro( "buffer cannot be smaller than computed buffer length" );
return false;
diff --git a/Source/MediaStorageAndFileFormat/gdcmImageWriter.cxx b/Source/MediaStorageAndFileFormat/gdcmImageWriter.cxx
index 48699cd..eea541a 100644
--- a/Source/MediaStorageAndFileFormat/gdcmImageWriter.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmImageWriter.cxx
@@ -35,17 +35,12 @@ ImageWriter::~ImageWriter()
{
}
-//void ImageWriter::SetImage(Image const &img)
-//{
-// PixelData = img;
-//}
-
-bool ImageWriter::Write()
+MediaStorage ImageWriter::ComputeTargetMediaStorage()
{
MediaStorage ms;
if( !ms.SetFromFile( GetFile() ) )
{
- // Let's fix some old ACR-NAME stuff:
+ // Let's fix some old ACR-NEMA stuff:
ms = ImageHelper::ComputeMediaStorageFromModality( ms.GetModality(),
PixelData->GetNumberOfDimensions(),
PixelData->GetPixelFormat(),
@@ -62,6 +57,12 @@ bool ImageWriter::Write()
PixelData->GetPhotometricInterpretation(),
GetImage().GetIntercept(), GetImage().GetSlope() );
}
+ return ms;
+}
+
+bool ImageWriter::Write()
+{
+ const MediaStorage ms = ComputeTargetMediaStorage();
if( !PrepareWrite( ms ) ) return false;
//assert( Stream.is_open() );
diff --git a/Source/MediaStorageAndFileFormat/gdcmImageWriter.h b/Source/MediaStorageAndFileFormat/gdcmImageWriter.h
index 666e391..4b67fd3 100644
--- a/Source/MediaStorageAndFileFormat/gdcmImageWriter.h
+++ b/Source/MediaStorageAndFileFormat/gdcmImageWriter.h
@@ -40,6 +40,9 @@ public:
/// Write
bool Write(); // Execute()
+ /// internal function used to compute a target MediaStorage the most appropriate
+ /// User may want to call this function ahead of time (before Write)
+ MediaStorage ComputeTargetMediaStorage();
protected:
private:
diff --git a/Source/MediaStorageAndFileFormat/gdcmJPEG2000Codec.cxx b/Source/MediaStorageAndFileFormat/gdcmJPEG2000Codec.cxx
index 906c486..51d4e15 100644
--- a/Source/MediaStorageAndFileFormat/gdcmJPEG2000Codec.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmJPEG2000Codec.cxx
@@ -233,7 +233,7 @@ void JPEG2000Codec::SetRate(unsigned int idx, double rate)
double JPEG2000Codec::GetRate(unsigned int idx ) const
{
- return Internals->coder_param.tcp_rates[idx];
+ return (double)Internals->coder_param.tcp_rates[idx];
}
void JPEG2000Codec::SetQuality(unsigned int idx, double q)
@@ -248,7 +248,7 @@ void JPEG2000Codec::SetQuality(unsigned int idx, double q)
double JPEG2000Codec::GetQuality(unsigned int idx) const
{
- return Internals->coder_param.tcp_distoratio[idx];
+ return (double)Internals->coder_param.tcp_distoratio[idx];
}
void JPEG2000Codec::SetTileSize(unsigned int tx, unsigned int ty)
@@ -1307,6 +1307,7 @@ bool JPEG2000Codec::GetHeaderInfo(const char * dummy_buffer, size_t buf_size, Tr
#endif // OPENJPEG_MAJOR_VERSION == 1
int reversible;
+ int mct;
#if OPENJPEG_MAJOR_VERSION == 1
opj_j2k_t* j2k = NULL;
opj_jp2_t* jp2 = NULL;
@@ -1317,11 +1318,13 @@ bool JPEG2000Codec::GetHeaderInfo(const char * dummy_buffer, size_t buf_size, Tr
j2k = (opj_j2k_t*)dinfo->j2k_handle;
assert( j2k );
reversible = j2k->cp->tcps->tccps->qmfbid;
+ mct = j2k->cp->tcps->mct;
break;
case JP2_CFMT:
jp2 = (opj_jp2_t*)dinfo->jp2_handle;
assert( jp2 );
reversible = jp2->j2k->cp->tcps->tccps->qmfbid;
+ mct = jp2->j2k->cp->tcps->mct;
break;
default:
gdcmErrorMacro( "Impossible happen" );
@@ -1330,6 +1333,8 @@ bool JPEG2000Codec::GetHeaderInfo(const char * dummy_buffer, size_t buf_size, Tr
#else
reversible = opj_get_reversible(dinfo, ¶meters );
assert( reversible == 0 || reversible == 1 );
+ // FIXME
+ assert( mct == 0 || mct == 1 );
#endif // OPENJPEG_MAJOR_VERSION == 1
LossyFlag = !reversible;
@@ -1421,7 +1426,10 @@ bool JPEG2000Codec::GetHeaderInfo(const char * dummy_buffer, size_t buf_size, Tr
profiles. Note in particular that the JP2 file header is not sent in the JPEG
2000 bitstream that is encapsulated in DICOM.
*/
- PI = PhotometricInterpretation::YBR_RCT;
+ if( mct )
+ PI = PhotometricInterpretation::YBR_RCT;
+ else
+ PI = PhotometricInterpretation::RGB;
this->PF.SetSamplesPerPixel( 3 );
}
else if( image->numcomps == 4 )
@@ -1440,10 +1448,10 @@ bool JPEG2000Codec::GetHeaderInfo(const char * dummy_buffer, size_t buf_size, Tr
return false;
}
- assert( PI != PhotometricInterpretation::UNKNOW );
+ assert( PI != PhotometricInterpretation::UNKNOWN );
- bool mct = false;
- if( mct )
+ bool bmct = false;
+ if( bmct )
{
if( reversible )
{
@@ -1602,7 +1610,7 @@ bool JPEG2000Codec::DecodeExtent(
//std::streamoff relstart = is.tellg();
//assert( relstart - thestart == 8 );
std::streamoff off = frag.GetVL();
- offsets.push_back( off );
+ offsets.push_back( (size_t)off );
is.seekg( off, std::ios::cur );
++numfrags;
}
diff --git a/Source/MediaStorageAndFileFormat/gdcmJPEGBITSCodec.cxx b/Source/MediaStorageAndFileFormat/gdcmJPEGBITSCodec.cxx
index 821736b..cf7b904 100644
--- a/Source/MediaStorageAndFileFormat/gdcmJPEGBITSCodec.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmJPEGBITSCodec.cxx
@@ -1238,7 +1238,7 @@ bool JPEGBITSCodec::InternalCode(const char* input, unsigned long len, std::ostr
case PhotometricInterpretation::ARGB:
case PhotometricInterpretation::CMYK:
// TODO !
- case PhotometricInterpretation::UNKNOW:
+ case PhotometricInterpretation::UNKNOWN:
case PhotometricInterpretation::PI_END: // To please compiler
return false;
}
@@ -1451,7 +1451,7 @@ bool JPEGBITSCodec::EncodeBuffer(std::ostream &os, const char *data, size_t data
case PhotometricInterpretation::ARGB:
case PhotometricInterpretation::CMYK:
// TODO !
- case PhotometricInterpretation::UNKNOW:
+ case PhotometricInterpretation::UNKNOWN:
case PhotometricInterpretation::PI_END: // To please compiler
return false;
}
diff --git a/Source/MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx b/Source/MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx
index 256befe..a56d6b1 100644
--- a/Source/MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx
@@ -454,6 +454,12 @@ bool JPEGLSCodec::DecodeExtent(
const unsigned int colsize = ymax - ymin + 1;
const unsigned int bytesPerPixel = pf.GetPixelSize();
+ if( outv.size() != dimensions[0] * dimensions[1] * bytesPerPixel )
+ {
+ gdcmDebugMacro( "Inconsistant buffer size. Giving up" );
+ return false;
+ }
+
const unsigned char *tmpBuffer1 = raw;
unsigned int z = 0;
for (unsigned int y = ymin; y <= ymax; ++y)
@@ -477,7 +483,7 @@ bool JPEGLSCodec::DecodeExtent(
//std::streamoff relstart = is.tellg();
//assert( relstart - thestart == 8 );
std::streamoff off = frag.GetVL();
- offsets.push_back( off );
+ offsets.push_back( (size_t)off );
is.seekg( off, std::ios::cur );
++numfrags;
}
@@ -510,6 +516,12 @@ bool JPEGLSCodec::DecodeExtent(
const unsigned int colsize = ymax - ymin + 1;
const unsigned int bytesPerPixel = pf.GetPixelSize();
+ if( outv.size() != dimensions[0] * dimensions[1] * bytesPerPixel )
+ {
+ gdcmDebugMacro( "Inconsistant buffer size. Giving up" );
+ return false;
+ }
+
const unsigned char *tmpBuffer1 = raw;
for (unsigned int y = ymin; y <= ymax; ++y)
{
diff --git a/Source/MediaStorageAndFileFormat/gdcmOverlay.cxx b/Source/MediaStorageAndFileFormat/gdcmOverlay.cxx
index ee82711..6d44a75 100644
--- a/Source/MediaStorageAndFileFormat/gdcmOverlay.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmOverlay.cxx
@@ -270,6 +270,7 @@ bool Overlay::GrabOverlayFromPixelData(DataSet const &ds)
if( !bv )
{
// XA_GE_JPEG_02_with_Overlays.dcm
+ gdcmWarningMacro("Could not extract overlay from encapsulated stream." );
return false;
}
assert( bv );
@@ -283,6 +284,7 @@ bool Overlay::GrabOverlayFromPixelData(DataSet const &ds)
assert( 8 * ovlength == (unsigned int)Internal->Rows * Internal->Columns );
if( Internal->Data.empty() )
{
+ gdcmWarningMacro("Internal Data is empty." );
return false;
}
unsigned char * overlay = (unsigned char*)&Internal->Data[0];
diff --git a/Source/MediaStorageAndFileFormat/gdcmOverlay.h b/Source/MediaStorageAndFileFormat/gdcmOverlay.h
index b02e8e5..781e3cb 100644
--- a/Source/MediaStorageAndFileFormat/gdcmOverlay.h
+++ b/Source/MediaStorageAndFileFormat/gdcmOverlay.h
@@ -109,7 +109,7 @@ public:
/// return if the Overlay is stored in the pixel data or not
bool IsInPixelData() const;
- /// Set wether or no the OverlayData is in the Pixel Data:
+ /// Set whether or no the OverlayData is in the Pixel Data:
void IsInPixelData(bool b);
/// Decode the internal OverlayData (packed bits) into unpacked representation
diff --git a/Source/MediaStorageAndFileFormat/gdcmPhotometricInterpretation.cxx b/Source/MediaStorageAndFileFormat/gdcmPhotometricInterpretation.cxx
index 1173345..a46c277 100644
--- a/Source/MediaStorageAndFileFormat/gdcmPhotometricInterpretation.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmPhotometricInterpretation.cxx
@@ -43,7 +43,7 @@ namespace gdcm
*/
static const char *PIStrings[] = {
- "UNKNOW",
+ "UNKNOWN",
"MONOCHROME1 ",
"MONOCHROME2 ",
"PALETTE COLOR ",
@@ -111,7 +111,7 @@ bool PhotometricInterpretation::IsRetired(PIType pi)
unsigned short PhotometricInterpretation::GetSamplesPerPixel() const
{
- if ( PIField == UNKNOW ) return 0;
+ if ( PIField == UNKNOWN ) return 0;
else if( PIField == MONOCHROME1
|| PIField == MONOCHROME2
|| PIField == PALETTE_COLOR )
@@ -171,7 +171,7 @@ bool PhotometricInterpretation::IsLossless() const
return false;
}
- assert( 0 ); // technically one should not reach here, unless UNKNOW ...
+ assert( 0 ); // technically one should not reach here, unless UNKNOWN ...
return false;
}
diff --git a/Source/MediaStorageAndFileFormat/gdcmPhotometricInterpretation.h b/Source/MediaStorageAndFileFormat/gdcmPhotometricInterpretation.h
index 3e0526e..1669499 100644
--- a/Source/MediaStorageAndFileFormat/gdcmPhotometricInterpretation.h
+++ b/Source/MediaStorageAndFileFormat/gdcmPhotometricInterpretation.h
@@ -29,7 +29,7 @@ class GDCM_EXPORT PhotometricInterpretation
{
public:
typedef enum {
- UNKNOW = 0,
+ UNKNOWN = 0,
MONOCHROME1,
MONOCHROME2,
PALETTE_COLOR,
@@ -49,7 +49,7 @@ public:
PI_END // Helpfull for internal implementation
} PIType; // PhotometricInterpretationType
- PhotometricInterpretation(PIType pi = UNKNOW):PIField(pi) {}
+ PhotometricInterpretation(PIType pi = UNKNOWN):PIField(pi) {}
static const char *GetPIString(PIType pi);
diff --git a/Source/MediaStorageAndFileFormat/gdcmPixmapReader.cxx b/Source/MediaStorageAndFileFormat/gdcmPixmapReader.cxx
index d136e96..6336093 100644
--- a/Source/MediaStorageAndFileFormat/gdcmPixmapReader.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmPixmapReader.cxx
@@ -254,7 +254,7 @@ void DoIconImage(const DataSet& rootds, Pixmap& image)
pi = PhotometricInterpretation::GetPIType(
photometricinterpretation_str.c_str());
}
- assert( pi != PhotometricInterpretation::UNKNOW);
+ assert( pi != PhotometricInterpretation::UNKNOWN);
pixeldata.SetPhotometricInterpretation( pi );
//
@@ -494,11 +494,12 @@ unsigned int GetNumberOfOverlaysInternal(DataSet const & ds, std::vector<uint16_
bool DoOverlays(const DataSet& ds, Pixmap& pixeldata)
{
- bool updateoverlayinfo = false;
unsigned int numoverlays;
std::vector<uint16_t> overlaylist;
+ std::vector<bool> updateoverlayinfo;
if( (numoverlays = GetNumberOfOverlaysInternal( ds, overlaylist )) )
{
+ updateoverlayinfo.resize(numoverlays, false);
pixeldata.SetNumberOfOverlays( numoverlays );
for( unsigned int idxoverlays = 0; idxoverlays < numoverlays; ++idxoverlays )
@@ -549,7 +550,7 @@ bool DoOverlays(const DataSet& ds, Pixmap& pixeldata)
gdcmWarningMacro( "Could not extract Overlay from Pixel Data" );
//throw Exception("TODO: Could not extract Overlay Data");
}
- updateoverlayinfo = true;
+ updateoverlayinfo[idxoverlays] = true;
}
}
//std::cout << "Num of Overlays: " << numoverlays << std::endl;
@@ -569,15 +570,15 @@ bool DoOverlays(const DataSet& ds, Pixmap& pixeldata)
if( obp < pf.GetBitsStored() )
{
pixeldata.RemoveOverlay( ov );
+ updateoverlayinfo.erase( updateoverlayinfo.begin() + ov );
gdcmWarningMacro( "Invalid BitPosition: " << obp << " for overlay #" <<
ov << " removing it." );
}
}
}
- if( updateoverlayinfo )
- {
- for( size_t ov = 0; ov < pixeldata.GetNumberOfOverlays(); ++ov )
+ for( size_t ov = 0;
+ ov < pixeldata.GetNumberOfOverlays() && updateoverlayinfo[ov] ; ++ov )
{
Overlay& o = pixeldata.GetOverlay(ov);
// We need to update information
@@ -588,11 +589,10 @@ bool DoOverlays(const DataSet& ds, Pixmap& pixeldata)
}
else
{
- gdcmErrorMacro( "Overlay is not supported" );
+ gdcmErrorMacro( "Overlay #" << ov << " is not supported" );
return false;
}
}
- }
return true;
}
@@ -714,7 +714,7 @@ bool PixmapReader::ReadImageInternal(MediaStorage const &ms, bool handlepixeldat
const Tag tphotometricinterpretation(0x0028, 0x0004);
const ByteValue *photometricinterpretation
= ImageHelper::GetPointerFromElement( tphotometricinterpretation, *F );
- PhotometricInterpretation pi = PhotometricInterpretation::UNKNOW;
+ PhotometricInterpretation pi = PhotometricInterpretation::UNKNOWN;
if( photometricinterpretation )
{
std::string photometricinterpretation_str(
@@ -756,14 +756,14 @@ bool PixmapReader::ReadImageInternal(MediaStorage const &ms, bool handlepixeldat
assert( pi != PhotometricInterpretation::PI_END );
if( !pf.GetSamplesPerPixel() || (pi.GetSamplesPerPixel() != pf.GetSamplesPerPixel()) )
{
- if( pi != PhotometricInterpretation::UNKNOW )
+ if( pi != PhotometricInterpretation::UNKNOWN )
{
pf.SetSamplesPerPixel( pi.GetSamplesPerPixel() );
}
else if ( isacrnema )
{
assert ( pf.GetSamplesPerPixel() == 0 );
- assert ( pi == PhotometricInterpretation::UNKNOW );
+ assert ( pi == PhotometricInterpretation::UNKNOWN );
pf.SetSamplesPerPixel( 1 );
pi = PhotometricInterpretation::MONOCHROME2;
}
@@ -783,7 +783,7 @@ bool PixmapReader::ReadImageInternal(MediaStorage const &ms, bool handlepixeldat
{
return false;
}
- if( pi == PhotometricInterpretation::UNKNOW ) return false;
+ if( pi == PhotometricInterpretation::UNKNOWN ) return false;
PixelData->SetPhotometricInterpretation( pi );
// 4. Planar Configuration
@@ -1013,7 +1013,7 @@ bool PixmapReader::ReadImageInternal(MediaStorage const &ms, bool handlepixeldat
if( !sqf )
{
// TODO: It would be nice to recognize file such as JPEGDefinedLengthSequenceOfFragments.dcm
- gdcmDebugMacro( "File is declared as JPEG compressed but does not contains Fragmens explicitly." );
+ gdcmDebugMacro( "File is declared as JPEG compressed but does not contains Fragments explicitly." );
return false;
}
sqf->WriteBuffer( ss );
@@ -1063,12 +1063,15 @@ bool PixmapReader::ReadImageInternal(MediaStorage const &ms, bool handlepixeldat
licat.SetFromDataSet( ds ); // could be empty
const CSComp & v = licat.GetValue();
lossyflag = atoi( v.c_str() ) == 1;
+ // Note: technically one can decompress into uncompressed form (eg.
+ // Implicit Little Endian) an input JPEG Lossy. So we need to check
+ // the attribute LossyImageCompression value:
PixelData->SetLossyFlag(lossyflag);
}
// Two cases:
// - DataSet did not specify the lossyflag
- // - DataSet specify it to be 0, but there is still a change it could be wrong:
+ // - DataSet specify it to be 0, but there is still a chance it could be wrong:
if( !haslossyflag || !lossyflag )
{
PixelData->ComputeLossyFlag();
diff --git a/Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx b/Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx
index 05bc6b6..ed3633a 100644
--- a/Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx
@@ -283,7 +283,7 @@ bool PixmapWriter::PrepareWrite( MediaStorage const & ref_ms )
}
{
- assert( pi != PhotometricInterpretation::UNKNOW );
+ assert( pi != PhotometricInterpretation::UNKNOWN );
const char *pistr = PhotometricInterpretation::GetPIString(pi);
DataElement de( Tag(0x0028, 0x0004 ) );
VL::Type strlenPistr = (VL::Type)strlen(pistr);
diff --git a/Source/MediaStorageAndFileFormat/gdcmStreamImageReader.cxx b/Source/MediaStorageAndFileFormat/gdcmStreamImageReader.cxx
index 1fbd232..6741c45 100644
--- a/Source/MediaStorageAndFileFormat/gdcmStreamImageReader.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmStreamImageReader.cxx
@@ -390,7 +390,7 @@ bool StreamImageReader::ReadImageInformation()
{
if( !ds_t.FindDataElement( Tag(0x0048,0x0200) ) )
{
- gdcmWarningMacro( "error occured in WSI File read" );
+ gdcmWarningMacro( "error occurred in WSI File read" );
return false;
}
@@ -403,7 +403,7 @@ bool StreamImageReader::ReadImageInformation()
if( !subds_L.FindDataElement( Tag(0x0008,0x1160) ) )
{
- gdcmWarningMacro( "Error occured during WSI File Read" );
+ gdcmWarningMacro( "Error occurred during WSI File Read" );
return false;
}
@@ -426,7 +426,7 @@ bool StreamImageReader::ReadImageInformation()
if( !subds_H.FindDataElement( Tag(0x0008,0x1160) ) )
{
- gdcmWarningMacro( "Error occured during WSI File Read" );
+ gdcmWarningMacro( "Error occurred during WSI File Read" );
return false;
}
diff --git a/Source/MediaStorageAndFileFormat/gdcmSurfaceHelper.cxx b/Source/MediaStorageAndFileFormat/gdcmSurfaceHelper.cxx
index 1844f2f..234ec46 100644
--- a/Source/MediaStorageAndFileFormat/gdcmSurfaceHelper.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmSurfaceHelper.cxx
@@ -27,24 +27,24 @@ std::vector< float > SurfaceHelper::RGBToXYZ(const std::vector<float> & RGB)
tmp[1] = RGB[1];
tmp[2] = RGB[2];
- const float A = (float)(1. / 12.92);
- const float B = (float)(1. / 1.055);
+ const float A = 1.0f / 12.92f;
+ const float B = 1.0f / 1.055f;
- if ( tmp[0] > 0.04045 ) tmp[0] = powf( (float)( ( tmp[0] + 0.055 ) * B ), 2.4f);
- else tmp[0] *= A;
- if ( tmp[1] > 0.04045 ) tmp[1] = powf( (float)( ( tmp[1] + 0.055 ) * B ), 2.4f);
- else tmp[1] *= A;
- if ( tmp[2] > 0.04045 ) tmp[2] = powf( (float)( ( tmp[2] + 0.055 ) * B ), 2.4f);
- else tmp[2] *= A;
+ if ( tmp[0] > 0.04045f ) tmp[0] = powf( ( tmp[0] + 0.055f ) * B, 2.4f);
+ else tmp[0] *= A;
+ if ( tmp[1] > 0.04045f ) tmp[1] = powf( ( tmp[1] + 0.055f ) * B, 2.4f);
+ else tmp[1] *= A;
+ if ( tmp[2] > 0.04045f ) tmp[2] = powf( ( tmp[2] + 0.055f ) * B, 2.4f);
+ else tmp[2] *= A;
tmp[0] *= 100;
tmp[1] *= 100;
tmp[2] *= 100;
//Observer. = 2°, Illuminant = D65
- XYZ[0] = (float)(tmp[0] * 0.4124 + tmp[1] * 0.3576 + tmp[2] * 0.1805);
- XYZ[1] = (float)(tmp[0] * 0.2126 + tmp[1] * 0.7152 + tmp[2] * 0.0722);
- XYZ[2] = (float)(tmp[0] * 0.0193 + tmp[1] * 0.1192 + tmp[2] * 0.9505);
+ XYZ[0] = (tmp[0] * 0.4124f + tmp[1] * 0.3576f + tmp[2] * 0.1805f);
+ XYZ[1] = (tmp[0] * 0.2126f + tmp[1] * 0.7152f + tmp[2] * 0.0722f);
+ XYZ[2] = (tmp[0] * 0.0193f + tmp[1] * 0.1192f + tmp[2] * 0.9505f);
return XYZ;
}
@@ -63,18 +63,18 @@ std::vector< float > SurfaceHelper::XYZToRGB(const std::vector<float> & XYZ)
tmp[1] *= 0.01f; //Y from 0 to 100.000
tmp[2] *= 0.01f; //Z from 0 to 108.883
- RGB[0] = (float)(tmp[0] * 3.2406 + tmp[1] * -1.5372 + tmp[2] * -0.4986);
- RGB[1] = (float)(tmp[0] * -0.9689 + tmp[1] * 1.8758 + tmp[2] * 0.0415);
- RGB[2] = (float)(tmp[0] * 0.0557 + tmp[1] * -0.2040 + tmp[2] * 1.0570);
+ RGB[0] = (tmp[0] * 3.2406f + tmp[1] * -1.5372f + tmp[2] * -0.4986f);
+ RGB[1] = (tmp[0] * -0.9689f + tmp[1] * 1.8758f + tmp[2] * 0.0415f);
+ RGB[2] = (tmp[0] * 0.0557f + tmp[1] * -0.2040f + tmp[2] * 1.0570f);
- const float A = (float)(1. / 2.4);
+ const float A = 1.0f / 2.4f;
- if ( RGB[0] > 0.0031308 ) RGB[0] = 1.055f * powf( RGB[0], A) - 0.055f;
- else RGB[0] *= 12.92f;
- if ( RGB[1] > 0.0031308 ) RGB[1] = 1.055f * powf( RGB[1], A) - 0.055f;
- else RGB[1] *= 12.92f;
- if ( RGB[2] > 0.0031308 ) RGB[2] = 1.055f * powf( RGB[2], A) - 0.055f;
- else RGB[2] *= 12.92f;
+ if ( RGB[0] > 0.0031308f ) RGB[0] = 1.055f * powf( RGB[0], A) - 0.055f;
+ else RGB[0] *= 12.92f;
+ if ( RGB[1] > 0.0031308f ) RGB[1] = 1.055f * powf( RGB[1], A) - 0.055f;
+ else RGB[1] *= 12.92f;
+ if ( RGB[2] > 0.0031308f ) RGB[2] = 1.055f * powf( RGB[2], A) - 0.055f;
+ else RGB[2] *= 12.92f;
return RGB;
}
@@ -84,19 +84,19 @@ std::vector< float > SurfaceHelper::XYZToCIELab(const std::vector<float> & XYZ)
std::vector< float > CIELab(3);
float tmp[3];
- tmp[0] = (float)(XYZ[0] / 95.047); //ref_X = 95.047 Observer= 2°, Illuminant= D65
- tmp[1] = (float)(XYZ[1] * 0.01); //ref_Y = 100.000
- tmp[2] = (float)(XYZ[2] / 108.883); //ref_Z = 108.883
+ tmp[0] = (XYZ[0] / 95.047f); //ref_X = 95.047 Observer= 2°, Illuminant= D65
+ tmp[1] = (XYZ[1] * 0.01f); //ref_Y = 100.000
+ tmp[2] = (XYZ[2] / 108.883f); //ref_Z = 108.883
- const float A = (float)(1. / 3.);
- const float B = (float)(16. / 116.);
+ const float A = 1.0f / 3.0f;
+ const float B = 16.0f / 116.0f;
- if ( tmp[0] > 0.008856 ) tmp[0] = powf(tmp[0], A);
- else tmp[0] = (float)(7.787 * tmp[0] + B);
- if ( tmp[1] > 0.008856 ) tmp[1] = powf(tmp[1], A);
- else tmp[1] = (float)(7.787 * tmp[1] + B);
- if ( tmp[2] > 0.008856 ) tmp[2] = powf(tmp[2], A);
- else tmp[2] = (float)(7.787 * tmp[2] + B);
+ if ( tmp[0] > 0.008856f ) tmp[0] = powf(tmp[0], A);
+ else tmp[0] = (7.787f * tmp[0] + B);
+ if ( tmp[1] > 0.008856f ) tmp[1] = powf(tmp[1], A);
+ else tmp[1] = (7.787f * tmp[1] + B);
+ if ( tmp[2] > 0.008856f ) tmp[2] = powf(tmp[2], A);
+ else tmp[2] = (7.787f * tmp[2] + B);
CIELab[0] = ( 116 * tmp[1] ) - 16;
CIELab[1] = 500 * ( tmp[0] - tmp[1] );
@@ -110,28 +110,28 @@ std::vector< float > SurfaceHelper::CIELabToXYZ(const std::vector<float> & CIELa
std::vector< float > XYZ(3);
float tmp[3];
- tmp[1] = (float)(( CIELab[0] + 16 ) / 116.);
- tmp[0] = (float)(CIELab[1] * 0.002 + tmp[1]);
- tmp[2] = (float)(tmp[1] - CIELab[2] * 0.005);
+ tmp[1] = (( CIELab[0] + 16 ) / 116.0f);
+ tmp[0] = (CIELab[1] * 0.002f + tmp[1]);
+ tmp[2] = (tmp[1] - CIELab[2] * 0.005f);
// Compute t
const float A = tmp[0]*tmp[0]*tmp[0];
const float B = tmp[1]*tmp[1]*tmp[1];
const float C = tmp[2]*tmp[2]*tmp[2];
- const float D = (float)(16. / 116.);
+ const float D = 16.0f / 116.0f;
// Compute f(t)
if ( B > 0.008856f) tmp[1] = B;
- else tmp[1] = (float)(( tmp[1] - D ) / 7.787);
+ else tmp[1] = ( tmp[1] - D ) / 7.787f;
if ( A > 0.008856f) tmp[0] = A;
- else tmp[0] = (float)(( tmp[0] - D ) / 7.787);
+ else tmp[0] = ( tmp[0] - D ) / 7.787f;
if ( C > 0.008856f) tmp[2] = C;
- else tmp[2] = (float)(( tmp[2] - D ) / 7.787);
+ else tmp[2] = ( tmp[2] - D ) / 7.787f;
- XYZ[0] = (float)(tmp[0] * 95.047); //ref_X = 95.047 Observer= 2°, Illuminant= D65
- XYZ[1] = (float)(tmp[1] * 100.); //ref_Y = 100.000
- XYZ[2] = (float)(tmp[2] * 108.883); //ref_Z = 108.883
+ XYZ[0] = (tmp[0] * 95.047f); //ref_X = 95.047 Observer= 2°, Illuminant= D65
+ XYZ[1] = (tmp[1] * 100.0f); //ref_Y = 100.000
+ XYZ[2] = (tmp[2] * 108.883f); //ref_Z = 108.883
return XYZ;
}
diff --git a/Source/MediaStorageAndFileFormat/gdcmSurfaceHelper.h b/Source/MediaStorageAndFileFormat/gdcmSurfaceHelper.h
index ca375f8..4a4e7b4 100644
--- a/Source/MediaStorageAndFileFormat/gdcmSurfaceHelper.h
+++ b/Source/MediaStorageAndFileFormat/gdcmSurfaceHelper.h
@@ -107,7 +107,7 @@ unsigned short SurfaceHelper::RGBToRecommendedDisplayGrayscale(const std::vector
unsigned short Grayscale = 0;
- const float inverseRangeMax = 1. / (float) rangeMax;
+ const float inverseRangeMax = 1.0f / (float) rangeMax;
// 0xFFFF "=" 255 "=" white
Grayscale = (unsigned short) ((0.2989 * RGB[0] + 0.5870 * RGB[1] + 0.1140 * RGB[2])
@@ -127,7 +127,7 @@ SurfaceHelper::ColorArray SurfaceHelper::RGBToRecommendedDisplayCIELab(const std
std::vector<float> tmp(3);
// Convert to range 0-1
- const float inverseRangeMax = 1. / (float) rangeMax;
+ const float inverseRangeMax = 1.0f / (float) rangeMax;
tmp[0] = (float) (RGB[0] * inverseRangeMax);
tmp[1] = (float) (RGB[1] * inverseRangeMax);
tmp[2] = (float) (RGB[2] * inverseRangeMax);
@@ -136,22 +136,22 @@ SurfaceHelper::ColorArray SurfaceHelper::RGBToRecommendedDisplayCIELab(const std
// Convert to range 0x0000-0xFFFF
// 0xFFFF "=" 127, 0x8080 "=" 0, 0x0000 "=" -128
- CIELab[0] = (unsigned short) ( 0xFFFF * (tmp[0]*0.01));
+ CIELab[0] = (unsigned short) ( 0xFFFF * (tmp[0]*0.01f));
if(tmp[1] >= -128 && tmp[1] <= 0)
{
- CIELab[1] = (unsigned short)(((float)(0x8080)/128.0)*tmp[1] + ((float)0x8080));
+ CIELab[1] = (unsigned short)(((float)(0x8080)/128.0f)*tmp[1] + ((float)0x8080));
}
else if(tmp[1] <= 127 && tmp[1] > 0)
{
- CIELab[1] = (unsigned short)(((float)(0xFFFF - 0x8080)/127.0)*tmp[1] + (float)(0x8080));
+ CIELab[1] = (unsigned short)(((float)(0xFFFF - 0x8080)/127.0f)*tmp[1] + (float)(0x8080));
}
if(tmp[2] >= -128 && tmp[2] <= 0)
{
- CIELab[2] = (unsigned short)(((float)0x8080/128.0)*tmp[2] + ((float)0x8080));
+ CIELab[2] = (unsigned short)(((float)0x8080/128.0f)*tmp[2] + ((float)0x8080));
}
else if(tmp[2] <= 127 && tmp[2] > 0)
{
- CIELab[2] = (unsigned short)(((float)(0xFFFF - 0x8080)/127.0)*tmp[2] + (float)(0x8080));
+ CIELab[2] = (unsigned short)(((float)(0xFFFF - 0x8080)/127.0f)*tmp[2] + (float)(0x8080));
}
return CIELab;
@@ -168,22 +168,22 @@ std::vector<T> SurfaceHelper::RecommendedDisplayCIELabToRGB(const ColorArray & C
// Convert to range 0-1
- tmp[0] = 100.0*CIELab[0] /(float)(0xFFFF);
+ tmp[0] = 100.0f*CIELab[0] /(float)(0xFFFF);
if(CIELab[1] >= 0x0000 && CIELab[1] <= 0x8080)
{
- tmp[1] = (float)(((CIELab[1] - 0x8080) * 128.0)/(float)0x8080);
+ tmp[1] = (float)(((CIELab[1] - 0x8080) * 128.0f)/(float)0x8080);
}
else if(CIELab[1] <= 0xFFFF && CIELab[1] > 0x8080)
{
- tmp[1] = (float)((CIELab[1]-0x8080)*127.0 / (float)(0xFFFF - 0x8080));
+ tmp[1] = (float)((CIELab[1]-0x8080)*127.0f / (float)(0xFFFF - 0x8080));
}
if(CIELab[2] >= 0x0000 && CIELab[2] <= 0x8080)
{
- tmp[2] = (float)(((CIELab[2] - 0x8080) * 128.0)/(float)0x8080);
+ tmp[2] = (float)(((CIELab[2] - 0x8080) * 128.0f)/(float)0x8080);
}
else if(CIELab[2] <= 0xFFFF && CIELab[2] > 0x8080)
{
- tmp[2] = (float)((CIELab[2]-0x8080)*127.0 / (float)(0XFFFF - 0x8080));
+ tmp[2] = (float)((CIELab[2]-0x8080)*127.0f / (float)(0XFFFF - 0x8080));
}
tmp = SurfaceHelper::XYZToRGB( SurfaceHelper::CIELabToXYZ( tmp ) );
diff --git a/Source/MediaStorageAndFileFormat/gdcmUIDGenerator.cxx b/Source/MediaStorageAndFileFormat/gdcmUIDGenerator.cxx
index e0d90c9..dc18652 100644
--- a/Source/MediaStorageAndFileFormat/gdcmUIDGenerator.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmUIDGenerator.cxx
@@ -212,6 +212,7 @@ bool UIDGenerator::IsValid(const char *uid_)
* this is considered as a separator for components
*/
+ if( !uid_ ) return false;
std::string uid = uid_;
if( uid.size() > 64 || uid.empty() )
{
diff --git a/Source/MediaStorageAndFileFormat/gdcmXMLPrinter.h b/Source/MediaStorageAndFileFormat/gdcmXMLPrinter.h
index 089b6e0..8d5593a 100644
--- a/Source/MediaStorageAndFileFormat/gdcmXMLPrinter.h
+++ b/Source/MediaStorageAndFileFormat/gdcmXMLPrinter.h
@@ -113,8 +113,8 @@ public:
//void PrintUID(std::ostream &os);
- /// Virtual function mecanism to allow application programmer to
- /// override the default mecanism for BulkData handling. By default
+ /// Virtual function mechanism to allow application programmer to
+ /// override the default mechanism for BulkData handling. By default
/// GDCM will simply discard the BulkData and only write the UUID
virtual void HandleBulkData(const char *uuid, const TransferSyntax &ts,
const char *bulkdata, size_t bulklen);
diff --git a/Testing/Source/DataStructureAndEncodingDefinition/Cxx/TestAttribute1.cxx b/Testing/Source/DataStructureAndEncodingDefinition/Cxx/TestAttribute1.cxx
index a91ad5e..77b905a 100644
--- a/Testing/Source/DataStructureAndEncodingDefinition/Cxx/TestAttribute1.cxx
+++ b/Testing/Source/DataStructureAndEncodingDefinition/Cxx/TestAttribute1.cxx
@@ -111,7 +111,7 @@ int TestAttributeDS()
if( ipp.GetNumberOfValues() != numvalues ) return 1;
for(unsigned int i = 0; i < numvalues; ++i)
- if( fabs(ipp.GetValue(i) - values[i]) > std::numeric_limits<float>::epsilon() ) return 1;
+ if( fabs(ipp.GetValue(i) - values[i]) > std::numeric_limits<double>::epsilon() ) return 1;
ipp.Print( std::cout );
std::cout << std::endl;
@@ -124,7 +124,7 @@ int TestAttributeDS()
if( ipp.GetNumberOfValues() != numvalues ) return 1;
for(unsigned int i = 0; i < numvalues; ++i)
- if( fabs(ipp.GetValue(i) - newvalues[i]) > std::numeric_limits<float>::epsilon() ) return 1;
+ if( fabs(ipp.GetValue(i) - newvalues[i]) > std::numeric_limits<double>::epsilon() ) return 1;
ipp.Print( std::cout );
std::cout << std::endl;
diff --git a/Testing/Source/MediaStorageAndFileFormat/Cxx/TestSurfaceWriter2.cxx b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestSurfaceWriter2.cxx
index ac17e84..101080c 100644
--- a/Testing/Source/MediaStorageAndFileFormat/Cxx/TestSurfaceWriter2.cxx
+++ b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestSurfaceWriter2.cxx
@@ -160,7 +160,7 @@ int TestSurfaceWriter2(const char *subdir, const char* filename)
return 1;
}
- if ( 0.41 > surf->GetSurfaceProcessingRatio() || surf->GetSurfaceProcessingRatio() > 0.43)
+ if ( 0.41f > surf->GetSurfaceProcessingRatio() || surf->GetSurfaceProcessingRatio() > 0.43f)
{
std::cerr << "Find different surface processing ratio"<< std::endl;
return 1;
diff --git a/Utilities/VTK/VTK4/vtkMedicalImageProperties.h b/Utilities/VTK/VTK4/vtkMedicalImageProperties.h
index cdedd98..7ae1103 100644
--- a/Utilities/VTK/VTK4/vtkMedicalImageProperties.h
+++ b/Utilities/VTK/VTK4/vtkMedicalImageProperties.h
@@ -55,7 +55,7 @@ public:
void PrintSelf(ostream& os, vtkIndent indent);
// Description:
- // Convenience method to reset all fields to an emptry string/value
+ // Convenience method to reset all fields to an empty string/value
virtual void Clear();
// Description:
diff --git a/Utilities/VTK/vtkGDCMImageReader.cxx b/Utilities/VTK/vtkGDCMImageReader.cxx
index 55681af..7b64dce 100644
--- a/Utilities/VTK/vtkGDCMImageReader.cxx
+++ b/Utilities/VTK/vtkGDCMImageReader.cxx
@@ -682,7 +682,7 @@ int vtkGDCMImageReader::RequestInformationCompat()
return 0;
}
// I do not think this is a good idea anyway to let the user decide
- // wether or not she wants *not* to apply shift/scale...
+ // whether or not she wants *not* to apply shift/scale...
if( !this->ApplyShiftScale )
{
vtkErrorMacro("ApplyShiftScale not compatible" );
diff --git a/Utilities/VTK/vtkGDCMImageReader2.cxx b/Utilities/VTK/vtkGDCMImageReader2.cxx
index 0b54b7f..5dafdbf 100644
--- a/Utilities/VTK/vtkGDCMImageReader2.cxx
+++ b/Utilities/VTK/vtkGDCMImageReader2.cxx
@@ -459,7 +459,7 @@ int vtkGDCMImageReader2::RequestInformationCompat()
return 0;
}
// I do not think this is a good idea anyway to let the user decide
- // wether or not she wants *not* to apply shift/scale...
+ // whether or not she wants *not* to apply shift/scale...
if( !this->ApplyShiftScale )
{
vtkErrorMacro("ApplyShiftScale not compatible" );
diff --git a/Utilities/VTK/vtkGDCMMedicalImageProperties.h b/Utilities/VTK/vtkGDCMMedicalImageProperties.h
index e6ab087..826d1b9 100644
--- a/Utilities/VTK/vtkGDCMMedicalImageProperties.h
+++ b/Utilities/VTK/vtkGDCMMedicalImageProperties.h
@@ -38,7 +38,7 @@ public:
void PrintSelf(ostream& os, vtkIndent indent);
// Description:
- // Convenience method to reset all fields to an emptry string/value
+ // Convenience method to reset all fields to an empty string/value
virtual void Clear();
/*
diff --git a/Utilities/VTK/vtkRTStructSetProperties.h b/Utilities/VTK/vtkRTStructSetProperties.h
index e47c757..a5aef7c 100644
--- a/Utilities/VTK/vtkRTStructSetProperties.h
+++ b/Utilities/VTK/vtkRTStructSetProperties.h
@@ -32,7 +32,7 @@ public:
void PrintSelf(ostream& os, vtkIndent indent);
// Description:
- // Convenience method to reset all fields to an emptry string/value
+ // Convenience method to reset all fields to an empty string/value
virtual void Clear();
// Description:
diff --git a/Utilities/doxygen/CMakeLists.txt b/Utilities/doxygen/CMakeLists.txt
index 5567e73..055cf3a 100644
--- a/Utilities/doxygen/CMakeLists.txt
+++ b/Utilities/doxygen/CMakeLists.txt
@@ -20,7 +20,7 @@ if(GDCM_DOCUMENTATION)
"${GDCM_SOURCE_DIR}/Source/*.h"
"${GDCM_SOURCE_DIR}/Wrapping/*.h"
"${GDCM_SOURCE_DIR}/Utilities/VTK/*.h"
- "${GDCM_SOURCE_DIR}/Utilities/doxygen/man/*.dox"
+ #"${GDCM_SOURCE_DIR}/Utilities/doxygen/man/*.dox"
)
list(REMOVE_ITEM headerfiles
"${GDCM_SOURCE_DIR}/Source/DataDictionary/gdcmTagKeywords.h"
@@ -187,26 +187,26 @@ ${CMAKE_CURRENT_BINARY_DIR}/latex/Makefile
# ${CMAKE_CURRENT_BINARY_DIR}/html/gdcmviewer.html
# DESTINATION ${GDCM_INSTALL_DOC_DIR} COMPONENT DebugDevel
#)
- install(FILES
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcm2vtk.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcm2pnm.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmconv.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmpap3.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmxml.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmanon.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmgendir.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmdump.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmdiff.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmimg.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcminfo.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmpdf.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmraw.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmscu.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmscanner.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmtar.1
- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmviewer.1
- DESTINATION ${GDCM_INSTALL_MAN_DIR}/man1 COMPONENT DebugDevel
- )
+ #install(FILES
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcm2vtk.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcm2pnm.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmconv.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmpap3.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmxml.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmanon.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmgendir.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmdump.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmdiff.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmimg.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcminfo.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmpdf.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmraw.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmscu.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmscanner.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmtar.1
+ # ${CMAKE_CURRENT_BINARY_DIR}/man/man1/gdcmviewer.1
+ # DESTINATION ${GDCM_INSTALL_MAN_DIR}/man1 COMPONENT DebugDevel
+ #)
install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html DESTINATION ${GDCM_INSTALL_DOC_DIR}
PATTERN "*.md5" EXCLUDE
PATTERN "*.dot" EXCLUDE
@@ -223,5 +223,49 @@ ${CMAKE_CURRENT_BINARY_DIR}/latex/Makefile
endif()
subdirs(vtk)
endif()
+endif()
+set(MANPAGES_XML
+ gdcm2pnm
+ gdcm2vtk
+ gdcmanon
+ gdcmconv
+ gdcmdiff
+ gdcmdump
+ gdcmgendir
+ gdcmimg
+ gdcminfo
+ gdcmpap3
+ gdcmpdf
+ gdcmraw
+ gdcmscanner
+ gdcmscu
+ gdcmtar
+ gdcmviewer
+ gdcmxml
+ )
+find_package(LibXslt)
+# need an XSLT 1.0 processor, use xsltproc, maybe add more implementations later
+if(LIBXSLT_XSLTPROC_EXECUTABLE)
+foreach(docbook ${MANPAGES_XML})
+ add_custom_command(
+ OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${docbook}.1
+ COMMAND ${LIBXSLT_XSLTPROC_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/man/${docbook}.xml
+ DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/man/${docbook}.xml
+ )
+ list(APPEND MANPAGES
+ ${CMAKE_CURRENT_BINARY_DIR}/${docbook}.1
+ )
+endforeach()
+add_custom_target(DOCBOOK_MANPAGES
+ ALL
+ DEPENDS ${MANPAGES}
+ COMMENT "docbook manpages"
+ )
+install(FILES
+ ${MANPAGES}
+ DESTINATION ${GDCM_INSTALL_MAN_DIR}/man1 COMPONENT DebugDevel
+)
+else()
+ message(WARNING "Cannot build man page from docbook (need xsltproc)")
endif()
diff --git a/Utilities/doxygen/doxyfile.in b/Utilities/doxygen/doxyfile.in
index dde8ff0..11d8333 100644
--- a/Utilities/doxygen/doxyfile.in
+++ b/Utilities/doxygen/doxyfile.in
@@ -1,110 +1,129 @@
-# Doxyfile 1.8.1.2
+# Doxyfile 1.8.9.1
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
#
-# All text after a hash (#) is considered a comment and will be ignored.
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
-# TAG = value [value, ...]
-# For lists items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ").
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the config file
-# that follow. The default is UTF-8 which is also the encoding used for all
-# text before the first occurrence of this tag. Doxygen uses libiconv (or the
-# iconv built into libc) for the transcoding. See
-# http://www.gnu.org/software/libiconv for the list of possible encodings.
+# that follow. The default is UTF-8 which is also the encoding used for all text
+# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
+# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
+# for the list of possible encodings.
+# The default value is: UTF-8.
DOXYFILE_ENCODING = UTF-8
-# The PROJECT_NAME tag is a single word (or sequence of words) that should
-# identify the project. Note that if you do not use Doxywizard you need
-# to put quotes around the project name if it contains spaces.
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
PROJECT_NAME = GDCM
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
PROJECT_NUMBER = @GDCM_VERSION@
# Using the PROJECT_BRIEF tag one can provide an optional one line description
-# for a project that appears at the top of each page and should give viewer
-# a quick idea about the purpose of the project. Keep the description short.
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF =
-# With the PROJECT_LOGO tag one can specify an logo or icon that is
-# included in the documentation. The maximum height of the logo should not
-# exceed 55 pixels and the maximum width should not exceed 200 pixels.
-# Doxygen will copy the logo to the output directory.
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
PROJECT_LOGO =
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
OUTPUT_DIRECTORY = @GDCM_BINARY_DIR@/Utilities/doxygen
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-# 4096 sub-directories (in 2 levels) under the output directory of each output
-# format and will distribute the generated files over these directories.
-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
+# directories (in 2 levels) under the output directory of each output format and
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
CREATE_SUBDIRS = NO
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES = NO
+
# The OUTPUT_LANGUAGE tag is used to specify the language in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
-# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
-# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
-# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
OUTPUT_LANGUAGE = English
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
BRIEF_MEMBER_DESC = YES
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
# brief descriptions will be completely suppressed.
+# The default value is: YES.
REPEAT_BRIEF = YES
-# This tag implements a quasi-intelligent brief description abbreviator
-# that is used to form the text in various listings. Each string
-# in this list, if found as the leading text of the brief description, will be
-# stripped from the text and the result after processing the whole list, is
-# used as the annotated text. Otherwise, the brief description is used as-is.
-# If left blank, the following values are used ("$name" is automatically
-# replaced with the name of the entity): "The $name class" "The $name widget"
-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
ABBREVIATE_BRIEF =
# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
+# doxygen will generate a detailed section even if there is only a brief
# description.
+# The default value is: NO.
ALWAYS_DETAILED_SEC = NO
@@ -112,237 +131,269 @@ ALWAYS_DETAILED_SEC = NO
# inherited members of a class in the documentation of that class as if those
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
+# The default value is: NO.
INLINE_INHERITED_MEMB = NO
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-# path before files name in the file list and in the header files. If set
-# to NO the shortest path that makes the file name unique will be used.
+# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
FULL_PATH_NAMES = NO
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
STRIP_FROM_PATH =
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-# the path mentioned in the documentation of a class, which tells
-# the reader which header file to include in order to use a class.
-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
STRIP_FROM_INC_PATH =
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful if your file system
-# doesn't support long names like on DOS, Mac, or CD-ROM.
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
SHORT_NAMES = NO
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like regular Qt-style comments
-# (thus requiring an explicit @brief command for a brief description.)
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
JAVADOC_AUTOBRIEF = NO
-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
-# interpret the first line (until the first dot) of a Qt-style
-# comment as the brief description. If set to NO, the comments
-# will behave just like regular Qt-style comments (thus requiring
-# an explicit \brief command for a brief description.)
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
QT_AUTOBRIEF = NO
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
-# description. Set this tag to YES if you prefer the old behaviour instead.
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
MULTILINE_CPP_IS_BRIEF = NO
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
INHERIT_DOCS = YES
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
SEPARATE_MEMBER_PAGES = NO
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
TAB_SIZE = 2
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines.
ALIASES =
# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding
-# "class=itcl::class" will allow you to use the command class in the
-# itcl::class meaning.
+# A mapping has the form "name=value". For example adding "class=itcl::class"
+# will allow you to use the command class in the itcl::class meaning.
TCL_SUBST =
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C = NO
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for
-# Java. For instance, namespaces will be presented as packages, qualified
-# scopes will look different, etc.
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA = NO
# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-# sources only. Doxygen will then generate output that is more tailored for
-# Fortran.
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
OPTIMIZE_FOR_FORTRAN = NO
# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-# sources. Doxygen will then generate output that is tailored for
-# VHDL.
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
OPTIMIZE_OUTPUT_VHDL = NO
# Doxygen selects the parser to use depending on the extension of the files it
-# parses. With this tag you can assign which parser to use for a given extension.
-# Doxygen has a built-in mapping, but you can override or extend it using this
-# tag. The format is ext=language, where ext is a file extension, and language
-# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
-# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
-# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
-# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
-# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
+# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
+# Fortran. In the later case the parser tries to guess whether the code is fixed
+# or free formatted code, this is the default for Fortran type files), VHDL. For
+# instance to make doxygen treat .inc files as Fortran files (default is PHP),
+# and .f files as C (default is Fortran), use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen.
EXTENSION_MAPPING =
-# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
-# comments according to the Markdown format, which allows for more readable
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
# documentation. See http://daringfireball.net/projects/markdown/ for details.
-# The output of markdown processing is further processed by doxygen, so you
-# can mix doxygen, HTML, and XML commands with Markdown formatting.
-# Disable only in case of backward compatibilities issues.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
MARKDOWN_SUPPORT = YES
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT = YES
+
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
-# to include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also makes the inheritance and collaboration
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
BUILTIN_STL_SUPPORT = YES
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
+# The default value is: NO.
CPP_CLI_SUPPORT = NO
-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
-# Doxygen will parse them like normal C++ but will assume all classes use public
-# instead of private inheritance when no explicit protection keyword is present.
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
SIP_SUPPORT = NO
-# For Microsoft's IDL there are propget and propput attributes to indicate getter
-# and setter methods for a property. Setting this option to YES (the default)
-# will make doxygen replace the get and set methods by a property in the
-# documentation. This will only work if the methods are indeed getting or
-# setting a simple type. If this is not the case, or you want to show the
-# methods anyway, you should set this option to NO.
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
+# tag is set to YES then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
+# The default value is: NO.
DISTRIBUTE_GROUP_DOC = NO
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
SUBGROUPING = YES
-# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
-# unions are shown inside the group in which they are included (e.g. using
-# @ingroup) instead of on a separate page (for HTML and Man pages) or
-# section (for LaTeX and RTF).
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
-# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
-# unions with only public data fields will be shown inline in the documentation
-# of the scope in which they are defined (i.e. file, namespace, or group
-# documentation), provided this scope is documented. If set to NO (the default),
-# structs, classes, and unions are shown on a separate page (for HTML and Man
-# pages) or section (for LaTeX and RTF).
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
-# is documented as struct, union, or enum with the name of the typedef. So
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
-# namespace, or class. And the struct will be named TypeS. This can typically
-# be useful for C code in case the coding convention dictates that all compound
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
-# determine which symbols to keep in memory and which to flush to disk.
-# When the cache is full, less often used symbols will be written to disk.
-# For small to medium size projects (<1000 input files) the default value is
-# probably good enough. For larger projects a too small cache size can cause
-# doxygen to be busy swapping symbols to and from disk most of the time
-# causing a significant performance penalty.
-# If the system has enough physical memory increasing the cache will improve the
-# performance by keeping more symbols in memory. Note that the value works on
-# a logarithmic scale so increasing the size by one will roughly double the
-# memory usage. The cache size is given by this formula:
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
-
-SYMBOL_CACHE_SIZE = 0
-
-# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
-# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
-# their name and scope. Since this can be an expensive process and often the
-# same symbol appear multiple times in the code, doxygen keeps a cache of
-# pre-resolved symbols. If the cache is too small doxygen will become slower.
-# If the cache is too large, memory is wasted. The cache size is given by this
-# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
@@ -350,310 +401,362 @@ LOOKUP_CACHE_SIZE = 0
# Build related configuration options
#---------------------------------------------------------------------------
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
EXTRACT_ALL = YES
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
EXTRACT_PRIVATE = NO
-# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal scope will be included in the documentation.
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
EXTRACT_PACKAGE = NO
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
EXTRACT_STATIC = YES
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
EXTRACT_LOCAL_CLASSES = YES
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base
-# name of the file that contains the anonymous namespace. By default
-# anonymous namespaces are hidden.
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = NO
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
INTERNAL_DOCS = NO
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
# allowed. This is useful if you have classes or files whose names only differ
# in case and if your file system supports case sensitive file names. Windows
# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
CASE_SENSE_NAMES = YES
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
HIDE_SCOPE_NAMES = NO
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
SHOW_INCLUDE_FILES = YES
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
-# will list include files with double quotes in the documentation
-# rather than with sharp brackets.
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
INLINE_INFO = YES
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
SORT_MEMBER_DOCS = YES
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
SORT_BRIEF_DOCS = YES
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
-# will sort the (brief and detailed) documentation of class members so that
-# constructors and destructors are listed first. If set to NO (the default)
-# the constructors will appear in the respective orders defined by
-# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
-# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
-# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = YES
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
-# hierarchy of group names into alphabetical order. If set to NO (the default)
-# the group names will appear in their defined order.
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
SORT_GROUP_NAMES = NO
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
SORT_BY_SCOPE_NAME = NO
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
-# do proper type resolution of all parameters of a function it will reject a
-# match between the prototype and the implementation of a member function even
-# if there is only one candidate or it is obvious which candidate to choose
-# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
-# will still accept a match between prototype and implementation in such cases.
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
STRICT_PROTO_MATCHING = NO
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
GENERATE_TODOLIST = YES
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
GENERATE_TESTLIST = YES
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
GENERATE_BUGLIST = YES
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
GENERATE_DEPRECATEDLIST= YES
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
ENABLED_SECTIONS =
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or macro consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and macros in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 30
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
SHOW_USED_FILES = YES
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
-# This will remove the Files entry from the Quick Index and from the
-# Folder Tree View (if specified). The default is YES.
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
SHOW_FILES = YES
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
-# Namespaces page.
-# This will remove the Namespaces entry from the Quick Index
-# and from the Folder Tree View (if specified). The default is YES.
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
SHOW_NAMESPACES = YES
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
FILE_VERSION_FILTER =
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
# by doxygen. The layout file controls the global structure of the generated
# output files in an output format independent way. To create the layout file
-# that represents doxygen's defaults, run doxygen with the -l option.
-# You can optionally specify a file name after the option, if omitted
-# DoxygenLayout.xml will be used as the name of the layout file.
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
LAYOUT_FILE =
-# The CITE_BIB_FILES tag can be used to specify one or more bib files
-# containing the references data. This must be a list of .bib files. The
-# .bib extension is automatically appended if omitted. Using this command
-# requires the bibtex tool to be installed. See also
-# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
-# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
-# feature you need bibtex and perl available in the search path.
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
+# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
QUIET = YES
# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
WARNINGS = YES
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
WARN_IF_DOC_ERROR = YES
-# The WARN_NO_PARAMDOC option can be enabled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
WARN_NO_PARAMDOC = NO
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
WARN_LOGFILE =
#---------------------------------------------------------------------------
-# configuration options related to the input files
+# Configuration options related to the input files
#---------------------------------------------------------------------------
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces.
+# Note: If this tag is empty the current directory is searched.
INPUT = @GDCM_SOURCE_DIR@/Source \
@GDCM_SOURCE_DIR@/Wrapping \
@@ -663,33 +766,36 @@ INPUT = @GDCM_SOURCE_DIR@/Source \
@GDCM_BINARY_DIR@/Utilities/doxygen/TestsList.txt
# This tag can be used to specify the character encoding of the source files
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
-# also the default input encoding. Doxygen uses libiconv (or the iconv built
-# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
-# the list of possible encodings.
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
-# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
-# *.f90 *.f *.for *.vhd *.vhdl
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank the
+# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii,
+# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp,
+# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown,
+# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
+# *.qsf, *.as and *.js.
FILE_PATTERNS = *.h \
*.dox
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
RECURSIVE = YES
# The EXCLUDE tag can be used to specify files and/or directories that should be
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
# Note that relative paths are relative to the directory from which doxygen is
# run.
@@ -703,14 +809,16 @@ EXCLUDE = @GDCM_SOURCE_DIR@/Source/DataDictionary/gdcmTagToType.h
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
+# The default value is: NO.
EXCLUDE_SYMLINKS = NO
# If the value of the INPUT tag contains directories, you can use the
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS = */.git/* \
*/VTK4/*
@@ -720,12 +828,15 @@ EXCLUDE_PATTERNS = */.git/* \
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
EXAMPLE_PATH = @GDCM_SOURCE_DIR@/Examples \
@GDCM_SOURCE_DIR@/Testing \
@@ -735,9 +846,9 @@ EXAMPLE_PATH = @GDCM_SOURCE_DIR@/Examples \
@GDCM_SOURCE_DIR@/Utilities/VTK/Applications
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
EXAMPLE_PATTERNS = *.cxx \
*.py \
@@ -745,738 +856,1110 @@ EXAMPLE_PATTERNS = *.cxx \
*.cs
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
EXAMPLE_RECURSIVE = YES
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
IMAGE_PATH =
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output.
-# If FILTER_PATTERNS is specified, this tag will be
-# ignored.
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis.
-# Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match.
-# The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty or if
-# non of the patterns match the file name, INPUT_FILTER is applied.
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
FILTER_PATTERNS =
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
FILTER_SOURCE_FILES = NO
# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
-# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
-# and it is also possible to disable source filtering for a specific pattern
-# using *.ext= (so without naming a filter). This option only has effect when
-# FILTER_SOURCE_FILES is enabled.
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
#---------------------------------------------------------------------------
-# configuration options related to source browsing
+# Configuration options related to source browsing
#---------------------------------------------------------------------------
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
SOURCE_BROWSER = NO
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
INLINE_SOURCES = NO
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C, C++ and Fortran comments will always remain visible.
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
STRIP_CODE_COMMENTS = YES
-# If the REFERENCED_BY_RELATION tag is set to YES
-# then for each documented function all documented
-# functions referencing it will be listed.
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
REFERENCED_BY_RELATION = YES
-# If the REFERENCES_RELATION tag is set to YES
-# then for each documented function all documented entities
-# called/used by that function will be listed.
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
REFERENCES_RELATION = YES
-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code.
-# Otherwise they will link to the documentation.
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
VERBATIM_HEADERS = YES
+# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
+# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
+# cost of reduced performance. This can be particularly helpful with template
+# rich C++ code for which doxygen's built-in parser lacks the necessary type
+# information.
+# Note: The availability of this option depends on whether or not doxygen was
+# compiled with the --with-libclang option.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# If clang assisted parsing is enabled you can provide the compiler with command
+# line options that you would normally use when invoking the compiler. Note that
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS =
+
#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
+# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
ALPHABETICAL_INDEX = YES
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
COLS_IN_ALPHA_INDEX = 3
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
-# configuration options related to the HTML output
+# Configuration options related to the HTML output
#---------------------------------------------------------------------------
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
GENERATE_HTML = YES
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .xhtml
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header. Note that when using a custom header you are responsible
-# for the proper inclusion of any scripts and style sheets that doxygen
-# needs, which is dependent on the configuration options used.
-# It is advised to generate a default header using "doxygen -w html
-# header.html footer.html stylesheet.css YourConfigFile" and then modify
-# that header. Note that the header is subject to change so you typically
-# have to redo this when upgrading to a newer version of doxygen or when
-# changing the value of configuration settings such as GENERATE_TREEVIEW!
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER = @GDCM_HTML_FOOTER@
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# style sheet in the HTML output directory as well, or it will be erased!
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET =
+
# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
# that these files will be copied to the base HTML output directory. Use the
-# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
-# files. In the HTML_STYLESHEET file, use the file name only. Also note that
-# the files will be copied as-is; there are no commands or markers available.
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES =
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
-# Doxygen will adjust the colors in the style sheet and background images
-# according to this color. Hue is specified as an angle on a colorwheel,
-# see http://en.wikipedia.org/wiki/Hue for more information.
-# For instance the value 0 represents red, 60 is yellow, 120 is green,
-# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
-# The allowed range is 0 to 359.
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 220
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
-# the colors in the HTML output. For a value of 0 the output will use
-# grayscales only. A value of 255 will produce the most vivid colors.
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 100
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
-# the luminance component of the colors in the HTML output. Values below
-# 100 gradually make the output lighter, whereas values above 100 make
-# the output darker. The value divided by 100 is the actual gamma applied,
-# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
-# and 100 does not change the gamma.
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting
-# this to NO can help when comparing the output of multiple runs.
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = NO
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = NO
-# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
-# entries shown in the various tree structured indices initially; the user
-# can expand and collapse entries dynamically later on. Doxygen will expand
-# the tree to such a level that at most the specified number of entries are
-# visible (unless a fully collapsed tree already exceeds this amount).
-# So setting the number of entries 1 will produce a full collapsed tree by
-# default. 0 is a special value representing an infinite number of entries
-# and will result in a full expanded tree by default.
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
-# If the GENERATE_DOCSET tag is set to YES, additional index files
-# will be generated that can be used as input for Apple's Xcode 3
-# integrated development environment, introduced with OSX 10.5 (Leopard).
-# To create a documentation set, doxygen will generate a Makefile in the
-# HTML output directory. Running make will produce the docset in that
-# directory and running "make install" will install the docset in
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
-# it at startup.
-# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = NO
-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
-# feed. A documentation feed provides an umbrella under which multiple
-# documentation sets from a single provider (such as a company or product suite)
-# can be grouped.
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Doxygen generated docs"
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
-# should uniquely identify the documentation set bundle. This should be a
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
-# will append .docset to the name.
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = org.doxygen.Project
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
# the documentation publisher. This should be a reverse domain-name style
# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
-# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
-# of the generated HTML documentation.
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
-# is used to encode HtmlHelp index (hhk), content (hhc) and project file
-# content.
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
-# that can be used as input for Qt's qhelpgenerator to generate a
-# Qt Compressed Help (.qch) of the generated HTML documentation.
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = NO
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
-# be used to specify the file name of the resulting .qch file.
-# The path specified is relative to the HTML output folder.
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE =
-# The QHP_NAMESPACE tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#namespace
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE =
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = doc
-# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
-# add. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#custom-filters
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
-# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
-# custom filter to add. For more information please see
-# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
-# Qt Help Project / Custom Filters</a>.
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
-# project's
-# filter section matches.
-# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
-# Qt Help Project / Filter Attributes</a>.
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS =
-# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
-# be used to specify the location of Qt's qhelpgenerator.
-# If non-empty doxygen will try to run qhelpgenerator on the generated
-# .qhp file.
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION =
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
-# will be generated, which together with the HTML files, form an Eclipse help
-# plugin. To install this plugin and make it available under the help contents
-# menu in Eclipse, the contents of the directory containing the HTML and XML
-# files needs to be copied into the plugins directory of eclipse. The name of
-# the directory within the plugins directory should be the same as
-# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
-# the help appears.
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
-# A unique identifier for the eclipse help plugin. When installing the plugin
-# the directory name containing the HTML and XML files should also have
-# this name.
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
-# at top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it. Since the tabs have the same information as the
-# navigation tree you can set this option to NO if you already set
-# GENERATE_TREEVIEW to YES.
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = NO
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information.
-# If the tag value is set to YES, a side panel will be generated
-# containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
-# Windows users are probably better off using the HTML help feature.
-# Since the tree basically has the same information as the tab index you
-# could consider to set DISABLE_INDEX to NO when enabling this option.
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = NO
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
-# (range [0,1..20]) that doxygen will group on one line in the generated HTML
-# documentation. Note that a value of 0 will completely suppress the enum
-# values from appearing in the overview section.
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 1
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 250
-# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
-# links to external symbols imported via tag files in a separate window.
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
-# Use this tag to change the font size of Latex formulas included
-# as images in the HTML documentation. The default is 10. Note that
-# when you change the font size after a successful doxygen run you need
-# to manually remove any form_*.png images from the HTML output directory
-# to force them to be regenerated.
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are
-# not supported properly for IE 6.0, but are supported on all modern browsers.
-# Note that when changing this option you need to delete any form_*.png files
-# in the HTML output before the changes have effect.
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
-# (see http://www.mathjax.org) which uses client side Javascript for the
-# rendering instead of using prerendered bitmaps. Use this if you do not
-# have LaTeX installed or if you want to formulas look prettier in the HTML
-# output. When enabled you may also need to install MathJax separately and
-# configure the path to it using the MATHJAX_RELPATH option.
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = NO
-# When MathJax is enabled you need to specify the location relative to the
-# HTML output directory using the MATHJAX_RELPATH option. The destination
-# directory should contain the MathJax.js script. For instance, if the mathjax
-# directory is located at the same level as the HTML output directory, then
-# MATHJAX_RELPATH should be ../mathjax. The default value points to
-# the MathJax Content Delivery Network so you can quickly see the result without
-# installing MathJax.
-# However, it is strongly recommended to install a local
-# copy of MathJax from http://www.mathjax.org before deployment.
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
-# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
-# names that should be enabled during MathJax rendering.
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box
-# for the HTML output. The underlying search engine uses javascript
-# and DHTML and should work on any modern browser. Note that when using
-# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
-# (GENERATE_DOCSET) there is already a search function so this one should
-# typically be disabled. For large projects the javascript based search engine
-# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
SEARCHENGINE = NO
# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a PHP enabled web server instead of at the web client
-# using Javascript. Doxygen will generate the search PHP script and index
-# file to put on the web server. The advantage of the server
-# based approach is that it scales better to large projects and allows
-# full text search. The disadvantages are that it is more difficult to setup
-# and does not have live searching capabilities.
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
SERVER_BASED_SEARCH = NO
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS =
+
#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
+# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
GENERATE_LATEX = YES
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-# Note that when enabling USE_PDFLATEX this option is only used for
-# generating bitmaps for formulas in the HTML output, but not in the
-# Makefile that is written to the output directory.
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_CMD_NAME = latex
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
MAKEINDEX_CMD_NAME = makeindex
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
COMPACT_LATEX = NO
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, letter, legal and
-# executive. If left blank a4wide will be used.
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
PAPER_TYPE = letter
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. To get the times font for
+# instance you can specify
+# EXTRA_PACKAGES=times
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
EXTRA_PACKAGES =
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HEADER =
-# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
-# the generated latex document. The footer should contain everything after
-# the last chapter. If it is left blank doxygen will generate a
-# standard footer. Notice: only use this tag if you know what you are doing!
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_FOOTER =
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
PDF_HYPERLINKS = YES
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = YES
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BATCHMODE = YES
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HIDE_INDICES = NO
-# If LATEX_SOURCE_CODE is set to YES then doxygen will include
-# source code with syntax highlighting in the LaTeX output.
-# Note that which sources are shown also depends on other settings
-# such as SOURCE_BROWSER.
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_SOURCE_CODE = NO
# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
-# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
-# http://en.wikipedia.org/wiki/BibTeX for more info.
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BIB_STYLE = plain
#---------------------------------------------------------------------------
-# configuration options related to the RTF output
+# Configuration options related to the RTF output
#---------------------------------------------------------------------------
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
GENERATE_RTF = NO
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_OUTPUT = rtf
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
COMPACT_RTF = NO
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_HYPERLINKS = NO
-# Load style sheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_STYLESHEET_FILE =
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_EXTENSIONS_FILE =
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE = NO
+
#---------------------------------------------------------------------------
-# configuration options related to the man page output
+# Configuration options related to the man page output
#---------------------------------------------------------------------------
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
-GENERATE_MAN = YES
+GENERATE_MAN = NO
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_OUTPUT = man
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_EXTENSION = .1
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_LINKS = NO
#---------------------------------------------------------------------------
-# configuration options related to the XML output
+# Configuration options related to the XML output
#---------------------------------------------------------------------------
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
GENERATE_XML = YES
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
XML_OUTPUT = xml
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING = YES
-XML_SCHEMA =
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
-XML_DTD =
+GENERATE_DOCBOOK = YES
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-XML_PROGRAMLISTING = YES
+DOCBOOK_OUTPUT = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
+# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sf.net) file that captures the
+# structure of the code including all documentation. Note that this feature is
+# still experimental and incomplete at the moment.
+# The default value is: NO.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
+# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
GENERATE_PERLMOD = NO
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_LATEX = NO
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader.
-# This is useful
-# if you want to understand what is going on.
-# On the other hand, if this
-# tag is set to NO the size of the Perl module output will be much smaller
-# and Perl will parse it just the same.
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_PRETTY = YES
-# The names of the make variables in the generated doxyrules.make file
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-# This is useful so different doxyrules.make files included by the same
-# Makefile don't overwrite each other's variables.
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_MAKEVAR_PREFIX =
@@ -1484,108 +1967,131 @@ PERLMOD_MAKEVAR_PREFIX =
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-# evaluate all C-preprocessor directives found in the sources and include
-# files.
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
ENABLE_PREPROCESSING = YES
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-# names in the source code. If set to NO (the default) only conditional
-# compilation will be performed. Macro expansion can be done in a controlled
-# way by setting EXPAND_ONLY_PREDEF to YES.
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
MACRO_EXPANSION = YES
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-# then the macro expansion is limited to the macros specified with the
-# PREDEFINED and EXPAND_AS_DEFINED tags.
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_ONLY_PREDEF = YES
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# pointed to by INCLUDE_PATH will be searched when a #include is found.
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SEARCH_INCLUDES = NO
# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by
-# the preprocessor.
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
INCLUDE_PATH =
# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will
-# be used.
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
INCLUDE_FILE_PATTERNS =
-# The PREDEFINED tag can be used to specify one or more macro names that
-# are defined before the preprocessor is started (similar to the -D option of
-# gcc). The argument of the tag is a list of macros of the form: name
-# or name=definition (no spaces). If the definition and the = are
-# omitted =1 is assumed. To prevent a macro definition from being
-# undefined via #undef or recursively expanded use the := operator
-# instead of the = operator.
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED = "GDCM_LEGACY(x)= x;" \
"gdcm_ns=gdcm" \
"gdcmEventMacro(classname,super)= class classname: public super {};"
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
-# this tag can be used to specify a list of macro names that should be expanded.
-# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition that
-# overrules the definition found in the source code.
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_AS_DEFINED =
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all references to function-like macros
-# that are alone on a line, have an all uppercase name, and do not end with a
-# semicolon, because these will confuse the parser if not removed.
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
-# Configuration::additions related to external references
+# Configuration options related to external references
#---------------------------------------------------------------------------
-# The TAGFILES option can be used to specify one or more tagfiles. For each
-# tag file the location of the external documentation should be added. The
-# format of a tag file without this location is as follows:
-#
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
# TAGFILES = file1 file2 ...
# Adding location for the tag files is done as follows:
-#
# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths
-# or URLs. Note that each tag file must have a unique name (where the name does
-# NOT include the path). If a tag file is not located in the directory in which
-# doxygen is run, you must also specify the path to the tagfile here.
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
TAGFILES =
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
GENERATE_TAGFILE = @GDCM_BINARY_DIR@/Utilities/doxygen/GDCM.tag
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
ALLEXTERNALS = NO
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
EXTERNAL_GROUPS = YES
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES = YES
+
# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
PERL_PATH = /usr/bin/perl
@@ -1593,222 +2099,308 @@ PERL_PATH = /usr/bin/perl
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option also works with HAVE_DOT disabled, but it is recommended to
-# install and use dot, since it yields more powerful graphs.
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
CLASS_DIAGRAMS = YES
# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see
-# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
# documentation. The MSCGEN_PATH tag allows you to specify the directory where
# the mscgen tool resides. If left empty the tool is assumed to be found in the
# default search path.
MSCGEN_PATH =
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH =
+
+# If set to YES the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
HIDE_UNDOC_RELATIONS = YES
# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: YES.
HAVE_DOT = YES
-# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
-# allowed to run in parallel. When set to 0 (the default) doxygen will
-# base this on the number of processors available in the system. You can set it
-# explicitly to a value larger than 0 to get control over the balance
-# between CPU load and processing speed.
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_NUM_THREADS = 1
-# By default doxygen will use the Helvetica font for all dot files that
-# doxygen generates. When you want a differently looking font you can specify
-# the font name using DOT_FONTNAME. You need to make sure dot is able to find
-# the font, which can be done by putting it in a standard location or by setting
-# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
-# directory containing the font.
+# When you want a differently looking font in the dot files that doxygen
+# generates you can specify the font name using DOT_FONTNAME. You need to make
+# sure dot is able to find the font, which can be done by putting it in a
+# standard location or by setting the DOTFONTPATH environment variable or by
+# setting DOT_FONTPATH to the directory containing the font.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTNAME = FreeSans
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
-# The default size is 10pt.
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTSIZE = 10
-# By default doxygen will tell dot to use the Helvetica font.
-# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
-# set the path where dot can find it.
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTPATH =
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# CLASS_DIAGRAMS tag to NO.
+# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
+# each documented class showing the direct and indirect inheritance relations.
+# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
CLASS_GRAPH = YES
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
COLLABORATION_GRAPH = YES
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for groups, showing the direct groups dependencies
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
GROUP_GRAPHS = YES
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
# collaboration diagrams in a style similar to the OMG's Unified Modeling
# Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
UML_LOOK = NO
-# If the UML_LOOK tag is enabled, the fields and methods are shown inside
-# the class node. If there are many fields or methods and many nodes the
-# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
-# threshold limits the number of items for each type to make the size more
-# managable. Set this to 0 for no limit. Note that the threshold may be
-# exceeded by 50% before the limit is enforced.
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
UML_LIMIT_NUM_FIELDS = 10
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
TEMPLATE_RELATIONS = YES
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDE_GRAPH = YES
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDED_BY_GRAPH = YES
-# If the CALL_GRAPH and HAVE_DOT options are set to YES then
-# doxygen will generate a call dependency graph for every global function
-# or class method. Note that enabling this option will significantly increase
-# the time of a run. So in most cases it will be better to enable call graphs
-# for selected functions only using the \callgraph command.
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
CALL_GRAPH = NO
-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
-# doxygen will generate a caller dependency graph for every global function
-# or class method. Note that enabling this option will significantly increase
-# the time of a run. So in most cases it will be better to enable caller
-# graphs for selected functions only using the \callergraph command.
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
CALLER_GRAPH = NO
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will generate a graphical hierarchy of all classes instead of a textual one.
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
GRAPHICAL_HIERARCHY = YES
-# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
-# then doxygen will show the dependencies a directory has on other directories
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
DIRECTORY_GRAPH = YES
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are svg, png, jpg, or gif.
-# If left blank png will be used. If you choose svg you need to set
-# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
-# visible in IE 9+ (other browsers do not have this requirement).
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+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
INTERACTIVE_SVG = NO
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+# The DOT_PATH tag can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_PATH = @DOXYGEN_DOT_PATH@
# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
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+# contain dot files that are included in the documentation (see the \dotfile
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+# This tag requires that the tag HAVE_DOT is set to YES.
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# The MSCFILE_DIRS tag can be used to specify one or more directories that
-# contain msc files that are included in the documentation (see the
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+# contain msc files that are included in the documentation (see the \mscfile
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-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
-# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file. If left blank, it is assumed
+# PlantUML is not used or called during a preprocessing step. Doxygen will
+# generate a warning when it encounters a \startuml command in this case and
+# will not generate output for the diagram.
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+PLANTUML_JAR_PATH =
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_GRAPH_MAX_NODES = 50
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-# graphs generated by dot. A depth value of 3 means that only nodes reachable
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-# that lay further from the root node will be omitted. Note that setting this
-# option to 1 or 2 may greatly reduce the computation time needed for large
-# code bases. Also note that the size of a graph can be further restricted by
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
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+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
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-# seem to support this out of the box. Warning: Depending on the platform used,
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+# background. This is disabled by default, because dot on Windows does not seem
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diff --git a/Utilities/doxygen/man/gdcm2pnm.dox b/Utilities/doxygen/man/gdcm2pnm.dox
deleted file mode 100644
index 88cb3c7..0000000
--- a/Utilities/doxygen/man/gdcm2pnm.dox
+++ /dev/null
@@ -1,71 +0,0 @@
-/*!
-
-\page gdcm2pnm off-screen rendering of DICOM images
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcm2pnm [options] file-in bitmap-out
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcm2pnm command line program takes as input a DICOM file and produces
-a rendered bitmap file.
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM input filename
-
-bitmap-out Bitmap output filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection options options
-\verbatim
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\section simple_usage Simple usage
-\b gdcm2pnm will take as input DICOM and render it into a bitmap file using the
-window/level attributes value.
-
-\verbatim
-$ gdcm2pnm input.dcm output.png
-\endverbatim
-
-It is much different from the gdcmraw or gdcmimg command line tool as it will
-render a DICOM image. This means that the output will be rendered in 8bits
-ready for display.
-
-\section see_also SEE ALSO
-
-<b>gdcm2vtk</b>(1), <b>gdcmimg</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcm2pnm.xml b/Utilities/doxygen/man/gdcm2pnm.xml
new file mode 100644
index 0000000..5ccb02c
--- /dev/null
+++ b/Utilities/doxygen/man/gdcm2pnm.xml
@@ -0,0 +1,82 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcm2pnm</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcm2pnm</refname>
+ <refpurpose>off-screen rendering of DICOM images</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcm2pnm_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcm2pnm [options] file-in bitmap-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcm2pnm_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcm2pnm</emphasis> command line program takes as input a DICOM file and produces a rendered bitmap file.</para>
+</refsection>
+<refsection xml:id="gdcm2pnm_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in DICOM input filename
+
+bitmap-out Bitmap output filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcm2pnm_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcm2pnm_1specific_options">
+<title>specific options</title>
+
+<para><literallayout></literallayout></para>
+</refsection>
+<refsection xml:id="gdcm2pnm_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmviewer_1simple_usage">
+<title>Simple usage</title>
+
+<para><emphasis role="bold">gdcm2pnm</emphasis> will take as input DICOM and render it into a bitmap file using the window/level attributes value.</para>
+
+<para><literallayout>$ gdcm2pnm input.dcm output.png
+</literallayout></para>
+
+<para>It is much different from the gdcmraw or gdcmimg command line tool as it will render a DICOM image. This means that the output will be rendered in 8bits ready for display.</para>
+</refsection>
+<refsection xml:id="gdcm2pnm_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcm2vtk</emphasis>(1), <emphasis role="bold">gdcmimg</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcm2vtk.dox b/Utilities/doxygen/man/gdcm2vtk.dox
deleted file mode 100644
index 4e2088e..0000000
--- a/Utilities/doxygen/man/gdcm2vtk.dox
+++ /dev/null
@@ -1,187 +0,0 @@
-/*!
-
-\page gdcm2vtk Convert a file supported by VTK into DICOM.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcm2vtk [options] file-in file-out
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcm2vtk takes as input any file supported by VTK (including DICOM file) and will generate as output
-a DICOM file.
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in input filename (DICOM or VTK supported)
-
-file-out output filename (DICOM or VTK supported)
-\endverbatim
-
-\section options OPTIONS
-
-\subsection options options
-\verbatim
- --force-rescale force rescale.
- --force-spacing force spacing.
- --palette-color when supported generate a PALETTE COLOR file.
- --argb when supported generate a ARGB file.
- --compress when supported generate a compressed file.
- --use-vtkdicom Use vtkDICOMImageReader (instead of GDCM).
- --modality set Modality.
- --lower-left set lower left.
- --shift set shift.
- --scale set scale.
- --compress set compression (MetaIO).
- -T --study-uid Study UID.
- -S --series-uid Series UID.
- --root-uid Root UID.
-\endverbatim
-
-\subsection compression_options compression options
-\verbatim
- -J --jpeg Compress image in jpeg.
- -K --j2k Compress image in j2k.
- -L --jpegls Compress image in jpeg-ls.
- -R --rle Compress image in rle (lossless only).
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\subsection environment_variable environment variable
-\verbatim
- GDCM_ROOT_UID Root UID
-\endverbatim
-
-\section description DESCRIPTION
-Convert a file supported by VTK into DICOM.
-
-Typical usage is:
-
-\verbatim
-$ gdcm2vtk inputfile output.dcm
-\endverbatim
-
-It uses the internal factory mechanism of VTK to recognize a file (CanRead function). See VTK supported file here:
-
- * What image file formats can VTK read and write? http://www.vtk.org/Wiki/VTK_FAQ#What_image_file_formats_can_VTK_read_and_write.3F
-
-If your input file has 4 components, the 4th comp (alpha) will be removed from the output file as DICOM does not support alpha component anymore (see --argb option).
-
-Special care was taken for the following file format:
-
-\verbatim
- 1. DICOM: Direction Cosines and vtkMedicalImageInformation are passed to the output
- 2. BMP: The file can be saved with a Lookup Table (see --palette-color)
- 3. GE Signa: vtkMedicalImageProperties is passed to the output
- 4. MINC: Direction Cosines is passed to the output
- 5. TIFF: vtkTIFFReader is currently in bad shape in VTK (different behavior in VTK 5.2 and git/master). Only use it, if you know what you are doing.
-\endverbatim
-
-\subsection convert_meta CONVERT MetaImage (mhd, mha)
-
-\verbatim
-$ gdcm2vtk inputfile output.mha
-\endverbatim
-
-This command will convert the input DICOM file: inputfile into a MetaImage .mha file. Same goes for .mhd file.
-
-\subsection convert_mha CONVERT MHA/MHD
-
-\verbatim
-$ gdcm2vtk inputfile output.mha
-\endverbatim
-or
-\verbatim
-$ gdcm2vtk inputfile output.mhd
-\endverbatim
-
-This command will convert the input DICOM file: inputfile into a MetaImageData .mha/.mhd file.
-
-\subsection convert_vti CONVERT VTI
-
-\verbatim
-$ gdcm2vtk inputfile output.vti
-\endverbatim
-
-This command will convert the input DICOM file: inputfile into a XML VTK ImageData .vti file.
-
-\subsection convert_vtk CONVERT VTK
-
-\verbatim
-$ gdcm2vtk inputfile output.vtk
-\endverbatim
-
-This command will convert the input DICOM file: inputfile into an old VTK Structured PointSets .vtk file.
-
-\section convert_dicom CONVERT DICOM
-
-\verbatim
-$ gdcm2vtk input.dcm output.dcm
-\endverbatim
-
-vtkGDCMImageReader will be used to read in a DICOM file, not the default vtkDICOMImageReader.
-See option --use-vtkdicom to use vtkDICOMImageReader.
-
-\section round_tripmhd RoundTrip DICOM to MHD to DICOM
-
-\verbatim
-$ gdcm2vtk input_ybr.dcm output.mhd
-$ gdcm2vtk --modality US --imageformat 7 output.mhd output.dcm
-\endverbatim
-
-The above section shows how to convert a DICOM using the Photometric Interpretation of YBR_FULL
-(or even YBR_FULL_422 is lossy) into another file format: MetaImage (mhd). Since this
-file format does not handle color space, we have to explicitly set it using the --imageformat
-command line option.
-The --modality command line option is required in this case since the default Secondary Capture
-Image Storage Class family does not allow for YBR Photometric Interpretation.
-
-\section gdcm2vtk_notes gdcm2vtk notes
-
-IMPORTANT NOTE: The internal VTK structured will be filled from the input
-DICOM, and then pass to the output DICOM writer. Some information might be lost
-during the conversion DICOM to VTK to DICOM. This option is mostly used to test
-the vtkGDCMImageReader/vtkGDCMImageWriter combination.
-
-IMPORTANT NOTE: When converting from a lossy format such as JPEG, the
-information of lossiness is important. The output DICOM will contains the
-required Lossy Image Compression attribute that indicates that image was
-lossy-compressed somewhere along the pipeline. See also gdcmimg (better
-handling of JPEG in general).
-
-IMPORTANT NOTE: When using --use-vtkdicom the output DICOM file will always be
-written as MR Image Storage as this information is not available from the
-reader itself. This allow setting the Image Orientation (Patient) properly.
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcmviewer</b>(1), <b>gdcmimg</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcm2vtk.xml b/Utilities/doxygen/man/gdcm2vtk.xml
new file mode 100644
index 0000000..ff5ad6f
--- /dev/null
+++ b/Utilities/doxygen/man/gdcm2vtk.xml
@@ -0,0 +1,184 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcm2vtk</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcm2vtk</refname>
+ <refpurpose>Convert a file supported by VTK into DICOM.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmxml_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcm2vtk [options] file-in file-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcm2vtk</emphasis> takes as input any file supported by VTK (including DICOM file) and will generate as output a DICOM file.</para>
+</refsection>
+<refsection xml:id="gdcmxml_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in input filename (DICOM or VTK supported)
+
+file-out output filename (DICOM or VTK supported)
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcmxml_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> --force-rescale force rescale.
+ --force-spacing force spacing.
+ --palette-color when supported generate a PALETTE COLOR file.
+ --argb when supported generate a ARGB file.
+ --compress when supported generate a compressed file.
+ --use-vtkdicom Use vtkDICOMImageReader (instead of GDCM).
+ --modality set Modality.
+ --lower-left set lower left.
+ --shift set shift.
+ --scale set scale.
+ --compress set compression (MetaIO).
+ -T --study-uid Study UID.
+ -S --series-uid Series UID.
+ --root-uid Root UID.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcm2vtk_1compression_options">
+<title>compression options</title>
+
+<para><literallayout> -J --jpeg Compress image in jpeg.
+ -K --j2k Compress image in j2k.
+ -L --jpegls Compress image in jpeg-ls.
+ -R --rle Compress image in rle (lossless only).
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1environment_variable">
+<title>environment variable</title>
+
+<para><literallayout> GDCM_ROOT_UID Root UID
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmxml_1description2">
+<title>DESCRIPTION</title>
+
+<para>Convert a file supported by VTK into DICOM.</para>
+
+<para>Typical usage is:</para>
+
+<para><literallayout>$ gdcm2vtk inputfile output.dcm
+</literallayout></para>
+
+<para>It uses the internal factory mechanism of VTK to recognize a file (CanRead function). See VTK supported file here: <literallayout> What image file formats can VTK read and write? http://www.vtk.org/Wiki/VTK_FAQ#What_image_file_formats_can_VTK_read_and_write.3F
+</literallayout></para>
+
+<para>If your input file has 4 components, the 4th comp (alpha) will be removed from the output file as DICOM does not support alpha component anymore (see –argb option).</para>
+
+<para>Special care was taken for the following file format:</para>
+
+<para><literallayout> 1. DICOM: Direction Cosines and vtkMedicalImageInformation are passed to the output
+ 2. BMP: The file can be saved with a Lookup Table (see --palette-color)
+ 3. GE Signa: vtkMedicalImageProperties is passed to the output
+ 4. MINC: Direction Cosines is passed to the output
+ 5. TIFF: vtkTIFFReader is currently in bad shape in VTK (different behavior in VTK 5.2 and git/master). Only use it, if you know what you are doing.
+</literallayout></para>
+<refsection xml:id="gdcm2vtk_1convert_meta">
+<title>CONVERT MetaImage (mhd, mha)</title>
+
+<para><literallayout>$ gdcm2vtk inputfile output.mha
+</literallayout></para>
+
+<para>This command will convert the input DICOM file: inputfile into a MetaImage .mha file. Same goes for .mhd file.</para>
+</refsection>
+<refsection xml:id="gdcm2vtk_1convert_mha">
+<title>CONVERT MHA/MHD</title>
+
+<para><literallayout>$ gdcm2vtk inputfile output.mha
+</literallayout> or <literallayout>$ gdcm2vtk inputfile output.mhd
+</literallayout></para>
+
+<para>This command will convert the input DICOM file: inputfile into a MetaImageData .mha/.mhd file.</para>
+</refsection>
+<refsection xml:id="gdcm2vtk_1convert_vti">
+<title>CONVERT VTI</title>
+
+<para><literallayout>$ gdcm2vtk inputfile output.vti
+</literallayout></para>
+
+<para>This command will convert the input DICOM file: inputfile into a XML VTK ImageData .vti file.</para>
+</refsection>
+<refsection xml:id="gdcm2vtk_1convert_vtk">
+<title>CONVERT VTK</title>
+
+<para><literallayout>$ gdcm2vtk inputfile output.vtk
+</literallayout></para>
+
+<para>This command will convert the input DICOM file: inputfile into an old VTK Structured PointSets .vtk file.</para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcm2vtk_1convert_dicom">
+<title>CONVERT DICOM</title>
+
+<para><literallayout>$ gdcm2vtk input.dcm output.dcm
+</literallayout></para>
+
+<para><emphasis>vtkGDCMImageReader</emphasis> will be used to read in a DICOM file, not the default vtkDICOMImageReader. See option –use-vtkdicom to use vtkDICOMImageReader.</para>
+</refsection>
+<refsection xml:id="gdcm2vtk_1round_tripmhd">
+<title>RoundTrip DICOM to MHD to DICOM</title>
+
+<para><literallayout>$ gdcm2vtk input_ybr.dcm output.mhd
+$ gdcm2vtk --modality US --imageformat 7 output.mhd output.dcm
+</literallayout></para>
+
+<para>The above refsection shows how to convert a DICOM using the Photometric Interpretation of YBR_FULL (or even YBR_FULL_422 is lossy) into another file format: MetaImage (mhd). Since this file format does not handle color space, we have to explicitly set it using the –imageformat command line option. The –modality command line option is required in this case since the default Secondary Capture Image Storage Class family does not allow for YBR Photometric Interpretation.</para>
+</refsection>
+<refsection xml:id="gdcm2vtk_1gdcm2vtk_notes">
+<title>gdcm2vtk notes</title>
+
+<para>IMPORTANT NOTE: The internal VTK structured will be filled from the input DICOM, and then pass to the output DICOM writer. Some information might be lost during the conversion DICOM to VTK to DICOM. This option is mostly used to test the vtkGDCMImageReader/vtkGDCMImageWriter combination.</para>
+
+<para>IMPORTANT NOTE: When converting from a lossy format such as JPEG, the information of lossiness is important. The output DICOM will contains the required Lossy Image Compression attribute that indicates that image was lossy-compressed somewhere along the pipeline. See also gdcmimg (better handling of JPEG in general).</para>
+
+<para>IMPORTANT NOTE: When using –use-vtkdicom the output DICOM file will always be written as MR Image Storage as this information is not available from the reader itself. This allow setting the Image Orientation (Patient) properly.</para>
+</refsection>
+<refsection xml:id="gdcmxml_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmviewer</emphasis>(1), <emphasis role="bold">gdcmimg</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmanon.dox b/Utilities/doxygen/man/gdcmanon.dox
deleted file mode 100644
index e44b8b7..0000000
--- a/Utilities/doxygen/man/gdcmanon.dox
+++ /dev/null
@@ -1,288 +0,0 @@
-/*!
-
-\page gdcmanon Tool to anonymize a DICOM file.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmanon [options] file-in file-out
-gdcmanon [options] dir-in dir-out
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmanon tool is an implementation of PS 3.15 / E.1 / Basic Application
-Level Confidentiality Profile (Implementation of E.1.1 De-identify & E.1.2
-Re-identify)
-
-This tool is split into two very different operating mode:
-\li An implementation of PS 3.15, see -e and -d flags
-\li A dumb mode, see --dumb
-
-Dumb mode and PS 3.15 do not work well together, you should really only use one
-type of anonymization. In case of doubt, avoid using --dumb.
-
-In order to use the PS 3.15 implementation (-d & -e flag), you'll need a
-certificate to do de-identification operations, and the associated private key
-to do the re-identification operation. If you are only doing a one-shot
-anonymization and do not need to properly re-identify the DICOM file, you can
-safely discard the private key and only keep the certificate. See OpenSSL
-section below for an example on how to generate the private key/certificate
-pair.
-
-gdcmanon will exit early if OpenSSL was not configured/build properly into the
-library (see GDCM_USE_SYSTEM_OPENSSL in cmake).
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM input filename
-
-file-out DICOM output filename
-\endverbatim
-
-or
-
-\verbatim
-file-in DICOM input directory
-
-file-out DICOM output directory
-\endverbatim
-
-\section options OPTIONS
-
-You need to specify at least one operating mode, from the following list (and
-only one):
-
-\subsection required_params Required parameters
-\verbatim
- -e --de-identify De-identify DICOM (default)
- -d --re-identify Re-identify DICOM
- --dumb Dumb mode anonymizer
-\endverbatim
-
-Warning when operating in dumb mode, you need to also specify an operation to
-do, such as 'remove' or 'empty' a tag, see below the dumb mode options.
-
-\subsection options options
-\verbatim
- -i --input DICOM filename / directory
- -o --output DICOM filename / directory
- -r --recursive recursively process (sub-)directories.
- --continue Do not stop when file found is not DICOM.
- --root-uid Root UID.
- --resources-path Resources path.
- -k --key Path to RSA Private Key.
- -c --certificate Path to Certificate.
-\endverbatim
-
-\subsection encryption_options encryption options
-\verbatim
- --des DES.
- --des3 Triple DES.
- --aes128 AES 128.
- --aes192 AES 192.
- --aes256 AES 256.
-\endverbatim
-
-\subsection dumb_mode_options dumb mode options
-\verbatim
- --empty %d,%d DICOM tag(s) to empty
- --remove %d,%d DICOM tag(s) to remove
- --replace %d,%d,%s DICOM tag(s) to replace
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\subsection environment_variable environment variable
-\verbatim
- GDCM_ROOT_UID Root UID
- GDCM_RESOURCES_PATH path pointing to resources files (Part3.xml, ...)
-\endverbatim
-
-\section usage Typical usage
-\subsection deident De-identification (anonymization, encrypt)
-
-The only thing required for this operation is a certificate file (in PEM
-format).
-
-\verbatim
-$ gdcmanon --certificate certificate.pem -e original.dcm original_anonymized.dcm
-\endverbatim
-
-You can use --asn1 option from gdcmdump to dump the generated DataSet
-as ASN1 structure (see <b>gdcmdump</b>(1) for example).
-
-\subsection reindent Re-identification (de-anonymization,decrypt)
-
-The only thing required for this operation is a private key (in PEM format). It
-is required that the private key used for the re-identification process, was
-the actual private key used to generate the certificate file (certificate.pem)
-used during the de-identification step.
-
-\verbatim
-$ gdcmanon --key privatekey.pem -d original_anonymized.dcm original_copy.dcm
-\endverbatim
-
-You can then check that original.dcm and original_copy.dcm are identical.
-
-\subsection caveat Multiple files caveat
-
-It is very important to understand the following section, when anonymizing more
-than one single file. When anonymizing multiple DICOM files, you are required
-to use the directory input. You cannot call multiple time the gdcmanon command
-line tool. Indeed the tool stores in memory during the process only a hash
-table of conversion so that each time a particular value is found it get always
-replaced by the same de-identified value (think: consistent Series Instance
-UID).
-
-\subsection dumb Dumb mode
-
-This functionality is not described in the DICOM standard. Users are advised
-that improper use of that mode is not recommended, meaning that important tag
-can be emptied/removed/replaced resulting in illegal/invalid DICOM file. Only
-use when you know what you are doing. If you delete a Type 1 attribute, chance
-is that your DICOM file will be not accepted in most DICOM third party viewer.
-Unfortunately this is often this mode that is implemented in popular DICOM
-Viewer, always prefer what the DICOM standard describes, and avoid the dumb
-mode.
-
-The following example shows how to use dumb mode and achieve 5 operations at the same time:
-\li Empty the tag (0010,0010) Patient's Name,
-\li Empty the tag (0010,0020) Patient ID,
-\li Remove the tag (0010,0040) Patient's Sex
-\li Remove the tag (0010,1010) Patient's Age
-\li Replace the tag (0010,1030) Patient's Weight with the value '10'
-
-You are required to check which DICOM attribute is Type 1 and Type 1C, before
-trying to \b 'Empty' or \b 'Remove' a particular DICOM attribute. For the same
-reason, you are required to check what are valid value in a replace operation.
-
-\verbatim
-$ gdcmanon --dumb --empty 10,10 --empty 10,20 --remove 10,40 --remove 10,1010 --replace 10,1030,10 012345.002.050.dcm out.dcm
-\endverbatim
-
-Multiple operation of --dumb mode can take place, just reuse the output of the
-previous operation. Always use gdcmdump on the input and output file to check
-what was actually achieved. You can use a diff program to check only what
-changed (see <b>gdcmdiff</b>(1) for example).
-
-\subsubsection irreversible_anon Irreversible Anonymization
-
-In some very rare cases, one would want to anonymize using the PS 3.15 mode so
-as to take benefit of the automatic conversion of all content that could
-contain Patient related information.
-
-In the end all Patient related information has been removed and has been
-secretly stored in the 0400,0500 DICOM attribute. However to make sure that
-no-one ever try to break that security using brute-force algorithm, one want
-want to remove completely this DICOM attribute. This will make the DICOM:
-
-\li Completely free of any Patient related information (as per PS 3.15 specification)
-\li Remove any mean of people to brute force attack the file to find out the identity of the Patient
-
-In this case one could simply do, as a first step execute the reversible anonymizer:
-
-\verbatim
-$ gdcmanon -c certificate.pem input.dcm anonymized_reversible.dcm
-\endverbatim
-
-and now completely remove the DICOM attribute containing the secretly encrypted Patient related
-information:
-
-\verbatim
-$ gdcmanon --dumb --remove 400,500 --remove 12,62 --remove 12,63 anonymized_reversible.dcm anonymized_irreversible.dcm
-\endverbatim
-
-\remark
-As mentionned in DICOM Sup 142, this anonymization is preferred over
-de-identification since:
-It is not required that the Encrypted Attributes Data Set be created; indeed,
-there may be circumstances where the Dataset is expected to be archived long
-enough that any contemporary encryption technology may be inadequate to provide
-long term protection against unauthorized recovery of identification
-
-\section openssl OpenSSL
-
-On most system you can have access to OpenSSL to generate the Private
-Key/Certificate pair.
-
-\subsection priv_key Generating a Private Key
-
-Command line to generate a rsa key (512bit)
-
-\verbatim
-$ openssl genrsa -out CA_key.pem
-\endverbatim
-
-Command line to generate a rsa key (2048bit)
-
-\verbatim
-$ openssl genrsa -out CA_key.pem 2048
-\endverbatim
-
-Command line to generate a rsa key (2048bit) + passphrase
-
-\verbatim
-$ openssl genrsa -des3 -out CA_key.pem 2048
-\endverbatim
-
-\subsection certificate Generating a Certificate
-
-From your previously generated Private Key, you can now generate a certificate
-in PEM (DER format is currently not supported).
-
-\verbatim
-$ openssl req -new -key CA_key.pem -x509 -days 365 -out CA_cert.cer
-\endverbatim
-
-\section dicom_standard DICOM Standard:
-
-Page to the DICOM Standard:
-
-http://dicom.nema.org/
-
-The DICOM Standard at the time of releasing gdcmanon is:
-
-ftp://medical.nema.org/medical/dicom/2008/
-
-Direct link to PS 3.15-2008:
-
-ftp://medical.nema.org/medical/dicom/2008/08_15pu.pdf
-
-\section gdcmanon_warnings Warnings
-
-Certain attributes may still contains Protected Health Information (PHI) after
-an anonymization step. This is typically the case for Patient's Address (0010,1040).
-The reason is that this particular attribute is not supposed to be in the composite
-IODs in the first place. DICOM Supp 142 includes it (however gdcmanon does not
-implement it).
-
-\section see_also SEE ALSO
-
-<b>gdcmconv</b>(1), <b>gdcmdump</b>(1), <b>gdcmdiff</b>(1), <b>openssl</b>(1), <b>dumpasn1</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmanon.xml b/Utilities/doxygen/man/gdcmanon.xml
new file mode 100644
index 0000000..49ff84c
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmanon.xml
@@ -0,0 +1,278 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmanon</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmanon</refname>
+ <refpurpose>Tool to anonymize a DICOM file.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmanon_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmanon [options] file-in file-out
+gdcmanon [options] dir-in dir-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmanon_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmanon</emphasis> tool is an implementation of PS 3.15 / E.1 / Basic Application Level Confidentiality Profile (Implementation of E.1.1 De-identify & E.1.2 Re-identify)</para>
+
+<para>This tool is split into two very different operating mode: <itemizedlist>
+<listitem>
+<para>An implementation of PS 3.15, see -e and -d flags </para>
+</listitem>
+<listitem>
+<para>A dumb mode, see –dumb</para>
+</listitem>
+</itemizedlist>
+Dumb mode and PS 3.15 do not work well together, you should really only use one type of anonymization. In case of doubt, avoid using –dumb.</para>
+
+<para>In order to use the PS 3.15 implementation (-d & -e flag), you'll need a certificate to do de-identification operations, and the associated private key to do the re-identification operation. If you are only doing a one-shot anonymization and do not need to properly re-identify the DICOM file, you can safely discard the private key and only keep the certificate. See OpenSSL refsection below for an example on how to generate the private key/certificate pair.</para>
+
+<para>gdcmanon will exit early if OpenSSL was not configured/build properly into the library (see GDCM_USE_SYSTEM_OPENSSL in cmake).</para>
+</refsection>
+<refsection xml:id="gdcmanon_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in DICOM input filename
+
+file-out DICOM output filename
+</literallayout></para>
+
+<para>or</para>
+
+<para><literallayout>file-in DICOM input directory
+
+file-out DICOM output directory
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmanon_1options">
+<title>OPTIONS</title>
+
+<para>You need to specify at least one operating mode, from the following list (and only one):</para>
+<refsection xml:id="gdcmanon_1required_params">
+<title>Required parameters</title>
+
+<para><literallayout> -e --de-identify De-identify DICOM (default)
+ -d --re-identify Re-identify DICOM
+ --dumb Dumb mode anonymizer
+</literallayout></para>
+
+<para>Warning when operating in dumb mode, you need to also specify an operation to do, such as 'remove' or 'empty' a tag, see below the dumb mode options.</para>
+</refsection>
+<refsection xml:id="gdcmanon_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> -i --input DICOM filename / directory
+ -o --output DICOM filename / directory
+ -r --recursive recursively process (sub-)directories.
+ --continue Do not stop when file found is not DICOM.
+ --root-uid Root UID.
+ --resources-path Resources path.
+ -k --key Path to RSA Private Key.
+ -c --certificate Path to Certificate.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmanon_1encryption_options">
+<title>encryption options</title>
+
+<para><literallayout> --des DES.
+ --des3 Triple DES.
+ --aes128 AES 128.
+ --aes192 AES 192.
+ --aes256 AES 256.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmanon_1dumb_mode_options">
+<title>dumb mode options</title>
+
+<para><literallayout> --empty %d,%d DICOM tag(s) to empty
+ --remove %d,%d DICOM tag(s) to remove
+ --replace %d,%d,%s DICOM tag(s) to replace
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmanon_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1environment_variable">
+<title>environment variable</title>
+
+<para><literallayout> GDCM_ROOT_UID Root UID
+ GDCM_RESOURCES_PATH path pointing to resources files (Part3.xml, ...)
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmviewer_1usage">
+<title>Typical usage</title>
+<refsection xml:id="gdcmanon_1deident">
+<title>De-identification (anonymization, encrypt)</title>
+
+<para>The only thing required for this operation is a certificate file (in PEM format).</para>
+
+<para><literallayout>$ gdcmanon --certificate certificate.pem -e original.dcm original_anonymized.dcm
+</literallayout></para>
+
+<para>You can use –asn1 option from gdcmdump to dump the generated DataSet as ASN1 structure (see <emphasis role="bold">gdcmdump</emphasis>(1) for example).</para>
+</refsection>
+<refsection xml:id="gdcmanon_1reindent">
+<title>Re-identification (de-anonymization,decrypt)</title>
+
+<para>The only thing required for this operation is a private key (in PEM format). It is required that the private key used for the re-identification process, was the actual private key used to generate the certificate file (certificate.pem) used during the de-identification step.</para>
+
+<para><literallayout>$ gdcmanon --key privatekey.pem -d original_anonymized.dcm original_copy.dcm
+</literallayout></para>
+
+<para>You can then check that original.dcm and original_copy.dcm are identical.</para>
+</refsection>
+<refsection xml:id="gdcmanon_1caveat">
+<title>Multiple files caveat</title>
+
+<para>It is very important to understand the following refsection, when anonymizing more than one single file. When anonymizing multiple DICOM files, you are required to use the directory input. You cannot call multiple time the gdcmanon command line tool. Indeed the tool stores in memory during the process only a hash table of conversion so that each time a particular value is found it get always replaced by the same de-identified value (think: consistent Series Instance UID).</para>
+</refsection>
+<refsection xml:id="gdcmanon_1dumb">
+<title>Dumb mode</title>
+
+<para>This functionality is not described in the DICOM standard. Users are advised that improper use of that mode is not recommended, meaning that important tag can be emptied/removed/replaced resulting in illegal/invalid DICOM file. Only use when you know what you are doing. If you delete a Type 1 attribute, chance is that your DICOM file will be not accepted in most DICOM third party viewer. Unfortunately this is often this mode that is implemented in popular DICOM Viewer, always prefe [...]
+
+<para>The following example shows how to use dumb mode and achieve 5 operations at the same time: <itemizedlist>
+<listitem>
+<para>Empty the tag (0010,0010) Patient's Name, </para>
+</listitem>
+<listitem>
+<para>Empty the tag (0010,0020) Patient ID, </para>
+</listitem>
+<listitem>
+<para>Remove the tag (0010,0040) Patient's Sex </para>
+</listitem>
+<listitem>
+<para>Remove the tag (0010,1010) Patient's Age </para>
+</listitem>
+<listitem>
+<para>Replace the tag (0010,1030) Patient's Weight with the value '10'</para>
+</listitem>
+</itemizedlist>
+You are required to check which DICOM attribute is Type 1 and Type 1C, before trying to <emphasis role="bold">'Empty'</emphasis> or <emphasis role="bold">'Remove'</emphasis> a particular DICOM attribute. For the same reason, you are required to check what are valid value in a replace operation.</para>
+
+<para><literallayout>$ gdcmanon --dumb --empty 10,10 --empty 10,20 --remove 10,40 --remove 10,1010 --replace 10,1030,10 012345.002.050.dcm out.dcm
+</literallayout></para>
+
+<para>Multiple operation of –dumb mode can take place, just reuse the output of the previous operation. Always use gdcmdump on the input and output file to check what was actually achieved. You can use a diff program to check only what changed (see <emphasis role="bold">gdcmdiff</emphasis>(1) for example).</para>
+<refsection xml:id="gdcmanon_1irreversible_anon">
+<title>Irreversible Anonymization</title>
+
+<para>In some very rare cases, one would want to anonymize using the PS 3.15 mode so as to take benefit of the automatic conversion of all content that could contain Patient related information.</para>
+
+<para>In the end all Patient related information has been removed and has been secretly stored in the 0400,0500 DICOM attribute. However to make sure that no-one ever try to break that security using brute-force algorithm, one want want to remove completely this DICOM attribute. This will make the DICOM:</para>
+
+<para><itemizedlist>
+<listitem>
+<para>Completely free of any Patient related information (as per PS 3.15 specification) </para>
+</listitem>
+<listitem>
+<para>Remove any mean of people to brute force attack the file to find out the identity of the Patient</para>
+</listitem>
+</itemizedlist>
+In this case one could simply do, as a first step execute the reversible anonymizer:</para>
+
+<para><literallayout>$ gdcmanon -c certificate.pem input.dcm anonymized_reversible.dcm
+</literallayout></para>
+
+<para>and now completely remove the DICOM attribute containing the secretly encrypted Patient related information:</para>
+
+<para><literallayout>$ gdcmanon --dumb --remove 400,500 --remove 12,62 --remove 12,63 anonymized_reversible.dcm anonymized_irreversible.dcm
+</literallayout></para>
+
+<para><formalpara><title>Remarks: </title>
+
+<para>As mentionned in DICOM Sup 142, this anonymization is preferred over de-identification since: It is not required that the Encrypted Attributes Data Set be created; indeed, there may be circumstances where the Dataset is expected to be archived long enough that any contemporary encryption technology may be inadequate to provide long term protection against unauthorized recovery of identification</para>
+</formalpara>
+</para>
+</refsection>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmanon_1openssl">
+<title>OpenSSL</title>
+
+<para>On most system you can have access to OpenSSL to generate the Private Key/Certificate pair.</para>
+<refsection xml:id="gdcmanon_1priv_key">
+<title>Generating a Private Key</title>
+
+<para>Command line to generate a rsa key (512bit)</para>
+
+<para><literallayout>$ openssl genrsa -out CA_key.pem
+</literallayout></para>
+
+<para>Command line to generate a rsa key (2048bit)</para>
+
+<para><literallayout>$ openssl genrsa -out CA_key.pem 2048
+</literallayout></para>
+
+<para>Command line to generate a rsa key (2048bit) + passphrase</para>
+
+<para><literallayout>$ openssl genrsa -des3 -out CA_key.pem 2048
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmanon_1certificate">
+<title>Generating a Certificate</title>
+
+<para>From your previously generated Private Key, you can now generate a certificate in PEM (DER format is currently not supported).</para>
+
+<para><literallayout>$ openssl req -new -key CA_key.pem -x509 -days 365 -out CA_cert.cer
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmanon_1dicom_standard">
+<title>DICOM Standard:</title>
+
+<para>Page to the DICOM Standard:</para>
+
+<para><link xlink:href="http://dicom.nema.org/">http://dicom.nema.org/</link></para>
+
+<para>The DICOM Standard at the time of releasing gdcmanon is:</para>
+
+<para><link xlink:href="ftp://medical.nema.org/medical/dicom/2008/">ftp://medical.nema.org/medical/dicom/2008/</link></para>
+
+<para>Direct link to PS 3.15-2008:</para>
+
+<para><link xlink:href="ftp://medical.nema.org/medical/dicom/2008/08_15pu.pdf">ftp://medical.nema.org/medical/dicom/2008/08_15pu.pdf</link></para>
+</refsection>
+<refsection xml:id="gdcmanon_1gdcmanon_warnings">
+<title>Warnings</title>
+
+<para>Certain attributes may still contains Protected Health Information (PHI) after an anonymization step. This is typically the case for Patient's Address (0010,1040). The reason is that this particular attribute is not supposed to be in the composite IODs in the first place. DICOM Supp 142 includes it (however gdcmanon does not implement it).</para>
+</refsection>
+<refsection xml:id="gdcmanon_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmconv</emphasis>(1), <emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmdiff</emphasis>(1), <emphasis role="bold">openssl</emphasis>(1), <emphasis role="bold">dumpasn1</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmconv.dox b/Utilities/doxygen/man/gdcmconv.dox
deleted file mode 100644
index 44c0e18..0000000
--- a/Utilities/doxygen/man/gdcmconv.dox
+++ /dev/null
@@ -1,396 +0,0 @@
-/*!
-
-\page gdcmconv Tool to convert DICOM to DICOM.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmconv [options] file-in file-out
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmconv command line program takes as input a DICOM file (file-in) and
-process it to generate an output DICOM file (file-out).
-The command line option dictate the type of operation(s) gdcmconv will use to
-generate the output file.
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM input filename
-
-file-out DICOM output filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection parameters parameters
-\verbatim
- -i --input DICOM filename
- -o --output DICOM filename
-\endverbatim
-
-\subsection options options
-\verbatim
- -X --explicit Change Transfer Syntax to explicit.
- -M --implicit Change Transfer Syntax to implicit.
- -U --use-dict Use dict for VR (only public by default).
- --with-private-dict Use private dict for VR (advanced user only).
- -C --check-meta Check File Meta Information (advanced user only).
- --root-uid Root UID.
- --remove-gl Remove group length (deprecated in DICOM 2008).
- --remove-private-tags Remove private tags.
- --remove-retired Remove retired tags.
-\endverbatim
-
-\subsection image_options image options
-\verbatim
- -l --apply-lut Apply LUT (non-standard, advanced user only).
- -P --photometric-interpretation %s Change Photometric Interpretation (when possible).
- -w --raw Decompress image.
- -d --deflated Compress using deflated (gzip).
- -J --jpeg Compress image in jpeg.
- -K --j2k Compress image in j2k.
- -L --jpegls Compress image in jpeg-ls.
- -R --rle Compress image in rle (lossless only).
- -F --force Force decompression/merging before recompression/splitting.
- --generate-icon Generate icon.
- --icon-minmax %d,%d Min/Max value for icon.
- --icon-auto-minmax Automatically commpute best Min/Max values for icon.
- --compress-icon Decide whether icon follows main TransferSyntax or remains uncompressed.
- --planar-configuration [01] Change planar configuration.
- -Y --lossy Use the lossy (if possible) compressor.
- -S --split %d Write 2D image with multiple fragments (using max size)
-\endverbatim
-
-\subsection jpeg_options JPEG options
-\verbatim
- -q --quality %*f set quality.
-\endverbatim
-
-\subsection jpegls_options JPEG-LS options
-\verbatim
- -e --lossy-error %*i set error.
-\endverbatim
-
-\subsection j2k_options J2K options
-\verbatim
- -r --rate %*f set rate.
- -q --quality %*f set quality.
- -t --tile %d,%d set tile size.
- -n --number-resolution %d set number of resolution.
- --irreversible set irreversible.
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\subsection special_options special options
-\verbatim
- -I --ignore-errors convert even if file is corrupted (advanced users only, see disclaimers).
-\endverbatim
-
-\subsection environment_variable environment variable
-\verbatim
- GDCM_ROOT_UID Root UID
-\endverbatim
-
-\section simple_usage Simple usage
-\b gdcmconv is a great tool to convert broken DICOM implementation into
-properly parsable DICOM file. Usage is simply:
-
-\verbatim
-$ gdcmconv input.dcm output.dcm
-\endverbatim
-
-or if you prefer being explicit:
-
-\verbatim
-$ gdcmconv -i input.dcm -o output.dcm
-\endverbatim
-
-Even though gdcmconv can overwrite directly on the same file (input.dcm =
-output.dcm), it is recommended that user should first convert into a different
-file to make sure the bug is properly handled by GDCM.
-
-Typical cases where you would want to use gdcmconv in its simple form:
-
-\li convert non-cp246 conforming file into conforming cp246,
-\li convert implicit little endian transfer syntax file meta header into proper explicit little endian transfer syntax,
-\li convert the GE-13 bytes bug,
-\li convert dual syntax file: implicit/explicit,
-\li convert Philips dual Little Endian/Big Endian file,
-\li convert GDCM 1.2.0 broken UN-2-bytes fields,
-\li \&...
-\li All other broken files listed in the supported section.
-
-When no option other is used, only the dataset is inspected. So encapsulated
-Pixel Data, for instance, is not inspected for well known bugs.
-
-When doing this kind of work, this is usually a good idea to perform some kind
-of quality control, see gdcmconv Quality Control section (down below).
-
-\section usage Typical usage
-\subsection file_meta File Meta Header
-
-Running
-
-\verbatim
-$ gdcmconv input.dcm output.dcm
-\endverbatim
-
-Is not enough to recompute file meta header, when input file is buggy. You may
-want to use: --check-meta
-
-\verbatim
-$ gdcmconv --check-meta input.dcm output.dcm
-\endverbatim
-
-See typical cases such as: GE_DLX-8-MONO2-PrivateSyntax.dcm or
-PICKER-16-MONO2-No_DicomV3_Preamble.dcm from gdcmData.
-
-\subsection explicit Conversion to Explicit Transfer Syntax
-
-To convert a file that was written using Implicit Transfer Syntax into Explicit
-Transfer Syntax simply use:
-
-\verbatim
-$ gdcmconv --explicit uncompressed.dcm compressed.dcm
-\endverbatim
-
-\subsection lossless_jpeg Compressing to lossless JPEG
-To compress an uncompressed DICOM file to a JPEG Lossless encapsulated format:
-
-\verbatim
-$ gdcmconv --jpeg uncompressed.dcm compressed.dcm
-\endverbatim
-
-\subsection lossy_jpeg Compressing to lossy JPEG
-To compress an uncompressed DICOM file to a JPEG Lossy encapsulated format:
-
-\verbatim
-$ gdcmconv --lossy --jpeg -q 90 uncompressed.dcm compressed.dcm
-\endverbatim
-
-Note:
-
- * -q is just one of the many way to specify lossy quality, you need to inspect the other cmd line flag to specify lossyness properties.
-
-\subsection lossless_jpegls Compressing to lossless JPEG-LS
-
-To compress an uncompressed DICOM file to a JPEG-LS Lossless encapsulated
-format:
-
-\verbatim
-$ gdcmconv --jpegls uncompressed.dcm compressed.dcm
-\endverbatim
-
-\subsection lossy_jpegls Compressing to lossy JPEG-LS
-
-To compress an uncompressed DICOM file to a JPEG-LS Lossy encapsulated format:
-
-\verbatim
-$ gdcmconv --lossy --jpegls -e 2 uncompressed.dcm lossy_compressed.dcm
-\endverbatim
-
-Note:
-
- -e (or --lossy-error) means that the maximum tolerate error is 2 for each pixel value
-
-\subsection lossless_j2k Compressing to lossless J2K
-
-To compress an uncompressed DICOM file to a JPEG-2000 Lossless encapsulated
-format:
-
-\verbatim
-$ gdcmconv --j2k uncompressed.dcm compressed.dcm
-\endverbatim
-
-\subsection lossy_j2k Compressing to lossy J2K
-
-To compress an uncompressed DICOM file to a JPEG-2000 Lossy encapsulated
-format:
-
-\verbatim
-$ gdcmconv --lossy -q 55,50,45 --j2k uncompressed.dcm lossy_compressed.dcm
-\endverbatim
-
-Note:
-
- * -q is just one of the many way to specify lossy quality, you need to inspect the other cmd line flag to specify lossyness properties.
-
-\subsection lossless_rle Compressing to lossless RLE
-
-To compress an uncompressed DICOM file to a RLE Lossless encapsulated format:
-
-\verbatim
-$ gdcmconv --rle uncompressed.dcm compressed.dcm
-\endverbatim
-
-There is no such thing as lossy RLE compression.
-
-\subsection split_encapsulated Split encapsulated DICOM:
-
-To split an encapsulated stream into smaller chunk (1024 bytes each):
-
-\verbatim
-$ gdcmconv --split 1024 rle.dcm rle_1024.dcm
-\endverbatim
-
-If an odd number of bytes is passed it will be rounded down to the next even
-number (eg. 1025 -> 1024) since DICOM only allow even number for Value Length.
-
-\subsection force Forcing (re)compression
-
-Sometime it is necessary to use the --force option. By default when user
-specify --j2k and input file is already in JPEG 2000 encapsulated DICOM format
-then no operation takes places. By using --force you make sure that
-(re)compression operation takes places.
-
-Real life example of why you would use --force:
-\li When Pixel Data is missing data / is padded with junk
-\li When you would like to make sure GDCM can handle decompression & recompression cycle
-
-\subsection decompress_raw Decompressing a Compressed DICOM
-
-\verbatim
-$ gdcmconv --raw compressed.dcm uncompressed.dcm
-\endverbatim
-
-\subsection compress_icon Compressing an uncompressed Icon
-
-By default when compressing a DICOM Image file, gdcmconv will not compress the
-icon. A user option needs to be turned on to explicitly force the compression
-of the Icon Image Sequence Pixel Data
-
-For example, by default we will not compress the Icon Image Sequence Pixel Data
-attribute:
-
-\verbatim
-$ gdcmconv --jpeg gdcmData/simpleImageWithIcon.dcm uncompressed_icon.dcm
-\endverbatim
-
-In the following example we will explicitly compress the Icon Image Sequence
-Pixel Data attibute. In that case the same Transfer Syntax is being used for
-both the main Pixel Data and the Pixel Data from the Icon Image Sequence:
-
-\verbatim
-$ gdcmconv --jpeg --compress-icon gdcmData/simpleImageWithIcon.dcm compressed_icon.dcm
-\endverbatim
-
-\subsection generate_icon Generating an Icon
-
-For some application it might be necessary to produce a small preview of the main image
-to be able to quickly load that short preview instead of the main image. In that case:
-
-\verbatim
-$ gdcmconv --raw --generate-icon gdcmData/test.acr test_icon.dcm
-\endverbatim
-
-In some cases the main Pixel Data element is expressed as pixel defined on
-16bits. Since Icon can only store at most pixel of size 8bits, a rescale
-operation needs to take place. In order to properly select a better interval
-for doing the rescale operation user can specify the min max used for the
-rescale operation:
-
-\verbatim
-$ gdcmconv --raw --generate-icon --icon-minmax 0,192 gdcmData/012345.002.050.dcm icon_minmax.dcm
-\endverbatim
-
-\subsection planar_configuration Changing the planar Configuration
-
-Often RLE files are compressed using a different Planar Configuration (RRR ...
-GGG... BBB...) instead of the usual triplet (RGB ... RGB ... RGB ). So upon
-decompression the Planar Configuration is 1. This is perfectly legal in DICOM,
-however this is unconventional, and thus it may be a good idea to also change
-the planar configuration and set it to the default :
-
-\verbatim
-$ gdcmconv --raw --planar-configuration 0 compressed.dcm uncompressed1.dcm
-\endverbatim
-
-To reinvert the planar configuration of file 'uncompressed1.dcm', simply do:
-
-\verbatim
-$ gdcmconv --raw --planar-configuration 1 uncompressed1.dcm uncompressed2.dcm
-\endverbatim
-
-\section lossless_conversion Lossless Conversion
-
-When talking about lossless conversion, there is an ambiguity that need to be
-understood. To achieve higher compression ratio, the RGB color space is usually
-not used, in favor of a YBR one. Changing from one color space to the other is
-(bit level) not lossless.
-
-For more detail, see what are the true lossless transformations as described:
-
-http://gdcm.sourceforge.net/wiki/index.php/Color_Space_Transformations
-
-\section quality_control Quality Control
-
-One important part when using gdcmconv it to have a way to quality control the
-output.
-
-You can use 3rd party tool to check the output of gdcmconv is correct.
-
-\subsection other_toolkit DCMTK / dicom3tools
-
-Using another DICOM implementation such as the one from DCMTK or dicom3tools
-can be a good process to check the output of gdcmconv.
-\li For DCMTK use: dcmdump
-\li For dicom3tools use: dcdump
-
-For reference, gdcmconv --raw will act as dcmdjpeg +cn +px, since it never
-tries to convert color space.
-
-\subsection vim VIM: vimdiff
-
-You can setup your favorite editor to compare the output, for instance in vim:
-
-\code
-autocmd BufReadPre *.dcm set ro
-autocmd BufReadPost *.dcm silent %!dcmdump -M +uc "%"
-\endcode
-
-then simply do:
-
-\code
-$ vimdiff input.dcm output.dcm
-\endcode
-
-\subsection binary_diff vbindiff
-
-On UNIX you can visually compare binary file using the vbindiff command:
-
-\code
-$ vbindiff input.dcm output.dcm
-\endcode
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcmraw</b>(1), <b>gdcminfo</b>(1), <b>gdcmdiff</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmconv.xml b/Utilities/doxygen/man/gdcmconv.xml
new file mode 100644
index 0000000..e207c76
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmconv.xml
@@ -0,0 +1,404 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmconv</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmconv</refname>
+ <refpurpose>Tool to convert DICOM to DICOM.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmconv_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmconv [options] file-in file-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmconv</emphasis> command line program takes as input a DICOM file (file-in) and process it to generate an output DICOM file (file-out). The command line option dictate the type of operation(s) gdcmconv will use to generate the output file.</para>
+</refsection>
+<refsection xml:id="gdcmconv_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in DICOM input filename
+
+file-out DICOM output filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1options">
+<title>OPTIONS</title>
+
+<para><literallayout> -i --input DICOM filename
+ -o --output DICOM filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> -X --explicit Change Transfer Syntax to explicit.
+ -M --implicit Change Transfer Syntax to implicit.
+ -U --use-dict Use dict for VR (only public by default).
+ --with-private-dict Use private dict for VR (advanced user only).
+ -C --check-meta Check File Meta Information (advanced user only).
+ --root-uid Root UID.
+ --remove-gl Remove group length (deprecated in DICOM 2008).
+ --remove-private-tags Remove private tags.
+ --remove-retired Remove retired tags.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1image_options">
+<title>image options</title>
+
+<para><literallayout> -l --apply-lut Apply LUT (non-standard, advanced user only).
+ -P --photometric-interpretation %s Change Photometric Interpretation (when possible).
+ -w --raw Decompress image.
+ -d --deflated Compress using deflated (gzip).
+ -J --jpeg Compress image in jpeg.
+ -K --j2k Compress image in j2k.
+ -L --jpegls Compress image in jpeg-ls.
+ -R --rle Compress image in rle (lossless only).
+ -F --force Force decompression/merging before recompression/splitting.
+ --generate-icon Generate icon.
+ --icon-minmax %d,%d Min/Max value for icon.
+ --icon-auto-minmax Automatically commpute best Min/Max values for icon.
+ --compress-icon Decide whether icon follows main TransferSyntax or remains uncompressed.
+ --planar-configuration [01] Change planar configuration.
+ -Y --lossy Use the lossy (if possible) compressor.
+ -S --split %d Write 2D image with multiple fragments (using max size)
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1jpeg_options">
+<title>JPEG options</title>
+
+<para><literallayout> -q --quality %*f set quality.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1jpegls_options">
+<title>JPEG-LS options</title>
+
+<para><literallayout> -e --lossy-error %*i set error.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1j2k_options">
+<title>J2K options</title>
+
+<para><literallayout> -r --rate %*f set rate.
+ -q --quality %*f set quality.
+ -t --tile %d,%d set tile size.
+ -n --number-resolution %d set number of resolution.
+ --irreversible set irreversible.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1special_options">
+<title>special options</title>
+
+<para><literallayout> -I --ignore-errors convert even if file is corrupted (advanced users only, see disclaimers).
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1environment_variable">
+<title>environment variable</title>
+
+<para><literallayout> GDCM_ROOT_UID Root UID
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmviewer_1simple_usage">
+<title>Simple usage</title>
+
+<para><emphasis role="bold">gdcmconv</emphasis> is a great tool to convert broken DICOM implementation into properly parsable DICOM file. Usage is simply:</para>
+
+<para><literallayout>$ gdcmconv input.dcm output.dcm
+</literallayout></para>
+
+<para>or if you prefer being explicit:</para>
+
+<para><literallayout>$ gdcmconv -i input.dcm -o output.dcm
+</literallayout></para>
+
+<para>Even though gdcmconv can overwrite directly on the same file (input.dcm = output.dcm), it is recommended that user should first convert into a different file to make sure the bug is properly handled by GDCM.</para>
+
+<para>Typical cases where you would want to use gdcmconv in its simple form:</para>
+
+<para><itemizedlist>
+<listitem>
+<para>convert non-cp246 conforming file into conforming cp246, </para>
+</listitem>
+<listitem>
+<para>convert implicit little endian transfer syntax file meta header into proper explicit little endian transfer syntax, </para>
+</listitem>
+<listitem>
+<para>convert the GE-13 bytes bug, </para>
+</listitem>
+<listitem>
+<para>convert dual syntax file: implicit/explicit, </para>
+</listitem>
+<listitem>
+<para>convert Philips dual Little Endian/Big Endian file, </para>
+</listitem>
+<listitem>
+<para>convert GDCM 1.2.0 broken UN-2-bytes fields, </para>
+</listitem>
+<listitem>
+<para>&... </para>
+</listitem>
+<listitem>
+<para>All other broken files listed in the supported refsection.</para>
+</listitem>
+</itemizedlist>
+When no option other is used, only the dataset is inspected. So encapsulated Pixel Data, for instance, is not inspected for well known bugs.</para>
+
+<para>When doing this kind of work, this is usually a good idea to perform some kind of quality control, see gdcmconv Quality Control refsection (down below).</para>
+</refsection>
+<refsection xml:id="gdcmviewer_1usage">
+<title>Typical usage</title>
+<refsection xml:id="gdcmconv_1file_meta">
+<title>File Meta Header</title>
+
+<para>Running</para>
+
+<para><literallayout>$ gdcmconv input.dcm output.dcm
+</literallayout></para>
+
+<para>Is not enough to recompute file meta header, when input file is buggy. You may want to use: –check-meta</para>
+
+<para><literallayout>$ gdcmconv --check-meta input.dcm output.dcm
+</literallayout></para>
+
+<para>See typical cases such as: GE_DLX-8-MONO2-PrivateSyntax.dcm or PICKER-16-MONO2-No_DicomV3_Preamble.dcm from gdcmData.</para>
+</refsection>
+<refsection xml:id="gdcmconv_1explicit">
+<title>Conversion to Explicit Transfer Syntax</title>
+
+<para>To convert a file that was written using Implicit Transfer Syntax into Explicit Transfer Syntax simply use:</para>
+
+<para><literallayout>$ gdcmconv --explicit uncompressed.dcm compressed.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1lossless_jpeg">
+<title>Compressing to lossless JPEG</title>
+
+<para>To compress an uncompressed DICOM file to a JPEG Lossless encapsulated format:</para>
+
+<para><literallayout>$ gdcmconv --jpeg uncompressed.dcm compressed.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1lossy_jpeg">
+<title>Compressing to lossy JPEG</title>
+
+<para>To compress an uncompressed DICOM file to a JPEG Lossy encapsulated format:</para>
+
+<para><literallayout>$ gdcmconv --lossy --jpeg -q 90 uncompressed.dcm compressed.dcm
+</literallayout></para>
+
+<para>Note: <literallayout> -q is just one of the many way to specify lossy quality, you need to inspect the other cmd line flag to specify lossyness properties.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1lossless_jpegls">
+<title>Compressing to lossless JPEG-LS</title>
+
+<para>To compress an uncompressed DICOM file to a JPEG-LS Lossless encapsulated format:</para>
+
+<para><literallayout>$ gdcmconv --jpegls uncompressed.dcm compressed.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1lossy_jpegls">
+<title>Compressing to lossy JPEG-LS</title>
+
+<para>To compress an uncompressed DICOM file to a JPEG-LS Lossy encapsulated format:</para>
+
+<para><literallayout>$ gdcmconv --lossy --jpegls -e 2 uncompressed.dcm lossy_compressed.dcm
+</literallayout></para>
+
+<para>Note:</para>
+
+<para>-e (or –lossy-error) means that the maximum tolerate error is 2 for each pixel value</para>
+</refsection>
+<refsection xml:id="gdcmconv_1lossless_j2k">
+<title>Compressing to lossless J2K</title>
+
+<para>To compress an uncompressed DICOM file to a JPEG-2000 Lossless encapsulated format:</para>
+
+<para><literallayout>$ gdcmconv --j2k uncompressed.dcm compressed.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1lossy_j2k">
+<title>Compressing to lossy J2K</title>
+
+<para>To compress an uncompressed DICOM file to a JPEG-2000 Lossy encapsulated format:</para>
+
+<para><literallayout>$ gdcmconv --lossy -q 55,50,45 --j2k uncompressed.dcm lossy_compressed.dcm
+</literallayout></para>
+
+<para>Note: <literallayout> -q is just one of the many way to specify lossy quality, you need to inspect the other cmd line flag to specify lossyness properties.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1lossless_rle">
+<title>Compressing to lossless RLE</title>
+
+<para>To compress an uncompressed DICOM file to a RLE Lossless encapsulated format:</para>
+
+<para><literallayout>$ gdcmconv --rle uncompressed.dcm compressed.dcm
+</literallayout></para>
+
+<para>There is no such thing as lossy RLE compression.</para>
+</refsection>
+<refsection xml:id="gdcmconv_1split_encapsulated">
+<title>Split encapsulated DICOM:</title>
+
+<para>To split an encapsulated stream into smaller chunk (1024 bytes each):</para>
+
+<para><literallayout>$ gdcmconv --split 1024 rle.dcm rle_1024.dcm
+</literallayout></para>
+
+<para>If an odd number of bytes is passed it will be rounded down to the next even number (eg. 1025 -> 1024) since DICOM only allow even number for Value Length.</para>
+</refsection>
+<refsection xml:id="gdcmconv_1force">
+<title>Forcing (re)compression</title>
+
+<para>Sometime it is necessary to use the –force option. By default when user specify –j2k and input file is already in JPEG 2000 encapsulated DICOM format then no operation takes places. By using –force you make sure that (re)compression operation takes places.</para>
+
+<para>Real life example of why you would use –force: <itemizedlist>
+<listitem>
+<para>When Pixel Data is missing data / is padded with junk </para>
+</listitem>
+<listitem>
+<para>When you would like to make sure GDCM can handle decompression & recompression cycle</para>
+</listitem>
+</itemizedlist>
+</para>
+</refsection>
+<refsection xml:id="gdcmconv_1decompress_raw">
+<title>Decompressing a Compressed DICOM</title>
+
+<para><literallayout>$ gdcmconv --raw compressed.dcm uncompressed.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1compress_icon">
+<title>Compressing an uncompressed Icon</title>
+
+<para>By default when compressing a DICOM Image file, gdcmconv will not compress the icon. A user option needs to be turned on to explicitly force the compression of the Icon Image Sequence Pixel Data</para>
+
+<para>For example, by default we will not compress the Icon Image Sequence Pixel Data attribute:</para>
+
+<para><literallayout>$ gdcmconv --jpeg gdcmData/simpleImageWithIcon.dcm uncompressed_icon.dcm
+</literallayout></para>
+
+<para>In the following example we will explicitly compress the Icon Image Sequence Pixel Data attibute. In that case the same Transfer Syntax is being used for both the main Pixel Data and the Pixel Data from the Icon Image Sequence:</para>
+
+<para><literallayout>$ gdcmconv --jpeg --compress-icon gdcmData/simpleImageWithIcon.dcm compressed_icon.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1generate_icon">
+<title>Generating an Icon</title>
+
+<para>For some application it might be necessary to produce a small preview of the main image to be able to quickly load that short preview instead of the main image. In that case:</para>
+
+<para><literallayout>$ gdcmconv --raw --generate-icon gdcmData/test.acr test_icon.dcm
+</literallayout></para>
+
+<para>In some cases the main Pixel Data element is expressed as pixel defined on 16bits. Since Icon can only store at most pixel of size 8bits, a rescale operation needs to take place. In order to properly select a better interval for doing the rescale operation user can specify the min max used for the rescale operation:</para>
+
+<para><literallayout>$ gdcmconv --raw --generate-icon --icon-minmax 0,192 gdcmData/012345.002.050.dcm icon_minmax.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1planar_configuration">
+<title>Changing the planar Configuration</title>
+
+<para>Often RLE files are compressed using a different Planar Configuration (RRR ... GGG... BBB...) instead of the usual triplet (RGB ... RGB ... RGB ). So upon decompression the Planar Configuration is 1. This is perfectly legal in DICOM, however this is unconventional, and thus it may be a good idea to also change the planar configuration and set it to the default :</para>
+
+<para><literallayout>$ gdcmconv --raw --planar-configuration 0 compressed.dcm uncompressed1.dcm
+</literallayout></para>
+
+<para>To reinvert the planar configuration of file 'uncompressed1.dcm', simply do:</para>
+
+<para><literallayout>$ gdcmconv --raw --planar-configuration 1 uncompressed1.dcm uncompressed2.dcm
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmconv_1lossless_conversion">
+<title>Lossless Conversion</title>
+
+<para>When talking about lossless conversion, there is an ambiguity that need to be understood. To achieve higher compression ratio, the RGB color space is usually not used, in favor of a YBR one. Changing from one color space to the other is (bit level) not lossless.</para>
+
+<para>For more detail, see what are the true lossless transformations as described:</para>
+
+<para><link xlink:href="http://gdcm.sourceforge.net/wiki/index.php/Color_Space_Transformations">http://gdcm.sourceforge.net/wiki/index.php/Color_Space_Transformations</link></para>
+</refsection>
+<refsection xml:id="gdcmconv_1quality_control">
+<title>Quality Control</title>
+
+<para>One important part when using gdcmconv it to have a way to quality control the output.</para>
+
+<para>You can use 3rd party tool to check the output of gdcmconv is correct.</para>
+<refsection xml:id="gdcmconv_1other_toolkit">
+<title>DCMTK / dicom3tools</title>
+
+<para>Using another DICOM implementation such as the one from DCMTK or dicom3tools can be a good process to check the output of gdcmconv. <itemizedlist>
+<listitem>
+<para>For DCMTK use: dcmdump </para>
+</listitem>
+<listitem>
+<para>For dicom3tools use: dcdump</para>
+</listitem>
+</itemizedlist>
+For reference, gdcmconv –raw will act as dcmdjpeg +cn +px, since it never tries to convert color space.</para>
+</refsection>
+<refsection xml:id="gdcmconv_1vim">
+<title>VIM: vimdiff</title>
+
+<para>You can setup your favorite editor to compare the output, for instance in vim:</para>
+
+<para><literallayout><computeroutput>autocmd BufReadPre *.dcm set ro
+autocmd BufReadPost *.dcm silent %!dcmdump -M +uc "%"
+</computeroutput></literallayout></para>
+
+<para>then simply do:</para>
+
+<para><literallayout><computeroutput>$ vimdiff input.dcm output.dcm
+</computeroutput></literallayout></para>
+</refsection>
+<refsection xml:id="gdcmconv_1binary_diff">
+<title>vbindiff</title>
+
+<para>On UNIX you can visually compare binary file using the vbindiff command:</para>
+
+<para><literallayout><computeroutput>$ vbindiff input.dcm output.dcm
+</computeroutput></literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmconv_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmraw</emphasis>(1), <emphasis role="bold">gdcminfo</emphasis>(1), <emphasis role="bold">gdcmdiff</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmdiff.dox b/Utilities/doxygen/man/gdcmdiff.dox
deleted file mode 100644
index 39d8690..0000000
--- a/Utilities/doxygen/man/gdcmdiff.dox
+++ /dev/null
@@ -1,68 +0,0 @@
-/*!
-
-\page gdcmdiff dumps differences of two DICOM files
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmdiff [options] file1 file2
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmdiff command line program takes as input two DICOM files: file1 and
-file2.
-
-\section parameters PARAMETERS
-
-\verbatim
-file1 DICOM input filename
-
-file2 DICOM output filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection options options
-\verbatim
- -m --meta Compare metainformation. Default is off.
- -t <n> --truncate <n> String values trimmed to n characters.
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\section simple_usage Simple usage
-\b gdcmdiff is a great tool to produce a diff in between two DICOM files. Usage
-is simply:
-
-\verbatim
-$ gdcmdiff input1.dcm input2.dcm
-\endverbatim
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcminfo</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-*/
diff --git a/Utilities/doxygen/man/gdcmdiff.xml b/Utilities/doxygen/man/gdcmdiff.xml
new file mode 100644
index 0000000..ccd35b9
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmdiff.xml
@@ -0,0 +1,82 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmdiff</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmdiff</refname>
+ <refpurpose>dumps differences of two DICOM files</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmdiff_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmdiff [options] file1 file2
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdiff_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmdiff</emphasis> command line program takes as input two DICOM files: file1 and file2.</para>
+</refsection>
+<refsection xml:id="gdcmdiff_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file1 DICOM input filename
+
+file2 DICOM output filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdiff_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcmdiff_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> -m --meta Compare metainformation. Default is off.
+ -t <n> --truncate <n> String values trimmed to n characters.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdiff_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmviewer_1simple_usage">
+<title>Simple usage</title>
+
+<para><emphasis role="bold">gdcmdiff</emphasis> is a great tool to produce a diff in between two DICOM files. Usage is simply:</para>
+
+<para><literallayout>$ gdcmdiff input1.dcm input2.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdiff_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcminfo</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmdump.dox b/Utilities/doxygen/man/gdcmdump.xml
similarity index 53%
rename from Utilities/doxygen/man/gdcmdump.dox
rename to Utilities/doxygen/man/gdcmdump.xml
index 56b8757..fe7de6d 100644
--- a/Utilities/doxygen/man/gdcmdump.dox
+++ b/Utilities/doxygen/man/gdcmdump.xml
@@ -1,36 +1,50 @@
-/*!
-
-\page gdcmdump dumps a DICOM file, it will display the structure and values contained in the specified DICOM file.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmdump [options] dcm_file
+<?xml version="1.0" encoding="utf-8"?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmdump</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmdump</refname>
+ <refpurpose>dumps a DICOM file, it will display the structure and values contained in the specified DICOM file.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmdump_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmdump [options] dcm_file
gdcmdump [options] dcm_directory
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmdump command line program dumps a DICOM file to the console.
-For those familiar with dcmdump (DCMTK) output, gdcmdump has some minor
-differences. Namely:
-\li For Implicit Transfer Syntax gdcmdump will print \b ?? instead of the dictionary VR
-
-gdcmdump has a limited private dictionary that is used to lookup private
-element whenever possible.
-
-\section parameters PARAMETERS
-
-\verbatim
-dcm_file DICOM input filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmdump</emphasis> command line program dumps a DICOM file to the console. For those familiar with dcmdump (DCMTK) output, gdcmdump has some minor differences. Namely: <itemizedlist>
+<listitem>
+<para>For Implicit Transfer Syntax gdcmdump will print <emphasis role="bold"></emphasis>?? instead of the dictionary VR</para>
+</listitem>
+</itemizedlist>
+gdcmdump has a limited private dictionary that is used to lookup private element whenever possible.</para>
+</refsection>
+<refsection xml:id="gdcmdump_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>dcm_file DICOM input filename
dcm_directory DICOM input directory
-\endverbatim
-
-\section options OPTIONS
-
-\subsection options options
-\verbatim
- -x --xml-dict generate the XML dict (only private elements for now).
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcmdump_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> -x --xml-dict generate the XML dict (only private elements for now).
-r --recursive recursive (input is a directory)
-d --dump dump value (limited use).
-p --print print value instead of simply dumping (default).
@@ -41,13 +55,14 @@ dcm_directory DICOM input directory
--vepro print VEPRO Protocol Information (0055,20,VEPRO VIF 3.0 DATA).
or VEPRO Protocol Information (0055,20,VEPRO VIM 5.0 DATA).
--sds print Philips MR Series Data Storage (1.3.46.670589.11.0.0.12.2) Information (2005,32,Philips MR Imaging DD 002).
- -A --asn1 print encapsulated ASN1 structure >(0400,0520).
+ -A --asn1 print encapsulated ASN1 structure >(0400,0520).
--map-uid-names map UID to names.
-\endverbatim
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1general_options">
+<title>general options</title>
-\subsection general_options general options
-\verbatim
- -h --help
+<para><literallayout> -h --help
print this help text and exit
-v --version
@@ -64,28 +79,29 @@ dcm_directory DICOM input directory
-D --debug
debug mode, print debug information
-\endverbatim
-
-\subsection special_options special options
-\verbatim
- -I --ignore-errors dumps even if file is corrupted (advanced users only, see disclaimers).
-\endverbatim
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1special_options">
+<title>special options</title>
-\section usage Typical usage
-\subsection implicit Printing Implicit Transfer Syntax
+<para><literallayout> -I --ignore-errors dumps even if file is corrupted (advanced users only, see disclaimers).
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmviewer_1usage">
+<title>Typical usage</title>
+<refsection xml:id="gdcmdump_1implicit">
+<title>Printing Implicit Transfer Syntax</title>
-The VR are not found in the file, thus are presented with a "(??)", and right
-next to it (if found) the correct VR.
+<para>The VR are not found in the file, thus are presented with a "(??)", and right next to it (if found) the correct VR.</para>
-Eg.:
+<para>Eg.:</para>
-\verbatim
-$ gdcmdump GE_DLX-8-MONO2-PrivateSyntax.dcm
-\endverbatim
+<para><literallayout>$ gdcmdump GE_DLX-8-MONO2-PrivateSyntax.dcm
+</literallayout></para>
-\verbatim
-# Dicom-File-Format
-\&...
+<para><literallayout># Dicom-File-Format
+\&...
(0008,0000) ?? (UL) 434 # 4,1 Generic Group Length
(0008,0005) ?? (CS) [ISO_IR 100] # 10,1-n Specific Character Set
(0008,0008) ?? (CS) [ORIGINAL\\PRIMARY\\SINGLE PLANE ] # 30,2-n Image Type
@@ -99,20 +115,18 @@ $ gdcmdump GE_DLX-8-MONO2-PrivateSyntax.dcm
(0008,0031) ?? (TM) [101229.000] # 10,1 Series Time
(0008,0032) ?? (TM) [102653.000] # 10,1 Acquisition Time
(0008,0033) ?? (TM) [102653.000] # 10,1 Content Time
-\&...
-\endverbatim
+\&...
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1private_attribute">
+<title>Print Private Attributes</title>
-\subsection private_attribute Print Private Attributes
+<para>GDCM has a limited private dictionary. Whenever possible, it will try to lookup the private data element.</para>
-GDCM has a limited private dictionary. Whenever possible, it will try to lookup
-the private data element.
+<para><literallayout>$ gdcmdump 012345.002.050.dcm
+</literallayout></para>
-\verbatim
-$ gdcmdump 012345.002.050.dcm
-\endverbatim
-
-\verbatim
-\&...
+<para><literallayout>\&...
(0009,0010) LO [GEMS_IDEN_01] # 12,1 Private Creator
(0009,1001) LO [GE_GENESIS_FF ] # 14,1 Full fidelity
(0009,1002) SH [MRCV] # 4,1 Suite id
@@ -124,94 +138,88 @@ $ gdcmdump 012345.002.050.dcm
(0009,10e6) SH [08] # 2,1 Genesis Version - now
(0009,10e7) UL 2757786872 # 4,1 Exam Record checksum
(0009,10e9) SL 985968523 # 4,1 Actual series data time stamp
-\&...
+\&...
(0019,0000) UL 1208 # 4,1 Generic Group Length
(0019,0010) LO [GEMS_ACQU_01] # 12,1 Private Creator
(0019,100f) DS [424.399994] # 10,1 Horiz. Frame of ref.
(0019,1011) SS 0 # 2,1 Series contrast
-\&...
-(0019,10e0) DS [0.000000] # 8,1 User data 24 {# DTI Diffusion Dir., release 10.0 & above}
+\&...
+(0019,10e0) DS [0.000000] # 8,1 User data 24 {# DTI Diffusion Dir., release 10.0 & above}
(0019,10e2) DS [0.000000] # 8,1 Velocity Encode Scale
(0019,10f2) SS 0 # 2,1 Fast phases
(0019,10f9) DS [98] # 2,1 Transmit gain
-\&...
+\&...
(0021,0000) UL 372 # 4,1 Generic Group Length
(0021,0010) LO [GEMS_RELA_01] # 12,1 Private Creator
(0021,1003) SS 0 # 2,1 Series from which Prescribed
-\&...
-\endverbatim
-
-\subsection siemens_csa SIEMENS CSA Header
+\&...
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1siemens_csa">
+<title>SIEMENS CSA Header</title>
-Using this option it is possible to dump as a readable text what is contained
-in the private attribute as found in typical SIEMENS MR DICOM file.
+<para>Using this option it is possible to dump as a readable text what is contained in the private attribute as found in typical SIEMENS MR DICOM file.</para>
-Eg.:
+<para>Eg.:</para>
-\verbatim
-$ gdcmdump --csa MR_SIEMENS_forceLoad29-1010_29-1020.dcm
-\endverbatim
+<para><literallayout>$ gdcmdump --csa MR_SIEMENS_forceLoad29-1010_29-1020.dcm
+</literallayout></para>
-\verbatim
-(0029,0010)siemens csa header
+<para><literallayout>(0029,0010)siemens csa header
Image shadow data (0029,xx10)
-0 - 'EchoLinePosition' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '64 '
-1 - 'EchoColumnPosition' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '64 '
-2 - 'EchoPartitionPosition' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '32 '
-3 - 'UsedChannelMask' VM 1, VR UL, SyngoDT 9, NoOfItems 6, Data '255 '
-4 - 'Actual3DImaPartNumber' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
-5 - 'ICE_Dims' VM 1, VR LO, SyngoDT 19, NoOfItems 6, Data 'X_1_1_1_1_1_1_31_1_1_1_1_19'
-6 - 'B_value' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '0 '
-7 - 'Filter1' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
-8 - 'Filter2' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
-\&...
-\endverbatim
-
-\subsection gems_pdb GEMS Protocol Data Block
-
-Using this option it is possible to dump as a readable text what is contained
-in the private attribute as found in typical GEMS MR DICOM file.
-
-Protocol Data Block : 0025,xx1b,GEMS_SERS_01
-
-\verbatim
-$ gdcmdump --pdb GE_MR_0025xx1bProtocolDataBlock.dcm
-\endverbatim
-
-\verbatim
-ENTRY "Head First"
-POSITION "Supine"
-ANREF "NA"
-COIL "HEAD"
-PLANE "OBLIQUE"
-SEDESCFLAG "1"
-SEDESC "AX FSE T2"
-IMODE "2D"
-PSEQ "FSE-XL"
-IOPT "FC, EDR, TRF, Fast"
-PLUG "22"
-FILTCHOICE "None"
-BWRT "-1"
-TRICKSIMG "1"
-TAG_SPACE "7"
-TAG_TYPE "None"
-\&...
-\endverbatim
-
-\subsection elscint_pi ELSCINT Protocol Information
-
-Using this option it is possible to dump as a readable text what is contained
-in the private attribute as found in typical ELSCINT CT DICOM file.
-
-ELSCINT Protocol Information: (01f7,26,ELSCINT1)
-
-\verbatim
-$ gdcmdump --elscint ELSCINT1_ProtocolInformation.dcm
-\endverbatim
-
-\verbatim
-ELSCINT1 Dumping info from tag (01f7,26,elscint1)
+0 - 'EchoLinePosition' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '64 '
+1 - 'EchoColumnPosition' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '64 '
+2 - 'EchoPartitionPosition' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '32 '
+3 - 'UsedChannelMask' VM 1, VR UL, SyngoDT 9, NoOfItems 6, Data '255 '
+4 - 'Actual3DImaPartNumber' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
+5 - 'ICE_Dims' VM 1, VR LO, SyngoDT 19, NoOfItems 6, Data 'X_1_1_1_1_1_1_31_1_1_1_1_19'
+6 - 'B_value' VM 1, VR IS, SyngoDT 6, NoOfItems 6, Data '0 '
+7 - 'Filter1' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
+8 - 'Filter2' VM 1, VR IS, SyngoDT 6, NoOfItems 0, Data
+\&...
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1gems_pdb">
+<title>GEMS Protocol Data Block</title>
+
+<para>Using this option it is possible to dump as a readable text what is contained in the private attribute as found in typical GEMS MR DICOM file.</para>
+
+<para>Protocol Data Block : 0025,xx1b,GEMS_SERS_01</para>
+
+<para><literallayout>$ gdcmdump --pdb GE_MR_0025xx1bProtocolDataBlock.dcm
+</literallayout></para>
+
+<para><literallayout>ENTRY "Head First"
+POSITION "Supine"
+ANREF "NA"
+COIL "HEAD"
+PLANE "OBLIQUE"
+SEDESCFLAG "1"
+SEDESC "AX FSE T2"
+IMODE "2D"
+PSEQ "FSE-XL"
+IOPT "FC, EDR, TRF, Fast"
+PLUG "22"
+FILTCHOICE "None"
+BWRT "-1"
+TRICKSIMG "1"
+TAG_SPACE "7"
+TAG_TYPE "None"
+\&...
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1elscint_pi">
+<title>ELSCINT Protocol Information</title>
+
+<para>Using this option it is possible to dump as a readable text what is contained in the private attribute as found in typical ELSCINT CT DICOM file.</para>
+
+<para>ELSCINT Protocol Information: (01f7,26,ELSCINT1)</para>
+
+<para><literallayout>$ gdcmdump --elscint ELSCINT1_ProtocolInformation.dcm
+</literallayout></para>
+
+<para><literallayout>ELSCINT1 Dumping info from tag (01f7,26,elscint1)
ELSCINT1/Item name: []
ApprovedStep [yes]
RefSurview [1\0]
@@ -233,22 +241,20 @@ ELSCINT1/Item name: [doseright]
ACS-learn-allowed [no]
ACS-water-radius [-1.000000]
ACS-water-radius-scan [-1]
-\&...
-\endverbatim
-
-\subsection vepro_pi VEPRO Protocol Information
+\&...
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1vepro_pi">
+<title>VEPRO Protocol Information</title>
-Using this option it is possible to dump as a readable text what is contained
-in the private attribute as found in typical VEPRO CT DICOM file.
+<para>Using this option it is possible to dump as a readable text what is contained in the private attribute as found in typical VEPRO CT DICOM file.</para>
-ELSCINT Protocol Information: (0055,20,VEPRO VIM 5.0 DATA)
+<para>ELSCINT Protocol Information: (0055,20,VEPRO VIM 5.0 DATA)</para>
-\verbatim
-$ gdcmdump --vepro VEPRO_ProtocolInformation.dcm
-\endverbatim
+<para><literallayout>$ gdcmdump --vepro VEPRO_ProtocolInformation.dcm
+</literallayout></para>
-\verbatim
-VIMDATA2: (0055,20,VEPRO VIM 5.0 DATA)
+<para><literallayout>VIMDATA2: (0055,20,VEPRO VIM 5.0 DATA)
ID: VIM
Version: 5.0
UserName:
@@ -284,35 +290,33 @@ VIMDATA2: (0055,20,VEPRO VIM 5.0 DATA)
StudyUID: 1.2.392.200036.9116.2.6.1.48.1214228007.1285934880.206831
SeriesUID: 1.2.392.200036.9116.2.6.1.48.1214228007.1285935201.938653
Modality: CT
-\endverbatim
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1pms_mr_sds">
+<title>Philips Private MR Series Data Storage (1.3.46.670589.11.0.0.12.2)</title>
-\subsection pms_mr_sds Philips Private MR Series Data Storage (1.3.46.670589.11.0.0.12.2)
+<para>Using this option it is possible to dump as a readable text what is contained in the private attribute as found in typical Philips Private MR Series Data Storage file.</para>
-Using this option it is possible to dump as a readable text what is contained
-in the private attribute as found in typical Philips Private MR Series Data Storage file.
+<para>PMS Series Data Storage (2005,32,Philips MR Imaging DD 002)</para>
-PMS Series Data Storage (2005,32,Philips MR Imaging DD 002)
+<para><literallayout>$ gdcmdump --sds PMS_SeriesDataStorage.dcm
+</literallayout></para>
-\verbatim
-$ gdcmdump --sds PMS_SeriesDataStorage.dcm
-\endverbatim
-
-\verbatim
-\&...
+<para><literallayout>\&...
PMS/Item name: [PDF_CONTROL_GEN_PARS/IEEE_PDF/Y ]
-\&...
+\&...
PMS/Item name: [PDF_CONTROL_PREP_PARS /IEEE_PDF/Y ]
-\&...
+\&...
PMS/Item name: [PDF_CONTROL_RECON_PARS/IEEE_PDF/Y ]
-\&...
+\&...
PMS/Item name: [PDF_CONTROL_SCAN_PARS /IEEE_PDF/Y ]
-\&...
+\&...
PMS/Item name: [PDF_EXAM_PARS /IEEE_PDF/Y ]
-\&...
+\&...
PMS/Item name: [PDF_HARDWARE_PARS /IEEE_PDF/Y ]
-\&...
+\&...
PMS/Item name: [PDF_PREP_PARS /IEEE_PDF/Y ]
-\&...
+\&...
PMS/Item name: [PDF_SPT_PARS/IEEE_PDF/Y ]
SP_scan_resol [256\256] # 2
SP_pda_profiles [0\0] # 2
@@ -336,35 +340,31 @@ PMS/Item name: [PDF_SPT_PARS/IEEE_PDF/Y ]
SP_rg_result [0] # 1
SP_dc_result [0] # 1
SP_ph_result [0] # 1
-\&...
-\endverbatim
-
-\subsection asn1 Encapsulated ASN1 Structure
+\&...
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmdump_1asn1">
+<title>Encapsulated ASN1 Structure</title>
-This option is mainly used for dumping the ASN1 structure of the encrypted
-Attribute (0040,0520)
+<para>This option is mainly used for dumping the ASN1 structure of the encrypted Attribute (0040,0520)</para>
-\verbatim
-$ gdcmdump encrypted.dcm
-\endverbatim
+<para><literallayout>$ gdcmdump encrypted.dcm
+</literallayout></para>
-\verbatim
-\&...
+<para><literallayout>\&...
(0400,0500) SQ # u/l,1 Encrypted Attributes Sequence
(fffe,e000) na (Item with undefined length)
(0400,0510) UI [1.2.840.10008.1.2] # 18,1 Encrypted Content Transfer Syntax UID
(0400,0520) OB 30\\82\\03\\ba\\06\\09\\2a\\86\\48\\55\\04\\08\\13 # 958,1 Encrypted Content
(fffe,e00d)
(fffe,e0dd)
-\&...
-\endverbatim
+\&...
+</literallayout></para>
-\verbatim
-$ gdcmdump --asn1 encrypted.dcm
-\endverbatim
+<para><literallayout>$ gdcmdump --asn1 encrypted.dcm
+</literallayout></para>
-\verbatim
- 0:d=0 hl=4 l= 954 cons: SEQUENCE
+<para><literallayout> 0:d=0 hl=4 l= 954 cons: SEQUENCE
4:d=1 hl=2 l= 9 prim: OBJECT :pkcs7-envelopedData
15:d=1 hl=4 l= 939 cons: cont [ 0 ]
19:d=2 hl=4 l= 935 cons: SEQUENCE
@@ -397,15 +397,12 @@ $ gdcmdump --asn1 encrypted.dcm
413:d=5 hl=2 l= 9 prim: OBJECT :aes-256-cbc
424:d=5 hl=2 l= 16 prim: OCTET STRING [HEX DUMP]:3B49AFE71749F2BFF1519EBAEA95A393
442:d=4 hl=4 l= 512 prim: cont [ 0 ]
-\endverbatim
-
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcmraw</b>(1), <b>gdcmanon</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmdump_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmraw</emphasis>(1), <emphasis role="bold">gdcmanon</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmgendir.dox b/Utilities/doxygen/man/gdcmgendir.dox
deleted file mode 100644
index 18e17f4..0000000
--- a/Utilities/doxygen/man/gdcmgendir.dox
+++ /dev/null
@@ -1,92 +0,0 @@
-/*!
-
-\page gdcmgendir Tool to generate a DICOMDIR file from a File-Set.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmgendir [options] file-in file-out
-\endverbatim
-
-\section description DESCRIPTION
-
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM input filename
-
-file-out DICOM output filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection params Parameters
-\verbatim
-\endverbatim
-
-\subsection options Options
-\verbatim
- -i --input DICOM filename or directory
- -o --output DICOM filename or directory
- -r --recursive recursive.
- --descriptor descriptor.
- --root-uid Root UID.
-\endverbatim
-
-\subsection general_options General Options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\subsection environment_variable environment variable
-\verbatim
- GDCM_ROOT_UID Root UID
-\endverbatim
-
-\section usage Typical usage
-
-\section note NOTE
-One may have to run some preliminary steps in order to get gdcmgendir to
-generate the DICOMDIR file. Namely two steps:
-\li Batch renaming of the DICOM filename into something compatible with ISO 9660 filename convention
-\li Convert all DICOM file into the Explicit VR Little Endian Uncompressed (1.2.840.10008.1.2.1)
-
-Step 1. can be solved in a numerous way. Eg. on UNIX environment this could
-either be solved using the mkisofs command line tool. Filenames should not
-contains any extension since the VR CS does not allow for the '.' character.
-Only upper case, digit 0-9, the space ' ' and the underscore '_' character are
-valid in VR CS, with a maximum of 8 bytes. Another simple tool that can be
-handy is 'rename' in conjunction with 'basename'.
-
-Step 2. can simply be achieved using the gdcmconv command line tool:
-
-\verbatim
- $ for i in `ls IMG*`; do gdcmconv --raw --force $i /tmp/out/$i; done
-\endverbatim
-
-\section see_also SEE ALSO
-
-<b>gdcmconv</b>(1), <b>gdcmanon</b>(1), <b>rename</b>(1), <b>mkisofs</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmgendir.xml b/Utilities/doxygen/man/gdcmgendir.xml
new file mode 100644
index 0000000..4e75d72
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmgendir.xml
@@ -0,0 +1,107 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmgendir</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmgendir</refname>
+ <refpurpose>Tool to generate a DICOMDIR file from a File-Set.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmgendir_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmgendir [options] file-in file-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmgendir_1description">
+<title>DESCRIPTION</title>
+</refsection>
+<refsection xml:id="gdcmgendir_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in DICOM input filename
+
+file-out DICOM output filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmgendir_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcmgendir_1params">
+<title>Parameters</title>
+
+<para><literallayout></literallayout></para>
+</refsection>
+<refsection xml:id="gdcmgendir_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> -i --input DICOM filename or directory
+ -o --output DICOM filename or directory
+ -r --recursive recursive.
+ --descriptor descriptor.
+ --root-uid Root UID.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmgendir_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1environment_variable">
+<title>environment variable</title>
+
+<para><literallayout> GDCM_ROOT_UID Root UID
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmviewer_1usage">
+<title>Typical usage</title>
+</refsection>
+<refsection xml:id="gdcmgendir_1note">
+<title>NOTE</title>
+
+<para>One may have to run some preliminary steps in order to get gdcmgendir to generate the DICOMDIR file. Namely two steps: <itemizedlist>
+<listitem>
+<para>Batch renaming of the DICOM filename into something compatible with ISO 9660 filename convention </para>
+</listitem>
+<listitem>
+<para>Convert all DICOM file into the Explicit VR Little Endian Uncompressed (1.2.840.10008.1.2.1)</para>
+</listitem>
+</itemizedlist>
+Step 1. can be solved in a numerous way. Eg. on UNIX environment this could either be solved using the mkisofs command line tool. Filenames should not contains any extension since the VR CS does not allow for the '.' character. Only upper case, digit 0-9, the space ' ' and the underscore '_' character are valid in VR CS, with a maximum of 8 bytes. Another simple tool that can be handy is 'rename' in conjunction with 'basename'.</para>
+
+<para>Step 2. can simply be achieved using the gdcmconv command line tool:</para>
+
+<para><literallayout> $ for i in `ls IMG*`; do gdcmconv --raw --force $i /tmp/out/$i; done
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmgendir_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmconv</emphasis>(1), <emphasis role="bold">gdcmanon</emphasis>(1), <emphasis role="bold">rename</emphasis>(1), <emphasis role="bold">mkisofs</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmimg.dox b/Utilities/doxygen/man/gdcmimg.dox
deleted file mode 100644
index 2a3a930..0000000
--- a/Utilities/doxygen/man/gdcmimg.dox
+++ /dev/null
@@ -1,290 +0,0 @@
-/*!
-
-\page gdcmimg Manipulate DICOM image file.
-
-gdcmimg is a low level tool to allow de-/encapsulation from/to DICOM image.
-This tool does not understand Transfer Syntax conversion. It will encapsulate
-the raw data as-is. This has some impact in some cases, see special warnings
-below.
-
-It is important to note that gdcmimg can only encapsulate proper input file,
-for instance JPG and or JP2 are accepted since an associated DICOM Transfer
-Syntax can be found. However input such as TIFF and/or PNG are not, since DICOM
-does not support those. See instead a tool such as gdcm2vtk.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmimg [options] file-in file-out
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmimg command line tool can be used in two fashions:
-\li 1. Converting a recognized file format into its encapsulated DICOM counterpart,
-\li 2. Anonymizing a rectangular portion of a DICOM file.
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in input filename (non-DICOM)
-
-file-out DICOM output filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection parameters parameters
-\verbatim
- -i --input Input filename
- -o --output Output filename
-\endverbatim
-
-\subsection options options
-\verbatim
- --endian %s Endianness (LSB/MSB).
- -d --depth %d Depth (Either 8/16/32 or BitsAllocated eg. 12 when known).
- --sign %s Pixel sign (0/1).
- --spp %d Sample Per Pixel (1/3).
- -s --size %d,%d Size.
- -C --sop-class-uid SOP Class UID (name or value).
- -T --study-uid Study UID.
- -S --series-uid Series UID.
- --root-uid Root UID.
-\endverbatim
-
-\subsection fill_options fill options
-\verbatim
- -R --region %d,%d Region.
- -F --fill %d Fill with pixel value specified.
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\subsection environment_variable environment variable
-\verbatim
- GDCM_ROOT_UID Root UID
-\endverbatim
-
-\section supported Supported File Format (appropriate file extension) gdcmimg
-will base it's conversion process based on the file extension. Follows the list
-of recognized file extension. When no extension is found, DICOM file is
-assumed.
-
-input format
-\verbatim
- * RAW (raw, rawl, gray, rgb)
- * RLE (rle)
- * PNM (pgm, pnm, ppm)
- * JPEG-LS (jls)
- * JPEG 2000 (jp2, j2k, j2c, jpx, jpc)
- * JPEG (jpg, jpeg, ljpg, ljpeg)
- * DICOM ()
-\endverbatim
-
-output format:
-\verbatim
- * PGM (pgm, pnm, ppm)
- * DICOM ()
-\endverbatim
-
-For RAW file format, you should take special care of the --endian option.
-For the (old) JPEG file format, both the lossy and lossless format are
-supported, user should pay attention to the --sign option.
-For file format such as RLE or RAW, user is expected to fill in information
-required to find the dimension and type of input data as there is no other way
-to find this information. For all other file format, the properties are derived
-from the file format itself.
-
-PNM file are supposed to be big endian (important for depth > 8)
-
-\section usage Typical usage
-\subsection blank_out Remove a rectangular part of the image
-
-To fill the region [0,100]x[0,100] of a DICOM image simply do:
-
-\verbatim
-$ gdcmimg --fill 0 --region 0,100,0,100 -i input.dcm -o output_black.dcm
-\endverbatim
-
-Warning: if the Pixel Data is compressed, the image is first decompressed so
-that pixel can be set to 0, but it is not re-compressed.
-
-\subsection convert_raw Convert RAW to DICOM
-
-Recognized extension is .raw, .rawl, .gray or .rgb (case insensitive)
-
-\verbatim
-$ gdcmimg --size 512,512 --depth 16 -i input.raw -o output.dcm
-\endverbatim
-
-the image will be a Secondary Capture.
-
-When the input is 3 component, one need to specify explicitly the Samples Per
-Pixel:
-
-\verbatim
-$ gdcmimg --size 512,512 --spp 3 input_rgb.raw output_rgb.dcm
-\endverbatim
-
-When the filename contains .rgb as file extension output is automatically
-recognized as RGB no need to specify --spp
-
-\verbatim
-$ gdcmimg --size 512,512 input.rgb output_rgb.dcm
-\endverbatim
-
-You can use the \b dd cmd line to skip any header you would like to discard,
-for instance, if you would like to skip the first 108 bytes, simply do:
-
-\verbatim
-$ dd skip=108 bs=1 if=input.raw of=output.raw
-\endverbatim
-
-.raw and .rawl extension are equivalent. You need to explicitly specify the
-endianness manually:
-
-\verbatim
-$ gdcmimg --endian MSB --size 512,512 --depth 16 -i input.raw -o output.dcm
-\endverbatim
-
-or
-
-\verbatim
-$ gdcmimg --endian LSB --size 512,512 --depth 16 -i input.raw -o output.dcm
-\endverbatim
-
-\subsection pnm Convert PGM/PNM/PPM to DICOM
-
-Recognized extensions are .pgm, .pnm, .ppm (case insensitive)
-
-\verbatim
-$ gdcmimg -i input.pgm -o output.dcm
-\endverbatim
-
-the image will be a Secondary Capture
-
-\subsection rle Convert RLE to DICOM
-
-Recognized extension is .rle (case insensitive)
-
-\verbatim
-$ gdcmimg --size 512,512 --depth 16 -i input.rle -o output.dcm
-\endverbatim
-
-the image will be a Secondary Capture
-\subsection jpeg Convert JPEG to DICOM
-
-Recognized extensions are .jpg, .jpeg, .ljpg, .ljpeg (case insensitive)
-
-\verbatim
-$ gdcmimg -i input.ljpeg -o output.dcm
-\endverbatim
-
-the image will be a Secondary Capture
-
-\subsection j2k Convert J2K to DICOM
-
-Recognized extensions are .j2k, .jp2, .jpc, jpx, j2c (case insensitive)
-
-\verbatim
-$ gdcmimg -i input.j2k -o output.dcm
-\endverbatim
-
-the image will be a Secondary Capture.
-
-All Pixel information (Bits Stored/Allocated...) will be derived from the
-image itself, and not from the command line options.
-
-\subsection sopclassuid Specifying a SOP Class UID
-
-Instead of the default Secondary Capture Image Storage, one may want to
-specify, say VL Photographic Image Storage.
-
-\verbatim
-$ gdcmimg --sop-class-uid 1.2.840.10008.5.1.4.1.1.77.1.4 input.jpg output.dcm
-\endverbatim
-
-\section multiple_files Multiple Files
-
-gdcmimg handle nicely a set of files (for instance jpeg):
-
-\verbatim
-$ gdcmimg -C 1.2.840.10008.5.1.4.1.1.12.1 1.jpg 2.jpg 3.jpg 4.jpg output.dcm
-\endverbatim
-
-It is important to specify an SOP Class that supports multi-frames images
-otherwise gdcmimg will fail.
-
-\section start_offset Start Offset
-
-In some case, one may want to create a 2D slice from an arbitrary volume (e.g
-3D). In which case --offset becomes handy:
-
-\verbatim
-$ gdcmimg --offset 4954104330 --size 1673,1673 Input3D_1673_1673_1775.raw slice_1770.dcm
-\endverbatim
-
-\section warning Warning
-
-There are a couple of issues with gdcmimg implementation:
-
-For RAW file, one should pay attention that when using --endian MSB the Pixel
-Data will be encapsulated as is (not touched by gdcmimg). Therefore the only
-possible transfer syntax available is Implicit VR Big Endian DLX (G.E Private).
-GDCM does handle this private Transfer Syntax. So if you need to convert this
-Transfer Syntax to another one (and allow Pixel Data manipulation), you can
-use:
-
-\verbatim
-$ gdcmconv --raw --force input_big_endian_dlx.raw -o output_implicit_vr_little_endian.dcm
-\endverbatim
-
-For JFIF file and JP2 file (with header) the header is copied into the Pixel
-Data element which is illegal for JP2.
-Use gdcmconv to properly re-encode a JP2/JFIF file into J2K/JPG.
-
-\verbatim
-$ gdcmimg input.jp2 output_jp2.dcm
-$ gdcmconv --j2k --force output_jp2.dcm output_j2k.dcm
-\endverbatim
-
-For RLE file, no check is done for crossing the row boundary. It is recommended
-to use gdcmconv --rle to re-encode into a proper RLE file in case of doubt.
-
-Of course if the compression is not ok with your setup, you can always
-de-encapsulated the DICOM file (typically JPEG) to a non-encapsulated form,
-using gdcmconv:
-
-\verbatim
-$ gdcmconv --raw input_jpeg.dcm output_raw.dcm
-\endverbatim
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcm2vtk</b>(1), <b>gdcmraw</b>(1), <b>convert</b>(1), <b>dd</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmimg.xml b/Utilities/doxygen/man/gdcmimg.xml
new file mode 100644
index 0000000..2911ce9
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmimg.xml
@@ -0,0 +1,271 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmimg</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmimg</refname>
+ <refpurpose>Manipulate DICOM image file.</refpurpose>
+</refnamediv>
+
+<para>gdcmimg is a low level tool to allow de-/encapsulation from/to DICOM image. This tool does not understand Transfer Syntax conversion. It will encapsulate the raw data as-is. This has some impact in some cases, see special warnings below.</para>
+
+<para>It is important to note that gdcmimg can only encapsulate proper input file, for instance JPG and or JP2 are accepted since an associated DICOM Transfer Syntax can be found. However input such as TIFF and/or PNG are not, since DICOM does not support those. See instead a tool such as gdcm2vtk.</para>
+<refsection xml:id="gdcmimg_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmimg [options] file-in file-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmimg_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmimg</emphasis> command line tool can be used in two fashions: <itemizedlist>
+<listitem>
+<para>1. Converting a recognized file format into its encapsulated DICOM counterpart, </para>
+</listitem>
+<listitem>
+<para>2. Anonymizing a rectangular portion of a DICOM file.</para>
+</listitem>
+</itemizedlist>
+</para>
+</refsection>
+<refsection xml:id="gdcmimg_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in input filename (non-DICOM)
+
+file-out DICOM output filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmimg_1options">
+<title>OPTIONS</title>
+
+<para><literallayout> -i --input Input filename
+ -o --output Output filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmimg_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> --endian %s Endianness (LSB/MSB).
+ -d --depth %d Depth (Either 8/16/32 or BitsAllocated eg. 12 when known).
+ --sign %s Pixel sign (0/1).
+ --spp %d Sample Per Pixel (1/3).
+ -s --size %d,%d Size.
+ -C --sop-class-uid SOP Class UID (name or value).
+ -T --study-uid Study UID.
+ -S --series-uid Series UID.
+ --root-uid Root UID.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmimg_1fill_options">
+<title>fill options</title>
+
+<para><literallayout> -R --region %d,%d Region.
+ -F --fill %d Fill with pixel value specified.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmimg_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1environment_variable">
+<title>environment variable</title>
+
+<para><literallayout> GDCM_ROOT_UID Root UID
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmimg_1supported">
+<title>Supported File Format (appropriate file extension)</title>
+
+<para>gdcmimg will base it's conversion process based on the file extension. Follows the list of recognized file extension. When no extension is found, DICOM file is assumed.</para>
+
+<para>input format <literallayout> * RAW (raw, rawl, gray, rgb)
+ * RLE (rle)
+ * PNM (pgm, pnm, ppm)
+ * JPEG-LS (jls)
+ * JPEG 2000 (jp2, j2k, j2c, jpx, jpc)
+ * JPEG (jpg, jpeg, ljpg, ljpeg)
+ * DICOM ()
+</literallayout></para>
+
+<para>output format: <literallayout> * PGM (pgm, pnm, ppm)
+ * DICOM ()
+</literallayout></para>
+
+<para>For RAW file format, you should take special care of the –endian option. For the (old) JPEG file format, both the lossy and lossless format are supported, user should pay attention to the –sign option. For file format such as RLE or RAW, user is expected to fill in information required to find the dimension and type of input data as there is no other way to find this information. For all other file format, the properties are derived from the file format itself.</para>
+
+<para>PNM file are supposed to be big endian (important for depth > 8)</para>
+</refsection>
+<refsection xml:id="gdcmviewer_1usage">
+<title>Typical usage</title>
+<refsection xml:id="gdcmimg_1blank_out">
+<title>Remove a rectangular part of the image</title>
+
+<para>To fill the region [0,100]x[0,100] of a DICOM image simply do:</para>
+
+<para><literallayout>$ gdcmimg --fill 0 --region 0,100,0,100 -i input.dcm -o output_black.dcm
+</literallayout></para>
+
+<para>Warning: if the Pixel Data is compressed, the image is first decompressed so that pixel can be set to 0, but it is not re-compressed.</para>
+</refsection>
+<refsection xml:id="gdcmimg_1convert_raw">
+<title>Convert RAW to DICOM</title>
+
+<para>Recognized extension is .raw, .rawl, .gray or .rgb (case insensitive)</para>
+
+<para><literallayout>$ gdcmimg --size 512,512 --depth 16 -i input.raw -o output.dcm
+</literallayout></para>
+
+<para>the image will be a Secondary Capture.</para>
+
+<para>When the input is 3 component, one need to specify explicitly the Samples Per Pixel:</para>
+
+<para><literallayout>$ gdcmimg --size 512,512 --spp 3 input_rgb.raw output_rgb.dcm
+</literallayout></para>
+
+<para>When the filename contains .rgb as file extension output is automatically recognized as RGB no need to specify –spp</para>
+
+<para><literallayout>$ gdcmimg --size 512,512 input.rgb output_rgb.dcm
+</literallayout></para>
+
+<para>You can use the <emphasis role="bold">dd</emphasis> cmd line to skip any header you would like to discard, for instance, if you would like to skip the first 108 bytes, simply do:</para>
+
+<para><literallayout>$ dd skip=108 bs=1 if=input.raw of=output.raw
+</literallayout></para>
+
+<para>.raw and .rawl extension are equivalent. You need to explicitly specify the endianness manually:</para>
+
+<para><literallayout>$ gdcmimg --endian MSB --size 512,512 --depth 16 -i input.raw -o output.dcm
+</literallayout></para>
+
+<para>or</para>
+
+<para><literallayout>$ gdcmimg --endian LSB --size 512,512 --depth 16 -i input.raw -o output.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmimg_1pnm">
+<title>Convert PGM/PNM/PPM to DICOM</title>
+
+<para>Recognized extensions are .pgm, .pnm, .ppm (case insensitive)</para>
+
+<para><literallayout>$ gdcmimg -i input.pgm -o output.dcm
+</literallayout></para>
+
+<para>the image will be a Secondary Capture</para>
+</refsection>
+<refsection xml:id="gdcmimg_1rle">
+<title>Convert RLE to DICOM</title>
+
+<para>Recognized extension is .rle (case insensitive)</para>
+
+<para><literallayout>$ gdcmimg --size 512,512 --depth 16 -i input.rle -o output.dcm
+</literallayout></para>
+
+<para>the image will be a Secondary Capture </para>
+</refsection>
+<refsection xml:id="gdcmimg_1jpeg">
+<title>Convert JPEG to DICOM</title>
+
+<para>Recognized extensions are .jpg, .jpeg, .ljpg, .ljpeg (case insensitive)</para>
+
+<para><literallayout>$ gdcmimg -i input.ljpeg -o output.dcm
+</literallayout></para>
+
+<para>the image will be a Secondary Capture</para>
+</refsection>
+<refsection xml:id="gdcmimg_1j2k">
+<title>Convert J2K to DICOM</title>
+
+<para>Recognized extensions are .j2k, .jp2, .jpc, jpx, j2c (case insensitive)</para>
+
+<para><literallayout>$ gdcmimg -i input.j2k -o output.dcm
+</literallayout></para>
+
+<para>the image will be a Secondary Capture.</para>
+
+<para>All Pixel information (Bits Stored/Allocated...) will be derived from the image itself, and not from the command line options.</para>
+</refsection>
+<refsection xml:id="gdcmimg_1sopclassuid">
+<title>Specifying a SOP Class UID</title>
+
+<para>Instead of the default Secondary Capture Image Storage, one may want to specify, say VL Photographic Image Storage.</para>
+
+<para><literallayout>$ gdcmimg --sop-class-uid 1.2.840.10008.5.1.4.1.1.77.1.4 input.jpg output.dcm
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmimg_1multiple_files">
+<title>Multiple Files</title>
+
+<para>gdcmimg handle nicely a set of files (for instance jpeg):</para>
+
+<para><literallayout>$ gdcmimg -C 1.2.840.10008.5.1.4.1.1.12.1 1.jpg 2.jpg 3.jpg 4.jpg output.dcm
+</literallayout></para>
+
+<para>It is important to specify an SOP Class that supports multi-frames images otherwise gdcmimg will fail.</para>
+</refsection>
+<refsection xml:id="gdcmimg_1start_offset">
+<title>Start Offset</title>
+
+<para>In some case, one may want to create a 2D slice from an arbitrary volume (e.g 3D). In which case –offset becomes handy:</para>
+
+<para><literallayout>$ gdcmimg --offset 4954104330 --size 1673,1673 Input3D_1673_1673_1775.raw slice_1770.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmimg_1warning">
+<title>Warning</title>
+
+<para>There are a couple of issues with gdcmimg implementation:</para>
+
+<para>For RAW file, one should pay attention that when using –endian MSB the Pixel Data will be encapsulated as is (not touched by gdcmimg). Therefore the only possible transfer syntax available is Implicit VR Big Endian DLX (G.E Private). GDCM does handle this private Transfer Syntax. So if you need to convert this Transfer Syntax to another one (and allow Pixel Data manipulation), you can use:</para>
+
+<para><literallayout>$ gdcmconv --raw --force input_big_endian_dlx.raw -o output_implicit_vr_little_endian.dcm
+</literallayout></para>
+
+<para>For JFIF file and JP2 file (with header) the header is copied into the Pixel Data element which is illegal for JP2. Use gdcmconv to properly re-encode a JP2/JFIF file into J2K/JPG.</para>
+
+<para><literallayout>$ gdcmimg input.jp2 output_jp2.dcm
+$ gdcmconv --j2k --force output_jp2.dcm output_j2k.dcm
+</literallayout></para>
+
+<para>For RLE file, no check is done for crossing the row boundary. It is recommended to use gdcmconv –rle to re-encode into a proper RLE file in case of doubt.</para>
+
+<para>Of course if the compression is not ok with your setup, you can always de-encapsulated the DICOM file (typically JPEG) to a non-encapsulated form, using gdcmconv:</para>
+
+<para><literallayout>$ gdcmconv --raw input_jpeg.dcm output_raw.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmimg_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcm2vtk</emphasis>(1), <emphasis role="bold">gdcmraw</emphasis>(1), <emphasis role="bold">convert</emphasis>(1), <emphasis role="bold">dd</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcminfo.dox b/Utilities/doxygen/man/gdcminfo.dox
deleted file mode 100644
index 6408fb6..0000000
--- a/Utilities/doxygen/man/gdcminfo.dox
+++ /dev/null
@@ -1,164 +0,0 @@
-/*!
-
-\page gdcminfo Display meta info about the input DICOM file.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcminfo [options] file-in
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcminfo command line program takes as input a DICOM file, or a
-directory and process it to extract meta- information about the DICOM file
-processed.
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM input filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection options options
-\verbatim
- -r --recursive recursive.
- -d --check-deflated check if file is proper deflated syntax.
- --resources-path Resources path.
- --md5sum Compute md5sum of Pixel Data attribute value.
- --check-compression check the encapsulated stream compression (lossless/lossy).
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\subsection environment_variable environment variable
-
- GDCM_RESOURCES_PATH path pointing to resources files (Part3.xml, ...)
-
-\section simple_usage Simple usage
-
-\subsection gdcmdata gdcmData
-Using data from gdcmData:
-
-\verbatim
-$ gdcminfo gdcmData/012345.002.050.dcm
-\endverbatim
-
-\verbatim
-MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
-NumberOfDimensions: 2
-Dimensions: (256,256)
-Origin: (-85,21.6,108.7)
-Spacing: (0.664062,0.664062,1.5)
-DirectionCosines: (1,0,0,0,0,-1)
-Rescale Intercept/Slope: (0,1)
-SamplesPerPixel :1
-BitsAllocated :16
-BitsStored :16
-HighBit :15
-PixelRepresentation:1
-Orientation Label: CORONAL
-\endverbatim
-
-\subsection dclunie Davie Clunie datasets:
-
-Using data from David Clunie datasets:
-
-\verbatim
-$ gdcminfo BRTUM001.dcm
-\endverbatim
-
-\verbatim
-MediaStorage is 1.2.840.10008.5.1.4.1.1.4.1 [Enhanced MR Image Storage]
-NumberOfDimensions: 3
-Dimensions: (256,256,15)
-Origin: (40,-105,105)
-Spacing: (0.820312,0.820312,6)
-DirectionCosines: (0,1,0,0,0,-1)
-Rescale Intercept/Slope: (0,1)
-SamplesPerPixel :1
-BitsAllocated :16
-BitsStored :16
-HighBit :15
-PixelRepresentation:1
-Orientation Label: SAGITTAL
-\endverbatim
-
-\subsection md5sum Checking the md5sum of the Pixel Data
-
-After compressing a DICOM file (see gdcmconv) using a lossless compression
-algorithm, it is fairly easy to compare the two files for differences at DICOM
-attribute level. However one operation is slightly easier to do: how to make
-sure the compression was actually lossless ? In this case one could use the
---md5sum operation.
-
-Take an uncompressed DICOM image file:
-
-\verbatim
-$ gdcminfo --md5sum SIEMENS_ImageLocationUN.dcm
-\endverbatim
-
-The tool return: 0621954acd5815e0b4f7b65fcc6506b1
-
-Now compress this file:
-
-\verbatim
-$ gdcmconv --jpegls SIEMENS_ImageLocationUN.dcm lossless_compressed.dcm
-\endverbatim
-
-and then check again the md5sum:
-
-\verbatim
-$ gdcminfo --md5sum lossless_compressed.dcm
-\endverbatim
-
-The tool return: 0621954acd5815e0b4f7b65fcc6506b1
-
-\subsection checking_lossless Checking if Pixel Data is lossless
-
-In some environment one wish to check whether or not the DICOM file is
-lossless. It is fairly easy to do that in most cases. Only in two occasion this
-is not clear from the sole DICOM Attribute. When the Transfer Syntax is JPEG
-2000 Image Compression (1.2.840.10008.1.2.4.91) and when the Transfer Syntax is
-JPEG-LS Lossy (Near-Lossless) Image Compression (1.2.840.10008.1.2.4.81).
-
-In this case, the only solution is to open the Pixel Data element, read the
-specific JPEG header and check whether or not the JPEG transformation was
-lossless or not:
-
-\verbatim
-$ gdcminfo --check-compression gdcmData/MAROTECH_CT_JP2Lossy.dcm
-\endverbatim
-
-The tool returns: "Encapsulated Stream was found to be: lossy"
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcmraw</b>(1), <b>gdcmconv</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcminfo.xml b/Utilities/doxygen/man/gdcminfo.xml
new file mode 100644
index 0000000..3affa95
--- /dev/null
+++ b/Utilities/doxygen/man/gdcminfo.xml
@@ -0,0 +1,170 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcminfo</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcminfo</refname>
+ <refpurpose>Display meta info about the input DICOM file.</refpurpose>
+</refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>gdcminfo</command>
+ <arg choice="opt">
+ <option>options</option>
+ </arg>
+ <arg choice="opt" rep="repeat">file-in/dir-in</arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+<refsection xml:id="gdcminfo_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcminfo</emphasis> command line program takes as input a DICOM file, or a directory and process it to extract meta-information about the DICOM file(s) processed.</para>
+</refsection>
+<refsection xml:id="gdcminfo_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in/dir-in DICOM input filename/dirname
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcminfo_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcminfo_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> -r --recursive recursive traversal of an input directory
+ -d --check-deflated check if file is proper deflated syntax.
+ --resources-path Resources path.
+ --md5sum Compute md5sum of Pixel Data attribute value.
+ --check-compression check the encapsulated stream compression (lossless/lossy).
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcminfo_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1environment_variable">
+<title>environment variable</title>
+
+<para><envar>GDCM_RESOURCES_PATH</envar> path pointing to resources files (Part3.xml, ...)</para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmviewer_1simple_usage">
+<title>Simple usage</title>
+<refsection xml:id="gdcminfo_1gdcmdata">
+<title>gdcmData</title>
+
+<para>Using data from gdcmData:</para>
+
+<para><literallayout>$ gdcminfo gdcmData/012345.002.050.dcm
+</literallayout></para>
+
+<para><literallayout>MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
+NumberOfDimensions: 2
+Dimensions: (256,256)
+Origin: (-85,21.6,108.7)
+Spacing: (0.664062,0.664062,1.5)
+DirectionCosines: (1,0,0,0,0,-1)
+Rescale Intercept/Slope: (0,1)
+SamplesPerPixel :1
+BitsAllocated :16
+BitsStored :16
+HighBit :15
+PixelRepresentation:1
+Orientation Label: CORONAL
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcminfo_1dclunie">
+<title>Davie Clunie datasets:</title>
+
+<para>Using data from David Clunie datasets:</para>
+
+<para><literallayout>$ gdcminfo BRTUM001.dcm
+</literallayout></para>
+
+<para><literallayout>MediaStorage is 1.2.840.10008.5.1.4.1.1.4.1 [Enhanced MR Image Storage]
+NumberOfDimensions: 3
+Dimensions: (256,256,15)
+Origin: (40,-105,105)
+Spacing: (0.820312,0.820312,6)
+DirectionCosines: (0,1,0,0,0,-1)
+Rescale Intercept/Slope: (0,1)
+SamplesPerPixel :1
+BitsAllocated :16
+BitsStored :16
+HighBit :15
+PixelRepresentation:1
+Orientation Label: SAGITTAL
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcminfo_1md5sum">
+<title>Checking the md5sum of the Pixel Data</title>
+
+<para>After compressing a DICOM file (see gdcmconv) using a lossless compression algorithm, it is fairly easy to compare the two files for differences at DICOM attribute level. However one operation is slightly easier to do: how to make sure the compression was actually lossless ? In this case one could use the –md5sum operation.</para>
+
+<para>Take an uncompressed DICOM image file:</para>
+
+<para><literallayout>$ gdcminfo --md5sum SIEMENS_ImageLocationUN.dcm
+</literallayout></para>
+
+<para>The tool return: 0621954acd5815e0b4f7b65fcc6506b1</para>
+
+<para>Now compress this file:</para>
+
+<para><literallayout>$ gdcmconv --jpegls SIEMENS_ImageLocationUN.dcm lossless_compressed.dcm
+</literallayout></para>
+
+<para>and then check again the md5sum:</para>
+
+<para><literallayout>$ gdcminfo --md5sum lossless_compressed.dcm
+</literallayout></para>
+
+<para>The tool return: 0621954acd5815e0b4f7b65fcc6506b1</para>
+</refsection>
+<refsection xml:id="gdcminfo_1checking_lossless">
+<title>Checking if Pixel Data is lossless</title>
+
+<para>In some environment one wish to check whether or not the DICOM file is lossless. It is fairly easy to do that in most cases. Only on two occasions this is not clear from the sole DICOM Attributes. When the Transfer Syntax is JPEG 2000 Image Compression (1.2.840.10008.1.2.4.91) and when the Transfer Syntax is JPEG-LS Lossy (Near-Lossless) Image Compression (1.2.840.10008.1.2.4.81).</para>
+
+<para>In this case, the only solution is to open the Pixel Data element, read the specific JPEG header and check whether or not the JPEG transformation was lossless or not:</para>
+
+<para><literallayout>$ gdcminfo --check-compression gdcmData/MAROTECH_CT_JP2Lossy.dcm
+</literallayout></para>
+
+<para>The tool returns: "Encapsulated Stream was found to be: lossy"</para>
+
+<para>Pay attention that this tool also checks the Image Lossy Compression attribute (0028,2110). This means <option>--check-compression</option> will also returns a value of lossy if a predecessor was found to be lossy compressed.</para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcminfo_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmraw</emphasis>(1), <emphasis role="bold">gdcmconv</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmpap3.dox b/Utilities/doxygen/man/gdcmpap3.dox
deleted file mode 100644
index 5a8869b..0000000
--- a/Utilities/doxygen/man/gdcmpap3.dox
+++ /dev/null
@@ -1,93 +0,0 @@
-/*!
-
-\page gdcmpap3 Tool to convert PAPYRUS 3.0 to DICOM.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmconv [options] file-in file-out
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmconv command line program takes as input a PAPYRUS 3.0 file (file-in) and
-process it to generate an output (pseudo) DICOM file (file-out).
-The command line option dictate the type of operation(s) gdcmconv will use to
-generate the output file.
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM input filename
-
-file-out DICOM output filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection parameters parameters
-\verbatim
- -i --input DICOM filename
- -o --output DICOM filename
-\endverbatim
-
-\subsection options options
-\verbatim
- -S --split Split multiframes PAPYRUS 3.0 into multiples DICOM files
- --decomp-pap3 Use PAPYRUS 3.0 for decompressing (can be combined with --split).
- --check-iop Check that the Image Orientation (Patient) Attribute is ok (see --split).
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\subsection environment_variable environment variable
-\verbatim
- GDCM_ROOT_UID Root UID
-\endverbatim
-
-\section simple_usage Simple usage
-\b gdcmconv is a great tool to convert broken PAPYRUS 3.0 implementation into
-properly parsable DICOM file. Usage is simply:
-
-\verbatim
-$ gdcmconv input.pa3 output.dcm
-\endverbatim
-
-or if you prefer being explicit:
-
-\verbatim
-$ gdcmconv -i input.pa3 -o output.dcm
-\endverbatim
-
-Even though gdcmpap3 can overwrite directly on the same file (input.pa3 =
-output.dcm), it is recommended that user should first convert into a different
-file to make sure the bug is properly handled by GDCM.
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcmconv</b>(1), <b>gdcminfo</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmpap3.xml b/Utilities/doxygen/man/gdcmpap3.xml
new file mode 100644
index 0000000..0b8bc58
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmpap3.xml
@@ -0,0 +1,99 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmpap3</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmpap3</refname>
+ <refpurpose>Tool to convert PAPYRUS 3.0 to DICOM.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmpap3_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmpap3 [options] file-in file-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmpap3_1description">
+<title>DESCRIPTION</title>
+
+<para>The <command>gdcmpap3</command> command line program takes as input a PAPYRUS 3.0 file (file-in) and process it to generate an output (pseudo) DICOM file (file-out). The command line option dictate the type of operation(s) <command>gdcmpap3</command> will use to generate the output file.</para>
+</refsection>
+<refsection xml:id="gdcmpap3_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in DICOM input filename
+
+file-out DICOM output filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmpap3_1options">
+<title>OPTIONS</title>
+
+<para><literallayout> -i --input DICOM filename
+ -o --output DICOM filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmpap3_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> -S --split Split multiframes PAPYRUS 3.0 into multiples DICOM files
+ --decomp-pap3 Use PAPYRUS 3.0 for decompressing (can be combined with --split).
+ --check-iop Check that the Image Orientation (Patient) Attribute is ok (see --split).
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmpap3_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmpap3_1environment_variable">
+<title>environment variable</title>
+
+<para><envar>GDCM_ROOT_UID</envar> Root UID</para>
+</refsection>
+<refsection xml:id="gdcmpap3_1simple_usage">
+<title>Simple usage</title>
+
+<para><command>gdcmpap3</command> is a great tool to convert broken PAPYRUS 3.0 implementation into properly parsable DICOM file. Usage is simply:</para>
+
+<para><literallayout>$ gdcmpap3 input.pa3 output.dcm
+</literallayout></para>
+
+<para>or if you prefer being explicit:</para>
+
+<para><literallayout>$ gdcmpap3 -i input.pa3 -o output.dcm
+</literallayout></para>
+
+<para>Even though <command>gdcmpap3</command> can overwrite directly on the same file (<userinput>input.pa3</userinput> = <userinput>output.dcm</userinput>), it is recommended that user should first convert into a different file to make sure the bug is properly handled by GDCM.</para>
+</refsection>
+<refsection xml:id="gdcmpap3_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmconv</emphasis>(1), <emphasis role="bold">gdcminfo</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmpdf.dox b/Utilities/doxygen/man/gdcmpdf.xml
similarity index 53%
rename from Utilities/doxygen/man/gdcmpdf.dox
rename to Utilities/doxygen/man/gdcmpdf.xml
index 221e672..961d214 100644
--- a/Utilities/doxygen/man/gdcmpdf.dox
+++ b/Utilities/doxygen/man/gdcmpdf.xml
@@ -1,33 +1,45 @@
-/*!
-
-\page gdcmpdf Tool to convert PDF to PDF/DICOM.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmpdf [options] file-in file-out
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmpdf tool convert a PDF file (any PDF version) into an encapsulated PDF/DICOM file.
-By default it will try to read the PDF meta information stored in the PDF and convert this
-information to some specific DICOM fields (see below). However it may fails (eg. wrong
-password on encrypted PDF file) in which case empty value are used.
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in PDF input filename
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmpdf</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmpdf</refname>
+ <refpurpose>Tool to convert PDF to PDF/DICOM.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmxml_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmpdf [options] file-in file-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmpdf</emphasis> tool convert a PDF file (any PDF version) into an encapsulated PDF/DICOM file. By default it will try to read the PDF meta information stored in the PDF and convert this information to some specific DICOM fields (see below). However it may fails (eg. wrong password on encrypted PDF file) in which case empty value are used.</para>
+</refsection>
+<refsection xml:id="gdcmxml_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in PDF input filename
file-out DICOM output filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection general_options general options
-\verbatim
- -h --help
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcmxml_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
print this help text and exit
-v --version
@@ -44,28 +56,28 @@ file-out DICOM output filename
-D --debug
debug mode, print debug information
-\endverbatim
-
-\section usage_example Usage Example
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmpdf_1usage_example">
+<title>Usage Example</title>
-\verbatim
-$ wget http://gdcm.sourceforge.net/gdcm.pdf
+<para><literallayout>$ wget http://gdcm.sourceforge.net/gdcm.pdf
$ gdcmpdf gdcm.pdf gdcm.dcm
-\endverbatim
+</literallayout></para>
-To re-extract the encapsulated PDF file:
+<para>To re-extract the encapsulated PDF file:</para>
-\verbatim
- $ gdcmraw -i gdcm.dcm -t 42,11 -o gdcm.dcm.pdf
+<para><literallayout> $ gdcmraw -i gdcm.dcm -t 42,11 -o gdcm.dcm.pdf
$ diff gdcm.pdf gdcm.dcm.pdf
-\endverbatim
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmpdf_1pdf_mapping">
+<title>PDF Info Mapping</title>
-\section pdf_mapping PDF Info Mapping
+<para>Here is how the PDF info is mapped to DICOM information (typical pdfinfo output):</para>
-Here is how the PDF info is mapped to DICOM information (typical pdfinfo output):
-
-\verbatim
-Title: GDCM Reference Manual
+<para><literallayout>Title: GDCM Reference Manual
Subject: Grassroots DICOM API reference
Keywords: GDCM,DICOM,JPEG,Lossless JPEG,JPEG-LS,J2K,JPEG 2000,RLE
Author: Mathieu Malaterre and co.
@@ -79,12 +91,11 @@ Page size: 612 x 792 pts (letter)
File size: 13756841 bytes
Optimized: yes
PDF version: 1.4
-\endverbatim
+</literallayout></para>
-Converted to DICOM this leads to:
+<para>Converted to DICOM this leads to:</para>
-\verbatim
-# Dicom-Data-Set
+<para><literallayout># Dicom-Data-Set
# Used TransferSyntax: Little Endian Explicit
(0008,0005) CS [ISO_IR 100] # 10, 1 SpecificCharacterSet
(0008,0012) DA [20090428] # 8, 1 InstanceCreationDate
@@ -117,33 +128,36 @@ Converted to DICOM this leads to:
(0042,0010) ST [GDCM Reference Manual] # 22, 1 DocumentTitle
(0042,0011) OB 25\\50\\44\\46\\2d\\31\\2e\\34\\0a\\25\\e7\\f3\\cf\\d3\\0a\\33\\32\\30\\37\\37\\20\\30... # 13756842, 1 EncapsulatedDocument
(0042,0012) LO [application/pdf] # 16, 1 MIMETypeOfEncapsulatedDocument
-\endverbatim
+</literallayout></para>
-\verbatim
-$ stat gdcm.pdf
- File: `gdcm.pdf'
+<para><literallayout>$ stat gdcm.pdf
+ File: `gdcm.pdf'
Size: 13756841 Blocks: 26912 IO Block: 4096 regular file
Device: fe01h/65025d Inode: 2675750 Links: 1
Access: (0644/-rw-r--r--) Uid: ( 1002/mmalaterre) Gid: ( 1002/mmalaterre)
Access: 2009-04-28 16:05:00.000000000 +0200
Modify: 2009-04-28 15:34:37.000000000 +0200
Change: 2009-04-28 16:05:00.000000000 +0200
-\endverbatim
-
-
-Explanation for the different Date/Time mappings:
-
-\li Study Date/Time, Instance Creation Date/Time are both equal to the current time gdcmpdf tool was run,
-\li Acquisition Date Time is set to the Modify Time of the actual PDF file,
-\li Content Date/Time are set from the actual PDF header info: CreationDate.
-
-
-\section see_also SEE ALSO
-
-<b>gdcmconv</b>(1), <b>gdcmraw</b>(1), <b>pdfinfo</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
+</literallayout></para>
+
+<para>Explanation for the different Date/Time mappings:</para>
+
+<para><itemizedlist>
+<listitem>
+<para>Study Date/Time, Instance Creation Date/Time are both equal to the current time gdcmpdf tool was run, </para>
+</listitem>
+<listitem>
+<para>Acquisition Date Time is set to the Modify Time of the actual PDF file, </para>
+</listitem>
+<listitem>
+<para>Content Date/Time are set from the actual PDF header info: CreationDate.</para>
+</listitem>
+</itemizedlist>
+</para>
+</refsection>
+<refsection xml:id="gdcmxml_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmconv</emphasis>(1), <emphasis role="bold">gdcmraw</emphasis>(1), <emphasis role="bold">pdfinfo</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmraw.dox b/Utilities/doxygen/man/gdcmraw.dox
deleted file mode 100644
index cee03e0..0000000
--- a/Utilities/doxygen/man/gdcmraw.dox
+++ /dev/null
@@ -1,213 +0,0 @@
-/*!
-
-\page gdcmraw Extract Data Element Value Field.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmraw [options] file-in file-out
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmraw tool is mostly used for development purpose. It is used to
-extract a specific binary field from a DICOM DataSet.
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM input filename
-
-file-out output filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection parameters parameters
-\verbatim
- -i --input Input filename
- -o --output Output filename
- -t --tag Specify tag to extract value from.
-\endverbatim
-
-\subsection options options
-\verbatim
- -S --split-frags Split fragments into multiple files.
- -p --pattern Specify trailing file pattern (see split-frags).
- -P --pixel-data Pixel Data trailing 0.
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\section usage Typical usage
-
-\subsection copy_attribute Copy Attribute Value to file
-
-This will extract the value at Tag (0025,101b):
-
-\verbatim
-$ gdcmraw -i GE_MR_0025xx1bProtocolDataBlock.dcm -t 25,101b -o pdb.raw
-\endverbatim
-
-\subsection extract_pixeldata Extract Pixel Data
-
-If you do not specify any tag, the Pixel Data element is the default one. So for instance to grab the Pixel Data from an image:
-
-\verbatim
-$ gdcmraw -i test.acr -o test.raw
-\endverbatim
-
-You can then for example compute the md5sum of this pixel data (very useful):
-
-\verbatim
-$ md5sum test.raw
-f845c8f283d39a0204c325654493ba53 test.raw
-\endverbatim
-
-\subsection encapsulated_syntax Encapsulated Syntax
-
-When the Pixel Data is encapsulated, multiple fragments can be used to store a single slice image:
-
-\verbatim
-$ gdcmdump D_CLUNIE_CT1_J2KR.dcm
-\endverbatim
-
-\verbatim
-\&...
-(7fe0,0010) OB # u/l,1 Pixel Data
- (fffe,e000) ?? [] # 0,1 Item
- (fffe,e000) ?? ff\\4f\\ff\\51\\00\\29\\00\\00\\00\\00\\02\\00\\00\\00\\02\\00\\00\\00\\00\\00\\00\\00\\00\\00\\00\\00\\02\\00\\00\\00\\02\\00 # 65536,1 Item
- (fffe,e000) ?? 2c\\b7\\ee\\68\\de\\e3\\93\\2d\\b3\\b8\\ba\\90\\7b\\42\\3e\\f8\\42\\16\\64\\88\\46\\30\\37\\d4\\50\\95\\9b\\b6\\a5\\c7\\38\\9b # 65536,1 Item
- (fffe,e000) ?? 48\\3c\\03\\e8\\c4\\3f\\44\\e1\\8a\\5c\\73\\3b\\02\\0a\\ad\\a5\\8f\\e4\\0c\\81\\76\\a2\\d7\\1b\\7f\\b7\\cd\\bc\\30\\c6\\6a\\6a # 43308,1 Item
-(fffe,e0dd) 0
-\endverbatim
-
-In order to create a J2K image out of it, we need to extract each fragments and concatenate them:
-
-\verbatim
-$ gdcmraw -i D_CLUNIE_CT1_J2KR.dcm -o D_CLUNIE_CT1_J2KR.j2k
-\endverbatim
-
-This is a valid J2K file, using the Kakadu software package:
-
-\verbatim
-$ kdu_expand -i D_CLUNIE_CT1_J2KR.j2k -o D_CLUNIE_CT1_J2KR.tiff -record D_CLUNIE_CT1_J2KR.txt
-\endverbatim
-
-\verbatim
-$ cat D_CLUNIE_CT1_J2KR.txt
-\endverbatim
-
-\verbatim
-Sprofile=PROFILE2
-Scap=no
-Sextensions=0
-Ssize={512,512}
-Sorigin={0,0}
-Stiles={512,512}
-Stile_origin={0,0}
-Scomponents=1
-Ssigned=yes
-Sprecision=16
-Ssampling={1,1}
-Sdims={512,512}
-Cycc=no
-Cmct=0
-Clayers=1
-Cuse_sop=no
-Cuse_eph=no
-Corder=LRCP
-Calign_blk_last={no,no}
-Clevels=5
-Cads=0
-Cdfs=0
-Cdecomp=B(-:-:-)
-Creversible=yes
-Ckernels=W5X3
-Catk=0
-Cuse_precincts=no
-Cblk={64,64}
-Cmodes=0
-Qguard=1
-Qabs_ranges=18,19,19,20,19,19,20,19,19,20,19,19,20,19,19,20
-
->> New attributes for tile 0:
-\endverbatim
-
-\subsection extract_fragments Extract fragments as single file
-
-Sometimes each fragments is in fact a single slice, so we would not need to concatenate them:
-
-
-\verbatim
-$ gdcmdump 00191113.dcm
-\endverbatim
-
-\verbatim
-\&...
-(7fe0,0010) OB # u/l,1 Pixel Data
- (fffe,e000) ?? 00\\00\\00\\00\\6b\\38\\01\\00\\10\\77\\02\\00\\37\\b6\\03\\00\\a7\\f4\\04\\00 # 20,1 Item
- (fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 79970,1 Item
- (fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 81564,1 Item
- (fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 81694,1 Item
- (fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 81511 (81512),1 Item
-(fffe,e0dd) 0
-\endverbatim
-
-Let's try to extract those 4 individual Lossless jpeg individually:
-
-\verbatim
-$ gdcmraw --split-frags -i 00191113.dcm -o jpeg --pattern %02d.ljpeg
-\endverbatim
-
-This will output 4 files:
-
-\verbatim
--rw-r--r-- 1 mathieu mathieu 81512 2008-08-08 22:10 jpeg03.ljpeg
--rw-r--r-- 1 mathieu mathieu 81694 2008-08-08 22:10 jpeg02.ljpeg
--rw-r--r-- 1 mathieu mathieu 81564 2008-08-08 22:10 jpeg01.ljpeg
--rw-r--r-- 1 mathieu mathieu 79970 2008-08-08 22:10 jpeg00.ljpeg
-\endverbatim
-
-\section footnote Footnote about JPEG files
-
-It is a common misunderstanding to interchange 'JPEG 8bits lossy' with simply
-JPEG file. The JPEG specification is much broader than simply the common lossy
-8bits file (as found on internet).
-
-You can have:
-
-\li JPEG Lossy 8bits
-\li JPEG Lossy 12bits
-\li JPEG Lossless 2-16bits
-
-Those are what is defined in ITU-T T.81, ISO/IEC IS 10918-1.
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcmraw</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmraw.xml b/Utilities/doxygen/man/gdcmraw.xml
new file mode 100644
index 0000000..6b3d316
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmraw.xml
@@ -0,0 +1,221 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmraw</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmraw</refname>
+ <refpurpose>Extract Data Element Value Field.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmraw_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmraw [options] file-in file-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmraw_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmraw</emphasis> tool is mostly used for development purpose. It is used to extract a specific binary field from a DICOM DataSet.</para>
+</refsection>
+<refsection xml:id="gdcmraw_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in DICOM input filename
+
+file-out output filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmraw_1options">
+<title>OPTIONS</title>
+
+<para><literallayout> -i --input Input filename
+ -o --output Output filename
+ -t --tag Specify tag to extract value from.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmraw_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> -S --split-frags Split fragments into multiple files.
+ -p --pattern Specify trailing file pattern (see split-frags).
+ -P --pixel-data Pixel Data trailing 0.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmraw_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmviewer_1usage">
+<title>Typical usage</title>
+<refsection xml:id="gdcmraw_1copy_attribute">
+<title>Copy Attribute Value to file</title>
+
+<para>This will extract the value at Tag (0025,101b):</para>
+
+<para><literallayout>$ gdcmraw -i GE_MR_0025xx1bProtocolDataBlock.dcm -t 25,101b -o pdb.raw
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmraw_1extract_pixeldata">
+<title>Extract Pixel Data</title>
+
+<para>If you do not specify any tag, the Pixel Data element is the default one. So for instance to grab the Pixel Data from an image:</para>
+
+<para><literallayout>$ gdcmraw -i test.acr -o test.raw
+</literallayout></para>
+
+<para>You can then for example compute the md5sum of this pixel data (very useful):</para>
+
+<para><literallayout>$ md5sum test.raw
+f845c8f283d39a0204c325654493ba53 test.raw
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmraw_1encapsulated_syntax">
+<title>Encapsulated Syntax</title>
+
+<para>When the Pixel Data is encapsulated, multiple fragments can be used to store a single slice image:</para>
+
+<para><literallayout>$ gdcmdump D_CLUNIE_CT1_J2KR.dcm
+</literallayout></para>
+
+<para><literallayout>\&...
+(7fe0,0010) OB # u/l,1 Pixel Data
+ (fffe,e000) ?? [] # 0,1 Item
+ (fffe,e000) ?? ff\\4f\\ff\\51\\00\\29\\00\\00\\00\\00\\02\\00\\00\\00\\02\\00\\00\\00\\00\\00\\00\\00\\00\\00\\00\\00\\02\\00\\00\\00\\02\\00 # 65536,1 Item
+ (fffe,e000) ?? 2c\\b7\\ee\\68\\de\\e3\\93\\2d\\b3\\b8\\ba\\90\\7b\\42\\3e\\f8\\42\\16\\64\\88\\46\\30\\37\\d4\\50\\95\\9b\\b6\\a5\\c7\\38\\9b # 65536,1 Item
+ (fffe,e000) ?? 48\\3c\\03\\e8\\c4\\3f\\44\\e1\\8a\\5c\\73\\3b\\02\\0a\\ad\\a5\\8f\\e4\\0c\\81\\76\\a2\\d7\\1b\\7f\\b7\\cd\\bc\\30\\c6\\6a\\6a # 43308,1 Item
+(fffe,e0dd) 0
+</literallayout></para>
+
+<para>In order to create a J2K image out of it, we need to extract each fragments and concatenate them:</para>
+
+<para><literallayout>$ gdcmraw -i D_CLUNIE_CT1_J2KR.dcm -o D_CLUNIE_CT1_J2KR.j2k
+</literallayout></para>
+
+<para>This is a valid J2K file, using the Kakadu software package:</para>
+
+<para><literallayout>$ kdu_expand -i D_CLUNIE_CT1_J2KR.j2k -o D_CLUNIE_CT1_J2KR.tiff -record D_CLUNIE_CT1_J2KR.txt
+</literallayout></para>
+
+<para><literallayout>$ cat D_CLUNIE_CT1_J2KR.txt
+</literallayout></para>
+
+<para><literallayout>Sprofile=PROFILE2
+Scap=no
+Sextensions=0
+Ssize={512,512}
+Sorigin={0,0}
+Stiles={512,512}
+Stile_origin={0,0}
+Scomponents=1
+Ssigned=yes
+Sprecision=16
+Ssampling={1,1}
+Sdims={512,512}
+Cycc=no
+Cmct=0
+Clayers=1
+Cuse_sop=no
+Cuse_eph=no
+Corder=LRCP
+Calign_blk_last={no,no}
+Clevels=5
+Cads=0
+Cdfs=0
+Cdecomp=B(-:-:-)
+Creversible=yes
+Ckernels=W5X3
+Catk=0
+Cuse_precincts=no
+Cblk={64,64}
+Cmodes=0
+Qguard=1
+Qabs_ranges=18,19,19,20,19,19,20,19,19,20,19,19,20,19,19,20
+
+>> New attributes for tile 0:
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmraw_1extract_fragments">
+<title>Extract fragments as single file</title>
+
+<para>Sometimes each fragments is in fact a single slice, so we would not need to concatenate them:</para>
+
+<para><literallayout>$ gdcmdump 00191113.dcm
+</literallayout></para>
+
+<para><literallayout>\&...
+(7fe0,0010) OB # u/l,1 Pixel Data
+ (fffe,e000) ?? 00\\00\\00\\00\\6b\\38\\01\\00\\10\\77\\02\\00\\37\\b6\\03\\00\\a7\\f4\\04\\00 # 20,1 Item
+ (fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 79970,1 Item
+ (fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 81564,1 Item
+ (fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 81694,1 Item
+ (fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 81511 (81512),1 Item
+(fffe,e0dd) 0
+</literallayout></para>
+
+<para>Let's try to extract those 4 individual Lossless jpeg individually:</para>
+
+<para><literallayout>$ gdcmraw --split-frags -i 00191113.dcm -o jpeg --pattern %02d.ljpeg
+</literallayout></para>
+
+<para>This will output 4 files:</para>
+
+<para><literallayout>-rw-r--r-- 1 mathieu mathieu 81512 2008-08-08 22:10 jpeg03.ljpeg
+-rw-r--r-- 1 mathieu mathieu 81694 2008-08-08 22:10 jpeg02.ljpeg
+-rw-r--r-- 1 mathieu mathieu 81564 2008-08-08 22:10 jpeg01.ljpeg
+-rw-r--r-- 1 mathieu mathieu 79970 2008-08-08 22:10 jpeg00.ljpeg
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmraw_1footnote">
+<title>Footnote about JPEG files</title>
+
+<para>It is a common misunderstanding to interchange 'JPEG 8bits lossy' with simply JPEG file. The JPEG specification is much broader than simply the common lossy 8bits file (as found on internet).</para>
+
+<para>You can have:</para>
+
+<para><itemizedlist>
+<listitem>
+<para>JPEG Lossy 8bits </para>
+</listitem>
+<listitem>
+<para>JPEG Lossy 12bits </para>
+</listitem>
+<listitem>
+<para>JPEG Lossless 2-16bits</para>
+</listitem>
+</itemizedlist>
+Those are what is defined in ITU-T T.81, ISO/IEC IS 10918-1.</para>
+</refsection>
+<refsection xml:id="gdcmraw_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmraw</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmscanner.dox b/Utilities/doxygen/man/gdcmscanner.dox
deleted file mode 100644
index 2678dd9..0000000
--- a/Utilities/doxygen/man/gdcmscanner.dox
+++ /dev/null
@@ -1,79 +0,0 @@
-/*!
-
-\page gdcmscanner Scan a directory containing DICOM files.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmscanner [options] directory
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmscanner is a command line tool to quickly extract value from a set
-of DICOM attribute in a DICOM File-Set.
-
-\subsection parameters parameters
-\verbatim
- -d --dir DICOM directory
- -t --tag %d,%d DICOM tag(s) to look for
-\endverbatim
-
-\subsection options options
-\verbatim
- -p --print Print output.
- -r --recursive Recusively descend directory.
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\section usage Typical usage
-\section simple_usage Simple usage
-In order to display all the value for Patient Name (0010,0010) in the directory
-name \b gdcmData, simply do:
-
-\verbatim
-$ gdcmscanner -t 10,10 -d gdcmData -p
-\endverbatim
-
-\section complex_usage Complex usage
-
-Because gdcmscanner does not support progress, you have to wait until all files
-are traversed to see any results. This is quite cumbersome, on UNIX this can
-be worked around with the following trick:
-
-\verbatim
-$ find gdcmData -type d -exec gdcmscanner -t 10,10 -d {} -p ';'
-\endverbatim
-
-So all directory are locally traversed (no child directory are recursively
-traversed), which means results comes out much faster.
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcmraw</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmscanner.xml b/Utilities/doxygen/man/gdcmscanner.xml
new file mode 100644
index 0000000..047d23a
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmscanner.xml
@@ -0,0 +1,91 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmscanner</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmscanner</refname>
+ <refpurpose>Scan a directory containing DICOM files.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmxml_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmscanner [options] directory
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmscanner</emphasis> is a command line tool to quickly extract value from a set of DICOM attribute in a DICOM File-Set.</para>
+<refsection xml:id="gdcmxml_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout> -d --dir DICOM directory
+ -t --tag %d,%d DICOM tag(s) to look for
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1options">
+<title>OPTIONS</title>
+
+<para><literallayout> -p --print Print output.
+ -r --recursive Recusively descend directory.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmviewer_1usage">
+<title>Typical usage</title>
+</refsection>
+<refsection xml:id="gdcmviewer_1simple_usage">
+<title>Simple usage</title>
+
+<para>In order to display all the value for Patient Name (0010,0010) in the directory name <emphasis role="bold">gdcmData</emphasis>, simply do:</para>
+
+<para><literallayout>$ gdcmscanner -t 10,10 -d gdcmData -p
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscanner_1complex_usage">
+<title>Complex usage</title>
+
+<para>Because gdcmscanner does not support progress, you have to wait until all files are traversed to see any results. This is quite cumbersome, on UNIX this can be worked around with the following trick:</para>
+
+<para><literallayout>$ find gdcmData -type d -exec gdcmscanner -t 10,10 -d {} -p ';'
+</literallayout></para>
+
+<para>So all directory are locally traversed (no child directory are recursively traversed), which means results comes out much faster.</para>
+</refsection>
+<refsection xml:id="gdcmxml_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmraw</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmscu.dox b/Utilities/doxygen/man/gdcmscu.dox
deleted file mode 100644
index 82140c9..0000000
--- a/Utilities/doxygen/man/gdcmscu.dox
+++ /dev/null
@@ -1,341 +0,0 @@
-/*!
-
-\page gdcmscu Tool to execute a DICOM Query/Retrieve operation
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmscu [OPTION]...[OPERATION]...HOSTNAME...[PORT]...
-\endverbatim
-Execute a DICOM Q/R operation to HOSTNAME, using port PORT (104 when not specified)
-
-\section description DESCRIPTION
-
-The \b gdcmscu command line program is the tool to execute DICOM Query/Retrieve operation.
-It supports:
-\li C-ECHO (SCU)
-\li C-FIND (SCU)
-\li C-STORE (SCU)
-\li C-MOVE (SCU/SCP)
-C-MOVE operation are executed using two different ports (one for the SCU and one for the SCP).
-
-\section parameters PARAMETERS
-
-\section options OPTIONS
-
-\subsection options options
-\verbatim
- -H --hostname %s Hostname.
- -p --port %d Port number.
- --aetitle %s Set calling AE Title.
- --call %s Set called AE Title.
-\endverbatim
-
-\subsection mode_options mode options
-\verbatim
- --echo C-ECHO (default when none).
- --store C-STORE.
- --find C-FIND.
- --move C-MOVE.
-\endverbatim
-
-\subsection cstore_options C-STORE options
-\verbatim
- -i --input %s DICOM filename
- -r --recursive recursively process (sub-)directories
- --store-query %s Store constructed query in file
-\endverbatim
-
-\subsection cfind_options C-FIND/C-MOVE options
-\verbatim
- --patientroot C-FIND Patient Root Model.
- --studyroot C-FIND Study Root Model.
-
- --patient C-FIND Query on Patient Info (cannot be used with --studyroot).
- --study C-FIND Query on Study Info.
- --series C-FIND Query on Series Info.
- --image C-FIND Query on Image Info.
- --key %d,%d[=%s] 0123,4567=VALUE for specifying search criteria (wildcard allowed)
- With --key, leave blank (ie, --key 10,20="" or --key 10,20) to retrieve values
-\endverbatim
-
-\subsection cmove_options C-MOVE options
-\verbatim
- -o --output %s DICOM filename / directory
- --port-scp %d Port for incoming associations
- --key %d,%d[=%s 0123,4567=VALUE for specifying search criteria (wildcard not allowed)
- Note that C-MOVE supports the same queries as C-FIND, but no wildcards are allowed
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-
- -L --log-file
- specify a filename where to write logs
-
- --queryhelp
- print query help
-\endverbatim
-
-\subsection environment_variable environment variable
-\verbatim
- GDCM_ROOT_UID Root UID
-\endverbatim
-
-\section cecho_usage C-ECHO usage
-
-\b gdcmscu is a great tool to test if a DICOM server is up. For example to send
-a C-ECHO to server dicom.example.com using port 104, use:
-
-\verbatim
-$ gdcmscu dicom.example.com
-\endverbatim
-
-or if you prefer being explicit:
-
-\verbatim
-$ gdcmscu --echo dicom.example.com 104
-\endverbatim
-
-Using basic security your DICOM server might require that you set the
-appropriate called AE-TITLE
-
-\verbatim
-$ gdcmscu --echo dicom.example.com 11112 --call SERVSCP
-\endverbatim
-
-If you want to specifiy your own AE-TITLE (default is GDCMSCU), simply use:
-
-\verbatim
-$ gdcmscu --echo dicom.example.com 11112 --call SERVSCP --aetitle MYSCU
-\endverbatim
-
-For example you could test on the DICOM server provided by DICOMObject team:
-
-\verbatim
-$ gdcmscu www.dicomserver.co.uk 11112
-\endverbatim
-
-\section cstore_usage C-STORE usage
-
-C-STORE is the operation that allow sending a DICOM file to a remote DICOM
-server. For instance to send a file called myfile.dcm
-
-\verbatim
-$ gdcmscu --store dicom.example.com 104 myfile.dcm
-\endverbatim
-
-or if you prefer being explicit:
-
-\verbatim
-$ gdcmscu --store dicom.example.com 104 -i myfile.dcm
-\endverbatim
-
-You can even send multiple files using the same association:
-
-\verbatim
-$ gdcmscu --store dicom.example.com 104 myfile1.dcm myfile2.dcm myfile3.dcm ...
-\endverbatim
-
-\section cfind_usage C-FIND usage
-
-\b gdcmscu also allow querying a DICOM server. This is the C-FIND operation,
-for example to find all DICOM Instance where PatientsName match a particular
-pattern, usage is simply:
-
-\verbatim
-$ gdcmscu --find --patient dicom.example.com 11112 --patientroot --key 10,10,"A*"
-\endverbatim
-
-We also support a DCMTK compatible convention:
-
-\verbatim
-$ gdcmscu --find --patient dicom.example.com 11112 --patientroot --key 10,10="A*"
-\endverbatim
-
-When an attribute is set without a value it will be part of the output result:
-
-\verbatim
-$ gdcmscu --find --patient dicom.example.com 11112 --call MI2B2 --patientroot -k 10,10="A*" -k 10,20
-\endverbatim
-
-\section cmove_usage C-MOVE usage
-
-C-MOVE is the operation to retrieve a DICOM instance from a remote DICOM
-server. Most of the time, it is a subsequent operation after a C-FIND query.
-To retrieve a DICOM instance where PatientID is ABCD1234, simply execute:
-
-\verbatim
-$ gdcmscu --move --patient --aetitle ACME1 --call ACME_STORE dicom.example.com 5678 --patientroot -k 10,20="ABCD1234" --port-scp 1234
-\endverbatim
-
-WARNING For this operation to work you need information from the DICOM server
-you are communicating with. Only the DICOM server you are sending a C-MOVE
-query will be responsible for sending back incoming associations (the actual
-C-STORE SCP).
-Therefore you need to make sure that you mapping of (AE-TITLE,PortNumber) is
-properly set on the DICOM server side as well as the port for incoming
-association (--port-scp).
-
-\b gdcmscu does not currently support external C-STORE association (C-STORE
-request sent to an external SCP application).
-
-\section patientroot_notes patientroot notes
-
-The flag --patientroot is just simply a wrapper around the syntax --key 8,52=PATIENT
-For instance one would write using DCMTK syntax:
-
-\verbatim
-$ findscu --patient dicom.example.com 11112 --key 8,52=PATIENT --key 10,10="F*"
-\endverbatim
-
-This would become using GDCM syntax:
-
-\verbatim
-$ gdcmscu --find --patient dicom.example.com 11112 --patientroot --key 10,10="F*"
-\endverbatim
-
-\section debugging Debugging
-
-This is sometime difficult to investigate why a connection to a remote DICOM server
-cannot be done. Some recommendations follows:
-
-Always try to do a simple C-ECHO at first. If you cannot get the C-ECHO to work
-none of the other operations will work
-
-Before trying to a C-MOVE operation, make sure you can execute the C-FIND equivalent
-query first.
-
-When doing a C-MOVE operation you really need to communicate with the PACS
-admin as the C-MOVE operation is different from the other lower level operation
-such as HTTP/GET. When doing a C-MOVE, the server will communicate back using
-another channel (could be different port) using it's internal database to map
-an AE-TITLE back to the destination IP.
-
-Indeed the C-MOVE operation by design does not always use your incoming IP
-address to send back the resulting dataset. Instead it uses a mapping of
-AE-TITLE to IP address to send back any results. So pay particular attention to
-the spelling of your AE-TITLE and your incoming port (which may be different
-from the port to connect to the server).
-
-\section gdcmscu_portwarnings Port Warning
-
-Watch out that port ranging [1-1024] are reserved for admin and not easily
-accessible unless granted special privileges. Therefore the default 104 DICOM
-port might not be accessible to all your users.
-
-\section gdcmscu_ctorewarnings C-STORE Warnings
-
-When constructing a C-STORE operation, gdcmscu will always use the Media
-Storage SOP Class UID as found in the file to be sent. For encapsulated DICOM
-file (eg. RLE Lossless) the receiving SCP server might not support this
-compression and will legitimately refuse the C-STORE operation. In this case
-users have to manually convert to a non-compressed form this particular file:
-
-\verbatim
-$ gdcmconv --raw compressed.dcm non_compressed.dcm
-\endverbatim
-
-\section gdcmscu_cmovewarnings C-MOVE Warnings
-
-At the moment \b gdcmscu only supports non-compressed transfer syntax. It will
-always request DataSet using Implicit VR Little Endian Transfer Syntax during a
-C-MOVE operation (both incoming and outgoing associations). This make gdcmscu
---move equivalent to DCMTK movescu syntax:
-
-\verbatim
-$ movescu -xi +xi ...
-\endverbatim
-
-\section gdcmscu_cfind_image C-FIND IMAGE level (Composite Object Instance)
-
-One should pay attention that gdcmscu --find and findscu are not completely
-equivalent. Using gdcmscu --find, all Unique Keys will be added automatically.
-One can therefore execute something like this:
-
-\verbatim
-$ gdcmscu --find --patientroot --image --key 8,18=1.2.3.4.5.6 dicom.example.com 11112
-\endverbatim
-
-instead of the more explicit form
-
-\verbatim
-$ gdcmscu --find --patientroot --image --key 8,18=1.2.3.4.5.6 dicom.example.com 11112 --key 10,20 --key 20,d --key 20,e
-\endverbatim
-
-This would also be equivalent to:
-
-\verbatim
-$ findscu --patient --key 8,52=IMAGE --key 8,18=1.2.3.4.5.6 dicom.example.com 11112 --key 10,20 --key 20,d --key 20,e
-\endverbatim
-
-\section gdcmscu_storing Storing the Query
-
-It is also possible to store the query:
-
-\verbatim
-gdcmscu --find --patient --patientroot dicom.example.com 11112 --key 10,20="*" --key 10,10 --store-query query.dcm
-\endverbatim
-
-One can then check the DataSet values send for the query:
-
-\verbatim
-$ gdcmdump query.dcm
-# Dicom-File-Format
-
-# Dicom-Meta-Information-Header
-# Used TransferSyntax:
-
-# Dicom-Data-Set
-# Used TransferSyntax: 1.2.840.10008.1.2
-(0008,0005) ?? (CS) [ISO_IR 192] # 10,1-n Specific Character Set
-(0008,0052) ?? (CS) [PATIENT ] # 8,1 Query/Retrieve Level
-(0010,0010) ?? (PN) (no value) # 0,1 Patient's Name
-(0010,0020) ?? (LO) [* ] # 2,1 Patient ID
-\endverbatim
-
-The Specific Character Set was set to "ISO_IR 192" as the locale encoding of
-the system was found automatically by gdcmscu to be UTF-8.
-
-This means that the following command line will properly setup the Query with
-the appropriate Charset to be executed correctly:
-
-\verbatim
-$ gdcmscu --find --patient --patientroot dicom.example.com 11112 --key 10,10="*Jérôme*"
-\endverbatim
-
-The query is always executed on the server side (SCP), some implementations
-does not support string matching with different Character Set.
-
-\section public_servers DICOM Public Servers
-
-An up to date list of DICOM Public Servers can be found at:
-
-http://www.dclunie.com/medical-image-faq/html/part8.html#DICOMPublicServers
-
-\section see_also SEE ALSO
-
-<b>gdcmconv</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright Insight Software Consortium
-
-*/
diff --git a/Utilities/doxygen/man/gdcmscu.xml b/Utilities/doxygen/man/gdcmscu.xml
new file mode 100644
index 0000000..083baa7
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmscu.xml
@@ -0,0 +1,318 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmscu</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmscu</refname>
+ <refpurpose>Tool to execute a DICOM Query/Retrieve operation</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmscu_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmscu [OPTION]...[OPERATION]...HOSTNAME...[PORT]...
+</literallayout> Execute a DICOM Q/R operation to HOSTNAME, using port PORT (104 when not specified)</para>
+</refsection>
+<refsection xml:id="gdcmscu_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmscu</emphasis> command line program is the tool to execute DICOM Query/Retrieve operation. It supports: <itemizedlist>
+<listitem>
+<para>C-ECHO (SCU) </para>
+</listitem>
+<listitem>
+<para>C-FIND (SCU) </para>
+</listitem>
+<listitem>
+<para>C-STORE (SCU) </para>
+</listitem>
+<listitem>
+<para>C-MOVE (SCU/SCP) C-MOVE operation are executed using two different ports (one for the SCU and one for the SCP).</para>
+</listitem>
+</itemizedlist>
+</para>
+</refsection>
+<refsection xml:id="gdcmscu_1parameters">
+<title>PARAMETERS</title>
+</refsection>
+<refsection xml:id="gdcmscu_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcmscu_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> -H --hostname %s Hostname.
+ -p --port %d Port number.
+ --aetitle %s Set calling AE Title.
+ --call %s Set called AE Title.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1mode_options">
+<title>mode options</title>
+
+<para><literallayout> --echo C-ECHO (default when none).
+ --store C-STORE.
+ --find C-FIND.
+ --move C-MOVE.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1cstore_options">
+<title>C-STORE options</title>
+
+<para><literallayout> -i --input %s DICOM filename
+ -r --recursive recursively process (sub-)directories
+ --store-query %s Store constructed query in file
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1cfind_options">
+<title>C-FIND/C-MOVE options</title>
+
+<para><literallayout> --patientroot C-FIND Patient Root Model.
+ --studyroot C-FIND Study Root Model.
+
+ --patient C-FIND Query on Patient Info (cannot be used with --studyroot).
+ --study C-FIND Query on Study Info.
+ --series C-FIND Query on Series Info.
+ --image C-FIND Query on Image Info.
+ --key %d,%d[=%s] 0123,4567=VALUE for specifying search criteria (wildcard allowed)
+ With --key, leave blank (ie, --key 10,20="" or --key 10,20) to retrieve values
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1cmove_options">
+<title>C-MOVE options</title>
+
+<para><literallayout> -o --output %s DICOM filename / directory
+ --port-scp %d Port for incoming associations
+ --key %d,%d[=%s 0123,4567=VALUE for specifying search criteria (wildcard not allowed)
+ Note that C-MOVE supports the same queries as C-FIND, but no wildcards are allowed
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+
+ -L --log-file
+ specify a filename where to write logs
+
+ --queryhelp
+ print query help
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1environment_variable">
+<title>environment variable</title>
+
+<para><literallayout> GDCM_ROOT_UID Root UID
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmscu_1cecho_usage">
+<title>C-ECHO usage</title>
+
+<para><emphasis role="bold">gdcmscu</emphasis> is a great tool to test if a DICOM server is up. For example to send a C-ECHO to server dicom.example.com using port 104, use:</para>
+
+<para><literallayout>$ gdcmscu dicom.example.com
+</literallayout></para>
+
+<para>or if you prefer being explicit:</para>
+
+<para><literallayout>$ gdcmscu --echo dicom.example.com 104
+</literallayout></para>
+
+<para>Using basic security your DICOM server might require that you set the appropriate called AE-TITLE</para>
+
+<para><literallayout>$ gdcmscu --echo dicom.example.com 11112 --call SERVSCP
+</literallayout></para>
+
+<para>If you want to specifiy your own AE-TITLE (default is GDCMSCU), simply use:</para>
+
+<para><literallayout>$ gdcmscu --echo dicom.example.com 11112 --call SERVSCP --aetitle MYSCU
+</literallayout></para>
+
+<para>For example you could test on the DICOM server provided by DICOMObject team:</para>
+
+<para><literallayout>$ gdcmscu www.dicomserver.co.uk 11112
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1cstore_usage">
+<title>C-STORE usage</title>
+
+<para>C-STORE is the operation that allow sending a DICOM file to a remote DICOM server. For instance to send a file called myfile.dcm</para>
+
+<para><literallayout>$ gdcmscu --store dicom.example.com 104 myfile.dcm
+</literallayout></para>
+
+<para>or if you prefer being explicit:</para>
+
+<para><literallayout>$ gdcmscu --store dicom.example.com 104 -i myfile.dcm
+</literallayout></para>
+
+<para>You can even send multiple files using the same association:</para>
+
+<para><literallayout>$ gdcmscu --store dicom.example.com 104 myfile1.dcm myfile2.dcm myfile3.dcm ...
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1cfind_usage">
+<title>C-FIND usage</title>
+
+<para><emphasis role="bold">gdcmscu</emphasis> also allow querying a DICOM server. This is the C-FIND operation, for example to find all DICOM Instance where PatientsName match a particular pattern, usage is simply:</para>
+
+<para><literallayout>$ gdcmscu --find --patient dicom.example.com 11112 --patientroot --key 10,10,"A*"
+</literallayout></para>
+
+<para>We also support a DCMTK compatible convention:</para>
+
+<para><literallayout>$ gdcmscu --find --patient dicom.example.com 11112 --patientroot --key 10,10="A*"
+</literallayout></para>
+
+<para>When an attribute is set without a value it will be part of the output result:</para>
+
+<para><literallayout>$ gdcmscu --find --patient dicom.example.com 11112 --call MI2B2 --patientroot -k 10,10="A*" -k 10,20
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1cmove_usage">
+<title>C-MOVE usage</title>
+
+<para>C-MOVE is the operation to retrieve a DICOM instance from a remote DICOM server. Most of the time, it is a subsequent operation after a C-FIND query. To retrieve a DICOM instance where PatientID is ABCD1234, simply execute:</para>
+
+<para><literallayout>$ gdcmscu --move --patient --aetitle ACME1 --call ACME_STORE dicom.example.com 5678 --patientroot -k 10,20="ABCD1234" --port-scp 1234
+</literallayout></para>
+
+<para>WARNING For this operation to work you need information from the DICOM server you are communicating with. Only the DICOM server you are sending a C-MOVE query will be responsible for sending back incoming associations (the actual C-STORE SCP). Therefore you need to make sure that you mapping of (AE-TITLE,PortNumber) is properly set on the DICOM server side as well as the port for incoming association (–port-scp).</para>
+
+<para><emphasis role="bold">gdcmscu</emphasis> does not currently support external C-STORE association (C-STORE request sent to an external SCP application).</para>
+</refsection>
+<refsection xml:id="gdcmscu_1patientroot_notes">
+<title>patientroot notes</title>
+
+<para>The flag –patientroot is just simply a wrapper around the syntax –key 8,52=PATIENT For instance one would write using DCMTK syntax:</para>
+
+<para><literallayout>$ findscu --patient dicom.example.com 11112 --key 8,52=PATIENT --key 10,10="F*"
+</literallayout></para>
+
+<para>This would become using GDCM syntax:</para>
+
+<para><literallayout>$ gdcmscu --find --patient dicom.example.com 11112 --patientroot --key 10,10="F*"
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1debugging">
+<title>Debugging</title>
+
+<para>This is sometime difficult to investigate why a connection to a remote DICOM server cannot be done. Some recommendations follows:</para>
+
+<para>Always try to do a simple C-ECHO at first. If you cannot get the C-ECHO to work none of the other operations will work</para>
+
+<para>Before trying to a C-MOVE operation, make sure you can execute the C-FIND equivalent query first.</para>
+
+<para>When doing a C-MOVE operation you really need to communicate with the PACS admin as the C-MOVE operation is different from the other lower level operation such as HTTP/GET. When doing a C-MOVE, the server will communicate back using another channel (could be different port) using it's internal database to map an AE-TITLE back to the destination IP.</para>
+
+<para>Indeed the C-MOVE operation by design does not always use your incoming IP address to send back the resulting dataset. Instead it uses a mapping of AE-TITLE to IP address to send back any results. So pay particular attention to the spelling of your AE-TITLE and your incoming port (which may be different from the port to connect to the server).</para>
+</refsection>
+<refsection xml:id="gdcmscu_1gdcmscu_portwarnings">
+<title>Port Warning</title>
+
+<para>Watch out that port ranging [1-1024] are reserved for admin and not easily accessible unless granted special privileges. Therefore the default 104 DICOM port might not be accessible to all your users.</para>
+</refsection>
+<refsection xml:id="gdcmscu_1gdcmscu_ctorewarnings">
+<title>C-STORE Warnings</title>
+
+<para>When constructing a C-STORE operation, gdcmscu will always use the Media Storage SOP Class UID as found in the file to be sent. For encapsulated DICOM file (eg. RLE Lossless) the receiving SCP server might not support this compression and will legitimately refuse the C-STORE operation. In this case users have to manually convert to a non-compressed form this particular file:</para>
+
+<para><literallayout>$ gdcmconv --raw compressed.dcm non_compressed.dcm
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1gdcmscu_cmovewarnings">
+<title>C-MOVE Warnings</title>
+
+<para>At the moment <emphasis role="bold">gdcmscu</emphasis> only supports non-compressed transfer syntax. It will always request DataSet using Implicit VR Little Endian Transfer Syntax during a C-MOVE operation (both incoming and outgoing associations). This make gdcmscu –move equivalent to DCMTK movescu syntax:</para>
+
+<para><literallayout>$ movescu -xi +xi ...
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1gdcmscu_cfind_image">
+<title>C-FIND IMAGE level (Composite Object Instance)</title>
+
+<para>One should pay attention that gdcmscu –find and findscu are not completely equivalent. Using gdcmscu –find, all Unique Keys will be added automatically. One can therefore execute something like this:</para>
+
+<para><literallayout>$ gdcmscu --find --patientroot --image --key 8,18=1.2.3.4.5.6 dicom.example.com 11112
+</literallayout></para>
+
+<para>instead of the more explicit form</para>
+
+<para><literallayout>$ gdcmscu --find --patientroot --image --key 8,18=1.2.3.4.5.6 dicom.example.com 11112 --key 10,20 --key 20,d --key 20,e
+</literallayout></para>
+
+<para>This would also be equivalent to:</para>
+
+<para><literallayout>$ findscu --patient --key 8,52=IMAGE --key 8,18=1.2.3.4.5.6 dicom.example.com 11112 --key 10,20 --key 20,d --key 20,e
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmscu_1gdcmscu_storing">
+<title>Storing the Query</title>
+
+<para>It is also possible to store the query:</para>
+
+<para><literallayout>gdcmscu --find --patient --patientroot dicom.example.com 11112 --key 10,20="*" --key 10,10 --store-query query.dcm
+</literallayout></para>
+
+<para>One can then check the DataSet values send for the query:</para>
+
+<para><literallayout>$ gdcmdump query.dcm
+# Dicom-File-Format
+
+# Dicom-Meta-Information-Header
+# Used TransferSyntax:
+
+# Dicom-Data-Set
+# Used TransferSyntax: 1.2.840.10008.1.2
+(0008,0005) ?? (CS) [ISO_IR 192] # 10,1-n Specific Character Set
+(0008,0052) ?? (CS) [PATIENT ] # 8,1 Query/Retrieve Level
+(0010,0010) ?? (PN) (no value) # 0,1 Patient's Name
+(0010,0020) ?? (LO) [* ] # 2,1 Patient ID
+</literallayout></para>
+
+<para>The Specific Character Set was set to "ISO_IR 192" as the locale encoding of the system was found automatically by gdcmscu to be UTF-8.</para>
+
+<para>This means that the following command line will properly setup the Query with the appropriate Charset to be executed correctly:</para>
+
+<para><literallayout>$ gdcmscu --find --patient --patientroot dicom.example.com 11112 --key 10,10="*Jérôme*"
+</literallayout></para>
+
+<para>The query is always executed on the server side (SCP), some implementations does not support string matching with different Character Set.</para>
+</refsection>
+<refsection xml:id="gdcmscu_1public_servers">
+<title>DICOM Public Servers</title>
+
+<para>An up to date list of DICOM Public Servers can be found at:</para>
+
+<para><link xlink:href="http://www.dclunie.com/medical-image-faq/html/part8.html#DICOMPublicServers">http://www.dclunie.com/medical-image-faq/html/part8.html#DICOMPublicServers</link></para>
+</refsection>
+<refsection xml:id="gdcmscu_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmconv</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmtar.dox b/Utilities/doxygen/man/gdcmtar.dox
deleted file mode 100644
index c508cea..0000000
--- a/Utilities/doxygen/man/gdcmtar.dox
+++ /dev/null
@@ -1,137 +0,0 @@
-/*!
-
-\page gdcmtar Concatenate/Extract DICOM files.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmtar [options] file-in file-out
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmtar is a command line tool used to tar/untar multi-frames images
-(including SIEMENS MOSAIC file)
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM input filename
-
-file-out DICOM output filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection options options
-\verbatim
- --enhance enhance (default)
- -U --unenhance unenhance
- -M --mosaic Split SIEMENS Mosaic image into multiple frames.
- -p --pattern Specify trailing file pattern.
- --root-uid Root UID.
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\subsection environment_variable environment variable
-\verbatim
- GDCM_ROOT_UID Root UID
-\endverbatim
-
-\section usage Typical usage
-\subsection mosaic SIEMENS Mosaic
-
-\verbatim
-$ gdcminfo MR-sonata-3D-as-Tile.dcm
-\endverbatim
-
-\verbatim
-MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
-TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
-NumberOfDimensions: 2
-Dimensions: (384,384,1)
-\&...
-\endverbatim
-
-\verbatim
-$ gdcmtar --mosaic -i MR-sonata-3D-as-Tile.dcm -o mosaic --pattern %03d.dcm
-\endverbatim
-
-Will output:
-
-\verbatim
--rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic000.dcm
--rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic001.dcm
--rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic002.dcm
--rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic003.dcm
--rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic004.dcm
--rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic005.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic006.dcm
--rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic007.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic008.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic009.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic010.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic011.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic012.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic013.dcm
--rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic014.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic015.dcm
--rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic016.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic017.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic018.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic019.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic020.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic021.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic022.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic023.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic024.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic025.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic026.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic027.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic028.dcm
--rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic029.dcm
--rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic030.dcm
-\endverbatim
-
-\verbatim
-$ gdcminfo mosaic000.dcm
-\endverbatim
-
-\verbatim
-MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
-TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
-NumberOfDimensions: 2
-Dimensions: (64,64,1)
-\&...
-\endverbatim
-
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcmraw</b>(1), <b>gdcminfo</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmtar.xml b/Utilities/doxygen/man/gdcmtar.xml
new file mode 100644
index 0000000..ac36457
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmtar.xml
@@ -0,0 +1,147 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmtar</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmtar</refname>
+ <refpurpose>Concatenate/Extract DICOM files.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmtar_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmtar [options] file-in file-out
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmtar</emphasis> is a command line tool used to tar/untar multi-frames images (including SIEMENS MOSAIC file)</para>
+</refsection>
+<refsection xml:id="gdcmtar_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in DICOM input filename
+
+file-out DICOM output filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcmtar_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> --enhance enhance (default)
+ -U --unenhance unenhance
+ -M --mosaic Split SIEMENS Mosaic image into multiple frames.
+ -p --pattern Specify trailing file pattern.
+ --root-uid Root UID.
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmtar_1environment_variable">
+<title>environment variable</title>
+
+<para><literallayout> GDCM_ROOT_UID Root UID
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmviewer_1usage">
+<title>Typical usage</title>
+<refsection xml:id="gdcmtar_1mosaic">
+<title>SIEMENS Mosaic</title>
+
+<para><literallayout>$ gdcminfo MR-sonata-3D-as-Tile.dcm
+</literallayout></para>
+
+<para><literallayout>MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
+TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
+NumberOfDimensions: 2
+Dimensions: (384,384,1)
+\&...
+</literallayout></para>
+
+<para><literallayout>$ gdcmtar --mosaic -i MR-sonata-3D-as-Tile.dcm -o mosaic --pattern %03d.dcm
+</literallayout></para>
+
+<para>Will output:</para>
+
+<para><literallayout>-rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic000.dcm
+-rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic001.dcm
+-rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic002.dcm
+-rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic003.dcm
+-rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic004.dcm
+-rw-r--r-- 1 mathieu mathieu 72886 2009-08-10 11:14 mosaic005.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic006.dcm
+-rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic007.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic008.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic009.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic010.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic011.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic012.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic013.dcm
+-rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic014.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic015.dcm
+-rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic016.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic017.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic018.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic019.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic020.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic021.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic022.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic023.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic024.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic025.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic026.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic027.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic028.dcm
+-rw-r--r-- 1 mathieu mathieu 72884 2009-08-10 11:14 mosaic029.dcm
+-rw-r--r-- 1 mathieu mathieu 72882 2009-08-10 11:14 mosaic030.dcm
+</literallayout></para>
+
+<para><literallayout>$ gdcminfo mosaic000.dcm
+</literallayout></para>
+
+<para><literallayout>MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
+TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
+NumberOfDimensions: 2
+Dimensions: (64,64,1)
+\&...
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmtar_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmraw</emphasis>(1), <emphasis role="bold">gdcminfo</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmviewer.dox b/Utilities/doxygen/man/gdcmviewer.dox
deleted file mode 100644
index 5a1caa4..0000000
--- a/Utilities/doxygen/man/gdcmviewer.dox
+++ /dev/null
@@ -1,88 +0,0 @@
-/*!
-
-\page gdcmviewer Simple DICOM viewer.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmviewer [options] file-in
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmviewer is a simple tool that show how to use vtkGDCMImageReader.
-The class that use gdcm to make a layer to VTK. \b gdcmviewer is basically only
-just a wrapper around VTK/GDCM.
-
-This tool is meant for testing integration of GDCM in VTK. You should see it as
-a demo tool. It does compile with VTK ranging from 4.2 to 5.10, but only with
-VTK 5.2 (or above) can play with the widgets (as described below).
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM input filename
-\endverbatim
-
-\section options OPTIONS
-
-\subsection options options
-\verbatim
- --force-rescale force rescale (advanced users)
- --force-spacing force spacing (advanced users)
- -r --recursive Recusively descend directory
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\section usage Typical usage
-\section simple_usage Simple usage
-
-For now gdcmviewer should be started from a command line prompt. The next
-argument should be the name of the DICOM file you wish to read. For instance:
-
-\verbatim
-$ gdcmviewer -V 012345.002.050.dcm
-\endverbatim
-
-gdcmviewer will try to read your file, and then print the vtk information
-associated with this file. Basically what kind of image you are looking at.
-
-\li ScalarType is the DICOM Real World Value type
-\li Dimensions is the dimension of the image
-\li Spacing is the spacing of the image
-\li NumberOfScalarComponents should be 1 for grayscale & PALETTE COLOR and 3 for RGB, YBR data.
-
-\section wiki_link Wiki Link
-
-The wiki page, with color pictures can be found at:
-http://gdcm.sourceforge.net/wiki/index.php/Gdcmviewer
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcm2vtk</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmviewer.xml b/Utilities/doxygen/man/gdcmviewer.xml
new file mode 100644
index 0000000..985e15e
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmviewer.xml
@@ -0,0 +1,109 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmviewer</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmviewer</refname>
+ <refpurpose>Simple DICOM viewer.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmviewer_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmviewer [options] file-in
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmviewer_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmviewer</emphasis> is a simple tool that show how to use <emphasis>vtkGDCMImageReader</emphasis>. The class that use gdcm to make a layer to VTK. <emphasis role="bold">gdcmviewer</emphasis> is basically only just a wrapper around VTK/GDCM.</para>
+
+<para>This tool is meant for testing integration of GDCM in VTK. You should see it as a demo tool. It does compile with VTK ranging from 4.2 to 5.10, but only with VTK 5.2 (or above) can play with the widgets (as described below).</para>
+</refsection>
+<refsection xml:id="gdcmviewer_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in DICOM input filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmviewer_1options">
+<title>OPTIONS</title>
+<refsection xml:id="gdcmviewer_1specific_options">
+<title>specific options</title>
+
+<para><literallayout> --force-rescale force rescale (advanced users)
+ --force-spacing force spacing (advanced users)
+ -r --recursive Recusively descend directory
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmviewer_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+</refsection>
+<refsection xml:id="gdcmviewer_1usage">
+<title>Typical usage</title>
+</refsection>
+<refsection xml:id="gdcmviewer_1simple_usage">
+<title>Simple usage</title>
+
+<para>For now gdcmviewer should be started from a command line prompt. The next argument should be the name of the DICOM file you wish to read. For instance:</para>
+
+<para><literallayout>$ gdcmviewer -V 012345.002.050.dcm
+</literallayout></para>
+
+<para>gdcmviewer will try to read your file, and then print the vtk information associated with this file. Basically what kind of image you are looking at.</para>
+
+<para><itemizedlist>
+<listitem>
+<para>ScalarType is the DICOM Real World Value type </para>
+</listitem>
+<listitem>
+<para>Dimensions is the dimension of the image </para>
+</listitem>
+<listitem>
+<para>Spacing is the spacing of the image </para>
+</listitem>
+<listitem>
+<para>NumberOfScalarComponents should be 1 for grayscale & PALETTE COLOR and 3 for RGB, YBR data.</para>
+</listitem>
+</itemizedlist>
+</para>
+</refsection>
+<refsection xml:id="gdcmviewer_1wiki_link">
+<title>Wiki Link</title>
+
+<para>The wiki page, with color pictures can be found at: <link xlink:href="http://gdcm.sourceforge.net/wiki/index.php/Gdcmviewer">http://gdcm.sourceforge.net/wiki/index.php/Gdcmviewer</link></para>
+</refsection>
+<refsection xml:id="gdcmviewer_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcm2vtk</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/doxygen/man/gdcmxml.dox b/Utilities/doxygen/man/gdcmxml.dox
deleted file mode 100644
index 7aee053..0000000
--- a/Utilities/doxygen/man/gdcmxml.dox
+++ /dev/null
@@ -1,77 +0,0 @@
-/*!
-
-\page gdcmxml provides a tool to convert a DICOM file into a XML infoset and vice-versa.
-
-\section synopsis SYNOPSIS
-
-\verbatim
-gdcmxml [options] file-in[DICOM or XML] file-out[XML or DICOM]
-\endverbatim
-
-\section description DESCRIPTION
-
-The \b gdcmxml command line program converts a DICOM file (DataSet) into an XML
-file (according to the Native DICOM Model) or vice-versa. For those familiar
-with DCMTK, this provides binary capabilities (i.e. functionality of both
-dcm2xml and xml2dcm).
-
-The XML infoset which is from the DICOM file gdcmXMLPrintet Class. This is in
-strict compliance with the Native DICOM Model as given in Supp 118.
-
-\section parameters PARAMETERS
-
-\verbatim
-file-in DICOM or XML input filename ( cannot be absent)
-
-file-out output filename (can be absent)
-\endverbatim
-
-\section options OPTIONS
-
-\subsection parameters parameters
-\verbatim
- -i --input DICOM filename
- -o --output DICOM filename
-\endverbatim
-
-\subsection options_dicom2xml Options for DICOM to XML:
-\verbatim
- -B --loadBulkData Loads bulk data into a binary file named "UUID" (by default UUID are written).
-\endverbatim
-
-\subsection options_xml2dicom Options for XML to DICOM:
-\verbatim
- -B --loadBulkData Loads bulk data from a binary file named as the "UUID" in XML file (by default UUID are written).
- -T --TransferSyntax Loads transfer syntax from file (default is LittleEndianImplicit)
-\endverbatim
-
-\subsection general_options general options
-\verbatim
- -h --help
- print this help text and exit
-
- -v --version
- print version information and exit
-
- -V --verbose
- verbose mode (warning+error).
-
- -W --warning
- warning mode, print warning information
-
- -E --error
- error mode, print error information
-
- -D --debug
- debug mode, print debug information
-\endverbatim
-
-\section see_also SEE ALSO
-
-<b>gdcmdump</b>(1), <b>gdcmconv</b>(1)
-
-\section copyright COPYRIGHT
-
-Copyright (c) 2006-2011 Mathieu Malaterre
-
-*/
diff --git a/Utilities/doxygen/man/gdcmxml.xml b/Utilities/doxygen/man/gdcmxml.xml
new file mode 100644
index 0000000..2803fbd
--- /dev/null
+++ b/Utilities/doxygen/man/gdcmxml.xml
@@ -0,0 +1,86 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl" ?>
+<refentry xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink">
+<info>
+<author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author>
+<copyright><year>2006</year><year>2011</year><holder>Mathieu Malaterre</holder></copyright>
+</info>
+ <refmeta>
+ <refentrytitle>gdcmxml</refentrytitle>
+ <manvolnum>1</manvolnum>
+ <refmiscinfo class="source">GDCM</refmiscinfo>
+ <refmiscinfo class="version">VER_FULL</refmiscinfo>
+ <refmiscinfo class="manual">DICOM Manipulation.</refmiscinfo>
+ </refmeta>
+ <refnamediv><refname>gdcmxml</refname>
+ <refpurpose>provides a tool to convert a DICOM file into a XML infoset and vice-versa.</refpurpose>
+</refnamediv>
+<refsection xml:id="gdcmxml_1synopsis">
+<title>SYNOPSIS</title>
+
+<para><literallayout>gdcmxml [options] file-in[DICOM or XML] file-out[XML or DICOM]
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1description">
+<title>DESCRIPTION</title>
+
+<para>The <emphasis role="bold">gdcmxml</emphasis> command line program converts a DICOM file (DataSet) into an XML file (according to the Native DICOM Model) or vice-versa. For those familiar with DCMTK, this provides binary capabilities (i.e. functionality of both dcm2xml and xml2dcm).</para>
+
+<para>The XML infoset which is from the DICOM file gdcmXMLPrintet Class. This is in strict compliance with the Native DICOM Model as given in Supp 118.</para>
+</refsection>
+<refsection xml:id="gdcmxml_1parameters">
+<title>PARAMETERS</title>
+
+<para><literallayout>file-in DICOM or XML input filename ( cannot be absent)
+
+file-out output filename (can be absent)
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1options">
+<title>OPTIONS</title>
+
+<para><literallayout> -i --input DICOM filename
+ -o --output DICOM filename
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1options_dicom2xml">
+<title>Options for DICOM to XML:</title>
+
+<para><literallayout> -B --loadBulkData Loads bulk data into a binary file named "UUID" (by default UUID are written).
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1options_xml2dicom">
+<title>Options for XML to DICOM:</title>
+
+<para><literallayout> -B --loadBulkData Loads bulk data from a binary file named as the "UUID" in XML file (by default UUID are written).
+ -T --TransferSyntax Loads transfer syntax from file (default is LittleEndianImplicit)
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1general_options">
+<title>general options</title>
+
+<para><literallayout> -h --help
+ print this help text and exit
+
+ -v --version
+ print version information and exit
+
+ -V --verbose
+ verbose mode (warning+error).
+
+ -W --warning
+ warning mode, print warning information
+
+ -E --error
+ error mode, print error information
+
+ -D --debug
+ debug mode, print debug information
+</literallayout></para>
+</refsection>
+<refsection xml:id="gdcmxml_1see_also">
+<title>SEE ALSO</title>
+
+<para><emphasis role="bold">gdcmdump</emphasis>(1), <emphasis role="bold">gdcmconv</emphasis>(1)</para>
+</refsection>
+</refentry>
diff --git a/Utilities/gdcmrle/info.h b/Utilities/gdcmrle/info.h
index eadf82c..4d61ae9 100644
--- a/Utilities/gdcmrle/info.h
+++ b/Utilities/gdcmrle/info.h
@@ -41,7 +41,7 @@ public:
/// return number of bits per pixel
int get_number_of_bits_per_pixel() const;
- /// return wether or not the number of segments `num_segments` is valid
+ /// return whether or not the number of segments `num_segments` is valid
static bool check_num_segments( const int num_segments );
private:
diff --git a/Utilities/gdcmrle/rle.cxx b/Utilities/gdcmrle/rle.cxx
index 21934e3..72986dd 100644
--- a/Utilities/gdcmrle/rle.cxx
+++ b/Utilities/gdcmrle/rle.cxx
@@ -43,7 +43,7 @@ struct rle_encoder::internal
// when writing, need to keep updating offsets:
header::ul comp_pos[16];
- // internal buffer mecanism:
+ // internal buffer mechanism:
std::vector<char> invalues;
std::vector<char> outvalues;
};
@@ -339,7 +339,7 @@ struct rle_decoder::internal
source ** sources;
int nsources;
- // scanline buffering mecanism:
+ // scanline buffering mechanism:
std::vector<char> scanline;
// row crossing handling. some RLE encoder are brain dead and do cross the
diff --git a/Wrapping/Python/docstrings.i b/Wrapping/Python/docstrings.i
index c33d83a..73f0831 100644
--- a/Wrapping/Python/docstrings.i
+++ b/Wrapping/Python/docstrings.i
@@ -960,6 +960,46 @@ gdcm::network::BaseCompositeMessage::ConstructPDV(const ULConnection
&inConnection, const BaseRootQuery *inRootQuery)=0 ";
+// File: classgdcm_1_1network_1_1BaseNormalizedMessage.xml
+%feature("docstring") gdcm::network::BaseNormalizedMessage "
+
+BaseNormalizedMessage The Normalized events described in section
+3.7-2011 of the DICOM standard all use their own messages. These
+messages are constructed using Presentation Data Values, from section
+3.8-2011 of the standard, and then fill in appropriate values in their
+datasets.
+
+So, for the five normalized: N-ACTION
+
+N-CREATE
+
+N-DELETE
+
+N-EVENT
+
+N-GET
+
+N-SET there are a series of messages. However, all of these messages
+are obtained as part of a PDataPDU, and all have to be placed there.
+Therefore, since they all have shared functionality and construction
+tropes, that will be put into a base class. Further, the base class
+will be then returned by the factory class,
+gdcmNormalizedMessageFactory.h. This is an abstract class. It cannot
+be instantiated on its own.
+
+C++ includes: gdcmBaseNormalizedMessage.h ";
+
+%feature("docstring")
+gdcm::network::BaseNormalizedMessage::~BaseNormalizedMessage "virtual
+gdcm::network::BaseNormalizedMessage::~BaseNormalizedMessage() ";
+
+%feature("docstring")
+gdcm::network::BaseNormalizedMessage::ConstructPDV "virtual
+std::vector<PresentationDataValue>
+gdcm::network::BaseNormalizedMessage::ConstructPDV(const ULConnection
+&inConnection, const BaseQuery *inQuery)=0 ";
+
+
// File: classgdcm_1_1network_1_1BasePDU.xml
%feature("docstring") gdcm::network::BasePDU "
@@ -1003,6 +1043,58 @@ std::ostream& gdcm::network::BasePDU::Write(std::ostream &os) const =0
";
+// File: classgdcm_1_1BaseQuery.xml
+%feature("docstring") gdcm::BaseQuery "
+
+BaseQuery contains: a baseclass which will produce a dataset for all
+dimse messages.
+
+C++ includes: gdcmBaseQuery.h ";
+
+%feature("docstring") gdcm::BaseQuery::~BaseQuery "virtual
+gdcm::BaseQuery::~BaseQuery() ";
+
+%feature("docstring") gdcm::BaseQuery::AddQueryDataSet "void
+gdcm::BaseQuery::AddQueryDataSet(const DataSet &ds) ";
+
+%feature("docstring") gdcm::BaseQuery::GetAbstractSyntaxUID "virtual
+UIDs::TSName gdcm::BaseQuery::GetAbstractSyntaxUID() const =0 ";
+
+%feature("docstring") gdcm::BaseQuery::GetQueryDataSet "DataSet
+const& gdcm::BaseQuery::GetQueryDataSet() const
+
+Set/Get the internal representation of the query as a DataSet. ";
+
+%feature("docstring") gdcm::BaseQuery::GetQueryDataSet "DataSet&
+gdcm::BaseQuery::GetQueryDataSet() ";
+
+%feature("docstring") gdcm::BaseQuery::GetSOPInstanceUID "std::string gdcm::BaseQuery::GetSOPInstanceUID() const ";
+
+%feature("docstring") gdcm::BaseQuery::Print "void
+gdcm::BaseQuery::Print(std::ostream &os) const ";
+
+%feature("docstring") gdcm::BaseQuery::SetSearchParameter "void
+gdcm::BaseQuery::SetSearchParameter(const Tag &inTag, const
+std::string &inValue) ";
+
+%feature("docstring") gdcm::BaseQuery::SetSearchParameter "void
+gdcm::BaseQuery::SetSearchParameter(const std::string &inKeyword,
+const std::string &inValue) ";
+
+%feature("docstring") gdcm::BaseQuery::SetSOPInstanceUID "void
+gdcm::BaseQuery::SetSOPInstanceUID(const std::string &iSopInstanceUID)
+";
+
+%feature("docstring") gdcm::BaseQuery::ValidateQuery "virtual bool
+gdcm::BaseQuery::ValidateQuery(bool inStrict=true) const =0 ";
+
+%feature("docstring") gdcm::BaseQuery::WriteHelpFile "const
+std::ostream& gdcm::BaseQuery::WriteHelpFile(std::ostream &os) ";
+
+%feature("docstring") gdcm::BaseQuery::WriteQuery "bool
+gdcm::BaseQuery::WriteQuery(const std::string &inFileName) ";
+
+
// File: classgdcm_1_1BaseRootQuery.xml
%feature("docstring") gdcm::BaseRootQuery "
@@ -1026,20 +1118,6 @@ C++ includes: gdcmBaseRootQuery.h ";
%feature("docstring") gdcm::BaseRootQuery::~BaseRootQuery "virtual
gdcm::BaseRootQuery::~BaseRootQuery() ";
-%feature("docstring") gdcm::BaseRootQuery::AddQueryDataSet "void
-gdcm::BaseRootQuery::AddQueryDataSet(const DataSet &ds) ";
-
-%feature("docstring") gdcm::BaseRootQuery::GetAbstractSyntaxUID "virtual UIDs::TSName gdcm::BaseRootQuery::GetAbstractSyntaxUID() const
-=0 ";
-
-%feature("docstring") gdcm::BaseRootQuery::GetQueryDataSet "DataSet
-const& gdcm::BaseRootQuery::GetQueryDataSet() const
-
-Set/Get the internal representation of the query as a DataSet. ";
-
-%feature("docstring") gdcm::BaseRootQuery::GetQueryDataSet "DataSet&
-gdcm::BaseRootQuery::GetQueryDataSet() ";
-
%feature("docstring") gdcm::BaseRootQuery::GetQueryLevelFromQueryRoot
"EQueryLevel
gdcm::BaseRootQuery::GetQueryLevelFromQueryRoot(ERootType roottype) ";
@@ -1058,17 +1136,6 @@ this function sets tag 8,52 to the appropriate value based on query
level also fills in the right unique tags, as per the standard's
requirements should allow for connection with dcmtk ";
-%feature("docstring") gdcm::BaseRootQuery::Print "void
-gdcm::BaseRootQuery::Print(std::ostream &os) const ";
-
-%feature("docstring") gdcm::BaseRootQuery::SetSearchParameter "void
-gdcm::BaseRootQuery::SetSearchParameter(const Tag &inTag, const
-std::string &inValue) ";
-
-%feature("docstring") gdcm::BaseRootQuery::SetSearchParameter "void
-gdcm::BaseRootQuery::SetSearchParameter(const std::string &inKeyword,
-const std::string &inValue) ";
-
%feature("docstring") gdcm::BaseRootQuery::ValidateQuery "virtual
bool gdcm::BaseRootQuery::ValidateQuery(bool inStrict=true) const =0
@@ -1087,12 +1154,6 @@ the current level and all higher levels are now considered valid. So,
if you're doing a non-strict series-level query, tags from the patient
and study level can be passed along as well. ";
-%feature("docstring") gdcm::BaseRootQuery::WriteHelpFile "const
-std::ostream& gdcm::BaseRootQuery::WriteHelpFile(std::ostream &os) ";
-
-%feature("docstring") gdcm::BaseRootQuery::WriteQuery "bool
-gdcm::BaseRootQuery::WriteQuery(const std::string &inFileName) ";
-
// File: structgdcm_1_1SegmentHelper_1_1BasicCodedEntry.xml
%feature("docstring") gdcm::SegmentHelper::BasicCodedEntry "
@@ -2233,7 +2294,7 @@ C++ includes: gdcmCStoreMessages.h ";
%feature("docstring") gdcm::network::CStoreRQ::ConstructPDV "std::vector<PresentationDataValue>
gdcm::network::CStoreRQ::ConstructPDV(const ULConnection
-&inConnection, const File &file) ";
+&inConnection, const File &file, bool writeDataSet=true) ";
// File: classgdcm_1_1network_1_1CStoreRSP.xml
@@ -3861,7 +3922,7 @@ FileChangeTransferSyntax.
This class is a file-based (limited) replacement of the in-memory
ImageChangeTransferSyntax.
-This class provide a file-based compression-only mecanism. It will
+This class provide a file-based compression-only mechanism. It will
take in an uncompressed DICOM image file (Pixel Data element). Then
produced as output a compressed DICOM file (Transfer Syntax will be
updated).
@@ -3909,6 +3970,40 @@ gdcm::FileChangeTransferSyntax::SetTransferSyntax(TransferSyntax const
Specify the Target Transfer Syntax. ";
+// File: classgdcm_1_1FileDecompressLookupTable.xml
+%feature("docstring") gdcm::FileDecompressLookupTable "
+
+FileDecompressLookupTable class It decompress the segmented LUT into
+linearized one (only PALETTE_COLOR images) Output will be a
+PhotometricInterpretation=RGB image.
+
+C++ includes: gdcmFileDecompressLookupTable.h ";
+
+%feature("docstring")
+gdcm::FileDecompressLookupTable::FileDecompressLookupTable "gdcm::FileDecompressLookupTable::FileDecompressLookupTable() ";
+
+%feature("docstring")
+gdcm::FileDecompressLookupTable::~FileDecompressLookupTable "gdcm::FileDecompressLookupTable::~FileDecompressLookupTable() ";
+
+%feature("docstring") gdcm::FileDecompressLookupTable::Change "bool
+gdcm::FileDecompressLookupTable::Change()
+
+Decompress. ";
+
+%feature("docstring") gdcm::FileDecompressLookupTable::GetFile "File& gdcm::FileDecompressLookupTable::GetFile() ";
+
+%feature("docstring") gdcm::FileDecompressLookupTable::GetPixmap "const Pixmap& gdcm::FileDecompressLookupTable::GetPixmap() const ";
+
+%feature("docstring") gdcm::FileDecompressLookupTable::GetPixmap "Pixmap& gdcm::FileDecompressLookupTable::GetPixmap() ";
+
+%feature("docstring") gdcm::FileDecompressLookupTable::SetFile "void
+gdcm::FileDecompressLookupTable::SetFile(const File &f)
+
+Set/Get File. ";
+
+%feature("docstring") gdcm::FileDecompressLookupTable::SetPixmap "void gdcm::FileDecompressLookupTable::SetPixmap(Pixmap const &img) ";
+
+
// File: classgdcm_1_1FileDerivation.xml
%feature("docstring") gdcm::FileDerivation "
@@ -4181,7 +4276,7 @@ Convert backslash (windows style) to UNIX style slash. ";
%feature("docstring") gdcm::Filename::ToWindowsSlashes "const char*
gdcm::Filename::ToWindowsSlashes()
-Convert foward slash (UNIX style) to windows style slash. ";
+Convert forward slash (UNIX style) to windows style slash. ";
// File: classgdcm_1_1FileNameEvent.xml
@@ -5327,6 +5422,12 @@ C++ includes: gdcmImageWriter.h ";
%feature("docstring") gdcm::ImageWriter::~ImageWriter "gdcm::ImageWriter::~ImageWriter() ";
+%feature("docstring") gdcm::ImageWriter::ComputeTargetMediaStorage "MediaStorage gdcm::ImageWriter::ComputeTargetMediaStorage()
+
+internal function used to compute a target MediaStorage the most
+appropriate User may want to call this function ahead of time (before
+Write) ";
+
%feature("docstring") gdcm::ImageWriter::GetImage "const Image&
gdcm::ImageWriter::GetImage() const
@@ -5596,7 +5697,10 @@ how it is defined in DICOM, advanced users may refers to:
http://gdcm.sourceforge.net/wiki/index.php/Imager_Pixel_Spacing
Bug There are currently a couple of bugs in this implementation:
-Gantry Tilt is not considered
+Gantry Tilt is not considered (always an error)
+
+Application programmer should only sort valid DataSet (eg.
+MRImageStorage, CTImageStorage, PETImageStorage)
C++ includes: gdcmIPPSorter.h ";
@@ -5637,14 +5741,14 @@ Sometimes IOP along a series is slightly changing for example:
\"0.999081\\\\\\\\0.0426952\\\\\\\\0.00369272\\\\\\\\-0.0419025\\\\\\\\0.955059\\\\\\\\0.293439\",
We need an API to define the tolerance which is allowed. Internally
the cross vector of each direction cosines is computed. The tolerance
-then define the the distance in between 1. to the dot product of those
+then define the distance in between 1.0 to the dot product of those
cross vectors. In a perfect world this dot product is of course 1.0
which imply a DirectionCosines tolerance of exactly 0.0 (default). ";
%feature("docstring") gdcm::IPPSorter::SetDropDuplicatePositions "void gdcm::IPPSorter::SetDropDuplicatePositions(bool b)
Makes the IPPSorter ignore multiple images located at the same
-position. Only the first occurence will be kept.
+position. Only the first occurrence will be kept.
DropDuplicatePositions defaults to false. ";
%feature("docstring") gdcm::IPPSorter::SetZSpacingTolerance "void
@@ -6492,6 +6596,68 @@ gdcm::MeshPrimitive::SetPrimitivesData(PrimitivesData const &DEs) ";
gdcm::MeshPrimitive::SetPrimitiveType(const MPType type) ";
+// File: classgdcm_1_1ModalityPerformedProcedureStepCreateQuery.xml
+%feature("docstring") gdcm::ModalityPerformedProcedureStepCreateQuery
+"
+
+ModalityPerformedProcedureStepCreateQuery contains: the class which
+will produce a dataset for n-create for Modality Performed Procedure
+Step sop class.
+
+C++ includes: gdcmModalityPerformedProcedureStepCreateQuery.h ";
+
+%feature("docstring")
+gdcm::ModalityPerformedProcedureStepCreateQuery::ModalityPerformedProcedureStepCreateQuery
+"gdcm::ModalityPerformedProcedureStepCreateQuery::ModalityPerformedProcedureStepCreateQuery(const
+std::string &iSopInstanceUID) ";
+
+%feature("docstring")
+gdcm::ModalityPerformedProcedureStepCreateQuery::GetAbstractSyntaxUID
+"UIDs::TSName
+gdcm::ModalityPerformedProcedureStepCreateQuery::GetAbstractSyntaxUID()
+const ";
+
+%feature("docstring")
+gdcm::ModalityPerformedProcedureStepCreateQuery::GetRequiredDataSet "gdcm::DataSet
+gdcm::ModalityPerformedProcedureStepCreateQuery::GetRequiredDataSet()
+const ";
+
+%feature("docstring")
+gdcm::ModalityPerformedProcedureStepCreateQuery::ValidateQuery "bool
+gdcm::ModalityPerformedProcedureStepCreateQuery::ValidateQuery(bool
+inStrict=true) const ";
+
+
+// File: classgdcm_1_1ModalityPerformedProcedureStepSetQuery.xml
+%feature("docstring") gdcm::ModalityPerformedProcedureStepSetQuery "
+
+ModalityPerformedProcedureStepSetQuery contains: the class which will
+produce a dataset for n-set for Modality Performed Procedure Step sop
+class.
+
+C++ includes: gdcmModalityPerformedProcedureStepSetQuery.h ";
+
+%feature("docstring")
+gdcm::ModalityPerformedProcedureStepSetQuery::ModalityPerformedProcedureStepSetQuery
+"gdcm::ModalityPerformedProcedureStepSetQuery::ModalityPerformedProcedureStepSetQuery(const
+std::string &iSopInstanceUID) ";
+
+%feature("docstring")
+gdcm::ModalityPerformedProcedureStepSetQuery::GetAbstractSyntaxUID "UIDs::TSName
+gdcm::ModalityPerformedProcedureStepSetQuery::GetAbstractSyntaxUID()
+const ";
+
+%feature("docstring")
+gdcm::ModalityPerformedProcedureStepSetQuery::GetRequiredDataSet "gdcm::DataSet
+gdcm::ModalityPerformedProcedureStepSetQuery::GetRequiredDataSet()
+const ";
+
+%feature("docstring")
+gdcm::ModalityPerformedProcedureStepSetQuery::ValidateQuery "bool
+gdcm::ModalityPerformedProcedureStepSetQuery::ValidateQuery(bool
+inStrict=true) const ";
+
+
// File: classgdcm_1_1ModifiedEvent.xml
%feature("docstring") gdcm::ModifiedEvent "C++ includes: gdcmEvent.h
";
@@ -6703,6 +6869,81 @@ if you're doing a non-strict series-level query, tags from the patient
and study level can be passed along as well. ";
+// File: classgdcm_1_1network_1_1NActionRQ.xml
+%feature("docstring") gdcm::network::NActionRQ "
+
+NActionRQ this file defines the messages for the NAction action.
+
+C++ includes: gdcmNActionMessages.h ";
+
+%feature("docstring") gdcm::network::NActionRQ::ConstructPDV "std::vector<PresentationDataValue>
+gdcm::network::NActionRQ::ConstructPDV(const ULConnection
+&inConnection, const BaseQuery *inQuery) ";
+
+
+// File: classgdcm_1_1network_1_1NActionRSP.xml
+%feature("docstring") gdcm::network::NActionRSP "
+
+NActionRSP this file defines the messages for the NAction action.
+
+C++ includes: gdcmNActionMessages.h ";
+
+%feature("docstring")
+gdcm::network::NActionRSP::ConstructPDVByDataSet "std::vector<PresentationDataValue>
+gdcm::network::NActionRSP::ConstructPDVByDataSet(const DataSet
+*inDataSet) ";
+
+
+// File: classgdcm_1_1network_1_1NCreateRQ.xml
+%feature("docstring") gdcm::network::NCreateRQ "
+
+NCreateRQ this file defines the messages for the ncreate action.
+
+C++ includes: gdcmNCreateMessages.h ";
+
+%feature("docstring") gdcm::network::NCreateRQ::ConstructPDV "std::vector<PresentationDataValue>
+gdcm::network::NCreateRQ::ConstructPDV(const ULConnection
+&inConnection, const BaseQuery *inQuery) ";
+
+
+// File: classgdcm_1_1network_1_1NCreateRSP.xml
+%feature("docstring") gdcm::network::NCreateRSP "
+
+NCreateRSP this file defines the messages for the ncreate action.
+
+C++ includes: gdcmNCreateMessages.h ";
+
+%feature("docstring")
+gdcm::network::NCreateRSP::ConstructPDVByDataSet "std::vector<PresentationDataValue>
+gdcm::network::NCreateRSP::ConstructPDVByDataSet(const DataSet
+*inDataSet) ";
+
+
+// File: classgdcm_1_1network_1_1NDeleteRQ.xml
+%feature("docstring") gdcm::network::NDeleteRQ "
+
+NDeleteRQ this file defines the messages for the ndelete action.
+
+C++ includes: gdcmNDeleteMessages.h ";
+
+%feature("docstring") gdcm::network::NDeleteRQ::ConstructPDV "std::vector<PresentationDataValue>
+gdcm::network::NDeleteRQ::ConstructPDV(const ULConnection
+&inConnection, const BaseQuery *inQuery) ";
+
+
+// File: classgdcm_1_1network_1_1NDeleteRSP.xml
+%feature("docstring") gdcm::network::NDeleteRSP "
+
+NDeleteRSP this file defines the messages for the ndelete action.
+
+C++ includes: gdcmNDeleteMessages.h ";
+
+%feature("docstring")
+gdcm::network::NDeleteRSP::ConstructPDVByDataSet "std::vector<PresentationDataValue>
+gdcm::network::NDeleteRSP::ConstructPDVByDataSet(const DataSet
+*inDataSet) ";
+
+
// File: classgdcm_1_1NestedModuleEntries.xml
%feature("docstring") gdcm::NestedModuleEntries "
@@ -6732,6 +6973,57 @@ gdcm::NestedModuleEntries::GetNumberOfModuleEntries "SizeType
gdcm::NestedModuleEntries::GetNumberOfModuleEntries() ";
+// File: classgdcm_1_1network_1_1NEventReportRQ.xml
+%feature("docstring") gdcm::network::NEventReportRQ "
+
+NEventReportRQ this file defines the messages for the neventreport
+action.
+
+C++ includes: gdcmNEventReportMessages.h ";
+
+%feature("docstring") gdcm::network::NEventReportRQ::ConstructPDV "std::vector<PresentationDataValue>
+gdcm::network::NEventReportRQ::ConstructPDV(const ULConnection
+&inConnection, const BaseQuery *inQuery) ";
+
+
+// File: classgdcm_1_1network_1_1NEventReportRSP.xml
+%feature("docstring") gdcm::network::NEventReportRSP "
+
+NEventReportRSP this file defines the messages for the neventreport
+action.
+
+C++ includes: gdcmNEventReportMessages.h ";
+
+%feature("docstring")
+gdcm::network::NEventReportRSP::ConstructPDVByDataSet "std::vector<PresentationDataValue>
+gdcm::network::NEventReportRSP::ConstructPDVByDataSet(const DataSet
+*inDataSet) ";
+
+
+// File: classgdcm_1_1network_1_1NGetRQ.xml
+%feature("docstring") gdcm::network::NGetRQ "
+
+NGetRQ this file defines the messages for the nget action.
+
+C++ includes: gdcmNGetMessages.h ";
+
+%feature("docstring") gdcm::network::NGetRQ::ConstructPDV "std::vector<PresentationDataValue>
+gdcm::network::NGetRQ::ConstructPDV(const ULConnection &inConnection,
+const BaseQuery *inQuery) ";
+
+
+// File: classgdcm_1_1network_1_1NGetRSP.xml
+%feature("docstring") gdcm::network::NGetRSP "
+
+NGetRSP this file defines the messages for the nget action.
+
+C++ includes: gdcmNGetMessages.h ";
+
+%feature("docstring") gdcm::network::NGetRSP::ConstructPDVByDataSet "std::vector<PresentationDataValue>
+gdcm::network::NGetRSP::ConstructPDVByDataSet(const DataSet
+*inDataSet) ";
+
+
// File: classgdcm_1_1NoEvent.xml
%feature("docstring") gdcm::NoEvent "
@@ -6740,6 +7032,66 @@ Define some common GDCM events
C++ includes: gdcmEvent.h ";
+// File: classgdcm_1_1network_1_1NormalizedMessageFactory.xml
+%feature("docstring") gdcm::network::NormalizedMessageFactory "C++
+includes: gdcmNormalizedMessageFactory.h ";
+
+
+// File: classgdcm_1_1NormalizedNetworkFunctions.xml
+%feature("docstring") gdcm::NormalizedNetworkFunctions "
+
+Normalized Network Functions These functions provide a generic API to
+the DICOM functions implemented in GDCM. Advanced users can use this
+code as a template for building their own versions of these functions
+(for instance, to provide progress bars or some other way of handling
+returned query information), but for most users, these functions
+should be sufficient to interface with a PACS to a local machine. Note
+that these functions are not contained within a static class or some
+other class-style interface, because multiple connections can be
+instantiated in the same program. The DICOM standard is much more
+function oriented rather than class oriented in this instance, so the
+design of this API reflects that functional approach. These functions
+implements the following SCU operations:
+
+N-EVENT-REPORT
+
+N-GET
+
+N-SET
+
+N-ACTION
+
+N-CREATE
+
+N-DELETE
+
+C++ includes: gdcmNormalizedNetworkFunctions.h ";
+
+
+// File: classgdcm_1_1network_1_1NSetRQ.xml
+%feature("docstring") gdcm::network::NSetRQ "
+
+NSetRQ this file defines the messages for the nset action.
+
+C++ includes: gdcmNSetMessages.h ";
+
+%feature("docstring") gdcm::network::NSetRQ::ConstructPDV "std::vector<PresentationDataValue>
+gdcm::network::NSetRQ::ConstructPDV(const ULConnection &inConnection,
+const BaseQuery *inQuery) ";
+
+
+// File: classgdcm_1_1network_1_1NSetRSP.xml
+%feature("docstring") gdcm::network::NSetRSP "
+
+NSetRSP this file defines the messages for the nset action.
+
+C++ includes: gdcmNSetMessages.h ";
+
+%feature("docstring") gdcm::network::NSetRSP::ConstructPDVByDataSet "std::vector<PresentationDataValue>
+gdcm::network::NSetRSP::ConstructPDVByDataSet(const DataSet
+*inDataSet) ";
+
+
// File: classgdcm_1_1Object.xml
%feature("docstring") gdcm::Object "
@@ -7024,7 +7376,7 @@ return if the Overlay is stored in the pixel data or not ";
%feature("docstring") gdcm::Overlay::IsInPixelData "void
gdcm::Overlay::IsInPixelData(bool b)
-Set wether or no the OverlayData is in the Pixel Data: ";
+Set whether or no the OverlayData is in the Pixel Data: ";
%feature("docstring") gdcm::Overlay::IsZero "bool
gdcm::Overlay::IsZero() const
@@ -7389,7 +7741,7 @@ C++ includes: gdcmPhotometricInterpretation.h ";
%feature("docstring")
gdcm::PhotometricInterpretation::PhotometricInterpretation "gdcm::PhotometricInterpretation::PhotometricInterpretation(PIType
-pi=UNKNOW) ";
+pi=UNKNOWN) ";
%feature("docstring")
gdcm::PhotometricInterpretation::GetSamplesPerPixel "unsigned short
@@ -7934,6 +8286,13 @@ C++ includes: gdcmPresentationContextGenerator.h ";
%feature("docstring")
gdcm::PresentationContextGenerator::PresentationContextGenerator "gdcm::PresentationContextGenerator::PresentationContextGenerator() ";
+%feature("docstring") gdcm::PresentationContextGenerator::AddFromFile
+"bool gdcm::PresentationContextGenerator::AddFromFile(const File
+&file)
+
+Add a single PresentationContext from a single File. Call multiple
+times when dealing with multiple files. ";
+
%feature("docstring")
gdcm::PresentationContextGenerator::GenerateFromFilenames "bool
gdcm::PresentationContextGenerator::GenerateFromFilenames(const
@@ -8719,6 +9078,11 @@ gdcm::Reader::SetStream(std::istream &input_stream)
Set the open-ed stream directly. ";
+// File: structgdcm_1_1RealWorldValueMappingContent.xml
+%feature("docstring") gdcm::RealWorldValueMappingContent "C++
+includes: gdcmImageHelper.h ";
+
+
// File: classgdcm_1_1Region.xml
%feature("docstring") gdcm::Region "
@@ -8991,8 +9355,7 @@ tags. ";
%feature("docstring") gdcm::Scanner::AddTag "void
gdcm::Scanner::AddTag(Tag const &t)
-Add a tag that will need to be read. Those are root level skip tags.
-";
+Add a tag that will need to be read. Those are root level tags. ";
%feature("docstring") gdcm::Scanner::Begin "ConstIterator
gdcm::Scanner::Begin() const ";
@@ -9393,6 +9756,12 @@ gdcm::SequenceOfItems::AddItem(Item const &item)
Appends an Item to the already added ones. ";
+%feature("docstring")
+gdcm::SequenceOfItems::AddNewUndefinedLengthItem "Item&
+gdcm::SequenceOfItems::AddNewUndefinedLengthItem()
+
+Appends an Item to the already added ones. ";
+
%feature("docstring") gdcm::SequenceOfItems::Begin "Iterator
gdcm::SequenceOfItems::Begin() ";
@@ -11968,7 +12337,8 @@ C++ includes: gdcmULConnectionManager.h ";
gdcm::network::ULConnectionManager::ULConnectionManager "gdcm::network::ULConnectionManager::ULConnectionManager() ";
%feature("docstring")
-gdcm::network::ULConnectionManager::~ULConnectionManager "gdcm::network::ULConnectionManager::~ULConnectionManager() ";
+gdcm::network::ULConnectionManager::~ULConnectionManager "virtual
+gdcm::network::ULConnectionManager::~ULConnectionManager() ";
%feature("docstring")
gdcm::network::ULConnectionManager::BreakConnection "bool
@@ -12024,11 +12394,64 @@ gdcm::network::ULConnectionManager::SendMove(const BaseRootQuery
return false upon error ";
+%feature("docstring") gdcm::network::ULConnectionManager::SendNAction
+"std::vector<DataSet>
+gdcm::network::ULConnectionManager::SendNAction(const BaseQuery
+*inQuery) ";
+
+%feature("docstring") gdcm::network::ULConnectionManager::SendNAction
+"void gdcm::network::ULConnectionManager::SendNAction(const BaseQuery
+*inQuery, ULConnectionCallback *inCallback) ";
+
+%feature("docstring") gdcm::network::ULConnectionManager::SendNCreate
+"std::vector<DataSet>
+gdcm::network::ULConnectionManager::SendNCreate(const BaseQuery
+*inQuery) ";
+
+%feature("docstring") gdcm::network::ULConnectionManager::SendNCreate
+"void gdcm::network::ULConnectionManager::SendNCreate(const BaseQuery
+*inQuery, ULConnectionCallback *inCallback) ";
+
+%feature("docstring") gdcm::network::ULConnectionManager::SendNDelete
+"std::vector<DataSet>
+gdcm::network::ULConnectionManager::SendNDelete(const BaseQuery
+*inQuery) ";
+
+%feature("docstring") gdcm::network::ULConnectionManager::SendNDelete
+"void gdcm::network::ULConnectionManager::SendNDelete(const BaseQuery
+*inQuery, ULConnectionCallback *inCallback) ";
+
+%feature("docstring")
+gdcm::network::ULConnectionManager::SendNEventReport "std::vector<DataSet>
+gdcm::network::ULConnectionManager::SendNEventReport(const BaseQuery
+*inQuery) ";
+
+%feature("docstring")
+gdcm::network::ULConnectionManager::SendNEventReport "void
+gdcm::network::ULConnectionManager::SendNEventReport(const BaseQuery
+*inQuery, ULConnectionCallback *inCallback) ";
+
+%feature("docstring") gdcm::network::ULConnectionManager::SendNGet "std::vector<DataSet>
+gdcm::network::ULConnectionManager::SendNGet(const BaseQuery *inQuery)
+";
+
+%feature("docstring") gdcm::network::ULConnectionManager::SendNGet "void gdcm::network::ULConnectionManager::SendNGet(const BaseQuery
+*inQuery, ULConnectionCallback *inCallback) ";
+
+%feature("docstring") gdcm::network::ULConnectionManager::SendNSet "std::vector<DataSet>
+gdcm::network::ULConnectionManager::SendNSet(const BaseQuery *inQuery)
+";
+
+%feature("docstring") gdcm::network::ULConnectionManager::SendNSet "void gdcm::network::ULConnectionManager::SendNSet(const BaseQuery
+*inQuery, ULConnectionCallback *inCallback) ";
+
%feature("docstring") gdcm::network::ULConnectionManager::SendStore "std::vector<DataSet>
-gdcm::network::ULConnectionManager::SendStore(const File &file) ";
+gdcm::network::ULConnectionManager::SendStore(const File &file,
+std::istream *pStream=NULL, std::streampos dataSetOffset=0) ";
%feature("docstring") gdcm::network::ULConnectionManager::SendStore "void gdcm::network::ULConnectionManager::SendStore(const File &file,
-ULConnectionCallback *inCallback)
+ULConnectionCallback *inCallback, std::istream *pStream=NULL,
+std::streampos dataSetOffset=0)
callback based API ";
@@ -12047,16 +12470,22 @@ associated event to destroy it!
C++ includes: gdcmULEvent.h ";
%feature("docstring") gdcm::network::ULEvent::ULEvent "gdcm::network::ULEvent::ULEvent(const EEventID &inEventID,
-std::vector< BasePDU * > const &inBasePDU) ";
+std::vector< BasePDU * > inBasePDU, std::istream *iStream=NULL,
+std::streampos posDataSet=0) ";
%feature("docstring") gdcm::network::ULEvent::ULEvent "gdcm::network::ULEvent::ULEvent(const EEventID &inEventID, BasePDU
-*inBasePDU) ";
+*inBasePDU, std::istream *iStream=NULL, std::streampos posDataSet=0)
+";
%feature("docstring") gdcm::network::ULEvent::~ULEvent "gdcm::network::ULEvent::~ULEvent() ";
+%feature("docstring") gdcm::network::ULEvent::GetDataSetPos "std::streampos gdcm::network::ULEvent::GetDataSetPos() const ";
+
%feature("docstring") gdcm::network::ULEvent::GetEvent "EEventID
gdcm::network::ULEvent::GetEvent() const ";
+%feature("docstring") gdcm::network::ULEvent::GetIStream "std::istream* gdcm::network::ULEvent::GetIStream() const ";
+
%feature("docstring") gdcm::network::ULEvent::GetPDUs "std::vector<BasePDU*> const& gdcm::network::ULEvent::GetPDUs() const
";
@@ -13427,6 +13856,51 @@ C++ includes: gdcmWaveform.h ";
%feature("docstring") gdcm::Waveform::Waveform "gdcm::Waveform::Waveform() ";
+// File: classgdcm_1_1WLMFindQuery.xml
+%feature("docstring") gdcm::WLMFindQuery "
+
+PatientRootQuery contains: the class which will produce a dataset for
+c-find with patient root.
+
+C++ includes: gdcmWLMFindQuery.h ";
+
+%feature("docstring") gdcm::WLMFindQuery::WLMFindQuery "gdcm::WLMFindQuery::WLMFindQuery() ";
+
+%feature("docstring") gdcm::WLMFindQuery::GetAbstractSyntaxUID "UIDs::TSName gdcm::WLMFindQuery::GetAbstractSyntaxUID() const ";
+
+%feature("docstring") gdcm::WLMFindQuery::GetTagListByLevel "std::vector<Tag> gdcm::WLMFindQuery::GetTagListByLevel(const
+EQueryLevel &inQueryLevel)
+
+this function will return all tags at a given query level, so that
+they maybe selected for searching. The boolean forFind is true if the
+query is a find query, or false for a move query. ";
+
+%feature("docstring") gdcm::WLMFindQuery::InitializeDataSet "void
+gdcm::WLMFindQuery::InitializeDataSet(const EQueryLevel &inQueryLevel)
+
+this function sets tag 8,52 to the appropriate value based on query
+level also fills in the right unique tags, as per the standard's
+requirements should allow for connection with dcmtk ";
+
+%feature("docstring") gdcm::WLMFindQuery::ValidateQuery "bool
+gdcm::WLMFindQuery::ValidateQuery(bool inStrict=true) const
+
+have to be able to ensure that 0x8,0x52 is set (which will be true if
+InitializeDataSet is called...) that the level is appropriate (ie, not
+setting PATIENT for a study query that the tags in the query match the
+right level (either required, unique, optional) by default, this
+function checks to see if the query is for finding, which is more
+permissive than for moving. For moving, only the unique tags are
+allowed. 10 Jan 2011: adding in the 'strict' mode. according to the
+standard (at least, how I've read it), only tags for a particular
+level should be allowed in a particular query (ie, just series level
+tags in a series level query). However, it seems that dcm4chee doesn't
+share that interpretation. So, if 'inStrict' is false, then tags from
+the current level and all higher levels are now considered valid. So,
+if you're doing a non-strict series-level query, tags from the patient
+and study level can be passed along as well. ";
+
+
// File: classgdcm_1_1Writer.xml
%feature("docstring") gdcm::Writer "
@@ -13537,8 +14011,8 @@ gdcm::XMLPrinter::GetPrintStyle() const ";
gdcm::XMLPrinter::HandleBulkData(const char *uuid, const
TransferSyntax &ts, const char *bulkdata, size_t bulklen)
-Virtual function mecanism to allow application programmer to override
-the default mecanism for BulkData handling. By default GDCM will
+Virtual function mechanism to allow application programmer to override
+the default mechanism for BulkData handling. By default GDCM will
simply discard the BulkData and only write the UUID ";
%feature("docstring") gdcm::XMLPrinter::Print "void
@@ -13623,12 +14097,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: namespacestd.xml
-// File: gdcm2pnm_8dox.xml
-
-
-// File: gdcm2vtk_8dox.xml
-
-
// File: gdcmAAbortPDU_8h.xml
@@ -13644,9 +14112,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmAbstractSyntax_8h.xml
-// File: gdcmanon_8dox.xml
-
-
// File: gdcmAnonymizeEvent_8h.xml
@@ -13686,9 +14151,15 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmBaseCompositeMessage_8h.xml
+// File: gdcmBaseNormalizedMessage_8h.xml
+
+
// File: gdcmBasePDU_8h.xml
+// File: gdcmBaseQuery_8h.xml
+
+
// File: gdcmBaseRootQuery_8h.xml
@@ -13755,9 +14226,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmConstCharWrapper_8h.xml
-// File: gdcmconv_8dox.xml
-
-
// File: gdcmCP246ExplicitDataElement_8h.xml
@@ -13836,9 +14304,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmDicts_8h.xml
-// File: gdcmdiff_8dox.xml
-
-
// File: gdcmDIMSE_8h.xml
@@ -13854,9 +14319,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmDummyValueGenerator_8h.xml
-// File: gdcmdump_8dox.xml
-
-
// File: gdcmDumper_8h.xml
@@ -13893,6 +14355,9 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmFileChangeTransferSyntax_8h.xml
+// File: gdcmFileDecompressLookupTable_8h.xml
+
+
// File: gdcmFileDerivation_8h.xml
@@ -13926,9 +14391,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmFragment_8h.xml
-// File: gdcmgendir_8dox.xml
-
-
// File: gdcmGlobal_8h.xml
@@ -13983,9 +14445,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmImageWriter_8h.xml
-// File: gdcmimg_8dox.xml
-
-
// File: gdcmImplementationClassUIDSub_8h.xml
@@ -13998,9 +14457,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmImplicitDataElement_8h.xml
-// File: gdcminfo_8dox.xml
-
-
// File: gdcmIOD_8h.xml
@@ -14070,6 +14526,12 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmMeshPrimitive_8h.xml
+// File: gdcmModalityPerformedProcedureStepCreateQuery_8h.xml
+
+
+// File: gdcmModalityPerformedProcedureStepSetQuery_8h.xml
+
+
// File: gdcmModule_8h.xml
@@ -14085,6 +14547,15 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmMoveStudyRootQuery_8h.xml
+// File: gdcmNActionMessages_8h.xml
+
+
+// File: gdcmNCreateMessages_8h.xml
+
+
+// File: gdcmNDeleteMessages_8h.xml
+
+
// File: gdcmNestedModuleEntries_8h.xml
@@ -14094,6 +14565,21 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmNetworkStateID_8h.xml
+// File: gdcmNEventReportMessages_8h.xml
+
+
+// File: gdcmNGetMessages_8h.xml
+
+
+// File: gdcmNormalizedMessageFactory_8h.xml
+
+
+// File: gdcmNormalizedNetworkFunctions_8h.xml
+
+
+// File: gdcmNSetMessages_8h.xml
+
+
// File: gdcmObject_8h.xml
@@ -14115,9 +14601,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmOverlay_8h.xml
-// File: gdcmpap3_8dox.xml
-
-
// File: gdcmParseException_8h.xml
@@ -14136,9 +14619,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmPDBHeader_8h.xml
-// File: gdcmpdf_8dox.xml
-
-
// File: gdcmPDFCodec_8h.xml
@@ -14223,9 +14703,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmQueryStudy_8h.xml
-// File: gdcmraw_8dox.xml
-
-
// File: gdcmRAWCodec_8h.xml
@@ -14244,15 +14721,9 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmRoleSelectionSub_8h.xml
-// File: gdcmscanner_8dox.xml
-
-
// File: gdcmScanner_8h.xml
-// File: gdcmscu_8dox.xml
-
-
// File: gdcmSegment_8h.xml
@@ -14376,9 +14847,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmTagToVR_8h.xml
-// File: gdcmtar_8dox.xml
-
-
// File: gdcmTerminal_8h.xml
@@ -14478,9 +14946,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmVersion_8h.xml
-// File: gdcmviewer_8dox.xml
-
-
// File: gdcmVL_8h.xml
@@ -14499,10 +14964,10 @@ gdcm::terminal::setmode(Mode m) ";
// File: gdcmWin32_8h.xml
-// File: gdcmWriter_8h.xml
+// File: gdcmWLMFindQuery_8h.xml
-// File: gdcmxml_8dox.xml
+// File: gdcmWriter_8h.xml
// File: gdcmXMLDictReader_8h.xml
@@ -14571,57 +15036,6 @@ gdcm::terminal::setmode(Mode m) ";
// File: vtkRTStructSetProperties_8h.xml
-// File: gdcm2pnm.xml
-
-
-// File: gdcm2vtk.xml
-
-
-// File: gdcmanon.xml
-
-
-// File: gdcmconv.xml
-
-
-// File: gdcmdiff.xml
-
-
-// File: gdcmdump.xml
-
-
-// File: gdcmgendir.xml
-
-
-// File: gdcmimg.xml
-
-
-// File: gdcminfo.xml
-
-
-// File: gdcmpap3.xml
-
-
-// File: gdcmpdf.xml
-
-
-// File: gdcmraw.xml
-
-
-// File: gdcmscanner.xml
-
-
-// File: gdcmscu.xml
-
-
-// File: gdcmtar.xml
-
-
-// File: gdcmviewer.xml
-
-
-// File: gdcmxml.xml
-
-
// File: todo.xml
@@ -14631,40 +15045,40 @@ gdcm::terminal::setmode(Mode m) ";
// File: bug.xml
-// File: dir_baa54b0fc0a51ae65b8ade5fc5834843.xml
+// File: dir_48be02fb937e08881437e02515417ab2.xml
-// File: dir_760652a266da5834cc3e97cfe417708e.xml
+// File: dir_dbdfee04788ce02e68d05e06d5e6d98f.xml
-// File: dir_c4773660235d6419cbce98ba7728c69c.xml
+// File: dir_422e8974cbd0b7203ed9c70ede735192.xml
-// File: dir_4eed16b43278c59f2ec90617aa823645.xml
+// File: dir_fc2dbd93ff698b14d78f486017ee822b.xml
-// File: dir_1b862fb7590f5660fca04cc43d96fb27.xml
+// File: dir_63e84970519399936bea68aa0151439e.xml
-// File: dir_a73f40d126d81357a14a94e26d2bdf1b.xml
+// File: dir_a3a231e2bd7f702d85036607d7d87964.xml
-// File: dir_a4ab8faed3a40b14352018492e6b9514.xml
+// File: dir_bfc3201f3b82d7ccf14c524caa3c389b.xml
-// File: dir_b6fa77c9e8690cb24913e26282ff8de3.xml
+// File: dir_9a6580727919559370fc2250dcaca6b8.xml
-// File: dir_9681c4dd247acdffddd07e8149decc60.xml
+// File: dir_087222ad62d2f517f4e0198672951648.xml
-// File: dir_1060e304b1e64f0c0a2e3f0d58ae4655.xml
+// File: dir_2a74275ceded0a5f3b0fb2e9bd792825.xml
-// File: dir_e1e30d61f6961475b2a4c887cfe98de1.xml
+// File: dir_acafdc7d686494cf0735517ddc7a7669.xml
-// File: dir_cff348c9442501173f15a3e4169a76d0.xml
+// File: dir_d2ab22b73e3ee89be3a207288d7a9056.xml
// File: AWTMedical3_8java-example.xml
@@ -14862,6 +15276,9 @@ gdcm::terminal::setmode(Mode m) ";
// File: FixJAIBugJPEGLS_8cxx-example.xml
+// File: FixOrientation_8cxx-example.xml
+
+
// File: gdcmorthoplanes_8cxx-example.xml
@@ -14970,6 +15387,9 @@ gdcm::terminal::setmode(Mode m) ";
// File: MagnifyFile_8cxx-example.xml
+// File: MakeTemplate_8cxx-example.xml
+
+
// File: ManipulateFile_8cs-example.xml
diff --git a/appveyor.yml b/appveyor.yml
index 03ac950..6860569 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -1,16 +1,38 @@
-version: 2.7.0.{build}
+# appveyor file
+# http://www.appveyor.com/docs/appveyor-yml
+
+# Set build version format here instead of in the admin panel.
+version: 2.6.2.{build}
+
+# http://www.appveyor.com/docs/build-cache#caching-chocolatey-packages
+# https://github.com/kvirc/KVIrc/blob/master/.appveyor.yml
+cache:
+ - C:\ProgramData\chocolatey\bin -> appveyor.yml
+ - C:\ProgramData\chocolatey\lib -> appveyor.yml
+ - 'c:\Program Files\NSIS'
environment:
matrix:
- - VS_GEN: Visual Studio 14 2015
- CONFIG: RelWithDebInfo
- B_NAME: Win32
- - VS_GEN: Visual Studio 14 2015 Win64
+ - VS_GEN: Visual Studio 10 2010
+ CONFIG: Release
+ B_NAME: Windows-x86
+ DO_REL: true
+ - VS_GEN: Visual Studio 10 2010 Win64
CONFIG: Release
- B_NAME: Win64
- - VS_GEN: Visual Studio 14 2015 ARM
- CONFIG: Debug
- B_NAME: ARM
+ B_NAME: Windows-x86_64
+ DO_REL: true
+# - VS_GEN: Visual Studio 14 2015 Win64
+# CONFIG: Release
+# B_NAME: Win64
+# - VS_GEN: MinGW Makefiles
+# CONFIG: None
+# B_NAME: MinGW
+# - VS_GEN: MSYS Makefiles
+# CONFIG: None
+# B_NAME: Msys
+# - VS_GEN: Visual Studio 14 2015 ARM
+# CONFIG: Debug
+# B_NAME: ARM
matrix:
fast_finish: true
@@ -20,41 +42,112 @@ os: Visual Studio 2015
branches:
except:
- coverity_scan
-skip_tags: true
+
+#You can disable builds on new tags through UI (General tab of project settings) or in appveyor.yml:
+#skip_tags: true
# scripts that are called at very beginning, before repo cloning
init:
- # Print environment info
- #- set
+ # Print environment info ( set / systeminfo)
- msbuild /version
- cmake --version
- python --version
- java -version
-
-# check nmake ?
-#- call "c:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" amd64
-#- cl
+ # https://github.com/chocolatey/chocolatey/issues/431
+ - del c:\programdata\chocolatey\bin\cpack.exe
# scripts that run after cloning repository
install:
# Fetch submodules
- - git submodule update --init --recursive
+ #- git submodule update --init --recursive
- choco install swig
- swig -version
+ # https://chocolatey.org/packages/nsis.install/
+ - ps: |
+ if (Test-Path "c:/Program Files/NSIS/makensis.exe") {
+ echo "using nsis from cache"
+ } else {
+ choco install nsis.install -pre -version 2.46.0.20150406
+ }
+ # Set VC variables for the platform
+ # - if %PLATFORM% == x64 call "C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin\x86_amd64\vcvarsx86_amd64.bat"
+ # - if %PLATFORM% == x86 call "C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin\vcvars32.bat"
+on_failure:
+ # Display error log file if generated
+ - if exist C:\ProgramData\chocolatey\logs\chocolatey.log type C:\ProgramData\chocolatey\logs\chocolatey.log
+
+# scripts to run before build
before_build:
- - cmake -Wno-dev -G"%VS_GEN%" -DCMAKE_BUILD_TYPE=%CONFIG% -DGDCM_BUILD_TESTING:BOOL=ON -DGDCM_BUILD_APPLICATIONS:BOOL=ON -DGDCM_BUILD_SHARED_LIBS:BOOL=ON -DGDCM_ALLOW_INSOURCE_BUILD:BOOL=ON -DBUILDNAME:STRING=%COMPUTERNAME%-%B_NAME% -DGDCM_WRAP_CSHARP:BOOL=ON -DGDCM_WRAP_JAVA:BOOL=ON -DGDCM_WRAP_PYTHON:BOOL=ON -DGDCM_USE_PVRG:BOOL=ON .
+ - cmake -Wno-dev -G"%VS_GEN%" -DCMAKE_BUILD_TYPE=%CONFIG% -DGDCM_BUILD_TESTING:BOOL=ON -DGDCM_BUILD_APPLICATIONS:BOOL=ON -DGDCM_BUILD_SHARED_LIBS:BOOL=ON -DBUILDNAME:STRING=%COMPUTERNAME%-%B_NAME% -DGDCM_WRAP_CSHARP:BOOL=ON -DGDCM_WRAP_JAVA:BOOL=ON -DGDCM_WRAP_PYTHON:BOOL=ON -DGDCM_USE_PVRG:BOOL=ON -DGDCM_JAVA_SOURCE_VERSION:STRING=1.7 -DGDCM_JAVA_TARGET_VERSION:STRING=1.7 -DCPACK_SYSTEM_NAME:STRING=%B_NAME% .
+ - ctest -D ExperimentalStart -C %CONFIG%
+# scripts to run after build
+after_build:
+ # create NSIS installer
+ - cpack -G NSIS -C %CONFIG%
+ # create binary zip
+ - cpack -G ZIP -C %CONFIG%
+ # on github it does make sense to do source package
+
+# to run your custom scripts instead of automatic MSBuild
build_script:
- - echo %CONFIG%
- # NUMBER_OF_PROCESSORS=2
- # msbuild /m => parallel
- #- msbuild gdcm.sln /m /p:Configuration=%config% /toolsversion:14.0 /p:Platform=x64 /p:PlatformToolset=v140
# Do not run Test=Update/Configure, only Start/Build/Test/Submit (TODO: Coverage)
- - ctest -D ExperimentalStart -C %CONFIG%
- - ctest -D ExperimentalBuild -j2 -C %CONFIG%
- - ctest -D ExperimentalTest -j2 -C %CONFIG% || true
- - ctest -D ExperimentalSubmit -C %CONFIG%
+ - ctest -D ExperimentalBuild -j %NUMBER_OF_PROCESSORS% -C %CONFIG% -Q
+
+# scripts to run before tests
+#before_test:
+# - echo %APPVEYOR_REPO_TAG_NAME%
+# - echo %APPVEYOR_REPO_TAG_NAME:~1%
+
+# scripts to run after tests
+after_test:
+
+# to run your custom scripts instead of automatic tests
+test_script:
+ - ctest -D ExperimentalTest -j %NUMBER_OF_PROCESSORS% -C %CONFIG% -Q || true
+ - ctest -D ExperimentalSubmit -C %CONFIG% -Q
+
+#---------------------------------#
+# artifacts configuration #
+#---------------------------------#
+
+artifacts:
+ - path: GDCM-*-$(B_NAME).exe
+ name: installer
+ - path: GDCM-*-$(B_NAME).zip
+ name: zip_executable
+ type: zip
+
+#---------------------------------#
+# deployment configuration #
+#---------------------------------#
+
+# scripts to run before deployment
+#before_deploy:
+
+# scripts to run after deployment
+#after_deploy:
+
+# to run your custom scripts instead of provider deployments
+#deploy_script:
-test: off
-deploy: off
+# Deploy to GitHub Releases http://www.appveyor.com/docs/deployment/github
+# http://www.appveyor.com/docs/branches
+# AppVeyor sets APPVEYOR_REPO_TAG environment variable to distinguish regular
+# commits from tags - the value is True if tag was pushed; otherwise it's
+# False. When it's True the name of tag is stored in APPVEYOR_REPO_TAG_NAME.
+deploy:
+ - provider: GitHub
+ auth_token:
+ secure: 7HmfZp9O7bVdQo2hRk6FjOUs7jJosftv2rZ6JPBNzjPcAOMXDTvLqv3lvzdAzBfy
+ release: $(appveyor_repo_tag_name)
+ description: 'Release of GDCM $(appveyor_repo_tag_name)'
+ # github automatically does source zip/tarball for us
+ artifact: installer,zip_executable
+ draft: false
+ prerelease: false
+ on:
+ branch: release # release from release branch only
+ appveyor_repo_tag: true # deploy on tag push only
+ do_rel: true
--
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