[med-svn] [mia] 01/04: Imported Upstream version 2.4.3
Gert Wollny
gert-guest at moszumanska.debian.org
Wed Aug 24 17:32:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
gert-guest pushed a commit to branch master
in repository mia.
commit 1bb7eb8c2f86404471d9b9dc917f5f619b7128d9
Author: Gert Wollny <gw.fossdev at gmail.com>
Date: Wed Aug 24 16:36:23 2016 +0000
Imported Upstream version 2.4.3
---
CMakeLists.txt | 23 ++++++++---
ChangeLog | 7 ++++
addons/dicom/dcm3d.cc | 20 +++++++---
addons/dicom/dicom4mia.cc | 2 +-
addons/vistaio/vistamesh.cc | 2 +-
mia/2d/cost/ngf.cc | 2 +-
mia/2d/filter/meanvar.cc | 4 +-
mia/2d/filter/medianmad.cc | 4 +-
mia/2d/filter/tmean.cc | 4 +-
mia/2d/fullcost.cc | 2 +-
mia/2d/fullcost/image.cc | 2 +-
mia/2d/fullcost/label.cc | 2 +-
mia/2d/fullcost/maskedimage.cc | 2 +-
mia/2d/segframe.cc | 4 +-
mia/2d/splinetransformpenalty.cc | 2 +-
mia/2d/test_filter.cc | 2 +-
mia/2d/test_splinetransformpenalty.cc | 4 +-
mia/2d/transform/test_spline.cc | 2 +-
mia/3d/2dimagefifofilter.cc | 2 +-
mia/3d/fifof/regiongrow.cc | 2 +-
mia/3d/fifof/rgg.cc | 4 +-
mia/3d/filter/growmask.cc | 2 +-
mia/3d/fullcost/image.cc | 2 +-
mia/3d/fullcost/label.cc | 2 +-
mia/3d/fullcost/maskedimage.cc | 2 +-
mia/3d/fullcost/taggedssd.cc | 2 +-
mia/3d/splinetransformpenalty.cc | 2 +-
mia/3d/test_landmarklistio.cc | 4 +-
mia/3d/test_splinetransformpenalty.cc | 4 +-
mia/3d/transform/spline.cc | 2 +-
mia/3d/transform/test_spline.cc | 2 +-
mia/core/attributes.hh | 4 +-
mia/core/delayedparameter.hh | 2 +-
mia/core/fftslopeclassifier.cc | 2 +-
mia/core/filetools.cc | 1 -
mia/core/handler.cxx | 5 +--
mia/core/handler.hh | 2 +-
mia/core/index.hh | 2 +-
mia/core/iohandler.hh | 2 +-
mia/core/minimizer/gdas.cc | 4 +-
mia/core/minimizer/gsl.cc | 2 +-
mia/core/property_flags.hh | 2 +-
mia/core/searchpath.cc | 20 +++++++---
mia/core/slopeclassifier.hh | 2 +-
mia/core/utils.cc | 73 +++--------------------------------
mia/core/vector.hh | 6 +--
mia/internal/pluginsettest.hh | 2 +-
src/2deval-transformquantity.cc | 2 +-
src/2dgroundtruthreg.cc | 2 +-
src/2dmyoica-full.cc | 4 +-
src/2dmyoica-nonrigid-parallel.cc | 2 +-
src/2dmyoica-nonrigid.cc | 2 +-
src/2dmyoicapgt.cc | 4 +-
src/2dmyopgt-nonrigid.cc | 2 +-
src/2dmyoseries-compdice.cc | 2 +-
src/2dsegment-local-cmeans.cc | 6 +--
src/2dsegment-local-kmeans.cc | 6 +--
src/2dsegment-per-pixel-kmeans.cc | 6 +--
src/2dseries2sets.cc | 16 ++++----
src/3ddistance-stats.cc | 2 +-
src/3deval-transformquantity.cc | 2 +-
src/3dlandmarks-distances.cc | 2 +-
src/fluid3d/main.cc | 4 +-
src/multihist.cc | 2 +-
src/plugin-help.cc | 2 +-
65 files changed, 149 insertions(+), 172 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2bd89a3..3fd2672 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -53,9 +53,9 @@ SET(VENDOR "Gert Wollny")
SET(PACKAGE_NAME "mia")
SET(MAJOR_VERSION 2)
SET(MINOR_VERSION 4)
-SET(MICRO_VERSION 2)
-SET(INTERFACE_AGE 0)
-SET(BINARY_AGE 0)
+SET(MICRO_VERSION 3)
+SET(INTERFACE_AGE 1)
+SET(BINARY_AGE 1)
#
#SET(CMAKE_BUILD_WITH_INSTALL_RPATH 1)
@@ -82,6 +82,9 @@ OPTION(ENABLE_DEBUG_MESSAGES "Enable debug and trace outputs" TRUE)
OPTION(ENABLE_COVERAGE "Enable code coverage tests" FALSE)
OPTION(DISABLE_PROGRAMS "Don't build the programs nor documentation (only for testing purposes)" FALSE)
OPTION(MIA_CREATE_USERDOC "Enable creation of html user documentation" TRUE)
+OPTION(MIA_USE_BOOST_REGEX "Use the boost::regex library (instead of c++11 build in) " FALSE)
+
+
INCLUDE(GNUInstallDirs)
@@ -216,7 +219,12 @@ MACRO(GET_BOOST_LINKERFLAG VAR LIBNAMES)
SET(${VAR} "${flags}")
ENDMACRO(GET_BOOST_LINKERFLAG)
-SET(BOOST_COMPONENTS filesystem regex unit_test_framework serialization system)
+SET(BOOST_COMPONENTS filesystem unit_test_framework serialization system)
+
+IF (MIA_USE_BOOST_REGEX)
+ SET(BOOST_COMPONENTS ${BOOST_COMPONENTS} regex)
+ENDIF()
+
IF (WIN32)
SET(BOOST_COMPONENTS ${BOOST_COMPONENTS} date_time)
ENDIF(WIN32)
@@ -231,7 +239,12 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
ADD_DEFINITIONS(-DBOOST_ALL_DYN_LINK)
ADD_DEFINITIONS(-DBOOST_FILESYSTEM_VERSION=3)
-SET(BOOST_DEPS ${Boost_REGEX_LIBRARY} ${Boost_FILESYSTEM_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+IF (MIA_USE_BOOST_REGEX)
+ SET(BOOST_DEPS ${Boost_REGEX_LIBRARY} ${Boost_FILESYSTEM_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+ELSE()
+ SET(BOOST_DEPS ${Boost_FILESYSTEM_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+ENDIF()
+
SET(BOOST_UNITTEST ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
IF (WIN32 AND NOT UNIX)
diff --git a/ChangeLog b/ChangeLog
index 6ea63c3..fb6adec 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,10 @@
+2.4.3
+
+ * m/c/utils.cc: Always define PATH_MAX when it is not defined by
+ system headers
+ * Correct spellings
+ * Replace use of boost::regex by std::regex
+
2.4.2
* correct installed headers
diff --git a/addons/dicom/dcm3d.cc b/addons/dicom/dcm3d.cc
index 33f1cf8..18dd317 100644
--- a/addons/dicom/dcm3d.cc
+++ b/addons/dicom/dcm3d.cc
@@ -26,7 +26,17 @@
#include <map>
#include <queue>
#include <boost/filesystem.hpp>
+
+#if __cplusplus >= 201103
+#include <regex>
+using std::regex;
+using std::regex_match;
+#else
#include <boost/regex.hpp>
+using boost::regex;
+using boost::regex_match;
+#endif
+
#include <mia/core/errormacro.hh>
#include <mia/core/file.hh>
@@ -78,7 +88,7 @@ struct image_instance_less {
typedef priority_queue<P2DImage, vector<P2DImage>, image_instance_less> CImageInstances;
typedef map<PAttribute, CImageInstances, attr_less> CImageSeries;
-typedef map<PAttribute, CImageSeries, attr_less> CAquisitions;
+typedef map<PAttribute, CImageSeries, attr_less> CAcquisitions;
struct C3DImageCreator: public TFilter<bool> {
C3DImageCreator(size_t nz): m_nz(nz),
@@ -184,7 +194,7 @@ C3DImageIOPlugin::PData CDicom3DImageIOPlugin::get_images(const vector<P2DImage>
PData result(new Data);
- CAquisitions acc;
+ CAcquisitions acc;
// read all the images into a map
for(auto i = candidates.begin(); i != candidates.end(); ++i) {
@@ -195,7 +205,7 @@ C3DImageIOPlugin::PData CDicom3DImageIOPlugin::get_images(const vector<P2DImage>
[(*i)->get_attribute(IDSeriesNumber)].push(*i);
}else{
cvwarn() << "Discard image because of no "
- << ((*i)->has_attribute(IDAcquisitionNumber) ? "" : "aquisition")
+ << ((*i)->has_attribute(IDAcquisitionNumber) ? "" : "acquisition")
<< ((*i)->has_attribute(IDInstanceNumber) ? "" : "instance")
<< ((*i)->has_attribute(IDSeriesNumber) ? "" : "series")
<< " number\n";
@@ -231,12 +241,12 @@ static void add_images(const string& fname, const string& study_id, vector<P2DIm
stringstream pattern;
pattern << ".*\\" << ext;
- boost::regex pat_expr(pattern.str());
+ regex pat_expr(pattern.str());
bfs::directory_iterator di(dir);
bfs::directory_iterator dend;
while (di != dend) {
- if (boost::regex_match(di->path().filename().string(), pat_expr) &&
+ if (regex_match(di->path().filename().string(), pat_expr) &&
di->path().filename().string() != fname) {
bfs::path f = di->path();
cvdebug() << "read file '" << f << "'\n";
diff --git a/addons/dicom/dicom4mia.cc b/addons/dicom/dicom4mia.cc
index 4316f90..ded4790 100644
--- a/addons/dicom/dicom4mia.cc
+++ b/addons/dicom/dicom4mia.cc
@@ -451,7 +451,7 @@ void CDicomReaderData::getAcquisitionTimeIfAvailable(CAttributedData& image)
OFTime of_time;
success = dcm_time->getOFTime(of_time);
if (!success.good()) {
- cverr() << "CDicomReader: Could not retrive OFTime string from DcmTime Element\n";
+ cverr() << "CDicomReader: Could not retrieve OFTime string from DcmTime Element\n";
return;
}
image.set_attribute(IDAcquisitionTime, of_time.getTimeInSeconds());
diff --git a/addons/vistaio/vistamesh.cc b/addons/vistaio/vistamesh.cc
index 35b8948..9d4833a 100644
--- a/addons/vistaio/vistamesh.cc
+++ b/addons/vistaio/vistamesh.cc
@@ -150,7 +150,7 @@ static CTriangleMesh::PTrianglefield read_triangles(VistaIOGraph graph, size_t
// set triangle values
*t++ = node->t;
}else{
- cverr() <<"adressing vertexes " << node->t << "but have only"<<v_size<< "vertices\n";
+ cverr() <<"addressing vertexes " << node->t << " but have only "<<v_size<< "vertices\n";
cverr() <<"Bougus mesh: Triangle vertex out of bounds - bailing out\n";
return CTriangleMesh::PTrianglefield();
}
diff --git a/mia/2d/cost/ngf.cc b/mia/2d/cost/ngf.cc
index a2797ea..3f6aedf 100644
--- a/mia/2d/cost/ngf.cc
+++ b/mia/2d/cost/ngf.cc
@@ -263,7 +263,7 @@ C2DImageCost *C2DNFGImageCostPlugin::do_create()const
const string C2DNFGImageCostPlugin::do_get_descr()const
{
return "This function evaluates the image similarity based on normalized gradient fields. "
- "Various evaluation kernels are availabe.";
+ "Various evaluation kernels are available.";
}
diff --git a/mia/2d/filter/meanvar.cc b/mia/2d/filter/meanvar.cc
index f2055fd..33ca2db 100644
--- a/mia/2d/filter/meanvar.cc
+++ b/mia/2d/filter/meanvar.cc
@@ -140,8 +140,8 @@ C2DMeanVarImageFilterFactory::C2DMeanVarImageFilterFactory():
m_thresh(0.0)
{
add_parameter("w", make_lc_param(m_hw, 1, false, "filter width parameter"));
- add_parameter("thresh", make_lc_param(m_thresh, 0.0, false, "Intensity threshholding parameter: Pixels with intensities "
- "below this threshhold will be set to zero, and also not used when evaluating mean "
+ add_parameter("thresh", make_lc_param(m_thresh, 0.0, false, "Intensity thresholding parameter: Pixels with intensities "
+ "below this threshold will be set to zero, and also not used when evaluating mean "
"and variation"));
add_parameter("varfile", new CStringParameter(m_varfilename, CCmdOptionFlags::required_output,
"name of the output file to save the variation image too.",
diff --git a/mia/2d/filter/medianmad.cc b/mia/2d/filter/medianmad.cc
index 8ecabff..370e2f0 100644
--- a/mia/2d/filter/medianmad.cc
+++ b/mia/2d/filter/medianmad.cc
@@ -153,8 +153,8 @@ C2DMedianMadImageFilterFactory::C2DMedianMadImageFilterFactory():
m_thresh(0.0)
{
add_parameter("w", make_lc_param(m_hw, 1, false, "filter width parameter"));
- add_parameter("thresh", make_lc_param(m_thresh, 0.0, false, "Intensity threshholding parameter: Pixels with intensities "
- "below this threshhold will be set to zero, and also not used when evaluating mean "
+ add_parameter("thresh", make_lc_param(m_thresh, 0.0, false, "Intensity thresholding parameter: Pixels with intensities "
+ "below this threshold will be set to zero, and also not used when evaluating mean "
"and variation"));
add_parameter("madfile", new CStringParameter(m_madfilename, CCmdOptionFlags::required_output,
"name of the output file to save the median absolute deviation image too.",
diff --git a/mia/2d/filter/tmean.cc b/mia/2d/filter/tmean.cc
index 8ae27ee..20d2008 100644
--- a/mia/2d/filter/tmean.cc
+++ b/mia/2d/filter/tmean.cc
@@ -132,8 +132,8 @@ C2DFilter *C2DTmeanFilterPlugin::do_create()const
const string C2DTmeanFilterPlugin::do_get_descr()const
{
return "2D image thresholded tmean filter: The output pixel value is zero if the input pixel "
- "value is below the given threshhold, otherwise the pixels in the evaluation windows "
- "are only considered if the input pixel intensity is above the threshhold.";
+ "value is below the given threshold, otherwise the pixels in the evaluation windows "
+ "are only considered if the input pixel intensity is above the threshold.";
}
extern "C" EXPORT CPluginBase *get_plugin_interface()
diff --git a/mia/2d/fullcost.cc b/mia/2d/fullcost.cc
index fb32c91..7a4dcc1 100644
--- a/mia/2d/fullcost.cc
+++ b/mia/2d/fullcost.cc
@@ -37,7 +37,7 @@ TPluginHandler<C2DFullCostPlugin>::m_help =
"This class of cost functions evaluates the cost resulting from the "
"use of a certain transformation. This may include a penalty term that ensures "
"the smoothness of a transformation or the evaluation of a similarity measure "
- "between a transformed study data set and a refernce data set.";
+ "between a transformed study data set and a reference data set.";
EXPLICIT_INSTANCE_PLUGIN(C2DFullCost);
diff --git a/mia/2d/fullcost/image.cc b/mia/2d/fullcost/image.cc
index c25d482..444221b 100644
--- a/mia/2d/fullcost/image.cc
+++ b/mia/2d/fullcost/image.cc
@@ -150,7 +150,7 @@ void C2DImageFullCost::do_reinit()
throw runtime_error("C2DImageFullCost only works with images of equal size");
if (m_src->get_pixel_size() != m_ref->get_pixel_size()) {
- cvwarn() << "C2DImageFullCost: src and reference image are of differnet pixel dimensions:"
+ cvwarn() << "C2DImageFullCost: src and reference image are of different pixel dimensions:"
<< m_src->get_pixel_size() << " vs " << m_ref->get_pixel_size()
<< " This code doesn't honour this.\n";
}
diff --git a/mia/2d/fullcost/label.cc b/mia/2d/fullcost/label.cc
index b0bca34..72b970d 100644
--- a/mia/2d/fullcost/label.cc
+++ b/mia/2d/fullcost/label.cc
@@ -272,7 +272,7 @@ void C2DLabelFullCost::do_reinit()
throw runtime_error("C2DLabelFullCost only works with images of equal size");
if (m_src->get_pixel_size() != m_ref->get_pixel_size()) {
- cvwarn() << "C2DLabelFullCost: src and reference image are of differnet pixel dimensions:"
+ cvwarn() << "C2DLabelFullCost: src and reference image are of different pixel dimensions:"
<< m_src->get_pixel_size() << " vs " << m_ref->get_pixel_size()
<< " This code doesn't honour this.\n";
}
diff --git a/mia/2d/fullcost/maskedimage.cc b/mia/2d/fullcost/maskedimage.cc
index 774d90c..82557d3 100644
--- a/mia/2d/fullcost/maskedimage.cc
+++ b/mia/2d/fullcost/maskedimage.cc
@@ -242,7 +242,7 @@ void C2DMaskedImageFullCost::do_reinit()
if (m_src->get_pixel_size() != m_ref->get_pixel_size()) {
- cvwarn() << "C2DMaskedImageFullCost: moving and reference image are of differnet pixel dimensions."
+ cvwarn() << "C2DMaskedImageFullCost: moving and reference image are of different pixel dimensions."
<< "unless you optimize a transformation that supports global scaling this might "
<< "not be what you want to do\n";
}
diff --git a/mia/2d/segframe.cc b/mia/2d/segframe.cc
index e960443..23bd4c5 100644
--- a/mia/2d/segframe.cc
+++ b/mia/2d/segframe.cc
@@ -113,7 +113,7 @@ CSegFrame::CSegFrame(const Node& node, int version):
else if ((*i)->get_name() == "section") {
m_sections.push_back(CSegSection(**i, version));
}else {
- cvinfo() << "ignoring unsuported element '" << (*i)->get_name() << "'\n";
+ cvinfo() << "ignoring unsupported element '" << (*i)->get_name() << "'\n";
}
}
@@ -161,7 +161,7 @@ const CSegFrame::Sections& CSegFrame::get_sections()const
const CSegStar& CSegFrame::get_star() const
{
if (!m_has_star)
- cvwarn() << "CSegFrame::get_star(): returing fake star";
+ cvwarn() << "CSegFrame::get_star(): returning fake star";
return m_star;
}
diff --git a/mia/2d/splinetransformpenalty.cc b/mia/2d/splinetransformpenalty.cc
index f93a50a..660be65 100644
--- a/mia/2d/splinetransformpenalty.cc
+++ b/mia/2d/splinetransformpenalty.cc
@@ -128,7 +128,7 @@ TPluginHandler<C2DSplineTransformPenaltyPlugin>::m_help =
"This class provides the penalty put on spline based transformations "
"when considering image registration. This penalty term ensures "
"the smoothness of a transformation or the evaluation of a similarity measure "
- "between a transformed study data set and a refernce data set.";
+ "between a transformed study data set and a reference data set.";
EXPLICIT_INSTANCE_DERIVED_FACTORY_HANDLER(C2DSplineTransformPenalty, C2DSplineTransformPenaltyPlugin);
diff --git a/mia/2d/test_filter.cc b/mia/2d/test_filter.cc
index d0964b0..09c0270 100644
--- a/mia/2d/test_filter.cc
+++ b/mia/2d/test_filter.cc
@@ -50,7 +50,7 @@ BOOST_AUTO_TEST_CASE(test_available_filters)
#ifdef HAVE_MAXFLOW
test_data.insert("maxflow");
#endif
- test_availabe_plugins(handler, test_data);
+ test_available_plugins(handler, test_data);
}
BOOST_AUTO_TEST_CASE(test_run_filters)
diff --git a/mia/2d/test_splinetransformpenalty.cc b/mia/2d/test_splinetransformpenalty.cc
index b2e3abe..dffe877 100644
--- a/mia/2d/test_splinetransformpenalty.cc
+++ b/mia/2d/test_splinetransformpenalty.cc
@@ -237,8 +237,8 @@ C2DSplineTransformPenalty *C2DSplinePenaltyMock::do_clone() const
return result;
}
-BOOST_AUTO_TEST_CASE(test_available_plugins)
+BOOST_AUTO_TEST_CASE(test_available_plugins_spline_penalty)
{
std::set<std::string> test_data = {"divcurl"};
- test_availabe_plugins(C2DSplineTransformPenaltyPluginHandler::instance(), test_data);
+ test_available_plugins(C2DSplineTransformPenaltyPluginHandler::instance(), test_data);
}
diff --git a/mia/2d/transform/test_spline.cc b/mia/2d/transform/test_spline.cc
index 6b8564a..a0dc8d2 100644
--- a/mia/2d/transform/test_spline.cc
+++ b/mia/2d/transform/test_spline.cc
@@ -414,7 +414,7 @@ BOOST_FIXTURE_TEST_CASE( test_splines_pertuberate, TransformSplineFixture )
fill(v.begin(), v.end(), vv);
- // this location is hand-picked and is not really the position ofthe maximun
+ // this location is hand-picked and is not really the position of the maximun
// but only an approximation
float gamma = stransf.pertuberate(v);
C2DFVector lmg(12* scalex, 27 * scaley);
diff --git a/mia/3d/2dimagefifofilter.cc b/mia/3d/2dimagefifofilter.cc
index 2754a8c..4aaf719 100644
--- a/mia/3d/2dimagefifofilter.cc
+++ b/mia/3d/2dimagefifofilter.cc
@@ -121,7 +121,7 @@ TPluginHandler<C2DFifoFilterPlugin>::m_help =
"These filters work on a stack of 2D images in a 3D manner by interpreting the images of the stack "
"as slices of a 3D image. For spacial filters with a fixed filter width that is small compared to "
"the number of slices the filter is applied in a true 3D manner. "
- "For other filters, that would normaly require to work on the whole image domain at once, the "
+ "For other filters, that would normally require to work on the whole image domain at once, the "
"image filter is only applied to a subset of the images at a time which results in a quasi-3D processing "
" that may require additional post-processing.";
diff --git a/mia/3d/fifof/regiongrow.cc b/mia/3d/fifof/regiongrow.cc
index a7587cc..322fd00 100644
--- a/mia/3d/fifof/regiongrow.cc
+++ b/mia/3d/fifof/regiongrow.cc
@@ -205,7 +205,7 @@ const string C2DRegiongrowFifoFilterPlugin::do_get_descr() const
"a 3D image. The region growing is based on class probabilities obtained from "
"a c-means classification of the pixel intensities. One seed thresh is use to initiate "
"a region, and another (lower) threshold is used to stop the region growing. "
- "By holding a number of 3D slices in the working memory to allow the region to grow \""
+ "By holding a number of 3D slices in the working memory to permit the region to grow \""
"backwards \" in the stack a Quasi-3D processing is achieved. However, with complex "
"structures the region growing may not properly be segmented.";
}
diff --git a/mia/3d/fifof/rgg.cc b/mia/3d/fifof/rgg.cc
index c97eeee..fbc43d3 100644
--- a/mia/3d/fifof/rgg.cc
+++ b/mia/3d/fifof/rgg.cc
@@ -162,12 +162,12 @@ C2DRGGStackFilterFactory::C2DRGGStackFilterFactory():
{
add_parameter("map", new CStringParameter(m_seed_map, CCmdOptionFlags::required_input, "class probability map"));
add_parameter("st", new CFloatParameter(m_seed_thresh, 0.0, 1.0,
- false, "seed probability threshhold"));
+ false, "seed probability threshold"));
add_parameter("depth", new CIntParameter(m_depth, 1, 30,
false, "number of slices to keep during processing"));
add_parameter("gt", new CFloatParameter(m_gradient_thresh, 4.0,
numeric_limits<float>::max(),
- false, "gradient threshhold"));
+ false, "gradient threshold"));
}
diff --git a/mia/3d/filter/growmask.cc b/mia/3d/filter/growmask.cc
index 185aeae..aec4963 100644
--- a/mia/3d/filter/growmask.cc
+++ b/mia/3d/filter/growmask.cc
@@ -177,7 +177,7 @@ C3DDoGrowmask::result_type C3DDoGrowmask::operator () (const T3DImage<T>& data)
queue <seed_t<T> > pool;
if (data.get_size() != m_start_mask.get_size())
- throw invalid_argument("C3DGrowmask::filter: seed mask and reference must be ofthe same size");
+ throw invalid_argument("C3DGrowmask::filter: seed mask and reference must be of the same size");
C3DBitImage *r = new C3DBitImage(m_start_mask);
r->set_attributes(data.begin_attributes(), data.end_attributes());
P3DImage result(r);
diff --git a/mia/3d/fullcost/image.cc b/mia/3d/fullcost/image.cc
index 7bc6eb9..cdda37e 100644
--- a/mia/3d/fullcost/image.cc
+++ b/mia/3d/fullcost/image.cc
@@ -122,7 +122,7 @@ void C3DImageFullCost::do_reinit()
throw runtime_error("C3DImageFullCost only works with images of equal size");
if (m_src->get_voxel_size() != m_ref->get_voxel_size()) {
- cverr() << "C3DImageFullCost: src and reference image are of differnet pixel dimensions."
+ cverr() << "C3DImageFullCost: src and reference image are of different pixel dimensions."
<< "This code doesn't honour this and a proper scaling should be applied first.";
}
m_cost_kernel->set_reference(*m_ref_scaled);
diff --git a/mia/3d/fullcost/label.cc b/mia/3d/fullcost/label.cc
index 339a719..d591a56 100644
--- a/mia/3d/fullcost/label.cc
+++ b/mia/3d/fullcost/label.cc
@@ -257,7 +257,7 @@ void C3DLabelFullCost::do_reinit()
throw runtime_error("C3DLabelFullCost only works with images of equal size");
if (m_src->get_voxel_size() != m_ref->get_voxel_size()) {
- cvwarn() << "C3DLabelFullCost: src and reference image are of differnet voxel dimensions:"
+ cvwarn() << "C3DLabelFullCost: src and reference image are of different voxel dimensions:"
<< m_src->get_voxel_size() << " vs " << m_ref->get_voxel_size()
<< " This code doesn't honour this.\n";
}
diff --git a/mia/3d/fullcost/maskedimage.cc b/mia/3d/fullcost/maskedimage.cc
index 04d00c1..348b283 100644
--- a/mia/3d/fullcost/maskedimage.cc
+++ b/mia/3d/fullcost/maskedimage.cc
@@ -256,7 +256,7 @@ void C3DMaskedImageFullCost::do_reinit()
if (m_src->get_voxel_size() != m_ref->get_voxel_size()) {
- cvwarn() << "C3DMaskedImageFullCost: moving and reference image are of differnet pixel dimensions."
+ cvwarn() << "C3DMaskedImageFullCost: moving and reference image are of different pixel dimensions."
<< "unless you optimize a transformation that supports global scaling this might "
<< "not be what you want to do\n";
}
diff --git a/mia/3d/fullcost/taggedssd.cc b/mia/3d/fullcost/taggedssd.cc
index b27c39b..8d5acf1 100644
--- a/mia/3d/fullcost/taggedssd.cc
+++ b/mia/3d/fullcost/taggedssd.cc
@@ -359,7 +359,7 @@ void C3DTaggedSSDCost::do_reinit()
if (m_src[i]->get_voxel_size() != m_ref[i]->get_voxel_size()) {
- cverr() << "C3DImageFullCost: src and reference image are of differnet pixel dimensions."
+ cverr() << "C3DImageFullCost: src and reference image are of different pixel dimensions."
<< "This code doesn't honour this and a proper scaling should be applied first.";
}
}
diff --git a/mia/3d/splinetransformpenalty.cc b/mia/3d/splinetransformpenalty.cc
index 4357393..f9689b6 100644
--- a/mia/3d/splinetransformpenalty.cc
+++ b/mia/3d/splinetransformpenalty.cc
@@ -127,7 +127,7 @@ TPluginHandler<C3DSplineTransformPenaltyPlugin>::m_help =
"This class provides the penalty put on spline based transformations "
"when considering image registration. This penalty term ensures "
"the smoothness of a transformation or the evaluation of a similarity measure "
- "between a transformed study data set and a refernce data set.";
+ "between a transformed study data set and a reference data set.";
EXPLICIT_INSTANCE_DERIVED_FACTORY_HANDLER(C3DSplineTransformPenalty, C3DSplineTransformPenaltyPlugin);
diff --git a/mia/3d/test_landmarklistio.cc b/mia/3d/test_landmarklistio.cc
index 3bba025..fad01ff 100644
--- a/mia/3d/test_landmarklistio.cc
+++ b/mia/3d/test_landmarklistio.cc
@@ -26,10 +26,10 @@
NS_MIA_USE
using namespace std;
-BOOST_AUTO_TEST_CASE( test_available_plugins )
+BOOST_AUTO_TEST_CASE( test_available_plugins_landmarklistio )
{
set<string> expected_plugins = {"lmx", "datapool"};
- test_availabe_plugins(C3DLandmarklistIOPluginHandler::instance(), expected_plugins);
+ test_available_plugins(C3DLandmarklistIOPluginHandler::instance(), expected_plugins);
}
BOOST_AUTO_TEST_CASE( test_load_landmarklist_lmx )
diff --git a/mia/3d/test_splinetransformpenalty.cc b/mia/3d/test_splinetransformpenalty.cc
index 6fedc79..90ea3df 100644
--- a/mia/3d/test_splinetransformpenalty.cc
+++ b/mia/3d/test_splinetransformpenalty.cc
@@ -259,8 +259,8 @@ C3DSplineTransformPenalty *C3DSplinePenaltyMock::do_clone() const
}
-BOOST_AUTO_TEST_CASE(test_available_plugins)
+BOOST_AUTO_TEST_CASE(test_available_plugins_spline_penalty)
{
std::set<std::string> test_data = {"divcurl"};
- test_availabe_plugins(C3DSplineTransformPenaltyPluginHandler::instance(), test_data);
+ test_available_plugins(C3DSplineTransformPenaltyPluginHandler::instance(), test_data);
}
diff --git a/mia/3d/transform/spline.cc b/mia/3d/transform/spline.cc
index 4ebcf5f..2d8541c 100644
--- a/mia/3d/transform/spline.cc
+++ b/mia/3d/transform/spline.cc
@@ -999,7 +999,7 @@ C3DSplineTransformCreatorPlugin::C3DSplineTransformCreatorPlugin():
"will be overwritten by the 'rate' value."));
add_parameter("debug",
- new CBoolParameter(m_debug, false, "enable additional debuging output"));
+ new CBoolParameter(m_debug, false, "enable additional debugging output"));
add_parameter("penalty", make_param(m_penalty, "", false, "transformation penalty energy term"));
}
diff --git a/mia/3d/transform/test_spline.cc b/mia/3d/transform/test_spline.cc
index 67be069..f065978 100644
--- a/mia/3d/transform/test_spline.cc
+++ b/mia/3d/transform/test_spline.cc
@@ -556,7 +556,7 @@ BOOST_FIXTURE_TEST_CASE( test_splines_pertuberate, TransformSplineFixture )
fill(v.begin(), v.end(), vv);
- // this location is hand-picked and is not really the position ofthe maximun
+ // this location is hand-picked and is not really the position of the maximun
// but only an approximation
float gamma = stransf.pertuberate(v);
C3DFVector lmg(12* scalex, 27 * scaley);
diff --git a/mia/core/attributes.hh b/mia/core/attributes.hh
index ba71bd0..99d9a2b 100644
--- a/mia/core/attributes.hh
+++ b/mia/core/attributes.hh
@@ -150,7 +150,7 @@ private:
\ingroup basic
Helper function to get the value of an attribute. Thr function throws a bad_cast exception,
- if the attribute doesn't hold a value ofthe requested type T
+ if the attribute doesn't hold a value of the requested type T
\tparam T target type
\param attr attribute to be read
*/
@@ -250,7 +250,7 @@ EXPORT_CORE std::ostream& operator << (std::ostream& os, const CAttributeMap& d
\brief A collection of attributes
This is the base class for all data that uses attributes. It provides all the needed functions to store
- and retrive attributes.
+ and retrieve attributes.
*/
class EXPORT_CORE CAttributedData {
public:
diff --git a/mia/core/delayedparameter.hh b/mia/core/delayedparameter.hh
index 9a26e5d..97e71c8 100644
--- a/mia/core/delayedparameter.hh
+++ b/mia/core/delayedparameter.hh
@@ -91,7 +91,7 @@ const T TDelayedParameter<T>::get() const
{
if (!(CDatapool::instance().has_key(m_key))) {
throw create_exception<std::invalid_argument>("TDelayedParameter::get(): Key '", m_key,
- "' is not availabe in the data pool");
+ "' is not available in the data pool");
}
return boost::any_cast<T>(CDatapool::instance().get(m_key));
}
diff --git a/mia/core/fftslopeclassifier.cc b/mia/core/fftslopeclassifier.cc
index 84a19e7..0fe7b5d 100644
--- a/mia/core/fftslopeclassifier.cc
+++ b/mia/core/fftslopeclassifier.cc
@@ -215,7 +215,7 @@ CFFTSlopeClassifierImpl::CFFTSlopeClassifierImpl(const CFFTSlopeClassifier::Colu
/* mechanics for classifying the mixing curves:
- - sort the slopes that are below the periodic threshhold for high range and eliminate the
+ - sort the slopes that are below the periodic threshold for high range and eliminate the
other curves, they are perfusion or baseline
- sort these two curves by the order in which the high peaks appear to identify
which is RV (peak comes first) and which LV
diff --git a/mia/core/filetools.cc b/mia/core/filetools.cc
index aae1e3b..85e0e81 100644
--- a/mia/core/filetools.cc
+++ b/mia/core/filetools.cc
@@ -25,7 +25,6 @@
#include <boost/filesystem/path.hpp>
#include <boost/filesystem/operations.hpp> // includes boost/filesystem/path.hpp
#include <boost/filesystem/fstream.hpp> // ditto
-#include <boost/regex.hpp>
#include <mia/core/msgstream.hh>
#include <mia/core/filetools.hh>
diff --git a/mia/core/handler.cxx b/mia/core/handler.cxx
index 6ca3fc4..bda493d 100644
--- a/mia/core/handler.cxx
+++ b/mia/core/handler.cxx
@@ -28,7 +28,6 @@
#include <iterator>
#include <climits>
-#include <boost/regex.hpp>
#include <boost/filesystem/operations.hpp>
#include <mia/core/module.hh>
@@ -315,10 +314,10 @@ T& THandlerSingleton<T>::do_instance(bool require_initialization)
if (require_initialization) {
if (!m_is_initialized) {
- TRACE("Unitialized state");
+ TRACE("Uninitialized state");
CScopedLock lock_init(m_initialization_mutex);
if (!m_is_initialized) {
- TRACE("Enter locked unitialized state");
+ TRACE("Enter locked uninitialized state");
lock.release();
cvdebug() << "not yet initialized: second check passed\n";
me.initialise(m_searchpath);
diff --git a/mia/core/handler.hh b/mia/core/handler.hh
index 4788ec0..89ae04d 100644
--- a/mia/core/handler.hh
+++ b/mia/core/handler.hh
@@ -60,7 +60,7 @@ public:
typedef std::shared_ptr<I> PInterface;
- /// a map containing the names and theavailabe plug-ins
+ /// a map containing the names and the available plug-ins
typedef std::map<std::string, PInterface> CPluginMap;
/// the iterator to walk over the available plug-ins
diff --git a/mia/core/index.hh b/mia/core/index.hh
index 97af55f..d3812ee 100644
--- a/mia/core/index.hh
+++ b/mia/core/index.hh
@@ -39,7 +39,7 @@ class EXPORT_CORE CCircularIndex {
public:
/**
Construct the buffer
- \param size size ofthe buffer
+ \param size size of the buffer
\param start start index
*/
CCircularIndex(unsigned int size, unsigned int start);
diff --git a/mia/core/iohandler.hh b/mia/core/iohandler.hh
index 4c3511d..bb5f20f 100644
--- a/mia/core/iohandler.hh
+++ b/mia/core/iohandler.hh
@@ -53,7 +53,7 @@ public:
/// the IO interface provided by this handler
typedef typename TPluginHandler<I>::Interface Interface;
- /// an iterator over the availabe plug-ins
+ /// an iterator over the available plug-ins
typedef typename TPluginHandler<I>::const_iterator const_iterator;
/// The map that maps file name suffixes to IO plug-ins
diff --git a/mia/core/minimizer/gdas.cc b/mia/core/minimizer/gdas.cc
index 3d35c52..1478e4e 100644
--- a/mia/core/minimizer/gdas.cc
+++ b/mia/core/minimizer/gdas.cc
@@ -89,7 +89,7 @@ int CGDSAMinimizer::do_run(CDoubleVector& x)
if (f < f_old) {
- cvinfo() << "Successfull step: [" << iter << "]: f=" << f
+ cvinfo() << "Successful step: [" << iter << "]: f=" << f
<< ", gmax = " << gmax << ", step=" << step << "\n";
tries = 0;
@@ -140,7 +140,7 @@ int CGDSAMinimizer::do_run(CDoubleVector& x)
cvmsg() << "Stop: dx below given limit\n";
if (success & SUCCESS_FTOLR)
- cvmsg() << "Stop: relative cost funtion value decrease below limit "<< m_ftolr << ".\n";
+ cvmsg() << "Stop: relative cost function value decrease below limit "<< m_ftolr << ".\n";
return CMinimizer::success;
}
diff --git a/mia/core/minimizer/gsl.cc b/mia/core/minimizer/gsl.cc
index ce03afa..2828123 100644
--- a/mia/core/minimizer/gsl.cc
+++ b/mia/core/minimizer/gsl.cc
@@ -277,7 +277,7 @@ CGSLMinimizerPlugin::CGSLMinimizerPlugin():
const std::string CGSLMinimizerPlugin::do_get_descr() const
{
- return "optimizer plugin based on the multimin optimizers of"
+ return "optimizer plugin based on the multimin optimizers of "
"the GNU Scientific Library (GSL) https://www.gnu.org/software/gsl/";
}
diff --git a/mia/core/property_flags.hh b/mia/core/property_flags.hh
index 9e44509..cec0577 100644
--- a/mia/core/property_flags.hh
+++ b/mia/core/property_flags.hh
@@ -65,7 +65,7 @@ public:
bool has_all_in(const CPropertyFlagHolder& testset)const;
/**
- Evalaute the set of properties that is availabe in the testset but not in this one
+ Evalaute the set of properties that is available in the testset but not in this one
@param testset
@return set of missing flags
*/
diff --git a/mia/core/searchpath.cc b/mia/core/searchpath.cc
index 9ddb14f..def3102 100644
--- a/mia/core/searchpath.cc
+++ b/mia/core/searchpath.cc
@@ -17,15 +17,24 @@
* along with MIA; if not, see <http://www.gnu.org/licenses/>.
*
*/
+#include <mia/core/searchpath.hh>
+#include <mia/core/msgstream.hh>
+
#include <stdexcept>
#include <sstream>
#include <cstdlib>
-#include <mia/core/searchpath.hh>
-#include <mia/core/msgstream.hh>
-
+#if __cplusplus >= 201103
+#include <regex>
+using std::regex;
+using std::regex_match;
+#else
#include <boost/regex.hpp>
+using boost::regex;
+using boost::regex_match;
+#endif
+
#include <boost/filesystem/operations.hpp>
#include <config.h>
@@ -115,7 +124,8 @@ std::vector<PPluginModule> CPluginSearchpath::find_modules(const std::string& da
std::stringstream pattern;
pattern << ".*\\."<< MIA_MODULE_SUFFIX << "$";
- boost::regex pat_expr(pattern.str());
+
+ regex pat_expr(pattern.str());
std::vector<PPluginModule> result;
@@ -138,7 +148,7 @@ std::vector<PPluginModule> CPluginSearchpath::find_modules(const std::string& da
while (di != dend) {
cvdebug() << " candidate:'" << di->path().string() << "'";
- if (boost::regex_match(di->path().string(), pat_expr)) {
+ if (regex_match(di->path().string(), pat_expr)) {
candidates.push_back(*di);
cverb << " add\n";
}else
diff --git a/mia/core/slopeclassifier.hh b/mia/core/slopeclassifier.hh
index 023e4cd..ccc84f4 100644
--- a/mia/core/slopeclassifier.hh
+++ b/mia/core/slopeclassifier.hh
@@ -91,7 +91,7 @@ public:
/// @return the time index of the LV peak image or -1 if not identified
int get_LV_peak() const;
- /// \returns the absolute difference between the length ofthe longest and second longest curve in the list
+ /// \returns the absolute difference between the length of the longest and second longest curve in the list
float get_max_slope_length_diff() const;
/// \returns the maximum value of the correlation between the curves and the rows for which it occures
diff --git a/mia/core/utils.cc b/mia/core/utils.cc
index 6903f2a..73d23ea 100644
--- a/mia/core/utils.cc
+++ b/mia/core/utils.cc
@@ -22,14 +22,10 @@
#include <unistd.h>
#endif
-#ifndef WIN32
-#include <regex.h>
-#include <dirent.h>
-#else
+#ifdef WIN32
#include <direct.h>
#define getcwd _getcwd
#define chdir _chdir
-#define PATH_MAX 1024
#endif
#include <limits.h>
@@ -45,6 +41,11 @@
#include <mia/core/utils.hh>
#include <mia/core/msgstream.hh>
+// WIN32 and HURD don't define this
+#ifndef PATH_MAX
+#define PATH_MAX 1024
+#endif
+
NS_MIA_BEGIN
CCWDSaver::CCWDSaver():
@@ -64,68 +65,6 @@ CCWDSaver::~CCWDSaver()
delete[] cwd;
}
-#if 0
-static bool scan_dir(const std::string& path, const std::string& pattern, std::list<std::string>& list)
-{
- class TFindRegExp {
- regex_t preg;
- public:
- TFindRegExp(const std::string& pattern) {
- char buf[1024];
- int status = regcomp (&preg, pattern.c_str(), REG_EXTENDED |REG_NOSUB);
- if (status) {
- regerror(status, &preg, buf, 1024);
- std::cerr << buf << std::endl;
- }
- }
-
- ~TFindRegExp() {
- regfree(&preg);
- }
- bool check(const char *s) {
- return !regexec(&preg, s,0, NULL, 0);
- }
- };
-
-
- CCWDSaver __saver;
-
- if (chdir(path.c_str())) {
- //std::cerr << path << ":" << strerror(errno) << std::endl;
- return false;
- }
-
- struct dirent **namelist;
- int nfiles = scandir(".", &namelist, NULL , NULL);
-
- TFindRegExp searcher(pattern);
- for (int i = 0; i < nfiles; i++) {
- if (searcher.check(namelist[i]->d_name))
- list.push_back(path + std::string("/") + std::string(namelist[i]->d_name));
- free(namelist[i]);
-
- }
- free(namelist);
-
- return true;
-}
-
-
-FSearchFiles::FSearchFiles(std::list<std::string>& __result, const std::string& __pattern):
- result(__result),
- pattern(__pattern)
-{
-}
-
-void FSearchFiles::operator()(const std::string& path) {
- try {
- scan_dir(path, pattern, result);
- }
- catch (std::exception& e) {
- std::cerr << e.what();
- }
-}
-#endif
#ifndef _GNU_SOURCE
// there should be an intrinsic (at least on intel)
diff --git a/mia/core/vector.hh b/mia/core/vector.hh
index e1d79c7..c72a9af 100644
--- a/mia/core/vector.hh
+++ b/mia/core/vector.hh
@@ -151,7 +151,7 @@ public:
reference operator[] (size_t i) {
assert(i < m_size);
DEBUG_ASSERT_RELEASE_THROW(m_data && m_data.unique(),
- "TCArrayWrapper::operator[]: No writeable data availabe or not unique,"
+ "TCArrayWrapper::operator[]: No writeable data available or not unique,"
" call TCArrayWrapper::make_unique() first or enforce the use of "
"'TCArrayWrapper::operator[](...) const'");
return m_data.get()[i];
@@ -170,7 +170,7 @@ public:
*/
iterator begin() {
DEBUG_ASSERT_RELEASE_THROW(m_data && m_data.unique(),
- "TCArrayWrapper::begin(): No writeable data availabe or not unique, "
+ "TCArrayWrapper::begin(): No writeable data available or not unique, "
"call TCArrayWrapper::make_unique() first or enforce the use of "
"'TCArrayWrapper::begin() const'");
return m_data.get();
@@ -181,7 +181,7 @@ public:
*/
iterator end() {
DEBUG_ASSERT_RELEASE_THROW(m_data && m_data.unique(),
- "TCArrayWrapper::begin(): No writeable data availabe or not unique, "
+ "TCArrayWrapper::begin(): No writeable data available or not unique, "
"call TCArrayWrapper::make_unique() first or enforce the use of "
"'TCArrayWrapper::end() const'");
return m_data.get() + m_size;
diff --git a/mia/internal/pluginsettest.hh b/mia/internal/pluginsettest.hh
index be819de..8d2e185 100644
--- a/mia/internal/pluginsettest.hh
+++ b/mia/internal/pluginsettest.hh
@@ -26,7 +26,7 @@
#include <boost/test/unit_test.hpp>
template <typename Hander>
-void test_availabe_plugins(const Hander& handler, const std::set<std::string>& test)
+void test_available_plugins(const Hander& handler, const std::set<std::string>& test)
{
auto data = handler.get_set();
BOOST_CHECK_EQUAL(data.size(), test.size());
diff --git a/src/2deval-transformquantity.cc b/src/2deval-transformquantity.cc
index b0f7c83..e00ddca 100644
--- a/src/2deval-transformquantity.cc
+++ b/src/2deval-transformquantity.cc
@@ -160,7 +160,7 @@ int do_main( int argc, char *argv[] )
options.set_group("\nFile-IO");
options.add(make_opt( in_filename, "in-file", 'i',
"input point set, if this parameter is given a sparse evaluation "
- "of the quantity will be done, otherwise the quantity is evalutated "
+ "of the quantity will be done, otherwise the quantity is evaluated "
"for each grid point of the transformation range.", CCmdOptionFlags::required_input));
options.add(make_opt( out_filename, "out-file", 'o',
"output strains file, for a format description see above.", CCmdOptionFlags::required_output));
diff --git a/src/2dgroundtruthreg.cc b/src/2dgroundtruthreg.cc
index 3695512..dc141d4 100644
--- a/src/2dgroundtruthreg.cc
+++ b/src/2dgroundtruthreg.cc
@@ -45,7 +45,7 @@ const SProgramDescription g_description = {
{pdi_short, "Registration of a series of 2D images"},
{pdi_description, "This program implements the non-linear registration based on Pseudo "
"Ground Thruth for motion compensation of series of myocardial perfusion images as "
- "decribed in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion "
+ "described in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion "
"MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted "
"Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction "
"a preceding linear registration step is usually required."},
diff --git a/src/2dmyoica-full.cc b/src/2dmyoica-full.cc
index ed8376f..933c09d 100644
--- a/src/2dmyoica-full.cc
+++ b/src/2dmyoica-full.cc
@@ -365,7 +365,7 @@ float get_relative_min_breathing_frequency(const C2DImageSeries& images, int ski
double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
image_begin->get_attribute_as<double>(IDAcquisitionTime);
if (aq_time < 0)
- throw create_exception<runtime_error>("Got non-postive aquisition time range ", aq_time,
+ throw create_exception<runtime_error>("Got non-postive acquisition time range ", aq_time,
", can't handle this");
double heart_rate = 60 * n_heartbeats / aq_time;
@@ -493,7 +493,7 @@ int do_main( int argc, char *argv[] )
options.add(make_opt(min_breathing_frequency, "min-breathing-frequency", 'b',
"minimal mean frequency a mixing curve can have to be considered to stem from brething. "
"A healthy rest breating rate is 12 per minute. A negative value disables the test. "
- "A value 0.0 forces the series to be indentified as acquired with initial breath hold."));
+ "A value 0.0 forces the series to be identified as acquired with initial breath hold."));
if (options.parse(argc, argv) != CCmdOptionList::hr_no)
diff --git a/src/2dmyoica-nonrigid-parallel.cc b/src/2dmyoica-nonrigid-parallel.cc
index 0475779..929bfe4 100644
--- a/src/2dmyoica-nonrigid-parallel.cc
+++ b/src/2dmyoica-nonrigid-parallel.cc
@@ -199,7 +199,7 @@ float get_relative_min_breathing_frequency(const C2DImageSeries& images, int ski
double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
image_begin->get_attribute_as<double>(IDAcquisitionTime);
if (aq_time < 0)
- throw create_exception<runtime_error>("Got non-postive aquisition time range ", aq_time,
+ throw create_exception<runtime_error>("Got non-postive acquisition time range ", aq_time,
", can't handle this");
double heart_rate = 60 * n_heartbeats / aq_time;
diff --git a/src/2dmyoica-nonrigid.cc b/src/2dmyoica-nonrigid.cc
index 0c9fc55..3e79a16 100644
--- a/src/2dmyoica-nonrigid.cc
+++ b/src/2dmyoica-nonrigid.cc
@@ -163,7 +163,7 @@ float get_relative_min_breathing_frequency(const C2DImageSeries& images, int ski
double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
image_begin->get_attribute_as<double>(IDAcquisitionTime);
if (aq_time < 0)
- throw create_exception<runtime_error>("Got non-postive aquisition time range ", aq_time,
+ throw create_exception<runtime_error>("Got non-postive acquisition time range ", aq_time,
", can't handle this");
double heart_rate = 60 * n_heartbeats / aq_time;
diff --git a/src/2dmyoicapgt.cc b/src/2dmyoicapgt.cc
index 40f8ede..6b7c0c7 100644
--- a/src/2dmyoicapgt.cc
+++ b/src/2dmyoicapgt.cc
@@ -336,7 +336,7 @@ float get_relative_min_breathing_frequency(const C2DImageSeries& images, int ski
double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
image_begin->get_attribute_as<double>(IDAcquisitionTime);
if (aq_time < 0)
- throw create_exception<runtime_error>("Got non-postive aquisition time range ", aq_time,
+ throw create_exception<runtime_error>("Got non-postive acquisition time range ", aq_time,
", can't handle this");
double heart_rate = 60 * n_heartbeats / aq_time;
@@ -470,7 +470,7 @@ int do_main( int argc, char *argv[] )
options.add(make_opt(min_breathing_frequency, "min-breathing-frequency", 'b',
"minimal mean frequency a mixing curve can have to be considered to stem from brething. "
"A healthy rest breating rate is 12 per minute. A negative value disables the test. "
- "A value 0.0 forces the series to be indentified as acquired with initial breath hold."));
+ "A value 0.0 forces the series to be identified as acquired with initial breath hold."));
options.set_group("\nPseudo Ground Thruth estimation");
diff --git a/src/2dmyopgt-nonrigid.cc b/src/2dmyopgt-nonrigid.cc
index 212eafc..dab8d2e 100644
--- a/src/2dmyopgt-nonrigid.cc
+++ b/src/2dmyopgt-nonrigid.cc
@@ -44,7 +44,7 @@ const SProgramDescription g_description = {
{pdi_short, "Run a registration of a series of 2D images."},
{pdi_description, "This program implements the non-linear registration based on Pseudo Ground "
"Thruth for motion compensation of series of myocardial perfusion images given as a "
- "data set as decribed in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion "
+ "data set as described in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion "
"MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted "
"Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction "
"a preceding linear registration step is usually required."},
diff --git a/src/2dmyoseries-compdice.cc b/src/2dmyoseries-compdice.cc
index 80a180b..5da3c63 100644
--- a/src/2dmyoseries-compdice.cc
+++ b/src/2dmyoseries-compdice.cc
@@ -89,7 +89,7 @@ int do_main( int argc, char *argv[] )
throw invalid_argument("Both series must contain the same number of frames");
if (skip >= original_frames.size())
- throw create_exception<invalid_argument>( "skip (", skip, ") must be smaller then number of availabe frames(",
+ throw create_exception<invalid_argument>( "skip (", skip, ") must be smaller then number of available frames(",
original_frames.size(), ")");
diff --git a/src/2dsegment-local-cmeans.cc b/src/2dsegment-local-cmeans.cc
index a8a3cb4..fce6bc8 100644
--- a/src/2dsegment-local-cmeans.cc
+++ b/src/2dsegment-local-cmeans.cc
@@ -44,9 +44,9 @@ const SProgramDescription g_description = {
"in the image. The approach evaluates a global c-means clustering, and then "
"separates the image into overlapping regions where more c-means iterations "
"are run only including the locally present classes, i.e. the classes that "
- "relatively contain more pixels than a given threshhold."},
+ "relatively contain more pixels than a given threshold."},
{pdi_example_descr, "Run the segmentation on image test.png using three classes, "
- "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshhold of 0.01." },
+ "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01." },
{pdi_example_code, "-i test.png -o label.png -n 3 -g 20 -t 0.01"}
};
@@ -148,7 +148,7 @@ int do_main(int argc, char *argv[])
opts.add(make_opt( cmeans_epsilon, EParameterBounds::bf_min_open,
{0.0}, "c-means-epsilon", 'e', "c-means breaking condition for update tolerance"));
opts.add(make_opt( rel_cluster_threshold, EParameterBounds::bf_min_closed | EParameterBounds::bf_max_open,
- {0.0,1.0}, "relative-cluster-threshhold", 't', "Number of intensity classes to segment"));
+ {0.0,1.0}, "relative-cluster-threshold", 't', "Number of intensity classes to segment"));
if (opts.parse(argc, argv) != CCmdOptionList::hr_no)
diff --git a/src/2dsegment-local-kmeans.cc b/src/2dsegment-local-kmeans.cc
index c2a444c..a2210ad 100644
--- a/src/2dsegment-local-kmeans.cc
+++ b/src/2dsegment-local-kmeans.cc
@@ -43,9 +43,9 @@ const SProgramDescription g_description = {
"in the image. The approach evaluates a global k-means clustering, and then "
"separates the image into overlapping regions where more k-means iterations "
"are run only including the locally present classes, i.e. the classes that "
- "relatively contain more pixels than a given threshhold."},
+ "relatively contain more pixels than a given threshold."},
{pdi_example_descr, "Run the segmentation on image test.png using three classes, "
- "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshhold of 0.01." },
+ "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01." },
{pdi_example_code, "-i test.png -o label.png -n 3 -g 20 -t 0.01"}
};
@@ -110,7 +110,7 @@ int do_main(int argc, char *argv[])
opts.add(make_opt( n_classes, EParameterBounds::bf_closed_interval, {2u,127u},
"nclasses", 'n', "Number of intensity classes to segment"));
opts.add(make_opt( rel_cluster_threshold, EParameterBounds::bf_min_closed | EParameterBounds::bf_max_open,
- {0.0,1.0}, "relative-cluster-threshhold", 't', "Number of intensity classes to segment"));
+ {0.0,1.0}, "relative-cluster-threshold", 't', "Number of intensity classes to segment"));
diff --git a/src/2dsegment-per-pixel-kmeans.cc b/src/2dsegment-per-pixel-kmeans.cc
index 1098e37..e60ec24 100644
--- a/src/2dsegment-per-pixel-kmeans.cc
+++ b/src/2dsegment-per-pixel-kmeans.cc
@@ -45,9 +45,9 @@ const SProgramDescription g_description = {
"in the image. The approach evaluates a global k-means clustering, and then "
"separates the image into overlapping regions where more k-means iterations "
"are run only including the locally present classes, i.e. the classes that "
- "relatively contain more pixels than a given threshhold."},
+ "relatively contain more pixels than a given threshold."},
{pdi_example_descr, "Run the segmentation on image test.png using three classes, "
- "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshhold of 0.01." },
+ "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01." },
{pdi_example_code, "-i test.png -o label.png -n 3 -g 20 -t 0.01"}
};
@@ -106,7 +106,7 @@ int do_main(int argc, char *argv[])
opts.add(make_opt( n_classes, EParameterBounds::bf_closed_interval, {2u,127u},
"nclasses", 'n', "Number of intensity classes to segment"));
opts.add(make_opt( rel_cluster_threshold, EParameterBounds::bf_min_closed | EParameterBounds::bf_max_open,
- {0.0,1.0}, "relative-cluster-threshhold", 't', "Number of intensity classes to segment"));
+ {0.0,1.0}, "relative-cluster-threshold", 't', "Number of intensity classes to segment"));
diff --git a/src/2dseries2sets.cc b/src/2dseries2sets.cc
index e7220af..d23bcbd 100644
--- a/src/2dseries2sets.cc
+++ b/src/2dseries2sets.cc
@@ -41,9 +41,9 @@ const SProgramDescription g_description = {
"Used information is the z-location of the slice and the acquisition number. "
"The code is taylored to used the according descriptors defined in the DICOM standard. "
"All images with the same slice location will be grouped together in one segmentation "
- "set and ordered according to their aquisition number. "
+ "set and ordered according to their acquisition number. "
"Slice locations are rounded to three digits accuracy to make proper comparison "
- "of floating point values feasable."},
+ "of floating point values feasible."},
{pdi_example_descr, "Create the segmentation sets from a series of DICOM images and "
"copy the files to the output directory (copying is the default)."},
{pdi_example_code, "-o /home/user/series /net/dicoms/patient1/series1/*.dcm"}
@@ -60,8 +60,8 @@ vector<C2DImageVectorWithName> separate_slices(const C2DImageVectorWithName &ima
// collect series
// \todo maybe one should also look for SeriesNumber
typedef map<int, SImage> InstanceSeries;
- typedef map<int, InstanceSeries> AquisitionSeries;
- map<float, AquisitionSeries> series;
+ typedef map<int, InstanceSeries> AcquisitionSeries;
+ map<float, AcquisitionSeries> series;
int aq_number = 0;
int is_number = 0;
for (auto i = images.begin(); i != images.end(); ++i) {
@@ -74,10 +74,10 @@ vector<C2DImageVectorWithName> separate_slices(const C2DImageVectorWithName &ima
}
if (series.find(slice_location) == series.end()) {
cvmsg() << "Add location " << slice_location << "\n";
- series[slice_location] = AquisitionSeries();
+ series[slice_location] = AcquisitionSeries();
}
- AquisitionSeries& aqs = series[slice_location];
+ AcquisitionSeries& aqs = series[slice_location];
auto pAcquisitionNumber = dynamic_cast<const CIntAttribute *>(i->first->get_attribute(IDAcquisitionNumber).get());
if (pAcquisitionNumber) {
@@ -85,7 +85,7 @@ vector<C2DImageVectorWithName> separate_slices(const C2DImageVectorWithName &ima
}else {
++aq_number;
}
- cvmsg() << "Add aquisition " << aq_number << "\n";
+ cvmsg() << "Add acquisition " << aq_number << "\n";
if (aqs.find(aq_number) == aqs.end()) {
aqs[aq_number] = InstanceSeries();
@@ -102,7 +102,7 @@ vector<C2DImageVectorWithName> separate_slices(const C2DImageVectorWithName &ima
cvmsg() << "Add instance " << is_number << "\n";
if (is.find(is_number) != is.end()) {
- cvwarn() << "got duplicate slice aquisition/instance/location = "
+ cvwarn() << "got duplicate slice acquisition/instance/location = "
<< aq_number << "/" << is_number << "/" << slice_location
<< ", Ignoring this slice\n";
}else {
diff --git a/src/3ddistance-stats.cc b/src/3ddistance-stats.cc
index 4f14c90..467b664 100644
--- a/src/3ddistance-stats.cc
+++ b/src/3ddistance-stats.cc
@@ -50,7 +50,7 @@ const SProgramDescription g_description = {
" cat(result)\n"
" }\n\n"
},
- {pdi_example_descr, "Evaluate the distances for each label availabe in image.v to the "
+ {pdi_example_descr, "Evaluate the distances for each label available in image.v to the "
"corresponding labels in the image reference.v ans store the result "
"a coma separated list of values, i.e. distances.csv."},
{pdi_example_code, "-i image.v -r reference.v -o distances.csv" }
diff --git a/src/3deval-transformquantity.cc b/src/3deval-transformquantity.cc
index ff96582..911273f 100644
--- a/src/3deval-transformquantity.cc
+++ b/src/3deval-transformquantity.cc
@@ -160,7 +160,7 @@ int do_main( int argc, char *argv[] )
options.set_group("\nFile-IO");
options.add(make_opt( in_filename, "in-file", 'i',
"input point set, if this parameter is given a sparse evaluation "
- "of the quantity will be done, otherwise the quantity is evalutated "
+ "of the quantity will be done, otherwise the quantity is evaluated "
"for each grid point of the transformation range.", CCmdOptionFlags::input));
options.add(make_opt( out_filename, "out-file", 'o',
"output strains file, for a format description see above.", CCmdOptionFlags::required_output));
diff --git a/src/3dlandmarks-distances.cc b/src/3dlandmarks-distances.cc
index 2f1aed8..60d2031 100644
--- a/src/3dlandmarks-distances.cc
+++ b/src/3dlandmarks-distances.cc
@@ -34,7 +34,7 @@ const SProgramDescription g_description = {
{pdi_description,
"Evaluate Euclidian distances between the corresponding landmarks in two landmark sets. "
- "The programs prints out only values for landmarks that are availabe and have location "
+ "The programs prints out only values for landmarks that are available and have location "
"values in both sets "},
{pdi_example_descr,
diff --git a/src/fluid3d/main.cc b/src/fluid3d/main.cc
index 4cb57b2..66a18b5 100644
--- a/src/fluid3d/main.cc
+++ b/src/fluid3d/main.cc
@@ -63,7 +63,7 @@ enum TMethod { meth_sor,
const TDictMap<TMethod>::Table method_dict[] = {
- {"sor", meth_sor, "succesive overrelaxation"}
+ {"sor", meth_sor, "successive overrelaxation"}
,{"sora",meth_sorex, "Gauss Southwell relexation"}
// ,{"sorap",meth_sorap}
,{NULL, meth_sor, ""}
@@ -139,7 +139,7 @@ int do_main(int argc, char *argv[])
options.add(make_opt( params.InitialStepsize, "step", 0, "Initial stepsize"));
options.add(make_opt( interpolator_kernel, "bspline:d=3", "interpolator", 'p', "image interpolator kernel"));
options.add(make_opt( params.Overrelaxation, "relax", 0, "overrelaxation factor vor method sor"));
- options.add(make_opt( params.maxiter, "maxiter", 0, "maxium iterations"));
+ options.add(make_opt( params.maxiter, "maxiter", 0, "maximum iterations"));
options.add(make_opt( params.factor, "epsilon", 0, "truncation condition"));
options.add(make_opt( params.matter_threshold, "matter", 0, "intensity above which real "
"matter is assumed (experimental)"));
diff --git a/src/multihist.cc b/src/multihist.cc
index 1fb360e..0424f30 100644
--- a/src/multihist.cc
+++ b/src/multihist.cc
@@ -185,7 +185,7 @@ int do_main( int argc, char *argv[] )
options.add(make_opt( hmin, "min", 0, "minimum of histogram range"));
options.add(make_opt( hmax, "max", 0, "maximum of histogram range"));
options.add(make_opt( bins, "bins", 0, "number of histogram bins, set to zero to create a bin for "
- "each intensity value availabe in the input data. In this case the histogram "
+ "each intensity value available in the input data. In this case the histogram "
"range is also evaluated automatically"));
if (options.parse(argc, argv) != CCmdOptionList::hr_no)
diff --git a/src/plugin-help.cc b/src/plugin-help.cc
index 24768c4..3987a9a 100644
--- a/src/plugin-help.cc
+++ b/src/plugin-help.cc
@@ -33,7 +33,7 @@ NS_MIA_USE;
const SProgramDescription description = {
{pdi_group, "Help"},
{pdi_short, "Print help about plug-in groups"},
- {pdi_description, "This program is used to print out help about the availabel plug-ins\n"},
+ {pdi_description, "This program is used to print out help about the available plug-ins\n"},
{pdi_example_descr, "Print out the help about the 2D filter plugins .\n"},
{pdi_example_code, "filter/2d"}
};
--
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