[med-svn] [mia] 03/04: d/p: remove patches applied upstream
Gert Wollny
gert-guest at moszumanska.debian.org
Wed Aug 24 17:32:37 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 b10cba7360d6d8375d74f2c73b9daae7de177a14
Author: Gert Wollny <gw.fossdev at gmail.com>
Date: Wed Aug 24 16:37:09 2016 +0000
d/p: remove patches applied upstream
---
debian/patches/mia_242_remove_boost_regex.patch | 245 ------
debian/patches/mia_242_spellcheck.patch | 981 ------------------------
debian/patches/series | 2 -
3 files changed, 1228 deletions(-)
diff --git a/debian/patches/mia_242_remove_boost_regex.patch b/debian/patches/mia_242_remove_boost_regex.patch
deleted file mode 100644
index 120b45a..0000000
--- a/debian/patches/mia_242_remove_boost_regex.patch
+++ /dev/null
@@ -1,245 +0,0 @@
-commit 1bf22a5ff3e137c9bf205ae966a323c9b3cc82eb
-Author: Gert Wollny <gw.fossdev at gmail.com>
-Date: Sun Jul 24 22:58:16 2016 +0200
-
- Enable use of std::regex
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 2bd89a3..4d8d5e2 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -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/addons/dicom/dcm3d.cc b/addons/dicom/dcm3d.cc
-index 33f1cf8..925831d 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>
-@@ -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/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..92c8fcf 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>
-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/utils.cc b/mia/core/utils.cc
-index 6903f2a..53e6027 100644
---- a/mia/core/utils.cc
-+++ b/mia/core/utils.cc
-@@ -22,10 +22,7 @@
- #include <unistd.h>
- #endif
-
--#ifndef WIN32
--#include <regex.h>
--#include <dirent.h>
--#else
-+#ifdef WIN32
- #include <direct.h>
- #define getcwd _getcwd
- #define chdir _chdir
-@@ -64,68 +61,6 @@ 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/debian/patches/mia_242_spellcheck.patch b/debian/patches/mia_242_spellcheck.patch
deleted file mode 100644
index a3c6d36..0000000
--- a/debian/patches/mia_242_spellcheck.patch
+++ /dev/null
@@ -1,981 +0,0 @@
-commit 7184c30f3611d785853821e8ada4f61bcfb634b5
-Author: Gert Wollny <gw.fossdev at gmail.com>
-Date: Wed Jul 27 22:51:41 2016 +0200
-
- correct spellings
-
-diff --git a/addons/dicom/dcm3d.cc b/addons/dicom/dcm3d.cc
-index 925831d..18dd317 100644
---- a/addons/dicom/dcm3d.cc
-+++ b/addons/dicom/dcm3d.cc
-@@ -88,7 +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),
-@@ -194,7 +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) {
-@@ -205,7 +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";
-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/handler.cxx b/mia/core/handler.cxx
-index 92c8fcf..bda493d 100644
---- a/mia/core/handler.cxx
-+++ b/mia/core/handler.cxx
-@@ -314,10 +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/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/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"}
- };
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 2d46791..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,2 +0,0 @@
-mia_242_remove_boost_regex.patch
-mia_242_spellcheck.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mia.git
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