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commit b10cba7360d6d8375d74f2c73b9daae7de177a14 Author: Gert Wollny <[email protected]> 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 <[email protected]> -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 <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
