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