[med-svn] [mia] 04/04: Update spellcheck patch
Gert Wollny
gert-guest at moszumanska.debian.org
Wed Jul 27 22:11:44 UTC 2016
This is an automated email from the git hooks/post-receive script.
gert-guest pushed a commit to branch master
in repository mia.
commit 3a0dcdf7841c7f31a4ea74917b7f5f0de58524df
Author: Gert Wollny <gw.fossdev at gmail.com>
Date: Wed Jul 27 22:10:58 2016 +0000
Update spellcheck patch
---
debian/patches/mia_242_spellcheck.patch | 234 ++++++++++----------------------
1 file changed, 75 insertions(+), 159 deletions(-)
diff --git a/debian/patches/mia_242_spellcheck.patch b/debian/patches/mia_242_spellcheck.patch
index 01b0a58..a636d25 100644
--- a/debian/patches/mia_242_spellcheck.patch
+++ b/debian/patches/mia_242_spellcheck.patch
@@ -4,11 +4,9 @@ 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 {
+@@ -88,7 +88,7 @@
typedef priority_queue<P2DImage, vector<P2DImage>, image_instance_less> CImageInstances;
typedef map<PAttribute, CImageInstances, attr_less> CImageSeries;
@@ -17,7 +15,7 @@ index 925831d..18dd317 100644
struct C3DImageCreator: public TFilter<bool> {
C3DImageCreator(size_t nz): m_nz(nz),
-@@ -194,7 +194,7 @@ C3DImageIOPlugin::PData CDicom3DImageIOPlugin::get_images(const vector<P2DImage>
+@@ -194,7 +194,7 @@
PData result(new Data);
@@ -26,7 +24,7 @@ index 925831d..18dd317 100644
// 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>
+@@ -205,7 +205,7 @@
[(*i)->get_attribute(IDSeriesNumber)].push(*i);
}else{
cvwarn() << "Discard image because of no "
@@ -35,11 +33,9 @@ index 925831d..18dd317 100644
<< ((*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)
+@@ -451,7 +451,7 @@
OFTime of_time;
success = dcm_time->getOFTime(of_time);
if (!success.good()) {
@@ -48,11 +44,9 @@ index 4316f90..ded4790 100644
return;
}
image.set_attribute(IDAcquisitionTime, of_time.getTimeInSeconds());
-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
+@@ -263,7 +263,7 @@
const string C2DNFGImageCostPlugin::do_get_descr()const
{
return "This function evaluates the image similarity based on normalized gradient fields. "
@@ -61,11 +55,9 @@ index a2797ea..3f6aedf 100644
}
-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():
+@@ -140,8 +140,8 @@
m_thresh(0.0)
{
add_parameter("w", make_lc_param(m_hw, 1, false, "filter width parameter"));
@@ -76,11 +68,9 @@ index f2055fd..33ca2db 100644
"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():
+@@ -153,8 +153,8 @@
m_thresh(0.0)
{
add_parameter("w", make_lc_param(m_hw, 1, false, "filter width parameter"));
@@ -91,11 +81,9 @@ index 8ecabff..370e2f0 100644
"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
+@@ -132,8 +132,8 @@
const string C2DTmeanFilterPlugin::do_get_descr()const
{
return "2D image thresholded tmean filter: The output pixel value is zero if the input pixel "
@@ -106,11 +94,9 @@ index 8ae27ee..20d2008 100644
}
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 =
+@@ -37,7 +37,7 @@
"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 "
@@ -119,11 +105,9 @@ index fb32c91..7a4dcc1 100644
EXPLICIT_INSTANCE_PLUGIN(C2DFullCost);
-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 =
+@@ -128,7 +128,7 @@
"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 "
@@ -132,11 +116,9 @@ index f93a50a..660be65 100644
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)
+@@ -50,7 +50,7 @@
#ifdef HAVE_MAXFLOW
test_data.insert("maxflow");
#endif
@@ -145,22 +127,22 @@ index d0964b0..09c0270 100644
}
BOOST_AUTO_TEST_CASE(test_run_filters)
-diff --git a/mia/2d/test_splinetransformpenalty.cc b/mia/2d/test_splinetransformpenalty.cc
-index b2e3abe..75f1e21 100644
--- a/mia/2d/test_splinetransformpenalty.cc
+++ b/mia/2d/test_splinetransformpenalty.cc
-@@ -240,5 +240,5 @@ C2DSplineTransformPenalty *C2DSplinePenaltyMock::do_clone() const
- BOOST_AUTO_TEST_CASE(test_available_plugins)
+@@ -237,8 +237,8 @@
+ 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 )
+@@ -414,7 +414,7 @@
fill(v.begin(), v.end(), vv);
@@ -169,11 +151,9 @@ index 6b8564a..a0dc8d2 100644
// 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 =
+@@ -121,7 +121,7 @@
"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. "
@@ -182,11 +162,9 @@ index 2754a8c..4aaf719 100644
"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/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():
+@@ -162,12 +162,12 @@
{
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,
@@ -201,11 +179,9 @@ index c97eeee..fbc43d3 100644
}
-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)
+@@ -177,7 +177,7 @@
queue <seed_t<T> > pool;
if (data.get_size() != m_start_mask.get_size())
@@ -214,11 +190,9 @@ index 185aeae..aec4963 100644
C3DBitImage *r = new C3DBitImage(m_start_mask);
r->set_attributes(data.begin_attributes(), data.end_attributes());
P3DImage result(r);
-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 =
+@@ -127,7 +127,7 @@
"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 "
@@ -227,12 +201,14 @@ index 4357393..f9689b6 100644
EXPLICIT_INSTANCE_DERIVED_FACTORY_HANDLER(C3DSplineTransformPenalty, C3DSplineTransformPenaltyPlugin);
-diff --git a/mia/3d/test_landmarklistio.cc b/mia/3d/test_landmarklistio.cc
-index 3bba025..e54dd76 100644
--- a/mia/3d/test_landmarklistio.cc
+++ b/mia/3d/test_landmarklistio.cc
-@@ -29,7 +29,7 @@ using namespace std;
- BOOST_AUTO_TEST_CASE( test_available_plugins )
+@@ -26,10 +26,10 @@
+ NS_MIA_USE
+ using namespace std;
+
+-BOOST_AUTO_TEST_CASE( test_available_plugins )
++BOOST_AUTO_TEST_CASE( test_available_plugins_landmark_listio )
{
set<string> expected_plugins = {"lmx", "datapool"};
- test_availabe_plugins(C3DLandmarklistIOPluginHandler::instance(), expected_plugins);
@@ -240,22 +216,22 @@ index 3bba025..e54dd76 100644
}
BOOST_AUTO_TEST_CASE( test_load_landmarklist_lmx )
-diff --git a/mia/3d/test_splinetransformpenalty.cc b/mia/3d/test_splinetransformpenalty.cc
-index 6fedc79..dd790ec 100644
--- a/mia/3d/test_splinetransformpenalty.cc
+++ b/mia/3d/test_splinetransformpenalty.cc
-@@ -262,5 +262,5 @@ C3DSplineTransformPenalty *C3DSplinePenaltyMock::do_clone() const
- BOOST_AUTO_TEST_CASE(test_available_plugins)
+@@ -259,8 +259,8 @@
+ }
+
+
+-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():
+@@ -999,7 +999,7 @@
"will be overwritten by the 'rate' value."));
add_parameter("debug",
@@ -264,11 +240,9 @@ index 4ebcf5f..2d8541c 100644
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 )
+@@ -556,7 +556,7 @@
fill(v.begin(), v.end(), vv);
@@ -277,11 +251,9 @@ index 67be069..f065978 100644
// 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:
+@@ -150,7 +150,7 @@
\ingroup basic
Helper function to get the value of an attribute. Thr function throws a bad_cast exception,
@@ -290,7 +262,7 @@ index ba71bd0..99d9a2b 100644
\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
+@@ -250,7 +250,7 @@
\brief A collection of attributes
This is the base class for all data that uses attributes. It provides all the needed functions to store
@@ -299,11 +271,9 @@ index ba71bd0..99d9a2b 100644
*/
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
+@@ -91,7 +91,7 @@
{
if (!(CDatapool::instance().has_key(m_key))) {
throw create_exception<std::invalid_argument>("TDelayedParameter::get(): Key '", m_key,
@@ -312,11 +282,9 @@ index 9a26e5d..97e71c8 100644
}
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
+@@ -215,7 +215,7 @@
/* mechanics for classifying the mixing curves:
@@ -325,11 +293,9 @@ index 84a19e7..0fe7b5d 100644
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..377791b 100644
--- a/mia/core/handler.cxx
+++ b/mia/core/handler.cxx
-@@ -314,7 +314,7 @@ T& THandlerSingleton<T>::do_instance(bool require_initialization)
+@@ -314,7 +314,7 @@
if (require_initialization) {
if (!m_is_initialized) {
@@ -338,11 +304,9 @@ index 92c8fcf..377791b 100644
CScopedLock lock_init(m_initialization_mutex);
if (!m_is_initialized) {
TRACE("Enter locked unitialized state");
-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:
+@@ -60,7 +60,7 @@
typedef std::shared_ptr<I> PInterface;
@@ -351,11 +315,9 @@ index 4788ec0..89ae04d 100644
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 {
+@@ -39,7 +39,7 @@
public:
/**
Construct the buffer
@@ -364,11 +326,9 @@ index 97af55f..d3812ee 100644
\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:
+@@ -53,7 +53,7 @@
/// the IO interface provided by this handler
typedef typename TPluginHandler<I>::Interface Interface;
@@ -377,11 +337,9 @@ index 4c3511d..bb5f20f 100644
typedef typename TPluginHandler<I>::const_iterator const_iterator;
/// The map that maps file name suffixes to IO plug-ins
-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:
+@@ -65,7 +65,7 @@
bool has_all_in(const CPropertyFlagHolder& testset)const;
/**
@@ -390,11 +348,9 @@ index 9e44509..cec0577 100644
@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:
+@@ -91,7 +91,7 @@
/// @return the time index of the LV peak image or -1 if not identified
int get_LV_peak() const;
@@ -403,11 +359,9 @@ index 023e4cd..ccc84f4 100644
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..26729a4 100644
--- a/mia/core/vector.hh
+++ b/mia/core/vector.hh
-@@ -151,7 +151,7 @@ public:
+@@ -151,7 +151,7 @@
reference operator[] (size_t i) {
assert(i < m_size);
DEBUG_ASSERT_RELEASE_THROW(m_data && m_data.unique(),
@@ -416,7 +370,7 @@ index e1d79c7..26729a4 100644
" call TCArrayWrapper::make_unique() first or enforce the use of "
"'TCArrayWrapper::operator[](...) const'");
return m_data.get()[i];
-@@ -170,7 +170,7 @@ public:
+@@ -170,7 +170,7 @@
*/
iterator begin() {
DEBUG_ASSERT_RELEASE_THROW(m_data && m_data.unique(),
@@ -425,8 +379,6 @@ index e1d79c7..26729a4 100644
"call TCArrayWrapper::make_unique() first or enforce the use of "
"'TCArrayWrapper::begin() const'");
return m_data.get();
-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 @@
@@ -438,11 +390,9 @@ index be819de..8d2e185 100644
{
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[] )
+@@ -160,7 +160,7 @@
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 "
@@ -451,11 +401,9 @@ index b0f7c83..e00ddca 100644
"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 = {
+@@ -45,7 +45,7 @@
{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 "
@@ -464,11 +412,9 @@ index 3695512..dc141d4 100644
"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..5066e22 100644
--- a/src/2dmyoica-full.cc
+++ b/src/2dmyoica-full.cc
-@@ -493,7 +493,7 @@ int do_main( int argc, char *argv[] )
+@@ -493,7 +493,7 @@
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. "
@@ -477,11 +423,9 @@ index ed8376f..5066e22 100644
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
+@@ -199,7 +199,7 @@
double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
image_begin->get_attribute_as<double>(IDAcquisitionTime);
if (aq_time < 0)
@@ -490,11 +434,9 @@ index 0475779..929bfe4 100644
", 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
+@@ -163,7 +163,7 @@
double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
image_begin->get_attribute_as<double>(IDAcquisitionTime);
if (aq_time < 0)
@@ -503,11 +445,9 @@ index 0c9fc55..3e79a16 100644
", 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
+@@ -336,7 +336,7 @@
double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
image_begin->get_attribute_as<double>(IDAcquisitionTime);
if (aq_time < 0)
@@ -516,7 +456,7 @@ index 40f8ede..6b7c0c7 100644
", can't handle this");
double heart_rate = 60 * n_heartbeats / aq_time;
-@@ -470,7 +470,7 @@ int do_main( int argc, char *argv[] )
+@@ -470,7 +470,7 @@
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. "
@@ -525,11 +465,9 @@ index 40f8ede..6b7c0c7 100644
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 = {
+@@ -44,7 +44,7 @@
{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 "
@@ -538,11 +476,9 @@ index 212eafc..dab8d2e 100644
"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[] )
+@@ -89,7 +89,7 @@
throw invalid_argument("Both series must contain the same number of frames");
if (skip >= original_frames.size())
@@ -551,11 +487,9 @@ index 80a180b..5da3c63 100644
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 = {
+@@ -44,9 +44,9 @@
"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 "
@@ -567,7 +501,7 @@ index a8a3cb4..fce6bc8 100644
{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[])
+@@ -148,7 +148,7 @@
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,
@@ -576,11 +510,9 @@ index a8a3cb4..fce6bc8 100644
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 = {
+@@ -43,9 +43,9 @@
"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 "
@@ -592,7 +524,7 @@ index c2a444c..a2210ad 100644
{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[])
+@@ -110,7 +110,7 @@
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,
@@ -601,11 +533,9 @@ index c2a444c..a2210ad 100644
-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 = {
+@@ -45,9 +45,9 @@
"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 "
@@ -617,7 +547,7 @@ index 1098e37..e60ec24 100644
{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[])
+@@ -106,7 +106,7 @@
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,
@@ -626,11 +556,9 @@ index 1098e37..e60ec24 100644
-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 = {
+@@ -41,9 +41,9 @@
"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 "
@@ -642,7 +570,7 @@ index e7220af..d23bcbd 100644
{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
+@@ -60,8 +60,8 @@
// collect series
// \todo maybe one should also look for SeriesNumber
typedef map<int, SImage> InstanceSeries;
@@ -653,7 +581,7 @@ index e7220af..d23bcbd 100644
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
+@@ -74,10 +74,10 @@
}
if (series.find(slice_location) == series.end()) {
cvmsg() << "Add location " << slice_location << "\n";
@@ -666,7 +594,7 @@ index e7220af..d23bcbd 100644
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
+@@ -85,7 +85,7 @@
}else {
++aq_number;
}
@@ -675,7 +603,7 @@ index e7220af..d23bcbd 100644
if (aqs.find(aq_number) == aqs.end()) {
aqs[aq_number] = InstanceSeries();
-@@ -102,7 +102,7 @@ vector<C2DImageVectorWithName> separate_slices(const C2DImageVectorWithName &ima
+@@ -102,7 +102,7 @@
cvmsg() << "Add instance " << is_number << "\n";
if (is.find(is_number) != is.end()) {
@@ -684,11 +612,9 @@ index e7220af..d23bcbd 100644
<< 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 = {
+@@ -50,7 +50,7 @@
" cat(result)\n"
" }\n\n"
},
@@ -697,11 +623,9 @@ index 4f14c90..467b664 100644
"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[] )
+@@ -160,7 +160,7 @@
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 "
@@ -710,11 +634,9 @@ index ff96582..911273f 100644
"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 = {
+@@ -34,7 +34,7 @@
{pdi_description,
"Evaluate Euclidian distances between the corresponding landmarks in two landmark sets. "
@@ -723,11 +645,9 @@ index 2f1aed8..60d2031 100644
"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,
+@@ -63,7 +63,7 @@
const TDictMap<TMethod>::Table method_dict[] = {
@@ -736,7 +656,7 @@ index 4cb57b2..66a18b5 100644
,{"sora",meth_sorex, "Gauss Southwell relexation"}
// ,{"sorap",meth_sorap}
,{NULL, meth_sor, ""}
-@@ -139,7 +139,7 @@ int do_main(int argc, char *argv[])
+@@ -139,7 +139,7 @@
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"));
@@ -745,11 +665,9 @@ index 4cb57b2..66a18b5 100644
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[] )
+@@ -185,7 +185,7 @@
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 "
@@ -758,11 +676,9 @@ index 1fb360e..0424f30 100644
"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;
+@@ -33,7 +33,7 @@
const SProgramDescription description = {
{pdi_group, "Help"},
{pdi_short, "Print help about plug-in groups"},
--
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