[med-svn] [mia] 01/03: add spellcheck patch
Gert Wollny
gert-guest at moszumanska.debian.org
Thu Jul 28 18:53:22 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 901c5c7c88e3b0800555214aebc70b2fca8639f9
Author: Gert Wollny <gw.fossdev at gmail.com>
Date: Wed Jul 27 20:50:40 2016 +0000
add spellcheck patch
---
debian/patches/mia_242_spellcheck.patch | 981 ++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
2 files changed, 982 insertions(+)
diff --git a/debian/patches/mia_242_spellcheck.patch b/debian/patches/mia_242_spellcheck.patch
new file mode 100644
index 0000000..a3c6d36
--- /dev/null
+++ b/debian/patches/mia_242_spellcheck.patch
@@ -0,0 +1,981 @@
+commit 7184c30f3611d785853821e8ada4f61bcfb634b5
+Author: Gert Wollny <gw.fossdev at gmail.com>
+Date: Wed Jul 27 22:51:41 2016 +0200
+
+ correct spellings
+
+diff --git a/addons/dicom/dcm3d.cc b/addons/dicom/dcm3d.cc
+index 925831d..18dd317 100644
+--- a/addons/dicom/dcm3d.cc
++++ b/addons/dicom/dcm3d.cc
+@@ -88,7 +88,7 @@ struct image_instance_less {
+
+ typedef priority_queue<P2DImage, vector<P2DImage>, image_instance_less> CImageInstances;
+ typedef map<PAttribute, CImageInstances, attr_less> CImageSeries;
+-typedef map<PAttribute, CImageSeries, attr_less> CAquisitions;
++typedef map<PAttribute, CImageSeries, attr_less> CAcquisitions;
+
+ struct C3DImageCreator: public TFilter<bool> {
+ C3DImageCreator(size_t nz): m_nz(nz),
+@@ -194,7 +194,7 @@ C3DImageIOPlugin::PData CDicom3DImageIOPlugin::get_images(const vector<P2DImage>
+
+ PData result(new Data);
+
+- CAquisitions acc;
++ CAcquisitions acc;
+
+ // read all the images into a map
+ for(auto i = candidates.begin(); i != candidates.end(); ++i) {
+@@ -205,7 +205,7 @@ C3DImageIOPlugin::PData CDicom3DImageIOPlugin::get_images(const vector<P2DImage>
+ [(*i)->get_attribute(IDSeriesNumber)].push(*i);
+ }else{
+ cvwarn() << "Discard image because of no "
+- << ((*i)->has_attribute(IDAcquisitionNumber) ? "" : "aquisition")
++ << ((*i)->has_attribute(IDAcquisitionNumber) ? "" : "acquisition")
+ << ((*i)->has_attribute(IDInstanceNumber) ? "" : "instance")
+ << ((*i)->has_attribute(IDSeriesNumber) ? "" : "series")
+ << " number\n";
+diff --git a/addons/dicom/dicom4mia.cc b/addons/dicom/dicom4mia.cc
+index 4316f90..ded4790 100644
+--- a/addons/dicom/dicom4mia.cc
++++ b/addons/dicom/dicom4mia.cc
+@@ -451,7 +451,7 @@ void CDicomReaderData::getAcquisitionTimeIfAvailable(CAttributedData& image)
+ OFTime of_time;
+ success = dcm_time->getOFTime(of_time);
+ if (!success.good()) {
+- cverr() << "CDicomReader: Could not retrive OFTime string from DcmTime Element\n";
++ cverr() << "CDicomReader: Could not retrieve OFTime string from DcmTime Element\n";
+ return;
+ }
+ image.set_attribute(IDAcquisitionTime, of_time.getTimeInSeconds());
+diff --git a/addons/vistaio/vistamesh.cc b/addons/vistaio/vistamesh.cc
+index 35b8948..9d4833a 100644
+--- a/addons/vistaio/vistamesh.cc
++++ b/addons/vistaio/vistamesh.cc
+@@ -150,7 +150,7 @@ static CTriangleMesh::PTrianglefield read_triangles(VistaIOGraph graph, size_t
+ // set triangle values
+ *t++ = node->t;
+ }else{
+- cverr() <<"adressing vertexes " << node->t << "but have only"<<v_size<< "vertices\n";
++ cverr() <<"addressing vertexes " << node->t << " but have only "<<v_size<< "vertices\n";
+ cverr() <<"Bougus mesh: Triangle vertex out of bounds - bailing out\n";
+ return CTriangleMesh::PTrianglefield();
+ }
+diff --git a/mia/2d/cost/ngf.cc b/mia/2d/cost/ngf.cc
+index a2797ea..3f6aedf 100644
+--- a/mia/2d/cost/ngf.cc
++++ b/mia/2d/cost/ngf.cc
+@@ -263,7 +263,7 @@ C2DImageCost *C2DNFGImageCostPlugin::do_create()const
+ const string C2DNFGImageCostPlugin::do_get_descr()const
+ {
+ return "This function evaluates the image similarity based on normalized gradient fields. "
+- "Various evaluation kernels are availabe.";
++ "Various evaluation kernels are available.";
+ }
+
+
+diff --git a/mia/2d/filter/meanvar.cc b/mia/2d/filter/meanvar.cc
+index f2055fd..33ca2db 100644
+--- a/mia/2d/filter/meanvar.cc
++++ b/mia/2d/filter/meanvar.cc
+@@ -140,8 +140,8 @@ C2DMeanVarImageFilterFactory::C2DMeanVarImageFilterFactory():
+ m_thresh(0.0)
+ {
+ add_parameter("w", make_lc_param(m_hw, 1, false, "filter width parameter"));
+- add_parameter("thresh", make_lc_param(m_thresh, 0.0, false, "Intensity threshholding parameter: Pixels with intensities "
+- "below this threshhold will be set to zero, and also not used when evaluating mean "
++ add_parameter("thresh", make_lc_param(m_thresh, 0.0, false, "Intensity thresholding parameter: Pixels with intensities "
++ "below this threshold will be set to zero, and also not used when evaluating mean "
+ "and variation"));
+ add_parameter("varfile", new CStringParameter(m_varfilename, CCmdOptionFlags::required_output,
+ "name of the output file to save the variation image too.",
+diff --git a/mia/2d/filter/medianmad.cc b/mia/2d/filter/medianmad.cc
+index 8ecabff..370e2f0 100644
+--- a/mia/2d/filter/medianmad.cc
++++ b/mia/2d/filter/medianmad.cc
+@@ -153,8 +153,8 @@ C2DMedianMadImageFilterFactory::C2DMedianMadImageFilterFactory():
+ m_thresh(0.0)
+ {
+ add_parameter("w", make_lc_param(m_hw, 1, false, "filter width parameter"));
+- add_parameter("thresh", make_lc_param(m_thresh, 0.0, false, "Intensity threshholding parameter: Pixels with intensities "
+- "below this threshhold will be set to zero, and also not used when evaluating mean "
++ add_parameter("thresh", make_lc_param(m_thresh, 0.0, false, "Intensity thresholding parameter: Pixels with intensities "
++ "below this threshold will be set to zero, and also not used when evaluating mean "
+ "and variation"));
+ add_parameter("madfile", new CStringParameter(m_madfilename, CCmdOptionFlags::required_output,
+ "name of the output file to save the median absolute deviation image too.",
+diff --git a/mia/2d/filter/tmean.cc b/mia/2d/filter/tmean.cc
+index 8ae27ee..20d2008 100644
+--- a/mia/2d/filter/tmean.cc
++++ b/mia/2d/filter/tmean.cc
+@@ -132,8 +132,8 @@ C2DFilter *C2DTmeanFilterPlugin::do_create()const
+ const string C2DTmeanFilterPlugin::do_get_descr()const
+ {
+ return "2D image thresholded tmean filter: The output pixel value is zero if the input pixel "
+- "value is below the given threshhold, otherwise the pixels in the evaluation windows "
+- "are only considered if the input pixel intensity is above the threshhold.";
++ "value is below the given threshold, otherwise the pixels in the evaluation windows "
++ "are only considered if the input pixel intensity is above the threshold.";
+ }
+
+ extern "C" EXPORT CPluginBase *get_plugin_interface()
+diff --git a/mia/2d/fullcost.cc b/mia/2d/fullcost.cc
+index fb32c91..7a4dcc1 100644
+--- a/mia/2d/fullcost.cc
++++ b/mia/2d/fullcost.cc
+@@ -37,7 +37,7 @@ TPluginHandler<C2DFullCostPlugin>::m_help =
+ "This class of cost functions evaluates the cost resulting from the "
+ "use of a certain transformation. This may include a penalty term that ensures "
+ "the smoothness of a transformation or the evaluation of a similarity measure "
+- "between a transformed study data set and a refernce data set.";
++ "between a transformed study data set and a reference data set.";
+
+
+ EXPLICIT_INSTANCE_PLUGIN(C2DFullCost);
+diff --git a/mia/2d/fullcost/image.cc b/mia/2d/fullcost/image.cc
+index c25d482..444221b 100644
+--- a/mia/2d/fullcost/image.cc
++++ b/mia/2d/fullcost/image.cc
+@@ -150,7 +150,7 @@ void C2DImageFullCost::do_reinit()
+ throw runtime_error("C2DImageFullCost only works with images of equal size");
+
+ if (m_src->get_pixel_size() != m_ref->get_pixel_size()) {
+- cvwarn() << "C2DImageFullCost: src and reference image are of differnet pixel dimensions:"
++ cvwarn() << "C2DImageFullCost: src and reference image are of different pixel dimensions:"
+ << m_src->get_pixel_size() << " vs " << m_ref->get_pixel_size()
+ << " This code doesn't honour this.\n";
+ }
+diff --git a/mia/2d/fullcost/label.cc b/mia/2d/fullcost/label.cc
+index b0bca34..72b970d 100644
+--- a/mia/2d/fullcost/label.cc
++++ b/mia/2d/fullcost/label.cc
+@@ -272,7 +272,7 @@ void C2DLabelFullCost::do_reinit()
+ throw runtime_error("C2DLabelFullCost only works with images of equal size");
+
+ if (m_src->get_pixel_size() != m_ref->get_pixel_size()) {
+- cvwarn() << "C2DLabelFullCost: src and reference image are of differnet pixel dimensions:"
++ cvwarn() << "C2DLabelFullCost: src and reference image are of different pixel dimensions:"
+ << m_src->get_pixel_size() << " vs " << m_ref->get_pixel_size()
+ << " This code doesn't honour this.\n";
+ }
+diff --git a/mia/2d/fullcost/maskedimage.cc b/mia/2d/fullcost/maskedimage.cc
+index 774d90c..82557d3 100644
+--- a/mia/2d/fullcost/maskedimage.cc
++++ b/mia/2d/fullcost/maskedimage.cc
+@@ -242,7 +242,7 @@ void C2DMaskedImageFullCost::do_reinit()
+
+
+ if (m_src->get_pixel_size() != m_ref->get_pixel_size()) {
+- cvwarn() << "C2DMaskedImageFullCost: moving and reference image are of differnet pixel dimensions."
++ cvwarn() << "C2DMaskedImageFullCost: moving and reference image are of different pixel dimensions."
+ << "unless you optimize a transformation that supports global scaling this might "
+ << "not be what you want to do\n";
+ }
+diff --git a/mia/2d/segframe.cc b/mia/2d/segframe.cc
+index e960443..23bd4c5 100644
+--- a/mia/2d/segframe.cc
++++ b/mia/2d/segframe.cc
+@@ -113,7 +113,7 @@ CSegFrame::CSegFrame(const Node& node, int version):
+ else if ((*i)->get_name() == "section") {
+ m_sections.push_back(CSegSection(**i, version));
+ }else {
+- cvinfo() << "ignoring unsuported element '" << (*i)->get_name() << "'\n";
++ cvinfo() << "ignoring unsupported element '" << (*i)->get_name() << "'\n";
+ }
+ }
+
+@@ -161,7 +161,7 @@ const CSegFrame::Sections& CSegFrame::get_sections()const
+ const CSegStar& CSegFrame::get_star() const
+ {
+ if (!m_has_star)
+- cvwarn() << "CSegFrame::get_star(): returing fake star";
++ cvwarn() << "CSegFrame::get_star(): returning fake star";
+ return m_star;
+ }
+
+diff --git a/mia/2d/splinetransformpenalty.cc b/mia/2d/splinetransformpenalty.cc
+index f93a50a..660be65 100644
+--- a/mia/2d/splinetransformpenalty.cc
++++ b/mia/2d/splinetransformpenalty.cc
+@@ -128,7 +128,7 @@ TPluginHandler<C2DSplineTransformPenaltyPlugin>::m_help =
+ "This class provides the penalty put on spline based transformations "
+ "when considering image registration. This penalty term ensures "
+ "the smoothness of a transformation or the evaluation of a similarity measure "
+- "between a transformed study data set and a refernce data set.";
++ "between a transformed study data set and a reference data set.";
+
+
+ EXPLICIT_INSTANCE_DERIVED_FACTORY_HANDLER(C2DSplineTransformPenalty, C2DSplineTransformPenaltyPlugin);
+diff --git a/mia/2d/test_filter.cc b/mia/2d/test_filter.cc
+index d0964b0..09c0270 100644
+--- a/mia/2d/test_filter.cc
++++ b/mia/2d/test_filter.cc
+@@ -50,7 +50,7 @@ BOOST_AUTO_TEST_CASE(test_available_filters)
+ #ifdef HAVE_MAXFLOW
+ test_data.insert("maxflow");
+ #endif
+- test_availabe_plugins(handler, test_data);
++ test_available_plugins(handler, test_data);
+ }
+
+ BOOST_AUTO_TEST_CASE(test_run_filters)
+diff --git a/mia/2d/test_splinetransformpenalty.cc b/mia/2d/test_splinetransformpenalty.cc
+index b2e3abe..dffe877 100644
+--- a/mia/2d/test_splinetransformpenalty.cc
++++ b/mia/2d/test_splinetransformpenalty.cc
+@@ -237,8 +237,8 @@ C2DSplineTransformPenalty *C2DSplinePenaltyMock::do_clone() const
+ return result;
+ }
+
+-BOOST_AUTO_TEST_CASE(test_available_plugins)
++BOOST_AUTO_TEST_CASE(test_available_plugins_spline_penalty)
+ {
+ std::set<std::string> test_data = {"divcurl"};
+- test_availabe_plugins(C2DSplineTransformPenaltyPluginHandler::instance(), test_data);
++ test_available_plugins(C2DSplineTransformPenaltyPluginHandler::instance(), test_data);
+ }
+diff --git a/mia/2d/transform/test_spline.cc b/mia/2d/transform/test_spline.cc
+index 6b8564a..a0dc8d2 100644
+--- a/mia/2d/transform/test_spline.cc
++++ b/mia/2d/transform/test_spline.cc
+@@ -414,7 +414,7 @@ BOOST_FIXTURE_TEST_CASE( test_splines_pertuberate, TransformSplineFixture )
+
+ fill(v.begin(), v.end(), vv);
+
+- // this location is hand-picked and is not really the position ofthe maximun
++ // this location is hand-picked and is not really the position of the maximun
+ // but only an approximation
+ float gamma = stransf.pertuberate(v);
+ C2DFVector lmg(12* scalex, 27 * scaley);
+diff --git a/mia/3d/2dimagefifofilter.cc b/mia/3d/2dimagefifofilter.cc
+index 2754a8c..4aaf719 100644
+--- a/mia/3d/2dimagefifofilter.cc
++++ b/mia/3d/2dimagefifofilter.cc
+@@ -121,7 +121,7 @@ TPluginHandler<C2DFifoFilterPlugin>::m_help =
+ "These filters work on a stack of 2D images in a 3D manner by interpreting the images of the stack "
+ "as slices of a 3D image. For spacial filters with a fixed filter width that is small compared to "
+ "the number of slices the filter is applied in a true 3D manner. "
+- "For other filters, that would normaly require to work on the whole image domain at once, the "
++ "For other filters, that would normally require to work on the whole image domain at once, the "
+ "image filter is only applied to a subset of the images at a time which results in a quasi-3D processing "
+ " that may require additional post-processing.";
+
+diff --git a/mia/3d/fifof/regiongrow.cc b/mia/3d/fifof/regiongrow.cc
+index a7587cc..322fd00 100644
+--- a/mia/3d/fifof/regiongrow.cc
++++ b/mia/3d/fifof/regiongrow.cc
+@@ -205,7 +205,7 @@ const string C2DRegiongrowFifoFilterPlugin::do_get_descr() const
+ "a 3D image. The region growing is based on class probabilities obtained from "
+ "a c-means classification of the pixel intensities. One seed thresh is use to initiate "
+ "a region, and another (lower) threshold is used to stop the region growing. "
+- "By holding a number of 3D slices in the working memory to allow the region to grow \""
++ "By holding a number of 3D slices in the working memory to permit the region to grow \""
+ "backwards \" in the stack a Quasi-3D processing is achieved. However, with complex "
+ "structures the region growing may not properly be segmented.";
+ }
+diff --git a/mia/3d/fifof/rgg.cc b/mia/3d/fifof/rgg.cc
+index c97eeee..fbc43d3 100644
+--- a/mia/3d/fifof/rgg.cc
++++ b/mia/3d/fifof/rgg.cc
+@@ -162,12 +162,12 @@ C2DRGGStackFilterFactory::C2DRGGStackFilterFactory():
+ {
+ add_parameter("map", new CStringParameter(m_seed_map, CCmdOptionFlags::required_input, "class probability map"));
+ add_parameter("st", new CFloatParameter(m_seed_thresh, 0.0, 1.0,
+- false, "seed probability threshhold"));
++ false, "seed probability threshold"));
+ add_parameter("depth", new CIntParameter(m_depth, 1, 30,
+ false, "number of slices to keep during processing"));
+ add_parameter("gt", new CFloatParameter(m_gradient_thresh, 4.0,
+ numeric_limits<float>::max(),
+- false, "gradient threshhold"));
++ false, "gradient threshold"));
+ }
+
+
+diff --git a/mia/3d/filter/growmask.cc b/mia/3d/filter/growmask.cc
+index 185aeae..aec4963 100644
+--- a/mia/3d/filter/growmask.cc
++++ b/mia/3d/filter/growmask.cc
+@@ -177,7 +177,7 @@ C3DDoGrowmask::result_type C3DDoGrowmask::operator () (const T3DImage<T>& data)
+ queue <seed_t<T> > pool;
+
+ if (data.get_size() != m_start_mask.get_size())
+- throw invalid_argument("C3DGrowmask::filter: seed mask and reference must be ofthe same size");
++ throw invalid_argument("C3DGrowmask::filter: seed mask and reference must be of the same size");
+ C3DBitImage *r = new C3DBitImage(m_start_mask);
+ r->set_attributes(data.begin_attributes(), data.end_attributes());
+ P3DImage result(r);
+diff --git a/mia/3d/fullcost/image.cc b/mia/3d/fullcost/image.cc
+index 7bc6eb9..cdda37e 100644
+--- a/mia/3d/fullcost/image.cc
++++ b/mia/3d/fullcost/image.cc
+@@ -122,7 +122,7 @@ void C3DImageFullCost::do_reinit()
+ throw runtime_error("C3DImageFullCost only works with images of equal size");
+
+ if (m_src->get_voxel_size() != m_ref->get_voxel_size()) {
+- cverr() << "C3DImageFullCost: src and reference image are of differnet pixel dimensions."
++ cverr() << "C3DImageFullCost: src and reference image are of different pixel dimensions."
+ << "This code doesn't honour this and a proper scaling should be applied first.";
+ }
+ m_cost_kernel->set_reference(*m_ref_scaled);
+diff --git a/mia/3d/fullcost/label.cc b/mia/3d/fullcost/label.cc
+index 339a719..d591a56 100644
+--- a/mia/3d/fullcost/label.cc
++++ b/mia/3d/fullcost/label.cc
+@@ -257,7 +257,7 @@ void C3DLabelFullCost::do_reinit()
+ throw runtime_error("C3DLabelFullCost only works with images of equal size");
+
+ if (m_src->get_voxel_size() != m_ref->get_voxel_size()) {
+- cvwarn() << "C3DLabelFullCost: src and reference image are of differnet voxel dimensions:"
++ cvwarn() << "C3DLabelFullCost: src and reference image are of different voxel dimensions:"
+ << m_src->get_voxel_size() << " vs " << m_ref->get_voxel_size()
+ << " This code doesn't honour this.\n";
+ }
+diff --git a/mia/3d/fullcost/maskedimage.cc b/mia/3d/fullcost/maskedimage.cc
+index 04d00c1..348b283 100644
+--- a/mia/3d/fullcost/maskedimage.cc
++++ b/mia/3d/fullcost/maskedimage.cc
+@@ -256,7 +256,7 @@ void C3DMaskedImageFullCost::do_reinit()
+
+
+ if (m_src->get_voxel_size() != m_ref->get_voxel_size()) {
+- cvwarn() << "C3DMaskedImageFullCost: moving and reference image are of differnet pixel dimensions."
++ cvwarn() << "C3DMaskedImageFullCost: moving and reference image are of different pixel dimensions."
+ << "unless you optimize a transformation that supports global scaling this might "
+ << "not be what you want to do\n";
+ }
+diff --git a/mia/3d/fullcost/taggedssd.cc b/mia/3d/fullcost/taggedssd.cc
+index b27c39b..8d5acf1 100644
+--- a/mia/3d/fullcost/taggedssd.cc
++++ b/mia/3d/fullcost/taggedssd.cc
+@@ -359,7 +359,7 @@ void C3DTaggedSSDCost::do_reinit()
+
+
+ if (m_src[i]->get_voxel_size() != m_ref[i]->get_voxel_size()) {
+- cverr() << "C3DImageFullCost: src and reference image are of differnet pixel dimensions."
++ cverr() << "C3DImageFullCost: src and reference image are of different pixel dimensions."
+ << "This code doesn't honour this and a proper scaling should be applied first.";
+ }
+ }
+diff --git a/mia/3d/splinetransformpenalty.cc b/mia/3d/splinetransformpenalty.cc
+index 4357393..f9689b6 100644
+--- a/mia/3d/splinetransformpenalty.cc
++++ b/mia/3d/splinetransformpenalty.cc
+@@ -127,7 +127,7 @@ TPluginHandler<C3DSplineTransformPenaltyPlugin>::m_help =
+ "This class provides the penalty put on spline based transformations "
+ "when considering image registration. This penalty term ensures "
+ "the smoothness of a transformation or the evaluation of a similarity measure "
+- "between a transformed study data set and a refernce data set.";
++ "between a transformed study data set and a reference data set.";
+
+
+ EXPLICIT_INSTANCE_DERIVED_FACTORY_HANDLER(C3DSplineTransformPenalty, C3DSplineTransformPenaltyPlugin);
+diff --git a/mia/3d/test_landmarklistio.cc b/mia/3d/test_landmarklistio.cc
+index 3bba025..fad01ff 100644
+--- a/mia/3d/test_landmarklistio.cc
++++ b/mia/3d/test_landmarklistio.cc
+@@ -26,10 +26,10 @@
+ NS_MIA_USE
+ using namespace std;
+
+-BOOST_AUTO_TEST_CASE( test_available_plugins )
++BOOST_AUTO_TEST_CASE( test_available_plugins_landmarklistio )
+ {
+ set<string> expected_plugins = {"lmx", "datapool"};
+- test_availabe_plugins(C3DLandmarklistIOPluginHandler::instance(), expected_plugins);
++ test_available_plugins(C3DLandmarklistIOPluginHandler::instance(), expected_plugins);
+ }
+
+ BOOST_AUTO_TEST_CASE( test_load_landmarklist_lmx )
+diff --git a/mia/3d/test_splinetransformpenalty.cc b/mia/3d/test_splinetransformpenalty.cc
+index 6fedc79..90ea3df 100644
+--- a/mia/3d/test_splinetransformpenalty.cc
++++ b/mia/3d/test_splinetransformpenalty.cc
+@@ -259,8 +259,8 @@ C3DSplineTransformPenalty *C3DSplinePenaltyMock::do_clone() const
+ }
+
+
+-BOOST_AUTO_TEST_CASE(test_available_plugins)
++BOOST_AUTO_TEST_CASE(test_available_plugins_spline_penalty)
+ {
+ std::set<std::string> test_data = {"divcurl"};
+- test_availabe_plugins(C3DSplineTransformPenaltyPluginHandler::instance(), test_data);
++ test_available_plugins(C3DSplineTransformPenaltyPluginHandler::instance(), test_data);
+ }
+diff --git a/mia/3d/transform/spline.cc b/mia/3d/transform/spline.cc
+index 4ebcf5f..2d8541c 100644
+--- a/mia/3d/transform/spline.cc
++++ b/mia/3d/transform/spline.cc
+@@ -999,7 +999,7 @@ C3DSplineTransformCreatorPlugin::C3DSplineTransformCreatorPlugin():
+ "will be overwritten by the 'rate' value."));
+
+ add_parameter("debug",
+- new CBoolParameter(m_debug, false, "enable additional debuging output"));
++ new CBoolParameter(m_debug, false, "enable additional debugging output"));
+ add_parameter("penalty", make_param(m_penalty, "", false, "transformation penalty energy term"));
+
+ }
+diff --git a/mia/3d/transform/test_spline.cc b/mia/3d/transform/test_spline.cc
+index 67be069..f065978 100644
+--- a/mia/3d/transform/test_spline.cc
++++ b/mia/3d/transform/test_spline.cc
+@@ -556,7 +556,7 @@ BOOST_FIXTURE_TEST_CASE( test_splines_pertuberate, TransformSplineFixture )
+
+ fill(v.begin(), v.end(), vv);
+
+- // this location is hand-picked and is not really the position ofthe maximun
++ // this location is hand-picked and is not really the position of the maximun
+ // but only an approximation
+ float gamma = stransf.pertuberate(v);
+ C3DFVector lmg(12* scalex, 27 * scaley);
+diff --git a/mia/core/attributes.hh b/mia/core/attributes.hh
+index ba71bd0..99d9a2b 100644
+--- a/mia/core/attributes.hh
++++ b/mia/core/attributes.hh
+@@ -150,7 +150,7 @@ private:
+ \ingroup basic
+
+ Helper function to get the value of an attribute. Thr function throws a bad_cast exception,
+- if the attribute doesn't hold a value ofthe requested type T
++ if the attribute doesn't hold a value of the requested type T
+ \tparam T target type
+ \param attr attribute to be read
+ */
+@@ -250,7 +250,7 @@ EXPORT_CORE std::ostream& operator << (std::ostream& os, const CAttributeMap& d
+ \brief A collection of attributes
+
+ This is the base class for all data that uses attributes. It provides all the needed functions to store
+- and retrive attributes.
++ and retrieve attributes.
+ */
+ class EXPORT_CORE CAttributedData {
+ public:
+diff --git a/mia/core/delayedparameter.hh b/mia/core/delayedparameter.hh
+index 9a26e5d..97e71c8 100644
+--- a/mia/core/delayedparameter.hh
++++ b/mia/core/delayedparameter.hh
+@@ -91,7 +91,7 @@ const T TDelayedParameter<T>::get() const
+ {
+ if (!(CDatapool::instance().has_key(m_key))) {
+ throw create_exception<std::invalid_argument>("TDelayedParameter::get(): Key '", m_key,
+- "' is not availabe in the data pool");
++ "' is not available in the data pool");
+ }
+ return boost::any_cast<T>(CDatapool::instance().get(m_key));
+ }
+diff --git a/mia/core/fftslopeclassifier.cc b/mia/core/fftslopeclassifier.cc
+index 84a19e7..0fe7b5d 100644
+--- a/mia/core/fftslopeclassifier.cc
++++ b/mia/core/fftslopeclassifier.cc
+@@ -215,7 +215,7 @@ CFFTSlopeClassifierImpl::CFFTSlopeClassifierImpl(const CFFTSlopeClassifier::Colu
+
+
+ /* mechanics for classifying the mixing curves:
+- - sort the slopes that are below the periodic threshhold for high range and eliminate the
++ - sort the slopes that are below the periodic threshold for high range and eliminate the
+ other curves, they are perfusion or baseline
+ - sort these two curves by the order in which the high peaks appear to identify
+ which is RV (peak comes first) and which LV
+diff --git a/mia/core/handler.cxx b/mia/core/handler.cxx
+index 92c8fcf..bda493d 100644
+--- a/mia/core/handler.cxx
++++ b/mia/core/handler.cxx
+@@ -314,10 +314,10 @@ T& THandlerSingleton<T>::do_instance(bool require_initialization)
+
+ if (require_initialization) {
+ if (!m_is_initialized) {
+- TRACE("Unitialized state");
++ TRACE("Uninitialized state");
+ CScopedLock lock_init(m_initialization_mutex);
+ if (!m_is_initialized) {
+- TRACE("Enter locked unitialized state");
++ TRACE("Enter locked uninitialized state");
+ lock.release();
+ cvdebug() << "not yet initialized: second check passed\n";
+ me.initialise(m_searchpath);
+diff --git a/mia/core/handler.hh b/mia/core/handler.hh
+index 4788ec0..89ae04d 100644
+--- a/mia/core/handler.hh
++++ b/mia/core/handler.hh
+@@ -60,7 +60,7 @@ public:
+
+ typedef std::shared_ptr<I> PInterface;
+
+- /// a map containing the names and theavailabe plug-ins
++ /// a map containing the names and the available plug-ins
+ typedef std::map<std::string, PInterface> CPluginMap;
+
+ /// the iterator to walk over the available plug-ins
+diff --git a/mia/core/index.hh b/mia/core/index.hh
+index 97af55f..d3812ee 100644
+--- a/mia/core/index.hh
++++ b/mia/core/index.hh
+@@ -39,7 +39,7 @@ class EXPORT_CORE CCircularIndex {
+ public:
+ /**
+ Construct the buffer
+- \param size size ofthe buffer
++ \param size size of the buffer
+ \param start start index
+ */
+ CCircularIndex(unsigned int size, unsigned int start);
+diff --git a/mia/core/iohandler.hh b/mia/core/iohandler.hh
+index 4c3511d..bb5f20f 100644
+--- a/mia/core/iohandler.hh
++++ b/mia/core/iohandler.hh
+@@ -53,7 +53,7 @@ public:
+ /// the IO interface provided by this handler
+ typedef typename TPluginHandler<I>::Interface Interface;
+
+- /// an iterator over the availabe plug-ins
++ /// an iterator over the available plug-ins
+ typedef typename TPluginHandler<I>::const_iterator const_iterator;
+
+ /// The map that maps file name suffixes to IO plug-ins
+diff --git a/mia/core/minimizer/gdas.cc b/mia/core/minimizer/gdas.cc
+index 3d35c52..1478e4e 100644
+--- a/mia/core/minimizer/gdas.cc
++++ b/mia/core/minimizer/gdas.cc
+@@ -89,7 +89,7 @@ int CGDSAMinimizer::do_run(CDoubleVector& x)
+
+
+ if (f < f_old) {
+- cvinfo() << "Successfull step: [" << iter << "]: f=" << f
++ cvinfo() << "Successful step: [" << iter << "]: f=" << f
+ << ", gmax = " << gmax << ", step=" << step << "\n";
+
+ tries = 0;
+@@ -140,7 +140,7 @@ int CGDSAMinimizer::do_run(CDoubleVector& x)
+ cvmsg() << "Stop: dx below given limit\n";
+
+ if (success & SUCCESS_FTOLR)
+- cvmsg() << "Stop: relative cost funtion value decrease below limit "<< m_ftolr << ".\n";
++ cvmsg() << "Stop: relative cost function value decrease below limit "<< m_ftolr << ".\n";
+
+ return CMinimizer::success;
+ }
+diff --git a/mia/core/minimizer/gsl.cc b/mia/core/minimizer/gsl.cc
+index ce03afa..2828123 100644
+--- a/mia/core/minimizer/gsl.cc
++++ b/mia/core/minimizer/gsl.cc
+@@ -277,7 +277,7 @@ CGSLMinimizerPlugin::CGSLMinimizerPlugin():
+
+ const std::string CGSLMinimizerPlugin::do_get_descr() const
+ {
+- return "optimizer plugin based on the multimin optimizers of"
++ return "optimizer plugin based on the multimin optimizers of "
+ "the GNU Scientific Library (GSL) https://www.gnu.org/software/gsl/";
+ }
+
+diff --git a/mia/core/property_flags.hh b/mia/core/property_flags.hh
+index 9e44509..cec0577 100644
+--- a/mia/core/property_flags.hh
++++ b/mia/core/property_flags.hh
+@@ -65,7 +65,7 @@ public:
+ bool has_all_in(const CPropertyFlagHolder& testset)const;
+
+ /**
+- Evalaute the set of properties that is availabe in the testset but not in this one
++ Evalaute the set of properties that is available in the testset but not in this one
+ @param testset
+ @return set of missing flags
+ */
+diff --git a/mia/core/slopeclassifier.hh b/mia/core/slopeclassifier.hh
+index 023e4cd..ccc84f4 100644
+--- a/mia/core/slopeclassifier.hh
++++ b/mia/core/slopeclassifier.hh
+@@ -91,7 +91,7 @@ public:
+ /// @return the time index of the LV peak image or -1 if not identified
+ int get_LV_peak() const;
+
+- /// \returns the absolute difference between the length ofthe longest and second longest curve in the list
++ /// \returns the absolute difference between the length of the longest and second longest curve in the list
+ float get_max_slope_length_diff() const;
+
+ /// \returns the maximum value of the correlation between the curves and the rows for which it occures
+diff --git a/mia/core/vector.hh b/mia/core/vector.hh
+index e1d79c7..c72a9af 100644
+--- a/mia/core/vector.hh
++++ b/mia/core/vector.hh
+@@ -151,7 +151,7 @@ public:
+ reference operator[] (size_t i) {
+ assert(i < m_size);
+ DEBUG_ASSERT_RELEASE_THROW(m_data && m_data.unique(),
+- "TCArrayWrapper::operator[]: No writeable data availabe or not unique,"
++ "TCArrayWrapper::operator[]: No writeable data available or not unique,"
+ " call TCArrayWrapper::make_unique() first or enforce the use of "
+ "'TCArrayWrapper::operator[](...) const'");
+ return m_data.get()[i];
+@@ -170,7 +170,7 @@ public:
+ */
+ iterator begin() {
+ DEBUG_ASSERT_RELEASE_THROW(m_data && m_data.unique(),
+- "TCArrayWrapper::begin(): No writeable data availabe or not unique, "
++ "TCArrayWrapper::begin(): No writeable data available or not unique, "
+ "call TCArrayWrapper::make_unique() first or enforce the use of "
+ "'TCArrayWrapper::begin() const'");
+ return m_data.get();
+@@ -181,7 +181,7 @@ public:
+ */
+ iterator end() {
+ DEBUG_ASSERT_RELEASE_THROW(m_data && m_data.unique(),
+- "TCArrayWrapper::begin(): No writeable data availabe or not unique, "
++ "TCArrayWrapper::begin(): No writeable data available or not unique, "
+ "call TCArrayWrapper::make_unique() first or enforce the use of "
+ "'TCArrayWrapper::end() const'");
+ return m_data.get() + m_size;
+diff --git a/mia/internal/pluginsettest.hh b/mia/internal/pluginsettest.hh
+index be819de..8d2e185 100644
+--- a/mia/internal/pluginsettest.hh
++++ b/mia/internal/pluginsettest.hh
+@@ -26,7 +26,7 @@
+ #include <boost/test/unit_test.hpp>
+
+ template <typename Hander>
+-void test_availabe_plugins(const Hander& handler, const std::set<std::string>& test)
++void test_available_plugins(const Hander& handler, const std::set<std::string>& test)
+ {
+ auto data = handler.get_set();
+ BOOST_CHECK_EQUAL(data.size(), test.size());
+diff --git a/src/2deval-transformquantity.cc b/src/2deval-transformquantity.cc
+index b0f7c83..e00ddca 100644
+--- a/src/2deval-transformquantity.cc
++++ b/src/2deval-transformquantity.cc
+@@ -160,7 +160,7 @@ int do_main( int argc, char *argv[] )
+ options.set_group("\nFile-IO");
+ options.add(make_opt( in_filename, "in-file", 'i',
+ "input point set, if this parameter is given a sparse evaluation "
+- "of the quantity will be done, otherwise the quantity is evalutated "
++ "of the quantity will be done, otherwise the quantity is evaluated "
+ "for each grid point of the transformation range.", CCmdOptionFlags::required_input));
+ options.add(make_opt( out_filename, "out-file", 'o',
+ "output strains file, for a format description see above.", CCmdOptionFlags::required_output));
+diff --git a/src/2dgroundtruthreg.cc b/src/2dgroundtruthreg.cc
+index 3695512..dc141d4 100644
+--- a/src/2dgroundtruthreg.cc
++++ b/src/2dgroundtruthreg.cc
+@@ -45,7 +45,7 @@ const SProgramDescription g_description = {
+ {pdi_short, "Registration of a series of 2D images"},
+ {pdi_description, "This program implements the non-linear registration based on Pseudo "
+ "Ground Thruth for motion compensation of series of myocardial perfusion images as "
+- "decribed in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion "
++ "described in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion "
+ "MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted "
+ "Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction "
+ "a preceding linear registration step is usually required."},
+diff --git a/src/2dmyoica-full.cc b/src/2dmyoica-full.cc
+index ed8376f..933c09d 100644
+--- a/src/2dmyoica-full.cc
++++ b/src/2dmyoica-full.cc
+@@ -365,7 +365,7 @@ float get_relative_min_breathing_frequency(const C2DImageSeries& images, int ski
+ double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
+ image_begin->get_attribute_as<double>(IDAcquisitionTime);
+ if (aq_time < 0)
+- throw create_exception<runtime_error>("Got non-postive aquisition time range ", aq_time,
++ throw create_exception<runtime_error>("Got non-postive acquisition time range ", aq_time,
+ ", can't handle this");
+
+ double heart_rate = 60 * n_heartbeats / aq_time;
+@@ -493,7 +493,7 @@ int do_main( int argc, char *argv[] )
+ options.add(make_opt(min_breathing_frequency, "min-breathing-frequency", 'b',
+ "minimal mean frequency a mixing curve can have to be considered to stem from brething. "
+ "A healthy rest breating rate is 12 per minute. A negative value disables the test. "
+- "A value 0.0 forces the series to be indentified as acquired with initial breath hold."));
++ "A value 0.0 forces the series to be identified as acquired with initial breath hold."));
+
+
+ if (options.parse(argc, argv) != CCmdOptionList::hr_no)
+diff --git a/src/2dmyoica-nonrigid-parallel.cc b/src/2dmyoica-nonrigid-parallel.cc
+index 0475779..929bfe4 100644
+--- a/src/2dmyoica-nonrigid-parallel.cc
++++ b/src/2dmyoica-nonrigid-parallel.cc
+@@ -199,7 +199,7 @@ float get_relative_min_breathing_frequency(const C2DImageSeries& images, int ski
+ double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
+ image_begin->get_attribute_as<double>(IDAcquisitionTime);
+ if (aq_time < 0)
+- throw create_exception<runtime_error>("Got non-postive aquisition time range ", aq_time,
++ throw create_exception<runtime_error>("Got non-postive acquisition time range ", aq_time,
+ ", can't handle this");
+
+ double heart_rate = 60 * n_heartbeats / aq_time;
+diff --git a/src/2dmyoica-nonrigid.cc b/src/2dmyoica-nonrigid.cc
+index 0c9fc55..3e79a16 100644
+--- a/src/2dmyoica-nonrigid.cc
++++ b/src/2dmyoica-nonrigid.cc
+@@ -163,7 +163,7 @@ float get_relative_min_breathing_frequency(const C2DImageSeries& images, int ski
+ double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
+ image_begin->get_attribute_as<double>(IDAcquisitionTime);
+ if (aq_time < 0)
+- throw create_exception<runtime_error>("Got non-postive aquisition time range ", aq_time,
++ throw create_exception<runtime_error>("Got non-postive acquisition time range ", aq_time,
+ ", can't handle this");
+
+ double heart_rate = 60 * n_heartbeats / aq_time;
+diff --git a/src/2dmyoicapgt.cc b/src/2dmyoicapgt.cc
+index 40f8ede..6b7c0c7 100644
+--- a/src/2dmyoicapgt.cc
++++ b/src/2dmyoicapgt.cc
+@@ -336,7 +336,7 @@ float get_relative_min_breathing_frequency(const C2DImageSeries& images, int ski
+ double aq_time = image_end->get_attribute_as<double>(IDAcquisitionTime) -
+ image_begin->get_attribute_as<double>(IDAcquisitionTime);
+ if (aq_time < 0)
+- throw create_exception<runtime_error>("Got non-postive aquisition time range ", aq_time,
++ throw create_exception<runtime_error>("Got non-postive acquisition time range ", aq_time,
+ ", can't handle this");
+
+ double heart_rate = 60 * n_heartbeats / aq_time;
+@@ -470,7 +470,7 @@ int do_main( int argc, char *argv[] )
+ options.add(make_opt(min_breathing_frequency, "min-breathing-frequency", 'b',
+ "minimal mean frequency a mixing curve can have to be considered to stem from brething. "
+ "A healthy rest breating rate is 12 per minute. A negative value disables the test. "
+- "A value 0.0 forces the series to be indentified as acquired with initial breath hold."));
++ "A value 0.0 forces the series to be identified as acquired with initial breath hold."));
+
+
+ options.set_group("\nPseudo Ground Thruth estimation");
+diff --git a/src/2dmyopgt-nonrigid.cc b/src/2dmyopgt-nonrigid.cc
+index 212eafc..dab8d2e 100644
+--- a/src/2dmyopgt-nonrigid.cc
++++ b/src/2dmyopgt-nonrigid.cc
+@@ -44,7 +44,7 @@ const SProgramDescription g_description = {
+ {pdi_short, "Run a registration of a series of 2D images."},
+ {pdi_description, "This program implements the non-linear registration based on Pseudo Ground "
+ "Thruth for motion compensation of series of myocardial perfusion images given as a "
+- "data set as decribed in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion "
++ "data set as described in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion "
+ "MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted "
+ "Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction "
+ "a preceding linear registration step is usually required."},
+diff --git a/src/2dmyoseries-compdice.cc b/src/2dmyoseries-compdice.cc
+index 80a180b..5da3c63 100644
+--- a/src/2dmyoseries-compdice.cc
++++ b/src/2dmyoseries-compdice.cc
+@@ -89,7 +89,7 @@ int do_main( int argc, char *argv[] )
+ throw invalid_argument("Both series must contain the same number of frames");
+
+ if (skip >= original_frames.size())
+- throw create_exception<invalid_argument>( "skip (", skip, ") must be smaller then number of availabe frames(",
++ throw create_exception<invalid_argument>( "skip (", skip, ") must be smaller then number of available frames(",
+ original_frames.size(), ")");
+
+
+diff --git a/src/2dsegment-local-cmeans.cc b/src/2dsegment-local-cmeans.cc
+index a8a3cb4..fce6bc8 100644
+--- a/src/2dsegment-local-cmeans.cc
++++ b/src/2dsegment-local-cmeans.cc
+@@ -44,9 +44,9 @@ const SProgramDescription g_description = {
+ "in the image. The approach evaluates a global c-means clustering, and then "
+ "separates the image into overlapping regions where more c-means iterations "
+ "are run only including the locally present classes, i.e. the classes that "
+- "relatively contain more pixels than a given threshhold."},
++ "relatively contain more pixels than a given threshold."},
+ {pdi_example_descr, "Run the segmentation on image test.png using three classes, "
+- "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshhold of 0.01." },
++ "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01." },
+ {pdi_example_code, "-i test.png -o label.png -n 3 -g 20 -t 0.01"}
+ };
+
+@@ -148,7 +148,7 @@ int do_main(int argc, char *argv[])
+ opts.add(make_opt( cmeans_epsilon, EParameterBounds::bf_min_open,
+ {0.0}, "c-means-epsilon", 'e', "c-means breaking condition for update tolerance"));
+ opts.add(make_opt( rel_cluster_threshold, EParameterBounds::bf_min_closed | EParameterBounds::bf_max_open,
+- {0.0,1.0}, "relative-cluster-threshhold", 't', "Number of intensity classes to segment"));
++ {0.0,1.0}, "relative-cluster-threshold", 't', "Number of intensity classes to segment"));
+
+
+ if (opts.parse(argc, argv) != CCmdOptionList::hr_no)
+diff --git a/src/2dsegment-local-kmeans.cc b/src/2dsegment-local-kmeans.cc
+index c2a444c..a2210ad 100644
+--- a/src/2dsegment-local-kmeans.cc
++++ b/src/2dsegment-local-kmeans.cc
+@@ -43,9 +43,9 @@ const SProgramDescription g_description = {
+ "in the image. The approach evaluates a global k-means clustering, and then "
+ "separates the image into overlapping regions where more k-means iterations "
+ "are run only including the locally present classes, i.e. the classes that "
+- "relatively contain more pixels than a given threshhold."},
++ "relatively contain more pixels than a given threshold."},
+ {pdi_example_descr, "Run the segmentation on image test.png using three classes, "
+- "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshhold of 0.01." },
++ "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01." },
+ {pdi_example_code, "-i test.png -o label.png -n 3 -g 20 -t 0.01"}
+ };
+
+@@ -110,7 +110,7 @@ int do_main(int argc, char *argv[])
+ opts.add(make_opt( n_classes, EParameterBounds::bf_closed_interval, {2u,127u},
+ "nclasses", 'n', "Number of intensity classes to segment"));
+ opts.add(make_opt( rel_cluster_threshold, EParameterBounds::bf_min_closed | EParameterBounds::bf_max_open,
+- {0.0,1.0}, "relative-cluster-threshhold", 't', "Number of intensity classes to segment"));
++ {0.0,1.0}, "relative-cluster-threshold", 't', "Number of intensity classes to segment"));
+
+
+
+diff --git a/src/2dsegment-per-pixel-kmeans.cc b/src/2dsegment-per-pixel-kmeans.cc
+index 1098e37..e60ec24 100644
+--- a/src/2dsegment-per-pixel-kmeans.cc
++++ b/src/2dsegment-per-pixel-kmeans.cc
+@@ -45,9 +45,9 @@ const SProgramDescription g_description = {
+ "in the image. The approach evaluates a global k-means clustering, and then "
+ "separates the image into overlapping regions where more k-means iterations "
+ "are run only including the locally present classes, i.e. the classes that "
+- "relatively contain more pixels than a given threshhold."},
++ "relatively contain more pixels than a given threshold."},
+ {pdi_example_descr, "Run the segmentation on image test.png using three classes, "
+- "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshhold of 0.01." },
++ "local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01." },
+ {pdi_example_code, "-i test.png -o label.png -n 3 -g 20 -t 0.01"}
+ };
+
+@@ -106,7 +106,7 @@ int do_main(int argc, char *argv[])
+ opts.add(make_opt( n_classes, EParameterBounds::bf_closed_interval, {2u,127u},
+ "nclasses", 'n', "Number of intensity classes to segment"));
+ opts.add(make_opt( rel_cluster_threshold, EParameterBounds::bf_min_closed | EParameterBounds::bf_max_open,
+- {0.0,1.0}, "relative-cluster-threshhold", 't', "Number of intensity classes to segment"));
++ {0.0,1.0}, "relative-cluster-threshold", 't', "Number of intensity classes to segment"));
+
+
+
+diff --git a/src/2dseries2sets.cc b/src/2dseries2sets.cc
+index e7220af..d23bcbd 100644
+--- a/src/2dseries2sets.cc
++++ b/src/2dseries2sets.cc
+@@ -41,9 +41,9 @@ const SProgramDescription g_description = {
+ "Used information is the z-location of the slice and the acquisition number. "
+ "The code is taylored to used the according descriptors defined in the DICOM standard. "
+ "All images with the same slice location will be grouped together in one segmentation "
+- "set and ordered according to their aquisition number. "
++ "set and ordered according to their acquisition number. "
+ "Slice locations are rounded to three digits accuracy to make proper comparison "
+- "of floating point values feasable."},
++ "of floating point values feasible."},
+ {pdi_example_descr, "Create the segmentation sets from a series of DICOM images and "
+ "copy the files to the output directory (copying is the default)."},
+ {pdi_example_code, "-o /home/user/series /net/dicoms/patient1/series1/*.dcm"}
+@@ -60,8 +60,8 @@ vector<C2DImageVectorWithName> separate_slices(const C2DImageVectorWithName &ima
+ // collect series
+ // \todo maybe one should also look for SeriesNumber
+ typedef map<int, SImage> InstanceSeries;
+- typedef map<int, InstanceSeries> AquisitionSeries;
+- map<float, AquisitionSeries> series;
++ typedef map<int, InstanceSeries> AcquisitionSeries;
++ map<float, AcquisitionSeries> series;
+ int aq_number = 0;
+ int is_number = 0;
+ for (auto i = images.begin(); i != images.end(); ++i) {
+@@ -74,10 +74,10 @@ vector<C2DImageVectorWithName> separate_slices(const C2DImageVectorWithName &ima
+ }
+ if (series.find(slice_location) == series.end()) {
+ cvmsg() << "Add location " << slice_location << "\n";
+- series[slice_location] = AquisitionSeries();
++ series[slice_location] = AcquisitionSeries();
+ }
+
+- AquisitionSeries& aqs = series[slice_location];
++ AcquisitionSeries& aqs = series[slice_location];
+
+ auto pAcquisitionNumber = dynamic_cast<const CIntAttribute *>(i->first->get_attribute(IDAcquisitionNumber).get());
+ if (pAcquisitionNumber) {
+@@ -85,7 +85,7 @@ vector<C2DImageVectorWithName> separate_slices(const C2DImageVectorWithName &ima
+ }else {
+ ++aq_number;
+ }
+- cvmsg() << "Add aquisition " << aq_number << "\n";
++ cvmsg() << "Add acquisition " << aq_number << "\n";
+
+ if (aqs.find(aq_number) == aqs.end()) {
+ aqs[aq_number] = InstanceSeries();
+@@ -102,7 +102,7 @@ vector<C2DImageVectorWithName> separate_slices(const C2DImageVectorWithName &ima
+ cvmsg() << "Add instance " << is_number << "\n";
+
+ if (is.find(is_number) != is.end()) {
+- cvwarn() << "got duplicate slice aquisition/instance/location = "
++ cvwarn() << "got duplicate slice acquisition/instance/location = "
+ << aq_number << "/" << is_number << "/" << slice_location
+ << ", Ignoring this slice\n";
+ }else {
+diff --git a/src/3ddistance-stats.cc b/src/3ddistance-stats.cc
+index 4f14c90..467b664 100644
+--- a/src/3ddistance-stats.cc
++++ b/src/3ddistance-stats.cc
+@@ -50,7 +50,7 @@ const SProgramDescription g_description = {
+ " cat(result)\n"
+ " }\n\n"
+ },
+- {pdi_example_descr, "Evaluate the distances for each label availabe in image.v to the "
++ {pdi_example_descr, "Evaluate the distances for each label available in image.v to the "
+ "corresponding labels in the image reference.v ans store the result "
+ "a coma separated list of values, i.e. distances.csv."},
+ {pdi_example_code, "-i image.v -r reference.v -o distances.csv" }
+diff --git a/src/3deval-transformquantity.cc b/src/3deval-transformquantity.cc
+index ff96582..911273f 100644
+--- a/src/3deval-transformquantity.cc
++++ b/src/3deval-transformquantity.cc
+@@ -160,7 +160,7 @@ int do_main( int argc, char *argv[] )
+ options.set_group("\nFile-IO");
+ options.add(make_opt( in_filename, "in-file", 'i',
+ "input point set, if this parameter is given a sparse evaluation "
+- "of the quantity will be done, otherwise the quantity is evalutated "
++ "of the quantity will be done, otherwise the quantity is evaluated "
+ "for each grid point of the transformation range.", CCmdOptionFlags::input));
+ options.add(make_opt( out_filename, "out-file", 'o',
+ "output strains file, for a format description see above.", CCmdOptionFlags::required_output));
+diff --git a/src/3dlandmarks-distances.cc b/src/3dlandmarks-distances.cc
+index 2f1aed8..60d2031 100644
+--- a/src/3dlandmarks-distances.cc
++++ b/src/3dlandmarks-distances.cc
+@@ -34,7 +34,7 @@ const SProgramDescription g_description = {
+
+ {pdi_description,
+ "Evaluate Euclidian distances between the corresponding landmarks in two landmark sets. "
+- "The programs prints out only values for landmarks that are availabe and have location "
++ "The programs prints out only values for landmarks that are available and have location "
+ "values in both sets "},
+
+ {pdi_example_descr,
+diff --git a/src/fluid3d/main.cc b/src/fluid3d/main.cc
+index 4cb57b2..66a18b5 100644
+--- a/src/fluid3d/main.cc
++++ b/src/fluid3d/main.cc
+@@ -63,7 +63,7 @@ enum TMethod { meth_sor,
+
+
+ const TDictMap<TMethod>::Table method_dict[] = {
+- {"sor", meth_sor, "succesive overrelaxation"}
++ {"sor", meth_sor, "successive overrelaxation"}
+ ,{"sora",meth_sorex, "Gauss Southwell relexation"}
+ // ,{"sorap",meth_sorap}
+ ,{NULL, meth_sor, ""}
+@@ -139,7 +139,7 @@ int do_main(int argc, char *argv[])
+ options.add(make_opt( params.InitialStepsize, "step", 0, "Initial stepsize"));
+ options.add(make_opt( interpolator_kernel, "bspline:d=3", "interpolator", 'p', "image interpolator kernel"));
+ options.add(make_opt( params.Overrelaxation, "relax", 0, "overrelaxation factor vor method sor"));
+- options.add(make_opt( params.maxiter, "maxiter", 0, "maxium iterations"));
++ options.add(make_opt( params.maxiter, "maxiter", 0, "maximum iterations"));
+ options.add(make_opt( params.factor, "epsilon", 0, "truncation condition"));
+ options.add(make_opt( params.matter_threshold, "matter", 0, "intensity above which real "
+ "matter is assumed (experimental)"));
+diff --git a/src/multihist.cc b/src/multihist.cc
+index 1fb360e..0424f30 100644
+--- a/src/multihist.cc
++++ b/src/multihist.cc
+@@ -185,7 +185,7 @@ int do_main( int argc, char *argv[] )
+ options.add(make_opt( hmin, "min", 0, "minimum of histogram range"));
+ options.add(make_opt( hmax, "max", 0, "maximum of histogram range"));
+ options.add(make_opt( bins, "bins", 0, "number of histogram bins, set to zero to create a bin for "
+- "each intensity value availabe in the input data. In this case the histogram "
++ "each intensity value available in the input data. In this case the histogram "
+ "range is also evaluated automatically"));
+
+ if (options.parse(argc, argv) != CCmdOptionList::hr_no)
+diff --git a/src/plugin-help.cc b/src/plugin-help.cc
+index 24768c4..3987a9a 100644
+--- a/src/plugin-help.cc
++++ b/src/plugin-help.cc
+@@ -33,7 +33,7 @@ NS_MIA_USE;
+ const SProgramDescription description = {
+ {pdi_group, "Help"},
+ {pdi_short, "Print help about plug-in groups"},
+- {pdi_description, "This program is used to print out help about the availabel plug-ins\n"},
++ {pdi_description, "This program is used to print out help about the available plug-ins\n"},
+ {pdi_example_descr, "Print out the help about the 2D filter plugins .\n"},
+ {pdi_example_code, "filter/2d"}
+ };
diff --git a/debian/patches/series b/debian/patches/series
index 7523198..2d46791 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
mia_242_remove_boost_regex.patch
+mia_242_spellcheck.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mia.git
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