[med-svn] [Git][med-team/mia][master] 11 commits: Revert "Deactivate autopkgtest"
Yavor Doganov (@yavor-guest)
gitlab at salsa.debian.org
Mon Oct 20 11:40:56 BST 2025
Yavor Doganov pushed to branch master at Debian Med / mia
Commits:
b5f9c72b by Yavor Doganov at 2025-10-19T14:52:28+03:00
Revert "Deactivate autopkgtest"
This reverts commit 53185d85b28dd2eb4c8dbadf1a72c98c9bd4b2ba.
- - - - -
e5815100 by Yavor Doganov at 2025-10-19T20:28:41+03:00
Run the upstream testsuite as autopkgtest.
I couldn't find another (easy) way to test the library functionality.
- - - - -
1e2fe412 by Yavor Doganov at 2025-10-20T07:33:24+03:00
groff-warnings.patch: New.
- - - - -
f4566dbe by Yavor Doganov at 2025-10-20T09:05:09+03:00
spelling-errors.patch: New.
- - - - -
a50c9ae8 by Yavor Doganov at 2025-10-20T12:34:28+03:00
Fix DEP-3 headers.
- - - - -
30cc13a1 by Yavor Doganov at 2025-10-20T13:00:48+03:00
Remove unused lintian overrides.
- - - - -
115677f8 by Yavor Doganov at 2025-10-20T13:14:38+03:00
watch: Upgrade to version 5.
- - - - -
32a5412b by Yavor Doganov at 2025-10-20T13:15:43+03:00
copyright: Update copyright years for Debian packaging.
- - - - -
78eaf79d by Yavor Doganov at 2025-10-20T13:17:22+03:00
(Build-Depends): Require libvtk9-dev (>= 9.5) for the ongoing transition.
- - - - -
4b7ac1c2 by Yavor Doganov at 2025-10-20T13:18:13+03:00
(Rules-Requires-Root): Remove; it's the default.
- - - - -
d4c0ec86 by Yavor Doganov at 2025-10-20T13:20:34+03:00
(Standards-Version): Claim compliance with 4.7.2; no changes needed.
- - - - -
21 changed files:
- − debian/README.test
- debian/changelog
- debian/control
- debian/copyright
- − debian/docs
- debian/libmia-2.4-4.lintian-overrides
- debian/libmia-2.4-doc.examples
- debian/libmia-2.4-doc.install
- − debian/libmia-2.4-doc.lintian-overrides
- debian/mia-tools.lintian-overrides
- debian/patches/fix-g++11.diff
- debian/patches/fix-gcc-13.patch
- + debian/patches/groff-warnings.patch
- debian/patches/series
- + debian/patches/spelling-errors.patch
- debian/patches/vtk9.patch
- + debian/tests/control
- − debian/tests/control_autopkgtest_does_not_work
- − debian/tests/run-unit-test
- + debian/tests/testsuite
- debian/watch
Changes:
=====================================
debian/README.test deleted
=====================================
@@ -1,8 +0,0 @@
-Notes on how this package can be tested.
-────────────────────────────────────────
-
-This package can be tested by running the provided test:
-
- sh run-unit-test
-
-in order to confirm its integrity.
\ No newline at end of file
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-mia (2.4.7-14) UNRELEASED; urgency=medium
+mia (2.4.7-14) unstable; urgency=medium
[ ikeadeoyin ]
* Team upload.
@@ -7,6 +7,11 @@ mia (2.4.7-14) UNRELEASED; urgency=medium
[ Yavor Doganov ]
* debian/patches/gcc-14.patch: New; fix FTBFS with GCC 14 and 15
(Closes: #1075270).
+ * debian/patches/groff-warnings.patch: New.
+ * debian/patches/spelling-errors.patch: Likewise.
+ * debian/patches/vtk9.patch: Fix DEP-3 headers.
+ * debian/patches/fix-g++11.diff: Likewise.
+ * debian/patches/fix-gcc-13.patch: Likewise.
* debian/rules: Remove workarounds for mips and mipsel.
(DEB_CXXFLAGS_MAINT_APPEND): Define conditionally to reduce the log
size for the Salsa CI build only.
@@ -16,9 +21,32 @@ mia (2.4.7-14) UNRELEASED; urgency=medium
fails only on Salsa CI, probably due to some limitations there.
* debian/salsa-ci.yml (build): Forcefully delete .buildinfo/.changes.
Change build command to reduce the log and obtain something useful.
- * debian/control (libmia-2.4-4): Mark as Multi-Arch: same.
-
- -- ikeadeoyin <ikeadeoyin at gmail.com> Wed, 18 Oct 2023 21:43:53 -0400
+ * debian/control (Build-Depends): Require libvtk9-dev (>= 9.5) for the
+ ongoing vtk9 library transition.
+ (Rules-Requires-Root): Remove; it's the default.
+ (Standards-Version): Claim compliance with 4.7.2; no changes needed.
+ (libmia-2.4-4): Mark as Multi-Arch: same.
+ * debian/tests/testsuite: New test; run the whole testsuite. This is
+ likely to timeout on some architectures.
+ * debian/tests/control (Tests): Set to testsuite.
+ (Depends): Set to @builddeps@ only.
+ (Restrictions): Add build-needed.
+ * debian/tests/run-unit-test: Delete; these tests are part of the
+ testsuite and cannot be run in isolation without a built tree.
+ * debian/README.test: Delete.
+ * debian/docs: Likewise.
+ * debian/libmia-2.4-doc.install: Remove config.h.
+ * debian/libmia-2.4-doc.examples: Replace test/testdata with
+ examples/2d/filter/*. The latter is equally useless as examples but
+ at least silence a Lintian complaint in pedantic mode.
+ * debian/libmia-2.4-doc.lintian-overrides: Delete; unused.
+ * debian/libmia-2.4-4.lintian-overrides: Fix typo in the comment.
+ * debian/mia-tools.lintian-overrides: Remove
+ python-package-missing-depends-on-python; unused.
+ * debian/watch: Upgrade to version 5.
+ * debian/copyright: Update copyright years for Debian packaging.
+
+ -- Yavor Doganov <yavor at gnu.org> Mon, 20 Oct 2025 13:19:55 +0300
mia (2.4.7-13) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -23,7 +23,7 @@ Build-Depends: cmake,
libopenexr-dev,
libpng-dev,
libtiff-dev,
- libvtk9-dev,
+ libvtk9-dev (>= 9.5),
libvistaio-dev,
libxml2-dev,
python3-lxml
@@ -32,11 +32,10 @@ Build-Depends-Indep: docbook-xsl,
graphviz,
libjs-mathjax,
xsltproc
-Standards-Version: 4.6.2
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/mia
Vcs-Git: https://salsa.debian.org/med-team/mia.git
Homepage: https://mia.sourceforge.net
-Rules-Requires-Root: no
Package: libmia-2.4-4
Architecture: any
=====================================
debian/copyright
=====================================
@@ -5,13 +5,13 @@ Upstream-Contact: https://sourceforge.net/p/mia/discussion/
Files: *
Copyright: Gert Wollny <gw.fossdev at gmail.com>
-License: GPL-3.0+
+License: GPL-3+
Files: debian/*
-Copyright: 2012 wollny <gw.fossdev at gmail.com>
-License: GPL-3.0+
+Copyright: 2012-2025 wollny <gw.fossdev at gmail.com>
+License: GPL-3+
-License: GPL-3.0+
+License: GPL-3+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
=====================================
debian/docs deleted
=====================================
@@ -1,2 +0,0 @@
-debian/README.test
-debian/tests/run-unit-test
=====================================
debian/libmia-2.4-4.lintian-overrides
=====================================
@@ -16,7 +16,7 @@ libmia-2.4-4 binary: hardening-no-fortify-functions
libmia-2.4-4 binary: no-symbols-control-file
#
-# The libray command line parser is designed to call exit if a help
+# The library command line parser is designed to call exit if a help
# option was given.
#
libmia-2.4-4 binary: exit-in-shared-library
=====================================
debian/libmia-2.4-doc.examples
=====================================
@@ -1,3 +1 @@
-testdata
-# examples # seems not needed for test
-test
+examples/2d/filter/*
=====================================
debian/libmia-2.4-doc.install
=====================================
@@ -1,2 +1 @@
usr/share/doc/mia-2.4/libdoc/*
-obj-*/config.h usr/share/doc/libmia-2.4-dev/examples/test
=====================================
debian/libmia-2.4-doc.lintian-overrides deleted
=====================================
@@ -1,5 +0,0 @@
-# The embedded jquery.js is generated by Doxygen and can not be replaced
-# by the one provided by libjs-jquery.
-# For a rationale please see src::Doxygen/debian/README.jquery.
-
-libmia-2.4-doc binary: embedded-javascript-library
=====================================
debian/mia-tools.lintian-overrides
=====================================
@@ -3,10 +3,3 @@
# to detect that fortification is not needed
#
mia-tools binary: hardening-no-fortify-functions
-
-
-# The package provides python-nipype interface which is not required for
-# it to work, and too small to justify another package, hence
-# python-niṕype is only recommended
-#
-mia-tools binary: python-package-missing-depends-on-python
=====================================
debian/patches/fix-g++11.diff
=====================================
@@ -1,5 +1,9 @@
+Description: Fix FTBFS with GCC 11.
Author: Gert Wollny <gewo at debian.org>
-Debian-Bug: https://bugs.debian.org/984233
+Bug-Debian: https://bugs.debian.org/984233
+Last-Update: 2021-03-26
+---
+
--- a/mia/2d/test_segframe.cc
+++ b/mia/2d/test_segframe.cc
@@ -27,8 +27,9 @@
=====================================
debian/patches/fix-gcc-13.patch
=====================================
@@ -1,5 +1,6 @@
-Description: fix gcc-13 build issue
-Bug: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037775
+Description: fix gcc-13 build issue
+Author: Bo YU <tsu.yubo at gmail.com>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037775
Forwarded: https://sourceforge.net/p/mia/mailman/mia-devel/thread/20230730135701.jdurhx6hsmny6vyr%40debian/#msg37877723
Last-Update: 2023-07-30
---
=====================================
debian/patches/groff-warnings.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Fix a groff warning.
+Author: Yavor Doganov <yavor at gnu.org>
+Forwarded: no
+Last-Update: 2025-10-20
+---
+
+--- mia.orig/src/2dmyopgt-nonrigid.cc
++++ mia/src/2dmyopgt-nonrigid.cc
+@@ -47,6 +47,7 @@
+ "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](https://doi.org/10.1007/978-3-642-04268-3_21). "
++ "\n"
+ "Note that for this nonlinear motion correction a preceding linear registration step is usually required."
+ },
+ {
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,5 @@ openexr3.patch
fix-gcc-13.patch
fix-gsl-header-install.patch
gcc-14.patch
+groff-warnings.patch
+spelling-errors.patch
=====================================
debian/patches/spelling-errors.patch
=====================================
@@ -0,0 +1,387 @@
+Description: Fix some spelling errors.
+Author: Yavor Doganov <yavor at gnu.org>
+Forwarded: no
+Last-Update: 2025-10-20
+---
+
+--- mia.orig/mia/2d/filter/sortlabel.cc
++++ mia/mia/2d/filter/sortlabel.cc
+@@ -119,7 +119,7 @@
+ const std::string CSortLabelFilterPlugin::do_get_descr()const
+ {
+ return "This plug-in sorts the labels of a gray-scale image so that the lowest label "
+- "value corresponts to the lable with themost pixels. The background (0) is not touched";
++ "value corresponts to the label with themost pixels. The background (0) is not touched";
+ }
+
+ extern "C" EXPORT CPluginBase *get_plugin_interface()
+--- mia.orig/mia/template/seededwatershed.hh
++++ mia/mia/template/seededwatershed.hh
+@@ -310,7 +310,7 @@
+ m_input_is_gradient(false)
+ {
+ this->add_parameter("seed", new CStringParameter(m_seed_image_file, CCmdOptionFlags::required_input,
+- "seed input image containing the lables for the initial regions"));
++ "seed input image containing the labels for the initial regions"));
+ this->add_parameter("n", make_param(m_neighborhood, "sphere:r=1", false, "Neighborhood for watershead region growing"));
+ this->add_parameter("mark", new CBoolParameter(m_with_borders, false, "Mark the segmented watersheds with a special gray scale value"));
+ this->add_parameter("grad", new CBoolParameter(m_input_is_gradient, false, "Interpret the input image as gradient. "));
+--- mia.orig/src/2dfluid-syn-registration.cc
++++ mia/src/2dfluid-syn-registration.cc
+@@ -99,9 +99,9 @@
+ options.set_group("Registration");
+ options.add(make_opt( mg_levels, "mg-levels", 'l', "Number of multi-resolution levels to run the "
+ "registration on. Not that some registration parameters can be given as a "
+- "coma seperated list to indicate per level values. In these cases if the "
++ "coma separated list to indicate per level values. In these cases if the "
+ "number of given values is smaller than the number of multi-resolution "
+- "levels (this parameter), the the last given value is used for all subsequest "
++ "levels (this parameter), the the last given value is used for all subsequent "
+ "multi-resolution levels."));
+ options.add(make_opt(current_step, EParameterBounds::bf_min_open | EParameterBounds::bf_max_closed,
+ {0.0f, 0.5f}, "step", 'S', "Initial step size for all levels"));
+--- mia.orig/src/2dfuzzysegment.cc
++++ mia/src/2dfuzzysegment.cc
+@@ -64,7 +64,7 @@
+ CCmdOptionList options(g_description);
+ options.set_group("File-IO");
+ options.add(make_opt( in_filename, "in-file", 'i',
+- "input image(s) to be segmenetd", CCmdOptionFlags::required_input, &imageio));
++ "input image(s) to be segmented", CCmdOptionFlags::required_input, &imageio));
+ options.add(make_opt( cls_filename, "cls-file", 'c',
+ "output class probability images (floating point values and multi-image)",
+ CCmdOptionFlags::output, &imageio));
+--- mia.orig/src/2dmyocard-ica.cc
++++ mia/src/2dmyocard-ica.cc
+@@ -53,7 +53,7 @@
+
+ {
+ pdi_example_descr, "Evaluate the synthetic references from images imageXXXX.exr and save them to "
+- "refXXXX.exr by using five independend components, mean stripping, normalizing, "
++ "refXXXX.exr by using five independent components, mean stripping, normalizing, "
+ "and skipping 2 images."
+ },
+
+--- mia.orig/src/2dmyocard-icaseries.cc
++++ mia/src/2dmyocard-icaseries.cc
+@@ -55,7 +55,7 @@
+ },
+ {
+ pdi_example_descr, "Evaluate the synthetic references from set segment.set and save "
+- "them to refXXXX.??? by using five independend components, and skipping 2 images. "
++ "them to refXXXX.??? by using five independent components, and skipping 2 images. "
+ "Per default a bounding box around the LV will be segmented and scaled by 1.4 and "
+ "the cropped images will be saved to cropXXXX.??? and a segmentation set cropped.set "
+ " is created. The image file type ??? is deducted from the input images in segment.set."
+--- mia.orig/src/2dsegment-local-cmeans.cc
++++ mia/src/2dsegment-local-cmeans.cc
+@@ -153,7 +153,7 @@
+ 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,
+- {0.0, 1.0}, "relative-cluster-threshold", 't', "threshhold to ignore classes when initializing"
++ {0.0, 1.0}, "relative-cluster-threshold", 't', "threshold to ignore classes when initializing"
+ " the local cmeans from the global one."));
+
+ if (opts.parse(argc, argv) != CCmdOptionList::hr_no)
+--- mia.orig/src/2dsegseriesstats.cc
++++ mia/src/2dsegseriesstats.cc
+@@ -35,7 +35,7 @@
+
+ {
+ pdi_description, "This program is used evaluate various time-intensity curves over a series of images "
+- "given by a segmentation set. Specifically, the program is taylored to evaluate average "
++ "given by a segmentation set. Specifically, the program is tailored to evaluate average "
+ "intensities and variations of sections the left ventricle myocardium. "
+ "The segmentation set must contain the segmentations for all slices that will be accessed "
+ "during evaluation. "
+--- mia.orig/src/2dseries-mincorr.cc
++++ mia/src/2dseries-mincorr.cc
+@@ -37,7 +37,7 @@
+ {pdi_group, "Tools for Myocardial Perfusion Analysis"},
+ {pdi_short, "Evaluate minimal correlation of time-intensity curves."},
+ {
+- pdi_description, "Given a set of images of temporal sucession, this program evaluates the "
++ pdi_description, "Given a set of images of temporal succession, this program evaluates the "
+ "minimal correlation of the time-intensity curve between neighboring pixels."
+ },
+ {
+--- mia.orig/src/2dseries2sets.cc
++++ mia/src/2dseries2sets.cc
+@@ -39,7 +39,7 @@
+ pdi_description, "This program takes all image files that are given as free parameters "
+ "on the command line and creates segmentation sets based on information found in the images. "
+ "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. "
++ "The code is tailored to use 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 acquisition number. "
+ "Slice locations are rounded to three digits accuracy to make proper comparison "
+--- mia.orig/src/2dseriescorr.cc
++++ mia/src/2dseriescorr.cc
+@@ -40,7 +40,7 @@
+ {pdi_short, "Evaluate the time-intensity correlation in a series of images."},
+
+ {
+- pdi_description, "Given a set of images of temporal sucession, evaluates images that represent "
++ pdi_description, "Given a set of images of temporal succession, evaluates images that represent "
+ "the time-intensity correlation in horizontal and vertical direction as "
+ "well as average correlation of each pixel with its neighbors. "
+ "All input images must be of the same pixel type and size."
+--- mia.orig/src/2dseriesgradMAD.cc
++++ mia/src/2dseriesgradMAD.cc
+@@ -38,7 +38,7 @@
+ {pdi_group, "Tools for Myocardial Perfusion Analysis"},
+ {pdi_short, "Evaluate the time-intensity gradient MAD in a series of images."},
+ {
+- pdi_description, "Given a set of images of temporal sucession, evaluates the "
++ pdi_description, "Given a set of images of temporal succession, evaluates the "
+ "pixel-wise temporal gradient and then its median average distance (MAD) "
+ "and stores the result in an image. Spacial pre-filtering may be applied "
+ "as given additional plugin(s) (filter/2dimage)."
+--- mia.orig/src/2dseriesgradvariation.cc
++++ mia/src/2dseriesgradvariation.cc
+@@ -40,7 +40,7 @@
+ {pdi_short, "Evaluate the time-intensity gradient variation in a series of images."},
+
+ {
+- pdi_description, "Given a set of images of temporal sucession, this program evaluates the "
++ pdi_description, "Given a set of images of temporal succession, this program evaluates the "
+ "gradient variation of the pixel-wise time-intensity curves of this series. "
+ "If the input image set provides a segmentation, then this segmentation can "
+ "be used to create a bounding box and restrict evaluation to this box. "
+--- mia.orig/src/2dseriessmoothgradMAD.cc
++++ mia/src/2dseriessmoothgradMAD.cc
+@@ -40,7 +40,7 @@
+ {pdi_short, "Evaluate pixel-wise time-intensity gradient of a 2D image series."},
+
+ {
+- pdi_description, "Given a set of images of temporal sucession, evaluate the temporal "
++ pdi_description, "Given a set of images of temporal succession, evaluate the temporal "
+ "pixel-wise gaussian and evaluate pixel-wise its MAD."
+ "A spacial pre-filtering may be applied by specifying additional plugins "
+ "(filter/2dimage)"
+--- mia.orig/src/2dtransform.cc
++++ mia/src/2dtransform.cc
+@@ -36,7 +36,7 @@
+ {pdi_description, "This program is used to deform a 2D image using a given transformation."},
+
+ {
+- pdi_example_descr, "Transform an image input.png by the transfromation stored in trans.v "
++ pdi_example_descr, "Transform an image input.png by the transformation stored in trans.v "
+ "by using linear interpolation and zero boundary conditions and store the result in output.png"
+ },
+
+--- mia.orig/src/3dcrispsegment.cc
++++ mia/src/3dcrispsegment.cc
+@@ -31,7 +31,7 @@
+ {pdi_short, "Label segmentation according to probabilities."},
+ {
+ pdi_description, "This program creates a label image from a fuzzy segmentation. "
+- "or each pixel the label is set to the class with the higest probability plus a given offset"
++ "or each pixel the label is set to the class with the highest probability plus a given offset"
+ },
+ {
+ pdi_example_descr, "Set the labels based on the input class probability file cls.v "
+--- mia.orig/src/3dfluid-syn-registration.cc
++++ mia/src/3dfluid-syn-registration.cc
+@@ -98,10 +98,10 @@
+ {
+ options.set_group("Registration");
+ options.add(make_opt( mg_levels, "mg-levels", 'l', "Number of multi-resolution levels to run the registration on. "
+- "Not that some registration parameters can be given as a coma seperated list to "
++ "Not that some registration parameters can be given as a coma separated list to "
+ "indicate per level values. In these cases if the number of given values is smaller "
+ "than the number of multi-resolution levels (this parameter), the the last given value "
+- "is used for all subsequest multi-resolution levels."));
++ "is used for all subsequent multi-resolution levels."));
+ options.add(make_opt(current_step, EParameterBounds::bf_min_open | EParameterBounds::bf_max_closed,
+ {0.0f, 0.5f}, "step", 'S', "Initial step size for all levels"));
+ options.add(make_opt( cost, "ssd", "cost", 'c', "Image similarity function to be minimized"));
+--- mia.orig/src/3dfuzzysegment.cc
++++ mia/src/3dfuzzysegment.cc
+@@ -65,10 +65,10 @@
+ float residuum = 0.1;
+ const auto& imageio = C3DImageIOPluginHandler::instance();
+ CCmdOptionList options(g_description);
+- options.add(make_opt( in_filename, "in-file", 'i', "input image(s) to be segmenetd",
++ options.add(make_opt( in_filename, "in-file", 'i', "input image(s) to be segmented",
+ CCmdOptionFlags::required_input, &imageio));
+ options.add(make_opt( cls_filename, "cls-file", 'c', "output class probability images. Note, the "
+- "used file format must support multible images (best is to use vista)",
++ "used file format must support multiple images (best is to use vista)",
+ CCmdOptionFlags::output, &imageio));
+ options.add(make_opt( out_filename, "b0-file", 'o', "image corrected for intensity non-uniformity",
+ CCmdOptionFlags::output, &imageio));
+--- mia.orig/src/3dlandmarks-transform.cc
++++ mia/src/3dlandmarks-transform.cc
+@@ -47,7 +47,7 @@
+
+ {
+ pdi_example_descr,
+- "Transform the landmarks given in input.lmx by applyning the transfromation stored in trans.v "
++ "Transform the landmarks given in input.lmx by applying the transformation stored in trans.v "
+ "and store the result in output.lmx"
+ },
+
+--- mia.orig/src/3dmaskseeded.cc
++++ mia/src/3dmaskseeded.cc
+@@ -39,7 +39,7 @@
+ pdi_description, "3D image segmentation based on region growing from a seed point. "
+ "Neighboring points are added, either when their intensity is "
+ "equal or higher than that of the seed point, or of the intensity "
+- "is lower or equal then that of the neighoring point. "
++ "is lower or equal then that of the neighboring point. "
+ "After region growing is finished, this mask is used to zero out "
+ "the region in the original image yielding the resulting image. "
+ },
+--- mia.orig/src/3dsegment-local-cmeans.cc
++++ mia/src/3dsegment-local-cmeans.cc
+@@ -176,7 +176,7 @@
+ 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,
+- {0.0, 1.0}, "relative-cluster-threshold", 't', "threshhold to ignore classes when initializing"
++ {0.0, 1.0}, "relative-cluster-threshold", 't', "threshold to ignore classes when initializing"
+ " the local cmeans from the global one."));
+ opts.add(make_opt(ignore_partition_with_background, "ignore-background", 'B',
+ "Don't take background probablities into account when desiding whether classes are to be ignored"));
+--- mia.orig/src/3dtransform.cc
++++ mia/src/3dtransform.cc
+@@ -45,7 +45,7 @@
+
+ {
+ pdi_example_descr,
+- "Transform an image input.v by the transfromation stored in trans.v "
++ "Transform an image input.v by the transformation stored in trans.v "
+ "by using nearest neighbour interpolation ans store the result in output.v"
+ },
+
+--- mia.orig/src/raw2volume.cc
++++ mia/src/raw2volume.cc
+@@ -44,7 +44,7 @@
+
+ {
+ pdi_description, "This program is used to convert raw data into 3D images "
+- "with apropriate metadata."
++ "with appropriate metadata."
+ },
+
+ {pdi_example_descr, "pixel size of <1.2, 2.3, 3.4> to an Analyze file image.hdr"},
+--- mia.orig/mia/2d/perfusion.cc
++++ mia/mia/2d/perfusion.cc
+@@ -555,7 +555,7 @@
+ if (nc < 7)
+ goto retry;
+
+- cvmsg() << "Directional assumtion failed\n";
++ cvmsg() << "Directional assumption failed\n";
+ return result;
+ }
+
+--- mia.orig/mia/2d/segset.cc
++++ mia/mia/2d/segset.cc
+@@ -180,7 +180,7 @@
+ if (attr.empty())
+ cvwarn() << "CSegFrame: LVpeak without attribute";
+ else if (!from_string(attr, m_RV_peak)) {
+- cvwarn() << "Could't convert RV_peak attribute '" << attr
++ cvwarn() << "Couldn't convert RV_peak attribute '" << attr
+ << "' to an integer; ignoring\n";
+ m_RV_peak = -1;
+ }
+@@ -190,7 +190,7 @@
+ if (attr.empty())
+ cvwarn() << "CSegFrame: LVpeak without attribute";
+ else if (!from_string(attr, m_LV_peak)) {
+- cvwarn() << "Could't convert LV_peak attribute '" << attr
++ cvwarn() << "Couldn't convert LV_peak attribute '" << attr
+ << "' to an integer; ignoring\n";
+ m_LV_peak = -1;
+ }
+@@ -200,7 +200,7 @@
+ if (attr.empty())
+ cvwarn() << "CSegFrame: PreferedRef without attribute";
+ else if (!from_string(attr, m_preferred_reference)) {
+- cvwarn() << "Could't convert PreferedRef attribute '" << attr
++ cvwarn() << "Couldn't convert PreferedRef attribute '" << attr
+ << "' to an integer; ignoring\n";
+ m_preferred_reference = -1;
+ }
+--- mia.orig/mia/core/fastica/deflationnonlinearity.cc
++++ mia/mia/core/fastica/deflationnonlinearity.cc
+@@ -198,7 +198,7 @@
+ const std::string CFastICADeflGaussPlugin::do_get_descr()const
+ {
+ return "Implementation of the Gauss non-linearity for the deflation based "
+- "FastICA algorithm. Use it when the independend components are highly "
++ "FastICA algorithm. Use it when the independent components are highly "
+ "super-Gaussian or robustness is very important.";
+ }
+
+--- mia.orig/mia/core/fastica/fastica.cc
++++ mia/mia/core/fastica/fastica.cc
+@@ -150,7 +150,7 @@
+
+ // update the number of components
+ m_numOfIC = pca_result.eval.size();
+- cvdebug() << "Considering " << m_numOfIC << " independend components\n";
++ cvdebug() << "Considering " << m_numOfIC << " independent components\n";
+ cvdebug() << "PCA: eval= " << pca_result.eval << "\n";
+ cvdebug() << "PCA: evec= " << pca_result.evec << "\n";
+ evaluate_whiten_matrix(pca_result.evec, pca_result.eval);
+--- mia.orig/mia/core/handlerbase.cc
++++ mia/mia/core/handlerbase.cc
+@@ -66,7 +66,7 @@
+ if (handler_map.find(m_descriptor) != handler_map.end())
+ return;
+
+- cvdebug() << "Add '" << m_descriptor << "' to dependend handlers\n";
++ cvdebug() << "Add '" << m_descriptor << "' to dependent handlers\n";
+ handler_map[m_descriptor] = this;
+ do_add_dependend_handlers(handler_map);
+ }
+--- mia.orig/mia/core/ica.cc
++++ mia/mia/core/ica.cc
+@@ -65,7 +65,7 @@
+
+ template<> const char *const
+ TPluginHandler<TFactory<CIndepCompAnalysisFactory>>::m_help =
+- "These plug-ins provide implementations for the ICA algoritm.";
++ "These plug-ins provide implementations for the ICA algorithm.";
+
+ EXPLICIT_INSTANCE_HANDLER(CIndepCompAnalysisFactory);
+
+--- mia.orig/mia/core/plugin_base.cc
++++ mia/mia/core/plugin_base.cc
+@@ -74,7 +74,7 @@
+ void CPluginBase::add_dependend_handlers(HandlerHelpMap& handler_map)
+ {
+ TRACE_FUNCTION;
+- cvdebug() << "Add dependend handler for plugin '" << get_name() << "'\n";
++ cvdebug() << "Add dependent handler for plugin '" << get_name() << "'\n";
+ get_parameters().add_dependend_handlers(handler_map);
+ }
+
+--- mia.orig/src/2dmyocard-segment.cc
++++ mia/src/2dmyocard-segment.cc
+@@ -495,7 +495,7 @@
+ if (perf_idx < 0)
+ throw runtime_error("perfusion could not be identified");
+
+- cvmsg() << "Using " << test_components << " independend components\n";
++ cvmsg() << "Using " << test_components << " independent components\n";
+ // after running ICA get the related feature images
+ auto RV_feature = ica->get_feature_image(rv_idx);
+ auto LV_feature = ica->get_feature_image(lv_idx);
+--- mia.orig/src/wavelettrans.cc
++++ mia/src/wavelettrans.cc
+@@ -173,7 +173,7 @@
+ C1DWavelet wt(wt_type, k);
+
+ for (unsigned int i = 0; i < vx.size(); ++i) {
+- cvdebug() << "transfrom column of size " << table[i].size() << "\n";
++ cvdebug() << "transform column of size " << table[i].size() << "\n";
+ table[i] = wt.forward(table[i]);
+ cverb << " result size = " << table[i].size() << "\n";
+ }
=====================================
debian/patches/vtk9.patch
=====================================
@@ -1,7 +1,8 @@
Author: Francois Mazen <francois at mzf.fr>
-Last-Update: Sat, 11 Jun 2022 18:57:02 UTC
+Last-Update: 2022-06-11
Bug-Debian: https://bugs.debian.org/1012689
Description: Build against vtk9
+---
--- a/addons/vtk/CMakeLists.txt
+++ b/addons/vtk/CMakeLists.txt
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: testsuite
+Depends: @builddeps@
+Restrictions: allow-stderr build-needed
=====================================
debian/tests/control_autopkgtest_does_not_work deleted
=====================================
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @, build-essential
-Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test deleted
=====================================
@@ -1,53 +0,0 @@
-#!/bin/bash
-set -e
-
-pkg=mia
-# yes, examples in libmia-2.4-doc will be installed to libmia-2.4-dev!
-pkgdoc=lib${pkg}-2.4-dev
-CPP=c++
-
-set -x
-
-export LC_ALL=C.UTF-8
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
- AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- # trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cp -a /usr/share/doc/${pkgdoc}/examples/* "${AUTOPKGTEST_TMP}"
-
-cd "${AUTOPKGTEST_TMP}"
-
-# chmod a+x ./test
-
-cd test
-
-${CPP} -g -O2 -I. -I/usr/include/mia-2.4 -I/usr/lib/$(dpkg-architecture -qDEB_HOST_GNU_TYPE)/mia-2.4/include/ \
- -fstack-protector-strong -fstack-clash-protection -Wformat \
- -Werror=format-security -fcf-protection -Wdate-time \
- -D_FORTIFY_SOURCE=2 -fvisibility=hidden -Wl,-z,relro -Wl,-z,now \
- -fvisibility=hidden -rdynamic test_minimizer.cc -o test-minimizer \
- -lmiacore-2.4 -lboost_unit_test_framework \
- -lgsl -lgslcblas -lm -lboost_filesystem -lboost_system \
- -lpthread -Wl,-Bstatic -ldl -Wl,-Bdynamic -lfftw3f -lxml2
-# FIXME: this test fails to find plugins
-./test-minimizer
-
-# FIXME: This has linker errors
-${CPP} -DBOOST_ALL_DYN_LINK -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK \
- -DBOOST_FILESYSTEM_VERSION=3 -DBOOST_SYSTEM_DYN_LINK \
- -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DHAVE_CONFIG_H \
- -I. -I/usr/include/mia-2.4 -I/usr/lib/$(dpkg-architecture -qDEB_HOST_GNU_TYPE)/mia-2.4/include/ \
- -I/usr/include/eigen3 -I/usr/include/libxml2 \
- -g -O2 -fstack-protector-strong -fstack-clash-protection -Wformat \
- -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 \
- -fvisibility=hidden test_ioplugins.cc -o test_ioplugins.o
-${CPP} -g -O2 -fstack-protector-strong -fstack-clash-protection -Wformat \
- -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 \
- -fvisibility=hidden -Wl,-z,relro -Wl,-z,now -fvisibility=hidden \
- -rdynamic test_ioplugins.o -o test-ioplugins \
- -lmia3d-2.4 -lboost_unit_test_framework -lmia2d-2.4 -lmiacore-2.4 \
- -lgsl -lgslcblas -lm -lboost_filesystem -lboost_system \
- -lpthread -Wl,-Bstatic -ldl -Wl,-Bdynamic -lfftw3f -lxml2
-
-echo -e "\e[92m\e[1mPASS\e[0m"
=====================================
debian/tests/testsuite
=====================================
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+set -e
+
+dh_auto_test
=====================================
debian/watch
=====================================
@@ -1,3 +1,5 @@
-version=4
-opts="pgpsigurlmangle=s/$/.asc/" http://sf.net/mia/mia-([\d.]+)\.tar\.xz
+Version: 5
+Source: http://sf.net/mia/
+Matching-Pattern: mia-([\d.]+)\.tar\.xz
+Pgpsigurlmangle: s/$/.asc/
View it on GitLab: https://salsa.debian.org/med-team/mia/-/compare/4525398cec2c499f0d2576ddcb18c5ef3175968b...d4c0ec8615bd760bf77adc82b53e6b77f68b2a3d
--
View it on GitLab: https://salsa.debian.org/med-team/mia/-/compare/4525398cec2c499f0d2576ddcb18c5ef3175968b...d4c0ec8615bd760bf77adc82b53e6b77f68b2a3d
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