Merge branch 'feature/vtk7-compatibility' into 'develop'

Feature/vtk7 compatibility

See merge request !107

.gitlab/check.sh

@@ -15,3 +15,4 @@ fi
 
 pwd
 printenv
+ls -la $PROJECT_SOURCE_DIR

.gitlab/test.sh

@@ -6,9 +6,11 @@
 # This is ok on Linux but since gitlab-runner 11.7 on windows all path variables use backward slash instead of forward slash
 # → Replace all backslash to forward slash 
 export PROJECT_SOURCE_DIR=${PROJECT_SOURCE_DIR//\\//}
+export CI_PROJECT_DIR=${CI_PROJECT_DIR//\\//}
 
 echo "Job $CI_JOB_NAME"
 echo "PROJECT_SOURCE_DIR=$PROJECT_SOURCE_DIR"
+echo "CI_PROJECT_DIR=$CI_PROJECT_DIR"
 
 if ! grep -q TRIGGER_STAGE_TEST "${PROJECT_LOG_DIR}/trigger-stage.txt"; then
     echo "Job skipped as /test flag not in commit message and CAMITK_CI_STAGE < $STAGE_CONFIGURE"; 
@@ -16,12 +18,12 @@ if ! grep -q TRIGGER_STAGE_TEST "${PROJECT_LOG_DIR}/trigger-stage.txt"; then
 fi
 
 if [[ "$OS" != "win7" ]]; then
-    echo "===== Configuring xvfb =====" > >(tee ${PROJECT_LOG_DIR}/test.log) 2>&1
+    echo "===== Configuring xvfb =====" > >(tee --append ${PROJECT_LOG_DIR}/test.log) 2>&1
     # Starts the server first (try to avoid unexpected and random "QXcbConnection: Could not connect to display :99")
     export DISPLAY=":98"
     # create a specific file for xauth
     export XAUTHORITY=$(mktemp)
-    Xvfb $DISPLAY -screen 0 1280x1024x16 -ac -nolisten tcp -nolisten unix -auth $XAUTHORITY & > >(tee ${PROJECT_LOG_DIR}/test.log) 2>&1
+    Xvfb $DISPLAY -screen 0 1280x1024x16 -ac -nolisten tcp -nolisten unix -auth $XAUTHORITY & > >(tee --append ${PROJECT_LOG_DIR}/test.log) 2>&1
     trap "kill $! || true" EXIT
     # give some times to start the Xvfb
     sleep 10
@@ -42,16 +44,43 @@ ctest -VV \
       -DCI_PROJECT_LOG_DIRECTORY="$CI_PROJECT_DIR/$PROJECT_LOG_DIR" \
       -DCTEST_SOURCE_DIRECTORY="$PROJECT_SOURCE_DIR" \
       -DCTEST_BINARY_DIRECTORY="$PROJECT_BUILD_DIR" \
-      -S $PROJECT_SOURCE_DIR/sdk/cmake/ctest/ci-test.cmake > >(tee ${PROJECT_LOG_DIR}/test.log | grep --line-buffered -e "Test \#") 2>&1
+      -S $PROJECT_SOURCE_DIR/sdk/cmake/ctest/ci-test.cmake > >(tee --append ${PROJECT_LOG_DIR}/test.log | grep --line-buffered -e "Test \#") 2>&1
+
+# Rerun only the failed tests
+# There seems to be a bug in CMake, disabling for now
+# see https://gitlab.kitware.com/cmake/cmake/issues/17767
+# and https://gitlab.kitware.com/cmake/cmake/issues/16314
+#     echo "===== Re-running failed tests ====="
+#     ctest -VV \
+#         --rerun-failed \
+#         -DCTEST_SITE="$CDASH_SITE" \
+#         -DCI_MODE="$CAMITK_CI_MODE" \
+#         -DCI_ID="P $CI_PIPELINE_ID - J $CI_BUILD_ID" \
+#         -DCI_BRANCH="$CI_COMMIT_REF_NAME" \
+#         -DCI_BUILD_SETTINGS="$COMPILER_CONFIG" \
+#         -DCI_PROJECT_LOG_DIRECTORY="$CI_PROJECT_DIR/$PROJECT_LOG_DIR" \
+#         -DCTEST_SOURCE_DIRECTORY="$PROJECT_SOURCE_DIR" \
+#         -DCTEST_BINARY_DIRECTORY="$PROJECT_BUILD_DIR" \
+#         -S $PROJECT_SOURCE_DIR/sdk/cmake/ctest/ci-test.cmake > >(tee --append ${PROJECT_LOG_DIR}/test.log | grep --line-buffered -e "Test \#") 2>&1
 
 # if [[ "$OS" != "win7" ]]; then
 #     # shutdown xvfb
 #     kill $xvfbPid
 # fi
 
+echo
+echo "===== Not run (disabled) tests ====="
+grep -e "Not Run" $CI_PROJECT_DIR/$PROJECT_LOG_DIR/test.log
+
 # as ctest return a strange 255 error, check the log
 if grep --quiet "Fatal error" $CI_PROJECT_DIR/$PROJECT_LOG_DIR/ci-test.log; then
+    echo
+    echo "===== Fatal errors ====="
     echo "Found fatal error in $CI_PROJECT_DIR/$PROJECT_LOG_DIR/ci-test.log"
+    echo 
+    echo "===== Failed tests ====="
+    grep -e "\*\*\*Failed" -e "SegFault" $CI_PROJECT_DIR/$PROJECT_LOG_DIR/test.log
+    echo
     exit 1
 else
     echo "OK"

imaging/actions/itkfilters/CMakeLists.txt

@@ -20,27 +20,32 @@ camitk_extension(ACTION_EXTENSION
                  ENABLE_INTEGRATION_TEST
 )
 
-# Test failure due to ITK exception
-# For now consider these fail tests as passed until this can be taken care of in the save() method
-# TODO check if it possible to avoid this exception
-# For input file: biorad.pic
-# Applying action Gradient Magnitude With Smoothing...
-# camitk-testcomponents aborted by std exception: /usr/include/ITK-4.10/itkRecursiveSeparableImageFilter.hxx:245:
-# itk::ERROR: RecursiveGaussianImageFilter(0x55b3b21bc700): The number of pixels along direction 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed...
-set_tests_properties("action-itkfilters-level1-6" PROPERTIES WILL_FAIL true)
-# For input file: cthead1.lsm
-# Applying action Gradient Magnitude With Smoothing...
-# camitk-testcomponents aborted by std exception: /usr/include/ITK-4.10/itkRecursiveSeparableImageFilter.hxx:245:
-# itk::ERROR: RecursiveGaussianImageFilter(0x559652ac6cc0): The number of pixels along direction 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed..
-set_tests_properties("action-itkfilters-level1-8" PROPERTIES WILL_FAIL true)
-# For input file: mini-complex-slow1.nrrd
-# Applying action Gradient Magnitude With Smoothing...
-# camitk-testcomponents aborted by std exception: /usr/include/ITK-4.10/itkRecursiveSeparableImageFilter.hxx:245:
-# itk::ERROR: RecursiveGaussianImageFilter(0x55f942cacac0): The number of pixels along direction 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed.
-set_tests_properties("action-itkfilters-level1-14" PROPERTIES WILL_FAIL true)
+# --------------------------------
+# --- Specific test management ---
+# --------------------------------
+camitk_disable_tests(TESTS action-itkfilters-level1-6
+                           action-itkfilters-level1-8
+                           action-itkfilters-level1-14
+                     REASON " Test failure due to ITK exception.
+ For now disable these tests until this can be taken care of in the save() method
+ For input file: biorad.pic, cthead1.lsm, mini-complex-slow1.nrrd
+ When applying action Gradient Magnitude With Smoothing, the following exception is raised:
+ \"camitk-testcomponents aborted by std exception: /usr/include/ITK-4.10/itkRecursiveSeparableImageFilter.hxx:245:
+ itk::ERROR: RecursiveGaussianImageFilter(0x55b3b21bc700): The number of pixels along direction 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed...\""
+)
 
-# Tests fail due to OpenGL crashing when used inside a VM
-# As the test can be run directly on a "real" desktop, add the test but flag it with WILL_FAIL
-if(WIN32)
-    set_tests_properties(action-itkfilters-integration-test PROPERTIES WILL_FAIL true)
-endif()
+camitk_tests_requirement(TESTS action-itkfilters-integration-test
+                         REQUIRES "NOT WIN32"
+                         REASON "WIN32 OpenGL failure on a VM
+ This test will always fail when run inside a VM due to OpenGL crash.
+ This test will pass when run directly from a physical windows machine."
+)
+
+camitk_tests_requirement(TESTS action-itkfilters-integration-test
+                         REQUIRES "${VTK_VERSION} VERSION_EQUAL 6.3"
+                         REASON "VTK version is not equals than 6.3
+ The default test files are written using the currently supported version of VTK (VTK 6.3).
+ This test will therefore fail when comparing the input to the output if another version of VTK is used.
+ E.g., Ubuntu 16.04 LTS comes with VTK 6.2 and Debian buster comes with VTK 7.1
+ Although everything should work well on both OS, this test will unconditionnaly fail."
+)

imaging/components/itkimage/CMakeLists.txt

@@ -8,50 +8,46 @@ camitk_extension(COMPONENT_EXTENSION
                  ENABLE_AUTO_TEST
 )
 
-# Test failure due to ITK exception
-# For now consider these fail tests as passed until this can be taken care of in the save() method
-# TODO check if it possible to avoid this exception
-# Trying to save "biorad.pic" generates the following ITK Exception:
-# /build/insighttoolkit4-zpsE3g/insighttoolkit4-4.10.1-dfsg1/Modules/IO/BioRad/src/itkBioRadImageIO.cxx:484:
-# itk::ERROR: BioRadImageIO(0x55bf9bc9bb90): Component type not supported.
-set_tests_properties("component-itkimage-level3-9" PROPERTIES WILL_FAIL true)
-# Saving Error: problem occurs while saving file:/home/promayon/Dev/CamiTK/build/camitk/Testing/Temporary/component-itkimage-level3-10/cthead1.lsm: ITK Exception: /build/insighttoolkit4-zpsE3g/insighttoolkit4-4.10.1-dfsg1/Modules/IO/LSM/src/itkLSMImageIO.cxx:275:
-# itk::ERROR: LSMImageIO(0x55a165be7310): TIFF supports unsigned char and unsigned short
-set_tests_properties("component-itkimage-level3-10" PROPERTIES WILL_FAIL true)
+# --------------------------------
+# --- Specific test management ---
+# --------------------------------
 
-# Test failure due to bad export
-# TODO check why ITK cannot save BigEndian.spr properly
-set_tests_properties("component-itkimage-level3-3" PROPERTIES WILL_FAIL true)
-# TODO check why ITK cannot save LittleEndianZ.hdr properly
-set_tests_properties("component-itkimage-level3-19" PROPERTIES WILL_FAIL true)
-# TODO check why ITK cannot save LittleEndianZ.img.gz properly
-set_tests_properties("component-itkimage-level3-20" PROPERTIES WILL_FAIL true)
+camitk_disable_tests(TESTS component-itkimage-level3-3
+                           component-itkimage-level3-9 
+                           component-itkimage-level3-10
+                           component-itkimage-level3-19
+                           component-itkimage-level3-20
+                     REASON " Test failure due to ITK exception.
+ For now disable these tests until this can be dealt with (if possible)
+ For input file: biorad.pic, cthead1.lsm, BigEndian.spr, LittleEndianZ.hdr and LittleEndianZ.img.gz
+ When applying action Gradient Magnitude With Smoothing, the following exception is raised:
+ \"camitk-testcomponents aborted by std exception: /usr/include/ITK-4.10/itkRecursiveSeparableImageFilter.hxx:245:
+ itk::ERROR: RecursiveGaussianImageFilter(0x55b3b21bc700): The number of pixels along direction 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed...\""
+)
 
-if(WIN32)
-    # TODO check why BigEndianCompressed.img.gz does not work on Windows (maybe because of double suffix .im.gz?)
-    set_tests_properties(component-itkimage-level3-6 PROPERTIES WILL_FAIL true)
-    # same for LittleEndianCompressed.img.gz
-    set_tests_properties(component-itkimage-level3-16 PROPERTIES WILL_FAIL true)
-    # same for minimal.nii.gz
-    set_tests_properties(component-itkimage-level3-28 PROPERTIES WILL_FAIL true)
-endif()
+# TODO confirm diagnostic: check why BigEndianCompressed.img.gz, LittleEndianCompressed.img.gz and minimal.nii.gz does not work on Windows (maybe because of double suffix .im.gz?)
+camitk_tests_requirement(TESTS component-itkimage-level3-6 
+                               component-itkimage-level3-16 
+                               component-itkimage-level3-28
+                         REQUIRES "NOT WIN32"
+                         REASON "WIN32 failure (probably) due to double suffix .im.gz or .nii.gz
+ For input file: BigEndianCompressed.img.gz, LittleEndianCompressed.img.gz and minimal.nii.gz"
+)
 
-# On Ubuntu 18.04 LTS, the default ITK version is 4.12
-# ITK 4.12 handle export to some format differently that generates different file and therefore
-# test errors for level3
-# The following exception should be removed when all plateforms are based on ITK 4.12 or higher
-if("${ITK_VERSION}" VERSION_GREATER 4.11)
-    set_tests_properties(component-itkimage-level3-1
-                         component-itkimage-level3-4
-                         component-itkimage-level3-7
-                         component-itkimage-level3-11
-                         component-itkimage-level3-13
-                         component-itkimage-level3-15
-                         component-itkimage-level3-17
-                         component-itkimage-level3-21
-                         component-itkimage-level3-28
-                         PROPERTIES WILL_FAIL true)
-endif()
+camitk_tests_requirement(TESTS component-itkimage-level3-1
+                               component-itkimage-level3-4
+                               component-itkimage-level3-7
+                               component-itkimage-level3-11
+                               component-itkimage-level3-13
+                               component-itkimage-level3-15
+                               component-itkimage-level3-17
+                               component-itkimage-level3-21
+                               component-itkimage-level3-28
+                         REQUIRES "${ITK_VERSION} VERSION_LESS 4.12"
+                         REASON " ITK version is greater than 4.11
+ The default test files are written using the currently supported version of ITK (ITK 4.11).
+ This test will therefore fail when comparing the input to the output if another version of ITK is used."
+)
 
 # Additional test for SDK actions: this will add auto test for the given actions using the itkimage component
 camitk_additional_action_test(ACTION_EXTENSIONS cropvolume imagelut imageresampling multipicking pixelcolorchanger reconstruction reorientimage showin3d volumerendering

sdk/actions/image/reconstruction/CMakeLists.txt

@@ -10,14 +10,21 @@ camitk_extension(ACTION_EXTENSION
 # Recursively update the shiboken path variable containing the CamiTK SDK tree structure
 set(SHIBOKEN_CAMITK_SDK_PATH ${SHIBOKEN_CAMITK_SDK_PATH}:${CMAKE_CURRENT_SOURCE_DIR} CACHE INTERNAL "") 
 
-# On Ubuntu 16.04 LTS, the default VTK version is 6.2 not 6.3
-# VTK6.2 has a bug when it saves vtk files: it does not save the proper VTK file format version
-if("${VTK_VERSION}" VERSION_LESS 6.3)
-    set_tests_properties(action-reconstruction-integration-test PROPERTIES WILL_FAIL true)
-endif()
+# --------------------------------
+# --- Specific test management ---
+# --------------------------------
+camitk_tests_requirement(TESTS action-reconstruction-integration-test
+                         REQUIRES "${VTK_VERSION} VERSION_EQUAL 6.3"
+                         REASON "VTK version is not equals than 6.3
+ The default test files are written using the currently supported version of VTK (VTK 6.3).
+ This test will therefore fail when comparing the input to the output if another version of VTK is used.
+ E.g., Ubuntu 16.04 LTS comes with VTK 6.2 and Debian buster comes with VTK 7.1
+ Although everything should work well on both OS, this test will unconditionnaly fail."
+)
 
-# Tests fail due to OpenGL crashing when used inside a VM
-# As the test can be run directly on a "real" desktop, add the test but flag it with WILL_FAIL
-if(WIN32)
-    set_tests_properties(action-reconstruction-integration-test PROPERTIES WILL_FAIL true)
-endif()
+camitk_tests_requirement(TESTS action-reconstruction-integration-test
+                         REQUIRES "NOT WIN32"
+                         REASON "WIN32 OpenGL failure on a VM
+ This test will always fail when run inside a VM due to OpenGL crash.
+ This test will pass when run directly from a physical windows machine."
+)

sdk/actions/mesh/meshprocessing/MeshClipping.cpp

@@ -336,7 +336,6 @@ Action::ApplyStatus MeshClipping::clipMesh(MeshComponent* mesh, vtkSmartPointer
                 filter->SetInputConnection(mesh->getDataPort());
                 filter->ExtractInsideOn();
                 filter->SetImplicitFunction(plane);
-                filter->Update();
                 mesh->setDataConnection(filter->GetOutputPort());
                 if (save) {
                     new MeshComponent((vtkPointSet*)filter->GetOutput(), mesh->getName() + " clipped");

sdk/cmake/ctest/testdatavtk7/README

+This directory contains all the test data files required to pass the automatic tests when building CamiTK with VTK7.
+It is kepts here in order to simplify the future move to VTK7.
+
+As of 23 February 2019 CamiTK supports
+- VTK6 and all associated test
+- VTK7 with some test disabled (all the tests that depends on the VTK version)
+
+When CamiTK move to VTK7 only, just move the files of this directory to their respective location. All tests will
+then pass.

sdk/cmake/ctest/testdatavtk7/sdk/components/vtkmesh/testdata/check-with-color-pointdata.vtk

+# vtk DataFile Version 4.1
+color data (not implemented yet!)
+ASCII
+DATASET POLYDATA
+POINTS 25 float
+-0.0981577 0.0639953 -0.152536 0.0662411 0.913408 0.214962 -0.0256973 1.90475 0.0318697 
+-0.0732923 2.97639 -0.14693 -0.0907575 4.03827 0.424344 0.991426 0.088565 -0.439235 
+0.956044 1.03466 -0.119008 0.966296 1.9451 -0.376246 1.08769 2.93903 -0.257324 
+1.03252 4.02625 -0.19867 1.98952 -0.0785815 0.407174 2.07315 0.973676 -0.168316 
+2.02312 1.95903 -0.0489972 1.90072 3.05295 -0.0383131 2.01426 4.03996 0.337362 
+3.01026 -0.0131874 -0.19971 3.09593 1.03124 -0.335646 2.95806 2.0721 0.065351 
+3.07098 3.09579 0.13096 3.00829 3.92759 -0.215786 4.05534 0.0646894 0.175641 
+4.00035 0.955553 -0.0894418 3.95042 2.05852 0.0185222 4.06053 2.96645 -0.364692 
+3.92506 4.01263 0.0126824 
+POLYGONS 32 128
+3 11 6 5 
+3 12 8 7 
+3 5 1 0 
+3 7 3 2 
+3 15 11 10 
+3 20 16 15 
+3 6 2 1 
+3 9 4 3 
+3 6 1 5 
+3 7 2 6 
+3 8 3 7 
+3 9 3 8 
+3 12 7 6 
+3 19 14 13 
+3 11 5 10 
+3 13 9 8 
+3 12 6 11 
+3 13 8 12 
+3 14 9 13 
+3 17 12 11 
+3 17 13 12 
+3 16 11 15 
+3 17 11 16 
+3 18 13 17 
+3 19 13 18 
+3 22 17 16 
+3 22 18 17 
+3 21 16 20 
+3 24 19 18 
+3 22 16 21 
+3 23 18 22 
+3 24 18 23 
+
+POINT_DATA 25
+FIELD FieldData 1
+Colors 3 25 unsigned_char
+196 255 0 0 254 255 0 255 19 
+185 255 0 0 0 255 255 0 0 
+137 255 0 255 46 0 255 237 0 
+246 255 0 0 3 255 216 255 0 
+23 255 0 13 255 0 0 85 255 
+246 255 0 255 115 0 0 255 65 
+0 255 185 254 255 0 0 255 241 
+82 255 0 0 255 8 255 67 0 
+0 255 4 

sdk/cmake/ctest/testdatavtk7/sdk/components/vtkmesh/testdata/cube-with-point-and-cell-data.vtk

+# vtk DataFile Version 4.1
+Cube example
+ASCII
+DATASET POLYDATA
+POINTS 8 float
+0 0 0 1 0 0 1 1 0 
+0 1 0 0 0 1 1 0 1 
+1 1 1 0 1 1 
+POLYGONS 6 30
+4 0 1 2 3 
+4 4 5 6 7 
+4 0 1 5 4 
+4 2 3 7 6 
+4 0 4 7 3 
+4 1 2 6 5 
+
+CELL_DATA 6
+NORMALS cell_normals float
+0 0 -1 0 0 1 0 -1 0 
+0 1 0 -1 0 0 1 0 0 
+
+FIELD FieldData 1
+cell_scalars 1 6 int
+0 1 2 3 4 5 
+METADATA
+INFORMATION 0
+
+POINT_DATA 8
+FIELD FieldData 1
+my_scalars 1 8 float
+0 1 2 3 4 5 6 7 
+METADATA
+INFORMATION 0
+

sdk/cmake/ctest/testdatavtk7/sdk/components/vtkmesh/testdata/cube-with-tensors.vtk

+# vtk DataFile Version 4.1
+Random data to test tensors
+ASCII
+DATASET UNSTRUCTURED_GRID
+POINTS 8 float
+0 0 0 1 0 0 0 1 0 
+1 1 0 0 0 1 1 0 1 
+0 1 1 1 1 1 
+CELLS 1 9
+8 0 1 2 3 4 5 6 7 
+
+CELL_TYPES 1
+11
+
+POINT_DATA 8
+FIELD FieldData 3
+scalars 1 8 float
+0 1 2 3 4 3 2 0 
+METADATA
+INFORMATION 0
+
+other_scalars 1 8 float
+0 6 2 3 4 7 5 1 
+METADATA
+INFORMATION 0
+
+tensors1 9 8 float
+1 0 0 0 1 0 0 0 1 
+-2 0 0 0 -2 0 0 0 3 
+1 0 0 0 1 0 0 0 0.001 
+2 1 1 1 2 1 1 1 3 
+0.247186 0.490995 0.131325 0.490995 -0.371056 0.719072 0.131325 0.719072 -0.156008 
+0.280588 0.467439 0.934953 0.467439 0.0600321 -0.211376 0.934953 -0.211376 0.962976 
+0.062861 -0.0117908 -0.667617 -0.0117908 -0.390601 -0.957805 -0.667617 -0.957805 -0.19332 
+0 0 0 0 0 0 0 0 0 
+

sdk/cmake/ctest/testdatavtk7/sdk/components/vtkmesh/testdata/fieldfile.vtk

+# vtk DataFile Version 4.1
+cell attributes
+ASCII
+DATASET UNSTRUCTURED_GRID
+POINTS 18 float
+0.5 0.5 0.5 1.5 0.5 0.5 0.5 1.5 0.5 
+0.5 0.5 1.5 1.5 0.5 1.5 0.5 1.5 1.5 
+1.1 1.1 1 2.1 1.1 1 2.1 2.1 1 
+1.1 2.1 1 1.1 1.1 2 2.1 1.1 2 
+2.1 2.1 2 1.1 2.1 2 2.2 2.2 2 
+3.2 2.2 2 2.2 3.2 2 2.2 2.2 3 
+
+CELLS 3 27
+8 0 1 2 2 3 4 5 5 
+8 6 7 8 9 10 11 12 13 
+8 14 15 16 17 17 17 17 17 
+
+CELL_TYPES 3
+12
+12
+12
+
+CELL_DATA 3
+FIELD FieldData 3
+group 1 3 int
+1 2 1 
+METADATA
+INFORMATION 0
+
+material 1 3 int
+100 200 300 
+METADATA
+INFORMATION 0
+
+group_and_material 2 3 int
+1 100 2 200 1 300 

sdk/cmake/ctest/testdatavtk7/sdk/components/vtkmesh/testdata/imageBoundingBox.vtk

+# vtk DataFile Version 4.1
+ImageBoundingBox
+ASCII
+DATASET UNSTRUCTURED_GRID
+POINTS 8 float
+0 0 0 0 0 2 0 1 0 
+0 1 2 1 0 0 1 0 2 
+1 1 0 1 1 2 
+CELLS 1 9
+8 0 4 6 2 1 5 7 3 
+
+CELL_TYPES 1
+12
+