[Synchro] branch 4.1 (dev) receives bugfix from 4.0.3 to 4.0.7

.github/workflows/musicardio-macos.yml

@@ -0,0 +1,134 @@
+# This starter workflow is for a CMake project running on a single platform. There is a different starter workflow if you need cross-platform coverage.
+# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-multi-platform.yml
+name: MUSICardio on macOS
+
+on:
+  push:
+    branches: [ "4.1" ]
+  pull_request:
+    branches: [ "4.1" ]
+  workflow_dispatch:
+    inputs:
+      EXPIRATION_TIME:
+        description: 'Expiration time in month'
+        required: true
+        default: '12'
+        type: string
+  #schedule:
+  #  - cron: '0 0 * * 1'  # Each monday at 0h00, MIN HOUR DAY_IN_MONTH MONTH WEEK_DAY
+
+env:
+  BUILD_TYPE: Release
+  QT5_DIR: "/usr/local/opt/qt@5/lib/cmake/Qt5"
+  MSC_SSH_PLUGINS: ${{ secrets.MSC_SSH_PLUGINS }}
+  MSC_TOKEN: ${{ secrets.MSC_TOKEN }}
+
+jobs:
+  build:
+    # https://docs.github.com/en/actions/using-jobs/choosing-the-runner-for-a-job#standard-github-hosted-runners-for-public-repositories
+    runs-on: macos-13
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+          ref: 4.1
+
+    - name: Set up SSH
+      run: |
+        mkdir -p ~/.ssh
+        echo "$MSC_SSH_PLUGINS" > ~/.ssh/id_rsa
+        chmod 600 ~/.ssh/id_rsa
+        ssh-keyscan github.com >> ~/.ssh/known_hosts
+
+    - name: Install dependencies
+      run: |
+        brew install qt@5
+        brew install boost
+        brew install swig
+        brew install libomp
+        echo "OpenMP_ROOT=$(brew --prefix libomp)" >> $GITHUB_ENV
+        pip3 install dmgbuild
+        # brew info cmake
+
+    - name: Set default EXPIRATION_TIME if not provided (with non manual workflow)
+      run: echo "EXPIRATION_TIME=${{ inputs.EXPIRATION_TIME || '12' }}" >> $GITHUB_ENV
+
+    - name: Configure CMake
+      run: |
+        cmake -B ${{github.workspace}}/build \
+          -DUSE_GITHUB_SSH:BOOL=TRUE \
+          -DmedInria_BUILD_TYPE:STRING=$BUILD_TYPE \
+          -Dmusic-plugins_BUILD_TYPE:STRING=$BUILD_TYPE \
+          -DEP_CHECKBOX_CUSTOM_DIRS:BOOL=ON \
+          -DEP_CHECKBOX_ON_TOP_LEVEL:BOOL=OFF \
+          -DEP_CHECKBOX_SIDE_BY_SIDE:BOOL=OFF \
+          -DQt5_DIR=$QT5_DIR \
+          -DOpenMP_ROOT=$OpenMP_ROOT \
+          -DUSE_FFmpeg=ON \
+          -DEXPIRATION_TIME:STRING=$EXPIRATION_TIME \
+          -DUSE_RealTimeWorkspace=OFF
+
+    - name: Build
+      run: | 
+        CORES_TO_USE=$(($(sysctl -n hw.ncpu) - 1)) # Limit the number of used core otherwise the compilation crashes sometimes
+        echo "Using $CORES_TO_USE cores for the build"
+        cmake --build ${{github.workspace}}/build --config $BUILD_TYPE --parallel $CORES_TO_USE
+
+    - name: Package
+      run: |
+        cd ${{github.workspace}}/build
+        cpack -C $BUILD_TYPE
+
+    - name: Prepare DMG and update design
+      run: |
+        cd ${{github.workspace}}/build
+        dmg=$(ls *.dmg)
+        echo "The current package to adapt: $dmg"
+
+        if [ -n "$dmg" ]; then
+          # Attach to read-write format and retrieve mount path
+          path=$(hdiutil attach -owners on $dmg -shadow | grep -i 'Volumes' | cut -f 3)
+          echo "The current path: $path"
+
+          # Navigate to correct directory
+          cd "$path/MUSICardio.app/Contents/"
+
+          pathPluginsLegacy="${{github.workspace}}/build/medInria-build/bin/plugins_legacy"
+
+          # Change library paths for plugins
+          for f in PlugIns/*.dylib; do
+            install_name_tool -change $pathPluginsLegacy/libAAMeshInteractorPlugin.dylib  @executable_path/../PlugIns/libAAMeshInteractorPlugin.dylib $f
+            install_name_tool -change $pathPluginsLegacy/libAAAMeshUtilityPlugin.dylib    @executable_path/../PlugIns/libAAAMeshUtilityPlugin.dylib $f
+            install_name_tool -change $pathPluginsLegacy/libAAAmedPipelinePlugin.dylib    @executable_path/../PlugIns/libAAAmedPipelinePlugin.dylib $f
+            install_name_tool -change $pathPluginsLegacy/libmscPipelinesPlugin.dylib      @executable_path/../PlugIns/libmscPipelinesPlugin.dylib $f
+            install_name_tool -change $pathPluginsLegacy/libAAAEPMapPlugin.dylib          @executable_path/../PlugIns/libAAAEPMapPlugin.dylib $f
+            install_name_tool -change $pathPluginsLegacy/libAAMFSSimulationPlugin.dylib   @executable_path/../PlugIns/libAAMFSSimulationPlugin.dylib $f
+            install_name_tool -change $pathPluginsLegacy/libFEMForwardProblemPlugin.dylib @executable_path/../PlugIns/libFEMForwardProblemPlugin.dylib $f
+          done
+
+          # Go back to original path
+          cd "${{github.workspace}}/build"
+
+          # Update dmg design
+          echo "### Now we are going to update the dmg design"
+          volumeName=$(basename "$path")
+          dmgbuild -s ../packaging/apple/settings.json "$volumeName" MUSICardio.dmg
+
+          echo "End of the processes"
+        else
+          echo "A problem happened in MSC compilation, no dmg is built"
+        fi
+
+    - name: Upload binaries to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_name: Inria-Asclepios/msc_binaries
+        # A personal access token for the GitHub repository in which the release will be created and edited.
+        # It is recommended to create the access token with the following scopes: `repo, user, admin:repo_hook`.
+        repo_token: ${{ secrets.MSC_TOKEN }}
+        file: ${{github.workspace}}/build/MUSICardio.dmg
+        asset_name: MUSICardio.dmg
+        tag: latest
+        overwrite: true
+        body: "MUSICardio binaries"

CMakeLists.txt

@@ -20,7 +20,7 @@ endif()
 cmake_policy(SET CMP0074 NEW)
 
 if(NOT DEFINED ${MEDINRIA_SUPERBUILD_VERSION})
-    set(MEDINRIA_SUPERBUILD_VERSION 4.0.2)
+    set(MEDINRIA_SUPERBUILD_VERSION 4.0.7)
 endif()
 
 SET(CMAKE_CXX_STANDARD 17)

RELEASE_NOTES.txt

@@ -1,3 +1,33 @@
+MUSICardio 4.0.7:
+- PolygonROI:
+    * fix drawing a contour with shift-click to be able to change zoom/contrast with click.
+    * fix removing a last contour/node which reset the label tool and allow to draw again.
+- Registration step in pipelines allows to use Mouse Interaction Toolbox.
+- VOICutterToolBox fix a crash with metadata in pipelines sometimes if a cut has been made.
+
+MUSICardio 4.0.6:
+- Debug import of Carto .zip archives and .mesh files.
+- PolygonROI: remove shift-click to draw, fix contrast after deactivation of repulsor and hide deactivated widgets.
+- Pipelines: 
+    * put back the possibility of closing layers at result steps,
+    * fix VOICutter if no segmentation is done,
+    * fix Histogram Analysis non manual algorithms.
+    * fix pipeline crash when saving data.
+
+MUSICardio 4.0.5:
+- Allow to use data with different size or spacing in LCCLogDemons and DiffeomorphicDemons.
+- Manual Registration: enhance landmark numbers for better user understanding.
+- Fix Histogram Analysis width problem displaying multi-results.
+
+MUSICardio 4.0.4:
+- Fix some plugins wrongly loaded on Windows.
+
+MUSICardio 4.0.3:
+- Switch to Ubuntu 22.
+- PolygonROI: update icons, fix a glitch when users change ROI label, hide label panel in pipelines.
+- Histogram Analysis: enhance memory management and remove useless computation.
+- Pipelines: correct arithmetic filters computation. 
+
 MUSICardio 4.0.2:
 - Fix drawing problem in pipelines with custom step of PolygonROI.
 

packaging/apple/settings.json

@@ -7,7 +7,7 @@
     "window": { "position": { "x": 100, "y": 100 },
                 "size": { "width": 640, "height": 300 } },
     "contents": [
-        { "x": 140, "y": 165, "type": "file", "path": "/Volumes/MUSICardio 4.0.2/MUSICardio.app" },
+        { "x": 140, "y": 165, "type": "file", "path": "/Volumes/MUSICardio 4.0.7/MUSICardio.app" },
         { "x": 480, "y": 165, "type": "link", "path": "/Applications" }
     ]
 }

packaging/windows/WindowsPackaging.cmake

@@ -104,7 +104,7 @@ list(APPEND
   ${DCMTK_ROOT}/bin/Release
   ${VTK_ROOT}/bin/Release
   ${QtDCM_ROOT}/bin/Release
-  ${TTK_ROOT}/bin/Release
+  ${TTK_ROOT}/bin
   ${dtk_ROOT}/bin/Release
   ${RPI_ROOT}/bin/Release
   ${ZLIB_ROOT}/Release
@@ -121,12 +121,14 @@ file(GLOB_RECURSE itk_files LIST_DIRECTORIES true \"${ITK_ROOT}/bin/*.dll\")
 file(GLOB_RECURSE vtk_files LIST_DIRECTORIES true \"${VTK_ROOT}/bin/*.dll\")
 file(GLOB_RECURSE dtk_files LIST_DIRECTORIES true \"${dtk_ROOT}/bin/*.dll\")
 file(GLOB_RECURSE dcm_files LIST_DIRECTORIES true \"${QtDCM_ROOT}/bin/*.dll\")
+file(GLOB_RECURSE ttk_files LIST_DIRECTORIES true \"${TTK_DIR}/bin/*.dll\")
 file(GLOB_RECURSE qt5_files LIST_DIRECTORIES true \"${QT_BINARY_DIR}/*.dll\")
 file(GLOB_RECURSE zlib_files LIST_DIRECTORIES true \"${ZLIB_ROOT}/*.dll\")
 list(APPEND files \${itk_files})
 list(APPEND files \${vtk_files})
 list(APPEND files \${dtk_files})
 list(APPEND files \${dcm_files})
+list(APPEND files \${ttk_files})
 list(APPEND files \${qt5_files})
 list(APPEND files \${zlib_files})
 

src/CMakeLists.txt

@@ -16,7 +16,7 @@
 cmake_minimum_required(VERSION 3.19)
 
 if(NOT DEFINED ${medInria_VERSION})
-    set(medInria_VERSION 4.0.2)
+    set(medInria_VERSION 4.0.7)
 endif()
 
 project(medInria VERSION ${medInria_VERSION})

src/app/medInria/resources/medInria.qrc

@@ -146,8 +146,10 @@
         <file>pixmaps/radio-disabled.png</file>
         <file>pixmaps/radio-checked-disabled.png</file>
         <file>pixmaps/plus-button.png</file>
-        <file>pixmaps/plus.png</file>
-        <file>pixmaps/minus.png</file>
+        <file>pixmaps/plus_white.png</file>
+        <file>pixmaps/minus_white.png</file>
+        <file>pixmaps/plus_black.png</file>
+        <file>pixmaps/minus_black.png</file>
         <file>pixmaps/checkbox-disabled.png</file>
         <file>pixmaps/checkbox-checked-disabled.png</file>
         <file>pixmaps/arrow-top-disabled.png</file>

src/layers/legacy/medCoreLegacy/database/medAbstractDatabaseImporter.cpp

@@ -514,6 +514,7 @@ void medAbstractDatabaseImporter::importData()
 
     // Now, populate the database
     medDataIndex index = this->populateDatabaseAndGenerateThumbnails (  d->data, thumb_dir );
+    d->index = index;
 
     if (d->data->hasMetaData(medMetaDataKeys::Toolbox.key()) &&
     d->data->metadata(medMetaDataKeys::Toolbox.key())=="PolygonROI" &&

src/layers/legacy/medCoreLegacy/database/medAbstractDatabaseImporter.h

@@ -48,6 +48,8 @@ class MEDCORELEGACY_EXPORT medAbstractDatabaseImporter : public medJobItemL
                                 const QUuid &uuid);
     ~medAbstractDatabaseImporter() override;
 
+    medDataIndex index(void) const;
+
 signals:
     /**
      * This signal is emitted after a successful import/index.
@@ -74,7 +76,6 @@ public slots:
     bool indexWithoutImporting ( void );
     QMap<int, QString> volumeIdToImageFile ( void );
     QString callerUuid ( void );
-    medDataIndex index(void) const;
 
     void populateMissingMetadata ( medAbstractData* medData, const QString seriesDescription );
     void addAdditionalMetaData ( medAbstractData* imData, QString aggregatedFileName, QStringList aggregatedFilesPaths );

src/layers/legacy/medCoreLegacy/database/medDatabasePersistentController.cpp

@@ -80,6 +80,8 @@ void medDatabasePersistentControllerPrivate::buildMetaDataLookup()
     metaDataLookup.insert(medMetaDataKeys::StudyDate.key(),
                           TableEntryList() << TableEntry(T_study, "date"));
     // Series Data
+    metaDataLookup.insert(medMetaDataKeys::FilePaths.key(),
+                          TableEntryList() << TableEntry(T_series, "path"));
     metaDataLookup.insert(medMetaDataKeys::Size.key(),
                           TableEntryList() << TableEntry(T_series, "size"));
     metaDataLookup.insert(medMetaDataKeys::SeriesDescription.key(),

src/layers/legacy/medCoreLegacy/database/medDatabaseReader.cpp

@@ -203,6 +203,7 @@ medAbstractData* medDatabaseReader::run()
     QFileInfo fullThumbnailPathInfo(fullThumbnailPath);
     medMetaDataKeys::SeriesThumbnail.add (medData, fullThumbnailPath);
 
+    medMetaDataKeys::FilePaths.set ( medData, seriesPath );
     medMetaDataKeys::PatientID.set ( medData, patientId );
     medMetaDataKeys::PatientName.set ( medData, patientName );
     medMetaDataKeys::BirthDate.set ( medData, birthdate );

src/layers/legacy/medImageIO/itkDCMTKImageIO.cpp

@@ -54,8 +54,8 @@ DCMTKImageIO::DCMTKImageIO()
 {
     this->SetNumberOfDimensions(3);
     this->SetNumberOfComponents(1);
-    this->SetPixelType(SCALAR);
-    this->SetComponentType(CHAR);
+    this->SetPixelType(IOPixelEnum::SCALAR);
+    this->SetComponentType(itk::IOComponentEnum::CHAR);
 
     DcmRLEDecoderRegistration::registerCodecs();
     DJDecoderRegistration::registerCodecs();
@@ -356,11 +356,11 @@ void DCMTKImageIO::DetermineNumberOfPixelComponents()
 
     if( samplesPerPixel==1 )
     {
-        this->SetPixelType ( SCALAR );
+        this->SetPixelType (itk::IOPixelEnum::SCALAR );
     }
     else
     {
-        this->SetPixelType ( RGB );
+        this->SetPixelType ( itk::IOPixelEnum::RGB );
     }
 }
 
@@ -373,7 +373,7 @@ void DCMTKImageIO::DeterminePixelType()
 
     if (condition.bad())
     {
-        this->SetComponentType(UNKNOWNCOMPONENTTYPE);
+        this->SetComponentType(itk::IOComponentEnum::UNKNOWNCOMPONENTTYPE);
         return;
     }
 
@@ -387,36 +387,36 @@ void DCMTKImageIO::DeterminePixelType()
             switch( dmp->getRepresentation() )
             {
                 case EPR_Uint8:
-                    this->SetComponentType ( UCHAR );
+                    this->SetComponentType (itk::IOComponentEnum::UCHAR );
                     break;
 
                 case EPR_Sint8:
-                    this->SetComponentType ( CHAR );
+                    this->SetComponentType (itk::IOComponentEnum::CHAR );
                     break;
 
                 case EPR_Uint16:
-                    this->SetComponentType ( USHORT );
+                    this->SetComponentType (itk::IOComponentEnum::USHORT );
                     break;
 
                 case EPR_Sint16:
-                    this->SetComponentType ( SHORT );
+                    this->SetComponentType (itk::IOComponentEnum::SHORT );
                     break;
 
                 case EPR_Uint32:
-                    this->SetComponentType ( UINT );
+                    this->SetComponentType (itk::IOComponentEnum::UINT );
                     break;
 
                 case EPR_Sint32:
-                    this->SetComponentType ( INT );
+                    this->SetComponentType (itk::IOComponentEnum::INT );
                     break;
 
                 default:
-                    this->SetComponentType (UNKNOWNCOMPONENTTYPE);
+                    this->SetComponentType (itk::IOComponentEnum::UNKNOWNCOMPONENTTYPE);
             }
         }
         else
         {
-            this->SetComponentType (UNKNOWNCOMPONENTTYPE);
+            this->SetComponentType (itk::IOComponentEnum::UNKNOWNCOMPONENTTYPE);
         }
     }
 }
@@ -770,31 +770,31 @@ void DCMTKImageIO::InternalRead (void* buffer, int slice, unsigned long pixelCou
     size_t length = pixelCount * GetNumberOfComponents();
     switch( this->GetComponentType() )
     {
-        case CHAR:
+        case itk::IOComponentEnum::CHAR:
             length *= sizeof(char);
             break;
 
-        case UCHAR:
+        case itk::IOComponentEnum::UCHAR:
             length *= sizeof(Uint8);
             break;
 
-        case SHORT:
+        case itk::IOComponentEnum::SHORT:
             length *= sizeof(Sint16);
             break;
 
-        case USHORT:
+        case itk::IOComponentEnum::USHORT:
             length *= sizeof(Uint16);
             break;
 
-        case INT:
+        case itk::IOComponentEnum::INT:
             length *= sizeof(Sint32);
             break;
 
-        case UINT:
+        case itk::IOComponentEnum::UINT:
             length *= sizeof(Uint32);
             break;
 
-        case DOUBLE:
+        case itk::IOComponentEnum::DOUBLE:
             length *= sizeof(Float64);
             break;