MITK upgrade

.github/workflows/build.yml

@@ -20,8 +20,7 @@ jobs:
 
   Create-Release:
     runs-on: ubuntu-latest
-    # needs: [Variables, Build-Linux, Build-Windows, Build-macOS]
-    needs: [Variables, Build-Linux, Build-macOS]
+    needs: [Variables, Build-Linux, Build-Windows, Build-macOS]
     steps:
     - name: Download packages
       uses: actions/download-artifact@v4
@@ -39,15 +38,15 @@ jobs:
         asset_name: CemrgApp-Linux-${{ needs.Variables.outputs.tag }}.zip
         asset_content_type: application/zip
 
-    # - name: Upload Windows package
-    #   uses: actions/upload-release-asset@v1.0.2
-    #   env:
-    #     GITHUB_TOKEN: ${{ github.token }}
-    #   with:
-    #     upload_url: ${{ github.event.release.upload_url }}
-    #     asset_path: CemrgApp-Windows.zip
-    #     asset_name: CemrgApp-Windows-${{ needs.Variables.outputs.tag }}.zip
-    #     asset_content_type: application/zip
+    - name: Upload Windows package
+      uses: actions/upload-release-asset@v1.0.2
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      with:
+        upload_url: ${{ github.event.release.upload_url }}
+        asset_path: CemrgApp-Windows.zip
+        asset_name: CemrgApp-Windows-${{ needs.Variables.outputs.tag }}.zip
+        asset_content_type: application/zip
 
     - name: Upload macOS package
       uses: actions/upload-release-asset@v1.0.2
@@ -66,7 +65,7 @@ jobs:
     steps:
     - name: Download precompiled Build folder
       run: |
-        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/EU8n4C0PlPxDgLk6PFrprY8B4KwiDaYotmur5m0q3px81w?download=1
+        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/ETN8L5OcVupGiMInP8o9MtUBNflJb57nK1Dg-jnikW0iwg?download=1
         7z x Build.zip
         rm Build.zip
         sudo mv Build /
@@ -81,7 +80,7 @@ jobs:
     - name: Install missing packages
       run: |
         sudo apt update
-        sudo DEBIAN_FRONTEND=noninteractive apt install libxt-dev libtiff5-dev libfontconfig1 mesa-common-dev libglu1-mesa-dev libxcomposite1 libxcursor1 libxrender1 libxi6 libxtst6 libasound2 libnspr4 libnss3 libxkbcommon-dev libxkbcommon-x11-dev doxygen git cmake python3-pip gcc g++ -y
+        sudo DEBIAN_FRONTEND=noninteractive apt install doxygen graphviz libfreetype6-dev libglu1-mesa-dev libssl-dev libtiff5-dev libwrap0-dev libxcomposite1 libxcursor1 libxi-dev libxkbcommon-x11-0 libxt-dev mesa-common-dev -y
         sudo apt remove --auto-remove icu-devtools libicu-dev -y
 
     - name: Install Qt
@@ -91,9 +90,9 @@ jobs:
         sudo aqt install --outputdir /Qt 5.12.10 linux desktop -m qtcharts qtnetworkauth qtpurchasing qtdatavis3d qtscript qtvirtualkeyboard qtwebengine qtwebglplugin
 
     - name: Clone MITK
-      run: sudo git clone --branch v2018.04.2 https://phabricator.mitk.org/source/mitk.git /MITK
+      run: sudo git clone --branch v2022.10 https://phabricator.mitk.org/source/mitk.git /MITK
 
-    - name: Change timestamps of MITK directory
+    - name: Change timestamps of the MITK directory
       run: sudo find /MITK/ -exec touch -a -m -d 20210401 {} \;
 
     - name: Clone CemrgApp
@@ -120,7 +119,7 @@ jobs:
       run: |
         make package -j4
         cd _CPack_Packages/Linux/TGZ
-        mv MITK-v2018.04.2-linux-x86_64 CemrgApp-Linux
+        mv MITK-v2022.10-linux-x86_64 CemrgApp-Linux
         rm CemrgApp-Linux/Mitk*
         rm CemrgApp-Linux/bin/MitkWorkbench*
         mv /Externals/* CemrgApp-Linux/bin/
@@ -135,85 +134,86 @@ jobs:
         path: CemrgApp-Linux.zip
 
 
-  # Build-Windows:
-  #   runs-on: windows-2016
-  #   needs: [Variables]
-  #   steps:
-  #   - name: Uninstall NSIS
-  #     run: |
-  #       & 'C:/Program Files (x86)/NSIS/uninst-nsis.exe' /S
-  #
-  #   - name: Download precompiled Build folder
-  #     working-directory: c:\
-  #     run: |
-  #       c:\msys64\usr\bin\wget.exe -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/EUFa_AWPBI1OnnQwXA_ilu8Bq38U6OjiR4XKDcxDKo5wnw?download=1
-  #       7z x Build.zip
-  #       del Build.zip
-  #
-  #   - name: Download external libraries
-  #     working-directory: c:\
-  #     run: |
-  #       c:\msys64\usr\bin\wget.exe -q -O Externals.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/Ea8urj-xMS5CoEnt3lS-A9QBLoAi1EXfP3lM26MRn11OrA?download=1
-  #       7z x Externals.zip
-  #       del Externals.zip
-  #
-  #   - name: Install Qt
-  #     working-directory: c:\
-  #     run: |
-  #       pip install aqtinstall
-  #       mkdir Qt
-  #       python -m aqt install --outputdir Qt 5.12.10 windows desktop win64_msvc2017_64 -m qtcharts qtnetworkauth qtpurchasing qtdatavis3d qtscript qtvirtualkeyboard qtwebengine qtwebglplugin
-  #
-  #   - name: Clone MITK
-  #     run: git clone --branch v2018.04.2 https://phabricator.mitk.org/source/mitk.git c:\MITK
-  #
-  #   - name: Change timestamps of MITK directory
-  #     run: dir -R c:\MITK | foreach { $_.LastWriteTime = [DateTime]::ParseExact('01-04-21', 'dd-MM-yy', $null) }
-  #
-  #   - name: Clone CemrgApp
-  #     uses: actions/checkout@v4
-  #     with:
-  #       path: CemrgApp
-  #
-  #   - name: Copy CemrgApp to root
-  #     shell: cmd
-  #     run: |
-  #       mkdir c:\CemrgApp
-  #       xcopy /e .\CemrgApp\* c:\CemrgApp\
-  #       rd /s /q CemrgApp
-  #
-  #   - name: Update the CemrgApp version
-  #     working-directory: c:\CemrgApp
-  #     shell: powershell
-  #     run: |
-  #       rm CemrgApp/Applications/MainApp/version.txt
-  #       echo ${{ needs.Variables.outputs.tag }} >> CemrgApp/Applications/MainApp/version.txt
-  #       echo ${{ needs.Variables.outputs.sha }} >> CemrgApp/Applications/MainApp/version.txt
-  #
-  #   - name: Add MSBuild to PATH
-  #     uses: microsoft/setup-msbuild@v1.0.2
-  #
-  #   - name: Build
-  #     working-directory: c:\Build
-  #     run: MSBuild MITK-superbuild.sln /p:Configuration=Release /p:Platform=x64 -m:4
-  #
-  #   - name: Package
-  #     working-directory: c:\Build\MITK-build
-  #     run: |
-  #       MSBuild PACKAGE.vcxproj /p:Configuration=Release /p:Platform=x64 -m:4
-  #       cd _CPack_Packages\win64\ZIP
-  #       ren MITK-v2018.04.2-windows-x86_64 CemrgApp-Windows
-  #       xcopy /e c:\Externals\* .\CemrgApp-Windows\bin\
-  #       copy c:\CemrgApp\README.md .\CemrgApp-Windows\
-  #       del CemrgApp-Windows\bin\MitkWorkbench.*
-  #       7z a CemrgApp-Windows.zip CemrgApp-Windows
-  #       move CemrgApp-Windows.zip ${{ github.workspace }}\
-  #
-  #   - name: Upload package
-  #     uses: actions/upload-artifact@v4
-  #     with:
-  #       name: Packages-Windows
-  #       path: CemrgApp-Windows.zip
+  Build-Windows:
+    runs-on: windows-2016
+    needs: [Variables]
+    steps:
+    - name: Uninstall NSIS
+      run: |
+        & 'C:/Program Files (x86)/NSIS/uninst-nsis.exe' /S
+
+    - name: Download precompiled Build folder
+      working-directory: c:\
+      run: |
+        c:\msys64\usr\bin\wget.exe -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/EXJ2fam5aCNLvRW8kk1o6jwBzsI50I0iuZ1vfq4oOPRbJQ?download=1
+        7z x Build.zip
+        del Build.zip
+
+    - name: Download external libraries
+      working-directory: c:\
+      run: |
+        c:\msys64\usr\bin\wget.exe -q -O Externals.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/Ea8urj-xMS5CoEnt3lS-A9QBLoAi1EXfP3lM26MRn11OrA?download=1
+        7z x Externals.zip
+        del Externals.zip
+
+    - name: Install Qt
+      working-directory: c:\
+      run: |
+        pip install aqtinstall
+        mkdir Qt
+        python -m aqt install --outputdir Qt 5.12.10 windows desktop win64_msvc2017_64 -m qtcharts qtnetworkauth qtpurchasing qtdatavis3d qtscript qtvirtualkeyboard qtwebengine qtwebglplugin
+
+    - name: Clone MITK
+      run: git clone --branch v2022.10 https://phabricator.mitk.org/source/mitk.git c:\MITK
+
+    - name: Change timestamps of the MITK directory
+      run: dir -R c:\MITK | foreach { $_.LastWriteTime = [DateTime]::ParseExact('01-04-21', 'dd-MM-yy', $null) }
+
+    - name: Clone CemrgApp
+      uses: actions/checkout@v4
+      with:
+        path: CemrgApp
+
+    - name: Copy CemrgApp to root
+      shell: cmd
+      run: |
+        mkdir c:\CemrgApp
+        xcopy /e .\CemrgApp\* c:\CemrgApp\
+        rd /s /q CemrgApp
+
+    - name: Update the CemrgApp version
+      working-directory: c:\CemrgApp
+      shell: powershell
+      run: |
+        rm CemrgApp/Applications/MainApp/version.txt
+        echo ${{ needs.Variables.outputs.tag }} >> CemrgApp/Applications/MainApp/version.txt
+        echo ${{ needs.Variables.outputs.sha }} >> CemrgApp/Applications/MainApp/version.txt
+
+    - name: Add MSBuild to PATH
+      uses: microsoft/setup-msbuild@v1.0.2
+
+    - name: Build
+      working-directory: c:\Build
+      run: MSBuild MITK-superbuild.sln /p:Configuration=Release /p:Platform=x64 -m:4
+
+    - name: Package
+      working-directory: c:\Build\MITK-build
+      run: |
+        MSBuild PACKAGE.vcxproj /p:Configuration=Release /p:Platform=x64 -m:4
+        cd _CPack_Packages\win64\ZIP
+        ren MITK-v2022.10-windows-x86_64 CemrgApp-Windows
+        xcopy /e c:\Externals\* .\CemrgApp-Windows\bin\
+        copy c:\CemrgApp\README.md .\CemrgApp-Windows\
+        del CemrgApp-Windows\Mitk*
+        del CemrgApp-Windows\bin\MitkWorkbench.*
+        7z a CemrgApp-Windows.zip CemrgApp-Windows
+        move CemrgApp-Windows.zip ${{ github.workspace }}\
+
+    - name: Upload package
+      uses: actions/upload-artifact@v4
+      with:
+        name: Packages-Windows
+        path: CemrgApp-Windows.zip
 
 
   Build-macOS:
@@ -223,7 +223,7 @@ jobs:
     - name: Download precompiled Build folder
       working-directory: /Users/Shared
       run: |
-        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/EVzkObB3qiZLpEQsCLB3pdcBjaGDuzLapXFvujnDP_xr1A?download=1
+        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/EX4dERE2ilFNmuv2Od0GaOoBuUSgzBS_TzwEqf9KVtmsXQ?download=1
         7z x Build.zip
         rm Build.zip
 
@@ -234,15 +234,8 @@ jobs:
         7z x Externals.zip
         rm Externals.zip
 
-    - name: Download patch for MITK
-      working-directory: /Users/Shared
-      run: |
-        wget -q -O Patch.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/EQ5LKrqH_fZNt9eGA7RBcC4B9YyyF0SwFeo9hIm9zkqLTQ?download=1
-        7z x Patch.zip
-        rm Patch.zip
-
     - name: Install missing packages
-      run: brew install gmp doxygen llvm@9
+      run: brew install doxygen libomp
 
     - name: Install Qt
       working-directory: /Users/Shared
@@ -252,15 +245,9 @@ jobs:
         python3 -m aqt install --outputdir Qt 5.12.10 mac desktop -m qtcharts qtnetworkauth qtpurchasing qtdatavis3d qtscript qtvirtualkeyboard qtwebengine qtwebglplugin
 
     - name: Clone MITK
-      run: git clone --branch v2018.04.2 https://phabricator.mitk.org/source/mitk.git /Users/Shared/MITK
-
-    - name: Patch MITK
-      working-directory: /Users/Shared
-      run: |
-        cp Patch/usServiceListeners.cpp MITK/Modules/CppMicroServices/core/src/service/usServiceListeners.cpp
-        cp Patch/usListenerFunctors_p.h MITK/Modules/CppMicroServices/core/src/util/usListenerFunctors_p.h
+      run: git clone --branch v2022.10 https://phabricator.mitk.org/source/mitk.git /Users/Shared/MITK
 
-    - name: Change timestamps of MITK directory
+    - name: Change timestamps of the MITK directory
       run: find /Users/Shared/MITK/ -exec touch -a -m -t 202104010000 {} \;
 
     - name: Clone CemrgApp
@@ -278,17 +265,6 @@ jobs:
         sudo echo ${{ needs.Variables.outputs.tag }} >> CemrgApp/Applications/MainApp/version.txt
         sudo echo ${{ needs.Variables.outputs.sha }} >> CemrgApp/Applications/MainApp/version.txt
 
-    - name: Set environment variables
-      run: |
-        echo "/usr/local/opt/llvm@9/bin:$PATH" >> $GITHUB_PATH
-        echo "LDFLAGS=-L/usr/local/opt/llvm@9/lib" >> $GITHUB_ENV
-        echo "CPPFLAGS=-I/usr/local/opt/llvm@9/include" >> $GITHUB_ENV
-        echo "LLVM_VERSION=9.0" >> $GITHUB_ENV
-        echo "LLVM_DIRECTORY=/usr/local/opt/llvm@9" >> $GITHUB_ENV
-        echo "CC=/usr/local/opt/llvm@9/bin/clang" >> $GITHUB_ENV
-        echo "CXX=/usr/local/opt/llvm@9/bin/clang++" >> $GITHUB_ENV
-        echo "CPLUS_INCLUDE_PATH=/usr/local/opt/llvm@9/include/c++/v1:/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include" >> $GITHUB_ENV
-
     - name: Build
       working-directory: /Users/Shared/Build
       run: |
@@ -301,7 +277,7 @@ jobs:
       run: make package -j6
 
     - name: Create DMG
-      working-directory: /Users/Shared/Build/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-v2018.04.2-local_changes-macos-x86_64
+      working-directory: /Users/Shared/Build/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-v2022.10-macos-x86_64
       run: |
         rsync -au MitkWorkbench.app/Contents/Frameworks/ CemrgApp.app/Contents/Frameworks
         rsync -au MitkWorkbench.app/Contents/MacOS/ CemrgApp.app/Contents/MacOS

.github/workflows/test.yml

@@ -8,7 +8,7 @@ jobs:
     steps:
     - name: Download precompiled Build folder
       run: |
-        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/Ef5Vu6za325GoIIStbIcmg4BgWlVBGtUx6jp1GrxNLYrFw?download=1
+        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/ES5xxspvCyRGoHISDFTLifkBrcTmxNWCX4bzyUT_AkEnAg?download=1
         7z x Build.zip
         rm Build.zip
         sudo mv Build /
@@ -19,11 +19,11 @@ jobs:
         7z x Externals.zip
         rm Externals.zip
         sudo mv Externals /
-    
+
     - name: Install missing packages
       run: |
         sudo apt update
-        sudo DEBIAN_FRONTEND=noninteractive apt install libxt-dev libtiff5-dev libfontconfig1 mesa-common-dev libglu1-mesa-dev libxcomposite1 libxcursor1 libxrender1 libxi6 libxtst6 libasound2 libnspr4 libnss3 libxkbcommon-dev libxkbcommon-x11-dev libtbb2 doxygen git cmake python3-pip gcc g++ -y
+        sudo DEBIAN_FRONTEND=noninteractive apt install doxygen graphviz libfreetype6-dev libglu1-mesa-dev libssl-dev libtiff5-dev libwrap0-dev libxcomposite1 libxcursor1 libxi-dev libxkbcommon-x11-0 libxt-dev mesa-common-dev libtbb2 -y
         sudo apt remove --auto-remove icu-devtools libicu-dev -y
 
     - name: Install Qt
@@ -33,7 +33,7 @@ jobs:
         sudo aqt install --outputdir /Qt 5.12.10 linux desktop -m qtcharts qtnetworkauth qtpurchasing qtdatavis3d qtscript qtvirtualkeyboard qtwebengine qtwebglplugin
 
     - name: Clone MITK
-      run: sudo git clone --branch v2018.04.2 https://phabricator.mitk.org/source/mitk.git /MITK
+      run: sudo git clone --branch v2022.10 https://phabricator.mitk.org/source/mitk.git /MITK
 
     - name: Disable tests for CppMicroServices
       run: sudo sed -i 's/set(US_BUILD_TESTING ON)/set(US_BUILD_TESTING OFF)/' /MITK/Modules/CMakeLists.txt
@@ -61,7 +61,7 @@ jobs:
       env:
         QT_PLUGIN_PATH: /Qt/5.12.10/gcc_64/plugins
         QT_QPA_PLATFORM: minimal
-      run: ctest -R Cemrg -V
+      run: ctest -R Cemrg -C Debug -V
 
     - name: Code Coverage
       uses: codecov/codecov-action@v4

CemrgApp/Applications/MainApp/CMakeLists.txt

@@ -3,11 +3,6 @@ if(MITK_BUILD_APP_CemrgApp)
   project(MainApp)
 
   set(MY_APP_NAME CemrgApp)
-  set(_app_options)
-
-  if(MITK_SHOW_CONSOLE_WINDOW)
-    list(APPEND _app_options SHOW_CONSOLE)
-  endif()
 
   # Create a cache entry for the provisioning file which is used to export
   # the file name in the MITKConfig.cmake file. This will keep external projects
@@ -25,7 +20,7 @@ if(MITK_BUILD_APP_CemrgApp)
 
     org.mitk.gui.qt.datamanager
     org.mitk.gui.qt.basicimageprocessing
-    org.mitk.gui.qt.dicom
+    org.mitk.gui.qt.dicombrowser
     #org.mitk.gui.qt.diffusionimaging
     #org.mitk.gui.qt.diffusionimaging.registration
     org.mitk.gui.qt.pointsetinteraction
@@ -75,7 +70,6 @@ if(MITK_BUILD_APP_CemrgApp)
     #PLUGINS ${_plugins}
     EXCLUDE_PLUGINS ${_exclude_plugins}
     SOURCES ${_src_files}
-    ${_app_options}
   )
 
   mitk_use_modules(TARGET ${MY_APP_NAME}
@@ -101,5 +95,4 @@ if(MITK_BUILD_APP_CemrgApp)
     add_dependencies(${MY_APP_NAME} ${MITK_MODULES_ENABLED_PLUGINS})
   endif()
 
-
 endif()

CemrgApp/Applications/MainApp/CemrgApp.cpp

@@ -48,7 +48,7 @@ int main(int argc, char** argv) {
     splash.setWindowFlags(Qt::SplashScreen | Qt::WindowStaysOnTopHint | Qt::FramelessWindowHint);
     splash.show();
     if (!version.isEmpty())
-        splash.showMessage("CemrgApp " + version + " (" + sha + ")\nPowered by: MITK v2018.04.2", Qt::AlignLeft, Qt::white);
+        splash.showMessage("CemrgApp " + version + " (" + sha + ")\nPowered by: MITK v2022.10", Qt::AlignLeft, Qt::white);
     QTimer::singleShot(4000, &splash, SLOT(close()));
 
     // -------------------------------------------------------------------