REVERT_TO_MITKv18

Author: alonsoJASL

.github/workflows/build.yml

@@ -60,12 +60,12 @@ jobs:
 
 
   Build-Linux:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-18.04
     needs: [Variables]
     steps:
     - name: Download precompiled Build folder
       run: |
-        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/ETN8L5OcVupGiMInP8o9MtUBNflJb57nK1Dg-jnikW0iwg?download=1
+        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/EU8n4C0PlPxDgLk6PFrprY8B4KwiDaYotmur5m0q3px81w?download=1
         7z x Build.zip
         rm Build.zip
         sudo mv Build /
@@ -80,7 +80,7 @@ jobs:
     - name: Install missing packages
       run: |
         sudo apt update
-        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 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-6 g++-6 -y
         sudo apt remove --auto-remove icu-devtools libicu-dev -y
 
     - name: Install Qt
@@ -90,9 +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 v2021.02 https://phabricator.mitk.org/source/mitk.git /MITK
+      run: sudo git clone --branch v2018.04.2 https://phabricator.mitk.org/source/mitk.git /MITK
 
-    - name: Change timestamps of the MITK directory
+    - name: Change timestamps of MITK directory
       run: sudo find /MITK/ -exec touch -a -m -d 20210401 {} \;
 
     - name: Clone CemrgApp
@@ -119,7 +119,7 @@ jobs:
       run: |
         make package -j4
         cd _CPack_Packages/Linux/TGZ
-        mv MITK-v2021.02-linux-x86_64 CemrgApp-Linux
+        mv MITK-v2018.04.2-linux-x86_64 CemrgApp-Linux
         rm CemrgApp-Linux/Mitk*
         rm CemrgApp-Linux/bin/MitkWorkbench*
         mv /Externals/* CemrgApp-Linux/bin/
@@ -222,7 +222,7 @@ 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/EX4dERE2ilFNmuv2Od0GaOoBuUSgzBS_TzwEqf9KVtmsXQ?download=1
+        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/EVzkObB3qiZLpEQsCLB3pdcBjaGDuzLapXFvujnDP_xr1A?download=1
         7z x Build.zip
         rm Build.zip
 
@@ -233,8 +233,15 @@ 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 doxygen libomp
+      run: brew install gmp doxygen llvm@9
 
     - name: Install Qt
       working-directory: /Users/Shared
@@ -244,9 +251,15 @@ 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 v2021.02 https://phabricator.mitk.org/source/mitk.git /Users/Shared/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
 
-    - name: Change timestamps of the MITK directory
+    - name: Change timestamps of MITK directory
       run: find /Users/Shared/MITK/ -exec touch -a -m -t 202104010000 {} \;
 
     - name: Clone CemrgApp
@@ -264,6 +277,17 @@ 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: |
@@ -276,7 +300,7 @@ jobs:
       run: make package -j6
 
     - name: Create DMG
-      working-directory: /Users/Shared/Build/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-v2021.02-macos-x86_64
+      working-directory: /Users/Shared/Build/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-v2018.04.2-local_changes-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

@@ -4,11 +4,11 @@ on: [push, pull_request]
 
 jobs:
   Test-n-Coverage:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-18.04
     steps:
     - name: Download precompiled Build folder
       run: |
-        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/ES5xxspvCyRGoHISDFTLifkBrcTmxNWCX4bzyUT_AkEnAg?download=1
+        wget -q -O Build.zip https://emckclac-my.sharepoint.com/:u:/g/personal/k2143219_kcl_ac_uk/Ef5Vu6za325GoIIStbIcmg4BgWlVBGtUx6jp1GrxNLYrFw?download=1
         7z x Build.zip
         rm Build.zip
         sudo mv Build /
@@ -19,27 +19,21 @@ 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 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 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-6 g++-6 -y
         sudo apt remove --auto-remove icu-devtools libicu-dev -y
-
+    
     - name: Install Qt
       run: |
         sudo pip3 install --upgrade setuptools
         sudo pip3 install aqtinstall
         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 v2021.02 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
-
-    - name: Change timestamps of the MITK directory
-      run: sudo find /MITK/ -exec touch -a -m -d 20210401 {} \;
+      run: sudo git clone --branch v2018.04.2 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
@@ -54,7 +48,7 @@ jobs:
 
     - name: Move CemrgApp to root
       run: sudo mv CemrgApp /
-
+    
     - name: Build
       working-directory: /Build
       env:
@@ -67,7 +61,7 @@ jobs:
       env:
         QT_PLUGIN_PATH: /Qt/5.12.10/gcc_64/plugins
         QT_QPA_PLATFORM: minimal
-      run: ctest -R Cemrg -C Debug -V
+      run: ctest -R Cemrg -V
 
     - name: Code Coverage
       uses: codecov/codecov-action@v1

CemrgApp/Applications/MainApp/CMakeLists.txt

@@ -3,6 +3,11 @@ 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
@@ -20,7 +25,7 @@ if(MITK_BUILD_APP_CemrgApp)
 
     org.mitk.gui.qt.datamanager
     org.mitk.gui.qt.basicimageprocessing
-    org.mitk.gui.qt.dicombrowser
+    org.mitk.gui.qt.dicom
     #org.mitk.gui.qt.diffusionimaging
     #org.mitk.gui.qt.diffusionimaging.registration
     org.mitk.gui.qt.pointsetinteraction
@@ -31,6 +36,7 @@ if(MITK_BUILD_APP_CemrgApp)
     kcl.cemrgapp.mainapp
     kcl.cemrgapp.easi
     kcl.cemrgapp.powertrans
+    kcl.cemrgapp.atrialfibres
     kcl.cemrgapp.mmcwplugin
     kcl.cemrgapp.mmeasurement
     kcl.cemrgapp.scar
@@ -69,6 +75,7 @@ if(MITK_BUILD_APP_CemrgApp)
     #PLUGINS ${_plugins}
     EXCLUDE_PLUGINS ${_exclude_plugins}
     SOURCES ${_src_files}
+    ${_app_options}
   )
 
   mitk_use_modules(TARGET ${MY_APP_NAME}
@@ -94,4 +101,5 @@ if(MITK_BUILD_APP_CemrgApp)
     add_dependencies(${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 v2021.10", Qt::AlignLeft, Qt::white);
+        splash.showMessage("CemrgApp " + version + " (" + sha + ")\nPowered by: MITK v2018.04.2", Qt::AlignLeft, Qt::white);
     QTimer::singleShot(4000, &splash, SLOT(close()));
 
     // -------------------------------------------------------------------
@@ -61,4 +61,4 @@ int main(int argc, char** argv) {
     //myApp.setProperty(mitk::BaseApplication::PROP_APPLICATION, "org.mitk.qt.extapplication");
     myApp.setProperty(mitk::BaseApplication::PROP_APPLICATION, "kcl.cemrgapp.mainapp");
     return myApp.run();
-}
+}

CemrgApp/Applications/MainApp/target_libraries.cmake

@@ -7,7 +7,7 @@ set(target_libraries
 
   org_mitk_gui_qt_datamanager
   org_mitk_gui_qt_basicimageprocessing
-  org_mitk_gui_qt_dicombrowser
+  org_mitk_gui_qt_dicom
   #org_mitk_gui_qt_diffusionimaging
   #org_mitk_gui_qt_diffusionimaging_registration
   org_mitk_gui_qt_pointsetinteraction

CemrgApp/Applications/MainApp/version.txt

@@ -1,2 +1,2 @@
-3.0-alpha
-d9581d2
+2.2
+69e5e1e

CemrgApp/CMakeExternals/VMTK.cmake

@@ -34,8 +34,8 @@ if(MITK_USE_VMTK)
       )
     endif()
 
-    set(VMTK_GIT_REPOSITORY "https://github.com/CemrgDevelopers/vmtk.git" CACHE STRING "The git repository for cloning VMTK")
-    set(VMTK_GIT_TAG "f9ed6280b40fbfabd11f2b54c4a432a0a9b382f9" CACHE STRING "The git tag/hash to be used when cloning from VMTK_GIT_REPOSITORY")
+    set(VMTK_GIT_REPOSITORY "https://github.com/vmtk/vmtk.git" CACHE STRING "The git repository for cloning VMTK")
+    set(VMTK_GIT_TAG "v1.4.0" CACHE STRING "The git tag/hash to be used when cloning from VMTK_GIT_REPOSITORY")
     mark_as_advanced(VMTK_GIT_REPOSITORY VMTK_GIT_TAG)
 
     if (UNIX)

CemrgApp/Modules/CemrgAppModule/cmdapps/CMakeLists.txt

@@ -4,8 +4,11 @@ option(BUILD_CEMRG_PROJECTION_OPTS "Build Scar Map Projection Options command li
 option(BUILD_CEMRG_CLIPPINGTOOL "Build clipping valve command line app. " ON)
 option(BUILD_CEMRG_PROJECTLGE "Build lge projection command line app. " ON)
 option(BUILD_CEMRG_IM2INR "Build image to inr command line app. " ON)
+option(BUILD_CEMRG_COLOURSURF "Build colour surface command line app. " ON)
 option(BUILD_CEMRG_VENTRICLE_SEGMENTATION_RELABEL "Build ventricle segmentation relabelling command line app" ON)
 option(BUILD_CEMRG_MORPH_ANALYSIS "Build atrial morph analysis" ON)
+option(BUILD_CEMRG_IMAGE_CONVERT "Build image convert format" ON)
+option(BUILD_CEMRG_SURFACE_AREA "Build surface area calculator" ON)
 
 if(BUILD_CemrgCMDApps)
   mitkFunctionCreateCommandLineApp(
@@ -55,6 +58,14 @@ if(BUILD_CEMRG_IM2INR)
   )
 endif()
 
+if(BUILD_CEMRG_COLOURSURF)
+  mitkFunctionCreateCommandLineApp(
+    NAME CemrgColourSurface
+    DEPENDS MitkCemrgAppModule
+    CPP_FILES CemrgColourSurface.cpp
+  )
+endif()
+
 if(BUILD_CEMRG_VENTRICLE_SEGMENTATION_RELABEL)
   mitkFunctionCreateCommandLineApp(
     NAME CemrgVentricleSegmRelabel
@@ -70,3 +81,19 @@ if(BUILD_CEMRG_MORPH_ANALYSIS)
     CPP_FILES CemrgMorphAnalysis.cpp
   )
 endif()
+
+if(BUILD_CEMRG_IMAGE_CONVERT)
+  mitkFunctionCreateCommandLineApp(
+    NAME CemrgImageConvertFormat
+    DEPENDS MitkSegmentation MitkCemrgAppModule
+    CPP_FILES CemrgImageConvertFormat.cpp
+  )
+endif()
+
+IF(BUILD_CEMRG_SURFACE_AREA)
+    mitkFunctionCreateCommandLineApp(
+        NAME CemrgAreaFromThreshold
+        DEPENDS MitkSegmentation MitkCemrgAppModule
+        CPP_FILES CemrgAreaFromThreshold.cpp
+    )
+ENDIF()

CemrgApp/Modules/CemrgAppModule/cmdapps/CemrgAppCmdTemplate.cpp

@@ -49,23 +49,23 @@ int main(int argc, char* argv[]) {
     // How should arguments be prefixed
     parser.setArgumentPrefix("--", "-");
 
-  // Add arguments. Unless specified otherwise, each argument is optional.
-  // See mitkCommandLineParser::addArgument() for more information.
-  parser.addArgument(
-    "input", "i", mitkCommandLineParser::File,
-    "Input Image", "Any image format known to MITK.",
-    us::Any(), false);
-  parser.addArgument(
-    "output", "o", mitkCommandLineParser::File,
-    "Output file", "Where to save the output.",
-    us::Any(), false);
-  parser.addArgument(
-    "offset", "f", mitkCommandLineParser::Int,
-    "Offset", "the offset integer to add to each voxel.",
-    us::Any(), false);
-  parser.addArgument( // optional
-    "verbose", "v", mitkCommandLineParser::Bool,
-    "Verbose Output", "Whether to produce verbose output");
+    // Add arguments. Unless specified otherwise, each argument is optional.
+    // See mitkCommandLineParser::addArgument() for more information.
+    parser.addArgument(
+        "input", "i", mitkCommandLineParser::InputFile,
+        "Input Image", "Any image format known to MITK.",
+        us::Any(), false);
+    parser.addArgument(
+        "output", "o", mitkCommandLineParser::OutputFile,
+        "Output file", "Where to save the output.",
+        us::Any(), false);
+    parser.addArgument(
+        "offset", "f", mitkCommandLineParser::Int,
+        "Offset", "the offset integer to add to each voxel.",
+        us::Any(), false);
+    parser.addArgument( // optional
+        "verbose", "v", mitkCommandLineParser::Bool,
+        "Verbose Output", "Whether to produce verbose output");
 
     // Parse arguments.
     // This method returns a mapping of long argument names to their values.