410

slicer-base/Dockerfile

@@ -1,7 +1,7 @@
 FROM slicer/buildenv-qt5-centos7:latest
 
 # Slicer master 2018-12-13
-ENV SLICER_VERSION 27630
+ENV SLICER_VERSION 27501
 
 RUN \
   #
@@ -21,7 +21,8 @@ RUN \
     -DQt5_DIR:PATH=${Qt5_DIR} \
     -DSlicer_BUILD_ITKPython:BOOL=OFF \
     -DSlicer_INSTALL_ITKPython:BOOL=OFF \
-      /usr/src/Slicer && \
+      /usr/src/Slicer
+RUN \
   #
   # Split the superbuild commands (what is executed by ninja) into building Slicer's
   # dependencies, and building Slicer itself.
@@ -52,22 +53,22 @@ RUN \
     echo "cmake --build /usr/src/Slicer-build/Slicer-build --target package -- \$BUILD_TOOL_FLAGS | tee /usr/src/Slicer-build/Slicer-build/PACKAGES.txt" >> BuildSlicer.sh && \
     echo "cat /usr/src/Slicer-build/Slicer-build/PACKAGES.txt | gawk 'match(\$0, /CPack: - package: (.*) generated/, a) {print a[1]}' > /usr/src/Slicer-build/Slicer-build/PACKAGE_FILE.txt" >> BuildSlicer.sh && \
     chmod +x BuildSlicer.sh && \
-    rm xx01 xx01-no-slicer-build && \
-  #
+    rm xx01 xx01-no-slicer-build
+RUN \
+   cd /usr/src/Slicer-build && \
   # Build dependencies
   #
-  ./BuildSlicerDependencies.sh && \
+  ./BuildSlicerDependencies.sh
+RUN \
   #
   # Cleanup
   #
+  cd /usr/src/Slicer-build && \ 
   # Remove all object files
   find . -name '*.o' -delete && \
   # Remove all git directories
   find . -name .git -type d -prune -exec rm -rf "{}" \; && \
   # Remove files
-  rm -f *.cmake *.txt *.applied *.updated *.in *.tcl Makefile && \
-  rm -f *.tgz *.tar.gz *.zip && \
-  rm -rf CMakeFiles && \
   # Remove all python-* directories except python-install
   find . -maxdepth 1 -type d  -name python-install -o -type d -name "python-*" -exec rm -rf "{}" \; && \
   rm -rf NUMPY && \
@@ -92,8 +93,7 @@ RUN \
   find DCMTK -name '*.cc' -delete && \
   find ITK -name '*.cxx' -delete -o -name '*.cpp' -delete && \
   find VTK -name '*.cxx' -delete -o -name '*.cpp' -delete && \
-  rm -rf CTK-build/PythonQt/generated* && \
-  rm -rf /usr/src/Slicer
+  rm -rf CTK-build/PythonQt/generated*
 
 WORKDIR /usr/src/Slicer-build
 

slicer-build/Dockerfile

@@ -1,4 +1,11 @@
-FROM slicer/slicer-base:latest
+FROM slicer/slicer-base:410
+
+
+# Update packages and install new ones for opengl
+RUN \
+  # UPDATE
+  yum -y update && \
+  yum -y install xorg-x11-drv-intel mesa-dri-drivers mesa-libGL
 
 RUN \
   #
@@ -18,8 +25,37 @@ RUN \
   find lib -name '*.a' -delete && \
   rm -rf _CPack_Packages
 
+RUN \
+  cd /usr/src/Slicer-build/Slicer-build && \
+  ninja install
+
+# Install dependencies we need:
+RUN \
+  # SlicerOpenIGTLink (should also grab and build https://github.com/openigtlink/OpenIGTLink)
+  cd /usr/src && \
+  git clone https://github.com/openigtlink/SlicerOpenIGTLink.git && \
+  cd SlicerOpenIGTLink && \
+  git checkout 4.10 && \
+  mkdir build && \
+  cd build && \
+  cmake .. -GNinja -DADDITIONAL_CXX_FLAGS="-O" -DSlicer_DIR="/usr/src/Slicer-build/Slicer-build" && \
+  ninja
+
+RUN \
+  # SlicerIGT
+  cd /usr/src && \
+  git clone https://github.com/SlicerIGT/SlicerIGT.git && \
+  cd SlicerIGT && \
+  mkdir build && \
+  cd build && \
+  cmake .. -GNinja -DADDITIONAL_CXX_FLAGS="-O" -DSlicer_DIR="/usr/src/Slicer-build/Slicer-build" && \
+  ninja && \
+  ninja install
+
 WORKDIR /usr/src/Slicer-build/Slicer-build
 
+ADD local_home_config /root/.config
+
 CMD bash
 
 # Build-time metadata as defined at http://label-schema.org

slicer-build/local_home_config/NA-MIC/Slicer-0.ini

@@ -0,0 +1,68 @@
+[Extensions]
+InstallPath=/root/.config/NA-MIC/Extensions-0
+ManagerEnabled=true
+ServerUrl=http://slicer.kitware.com/midas3
+
+[LogFiles]
+000=/tmp/Slicer-/Slicer_0_20190104_171028.log
+001=/tmp/Slicer-/Slicer_0_20190104_170906.log
+002=/tmp/Slicer-/Slicer_0_20190104_170706.log
+003=/tmp/Slicer-/Slicer_0_20190104_170134.log
+004=/tmp/Slicer-/Slicer_0_20190104_165856.log
+005=/tmp/Slicer-/Slicer_0_20190104_165744.log
+NumberOfFilesToKeep=10
+
+[Modules]
+AdditionalPaths=/usr/src/SlicerOpenIGTLink/build/inner-build/lib/Slicer-4.10/qt-loadable-modules, /usr/src/SlicerOpenIGTLink/build/inner-build/lib/Slicer-4.10/qt-scripted-modules, /usr/src/SlicerIGT/build/lib/Slicer-4.10/qt-loadable-modules, /usr/src/SlicerIGT/build/lib/Slicer-4.10/qt-scripted-modules
+IgnoreModules=@Invalid()
+MostRecentlySelectedPath=/usr/src/SlicerIGT/build/lib/Slicer-4.10/qt-scripted-modules
+
+[frequency]
+coefficient=1
+id=vtkMRMLUnitNodeApplicationFrequency
+maximum=10000
+minimum=-10000
+offset=0
+precision=3
+prefix=
+suffix=Hz
+
+[intensity]
+coefficient=1
+id=vtkMRMLUnitNodeApplicationIntensity
+maximum=10000
+minimum=-10000
+offset=0
+precision=3
+prefix=
+suffix=W/m^2
+
+[length]
+coefficient=1
+id=vtkMRMLUnitNodeApplicationLength
+maximum=10000
+minimum=-10000
+offset=0
+precision=3
+prefix=
+suffix=mm
+
+[time]
+coefficient=1
+id=vtkMRMLUnitNodeApplicationTime
+maximum=10000
+minimum=-10000
+offset=0
+precision=3
+prefix=
+suffix=s
+
+[velocity]
+coefficient=1
+id=vtkMRMLUnitNodeApplicationVelocity
+maximum=10000
+minimum=-10000
+offset=0
+precision=3
+prefix=
+suffix=m/s

slicer-build/local_home_config/NA-MIC/Slicer.ini

@@ -0,0 +1,122 @@
+[General]
+DefaultScenePath=/root/Documents
+SlicerWikiURL=http://www.slicer.org/slicerWiki/index.php
+disable-builtin-cli-modules=false
+disable-builtin-loadable-modules=false
+disable-builtin-scripted-loadable-modules=false
+disable-cli-modules=false
+disable-loadable-modules=false
+disable-scripted-loadable-modules=false
+font=@Variant(\0\0\0@\0\0\0\x14\0S\0\x61\0n\0s\0 \0S\0\x65\0r\0i\0\x66@\"\0\0\0\0\0\0\xff\xff\xff\xff\x5\x1\0\x32\x10)
+language=
+no-splash=false
+no-tooltip=false
+
+[Cache]
+ForceRedownload=false
+FreeBufferSize=10
+Path=/tmp/Slicer-/RemoteIO
+Size=200
+
+[DICOM]
+PreferredMultiVolumeImportFormat=default
+ScalarVolume\AcquisitionGeometryRegularization=default
+ScalarVolume\AllowLoadingByTime=0
+ScalarVolume\ReaderApproach=0
+automaticallyLoadReferences=-1
+
+[Default3DView]
+AxisLabelsVisibility=true
+BoxVisibility=true
+OrientationMarkerSize=medium
+OrientationMarkerType=none
+RulerType=none
+UseDepthPeeling=false
+UseOrthographicProjection=false
+
+[DefaultSliceView]
+OrientationMarkerSize=medium
+OrientationMarkerType=none
+RulerType=none
+
+[Developer]
+DeveloperMode=false
+
+[ExtensionCheckOnStartup]
+dontCheck=false
+
+[ExtensionWizard]
+TemplatePaths=@Invalid()
+TemplatePaths\extensions=@Invalid()
+TemplatePaths\modules=@Invalid()
+
+[Extensions]
+AutoUpdate=false
+
+[ExtensionsHistory]
+Revisions\0=@Invalid()
+ScheduledForRemoval=
+
+[MainWindow]
+DontConfirmExit=-1
+DontConfirmRestart=-1
+DontConfirmSceneClose=-1
+DontShowDisclaimerMessage=-1
+RestoreGeometry=true
+ShowToolButtonText=false
+geometry=@ByteArray(\x1\xd9\xd0\xcb\0\x2\0\0\0\0\vJ\0\0\x1\r\0\0\x10m\0\0\x3\xf3\0\0\vJ\0\0\x1\x32\0\0\x10m\0\0\x3\xf3\0\0\0\x1\0\0\0\0\n\0)
+layout=0
+windowState=@ByteArray(\0\0\0\xff\0\0\0\0\xfd\0\0\0\x2\0\0\0\0\0\0\x1\x81\0\0\x1\x99\xfc\x2\0\0\0\x1\xfb\0\0\0\x1e\0P\0\x61\0n\0\x65\0l\0\x44\0o\0\x63\0k\0W\0i\0\x64\0g\0\x65\0t\x1\0\0\0\x32\0\0\x1\x99\0\0\0\xf3\0\xff\xff\xff\0\0\0\x3\0\0\x5$\0\0\0\xcf\xfc\x1\0\0\0\x1\xfb\0\0\0.\0P\0y\0t\0h\0o\0n\0\x43\0o\0n\0s\0o\0l\0\x65\0\x44\0o\0\x63\0k\0W\0i\0\x64\0g\0\x65\0t\x1\0\0\0\0\0\0\x5$\0\0\0.\0\xff\xff\xff\0\0\x3\x9f\0\0\x1\x99\0\0\0\x4\0\0\0\x4\0\0\0\b\0\0\0\b\xfc\0\0\0\x1\0\0\0\x2\0\0\0\b\0\0\0\x16\0M\0\x61\0i\0n\0T\0o\0o\0l\0\x42\0\x61\0r\x1\0\0\0\0\xff\xff\xff\xff\0\0\0\0\0\0\0\0\0\0\0*\0M\0o\0\x64\0u\0l\0\x65\0S\0\x65\0l\0\x65\0\x63\0t\0o\0r\0T\0o\0o\0l\0\x42\0\x61\0r\x1\0\0\0R\xff\xff\xff\xff\0\0\0\0\0\0\0\0\0\0\0\x1a\0M\0o\0\x64\0u\0l\0\x65\0T\0o\0o\0l\0\x42\0\x61\0r\x1\0\0\x1v\xff\xff\xff\xff\0\0\0\0\0\0\0\0\0\0\0\x16\0V\0i\0\x65\0w\0T\0o\0o\0l\0\x42\0\x61\0r\x1\0\0\x2\x10\xff\xff\xff\xff\0\0\0\0\0\0\0\0\0\0\0 \0M\0o\0u\0s\0\x65\0M\0o\0\x64\0\x65\0T\0o\0o\0l\0\x42\0\x61\0r\x1\0\0\x2\x32\xff\xff\xff\xff\0\0\0\0\0\0\0\0\0\0\0\x1c\0\x43\0\x61\0p\0t\0u\0r\0\x65\0T\0o\0o\0l\0\x42\0\x61\0r\x1\0\0\x2\\\xff\xff\xff\xff\0\0\0\0\0\0\0\0\0\0\0\x1c\0V\0i\0\x65\0w\0\x65\0r\0s\0T\0o\0o\0l\0\x42\0\x61\0r\x1\0\0\x2\xae\xff\xff\xff\xff\0\0\0\0\0\0\0\0\0\0\0\x1a\0\x44\0i\0\x61\0l\0o\0g\0T\0o\0o\0l\0\x42\0\x61\0r\x1\0\0\x2\xd8\xff\xff\xff\xff\0\0\0\0\0\0\0\0)
+
+[Modules]
+FavoriteModules=Data, Volumes, Models, Transforms, Markups, SegmentEditor
+HomeModule=Welcome
+PreferExecutableCLI=true
+ShowHiddenModules=false
+TemporaryDirectory=/tmp/Slicer-
+
+[Python]
+BackgroundColor=@Variant(\0\0\0\x43\x1\xff\xff\xff\xff\xff\xff\xff\xff\0\0)
+CommandTextColor=@Variant(\0\0\0\x43\x1\xff\xff\0\0\0\0\x96\x96\0\0)
+DockableWindow=true
+ErrorTextColor=@Variant(\0\0\0\x43\x1\xff\xff\xff\xff\0\0\0\0\0\0)
+Font=@Variant(\0\0\0@\0\0\0\xe\0\x43\0o\0u\0r\0i\0\x65\0r@\"\0\0\0\0\0\0\xff\xff\xff\xff\x2\x1\0\x32\x18)
+OutputTextColor=@Variant(\0\0\0\x43\x1\xff\xff\0\0\x96\x96\0\0\0\0)
+PromptColor=@Variant(\0\0\0\x43\x1\xff\xff\0\0\0\0\0\0\0\0)
+ScrollBarPolicy=0
+StdinTextColor=@Variant(\0\0\0\x43\x1\xff\xff\x80\x80\x80\x80\x80\x80\0\0)
+WelcomeTextColor=@Variant(\0\0\0\x43\x1\xff\xff\0\0\0\0\xff\xff\0\0)
+
+[QtTesting]
+Enabled=false
+
+[RecentlyLoadedFiles]
+NumberToKeep=10
+RecentFiles\size=0
+
+[Segmentations]
+AutoOpacities=true
+
+[Styles]
+AdditionalPaths=@Invalid()
+Style=Slicer
+
+[SubjectHierarchy]
+AutoDeleteSubjectHierarchyChildren=false
+DisplayPatientBirthDateInSubjectHierarchyItemName=false
+DisplayPatientIDInSubjectHierarchyItemName=true
+DisplayStudyDateInSubjectHierarchyItemName=true
+DisplayStudyIDInSubjectHierarchyItemName=false
+
+[Views]
+MSAA=Off
+
+[VolumeRendering]
+DefaultInteractiveSpeed=8
+DefaultQuality=Adaptive
+DefaultSurfaceSmoothing=false
+GPUMemorySize=
+RenderingMethod=vtkMRMLCPURayCastVolumeRenderingDisplayNode
+
+[ioManager]
+favoritesPaths=file:///root

slicer-build/local_home_config/Qt/Qt Apps.conf

@@ -0,0 +1,2 @@
+[General]
+uuid=78f4cc81-da17-4de7-b628-2ae94d61b19d

slicer-build/local_home_config/QtProject.conf

@@ -0,0 +1,8 @@
+[FileDialog]
+history=file:///usr/src/SlicerOpenIGTLink/build/inner-build/lib/Slicer-4.10, file:///usr/src/SlicerIGT/build/lib/Slicer-4.10
+lastVisited=file:///usr/src/SlicerIGT/build/lib/Slicer-4.10
+qtVersion=5.11.2
+shortcuts=file:, file:///root
+sidebarWidth=71
+treeViewHeader=@ByteArray(\0\0\0\xff\0\0\0\0\0\0\0\x1\0\0\0\0\0\0\0\0\x1\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\x1H\0\0\0\x4\x1\x1\0\0\0\0\0\0\0\0\0\0\0\0\0\0\x44\xff\xff\xff\xff\0\0\0\x81\0\0\0\0\0\0\0\x4\0\0\0\xaa\0\0\0\x1\0\0\0\0\0\0\0*\0\0\0\x1\0\0\0\0\0\0\0+\0\0\0\x1\0\0\0\0\0\0\0I\0\0\0\x1\0\0\0\0\0\0\x3\xe8\0\xff\xff\xff\xff)
+viewMode=Detail