ENH: Add black style pre-commit hook

Black is installed by the Superbuild and run on all changed Python
files during commit. A system version can also be used or configured
with the `black.executable` git configuration value.

Author: thewtex

.gitattributes

@@ -8,6 +8,7 @@
 *.txx            our-c-style
 *.txt            whitespace=tab-in-indent,no-lf-at-eof
 *.cmake          whitespace=tab-in-indent,no-lf-at-eof
+*.py             hooks.style=black
 
 # ExternalData content links must have LF newlines
 *.md5            crlf=input

Superbuild/External-Python.cmake

@@ -4,14 +4,19 @@ set(_itk_venv "${CMAKE_CURRENT_BINARY_DIR}/itkpython")
 if(WIN32)
   set(ITKPYTHON_EXECUTABLE "${_itk_venv}/python.exe" CACHE FILEPATH "Python executable with the ITK package installed" FORCE)
   set(SPHINX_EXECUTABLE "${_itk_venv}/Scripts/sphinx-build.exe" CACHE FILEPATH "Sphinx executable" FORCE)
+  set(BLACK_EXECUTABLE "${_itk_venv}/Scripts/black.exe" CACHE FILEPATH "black executable" FORCE)
 else()
   set(ITKPYTHON_EXECUTABLE "${_itk_venv}/bin/python" CACHE FILEPATH "Python executable with the ITK package installed" FORCE)
   set(SPHINX_EXECUTABLE "${_itk_venv}/bin/sphinx-build" CACHE FILEPATH "Sphinx executable" FORCE)
+  set(BLACK_EXECUTABLE "${_itk_venv}/bin/black" CACHE FILEPATH "black executable" FORCE)
 endif()
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/ITKBlackConfig.cmake.in"
+               "${CMAKE_CURRENT_BINARY_DIR}/ITKBlackConfig.cmake" @ONLY)
 
 ExternalProject_Add(ITKPython
   DOWNLOAD_COMMAND ""
   CONFIGURE_COMMAND ${PYTHON_EXECUTABLE} -m venv "${_itk_venv}"
   BUILD_COMMAND ${ITKPYTHON_EXECUTABLE} -m pip install --upgrade pip
-  INSTALL_COMMAND ${ITKPYTHON_EXECUTABLE} -m pip install --ignore-installed itk>=5.2rc3 sphinx==3.0.4 six
+  INSTALL_COMMAND ${ITKPYTHON_EXECUTABLE} -m pip install --ignore-installed itk>=5.2rc3 sphinx==3.0.4 six black
+  COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/ITKBlackConfig.cmake
   )

Superbuild/ITKBlackConfig.cmake.in

@@ -0,0 +1,17 @@
+set(ITKExamples_SOURCE_DIR "@ITKExamples_SOURCE_DIR@")
+set(CMAKE_SOURCE_DIR "@CMAKE_SOURCE_DIR@")
+set(BLACK_EXECUTABLE "@BLACK_EXECUTABLE@")
+
+set(WORKING_DIR "")
+if(ITKExamples_SOURCE_DIR)
+  set(WORKING_DIR "${ITKExamples_SOURCE_DIR}/..")
+else()
+  set(WORKING_DIR "${CMAKE_SOURCE_DIR}/..")
+endif()
+
+find_package(Git)
+if(GIT_FOUND AND EXISTS "${WORKING_DIR}/.git/config")
+  execute_process(COMMAND ${GIT_EXECUTABLE} config black.executable
+    "${BLACK_EXECUTABLE}"
+    WORKING_DIRECTORY ${WORKING_DIR})
+endif()

Utilities/Hooks/pre-commit-style.bash

@@ -14,7 +14,7 @@
 # limitations under the License.
 #=============================================================================
 
-# Run clangformat and KWStyle pre-commit hooks.
+# Run clangformat, KWStyle, black pre-commit hooks.
 #
 # 'git config' is used to enable the hooks and set their configuration files.
 # The repository .gitattributes must also enable the hooks on the targeted
@@ -32,6 +32,8 @@ do_KWStyle=$(git config --bool hooks.KWStyle) || do_KWStyle=false
 
 do_clangformat=$(git config --bool hooks.clangformat) || do_clangformat=true
 
+do_black=$(git config --bool hooks.blackformat) || do_blackformat=true
+
 #-----------------------------------------------------------------------------
 # Check if we want to run the style on a given file.  Uses git attributes.  If
 # the hook.style attribute is set, then all styles are executed.  If the
@@ -164,8 +166,8 @@ check_for_clangformat() {
   clangformat_path=$(type -p "$system_clang_format" >/dev/null) ||
   die "clang-format executable was not found.
 
-A clang-format binary will be downloaded and configured when ITK
-is built with the BUILD_TESTING CMake configuration option enabled.
+A clang-format binary will be downloaded and configured when the ITKExamples
+Superbuild is built with the BUILD_TESTING CMake configuration option enabled.
 
 Alternatively, install clang-format version $clangformat_required_version or set the executable location with
 
@@ -292,25 +294,81 @@ For more information, see
   done # end for changed files
 }
 
+#-----------------------------------------------------------------------------
+# black.
+check_for_black() {
+  system_black=""
+  if type -p "black" >/dev/null; then
+    system_black="black"
+  fi
+  black_path=$(git config black.executable) ||
+  black_path=$(type -p "$system_black" >/dev/null) ||
+  die "black executable was not found.
+
+A black Python formatting tool will be downloaded and configured when the ITKExamples
+Superbuild is built with the BUILD_TESTING CMake configuration option enabled.
+
+Alternatively, install black with:
+
+  python -m pip install black
+
+and set the executable location with
+
+  git config black.executable /path/to/black
+
+if it is not in the system's PATH.
+"
+}
+
+run_black_on_file() {
+  "$black_path" "$1"
+
+  if test $? -ne 0; then
+    die "black style application failed."
+  fi
+  return 0
+}
+
+run_black() {
+  $do_black && check_for_black
+  if test $?; then
+    have_black=true
+  else
+    have_black=false
+  fi
+
+  git diff-index --cached --diff-filter=ACMR --name-only HEAD -- |
+  while read f; do
+    if run_style_on_file "$f" "black"; then
+      run_black_on_file "$f"
+    fi || return
+  done
+}
+
 # Do not run during merge commits for now.
 if test -f "$GIT_DIR/MERGE_HEAD"; then
   :
-elif $do_clangformat; then
-  # We use git-mergetool settings to review the clangformat changes.
-  TOOL_MODE=merge
-  . "$(git --exec-path)/git-mergetool--lib"
-  # Redefine check_unchanged because we do not need to check if the merge was
-  # successful.
-  check_unchanged() {
-    status=0
-  }
-  check_for_clangformat
-  run_clangformat || exit 1
-# do_clangformat will run KWStyle on the files incrementally so excessive
-# clangformat merges do not have to occur.
-elif $do_KWStyle; then
-  if check_for_KWStyle; then
-    run_KWStyle || exit 1
+else
+  if $do_clangformat; then
+    # We use git-mergetool settings to review the clangformat changes.
+    TOOL_MODE=merge
+    . "$(git --exec-path)/git-mergetool--lib"
+    # Redefine check_unchanged because we do not need to check if the merge was
+    # successful.
+    check_unchanged() {
+      status=0
+    }
+    check_for_clangformat
+    run_clangformat || exit 1
+    # do_clangformat will run KWStyle on the files incrementally so excessive
+    # clangformat merges do not have to occur.
+  elif $do_KWStyle; then
+    if check_for_KWStyle; then
+      run_KWStyle || exit 1
+    fi
+  fi
+  if $do_black; then
+    run_black || exit 1
   fi
 fi
 

src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Code.py

@@ -21,10 +21,13 @@
     print(
         "Usage: " + sys.argv[0] + "<InputFileName>  <OutputFileName>"
         " <seedX> <seedY> <InitialDistance> <Sigma> <SigmoidAlpha> "
-        "<SigmoidBeta> <PropagationScaling> <NumberOfIterations>")
+        "<SigmoidBeta> <PropagationScaling> <NumberOfIterations>"
+    )
     sys.exit(1)
 
 inputFileName = sys.argv[1]
+
+
 outputFileName = sys.argv[2]
 seedPosX = int(sys.argv[3])
 seedPosY = int(sys.argv[4])
@@ -52,15 +55,17 @@
 reader.SetFileName(inputFileName)
 
 SmoothingFilterType = itk.CurvatureAnisotropicDiffusionImageFilter[
-    InputImageType, InputImageType]
+    InputImageType, InputImageType
+]
 smoothing = SmoothingFilterType.New()
 smoothing.SetTimeStep(0.125)
 smoothing.SetNumberOfIterations(5)
 smoothing.SetConductanceParameter(9.0)
 smoothing.SetInput(reader.GetOutput())
 
 GradientFilterType = itk.GradientMagnitudeRecursiveGaussianImageFilter[
-    InputImageType, InputImageType]
+    InputImageType, InputImageType
+]
 gradientMagnitude = GradientFilterType.New()
 gradientMagnitude.SetSigma(sigma)
 gradientMagnitude.SetInput(smoothing.GetOutput())
@@ -73,12 +78,12 @@
 sigmoid.SetBeta(beta)
 sigmoid.SetInput(gradientMagnitude.GetOutput())
 
-FastMarchingFilterType = itk.FastMarchingImageFilter[
-    InputImageType, InputImageType]
+FastMarchingFilterType = itk.FastMarchingImageFilter[InputImageType, InputImageType]
 fastMarching = FastMarchingFilterType.New()
 
 GeoActiveContourFilterType = itk.GeodesicActiveContourLevelSetImageFilter[
-    InputImageType, InputImageType, InputPixelType]
+    InputImageType, InputImageType, InputPixelType
+]
 geodesicActiveContour = GeoActiveContourFilterType.New()
 geodesicActiveContour.SetPropagationScaling(propagationScaling)
 geodesicActiveContour.SetCurvatureScaling(1.0)
@@ -88,8 +93,7 @@
 geodesicActiveContour.SetInput(fastMarching.GetOutput())
 geodesicActiveContour.SetFeatureImage(sigmoid.GetOutput())
 
-ThresholdingFilterType = itk.BinaryThresholdImageFilter[
-    InputImageType, OutputImageType]
+ThresholdingFilterType = itk.BinaryThresholdImageFilter[InputImageType, OutputImageType]
 thresholder = ThresholdingFilterType.New()
 thresholder.SetLowerThreshold(-1000.0)
 thresholder.SetUpperThreshold(0.0)
@@ -105,16 +109,14 @@
 node.SetValue(seedValue)
 node.SetIndex(seedPosition)
 
-seeds = itk.VectorContainer[
-    itk.UI, itk.LevelSetNode[InputPixelType, Dimension]].New()
+seeds = itk.VectorContainer[itk.UI, itk.LevelSetNode[InputPixelType, Dimension]].New()
 seeds.Initialize()
 seeds.InsertElement(0, node)
 
 fastMarching.SetTrialPoints(seeds)
 fastMarching.SetSpeedConstant(1.0)
 
-CastFilterType = itk.RescaleIntensityImageFilter[
-    InputImageType, OutputImageType]
+CastFilterType = itk.RescaleIntensityImageFilter[InputImageType, OutputImageType]
 
 caster1 = CastFilterType.New()
 caster2 = CastFilterType.New()
@@ -153,23 +155,22 @@
 caster4.SetOutputMinimum(itk.NumericTraits[OutputPixelType].min())
 caster4.SetOutputMaximum(itk.NumericTraits[OutputPixelType].max())
 
-fastMarching.SetOutputSize(
-    reader.GetOutput().GetBufferedRegion().GetSize())
+fastMarching.SetOutputSize(reader.GetOutput().GetBufferedRegion().GetSize())
 
 writer = WriterType.New()
 writer.SetFileName(outputFileName)
 writer.SetInput(thresholder.GetOutput())
 writer.Update()
 
 print(
-    "Max. no. iterations: " +
-    str(geodesicActiveContour.GetNumberOfIterations()) + "\n")
-print(
-    "Max. RMS error: " +
-    str(geodesicActiveContour.GetMaximumRMSError()) + "\n")
+    "Max. no. iterations: " + str(geodesicActiveContour.GetNumberOfIterations()) + "\n"
+)
+print("Max. RMS error: " + str(geodesicActiveContour.GetMaximumRMSError()) + "\n")
 print(
-    "No. elpased iterations: " +
-    str(geodesicActiveContour.GetElapsedIterations()) + "\n")
+    "No. elpased iterations: "
+    + str(geodesicActiveContour.GetElapsedIterations())
+    + "\n"
+)
 print("RMS change: " + str(geodesicActiveContour.GetRMSChange()) + "\n")
 
 writer4.Update()

src/Segmentation/Watersheds/SegmentWithWatershedImageFilter/Code.py

@@ -21,43 +21,44 @@
 # (A rule of thumb is to set the Threshold to be about 1 / 100 of the Level.)
 #
 #  threshold: absolute minimum height value used during processing.
-#        Raising this threshold percentage effectively decreases the number of local minima in the input, 
-#        resulting in an initial segmentation with fewer regions. 
+#        Raising this threshold percentage effectively decreases the number of local minima in the input,
+#        resulting in an initial segmentation with fewer regions.
 #        The assumption is that the shallow regions that thresholding removes are of of less interest.
-#  level: parameter controls the depth of metaphorical flooding of the image. 
-#        That is, it sets the maximum saliency value of interest in the result. 
-#        Raising and lowering the Level influences the number of segments 
-#        in the basic segmentation that are merged to produce the final output. 
-#        A level of 1.0 is analogous to flooding the image up to a 
-#        depth that is 100 percent of the maximum value in the image. 
-#        A level of 0.0 produces the basic segmentation, which will typically be very oversegmented. 
+#  level: parameter controls the depth of metaphorical flooding of the image.
+#        That is, it sets the maximum saliency value of interest in the result.
+#        Raising and lowering the Level influences the number of segments
+#        in the basic segmentation that are merged to produce the final output.
+#        A level of 1.0 is analogous to flooding the image up to a
+#        depth that is 100 percent of the maximum value in the image.
+#        A level of 0.0 produces the basic segmentation, which will typically be very oversegmented.
 #        Level values of interest are typically low (i.e. less than about 0.40 or 40%),
 #        since higher values quickly start to undersegment the image.
 
 import sys
 import itk
 
 if len(sys.argv) != 5:
-    print('Usage: ' + sys.argv[0] +
-          ' <InputFileName> <OutputFileName> <Threshold> <Level>')
+    print(
+        "Usage: "
+        + sys.argv[0]
+        + " <InputFileName> <OutputFileName> <Threshold> <Level>"
+    )
     sys.exit(1)
 
 inputFileName = sys.argv[1]
 outputFileName = sys.argv[2]
 
 Dimension = 2
 
-FloatPixelType = itk.ctype('float')
+FloatPixelType = itk.ctype("float")
 FloatImageType = itk.Image[FloatPixelType, Dimension]
 
 reader = itk.ImageFileReader[FloatImageType].New()
 reader.SetFileName(inputFileName)
 
-gradientMagnitude = \
-    itk.GradientMagnitudeImageFilter.New(Input=reader.GetOutput())
+gradientMagnitude = itk.GradientMagnitudeImageFilter.New(Input=reader.GetOutput())
 
-watershed = \
-    itk.WatershedImageFilter.New(Input=gradientMagnitude.GetOutput())
+watershed = itk.WatershedImageFilter.New(Input=gradientMagnitude.GetOutput())
 
 threshold = float(sys.argv[3])
 level = float(sys.argv[4])
@@ -66,14 +67,17 @@
 
 LabeledImageType = type(watershed.GetOutput())
 
-PixelType = itk.ctype('unsigned char')
+PixelType = itk.ctype("unsigned char")
 RGBPixelType = itk.RGBPixel[PixelType]
 RGBImageType = itk.Image[RGBPixelType, Dimension]
 
-ScalarToRGBColormapFilterType = \
-    itk.ScalarToRGBColormapImageFilter[LabeledImageType, RGBImageType]
+ScalarToRGBColormapFilterType = itk.ScalarToRGBColormapImageFilter[
+    LabeledImageType, RGBImageType
+]
 colormapImageFilter = ScalarToRGBColormapFilterType.New()
-colormapImageFilter.SetColormap(itk.ScalarToRGBColormapImageFilterEnums.RGBColormapFilter_Jet)
+colormapImageFilter.SetColormap(
+    itk.ScalarToRGBColormapImageFilterEnums.RGBColormapFilter_Jet
+)
 colormapImageFilter.SetInput(watershed.GetOutput())
 colormapImageFilter.Update()