ENH: Modified most Python examples to make use of argparse.

Author: kian-weimer

src/Bridge/VtkGlue/ConvertAnRGBitkImageTovtkImageData/Code.py

@@ -16,20 +16,21 @@
 
 import sys
 import itk
+import argparse
 
 from distutils.version import StrictVersion as VS
 
 if VS(itk.Version.GetITKVersion()) < VS("5.2.0"):
     print("ITK 5.2.0 is required.")
     sys.exit(1)
 
-if len(sys.argv) != 2:
-    print("Usage: " + sys.argv[0] + " <InputFileName>")
-    sys.exit(1)
-
-imageFileName = sys.argv[1]
+parser = argparse.ArgumentParser(
+    description="Convert An RBG itk Image to vtk Image Data."
+)
+parser.add_argument("input_image")
+args = parser.parse_args()
 
-inputImage = itk.imread(imageFileName)
+inputImage = itk.imread(args.input_image)
 
 vtkImage = itk.image_to_vtk_image(inputImage)
 

src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Code.py

@@ -16,20 +16,19 @@
 
 import sys
 import itk
+import argparse
 
 from distutils.version import StrictVersion as VS
 
 if VS(itk.Version.GetITKVersion()) < VS("5.2.0"):
     print("ITK 5.2.0 is required.")
     sys.exit(1)
 
-if len(sys.argv) != 2:
-    print("Usage: " + sys.argv[0] + " <InputFileName>")
-    sys.exit(1)
-
-imageFileName = sys.argv[1]
+parser = argparse.ArgumentParser(description="Convert An itk Image to vtk Image Data.")
+parser.add_argument("input_image")
+args = parser.parse_args()
 
-inputImage = itk.imread(imageFileName)
+inputImage = itk.imread(args.input_image)
 
 vtkImage = itk.image_to_vtk_image(inputImage)
 

src/Bridge/VtkGlue/ConvertRGBvtkImageDataToAnitkImage/Code.py

@@ -14,22 +14,23 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import sys
 import itk
 import vtk
+import argparse
 
-if len(sys.argv) < 2:
-    print("Usage: " + sys.argv[0] + " <InputFileName>")
-    sys.exit(1)
-imageFileName = sys.argv[1]
+parser = argparse.ArgumentParser(
+    description="Convert RBG vtk Image Data To An itk Image."
+)
+parser.add_argument("input_image")
+args = parser.parse_args()
 
 Dimension = 2
 PixelComponentType = itk.UC
 PixelType = itk.RGBPixel[PixelComponentType]
 ImageType = itk.Image[PixelType, Dimension]
 
 reader = vtk.vtkPNGReader()
-reader.SetFileName(imageFileName)
+reader.SetFileName(args.input_image)
 reader.SetDataScalarTypeToUnsignedChar()
 
 vtkToItkFilter = itk.VTKImageToImageFilter[ImageType].New()

src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Code.py

@@ -14,21 +14,20 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import sys
 import itk
 import vtk
+import argparse
 
-if len(sys.argv) < 2:
-    print("Usage: " + sys.argv[0] + " <InputFileName>")
-    sys.exit(1)
-imageFileName = sys.argv[1]
+parser = argparse.ArgumentParser(description="Convert vtk Image Data To An itk Image.")
+parser.add_argument("input_image")
+args = parser.parse_args()
 
 Dimension = 2
 PixelType = itk.UC
 ImageType = itk.Image[PixelType, Dimension]
 
 reader = vtk.vtkPNGReader()
-reader.SetFileName(imageFileName)
+reader.SetFileName(args.input_image)
 reader.SetDataScalarTypeToUnsignedChar()
 
 magnitude = vtk.vtkImageMagnitude()

src/Core/Common/GetImageSize/Code.py

@@ -14,17 +14,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import sys
 import numpy as np
 import itk
+import argparse
 
-if len(sys.argv) != 2:
-    print("Usage: " + sys.argv[0] + " <inputImageFile>")
-    sys.exit(1)
+parser = argparse.ArgumentParser(description="Get Image Size.")
+parser.add_argument("input_image")
+args = parser.parse_args()
 
-inputImageFile = sys.argv[1]
-
-image = itk.imread(inputImageFile, itk.UC)
+image = itk.imread(args.input_image, itk.UC)
 
 region = image.GetLargestPossibleRegion()
 size = region.GetSize()

src/Core/Common/ReadWriteVectorImage/Code.py

@@ -14,12 +14,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import sys
 import itk
+import argparse
 
-if len(sys.argv) != 3:
-    print("Usage: " + sys.argv[0] + " <InputFileName> <OutputFileName>")
-    sys.exit(1)
+parser = argparse.ArgumentParser(description="Read Write Vector Image.")
+parser.add_argument("input_image")
+parser.add_argument("output_image")
+args = parser.parse_args()
 
 VectorDimension = 4
 
@@ -30,9 +31,9 @@
 ImageType = itk.Image[PixelType, ImageDimension]
 
 reader = itk.ImageFileReader[ImageType].New()
-reader.SetFileName(sys.argv[1])
+reader.SetFileName(args.input_image)
 
 writer = itk.ImageFileWriter[ImageType].New()
-writer.SetFileName(sys.argv[2])
+writer.SetFileName(args.output_image)
 writer.SetInput(reader.GetOutput())
 writer.Update()

src/Core/Common/SetPixelValueInOneImage/Code.py

@@ -14,19 +14,17 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import sys
 import itk
+import argparse
 
-if len(sys.argv) != 2:
-    print("Usage: " + sys.argv[0] + " <OutputFileName>")
-    sys.exit(1)
+parser = argparse.ArgumentParser(description="Set Pixel Value In One Image.")
+parser.add_argument("output_image")
+args = parser.parse_args()
 
 Dimension = 2
 
 PixelType = itk.UC
 
-OutputFileName = sys.argv[1]
-
 ImageType = itk.Image[PixelType, Dimension]
 
 region = itk.ImageRegion[Dimension]()
@@ -96,4 +94,4 @@
 
 image.SetPixel(pixelIndex, 200)
 
-itk.imwrite(image, OutputFileName)
+itk.imwrite(image, args.output_image)

src/Core/Common/StreamAPipeline/Code.py

@@ -16,33 +16,33 @@
 
 import sys
 import itk
+import argparse
 
 from distutils.version import StrictVersion as VS
 
 if VS(itk.Version.GetITKVersion()) < VS("4.10.0"):
     print("ITK 4.10.0 is required.")
     sys.exit(1)
 
-if len(sys.argv) != 2:
-    print("Usage: " + sys.argv[0] + " <NumberOfSplits>")
-    sys.exit(1)
-numberOfSplits = int(sys.argv[1])
+parser = argparse.ArgumentParser(description="Stream A Pipeline.")
+parser.add_argument("number_of_splits", type=int)
+args = parser.parse_args()
 
 Dimension = 2
 PixelType = itk.UC
 ImageType = itk.Image[PixelType, Dimension]
 
 source = itk.RandomImageSource[ImageType].New()
 size = itk.Size[Dimension]()
-size.Fill(numberOfSplits)
+size.Fill(args.number_of_splits)
 source.SetSize(size)
 
 monitorFilter = itk.PipelineMonitorImageFilter[ImageType].New()
 monitorFilter.SetInput(source.GetOutput())
 
 streamingFilter = itk.StreamingImageFilter[ImageType, ImageType].New()
 streamingFilter.SetInput(monitorFilter.GetOutput())
-streamingFilter.SetNumberOfStreamDivisions(numberOfSplits)
+streamingFilter.SetNumberOfStreamDivisions(args.number_of_splits)
 
 streamingFilter.Update()
 

src/Core/ImageFunction/ResampleSegmentedImage/Code.py

@@ -15,45 +15,42 @@
 # limitations under the License.
 
 import itk
-import sys
+import argparse
 
-if len(sys.argv) != 6:
-    print(
-        f"Usage: {sys.argv[0]} input_image_file spacing_fraction sigma_fraction output_image_file_label_image_interpolator output_image_file_nearest_neighbor_interpolator"
-    )
-    sys.exit(1)
+parser = argparse.ArgumentParser(description="Resample Segmented Image.")
+parser.add_argument("input_image")
+parser.add_argument("spacing_fraction", type=float)
+parser.add_argument("sigma_fraction", type=float)
+parser.add_argument("output_image_file_label_image_interpolator")
+parser.add_argument("output_image_file_nearest_neighbor_interpolator")
+args = parser.parse_args()
 
-input_image_file = sys.argv[1]
-spacing_fraction = float(sys.argv[2])
-sigma_fraction = float(sys.argv[3])
-output_image_file_label_image_interpolator = sys.argv[4]
-output_image_file_nearest_neighbor_interpolator = sys.argv[5]
-
-input_image = itk.imread(input_image_file)
+input_image = itk.imread(args.input_image)
 
 resize_filter = itk.ResampleImageFilter.New(input_image)
 
 input_spacing = itk.spacing(input_image)
-output_spacing = [s * spacing_fraction for s in input_spacing]
+output_spacing = [s * args.spacing_fraction for s in input_spacing]
 resize_filter.SetOutputSpacing(output_spacing)
 
 input_size = itk.size(input_image)
 output_size = [
-    int(s * input_spacing[dim] / spacing_fraction) for dim, s in enumerate(input_size)
+    int(s * input_spacing[dim] / args.spacing_fraction)
+    for dim, s in enumerate(input_size)
 ]
 resize_filter.SetSize(output_size)
 
 gaussian_interpolator = itk.LabelImageGaussianInterpolateImageFunction.New(input_image)
-sigma = [s * sigma_fraction for s in output_spacing]
+sigma = [s * args.sigma_fraction for s in output_spacing]
 gaussian_interpolator.SetSigma(sigma)
 gaussian_interpolator.SetAlpha(3.0)
 resize_filter.SetInterpolator(gaussian_interpolator)
 
-itk.imwrite(resize_filter, output_image_file_label_image_interpolator)
+itk.imwrite(resize_filter, args.output_image_file_label_image_interpolator)
 
 nearest_neighbor_interpolator = itk.NearestNeighborInterpolateImageFunction.New(
     input_image
 )
 resize_filter.SetInterpolator(nearest_neighbor_interpolator)
 
-itk.imwrite(resize_filter, output_image_file_nearest_neighbor_interpolator)
+itk.imwrite(resize_filter, args.output_image_file_nearest_neighbor_interpolator)

src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Code.py

@@ -14,21 +14,16 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import sys
 import itk
+import argparse
 
-if len(sys.argv) != 6:
-    print(
-        "Usage: " + sys.argv[0] + " <inputImage> <outputImage> "
-        "<numberOfIterations> <timeStep> <conductance>"
-    )
-    sys.exit(1)
-
-inputImage = sys.argv[1]
-outputImage = sys.argv[2]
-numberOfIterations = int(sys.argv[3])
-timeStep = float(sys.argv[4])
-conductance = float(sys.argv[5])
+parser = argparse.ArgumentParser(description="Compute Curvature Anisotropic Diffusion.")
+parser.add_argument("input_image")
+parser.add_argument("output_image")
+parser.add_argument("number_of_iterations", type=int)
+parser.add_argument("time_step", type=float)
+parser.add_argument("conductance", type=float)
+args = parser.parse_args()
 
 InputPixelType = itk.F
 OutputPixelType = itk.UC
@@ -39,17 +34,17 @@
 
 ReaderType = itk.ImageFileReader[InputImageType]
 reader = ReaderType.New()
-reader.SetFileName(inputImage)
+reader.SetFileName(args.input_image)
 
 FilterType = itk.CurvatureAnisotropicDiffusionImageFilter[
     InputImageType, InputImageType
 ]
 curvatureAnisotropicDiffusionFilter = FilterType.New()
 
 curvatureAnisotropicDiffusionFilter.SetInput(reader.GetOutput())
-curvatureAnisotropicDiffusionFilter.SetNumberOfIterations(numberOfIterations)
-curvatureAnisotropicDiffusionFilter.SetTimeStep(timeStep)
-curvatureAnisotropicDiffusionFilter.SetConductanceParameter(conductance)
+curvatureAnisotropicDiffusionFilter.SetNumberOfIterations(args.number_of_iterations)
+curvatureAnisotropicDiffusionFilter.SetTimeStep(args.time_step)
+curvatureAnisotropicDiffusionFilter.SetConductanceParameter(args.conductance)
 
 RescaleFilterType = itk.RescaleIntensityImageFilter[InputImageType, OutputImageType]
 rescaler = RescaleFilterType.New()
@@ -63,7 +58,7 @@
 
 WriterType = itk.ImageFileWriter[OutputImageType]
 writer = WriterType.New()
-writer.SetFileName(outputImage)
+writer.SetFileName(args.output_image)
 writer.SetInput(rescaler.GetOutput())
 
 writer.Update()