Python/NeighborhoodConnectedImageFilter.py

"""=========================================================================
 '
 '  Copyright NumFOCUS
 '
 '  Licensed under the Apache License, Version 2.0 (the "License");
 '  you may not use this file except in compliance with the License.
 '  You may obtain a copy of the License at
 '
 '         http://www.apache.org/licenses/LICENSE-2.0.txt
 '
 '  Unless required by applicable law or agreed to in writing, software
 '  distributed under the License is distributed on an "AS IS" BASIS,
 '  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 '  See the License for the specific language governing permissions and
 '  limitations under the License.
 '
 '========================================================================="""
 
import os
import sys
 
import SimpleITK as sitk
 
#
# Check Command Line
#
if len(sys.argv) < 7:
    print(
        "Usage:",
        sys.argv[1],
        "inputImage outputImage lowerThreshold",
        "upperThreshold seedX seedY [seed2X seed2Y ... ]",
    )
    sys.exit(1)
 
#
# Read the image
#
reader = sitk.ImageFileReader()
reader.SetFileName(sys.argv[1])
image = reader.Execute()
 
#
# Blur using CurvatureFlowImageFilter
#
blurFilter = sitk.CurvatureFlowImageFilter()
blurFilter.SetNumberOfIterations(5)
blurFilter.SetTimeStep(0.125)
image = blurFilter.Execute(image)
 
#
# Set up NeighborhoodConnectedImageFilter for segmentation
#
segmentationFilter = sitk.NeighborhoodConnectedImageFilter()
segmentationFilter.SetLower(float(sys.argv[3]))
segmentationFilter.SetUpper(float(sys.argv[4]))
segmentationFilter.SetReplaceValue(255)
 
radius = [2, 2]
segmentationFilter.SetRadius(radius)
 
for i in range(5, len(sys.argv) - 1, 2):
    seed = [int(sys.argv[i]), int(sys.argv[i + 1])]
    segmentationFilter.AddSeed(seed)
    print("Adding seed at: ", seed, " with intensity: ", image.GetPixel(*seed))
 
# Run the segmentation filter
image = segmentationFilter.Execute(image)
 
#
# Write out the result
#
writer = sitk.ImageFileWriter()
writer.SetFileName(sys.argv[2])
writer.Execute(image)
 
if "SITK_NOSHOW" not in os.environ:
    sitk.Show(image, "NeighborhoodConnectedThreshold")