SphinxExamples/src/Nonunit/Review/SegmentBloodVesselsWithMultiScaleHessianBasedMeasure/Code.py

#!/usr/bin/env python
 
# 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
#
#        https://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 argparse
 
import itk
from distutils.version import StrictVersion as VS
 
if VS(itk.Version.GetITKVersion()) < VS("5.0.0"):
    print("ITK 5.0.0 or newer is required.")
    sys.exit(1)
 
parser = argparse.ArgumentParser(
    description="Segment blood vessels with multi-scale Hessian-based measure."
)
parser.add_argument("input_image")
parser.add_argument("output_image")
parser.add_argument("--sigma_minimum", type=float, default=1.0)
parser.add_argument("--sigma_maximum", type=float, default=10.0)
parser.add_argument("--number_of_sigma_steps", type=int, default=10)
args = parser.parse_args()
 
input_image = itk.imread(args.input_image, itk.F)
 
ImageType = type(input_image)
Dimension = input_image.GetImageDimension()
HessianPixelType = itk.SymmetricSecondRankTensor[itk.D, Dimension]
HessianImageType = itk.Image[HessianPixelType, Dimension]
 
objectness_filter = itk.HessianToObjectnessMeasureImageFilter[
    HessianImageType, ImageType
].New()
objectness_filter.SetBrightObject(False)
objectness_filter.SetScaleObjectnessMeasure(False)
objectness_filter.SetAlpha(0.5)
objectness_filter.SetBeta(1.0)
objectness_filter.SetGamma(5.0)
 
multi_scale_filter = itk.MultiScaleHessianBasedMeasureImageFilter[
    ImageType, HessianImageType, ImageType
].New()
multi_scale_filter.SetInput(input_image)
multi_scale_filter.SetHessianToMeasureFilter(objectness_filter)
multi_scale_filter.SetSigmaStepMethodToLogarithmic()
multi_scale_filter.SetSigmaMinimum(args.sigma_minimum)
multi_scale_filter.SetSigmaMaximum(args.sigma_maximum)
multi_scale_filter.SetNumberOfSigmaSteps(args.number_of_sigma_steps)
 
OutputPixelType = itk.UC
OutputImageType = itk.Image[OutputPixelType, Dimension]
 
rescale_filter = itk.RescaleIntensityImageFilter[ImageType, OutputImageType].New()
rescale_filter.SetInput(multi_scale_filter)
 
itk.imwrite(rescale_filter.GetOutput(), args.output_image)