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/*=========================================================================
*
* 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.
*
*=========================================================================*/
/**
*
* \author Ken Urish
*
* An example program to see how ThresholdMaximumConnectedComponentsImageFilter
* works for the Insight Journal:
*
* Urish KL, August J, Huard J. "Unsupervised segmentation for myofiber
* counting in immunoflourescent microscopy images". Insight Journal.
* ISC/NA-MIC/MICCAI Workshop on Open-Source Software (2005)
* https://insight-journal.org/browse/publication/40
*/
// itk header files
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkThresholdMaximumConnectedComponentsImageFilter.h"
#include "itkTestingMacros.h"
int
itkThresholdMaximumConnectedComponentsImageFilterTest(int argc, char * argv[])
{
if (argc < 3)
{
std::cerr << "Missing Parameters." << std::endl;
std::cerr << "Usage: " << itkNameOfTestExecutableMacro(argv) << " inputFileName outputFileName minimumPixelArea"
<< std::endl;
return EXIT_FAILURE;
}
using InputPixelType = unsigned char;
using OutputPixelType = unsigned char;
constexpr unsigned int Dimension = 2;
using InputImageType = itk::Image<InputPixelType, Dimension>;
using OutputImageType = itk::Image<OutputPixelType, Dimension>;
InputPixelType maxLabel = itk::NumericTraits<InputPixelType>::max();
InputPixelType minLabel = itk::NumericTraits<InputPixelType>::NonpositiveMin();
const unsigned int minimumPixelArea = std::stoi(argv[3]);
using ReaderType = itk::ImageFileReader<InputImageType>;
auto reader = ReaderType::New();
reader->SetFileName(argv[1]);
ITK_TRY_EXPECT_NO_EXCEPTION(reader->Update());
// Automatic Threshold Filter
// This filter essentially chooses the optimum place to threshold the object.
// It also indirectly will count the number of objects for you.
// As a note, SetInsideValue(maxLabel)/SetOutsideValue(minLabel) will count
// the number of light objects. If the reverse, it will count the number of
// dark objects.
unsigned int numberOfObjects;
unsigned int thresholdValue;
using ThresholdType = itk::ThresholdMaximumConnectedComponentsImageFilter<InputImageType>;
auto automaticThreshold = ThresholdType::New();
ITK_EXERCISE_BASIC_OBJECT_METHODS(
automaticThreshold, ThresholdMaximumConnectedComponentsImageFilter, ImageToImageFilter);
automaticThreshold->SetInput(reader->GetOutput());
automaticThreshold->SetMinimumObjectSizeInPixels(minimumPixelArea);
ITK_TEST_SET_GET_VALUE(minimumPixelArea, automaticThreshold->GetMinimumObjectSizeInPixels());
// For counting Myofibers, the inside value should be the minLabel
// If you wanted to count a solid object (ie dapi nuclei) set the
// inside value to minLabel.
//
automaticThreshold->SetInsideValue(minLabel);
ITK_TEST_SET_GET_VALUE(minLabel, automaticThreshold->GetInsideValue());
automaticThreshold->SetOutsideValue(maxLabel);
ITK_TEST_SET_GET_VALUE(maxLabel, automaticThreshold->GetOutsideValue());
typename ThresholdType::PixelType upperBoundary = itk::NumericTraits<ThresholdType::PixelType>::max();
automaticThreshold->SetUpperBoundary(upperBoundary);
ITK_TEST_SET_GET_VALUE(upperBoundary, automaticThreshold->GetUpperBoundary());
ITK_TRY_EXPECT_NO_EXCEPTION(automaticThreshold->Update());
numberOfObjects = automaticThreshold->GetNumberOfObjects();
thresholdValue = automaticThreshold->GetThresholdValue();
std::cout << "Number of Objects = " << numberOfObjects << std::endl;
std::cout << "Threshold Value = " << thresholdValue << std::endl;
using WriterType = itk::ImageFileWriter<OutputImageType>;
auto writer = WriterType::New();
writer->SetInput(automaticThreshold->GetOutput());
writer->SetFileName(argv[2]);
ITK_TRY_EXPECT_NO_EXCEPTION(writer->Update());
std::cout << "Test finished." << std::endl;
return EXIT_SUCCESS;
}
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