ENH: GDCMImageIO SINGLEBIT image type

[issakomi]

SINGLEBIT image type for GDCMImageIO. Closes #1969.

[issakomi]

Test file (original from TCIA)

Simple test:

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include <iostream>

int main(int, char * argv[])
{
  using ImageType  = itk::Image<unsigned char, 3>;
  using ReaderType = itk::ImageFileReader<ImageType>;
  using WriterType = itk::ImageFileWriter<ImageType>;
  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();
  try
  {
    reader->SetFileName(argv[1]);
    reader->Update();
    writer->SetFileName("from_singlebit.mha");
    writer->SetInput(reader->GetOutput());
    writer->Update();
  }
  catch (const itk::ExceptionObject & ex)
  {
    std::cout << ex << std::endl;
    return 1;
  }
  return 0;
}

Edit: BTW, missing sinlge-bit image type was also mentioned here 2 years ago
https://discourse.slicer.org/t/segmentation-storage-1-2-840-10008-5-1-4-1-1-66-4/4274

[dzenanz]

Do you want to add a regression test yourself? Reusing the read/write test should be easy if you follow the pattern.

[issakomi]

Thank you! Test program were probably easy, but unfortunately i don't know how it works with files, seems to be complicated, upload, links, etc. Is the file in above post OK, it is ~480 KB?

[dzenanz]

480KB is not bad, but a smaller one would be preferable. The simplest way is to use web interface to upload data, then use the web interface to download the hash file. Then reference it in test code just like the other input files.

[issakomi]

Found smaller file ~ 46KB, original from TCIA.
Edit: upload to data portal

[issakomi]

I have tried. Added

itk_add_test(NAME itkGDCM_ComplianceTest_singlebit
  COMMAND ITKIOGDCMTestDriver
    --compare DATA{Baseline/single-bit.mha}
      ${ITK_TEST_OUTPUT_DIR}/single-bit.mha
    itkGDCMImageReadWriteTest
      DATA{Input/single-bit.dcm}
      ${ITK_TEST_OUTPUT_DIR}/single-bit.mha
      scalar)

it produced compressed MHA file of float type: ElementType = MET_FLOAT, not sure it is good for binary mask. Also not sure do i need new function like function(AddComplianceTest fileName)

MET_FLOAT because test forces float.

  switch (pixelType)
  {
    case IOPixelType::SCALAR:
      ITK_TEST_EXPECT_EQUAL(numberOfComponents, 1);
      ITK_TEST_EXPECT_EQUAL(gdcmImageIO->GetPixelTypeAsString(pixelType), expectedPixelType);
      return ReadWrite<itk::Image<float, Dimension>>(inputImage, outputImage);

[issakomi]

I have to know about that float before i shall upload mha file.

[dzenanz]

Since it is a binary mask, it should compress really well and be small. It does not matter that it is float. I think it is OK to upload.

[issakomi]

OK, i have uploaded mha file and added sha512 files. The test seems to work

      Start 24: itkGDCM_ComplianceTest_singlebit
24/32 Test #24: itkGDCM_ComplianceTest_singlebit ................   Passed    0.04 sec

Another question, i see also md5 files for other input and baseline files, do i need to generate and add md5 file too?

[dzenanz]

You could, but this is usually done at the time of release by a script.

[dzenanz]

Can you amend the PR with the test+data?

[issakomi]

Oh, something went wrong, commits should be merged, but they are not, probably i have done something wrong.

[issakomi]

Somehow it is not correct. I am getting strange messages from git. I'll close the PR and re-create.

[issakomi]

S. #2010