mitkItkImageIOTest.cpp

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/*============================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

============================================================================*/

#include "mitkException.h"
#include <mitkStandardFileLocations.h>
#include <mitkTestFixture.h>
#include <mitkTestingMacros.h>

#include "mitkIOUtil.h"
#include "mitkITKImageImport.h"
#include <mitkExtractSliceFilter.h>

#include "itksys/SystemTools.hxx"
#include <itkImageRegionIterator.h>

#include <fstream>
#include <iostream>

#ifdef WIN32
#include "process.h"
#else
#include <unistd.h>
#endif

class mitkItkImageIOTestSuite : public mitk::TestFixture
{
  CPPUNIT_TEST_SUITE(mitkItkImageIOTestSuite);
  MITK_TEST(TestImageWriterJpg);
  MITK_TEST(TestImageWriterPng1);
  MITK_TEST(TestImageWriterPng2);
  MITK_TEST(TestImageWriterPng3);
  MITK_TEST(TestImageWriterSimple);
  MITK_TEST(TestWrite3DImageWithOnePlane);
  MITK_TEST(TestWrite3DImageWithTwoPlanes);
  MITK_TEST(TestWrite3DplusT_ArbitraryTG);
  MITK_TEST(TestWrite3DplusT_ProportionalTG);
  CPPUNIT_TEST_SUITE_END();

public:
  void setUp() override {}
  void tearDown() override {}
  void TestImageWriterJpg() { TestImageWriter("NrrdWritingTestImage.jpg"); }
  void TestImageWriterPng1() { TestImageWriter("Png2D-bw.png"); }
  void TestImageWriterPng2() { TestImageWriter("RenderingTestData/rgbImage.png"); }
  void TestImageWriterPng3() { TestImageWriter("RenderingTestData/rgbaImage.png"); }
  void TestWrite3DplusT_ArbitraryTG()
  {
    TestImageWriter("3D+t-ITKIO-TestData/LinearModel_4D_arbitrary_time_geometry.nrrd");
  }

  void TestWrite3DplusT_ProportionalTG()
  {
    TestImageWriter("3D+t-ITKIO-TestData/LinearModel_4D_prop_time_geometry.nrrd");
  }

  void TestImageWriterSimple()
  {
    // TODO
  }

  std::string AppendExtension(const std::string &filename, const char *extension)
  {
    std::string new_filename = filename;

    new_filename += extension;
    return new_filename;
  }

  bool CompareImageMetaData(mitk::Image::Pointer image, mitk::Image::Pointer reference, bool checkPixelType = true)
  {
    // switch to AreIdentical() methods as soon as Bug 11925 (Basic comparison operators) is fixed

    if (image->GetDimension() != reference->GetDimension())
    {
      MITK_ERROR << "The image dimension differs: IN (" << image->GetDimension() << ") REF("
                 << reference->GetDimension() << ")";
      return false;
    }

    // pixel type
    if (checkPixelType &&
        (image->GetPixelType() != reference->GetPixelType() &&
         image->GetPixelType().GetBitsPerComponent() != reference->GetPixelType().GetBitsPerComponent()))
    {
      MITK_ERROR << "Pixeltype differs ( image=" << image->GetPixelType().GetPixelTypeAsString() << "["
                 << image->GetPixelType().GetBitsPerComponent() << "]"
                 << " reference=" << reference->GetPixelType().GetPixelTypeAsString() << "["
                 << reference->GetPixelType().GetBitsPerComponent() << "]"
                 << " )";
      return false;
    }

    return true;
  }

  /*
  Test writing picture formats like *.bmp, *.png, *.tiff or *.jpg
  NOTE: Saving as picture format must ignore PixelType comparison - not all bits per components are supported (see
  specification of the format)
  */
  void TestPictureWriting(mitk::Image *image, const std::string &filename, const std::string &extension)
  {
    const std::string fullFileName = AppendExtension(filename, extension.c_str());

    mitk::Image::Pointer singleSliceImage = nullptr;
    if (image->GetDimension() == 3)
    {
      mitk::ExtractSliceFilter::Pointer extractFilter = mitk::ExtractSliceFilter::New();
      extractFilter->SetInput(image);
      extractFilter->SetWorldGeometry(image->GetSlicedGeometry()->GetPlaneGeometry(0));

      extractFilter->Update();
      singleSliceImage = extractFilter->GetOutput();

      // test 3D writing in format supporting only 2D
      mitk::IOUtil::Save(image, fullFileName);

      // test images
      unsigned int foundImagesCount = 0;

      // if the image only contains one sinlge slice the itkImageSeriesWriter won't add a number like
      // filename.XX.extension
      if (image->GetDimension(2) == 1)
      {
        std::stringstream series_filenames;
        series_filenames << filename << extension;
        mitk::Image::Pointer compareImage = mitk::IOUtil::Load<mitk::Image>(series_filenames.str());
        if (compareImage.IsNotNull())
        {
          foundImagesCount++;
          MITK_TEST_CONDITION(
            CompareImageMetaData(singleSliceImage, compareImage, false),
            "Image meta data unchanged after writing and loading again. "); // ignore bits per component
        }
        remove(series_filenames.str().c_str());
      }
      else // test the whole slice stack
      {
        for (unsigned int i = 0; i < image->GetDimension(2); i++)
        {
          std::stringstream series_filenames;
          series_filenames << filename << "." << i + 1 << extension;
          mitk::Image::Pointer compareImage = mitk::IOUtil::Load<mitk::Image>(series_filenames.str());
          if (compareImage.IsNotNull())
          {
            foundImagesCount++;
            MITK_TEST_CONDITION(
              CompareImageMetaData(singleSliceImage, compareImage, false),
              "Image meta data unchanged after writing and loading again. "); // ignore bits per component
          }
          remove(series_filenames.str().c_str());
        }
      }
      MITK_TEST_CONDITION(foundImagesCount == image->GetDimension(2),
                          "All 2D-Slices of a 3D image were stored correctly.");
    }
    else if (image->GetDimension() == 2)
    {
      singleSliceImage = image;
    }

    // test 2D writing
    if (singleSliceImage.IsNotNull())
    {
      try
      {
        mitk::IOUtil::Save(singleSliceImage, fullFileName);

        mitk::Image::Pointer compareImage = mitk::IOUtil::Load<mitk::Image>(fullFileName.c_str());
        MITK_TEST_CONDITION_REQUIRED(compareImage.IsNotNull(), "Image stored was succesfully loaded again");

        MITK_TEST_CONDITION_REQUIRED(
          CompareImageMetaData(singleSliceImage, compareImage, false),
          "Image meta data unchanged after writing and loading again. "); // ignore bits per component
        remove(fullFileName.c_str());
      }
      catch (itk::ExceptionObject &e)
      {
        MITK_TEST_FAILED_MSG(<< "Exception during file writing for ." << extension << ": " << e.what());
      }
    }
  }

  void TestNRRDWriting(const mitk::Image *image)
  {
    CPPUNIT_ASSERT_MESSAGE("Internal error. Passed reference image is null.", image);

    std::ofstream tmpStream;
    std::string tmpFilePath = mitk::IOUtil::CreateTemporaryFile(tmpStream, "XXXXXX.nrrd");
    tmpStream.close();

    try
    {
      mitk::IOUtil::Save(image, tmpFilePath);

      mitk::Image::Pointer compareImage = mitk::IOUtil::Load<mitk::Image>(tmpFilePath);
      CPPUNIT_ASSERT_MESSAGE("Image stored in NRRD format was succesfully loaded again", compareImage.IsNotNull());

      /*It would make sence to check the images as well (see commented cppunit assert),
        but currently there seems to be a problem (exception) with most of the test images
        (partly it seems to be a problem when try to access the pixel content by AccessByItk_1
        in mitk::CompareImageDataFilter.
        This problem should be dealt with in Bug 19533 - mitkITKImageIOTest needs improvement */
      // CPPUNIT_ASSERT_MESSAGE("Images are equal.", mitk::Equal(*image, *compareImage, mitk::eps, true));
      CPPUNIT_ASSERT_MESSAGE(
        "TimeGeometries are equal.",
        mitk::Equal(*(image->GetTimeGeometry()), *(compareImage->GetTimeGeometry()), mitk::eps, true));

      remove(tmpFilePath.c_str());
    }
    catch (...)
    {
      std::remove(tmpFilePath.c_str());
      CPPUNIT_FAIL("Exception during NRRD file writing");
    }
  }

  void TestMHDWriting(const mitk::Image *image)
  {
    CPPUNIT_ASSERT_MESSAGE("Internal error. Passed reference image is null.", image);

    std::ofstream tmpStream;
    std::string tmpFilePath = mitk::IOUtil::CreateTemporaryFile(tmpStream, "XXXXXX.mhd");
    tmpStream.close();

    std::string tmpFilePathWithoutExt = tmpFilePath.substr(0, tmpFilePath.size() - 4);

    try
    {
      mitk::IOUtil::Save(image, tmpFilePath);

      mitk::Image::Pointer compareImage = mitk::IOUtil::Load<mitk::Image>(tmpFilePath);
      CPPUNIT_ASSERT_MESSAGE("Image stored in MHD format was succesfully loaded again! ", compareImage.IsNotNull());

      CPPUNIT_ASSERT_MESSAGE(".mhd file exists",
                             itksys::SystemTools::FileExists((tmpFilePathWithoutExt + ".mhd").c_str()));
      CPPUNIT_ASSERT_MESSAGE(".raw or .zraw exists",
                             itksys::SystemTools::FileExists((tmpFilePathWithoutExt + ".raw").c_str()) ||
                               itksys::SystemTools::FileExists((tmpFilePathWithoutExt + ".zraw").c_str()));

      /*It would make sence to check the images as well (see commented cppunit assert),
      but currently there seems to be a problem (exception) with most of the test images
      (partly it seems to be a problem when try to access the pixel content by AccessByItk_1
      in mitk::CompareImageDataFilter.
      This problem should be dealt with in Bug 19533 - mitkITKImageIOTest needs improvement */
      // CPPUNIT_ASSERT_MESSAGE("Images are equal.", mitk::Equal(*image, *compareImage, mitk::eps, true));
      CPPUNIT_ASSERT_MESSAGE("TimeGeometries are equal.",
                             mitk::Equal(*(image->GetTimeGeometry()), *(compareImage->GetTimeGeometry()), 5e-4, true));

      // delete
      remove(tmpFilePath.c_str());
      remove((tmpFilePathWithoutExt + ".raw").c_str());
      remove((tmpFilePathWithoutExt + ".zraw").c_str());
    }
    catch (...)
    {
      CPPUNIT_FAIL("Exception during.mhd file writing");
    }
  }

  void TestImageWriter(std::string sourcefile)
  {
    sourcefile = GetTestDataFilePath(sourcefile);

    // load image
    CPPUNIT_ASSERT_MESSAGE("Checking whether source image exists", itksys::SystemTools::FileExists(sourcefile.c_str()));

    mitk::Image::Pointer image = nullptr;

    try
    {
      image = mitk::IOUtil::Load<mitk::Image>(sourcefile);
    }
    catch (...)
    {
      CPPUNIT_FAIL("Exception during file loading:");
    }

    CPPUNIT_ASSERT_MESSAGE("loaded image not nullptr", image.IsNotNull());

    // write ITK .mhd image (2D and 3D only)
    if (image->GetDimension() <= 3)
    {
      TestMHDWriting(image);
    }

    // testing more component image writing as nrrd files
    TestNRRDWriting(image);

    std::ofstream tmpStream;
    std::string tmpFilePath = mitk::IOUtil::CreateTemporaryFile(tmpStream, "XXXXXX");
    tmpStream.close();

    TestPictureWriting(image, tmpFilePath, ".png");
    TestPictureWriting(image, tmpFilePath, ".jpg");
    TestPictureWriting(image, tmpFilePath, ".tiff");
    TestPictureWriting(image, tmpFilePath, ".bmp");
    // always end with this!
  }

  void TestWrite3DImageWithOnePlane()
  {
    typedef itk::Image<unsigned char, 3> ImageType;

    ImageType::Pointer itkImage = ImageType::New();

    ImageType::IndexType start;
    start.Fill(0);

    ImageType::SizeType size;
    size[0] = 100;
    size[1] = 100;
    size[2] = 1;

    ImageType::RegionType region;
    region.SetSize(size);
    region.SetIndex(start);
    itkImage->SetRegions(region);
    itkImage->Allocate();
    itkImage->FillBuffer(0);

    itk::ImageRegionIterator<ImageType> imageIterator(itkImage, itkImage->GetLargestPossibleRegion());

    // Make two squares
    while (!imageIterator.IsAtEnd())
    {
      if ((imageIterator.GetIndex()[0] > 5 && imageIterator.GetIndex()[0] < 20) &&
          (imageIterator.GetIndex()[1] > 5 && imageIterator.GetIndex()[1] < 20))
      {
        imageIterator.Set(255);
      }

      if ((imageIterator.GetIndex()[0] > 50 && imageIterator.GetIndex()[0] < 70) &&
          (imageIterator.GetIndex()[1] > 50 && imageIterator.GetIndex()[1] < 70))
      {
        imageIterator.Set(60);
      }
      ++imageIterator;
    }

    mitk::Image::Pointer image = mitk::ImportItkImage(itkImage);

    mitk::IOUtil::Save(image, mitk::IOUtil::CreateTemporaryFile("3Dto2DTestImageXXXXXX.nrrd"));
    mitk::IOUtil::Save(image, mitk::IOUtil::CreateTemporaryFile("3Dto2DTestImageXXXXXX.png"));
  }

  void TestWrite3DImageWithTwoPlanes()
  {
    typedef itk::Image<unsigned char, 3> ImageType;

    ImageType::Pointer itkImage = ImageType::New();

    ImageType::IndexType start;
    start.Fill(0);

    ImageType::SizeType size;
    size[0] = 100;
    size[1] = 100;
    size[2] = 2;

    ImageType::RegionType region;
    region.SetSize(size);
    region.SetIndex(start);
    itkImage->SetRegions(region);
    itkImage->Allocate();
    itkImage->FillBuffer(0);

    itk::ImageRegionIterator<ImageType> imageIterator(itkImage, itkImage->GetLargestPossibleRegion());

    // Make two squares
    while (!imageIterator.IsAtEnd())
    {
      if ((imageIterator.GetIndex()[0] > 5 && imageIterator.GetIndex()[0] < 20) &&
          (imageIterator.GetIndex()[1] > 5 && imageIterator.GetIndex()[1] < 20))
      {
        imageIterator.Set(255);
      }
      if ((imageIterator.GetIndex()[0] > 50 && imageIterator.GetIndex()[0] < 70) &&
          (imageIterator.GetIndex()[1] > 50 && imageIterator.GetIndex()[1] < 70))
      {
        imageIterator.Set(60);
      }
      ++imageIterator;
    }
    mitk::Image::Pointer image = mitk::ImportItkImage(itkImage);

    mitk::IOUtil::Save(image, mitk::IOUtil::CreateTemporaryFile("3Dto2DTestImageXXXXXX.nrrd"));

    CPPUNIT_ASSERT_THROW(mitk::IOUtil::Save(image, mitk::IOUtil::CreateTemporaryFile("3Dto2DTestImageXXXXXX.png")),
                         mitk::Exception);
  }
};

MITK_TEST_SUITE_REGISTRATION(mitkItkImageIO)