Skip to content

Commit

Permalink
COMP: Reduce HTTP test coverage redundancy
Browse files Browse the repository at this point in the history 
Removes metadata validation from HTTP tests. Both metadata validation
and image buffer validation are now covered under baseline image
comparison after the test body completes.
  • Loading branch information
@tbirdso
tbirdso committed Aug 13, 2023
1 parent 197ebec commit 3d6984e
Showing 1 changed file with 40 additions and 110 deletions.
150 changes: 40 additions & 110 deletions test/itkOMEZarrNGFFHTTPTest.cxx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,14 @@ makeOutputName(const std::string & outputPrefix, size_t datasetIndex)
return outputPrefix + "_" + std::to_string(datasetIndex) + ".mha";
}

template <typename TImagePointer>
void
writeOutputImage(TImagePointer image, const std::string & outputPrefix, size_t datasetIndex)
{
std::string outputFilename = makeOutputName(outputPrefix, datasetIndex);
itk::WriteImage(image, outputFilename, USE_MHA_COMPRESSION);
}

bool
test2DImage(const std::string & outputPrefix)
{
Expand All @@ -45,67 +53,33 @@ test2DImage(const std::string & outputPrefix)

itk::OMEZarrNGFFImageIOFactory::RegisterOneFactory();

// Baseline image metadata
auto baselineImage0 = ImageType::New();
baselineImage0->SetRegions(itk::MakeSize(1024, 930));
// unit origin, spacing, direction

auto baselineImage1 = ImageType::New();
baselineImage1->SetRegions(itk::MakeSize(512, 465));
const float spacing1[2] = { 2.0, 2.0 };
baselineImage1->SetSpacing(spacing1);
// unit origin, direction

auto baselineImage2 = ImageType::New();
baselineImage2->SetRegions(itk::MakeSize(256, 232));
const float spacing2[2] = { 4.0, 4.0 };
baselineImage2->SetSpacing(spacing2);
// unit origin, direction

// Resolution 0
auto image = itk::ReadImage<ImageType>(resourceURL);
size_t resolution = 0;
auto image = itk::ReadImage<ImageType>(resourceURL);
image->Print(std::cout);

ITK_TEST_EXPECT_EQUAL(image->GetLargestPossibleRegion(), baselineImage0->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion(), baselineImage0->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetSpacing(), baselineImage0->GetSpacing());
ITK_TEST_EXPECT_EQUAL(image->GetOrigin(), baselineImage0->GetOrigin());
ITK_TEST_EXPECT_EQUAL(image->GetLargestPossibleRegion(), image->GetBufferedRegion());
writeOutputImage(image, outputPrefix, resolution);

std::string outputFilename = makeOutputName(outputPrefix, 0);
itk::WriteImage(image, outputFilename, USE_MHA_COMPRESSION);

// Resolution 1
resolution = 1;
auto imageIO = itk::OMEZarrNGFFImageIO::New();
imageIO->SetDatasetIndex(1);
imageIO->SetDatasetIndex(resolution);
auto reader1 = itk::ImageFileReader<ImageType>::New();
reader1->SetFileName(resourceURL);
reader1->SetImageIO(imageIO);
reader1->Update();
image = reader1->GetOutput();
image->Print(std::cout);
ITK_TEST_EXPECT_EQUAL(image->GetLargestPossibleRegion(), baselineImage1->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion(), baselineImage1->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetSpacing(), baselineImage1->GetSpacing());
ITK_TEST_EXPECT_EQUAL(image->GetOrigin(), baselineImage1->GetOrigin());

outputFilename = makeOutputName(outputPrefix, 1);
itk::WriteImage(image, outputFilename, USE_MHA_COMPRESSION);
writeOutputImage(image, outputPrefix, resolution);

// Resolution 2
imageIO->SetDatasetIndex(2);
imageIO->SetDatasetIndex(resolution);
auto reader2 = itk::ImageFileReader<ImageType>::New();
reader2->SetFileName(resourceURL);
reader2->SetImageIO(imageIO);
reader2->Update();
image = reader2->GetOutput();
image->Print(std::cout);
ITK_TEST_EXPECT_EQUAL(image->GetLargestPossibleRegion(), baselineImage2->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion(), baselineImage2->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetSpacing(), baselineImage2->GetSpacing());
ITK_TEST_EXPECT_EQUAL(image->GetOrigin(), baselineImage2->GetOrigin());

outputFilename = makeOutputName(outputPrefix, 2);
itk::WriteImage(image, outputFilename, USE_MHA_COMPRESSION);
writeOutputImage(image, outputPrefix, resolution);

return EXIT_SUCCESS;
}
Expand All @@ -116,68 +90,33 @@ test3DImage(const std::string & outputPrefix)
using ImageType = itk::Image<unsigned char, 3>;
const std::string resourceURL = "https://s3.embl.de/i2k-2020/ngff-example-data/v0.4/zyx.ome.zarr";

// Baseline image metadata
auto baselineImage0 = ImageType::New();
baselineImage0->SetRegions(itk::MakeSize(483, 393, 603));
const float spacing0[3] = { 64, 64, 64 };
baselineImage0->SetSpacing(spacing0);

auto baselineImage1 = ImageType::New();
baselineImage1->SetRegions(itk::MakeSize(242, 196, 302));
const float spacing1[3] = { 128, 128, 128 };
baselineImage1->SetSpacing(spacing1);

auto baselineImage2 = ImageType::New();
baselineImage2->SetRegions(itk::MakeSize(121, 98, 151));
const float spacing2[3] = { 256, 256, 256 };
baselineImage2->SetSpacing(spacing2);

itk::OMEZarrNGFFImageIOFactory::RegisterOneFactory();

// Resolution 0
auto image = itk::ReadImage<ImageType>(resourceURL);
size_t resolution = 0;
auto image = itk::ReadImage<ImageType>(resourceURL);
image->Print(std::cout);
writeOutputImage(image, outputPrefix, resolution);

ITK_TEST_EXPECT_EQUAL(image->GetLargestPossibleRegion(), baselineImage0->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion(), baselineImage0->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetSpacing(), baselineImage0->GetSpacing());
ITK_TEST_EXPECT_EQUAL(image->GetOrigin(), baselineImage0->GetOrigin());

std::string outputFilename = makeOutputName(outputPrefix, 0);
itk::WriteImage(image, outputFilename, USE_MHA_COMPRESSION);

// Resolution 1
resolution = 1;
auto imageIO = itk::OMEZarrNGFFImageIO::New();
imageIO->SetDatasetIndex(1);
imageIO->SetDatasetIndex(resolution);
auto reader1 = itk::ImageFileReader<ImageType>::New();
reader1->SetFileName(resourceURL);
reader1->SetImageIO(imageIO);
reader1->Update();
image = reader1->GetOutput();
image->Print(std::cout);
ITK_TEST_EXPECT_EQUAL(image->GetLargestPossibleRegion(), baselineImage1->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion(), baselineImage1->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetSpacing(), baselineImage1->GetSpacing());
ITK_TEST_EXPECT_EQUAL(image->GetOrigin(), baselineImage1->GetOrigin());
writeOutputImage(image, outputPrefix, resolution);

outputFilename = makeOutputName(outputPrefix, 1);
itk::WriteImage(image, outputFilename, USE_MHA_COMPRESSION);

// Resolution 2
imageIO->SetDatasetIndex(2);
resolution = 2;
imageIO->SetDatasetIndex(resolution);
auto reader2 = itk::ImageFileReader<ImageType>::New();
reader2->SetFileName(resourceURL);
reader2->SetImageIO(imageIO);
reader2->Update();
image = reader2->GetOutput();
image->Print(std::cout);
ITK_TEST_EXPECT_EQUAL(image->GetLargestPossibleRegion(), baselineImage2->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion(), baselineImage2->GetLargestPossibleRegion());
ITK_TEST_EXPECT_EQUAL(image->GetSpacing(), baselineImage2->GetSpacing());
ITK_TEST_EXPECT_EQUAL(image->GetOrigin(), baselineImage2->GetOrigin());

outputFilename = makeOutputName(outputPrefix, 2);
itk::WriteImage(image, outputFilename, USE_MHA_COMPRESSION);
writeOutputImage(image, outputPrefix, resolution);

return EXIT_SUCCESS;
}
Expand All @@ -187,11 +126,13 @@ testTimeSlice(const std::string & outputPrefix)
{
// Read a subregion of an arbitrary time point from a 3D image buffer into a 2D image
using ImageType = itk::Image<unsigned char, 2>;
const std::string resourceURL = "https://s3.embl.de/i2k-2020/ngff-example-data/v0.4/tyx.ome.zarr";
const std::string resourceURL = "https://s3.embl.de/i2k-2020/ngff-example-data/v0.4/tyx.ome.zarr";
static constexpr size_t RESOLUTION = 0;
static constexpr size_t TIME_INDEX = 2;

auto imageIO = itk::OMEZarrNGFFImageIO::New();
imageIO->SetDatasetIndex(0);
imageIO->SetTimeIndex(2);
imageIO->SetDatasetIndex(RESOLUTION);
imageIO->SetTimeIndex(TIME_INDEX);

auto requestedRegion = itk::ImageRegion<2>();
requestedRegion.SetSize(itk::MakeSize(50, 50));
Expand All @@ -212,13 +153,7 @@ testTimeSlice(const std::string & outputPrefix)
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion().GetSize(), requestedRegion.GetSize());
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion().GetIndex(), requestedRegion.GetIndex());

typename ImageType::SpacingType expectedSpacing;
expectedSpacing.Fill(0.65);
ITK_TEST_EXPECT_EQUAL(image->GetSpacing(), expectedSpacing);
ITK_TEST_EXPECT_EQUAL(image->GetOrigin(), itk::MakePoint(0.0, 0.0));

std::string outputFilename = makeOutputName(outputPrefix, 0);
itk::WriteImage(image, outputFilename, USE_MHA_COMPRESSION);
writeOutputImage(image, outputPrefix, RESOLUTION);

return EXIT_SUCCESS;
}
Expand All @@ -228,12 +163,15 @@ testTimeAndChannelSlice(const std::string & outputPrefix)
{
// Read a subregion of an arbitrary channel and time point from a 5D image buffer into a 3D image
using ImageType = itk::Image<unsigned char, 3>;
const std::string resourceURL = "https://s3.embl.de/i2k-2020/ngff-example-data/v0.4/tczyx.ome.zarr";
const std::string resourceURL = "https://s3.embl.de/i2k-2020/ngff-example-data/v0.4/tczyx.ome.zarr";
static constexpr size_t RESOLUTION = 2;
static constexpr size_t TIME_INDEX = 0;
static constexpr size_t CHANNEL_INDEX = 0;

auto imageIO = itk::OMEZarrNGFFImageIO::New();
imageIO->SetDatasetIndex(2);
imageIO->SetTimeIndex(0);
imageIO->SetChannelIndex(0);
imageIO->SetDatasetIndex(RESOLUTION);
imageIO->SetTimeIndex(TIME_INDEX);
imageIO->SetChannelIndex(CHANNEL_INDEX);

auto requestedRegion = itk::ImageRegion<3>();
requestedRegion.SetSize(itk::MakeSize(10, 20, 30));
Expand All @@ -254,15 +192,7 @@ testTimeAndChannelSlice(const std::string & outputPrefix)
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion().GetSize(), requestedRegion.GetSize());
ITK_TEST_EXPECT_EQUAL(image->GetBufferedRegion().GetIndex(), requestedRegion.GetIndex());

typename ImageType::SpacingType expectedSpacing;
expectedSpacing.SetElement(0, 2.6);
expectedSpacing.SetElement(1, 2.6);
expectedSpacing.SetElement(2, 4.0);
ITK_TEST_EXPECT_EQUAL(image->GetSpacing(), expectedSpacing);
ITK_TEST_EXPECT_EQUAL(image->GetOrigin(), itk::MakePoint(0.0, 0.0, 0.0));

std::string outputFilename = makeOutputName(outputPrefix, 2);
itk::WriteImage(image, outputFilename, USE_MHA_COMPRESSION);
writeOutputImage(image, outputPrefix, RESOLUTION);

return EXIT_SUCCESS;
}
Expand Down

0 comments on commit 3d6984e

Please sign in to comment.