void TestSetActiveLayer()
{
// Cache active layer
mitk::LabelSet::ConstPointer activeLayer = m_LabelSetImage->GetActiveLabelSet();
// Add new layer
mitk::LabelSet::Pointer newlayer = mitk::LabelSet::New();
mitk::Label::Pointer label1 = mitk::Label::New();
label1->SetName("Label1");
label1->SetValue(1);
mitk::Label::Pointer label2 = mitk::Label::New();
label2->SetName("Label2");
label2->SetValue(200);
newlayer->AddLabel(label1);
newlayer->AddLabel(label2);
newlayer->SetActiveLabel(200);
unsigned int layerID = m_LabelSetImage->AddLayer(newlayer);
// Set initial layer as active layer
m_LabelSetImage->SetActiveLayer(0);
CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*activeLayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true));
// Set previously added layer as active layer
m_LabelSetImage->SetActiveLayer(layerID);
CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true));
// Set a non existing layer as active layer - nothing should change
m_LabelSetImage->SetActiveLayer(10000);
CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true));
}
void TestRemoveLabels()
{
mitk::Image::Pointer image = mitk::IOUtil::LoadImage(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd"));
m_LabelSetImage->InitializeByLabeledImage(image);
CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 6",m_LabelSetImage->GetNumberOfLabels() == 6);
// 2ndMin because of the exterior label = 0
CPPUNIT_ASSERT_MESSAGE("Labels with value 1 and 3 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValue2ndMin() == 1);
CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 7);
CPPUNIT_ASSERT_MESSAGE("Label with ID 3 does not exists after initialization",m_LabelSetImage->ExistLabel(3) == true);
CPPUNIT_ASSERT_MESSAGE("Label with ID 7 does not exists after initialization",m_LabelSetImage->ExistLabel(7) == true);
std::vector<mitk::Label::PixelType> labelsToBeRemoved;
labelsToBeRemoved.push_back(1);
labelsToBeRemoved.push_back(3);
labelsToBeRemoved.push_back(7);
m_LabelSetImage->RemoveLabels(labelsToBeRemoved);
CPPUNIT_ASSERT_MESSAGE("Wrong number of labels after some have been removed", m_LabelSetImage->GetNumberOfLabels() == 3);
// Values within the image are 0, 1, 3, 5, 6, 7 - New Min/Max value should be 5 / 6
// 2ndMin because of the exterior label = 0
CPPUNIT_ASSERT_MESSAGE("Labels with value 1 and 3 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValue2ndMin() == 5);
CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 6);
}
void TestGetLabel()
{
mitk::Label::Pointer label1 = mitk::Label::New();
label1->SetName("Label1");
mitk::Label::PixelType value1 = 1;
label1->SetValue(value1);
mitk::Label::Pointer label2 = mitk::Label::New();
label2->SetName("Label2");
mitk::Label::PixelType value2 = 200;
label2->SetValue(value2);
m_LabelSetImage->GetActiveLabelSet()->AddLabel(label1);
m_LabelSetImage->AddLayer();
m_LabelSetImage->GetLabelSet(1)->AddLabel(label2);
CPPUNIT_ASSERT_MESSAGE("Wrong label retrieved for active layer", mitk::Equal(*m_LabelSetImage->GetLabel(1), *label1, 0.0001, true));
CPPUNIT_ASSERT_MESSAGE("Wrong label retrieved for layer 1", mitk::Equal(*m_LabelSetImage->GetLabel(200, 1), *label2, 0.0001, true));
// Try to get a non existing label
mitk::Label* label3 = m_LabelSetImage->GetLabel(1000);
CPPUNIT_ASSERT_MESSAGE("Non existing label should be NULL", label3 == NULL);
// Try to get a label from a non existing layer
label3 = m_LabelSetImage->GetLabel(200, 1000);
CPPUNIT_ASSERT_MESSAGE("Label from non existing layer should be NULL", label3 == NULL);
}
void setUp() override
{
// Create a new labelset image
m_LabelSetImage = mitk::LabelSetImage::New();
mitk::Image::Pointer regularImage = mitk::Image::New();
unsigned int dimensions[3] = {256, 256, 312};
regularImage->Initialize(mitk::MakeScalarPixelType<int>(), 3, dimensions);
m_LabelSetImage->Initialize(regularImage);
}
void TestReadWrite3DplusTLabelSetImage()
{
unsigned int dimensions[4] = {256, 256, 312, 10};
regularImage->Initialize(mitk::MakeScalarPixelType<int>(), 4, dimensions);
multilabelImage = mitk::LabelSetImage::New();
multilabelImage->Initialize(regularImage);
mitk::LabelSet::Pointer newlayer = mitk::LabelSet::New();
newlayer->SetLayer(1);
mitk::Label::Pointer label0 = mitk::Label::New();
label0->SetName("Background");
label0->SetValue(0);
mitk::Label::Pointer label1 = mitk::Label::New();
label1->SetName("Label1");
label1->SetValue(1);
mitk::Label::Pointer label2 = mitk::Label::New();
label2->SetName("Label2");
label2->SetValue(200);
newlayer->AddLabel(label0);
newlayer->AddLabel(label1);
newlayer->AddLabel(label2);
newlayer->SetActiveLabel(200);
multilabelImage->AddLayer(newlayer);
pathToImage = mitk::IOUtil::CreateTemporaryDirectory();
pathToImage.append("/LabelSetTestImage3DplusT.nrrd");
mitk::IOUtil::Save(multilabelImage, pathToImage);
mitk::LabelSetImage::Pointer loadedImage =
dynamic_cast<mitk::LabelSetImage *>(mitk::IOUtil::Load(pathToImage)[0].GetPointer());
// This information is currently not serialized but also checked within the Equals function
loadedImage->SetActiveLayer(multilabelImage->GetActiveLayer());
CPPUNIT_ASSERT_MESSAGE("Error reading label set image", loadedImage.IsNotNull());
CPPUNIT_ASSERT_MESSAGE("Error reading label set image", mitk::Equal(*multilabelImage, *loadedImage, 0.0001, true));
itksys::SystemTools::RemoveFile(pathToImage);
}
void TestGetTotalNumberOfLabels()
{
mitk::Label::Pointer label1 = mitk::Label::New();
label1->SetName("Label1");
mitk::Label::PixelType value1 = 1;
label1->SetValue(value1);
mitk::Label::Pointer label2 = mitk::Label::New();
label2->SetName("Label2");
mitk::Label::PixelType value2 = 200;
label2->SetValue(value2);
m_LabelSetImage->GetActiveLabelSet()->AddLabel(label1);
m_LabelSetImage->AddLayer();
m_LabelSetImage->GetLabelSet(1)->AddLabel(label2);
CPPUNIT_ASSERT_MESSAGE(
"Wrong total number of labels",
m_LabelSetImage->GetTotalNumberOfLabels() == 4); // added 2 labels + 2 exterior default labels
}
void TestGetActiveLabel()
{
mitk::Label::Pointer label1 = mitk::Label::New();
label1->SetName("Label1");
mitk::Label::PixelType value1 = 1;
label1->SetValue(value1);
mitk::Label::Pointer label2 = mitk::Label::New();
label2->SetName("Label2");
mitk::Label::PixelType value2 = 200;
label2->SetValue(value2);
m_LabelSetImage->GetActiveLabelSet()->AddLabel(label1);
m_LabelSetImage->GetActiveLabelSet()->AddLabel(label2);
m_LabelSetImage->GetActiveLabelSet()->SetActiveLabel(1);
CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active label is wrong",m_LabelSetImage->GetActiveLabel()->GetValue() == value1);
m_LabelSetImage->GetActiveLabelSet()->SetActiveLabel(value2);
CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active label is wrong",m_LabelSetImage->GetActiveLabel()->GetValue() == value2);
}
// Reduce contours with nth point
void TestInitialize()
{
// LabelSet image should always has the pixel type mitk::Label::PixelType
CPPUNIT_ASSERT_MESSAGE("LabelSetImage has wrong pixel type",
m_LabelSetImage->GetPixelType() == mitk::MakeScalarPixelType<mitk::Label::PixelType>());
mitk::Image::Pointer regularImage = mitk::Image::New();
unsigned int dimensions[3] = {256,256,312};
regularImage->Initialize(mitk::MakeScalarPixelType<int>(), 3, dimensions);
mitk::BaseGeometry::Pointer regularImageGeo = regularImage->GetGeometry();
mitk::BaseGeometry::Pointer labelImageGeo = m_LabelSetImage->GetGeometry();
MITK_ASSERT_EQUAL(labelImageGeo, regularImageGeo, "LabelSetImage has wrong geometry");
// By default one layer containing the exterior label should be added
CPPUNIT_ASSERT_MESSAGE("Image was not correctly initialized - number of layers is not one",m_LabelSetImage->GetNumberOfLayers() == 1);
CPPUNIT_ASSERT_MESSAGE("Image was not correctly initialized - active layer has wrong ID",m_LabelSetImage->GetActiveLayer() == 0);
CPPUNIT_ASSERT_MESSAGE("Image was not correctly initialized - active label is not the exterior label",m_LabelSetImage->GetActiveLabel()->GetValue() == 0);
}
void LabelSetImageIO::LoadLabelSetImagePreset(const std::string & presetFilename, mitk::LabelSetImage::Pointer& inputImage )
{
std::unique_ptr<TiXmlDocument> presetXmlDoc(new TiXmlDocument());
bool ok = presetXmlDoc->LoadFile(presetFilename);
if ( !ok )
return;
TiXmlElement * presetElem = presetXmlDoc->FirstChildElement("LabelSetImagePreset");
if(!presetElem)
{
MITK_INFO << "No valid preset XML";
return;
}
int numberOfLayers;
presetElem->QueryIntAttribute("layers", &numberOfLayers);
for(int i = 0 ; i < numberOfLayers; i++)
{
TiXmlElement * layerElem = presetElem->FirstChildElement("Layer");
int numberOfLabels;
layerElem->QueryIntAttribute("labels", &numberOfLabels);
if(inputImage->GetLabelSet(i) == NULL) inputImage->AddLayer();
TiXmlElement * labelElement = layerElem->FirstChildElement("Label");
if(labelElement == NULL) break;
for(int j = 0 ; j < numberOfLabels; j++)
{
mitk::Label::Pointer label = mitk::LabelSetImageIO::LoadLabelFromTiXmlDocument(labelElement);
inputImage->GetLabelSet()->AddLabel(label);
labelElement = labelElement->NextSiblingElement("Label");
if(labelElement == NULL) break;
}
}
}
void TestGetActiveLabelSet()
{
mitk::LabelSet::Pointer newlayer = mitk::LabelSet::New();
mitk::Label::Pointer label1 = mitk::Label::New();
label1->SetName("Label1");
label1->SetValue(1);
mitk::Label::Pointer label2 = mitk::Label::New();
label2->SetName("Label2");
label2->SetValue(200);
newlayer->AddLabel(label1);
newlayer->AddLabel(label2);
newlayer->SetActiveLabel(200);
unsigned int layerID = m_LabelSetImage->AddLayer(newlayer);
mitk::LabelSet::Pointer activeLayer = m_LabelSetImage->GetActiveLabelSet();
CPPUNIT_ASSERT_MESSAGE("Wrong layer ID was returned", layerID == 1);
CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *activeLayer, 0.00001, true));
}
void MitkImageToMitkLabelSetImage(itk::VectorImage< TPixel, VDimensions> * source, mitk::LabelSetImage::Pointer &output)
{
typedef itk::VectorImage< TPixel, VDimensions > VectorImageType;
typedef itk::Image< TPixel, VDimensions > ImageType;
typedef itk::VectorIndexSelectionCastImageFilter< VectorImageType, ImageType > VectorIndexSelectorType;
unsigned int numberOfComponents = source->GetVectorLength();
if (numberOfComponents < 1)
{
mitkThrow() << "At least one Component is required.";
}
typename VectorIndexSelectorType::Pointer vectorIndexSelector = VectorIndexSelectorType::New();
vectorIndexSelector->SetIndex(0);
vectorIndexSelector->SetInput(source);
vectorIndexSelector->Update();
mitk::Image::Pointer tempImage;
mitk::CastToMitkImage(vectorIndexSelector->GetOutput(), tempImage);
output = mitk::LabelSetImage::New();
output->InitializeByLabeledImage(tempImage);
for (unsigned int layer = 1; layer < numberOfComponents; ++layer)
{
typename VectorIndexSelectorType::Pointer vectorIndexSelectorLoop = VectorIndexSelectorType::New();
vectorIndexSelectorLoop->SetIndex(layer);
vectorIndexSelector->SetInput(source);
vectorIndexSelector->Update();
mitk::Image::Pointer loopImage;
mitk::CastToMitkImage(vectorIndexSelector->GetOutput(), loopImage);
output->AddLayer(loopImage);
}
}
void Result_Match_Expectation()
{
mitk::LabelSetImageSurfaceStampFilter::Pointer filter = mitk::LabelSetImageSurfaceStampFilter::New();
filter->SetSurface(m_Surface);
filter->SetForceOverwrite(true);
filter->SetInput(m_LabelSetImage);
filter->Update();
mitk::LabelSetImage::Pointer result = dynamic_cast<mitk::LabelSetImage *>(
m_LabelSetImage.GetPointer()); // dynamic_cast<mitk::LabelSetImage*>(filter->GetOutput());
// result->DisconnectPipeline();
// mitk::LabelSetImage::Pointer result
// =dynamic_cast<mitk::LabelSetImage*>(m_LabelSetImage->Clone().GetPointer());//dynamic_cast<mitk::LabelSetImage*>(filter->GetOutput());
mitk::LabelSetImage::Pointer expectedResult = dynamic_cast<mitk::LabelSetImage *>(
mitk::IOUtil::Load(GetTestDataFilePath("Multilabel/StampResultBasedOnEmptyML.nrrd"))[0].GetPointer());
MITK_ASSERT_EQUAL(result, expectedResult, "Result after stamping should be equal to the saved version");
}
void TestMergeLabel()
{
mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd"))[0].GetPointer());
m_LabelSetImage = 0;
m_LabelSetImage = mitk::LabelSetImage::New();
m_LabelSetImage->InitializeByLabeledImage(image);
CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 6", m_LabelSetImage->GetNumberOfLabels() == 6);
// 2ndMin because of the exterior label = 0
CPPUNIT_ASSERT_MESSAGE("Wrong MIN value", m_LabelSetImage->GetStatistics()->GetScalarValueMin() == 0);
CPPUNIT_ASSERT_MESSAGE("Wrong MAX value", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 7);
m_LabelSetImage->GetActiveLabelSet()->SetActiveLabel(6);
// Merge label 7 with label 0. Result should be that label 7 is not present any more
m_LabelSetImage->MergeLabel(6, 7);
CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 6);
m_LabelSetImage->GetStatistics()->GetScalarValue2ndMax();
// Count all pixels with value 7 = 823
// Count all pixels with value 6 = 507
// Check if merge label has 507 + 823 = 1330 pixels
CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not remove from the image", m_LabelSetImage->GetStatistics()->GetCountOfMaxValuedVoxels() == 1330);
}
void TestRemoveLayer()
{
// Cache active layer
mitk::LabelSet::ConstPointer activeLayer = m_LabelSetImage->GetActiveLabelSet();
// Add new layers
m_LabelSetImage->AddLayer();
mitk::LabelSet::Pointer newlayer = mitk::LabelSet::New();
mitk::Label::Pointer label1 = mitk::Label::New();
label1->SetName("Label1");
label1->SetValue(1);
mitk::Label::Pointer label2 = mitk::Label::New();
label2->SetName("Label2");
label2->SetValue(200);
newlayer->AddLabel(label1);
newlayer->AddLabel(label2);
newlayer->SetActiveLabel(200);
m_LabelSetImage->AddLayer(newlayer);
CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned",
mitk::Equal(*newlayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true));
m_LabelSetImage->RemoveLayer();
CPPUNIT_ASSERT_MESSAGE("Wrong number of layers, after a layer was removed",
m_LabelSetImage->GetNumberOfLayers() == 2);
CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(2) == false);
CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(1) == true);
CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(0) == true);
m_LabelSetImage->RemoveLayer();
CPPUNIT_ASSERT_MESSAGE("Wrong number of layers, after a layer was removed",
m_LabelSetImage->GetNumberOfLayers() == 1);
CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(1) == false);
CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(0) == true);
CPPUNIT_ASSERT_MESSAGE("Wrong active layer",
mitk::Equal(*activeLayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true));
m_LabelSetImage->RemoveLayer();
CPPUNIT_ASSERT_MESSAGE("Wrong number of layers, after a layer was removed",
m_LabelSetImage->GetNumberOfLayers() == 0);
CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(0) == false);
CPPUNIT_ASSERT_MESSAGE("Active layers is not nullptr although all layer have been removed",
m_LabelSetImage->GetActiveLabelSet() == 0);
}
void TestInitializeByLabeledImage()
{
mitk::Image::Pointer image = mitk::IOUtil::LoadImage(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd"));
m_LabelSetImage->InitializeByLabeledImage(image);
CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 6",m_LabelSetImage->GetNumberOfLabels() == 6);
}