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); }