diff --git a/Modules/Multilabel/Testing/files.cmake b/Modules/Multilabel/Testing/files.cmake
index 0a03695261..632cad3e3a 100644
--- a/Modules/Multilabel/Testing/files.cmake
+++ b/Modules/Multilabel/Testing/files.cmake
@@ -1,9 +1,8 @@
set(MODULE_TESTS
mitkLabelTest.cpp
- mitkLabelSetTest.cpp
mitkLabelSetImageTest.cpp
mitkLegacyLabelSetImageIOTest.cpp
mitkLabelSetImageSurfaceStampFilterTest.cpp
mitkTransferLabelTest.cpp
)
diff --git a/Modules/Multilabel/Testing/mitkLabelSetImageTest.cpp b/Modules/Multilabel/Testing/mitkLabelSetImageTest.cpp
index 700825fdaa..74ff7e4eae 100644
--- a/Modules/Multilabel/Testing/mitkLabelSetImageTest.cpp
+++ b/Modules/Multilabel/Testing/mitkLabelSetImageTest.cpp
@@ -1,514 +1,479 @@
/*============================================================================
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 <mitkIOUtil.h>
#include <mitkImageStatisticsHolder.h>
#include <mitkLabelSetImage.h>
#include <mitkTestFixture.h>
#include <mitkTestingMacros.h>
#include <mitkAutoCropImageFilter.h>
class mitkLabelSetImageTestSuite : public mitk::TestFixture
{
CPPUNIT_TEST_SUITE(mitkLabelSetImageTestSuite);
MITK_TEST(TestInitialize);
MITK_TEST(TestAddLayer);
MITK_TEST(TestGetActiveLabelSet);
MITK_TEST(TestGetActiveLabel);
MITK_TEST(TestInitializeByLabeledImage);
- MITK_TEST(TestGetLabelSet);
MITK_TEST(TestGetLabel);
MITK_TEST(TestSetUnlabeledLabelLock);
MITK_TEST(TestGetTotalNumberOfLabels);
MITK_TEST(TestExistsLabel);
MITK_TEST(TestExistsLabelSet);
MITK_TEST(TestSetActiveLayer);
MITK_TEST(TestRemoveLayer);
MITK_TEST(TestRemoveLabels);
MITK_TEST(TestEraseLabels);
MITK_TEST(TestMergeLabels);
MITK_TEST(TestCreateLabelMask);
CPPUNIT_TEST_SUITE_END();
private:
mitk::LabelSetImage::Pointer m_LabelSetImage;
public:
void setUp() override
{
// Create a new labelset image
m_LabelSetImage = mitk::LabelSetImage::New();
mitk::Image::Pointer regularImage = mitk::Image::New();
unsigned int dimensions[3] = { 96, 128, 52 };
regularImage->Initialize(mitk::MakeScalarPixelType<char>(), 3, dimensions);
m_LabelSetImage->Initialize(regularImage);
}
void tearDown() override
{
// Delete LabelSetImage
m_LabelSetImage = nullptr;
}
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] = { 96, 128, 52 };
regularImage->Initialize(mitk::MakeScalarPixelType<char>(), 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 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 - no active label should be selected",
m_LabelSetImage->GetActiveLabel() == nullptr);
}
void TestAddLayer()
{
CPPUNIT_ASSERT_MESSAGE("Number of layers is not zero", m_LabelSetImage->GetNumberOfLayers() == 1);
m_LabelSetImage->AddLayer();
CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - number of layers is not one",
m_LabelSetImage->GetNumberOfLayers() == 2);
CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active layer has wrong ID",
m_LabelSetImage->GetActiveLayer() == 1);
CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - no active label should be selected",
m_LabelSetImage->GetActiveLabel() == nullptr);
- 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);
+ const auto layerID = m_LabelSetImage->AddLayer({ label1, label2 });
+ m_LabelSetImage->SetActiveLabel(200);
CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - number of layers is not two",
m_LabelSetImage->GetNumberOfLayers() == 3);
CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active layer has wrong ID",
m_LabelSetImage->GetActiveLayer() == layerID);
CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active label is wrong",
- m_LabelSetImage->GetActiveLabel(layerID)->GetValue() == 200);
+ m_LabelSetImage->GetActiveLabel()->GetValue() == 200);
}
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::LabelSetImage::ConstLabelVectorType refLayer = { label1, label2 };
+ unsigned int layerID = m_LabelSetImage->AddLayer(refLayer);
+ m_LabelSetImage->SetActiveLabel(200);
- mitk::LabelSet::Pointer activeLayer = m_LabelSetImage->GetActiveLabelSet();
+ auto activeLayer = m_LabelSetImage->GetConstLabelsByValue(m_LabelSetImage->GetLabelValuesByGroup(m_LabelSetImage->GetActiveLayer()));
CPPUNIT_ASSERT_MESSAGE("Wrong layer ID was returned", layerID == 1);
- CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *activeLayer, 0.00001, true));
+ CPPUNIT_ASSERT_MESSAGE("Wrong layer ID was returned", layerID == m_LabelSetImage->GetActiveLayer());
- mitk::LabelSet::ConstPointer constActiveLayer = const_cast<const mitk::LabelSetImage*>(m_LabelSetImage.GetPointer())->GetActiveLabelSet();
- CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *constActiveLayer, 0.00001, true));
+ CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(refLayer, activeLayer, 0.00001, true));
}
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);
+ m_LabelSetImage->AddLabel(label1,0);
+ m_LabelSetImage->AddLabel(label2,0);
+ m_LabelSetImage->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);
+ m_LabelSetImage->SetActiveLabel(value2);
CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active label is wrong",
m_LabelSetImage->GetActiveLabel()->GetValue() == value2);
CPPUNIT_ASSERT_MESSAGE("Active Label was not correctly retreived with const getter",
const_cast<const mitk::LabelSetImage*>(m_LabelSetImage.GetPointer())->GetActiveLabel()->GetValue() == value2);
}
void TestInitializeByLabeledImage()
{
mitk::Image::Pointer image =
mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd"));
m_LabelSetImage->InitializeByLabeledImage(image);
CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 5", m_LabelSetImage->GetNumberOfLabels() == 5);
}
- void TestGetLabelSet()
- {
- // Test get non existing lset
- mitk::LabelSet::ConstPointer lset = m_LabelSetImage->GetLabelSet(10000);
- CPPUNIT_ASSERT_MESSAGE("Non existing labelset is not nullptr", lset.IsNull());
-
- lset = m_LabelSetImage->GetLabelSet(0);
- CPPUNIT_ASSERT_MESSAGE("Existing labelset is nullptr", lset.IsNotNull());
- }
-
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->AddLabel(label1,0);
m_LabelSetImage->AddLayer();
- m_LabelSetImage->GetLabelSet(1)->AddLabel(label2);
+ m_LabelSetImage->AddLabel(label2,1);
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));
+ mitk::Equal(*m_LabelSetImage->GetLabel(200), *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 nullptr", label3 == nullptr);
-
- // 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 nullptr", label3 == nullptr);
}
void TestSetUnlabeledLabelLock()
{
auto locked = m_LabelSetImage->GetUnlabeledLabelLock();
CPPUNIT_ASSERT_MESSAGE("Wrong UnlabeledLabelLock default state",
locked == false);
m_LabelSetImage->SetUnlabeledLabelLock(true);
locked = m_LabelSetImage->GetUnlabeledLabelLock();
CPPUNIT_ASSERT_MESSAGE("Wrong UnlabeledLabelLock state",
locked == true);
}
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->AddLabel(label1,0);
m_LabelSetImage->AddLayer();
- m_LabelSetImage->GetLabelSet(1)->AddLabel(label2);
+ m_LabelSetImage->AddLabel(label2,1);
CPPUNIT_ASSERT_MESSAGE(
"Wrong total number of labels",
m_LabelSetImage->GetTotalNumberOfLabels() == 2);
}
void TestExistsLabel()
{
mitk::Label::Pointer label = mitk::Label::New();
label->SetName("Label2");
mitk::Label::PixelType value = 200;
label->SetValue(value);
m_LabelSetImage->AddLayer();
- m_LabelSetImage->GetLabelSet(1)->AddLabel(label);
+ m_LabelSetImage->AddLabel(label,1);
m_LabelSetImage->SetActiveLayer(0);
CPPUNIT_ASSERT_MESSAGE("Existing label was not found", m_LabelSetImage->ExistLabel(value) == true);
CPPUNIT_ASSERT_MESSAGE("Non existing label was found", m_LabelSetImage->ExistLabel(10000) == false);
}
void TestExistsLabelSet()
{
- // 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);
-
- m_LabelSetImage->AddLayer(newlayer);
+ m_LabelSetImage->AddLayer({label1, label2});
CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(0) == true);
CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(1) == true);
CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(20) == false);
}
void TestSetActiveLayer()
{
// Cache active layer
- mitk::LabelSet::ConstPointer activeLayer = m_LabelSetImage->GetActiveLabelSet();
+ auto refActiveLayer = m_LabelSetImage->GetConstLabelsByValue(m_LabelSetImage->GetLabelValuesByGroup(m_LabelSetImage->GetActiveLayer()));
// 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);
-
+ mitk::LabelSetImage::ConstLabelVectorType newlayer = { label1, label2 };
unsigned int layerID = m_LabelSetImage->AddLayer(newlayer);
// Set initial layer as active layer
m_LabelSetImage->SetActiveLayer(0);
+ auto activeLayer = m_LabelSetImage->GetConstLabelsByValue(m_LabelSetImage->GetLabelValuesByGroup(m_LabelSetImage->GetActiveLayer()));
CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned",
- mitk::Equal(*activeLayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true));
+ mitk::Equal(refActiveLayer, activeLayer, 0.00001, true));
// Set previously added layer as active layer
m_LabelSetImage->SetActiveLayer(layerID);
+ activeLayer = m_LabelSetImage->GetConstLabelsByValue(m_LabelSetImage->GetLabelValuesByGroup(m_LabelSetImage->GetActiveLayer()));
CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned",
- mitk::Equal(*newlayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true));
+ mitk::Equal(newlayer, activeLayer, 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));
+ mitk::Equal(newlayer, activeLayer, 0.00001, true));
}
void TestRemoveLayer()
{
// Cache active layer
- mitk::LabelSet::ConstPointer activeLayer = m_LabelSetImage->GetActiveLabelSet();
+ auto refActiveLayer = m_LabelSetImage->GetConstLabelsByValue(m_LabelSetImage->GetLabelValuesByGroup(m_LabelSetImage->GetActiveLayer()));
// 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);
+ mitk::LabelSetImage::ConstLabelVectorType newlayer = { label1, label2 };
+ unsigned int layerID = m_LabelSetImage->AddLayer(newlayer);
+ auto activeLayer = m_LabelSetImage->GetConstLabelsByValue(m_LabelSetImage->GetLabelValuesByGroup(m_LabelSetImage->GetActiveLayer()));
CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned",
- mitk::Equal(*newlayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true));
+ mitk::Equal(newlayer, activeLayer, 0.00001, true));
- m_LabelSetImage->RemoveLayer();
+ m_LabelSetImage->RemoveGroup(1);
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();
+ m_LabelSetImage->RemoveGroup(1);
+ activeLayer = m_LabelSetImage->GetConstLabelsByValue(m_LabelSetImage->GetLabelValuesByGroup(m_LabelSetImage->GetActiveLayer()));
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));
+ mitk::Equal(refActiveLayer, activeLayer, 0.00001, true));
- m_LabelSetImage->RemoveLayer();
+ m_LabelSetImage->RemoveGroup(0);
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() == nullptr);
+ CPPUNIT_ASSERT_THROW_MESSAGE("GetActiveLayers does not fail although all layer have been removed",
+ m_LabelSetImage->GetActiveLayer(), mitk::Exception);
}
void TestRemoveLabels()
{
mitk::Image::Pointer image =
mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd"));
m_LabelSetImage = nullptr;
m_LabelSetImage = mitk::LabelSetImage::New();
m_LabelSetImage->InitializeByLabeledImage(image);
CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 6", m_LabelSetImage->GetNumberOfLabels() == 5);
// 2ndMin because of unlabeled pixels = 0
CPPUNIT_ASSERT_MESSAGE("Wrong MIN value", m_LabelSetImage->GetStatistics()->GetScalarValue2ndMin() == 1);
CPPUNIT_ASSERT_MESSAGE("Wrong MAX value", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 7);
CPPUNIT_ASSERT_MESSAGE("Label with ID 3 does not exist after initialization",
m_LabelSetImage->ExistLabel(3) == true);
m_LabelSetImage->RemoveLabel(1);
std::vector<mitk::Label::PixelType> labelsToBeRemoved;
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() == 2);
// Values within the image are 0, 1, 3, 5, 6, 7 - New Min / Max value should be 5 / 6
// 2ndMin because of unlabeled pixels = 0
CPPUNIT_ASSERT_MESSAGE("Labels with value 1 and 3 were not removed from the image",
m_LabelSetImage->GetStatistics()->GetScalarValue2ndMin() == 5);
CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not removed from the image",
m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 6);
}
void TestEraseLabels()
{
mitk::Image::Pointer image =
mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd"));
m_LabelSetImage = nullptr;
m_LabelSetImage = mitk::LabelSetImage::New();
m_LabelSetImage->InitializeByLabeledImage(image);
CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 6", m_LabelSetImage->GetNumberOfLabels() == 5);
// 2ndMin because of unlabeled pixels = 0
CPPUNIT_ASSERT_MESSAGE("Wrong MIN value", m_LabelSetImage->GetStatistics()->GetScalarValue2ndMin() == 1);
CPPUNIT_ASSERT_MESSAGE("Wrong MAX value", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 7);
CPPUNIT_ASSERT_MESSAGE("Label with ID 3 does not exist after initialization",
m_LabelSetImage->ExistLabel(3) == true);
m_LabelSetImage->EraseLabel(1);
std::vector<mitk::Label::PixelType> labelsToBeErased;
labelsToBeErased.push_back(3);
labelsToBeErased.push_back(7);
m_LabelSetImage->EraseLabels(labelsToBeErased);
CPPUNIT_ASSERT_MESSAGE("Wrong number of labels since none have been removed",
m_LabelSetImage->GetNumberOfLabels() == 5);
// Values within the image are 0, 1, 3, 5, 6, 7 - New Min / Max value should be 5 / 6
// 2ndMin because of unlabeled pixels = 0
CPPUNIT_ASSERT_MESSAGE("Labels with value 1 and 3 were not erased from the image",
m_LabelSetImage->GetStatistics()->GetScalarValue2ndMin() == 5);
CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not erased from the image",
m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 6);
}
void TestMergeLabels()
{
mitk::Image::Pointer image =
mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd"));
m_LabelSetImage = nullptr;
m_LabelSetImage = mitk::LabelSetImage::New();
m_LabelSetImage->InitializeByLabeledImage(image);
CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 6", m_LabelSetImage->GetNumberOfLabels() == 5);
// 2ndMin because of unlabeled pixels = 0
CPPUNIT_ASSERT_MESSAGE("Wrong MIN value", m_LabelSetImage->GetStatistics()->GetScalarValue2ndMin() == 1);
CPPUNIT_ASSERT_MESSAGE("Wrong MAX value", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 7);
CPPUNIT_ASSERT_MESSAGE("Label with ID 6 does not exist after initialization",
m_LabelSetImage->ExistLabel(6) == true);
// Merge label 7 with label 6. Result should be that label 7 is not present anymore.
m_LabelSetImage->MergeLabel(6, 7);
CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not removed from the image", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 6);
// Count all pixels with value 6 = 507
// Count all pixels with value 7 = 823
// Check if merged label has 507 + 823 = 1330 pixels
CPPUNIT_ASSERT_MESSAGE("Labels were not correctly merged", m_LabelSetImage->GetStatistics()->GetCountOfMaxValuedVoxels() == 1330);
CPPUNIT_ASSERT_MESSAGE("Label with ID 3 does not exist after initialization",
m_LabelSetImage->ExistLabel(3) == true);
CPPUNIT_ASSERT_MESSAGE("Label with ID 5 does not exist after initialization",
m_LabelSetImage->ExistLabel(5) == true);
// Merge labels 5 and 6 with 3. Result should be that labels 5 and 6 are not present anymore.
std::vector<mitk::Label::PixelType> vectorOfSourcePixelValues{ 5, 6 };
m_LabelSetImage->MergeLabels(3, vectorOfSourcePixelValues);
// Values within the image are 0, 1, 3, 5, 6, 7 - New Max value should be 3
CPPUNIT_ASSERT_MESSAGE("Labels with value 5 and 6 were not removed from the image", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 3);
// Count all pixels with value 3 = 1893
// Count all pixels with value 5 = 2143
// Count all pixels with value 6 = 1330
// Check if merged label has 1893 + 2143 + 1330 = 5366 pixels
CPPUNIT_ASSERT_MESSAGE("Labels were not correctly merged", m_LabelSetImage->GetStatistics()->GetCountOfMaxValuedVoxels() == 5366);
}
void TestCreateLabelMask()
{
mitk::Image::Pointer image =
mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd"));
m_LabelSetImage = nullptr;
m_LabelSetImage = mitk::LabelSetImage::New();
m_LabelSetImage->InitializeByLabeledImage(image);
auto labelMask = m_LabelSetImage->CreateLabelMask(6);
mitk::AutoCropImageFilter::Pointer cropFilter = mitk::AutoCropImageFilter::New();
cropFilter->SetInput(labelMask);
cropFilter->SetBackgroundValue(0);
cropFilter->SetMarginFactor(1.15);
cropFilter->Update();
auto maskImage = cropFilter->GetOutput();
// Count all pixels with value 6 = 507
CPPUNIT_ASSERT_MESSAGE("Label mask not correctly created", maskImage->GetStatistics()->GetCountOfMaxValuedVoxels() == 507);
}
};
MITK_TEST_SUITE_REGISTRATION(mitkLabelSetImage)
diff --git a/Modules/Multilabel/Testing/mitkLegacyLabelSetImageIOTest.cpp b/Modules/Multilabel/Testing/mitkLegacyLabelSetImageIOTest.cpp
index 80a7eb7fba..5dc15479d8 100644
--- a/Modules/Multilabel/Testing/mitkLegacyLabelSetImageIOTest.cpp
+++ b/Modules/Multilabel/Testing/mitkLegacyLabelSetImageIOTest.cpp
@@ -1,142 +1,145 @@
/*============================================================================
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 <mitkIOUtil.h>
#include <mitkLabelSetImage.h>
#include <mitkTestFixture.h>
#include <mitkTestingMacros.h>
#include <mitkArbitraryTimeGeometry.h>
#include <mitkCoreServices.h>
#include <mitkPropertyPersistenceInfo.h>
#include <mitkIPropertyPersistence.h>
std::string pathToImage;
class mitkLegacyLabelSetImageIOTestSuite : public mitk::TestFixture
{
CPPUNIT_TEST_SUITE(mitkLegacyLabelSetImageIOTestSuite);
MITK_TEST(TestRead3DLabelSetImage_Default);
MITK_TEST(TestRead3DLabelSetImage_Adapt);
MITK_TEST(TestRead3DLabelSetImage_Split);
MITK_TEST(TestRead3DplusTLabelSetImage);
CPPUNIT_TEST_SUITE_END();
private:
- mitk::LabelSet::Pointer m_labelSet1;
- mitk::LabelSet::Pointer m_labelSet2;
- mitk::LabelSet::Pointer m_labelSet2_adapted;
+ mitk::LabelSetImage::ConstLabelVectorType m_labelSet1;
+ mitk::LabelSetImage::ConstLabelVectorType m_labelSet2;
+ mitk::LabelSetImage::ConstLabelVectorType m_labelSet2_adapted;
public:
mitk::Label::Pointer GenerateLabel(mitk::Label::PixelType value, const std::string& name, float r, float g, float b) const
{
auto label = mitk::Label::New(value, name);
mitk::Color color;
color.SetRed(r);
color.SetGreen(g);
color.SetBlue(b);
label->SetColor(color);
return label;
}
void setUp() override
{
- m_labelSet1 = mitk::LabelSet::New();
auto label = GenerateLabel(1, "Label 1", 0.745098054f, 0.f, 0.196078435f);
- m_labelSet1->AddLabel(label,false);
- label = GenerateLabel(2, "Label 2", 0.952941179, 0.764705896, 0);
- m_labelSet1->AddLabel(label, false);
+ auto label2 = GenerateLabel(2, "Label 2", 0.952941179, 0.764705896, 0);
+ m_labelSet1 = { label, label2 };
- m_labelSet2 = mitk::LabelSet::New();
label = GenerateLabel(1, "Label 3", 0.552941203, 0.713725507, 0);
- m_labelSet2->AddLabel(label, false);
- label = GenerateLabel(2, "Label 4", 0.631372571, 0.792156875, 0.945098042);
- m_labelSet2->AddLabel(label, false);
- label = GenerateLabel(3, "Label 5", 0.639215708, 0.250980407, 0.725490212);
- m_labelSet2->AddLabel(label, false);
+ label2 = GenerateLabel(2, "Label 4", 0.631372571, 0.792156875, 0.945098042);
+ auto label3 = GenerateLabel(3, "Label 5", 0.639215708, 0.250980407, 0.725490212);
+ m_labelSet2 = { label, label2, label3 };
- m_labelSet2_adapted = mitk::LabelSet::New();
label = GenerateLabel(3, "Label 3", 0.552941203, 0.713725507, 0);
- m_labelSet2_adapted->AddLabel(label, false);
- label = GenerateLabel(4, "Label 4", 0.631372571, 0.792156875, 0.945098042);
- m_labelSet2_adapted->AddLabel(label, false);
- label = GenerateLabel(5, "Label 5", 0.639215708, 0.250980407, 0.725490212);
- m_labelSet2_adapted->AddLabel(label, false);
- m_labelSet2_adapted->SetLayer(1);
+ label2 = GenerateLabel(4, "Label 4", 0.631372571, 0.792156875, 0.945098042);
+ label3 = GenerateLabel(5, "Label 5", 0.639215708, 0.250980407, 0.725490212);
+ m_labelSet2_adapted = { label, label2, label3 };
}
void tearDown() override
{
- m_labelSet1 = nullptr;
- m_labelSet2 = nullptr;
- m_labelSet2_adapted = nullptr;
+ m_labelSet1.clear();
+ m_labelSet2.clear();
+ m_labelSet2_adapted.clear();
}
void TestRead3DLabelSetImage_Default()
{
auto testImages = mitk::IOUtil::Load(GetTestDataFilePath("Multilabel/LegacyLabelSetTestImage3D.nrrd"));
CPPUNIT_ASSERT_MESSAGE("Error reading label set image", testImages.size()==1);
auto lsimage1 = dynamic_cast<mitk::LabelSetImage*>(testImages[0].GetPointer());
CPPUNIT_ASSERT_MESSAGE("Number of layers is not correct", lsimage1->GetNumberOfLayers() == 2);
- CPPUNIT_ASSERT_MESSAGE("Error layer 0 is not equal", mitk::Equal(*m_labelSet1, *(lsimage1->GetLabelSet(0)), mitk::eps, true));
- CPPUNIT_ASSERT_MESSAGE("Error layer 1 is not equal", mitk::Equal(*m_labelSet2_adapted, *(lsimage1->GetLabelSet(1)), mitk::eps, true));
+
+ auto loadedLabels = lsimage1->GetConstLabelsByValue(lsimage1->GetLabelValuesByGroup(0));
+ CPPUNIT_ASSERT_MESSAGE("Error layer 0 is not equal", mitk::Equal(m_labelSet1, loadedLabels, mitk::eps, true));
+
+ loadedLabels = lsimage1->GetConstLabelsByValue(lsimage1->GetLabelValuesByGroup(1));
+ CPPUNIT_ASSERT_MESSAGE("Error layer 1 is not equal", mitk::Equal(m_labelSet2_adapted, loadedLabels, mitk::eps, true));
CPPUNIT_ASSERT_MESSAGE("Error, read image has different UID", "c236532b-f95a-4f22-a4c6-7abe4e41ad10"== lsimage1->GetUID());
}
void TestRead3DLabelSetImage_Adapt()
{
mitk::IFileReader::Options options = { {"Multi layer handling", us::Any(std::string("Adapt label values"))} };
auto testImages = mitk::IOUtil::Load(GetTestDataFilePath("Multilabel/LegacyLabelSetTestImage3D.nrrd"), options);
CPPUNIT_ASSERT_MESSAGE("Error reading label set image", testImages.size() == 1);
auto lsimage1 = dynamic_cast<mitk::LabelSetImage*>(testImages[0].GetPointer());
CPPUNIT_ASSERT_MESSAGE("Number of layers is not correct", lsimage1->GetNumberOfLayers() == 2);
- CPPUNIT_ASSERT_MESSAGE("Error layer 0 is not equal", mitk::Equal(*m_labelSet1, *(lsimage1->GetLabelSet(0)), mitk::eps, true));
- CPPUNIT_ASSERT_MESSAGE("Error layer 1 is not equal", mitk::Equal(*m_labelSet2_adapted, *(lsimage1->GetLabelSet(1)), mitk::eps, true));
+
+ auto loadedLabels = lsimage1->GetConstLabelsByValue(lsimage1->GetLabelValuesByGroup(0));
+ CPPUNIT_ASSERT_MESSAGE("Error layer 0 is not equal", mitk::Equal(m_labelSet1, loadedLabels, mitk::eps, true));
+
+ loadedLabels = lsimage1->GetConstLabelsByValue(lsimage1->GetLabelValuesByGroup(1));
+ CPPUNIT_ASSERT_MESSAGE("Error layer 1 is not equal", mitk::Equal(m_labelSet2_adapted, loadedLabels, mitk::eps, true));
CPPUNIT_ASSERT_MESSAGE("Error, read image has different UID", "c236532b-f95a-4f22-a4c6-7abe4e41ad10" == lsimage1->GetUID());
}
void TestRead3DLabelSetImage_Split()
{
mitk::IFileReader::Options options = { {"Multi layer handling", us::Any(std::string("Split layers"))} };
auto testImages = mitk::IOUtil::Load(GetTestDataFilePath("Multilabel/LegacyLabelSetTestImage3D.nrrd"), options);
CPPUNIT_ASSERT_MESSAGE("Error reading label set image", testImages.size() == 2);
auto lsimage1 = dynamic_cast<mitk::LabelSetImage*>(testImages[0].GetPointer());
auto lsimage2 = dynamic_cast<mitk::LabelSetImage*>(testImages[1].GetPointer());
CPPUNIT_ASSERT_MESSAGE("Number of layers in image 1 isnot correct", lsimage1->GetNumberOfLayers() == 1);
CPPUNIT_ASSERT_MESSAGE("Number of layers in image 2 is not correct", lsimage2->GetNumberOfLayers() == 1);
- CPPUNIT_ASSERT_MESSAGE("Error layer 0 is not equal", mitk::Equal(*m_labelSet1, *(lsimage1->GetLabelSet(0)), mitk::eps, true));
- CPPUNIT_ASSERT_MESSAGE("Error layer 1 is not equal", mitk::Equal(*m_labelSet2, *(lsimage2->GetLabelSet(0)), mitk::eps, true));
+
+ auto loadedLabels = lsimage1->GetConstLabelsByValue(lsimage1->GetLabelValuesByGroup(0));
+ CPPUNIT_ASSERT_MESSAGE("Error layer 0 is not equal", mitk::Equal(m_labelSet1, loadedLabels, mitk::eps, true));
+
+ loadedLabels = lsimage2->GetConstLabelsByValue(lsimage1->GetLabelValuesByGroup(0));
+ CPPUNIT_ASSERT_MESSAGE("Error layer 1 is not equal", mitk::Equal(m_labelSet2, loadedLabels, mitk::eps, true));
CPPUNIT_ASSERT_MESSAGE("Error, read image has same UID", "c236532b-f95a-4f22-a4c6-7abe4e41ad10" != lsimage1->GetUID());
}
void TestRead3DplusTLabelSetImage()
{
}
};
MITK_TEST_SUITE_REGISTRATION(mitkLegacyLabelSetImageIO)