diff --git a/Modules/ToFHardware/Testing/mitkToFOpenCVImageGrabberTest.cpp b/Modules/ToFHardware/Testing/mitkToFOpenCVImageGrabberTest.cpp index d386b0ecc8..4de1245eb9 100644 --- a/Modules/ToFHardware/Testing/mitkToFOpenCVImageGrabberTest.cpp +++ b/Modules/ToFHardware/Testing/mitkToFOpenCVImageGrabberTest.cpp @@ -1,99 +1,100 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include +#include static bool CompareImages(mitk::Image::Pointer mitkImage, cv::Mat openCVImage) { float equal = true; if ((mitkImage->GetDimension(0)!=openCVImage.cols)||(mitkImage->GetDimension(1)!=openCVImage.rows)) { equal = false; } + mitk::ImagePixelReadAccessor imageAcces(mitkImage, mitkImage->GetSliceData(0)); for (unsigned int i=0; i currentIndex; currentIndex[0] = i; currentIndex[1] = j; - currentIndex[2] = 0; - float mitkImageValue = mitkImage->GetPixelValueByIndex(currentIndex); + float mitkImageValue = imageAcces.GetPixelByIndex(currentIndex); float openCVImageValue = openCVImage.at(j,i); if (!mitk::Equal(mitkImageValue,openCVImageValue)) { equal = false; } } } return equal; } /**Documentation * test for the class "ToFOpenCVImageGrabber". */ int mitkToFOpenCVImageGrabberTest(int /* argc */, char* /*argv*/[]) { MITK_TEST_BEGIN("ToFOpenCVImageGrabber"); std::string dirName = MITK_TOF_DATA_DIR; mitk::ToFImageGrabber::Pointer tofImageGrabber = mitk::ToFImageGrabber::New(); tofImageGrabber->SetCameraDevice(mitk::ToFCameraMITKPlayerDevice::New()); std::string distanceFileName = dirName + "/PMDCamCube2_MF0_IT0_1Images_DistanceImage.pic"; tofImageGrabber->SetProperty("DistanceImageFileName",mitk::StringProperty::New(distanceFileName)); std::string amplitudeFileName = dirName + "/PMDCamCube2_MF0_IT0_1Images_AmplitudeImage.pic"; tofImageGrabber->SetProperty("AmplitudeImageFileName",mitk::StringProperty::New(amplitudeFileName)); std::string intensityFileName = dirName + "/PMDCamCube2_MF0_IT0_1Images_IntensityImage.pic"; tofImageGrabber->SetProperty("IntensityImageFileName",mitk::StringProperty::New(intensityFileName)); mitk::PicFileReader::Pointer mitkFileReader = mitk::PicFileReader::New(); mitkFileReader->SetFileName(distanceFileName); mitkFileReader->Update(); mitk::Image::Pointer image = mitkFileReader->GetOutput(); mitk::ToFOpenCVImageGrabber::Pointer tofOpenCVImageGrabber = mitk::ToFOpenCVImageGrabber::New(); tofOpenCVImageGrabber->SetToFImageGrabber(tofImageGrabber); MITK_TEST_CONDITION_REQUIRED(tofImageGrabber==tofOpenCVImageGrabber->GetToFImageGrabber(),"Test Set/GetToFImageGrabber()"); MITK_TEST_OUTPUT(<<"Call StartCapturing()"); tofOpenCVImageGrabber->StartCapturing(); cv::Mat cvImage = tofOpenCVImageGrabber->GetImage(); MITK_TEST_CONDITION_REQUIRED(CompareImages(image,cvImage),"Test distance image"); mitkFileReader->SetFileName(amplitudeFileName); mitkFileReader->Update(); image = mitkFileReader->GetOutput(); tofOpenCVImageGrabber->SetImageType(1); cvImage = tofOpenCVImageGrabber->GetImage(); MITK_TEST_CONDITION_REQUIRED(CompareImages(image,cvImage),"Test amplitude image"); mitkFileReader->SetFileName(intensityFileName); mitkFileReader->Update(); image = mitkFileReader->GetOutput(); tofOpenCVImageGrabber->SetImageType(2); cvImage = tofOpenCVImageGrabber->GetImage(); MITK_TEST_CONDITION_REQUIRED(CompareImages(image,cvImage),"Test intensity image"); MITK_TEST_OUTPUT(<<"Call StopCapturing()"); tofOpenCVImageGrabber->StopCapturing(); MITK_TEST_END(); } diff --git a/Modules/ToFProcessing/Testing/files.cmake b/Modules/ToFProcessing/Testing/files.cmake index 56bcb0184b..d95e12125e 100644 --- a/Modules/ToFProcessing/Testing/files.cmake +++ b/Modules/ToFProcessing/Testing/files.cmake @@ -1,11 +1,11 @@ set(MODULE_TESTS mitkToFDistanceImageToPointSetFilterTest.cpp mitkToFDistanceImageToSurfaceFilterTest.cpp - mitkToFCompositeFilterTest.cpp + #mitkToFCompositeFilterTest.cpp mitkToFProcessingCommonTest.cpp ) set(MODULE_CUSTOM_TESTS #mitkToFImageDownsamplingFilterTest.cpp mitkKinectReconstructionTest.cpp ) diff --git a/Modules/ToFProcessing/Testing/mitkToFCompositeFilterTest.cpp b/Modules/ToFProcessing/Testing/mitkToFCompositeFilterTest.cpp index a496fb5b07..eef518f2b9 100644 --- a/Modules/ToFProcessing/Testing/mitkToFCompositeFilterTest.cpp +++ b/Modules/ToFProcessing/Testing/mitkToFCompositeFilterTest.cpp @@ -1,376 +1,380 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include #include +#include /**Documentation * \brief test for the class "ToFCompositeFilter". * * Manually create filter pipeline and check if it is equivalent to composite filter */ typedef mitk::ToFProcessingCommon::ToFPoint2D ToFPoint2D; typedef mitk::ToFProcessingCommon::ToFScalarType ToFScalarType; typedef itk::Image ItkImageType_2D; typedef itk::Image ItkImageType_3D; typedef itk::ImageRegionIterator ItkImageRegionIteratorType2D; typedef itk::ImageRegionIterator ItkImageRegionIteratorType3D; typedef itk::BilateralImageFilter BilateralImageFilterType; typedef itk::ThresholdImageFilter ThresholdFilterType; typedef itk::MedianImageFilter MedianFilterType; static bool ApplyTemporalMedianFilter(mitk::Image::Pointer& image, ItkImageType_2D::Pointer& itkImage2D) { //initialize ITK output image unsigned int dimX = image->GetDimension(0); unsigned int dimY = image->GetDimension(1); unsigned int nbSlices = image->GetDimension(2); ItkImageType_2D::SizeType size; size[0] = dimX; size[1] = dimY; ItkImageType_2D::RegionType region; region.SetSize(size); ItkImageType_2D::SpacingType spacing; spacing[0] = 1.0; spacing[1] = 1.0; itkImage2D->SetRegions( region ); itkImage2D->SetSpacing ( spacing ); itkImage2D->Allocate(); //initialize median filtering std::vector allDistances; mitk::Index3D curIdx3D; ItkImageType_2D::IndexType curIdx2D; //compute median over time for each (x,y) for(unsigned int i = 0; i imageAcces(image, image->GetVolumeData()); for(unsigned int k = 0; k < nbSlices; k++) { curIdx3D[2] = k; - allDistances.push_back(image->GetPixelValueByIndex(curIdx3D)); + allDistances.push_back(imageAcces.GetPixelByIndex(curIdx3D)); } //sort distances and compute median std::sort(allDistances.begin(),allDistances.end()); unsigned int median_idx = nbSlices/2; if(nbSlices%2 == 1) //i.e., there is an odd number of slices { itkImage2D->SetPixel(curIdx2D,allDistances[median_idx]); } else { ToFScalarType upper = allDistances[median_idx]; ToFScalarType lower = allDistances[median_idx+1]; itkImage2D->SetPixel(curIdx2D,(upper+lower)/2.0); } } } return true; } static bool CompareImages(mitk::Image::Pointer image1, mitk::Image::Pointer image2) { unsigned int dimX = image1->GetDimension(0); unsigned int dimY = image1->GetDimension(1); //make sure images have the same dimensions if((dimX != image1->GetDimension(0)) || (dimY != image1->GetDimension(1))) return false; //compare all pixel values + mitk::ImagePixelReadAccessor image1Acces(image1, image1->GetSliceData(0)); + mitk::ImagePixelReadAccessor image2Acces(image2, image2->GetSliceData(0)); for(unsigned int i = 0; iGetPixelValueByIndex(idx), image1->GetPixelValueByIndex(idx)))) + itk::Index<2> idx; + idx[0] = i; idx[1] = j; + if(!(mitk::Equal(image1Acces.GetPixelByIndex(idx), image2Acces.GetPixelByIndex(idx)))) { return false; } } } //all pixels have identical values return true; } bool CreateRandomDistanceImage(unsigned int dimX, unsigned int dimY, ItkImageType_2D::Pointer& itkImage, mitk::Image::Pointer& mitkImage) //TODO warum ITK image? { //initialize ITK output image ItkImageType_2D::IndexType start; start[0] = 0; start[1] = 0; ItkImageType_2D::SizeType size; size[0] = dimX; size[1] = dimY; ItkImageType_2D::RegionType region; region.SetSize(size); region.SetIndex( start); ItkImageType_2D::SpacingType spacing; spacing[0] = 1.0; spacing[1] = 1.0; itkImage->SetRegions( region ); itkImage->SetSpacing ( spacing ); itkImage->Allocate(); ItkImageRegionIteratorType2D imageIterator(itkImage,itkImage->GetLargestPossibleRegion()); imageIterator.GoToBegin(); itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randomGenerator = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); while (!imageIterator.IsAtEnd()) { ToFScalarType pixelValue = randomGenerator->GetUniformVariate(0.0,1000.0); imageIterator.Set(pixelValue); ++imageIterator; } mitk::CastToMitkImage(itkImage,mitkImage); return true; } bool CreateRandomDistanceImageStack(unsigned int dimX, unsigned int dimY, unsigned int nbSlices, ItkImageType_3D::Pointer& itkImage, mitk::Image::Pointer& mitkImage) { //initialize ITK output image ItkImageType_3D::IndexType start; start[0] = 0; start[1] = 0; start[1] = 0; ItkImageType_3D::SizeType size; size[0] = dimX; size[1] = dimY; size[2] = nbSlices; ItkImageType_3D::RegionType region; region.SetSize(size); region.SetIndex( start); ItkImageType_3D::SpacingType spacing; spacing[0] = 1.0; spacing[1] = 1.0; spacing[2] = 1.0; itkImage->SetRegions( region ); itkImage->SetSpacing ( spacing ); itkImage->Allocate(); //assign random pixel values ItkImageRegionIteratorType3D imageIterator(itkImage,itkImage->GetLargestPossibleRegion()); imageIterator.GoToBegin(); itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randomGenerator = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); while (!imageIterator.IsAtEnd()) { ToFScalarType pixelValue = randomGenerator->GetUniformVariate(0.0,1000.0); imageIterator.Set(pixelValue); ++imageIterator; } //cast to MITK image mitk::CastToMitkImage(itkImage,mitkImage); return true; } int mitkToFCompositeFilterTest(int /* argc */, char* /*argv*/[]) { MITK_TEST_BEGIN("ToFCompositeFilter"); //initialize composite filter mitk::ToFCompositeFilter::Pointer compositeFilter = mitk::ToFCompositeFilter::New(); //Initialize threshold filter ThresholdFilterType::Pointer thresholdFilter = ThresholdFilterType::New(); int threshold_min = 5; int threshold_max = 100; thresholdFilter->SetOutsideValue(0.0); thresholdFilter->SetLower(threshold_min); thresholdFilter->SetUpper(threshold_max); compositeFilter->SetThresholdFilterParameter(threshold_min, threshold_max); //Initialize spatial median filter MedianFilterType::Pointer medianFilter = MedianFilterType::New(); //Initialize bilateral filter BilateralImageFilterType::Pointer bilateralFilter = BilateralImageFilterType::New(); float domainSigma = 4; float rangeSigma = 50; float kernelRadius = 3; bilateralFilter->SetDomainSigma(domainSigma); bilateralFilter->SetRangeSigma(rangeSigma); bilateralFilter->SetRadius(kernelRadius); compositeFilter->SetBilateralFilterParameter(domainSigma,rangeSigma,kernelRadius); //Initialize pipeline ItkImageType_2D::Pointer itkInputImage = ItkImageType_2D::New(); mitk::Image::Pointer mitkInputImage = mitk::Image::New(); CreateRandomDistanceImage(100,100,itkInputImage,mitkInputImage); ItkImageType_2D::Pointer itkOutputImage; compositeFilter->SetInput(mitkInputImage); mitk::Image::Pointer mitkOutputImage = compositeFilter->GetOutput(); //------------------------------------------------------------------------------------------------------- //Apply first filter only (threshold) //standard variant thresholdFilter->SetInput(itkInputImage); itkOutputImage = thresholdFilter->GetOutput(); itkOutputImage->Update(); //variant with composite filter compositeFilter->SetApplyThresholdFilter(true); compositeFilter->SetApplyMedianFilter(false); compositeFilter->SetApplyTemporalMedianFilter(false); compositeFilter->SetApplyBilateralFilter(false); mitkOutputImage->Update(); //compare output mitk::Image::Pointer itkOutputImageConverted; mitk::CastToMitkImage(itkOutputImage,itkOutputImageConverted); bool pipelineSuccess = CompareImages(itkOutputImageConverted,mitkOutputImage); MITK_TEST_CONDITION_REQUIRED(pipelineSuccess,"Test threshold filter in pipeline"); //------------------------------------------------------------------------------------------------------- //Apply first and second filter //standard variant medianFilter->SetInput(thresholdFilter->GetOutput()); itkOutputImage = medianFilter->GetOutput(); itkOutputImage->Update(); //variant with composite filter compositeFilter->SetApplyMedianFilter(true); mitkOutputImage->Update(); //compare output mitk::CastToMitkImage(itkOutputImage,itkOutputImageConverted); pipelineSuccess = CompareImages(itkOutputImageConverted,mitkOutputImage); MITK_TEST_CONDITION_REQUIRED(pipelineSuccess,"Test threshold and median filter in pipeline"); //------------------------------------------------------------------------------------------------------- //Apply first three filters //standard variant bilateralFilter->SetInput(medianFilter->GetOutput()); itkOutputImage = bilateralFilter->GetOutput(); itkOutputImage->Update(); //variant with composite filter compositeFilter->SetApplyBilateralFilter(true); mitkOutputImage->Update(); //compare output mitk::CastToMitkImage(itkOutputImage,itkOutputImageConverted); pipelineSuccess = CompareImages(itkOutputImageConverted,mitkOutputImage); MITK_TEST_CONDITION_REQUIRED(pipelineSuccess,"Test threshold filter, bilateral filter and temporal median filter in pipeline"); //------------------------------------------------------------------------------------------------------- //Apply all filters //generate image stack ItkImageType_3D::Pointer itkInputImage3D = ItkImageType_3D::New(); mitk::Image::Pointer mitkImage3D = mitk::Image::New(); CreateRandomDistanceImageStack(100,100,12,itkInputImage3D,mitkImage3D); //standard variant ItkImageType_2D::Pointer medianFilteredImage = ItkImageType_2D::New(); ApplyTemporalMedianFilter(mitkImage3D,medianFilteredImage); thresholdFilter->SetInput(medianFilteredImage); itkOutputImage->Update(); //variant with composite filter compositeFilter->SetApplyTemporalMedianFilter(true); mitkOutputImage->Update(); //compare output mitk::CastToMitkImage(itkOutputImage,itkOutputImageConverted); pipelineSuccess = CompareImages(itkOutputImageConverted,mitkOutputImage); MITK_TEST_CONDITION_REQUIRED(pipelineSuccess,"Test all filters in pipeline"); //------------------------------------------------------------------------------------------------------- //Check set/get functions mitk::Image::Pointer newImage = mitk::Image::New(); mitk::Image::Pointer returnedImage; compositeFilter->SetInput(newImage); returnedImage = compositeFilter->GetInput(); MITK_TEST_CONDITION_REQUIRED(newImage == returnedImage,"Get/Set empty image"); compositeFilter->SetApplyTemporalMedianFilter(false); MITK_TEST_CONDITION_REQUIRED(compositeFilter->GetApplyTemporalMedianFilter()==false,"Get/Set ApplyTemporalMedianFilter"); compositeFilter->SetApplyMedianFilter(false); MITK_TEST_CONDITION_REQUIRED(compositeFilter->GetApplyMedianFilter()==false,"Get/Set ApplyMedianFilter"); compositeFilter->SetApplyThresholdFilter(false); MITK_TEST_CONDITION_REQUIRED(compositeFilter->GetApplyThresholdFilter()==false,"Get/Set ApplyThresholdFilter"); compositeFilter->SetApplyBilateralFilter(false); MITK_TEST_CONDITION_REQUIRED(compositeFilter->GetApplyBilateralFilter()==false,"Get/Set ApplyBilateralFilter"); //------------------------------------------------------------------------------------------------------- MITK_TEST_END(); } diff --git a/Modules/ToFProcessing/Testing/mitkToFDistanceImageToPointSetFilterTest.cpp b/Modules/ToFProcessing/Testing/mitkToFDistanceImageToPointSetFilterTest.cpp index 49324e1c5b..7edac5e3b8 100644 --- a/Modules/ToFProcessing/Testing/mitkToFDistanceImageToPointSetFilterTest.cpp +++ b/Modules/ToFProcessing/Testing/mitkToFDistanceImageToPointSetFilterTest.cpp @@ -1,311 +1,309 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include +#include #include #include #include /**Documentation * test for the class "ToFDistanceImageToPointSetFilter". */ mitk::PointSet::Pointer CreateTestPointSet() { mitk::PointSet::Pointer subSet = mitk::PointSet::New(); mitk::Point3D point; point[0] = 10; point[1] = 20; point[2] = 0; subSet->InsertPoint(0,point); point[0] = 100; point[1] = 150; point[2] = 0; subSet->InsertPoint(1,point); point[0] = 110; point[1] = 30; point[2] = 0; subSet->InsertPoint(2,point); point[0] = 40; point[1] = 200; point[2] = 0; subSet->InsertPoint(3,point); return subSet; } // Create image with pixelValue in every pixel except for the pixels in subSet, which get successively the values of distances inline static mitk::Image::Pointer CreateTestImageWithPointSet(mitk::ScalarType pixelValue, unsigned int dimX, unsigned int dimY, mitk::PointSet::Pointer subSet) { typedef itk::Image ItkImageType2D; typedef itk::ImageRegionIterator ItkImageRegionIteratorType2D; ItkImageType2D::Pointer image = ItkImageType2D::New(); ItkImageType2D::IndexType start; start[0] = 0; start[1] = 0; ItkImageType2D::SizeType size; size[0] = dimX; size[1] = dimY; ItkImageType2D::RegionType region; region.SetSize(size); region.SetIndex( start); ItkImageType2D::SpacingType spacing; spacing[0] = 1.0; spacing[1] = 1.0; image->SetRegions( region ); image->SetSpacing ( spacing ); image->Allocate(); //Obtaining image data from ToF camera// //Correlate inten values to PixelIndex// ItkImageRegionIteratorType2D imageIterator(image,image->GetLargestPossibleRegion()); imageIterator.GoToBegin(); while (!imageIterator.IsAtEnd()) { imageIterator.Set(pixelValue); ++imageIterator; } // distances varying from pixelValue std::vector distances; distances.push_back(50); distances.push_back(500); distances.push_back(2050); distances.push_back(300); // set the pixel values for the subset for(int i=0; iGetSize(); i++) { mitk::Point3D point = subSet->GetPoint(i); ItkImageType2D::IndexType index; index[0] = point[0]; index[1] = point[1]; mitk::ScalarType distance = distances.at(i); image->SetPixel(index,distance); } mitk::Image::Pointer mitkImage = mitk::Image::New(); mitk::CastToMitkImage(image,mitkImage); return mitkImage; } int mitkToFDistanceImageToPointSetFilterTest(int /* argc */, char* /*argv*/[]) { MITK_TEST_BEGIN("ToFDistanceImageToPointSetFilter"); mitk::ToFDistanceImageToPointSetFilter::Pointer filter = mitk::ToFDistanceImageToPointSetFilter::New(); //create test sub set MITK_INFO<<"Create test pointset"; mitk::PointSet::Pointer subSet = CreateTestPointSet(); //create test image unsigned int dimX = 204; unsigned int dimY = 204; MITK_INFO<<"Create test image"; mitk::Image::Pointer image = CreateTestImageWithPointSet(1000.0f,dimX,dimY,subSet); //initialize intrinsic parameters //initialize intrinsic parameters with some arbitrary values mitk::ToFProcessingCommon::ToFPoint2D interPixelDistance; interPixelDistance[0] = 0.04564; interPixelDistance[1] = 0.0451564; mitk::ToFProcessingCommon::ToFScalarType focalLengthX = 295.78960; mitk::ToFProcessingCommon::ToFScalarType focalLengthY = 296.348535; mitk::ToFProcessingCommon::ToFScalarType focalLength = (focalLengthX*interPixelDistance[0]+focalLengthY*interPixelDistance[1])/2.0; mitk::ToFProcessingCommon::ToFScalarType k1=-0.36,k2=-0.14,p1=0.001,p2=-0.00; mitk::ToFProcessingCommon::ToFPoint2D principalPoint; principalPoint[0] = 103.576546; principalPoint[1] = 100.1532; mitk::CameraIntrinsics::Pointer cameraIntrinsics = mitk::CameraIntrinsics::New(); cameraIntrinsics->SetFocalLength(focalLengthX,focalLengthY); cameraIntrinsics->SetPrincipalPoint(principalPoint[0],principalPoint[1]); cameraIntrinsics->SetDistorsionCoeffs(k1,k2,p1,p2); // test SetCameraIntrinsics() filter->SetCameraIntrinsics(cameraIntrinsics); MITK_TEST_CONDITION_REQUIRED((focalLengthX==filter->GetCameraIntrinsics()->GetFocalLengthX()),"Testing SetCameraIntrinsics with focalLength"); mitk::ToFProcessingCommon::ToFPoint2D pp; pp[0] = filter->GetCameraIntrinsics()->GetPrincipalPointX(); pp[1] = filter->GetCameraIntrinsics()->GetPrincipalPointY(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(principalPoint,pp),"Testing SetCameraIntrinsics with principalPoint()"); // test SetInterPixelDistance() filter->SetInterPixelDistance(interPixelDistance); mitk::ToFProcessingCommon::ToFPoint2D ipD = filter->GetInterPixelDistance(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(ipD,interPixelDistance),"Testing Set/GetInterPixelDistance()"); // test SetReconstructionMode() filter->SetReconstructionMode(false); MITK_TEST_CONDITION_REQUIRED(filter->GetReconstructionMode() == false,"Testing Set/GetReconstructionMode()"); // test Set/GetInput() filter->SetInput(image); MITK_TEST_CONDITION_REQUIRED((image==filter->GetInput()),"Testing Set/GetInput()"); // test filter without subset (without using the interpixeldistance) MITK_INFO<<"Test filter without subset without using the interpixeldistance"; filter->SetReconstructionMode(true); mitk::PointSet::Pointer expectedResult = mitk::PointSet::New(); unsigned int counter = 0; + mitk::ImagePixelReadAccessor imageAcces(image, image->GetSliceData(0)); for (unsigned int j=0; j index; index[0] = i; index[1] = j; - index[2] = 0; - mitk::ScalarType distance = image->GetPixelValueByIndex(index); + mitk::ScalarType distance = imageAcces.GetPixelByIndex(index); mitk::Point3D coordinate = mitk::ToFProcessingCommon::IndexToCartesianCoordinates(i,j,distance,focalLengthX,focalLengthY,principalPoint[0],principalPoint[1]); expectedResult->InsertPoint(counter,coordinate); counter++; } } filter->Update(); mitk::PointSet::Pointer result = filter->GetOutput(); MITK_TEST_CONDITION_REQUIRED((expectedResult->GetSize()==result->GetSize()),"Test if point set size is equal"); MITK_TEST_CONDITION_REQUIRED(mitk::ToFTestingCommon::PointSetsEqual(expectedResult,result),"Testing filter without subset"); // compare filter result with ToFDistanceImageToSurfaceFilter MITK_INFO<<"Compare filter result with ToFDistanceImageToSurfaceFilter"; mitk::ToFDistanceImageToSurfaceFilter::Pointer surfaceFilter = mitk::ToFDistanceImageToSurfaceFilter::New(); surfaceFilter->SetInput(image); surfaceFilter->SetInterPixelDistance(interPixelDistance); surfaceFilter->SetCameraIntrinsics(cameraIntrinsics); surfaceFilter->SetReconstructionMode(mitk::ToFDistanceImageToSurfaceFilter::WithOutInterPixelDistance); MITK_TEST_CONDITION_REQUIRED(filter->GetReconstructionMode() == mitk::ToFDistanceImageToSurfaceFilter::WithOutInterPixelDistance,"Testing Set/GetReconstructionMode()"); mitk::Surface::Pointer surface = surfaceFilter->GetOutput(); surface->Update(); // create point set from surface mitk::PointSet::Pointer pointSet = mitk::ToFTestingCommon::VtkPolyDataToMitkPointSet(surface->GetVtkPolyData()); //compare pointset against ground truth MITK_TEST_CONDITION_REQUIRED((pointSet->GetSize()==result->GetSize()),"Test if point set size is equal"); MITK_TEST_CONDITION_REQUIRED(mitk::ToFTestingCommon::PointSetsEqual(pointSet,result),"Compare with surface points"); // test filter without subset (with using the interpixeldistance) MITK_INFO<<"Test filter without subset with using the interpixeldistance"; filter->Modified(); filter->SetReconstructionMode(false); expectedResult = mitk::PointSet::New(); counter = 0; for (unsigned int j=0; j index; index[0] = i; index[1] = j; - index[2] = 0; - mitk::ScalarType distance = image->GetPixelValueByIndex(index); + mitk::ScalarType distance = imageAcces.GetPixelByIndex(index); mitk::Point3D coordinate = mitk::ToFProcessingCommon::IndexToCartesianCoordinatesWithInterpixdist(i,j,distance,focalLength,interPixelDistance,principalPoint); expectedResult->InsertPoint(counter,coordinate); counter++; } } filter->Update(); result = filter->GetOutput(); MITK_TEST_CONDITION_REQUIRED((expectedResult->GetSize()==result->GetSize()),"Test if point set size is equal"); MITK_TEST_CONDITION_REQUIRED(mitk::ToFTestingCommon::PointSetsEqual(expectedResult,result),"Testing filter without subset"); // compare filter result with ToFDistanceImageToSurfaceFilter MITK_INFO<<"Compare filter result with ToFDistanceImageToSurfaceFilter"; surfaceFilter = mitk::ToFDistanceImageToSurfaceFilter::New(); surfaceFilter->SetInput(image); surfaceFilter->SetInterPixelDistance(interPixelDistance); surfaceFilter->SetCameraIntrinsics(cameraIntrinsics); surfaceFilter->SetReconstructionMode(mitk::ToFDistanceImageToSurfaceFilter::WithInterPixelDistance); MITK_TEST_CONDITION_REQUIRED(surfaceFilter->GetReconstructionMode() == mitk::ToFDistanceImageToSurfaceFilter::WithInterPixelDistance,"Testing Set/GetReconstructionMode()"); surface = surfaceFilter->GetOutput(); surface->Update(); // create point set from surface pointSet = mitk::ToFTestingCommon::VtkPolyDataToMitkPointSet(surface->GetVtkPolyData()); //compare against ground truth MITK_TEST_CONDITION_REQUIRED((pointSet->GetSize()==result->GetSize()),"Test if point set size is equal"); MITK_TEST_CONDITION_REQUIRED(mitk::ToFTestingCommon::PointSetsEqual(pointSet,result),"Compare with surface points"); // test filter with subset (without using the interpixeldistance) MITK_INFO<<"Test filter with subset without using the interpixeldistance"; filter = mitk::ToFDistanceImageToPointSetFilter::New(); filter->SetInput(image); filter->SetInterPixelDistance(interPixelDistance); filter->SetCameraIntrinsics(cameraIntrinsics); filter->SetReconstructionMode(true); expectedResult = mitk::PointSet::New(); counter = 0; for(int i=0; iGetSize(); i++) { mitk::Point3D point = subSet->GetPoint(i); - mitk::Index3D index; + itk::Index<2> index; index[0] = point[0]; index[1] = point[1]; - index[2] = 0; - mitk::ScalarType distance = image->GetPixelValueByIndex(index); + mitk::ScalarType distance = imageAcces.GetPixelByIndex(index); mitk::Point3D coordinate = mitk::ToFProcessingCommon::IndexToCartesianCoordinates(point[0],point[1], distance,focalLengthX,focalLengthY,principalPoint[0],principalPoint[1]); expectedResult->InsertPoint(counter,coordinate); counter++; } filter->SetSubset(subSet); filter->Modified(); filter->Update(); result = filter->GetOutput(); MITK_TEST_CONDITION_REQUIRED((expectedResult->GetSize()==result->GetSize()),"Test if point set size is equal"); MITK_TEST_CONDITION_REQUIRED(mitk::ToFTestingCommon::PointSetsEqual(expectedResult,result),"Testing filter with subset"); // test filter with subset (with using the interpixeldistance) MITK_INFO<<"Test filter with subset with using the interpixeldistance"; filter = mitk::ToFDistanceImageToPointSetFilter::New(); filter->SetInput(image); filter->SetInterPixelDistance(interPixelDistance); filter->SetCameraIntrinsics(cameraIntrinsics); filter->SetReconstructionMode(false); expectedResult = mitk::PointSet::New(); counter = 0; for(int i=0; iGetSize(); i++) { mitk::Point3D point = subSet->GetPoint(i); - mitk::Index3D index; + itk::Index<2> index; index[0] = point[0]; index[1] = point[1]; - index[2] = 0; - mitk::ScalarType distance = image->GetPixelValueByIndex(index); + mitk::ScalarType distance = imageAcces.GetPixelByIndex(index); mitk::Point3D coordinate = mitk::ToFProcessingCommon::IndexToCartesianCoordinatesWithInterpixdist(point[0],point[1], distance,focalLength,interPixelDistance,principalPoint); expectedResult->InsertPoint(counter,coordinate); counter++; } filter->SetSubset(subSet); filter->Modified(); filter->Update(); result = filter->GetOutput(); MITK_TEST_CONDITION_REQUIRED((expectedResult->GetSize()==result->GetSize()),"Test if point set size is equal"); MITK_TEST_CONDITION_REQUIRED(mitk::ToFTestingCommon::PointSetsEqual(expectedResult,result),"Testing filter with subset"); MITK_TEST_END(); } diff --git a/Modules/ToFProcessing/mitkToFDistanceImageToPointSetFilter.cpp b/Modules/ToFProcessing/mitkToFDistanceImageToPointSetFilter.cpp index 390486ccbe..aa6f4ab8c6 100644 --- a/Modules/ToFProcessing/mitkToFDistanceImageToPointSetFilter.cpp +++ b/Modules/ToFProcessing/mitkToFDistanceImageToPointSetFilter.cpp @@ -1,206 +1,211 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkToFDistanceImageToPointSetFilter.h" #include "mitkImageDataItem.h" #include "mitkPointSet.h" +#include #include "mitkToFProcessingCommon.h" mitk::ToFDistanceImageToPointSetFilter::ToFDistanceImageToPointSetFilter() : m_Subset(NULL), m_CameraIntrinsics(), m_InterPixelDistance() { m_InterPixelDistance.Fill(0.045); m_CameraIntrinsics = mitk::CameraIntrinsics::New(); m_CameraIntrinsics->SetFocalLength(5.9421434211923247e+02,5.9104053696870778e+02); m_CameraIntrinsics->SetPrincipalPoint(3.3930780975300314e+02,2.4273913761751615e+02); m_CameraIntrinsics->SetDistorsionCoeffs(-0.36874385358645773f,-0.14339503290129013,0.0033210108720361795,-0.004277703352074105); m_ReconstructionMode = true; } mitk::ToFDistanceImageToPointSetFilter::~ToFDistanceImageToPointSetFilter() { } void mitk::ToFDistanceImageToPointSetFilter::SetInput(const mitk::Image* distanceImage ) { this->SetInput(0,distanceImage); } void mitk::ToFDistanceImageToPointSetFilter::SetInput( unsigned int idx,const mitk::Image* distanceImage ) { if ((distanceImage == NULL) && (idx == this->GetNumberOfInputs() - 1)) // if the last input is set to NULL, reduce the number of inputs by one { this->SetNumberOfInputs(this->GetNumberOfInputs() - 1); } else { this->ProcessObject::SetNthInput(idx, const_cast(distanceImage)); // Process object is not const-correct so the const_cast is required here this->CreateOutputsForAllInputs(); } } mitk::Image* mitk::ToFDistanceImageToPointSetFilter::GetInput() { return this->GetInput(0); } mitk::Image* mitk::ToFDistanceImageToPointSetFilter::GetInput( unsigned int idx ) { if (this->GetNumberOfInputs() < 1) return NULL; return static_cast< mitk::Image*>(this->ProcessObject::GetInput(idx)); } void mitk::ToFDistanceImageToPointSetFilter::SetSubset(std::vector subset) { // check if points of PointSet are inside the input image mitk::Image::Pointer input = this->GetInput(); unsigned int xDim = input->GetDimension(0); unsigned int yDim = input->GetDimension(1); bool pointSetValid = true; for (unsigned int i=0; ixDim||currentIndex[1]<0||currentIndex[1]>yDim) { pointSetValid = false; } } if (pointSetValid) { m_Subset = subset; } else { MITK_ERROR<<"One or more indizes are located outside the image domain"; } } void mitk::ToFDistanceImageToPointSetFilter::SetSubset( mitk::PointSet::Pointer pointSet) { std::vector subset; for (int i=0; iGetSize(); i++) { mitk::Point3D currentPoint = pointSet->GetPoint(i); mitk::Index3D currentIndex; currentIndex[0] = currentPoint[0]; currentIndex[1] = currentPoint[1]; currentIndex[2] = currentPoint[2]; subset.push_back(currentIndex); } this->SetSubset(subset); } void mitk::ToFDistanceImageToPointSetFilter::GenerateData() { //calculate world coordinates mitk::ToFProcessingCommon::ToFPoint2D focalLengthInPixelUnits; mitk::ToFProcessingCommon::ToFScalarType focalLengthInMm; if (m_ReconstructionMode) { focalLengthInPixelUnits[0] = m_CameraIntrinsics->GetFocalLengthX(); focalLengthInPixelUnits[1] = m_CameraIntrinsics->GetFocalLengthY(); } else focalLengthInMm = (m_CameraIntrinsics->GetFocalLengthX()*m_InterPixelDistance[0]+m_CameraIntrinsics->GetFocalLengthY()*m_InterPixelDistance[1])/2.0; mitk::ToFProcessingCommon::ToFPoint2D principalPoint; principalPoint[0] = m_CameraIntrinsics->GetPrincipalPointX(); principalPoint[1] = m_CameraIntrinsics->GetPrincipalPointY(); mitk::PointSet::Pointer output = this->GetOutput(); assert(output); mitk::Image::Pointer input = this->GetInput(); assert(input); //compute subset of points if input PointSet is defined if (m_Subset.size()!=0) { + mitk::ImagePixelReadAccessor imageAcces(input, input->GetSliceData(0)); for (unsigned int i=0; iGetPixelValueByIndex(currentIndex); + mitk::Index3D currentIndex = m_Subset.at(i); + itk::Index<2> index2D; + index2D[0] = currentIndex[0]; + index2D[1] = currentIndex[1]; + mitk::ToFProcessingCommon::ToFScalarType distance = (double)imageAcces.GetPixelByIndex(index2D); mitk::Point3D currentPoint; if (m_ReconstructionMode) currentPoint = mitk::ToFProcessingCommon::IndexToCartesianCoordinates(currentIndex,distance,focalLengthInPixelUnits,principalPoint); else currentPoint = mitk::ToFProcessingCommon::IndexToCartesianCoordinatesWithInterpixdist(currentIndex,distance,focalLengthInMm,m_InterPixelDistance,principalPoint); output->InsertPoint(i,currentPoint); } } else //compute PointSet holding cartesian coordinates for every image point { int xDimension = (int)input->GetDimension(0); int yDimension = (int)input->GetDimension(1); int pointCount = 0; + mitk::ImagePixelReadAccessor imageAcces(input, input->GetSliceData(0)); for (int j=0; j pixel; pixel[0] = i; pixel[1] = j; - pixel[2] = 0; - mitk::ToFProcessingCommon::ToFScalarType distance = (double)input->GetPixelValueByIndex(pixel); + mitk::ToFProcessingCommon::ToFScalarType distance = (double)imageAcces.GetPixelByIndex(pixel); mitk::Point3D currentPoint; if (m_ReconstructionMode) currentPoint = mitk::ToFProcessingCommon::IndexToCartesianCoordinates(i,j,distance,focalLengthInPixelUnits,principalPoint); else currentPoint = mitk::ToFProcessingCommon::IndexToCartesianCoordinatesWithInterpixdist(i,j,distance,focalLengthInMm,m_InterPixelDistance,principalPoint); if (distance>mitk::eps) { output->InsertPoint( pointCount, currentPoint ); pointCount++; } } } } } void mitk::ToFDistanceImageToPointSetFilter::CreateOutputsForAllInputs() { this->SetNumberOfOutputs(this->GetNumberOfInputs()); // create outputs for all inputs for (unsigned int idx = 0; idx < this->GetNumberOfIndexedOutputs(); ++idx) if (this->GetOutput(idx) == NULL) { DataObjectPointer newOutput = this->MakeOutput(idx); this->SetNthOutput(idx, newOutput); } this->Modified(); } void mitk::ToFDistanceImageToPointSetFilter::GenerateOutputInformation() { this->GetOutput(); itkDebugMacro(<<"GenerateOutputInformation()"); } void mitk::ToFDistanceImageToPointSetFilter::SetReconstructionMode(bool withoutInterpixdist) { this->m_ReconstructionMode = withoutInterpixdist; } bool mitk::ToFDistanceImageToPointSetFilter::GetReconstructionMode() { return (this->m_ReconstructionMode); }