void mitk::PicFileReader::GenerateData() { Image::Pointer output = this->GetOutput(); // Check to see if we can read the file given the name or prefix // if ( m_FileName == "" && m_FilePrefix == "" ) { throw itk::ImageFileReaderException(__FILE__, __LINE__, "One of FileName or FilePrefix must be non-empty"); } if( m_FileName != "") { mitkIpPicDescriptor* outputPic = mitkIpPicNew(); outputPic = CastToIpPicDescriptor(output, outputPic); mitkIpPicDescriptor* pic=MITKipPicGet(const_cast<char *>(m_FileName.c_str()), outputPic); // comes upside-down (in MITK coordinates) from PIC file ConvertHandedness(pic); mitkIpPicTSV_t *tsv; if ( (tsv = mitkIpPicQueryTag( pic, "SOURCE HEADER" )) != NULL) { if(tsv->n[0]>1e+06) { mitkIpPicTSV_t *tsvSH; tsvSH = mitkIpPicDelTag( pic, "SOURCE HEADER" ); mitkIpPicFreeTag(tsvSH); } } if ( (tsv = mitkIpPicQueryTag( pic, "ICON80x80" )) != NULL) { mitkIpPicTSV_t *tsvSH; tsvSH = mitkIpPicDelTag( pic, "ICON80x80" ); mitkIpPicFreeTag(tsvSH); } if ( (tsv = mitkIpPicQueryTag( pic, "VELOCITY" )) != NULL) { mitkIpPicDescriptor* header = mitkIpPicCopyHeader(pic, NULL); header->data = tsv->value; ConvertHandedness(header); output->SetChannel(header->data, 1); header->data = NULL; mitkIpPicFree(header); mitkIpPicDelTag( pic, "VELOCITY" ); } //slice-wise reading //currently much too slow. //else //{ // int sstart, smax; // int tstart, tmax; // sstart=output->GetRequestedRegion().GetIndex(2); // smax=sstart+output->GetRequestedRegion().GetSize(2); // tstart=output->GetRequestedRegion().GetIndex(3); // tmax=tstart+output->GetRequestedRegion().GetSize(3); // int s,t; // for(s=sstart; s<smax; ++s) // { // for(t=tstart; t<tmax; ++t) // { // mitkIpPicDescriptor* pic=mitkIpPicGetSlice(const_cast<char *>(m_FileName.c_str()), NULL, t*smax+s+1); // output->SetPicSlice(pic,s,t); // } // } //} } else { int position; mitkIpPicDescriptor* pic=NULL; int zDim=(output->GetDimension()>2?output->GetDimensions()[2]:1); printf("\n zdim is %u \n",zDim); for (position = 0; position < zDim; ++position) { char fullName[1024]; sprintf(fullName, m_FilePattern.c_str(), m_FilePrefix.c_str(), m_StartFileIndex+position); pic=MITKipPicGet(fullName, pic); if(pic==NULL) { itkDebugMacro("Pic file '" << fullName << "' does not exist."); } /* FIXME else if(output->SetPicSlice(pic, position)==false) { itkDebugMacro("Image '" << fullName << "' could not be added to Image."); }*/ } if(pic!=NULL) mitkIpPicFree(pic); } }
mitk::GIFVolumetricStatistics::FeatureListType mitk::GIFVolumetricStatistics::CalculateFeatures(const Image::Pointer & image, const Image::Pointer &mask) { FeatureListType featureList; if (image->GetDimension() < 3) { return featureList; } AccessByItk_3(image, CalculateVolumeStatistic, mask, featureList, FeatureDescriptionPrefix()); AccessByItk_3(mask, CalculateLargestDiameter, image, featureList, FeatureDescriptionPrefix()); vtkSmartPointer<vtkImageMarchingCubes> mesher = vtkSmartPointer<vtkImageMarchingCubes>::New(); vtkSmartPointer<vtkMassProperties> stats = vtkSmartPointer<vtkMassProperties>::New(); mesher->SetInputData(mask->GetVtkImageData()); mesher->SetValue(0, 0.5); stats->SetInputConnection(mesher->GetOutputPort()); stats->Update(); double pi = vnl_math::pi; double meshVolume = stats->GetVolume(); double meshSurf = stats->GetSurfaceArea(); double pixelVolume = featureList[1].second; double pixelSurface = featureList[3].second; MITK_INFO << "Surface: " << pixelSurface << " Volume: " << pixelVolume; double compactness1 = pixelVolume / (std::sqrt(pi) * std::pow(meshSurf, 2.0 / 3.0)); double compactness1Pixel = pixelVolume / (std::sqrt(pi) * std::pow(pixelSurface, 2.0 / 3.0)); //This is the definition used by Aertz. However, due to 2/3 this feature is not demensionless. Use compactness3 instead. double compactness2 = 36 * pi*pixelVolume*pixelVolume / meshSurf / meshSurf / meshSurf; double compactness2MeshMesh = 36 * pi*meshVolume*meshVolume / meshSurf / meshSurf / meshSurf; double compactness2Pixel = 36 * pi*pixelVolume*pixelVolume / pixelSurface / pixelSurface / pixelSurface; double compactness3 = pixelVolume / (std::sqrt(pi) * std::pow(meshSurf, 3.0 / 2.0)); double compactness3MeshMesh = meshVolume / (std::sqrt(pi) * std::pow(meshSurf, 3.0 / 2.0)); double compactness3Pixel = pixelVolume / (std::sqrt(pi) * std::pow(pixelSurface, 3.0 / 2.0)); double sphericity = std::pow(pi, 1 / 3.0) *std::pow(6 * pixelVolume, 2.0 / 3.0) / meshSurf; double sphericityMesh = std::pow(pi, 1 / 3.0) *std::pow(6 * meshVolume, 2.0 / 3.0) / meshSurf; double sphericityPixel = std::pow(pi, 1 / 3.0) *std::pow(6 * pixelVolume, 2.0 / 3.0) / pixelSurface; double surfaceToVolume = meshSurf / meshVolume; double surfaceToVolumePixel = pixelSurface / pixelVolume; double sphericalDisproportion = meshSurf / 4 / pi / std::pow(3.0 / 4.0 / pi * pixelVolume, 2.0 / 3.0); double sphericalDisproportionMesh = meshSurf / 4 / pi / std::pow(3.0 / 4.0 / pi * meshVolume, 2.0 / 3.0); double sphericalDisproportionPixel = pixelSurface / 4 / pi / std::pow(3.0 / 4.0 / pi * pixelVolume, 2.0 / 3.0); double asphericity = std::pow(1.0/compactness2, (1.0 / 3.0)) - 1; double asphericityMesh = std::pow(1.0 / compactness2MeshMesh, (1.0 / 3.0)) - 1; double asphericityPixel = std::pow(1.0/compactness2Pixel, (1.0 / 3.0)) - 1; //Calculate center of mass shift int xx = mask->GetDimensions()[0]; int yy = mask->GetDimensions()[1]; int zz = mask->GetDimensions()[2]; double xd = mask->GetGeometry()->GetSpacing()[0]; double yd = mask->GetGeometry()->GetSpacing()[1]; double zd = mask->GetGeometry()->GetSpacing()[2]; vtkSmartPointer<vtkDoubleArray> dataset1Arr = vtkSmartPointer<vtkDoubleArray>::New(); vtkSmartPointer<vtkDoubleArray> dataset2Arr = vtkSmartPointer<vtkDoubleArray>::New(); vtkSmartPointer<vtkDoubleArray> dataset3Arr = vtkSmartPointer<vtkDoubleArray>::New(); dataset1Arr->SetNumberOfComponents(1); dataset2Arr->SetNumberOfComponents(1); dataset3Arr->SetNumberOfComponents(1); dataset1Arr->SetName("M1"); dataset2Arr->SetName("M2"); dataset3Arr->SetName("M3"); vtkSmartPointer<vtkDoubleArray> dataset1ArrU = vtkSmartPointer<vtkDoubleArray>::New(); vtkSmartPointer<vtkDoubleArray> dataset2ArrU = vtkSmartPointer<vtkDoubleArray>::New(); vtkSmartPointer<vtkDoubleArray> dataset3ArrU = vtkSmartPointer<vtkDoubleArray>::New(); dataset1ArrU->SetNumberOfComponents(1); dataset2ArrU->SetNumberOfComponents(1); dataset3ArrU->SetNumberOfComponents(1); dataset1ArrU->SetName("M1"); dataset2ArrU->SetName("M2"); dataset3ArrU->SetName("M3"); for (int x = 0; x < xx; x++) { for (int y = 0; y < yy; y++) { for (int z = 0; z < zz; z++) { itk::Image<int,3>::IndexType index; index[0] = x; index[1] = y; index[2] = z; mitk::ScalarType pxImage; mitk::ScalarType pxMask; mitkPixelTypeMultiplex5( mitk::FastSinglePixelAccess, image->GetChannelDescriptor().GetPixelType(), image, image->GetVolumeData(), index, pxImage, 0); mitkPixelTypeMultiplex5( mitk::FastSinglePixelAccess, mask->GetChannelDescriptor().GetPixelType(), mask, mask->GetVolumeData(), index, pxMask, 0); //Check if voxel is contained in segmentation if (pxMask > 0) { dataset1ArrU->InsertNextValue(x*xd); dataset2ArrU->InsertNextValue(y*yd); dataset3ArrU->InsertNextValue(z*zd); if (pxImage == pxImage) { dataset1Arr->InsertNextValue(x*xd); dataset2Arr->InsertNextValue(y*yd); dataset3Arr->InsertNextValue(z*zd); } } } } } vtkSmartPointer<vtkTable> datasetTable = vtkSmartPointer<vtkTable>::New(); datasetTable->AddColumn(dataset1Arr); datasetTable->AddColumn(dataset2Arr); datasetTable->AddColumn(dataset3Arr); vtkSmartPointer<vtkTable> datasetTableU = vtkSmartPointer<vtkTable>::New(); datasetTableU->AddColumn(dataset1ArrU); datasetTableU->AddColumn(dataset2ArrU); datasetTableU->AddColumn(dataset3ArrU); vtkSmartPointer<vtkPCAStatistics> pcaStatistics = vtkSmartPointer<vtkPCAStatistics>::New(); pcaStatistics->SetInputData(vtkStatisticsAlgorithm::INPUT_DATA, datasetTable); pcaStatistics->SetColumnStatus("M1", 1); pcaStatistics->SetColumnStatus("M2", 1); pcaStatistics->SetColumnStatus("M3", 1); pcaStatistics->RequestSelectedColumns(); pcaStatistics->SetDeriveOption(true); pcaStatistics->Update(); vtkSmartPointer<vtkDoubleArray> eigenvalues = vtkSmartPointer<vtkDoubleArray>::New(); pcaStatistics->GetEigenvalues(eigenvalues); pcaStatistics->SetInputData(vtkStatisticsAlgorithm::INPUT_DATA, datasetTableU); pcaStatistics->Update(); vtkSmartPointer<vtkDoubleArray> eigenvaluesU = vtkSmartPointer<vtkDoubleArray>::New(); pcaStatistics->GetEigenvalues(eigenvaluesU); std::vector<double> eigen_val(3); std::vector<double> eigen_valUC(3); eigen_val[2] = eigenvalues->GetValue(0); eigen_val[1] = eigenvalues->GetValue(1); eigen_val[0] = eigenvalues->GetValue(2); eigen_valUC[2] = eigenvaluesU->GetValue(0); eigen_valUC[1] = eigenvaluesU->GetValue(1); eigen_valUC[0] = eigenvaluesU->GetValue(2); double major = 4*sqrt(eigen_val[2]); double minor = 4*sqrt(eigen_val[1]); double least = 4*sqrt(eigen_val[0]); double elongation = (major == 0) ? 0 : sqrt(eigen_val[1] / eigen_val[2]); double flatness = (major == 0) ? 0 : sqrt(eigen_val[0] / eigen_val[2]); double majorUC = 4*sqrt(eigen_valUC[2]); double minorUC = 4*sqrt(eigen_valUC[1]); double leastUC = 4*sqrt(eigen_valUC[0]); double elongationUC = majorUC == 0 ? 0 : sqrt(eigen_valUC[1] / eigen_valUC[2]); double flatnessUC = majorUC == 0 ? 0 : sqrt(eigen_valUC[0] / eigen_valUC[2]); std::string prefix = FeatureDescriptionPrefix(); featureList.push_back(std::make_pair(prefix + "Volume (mesh based)",meshVolume)); featureList.push_back(std::make_pair(prefix + "Surface (mesh based)",meshSurf)); featureList.push_back(std::make_pair(prefix + "Surface to volume ratio (mesh based)",surfaceToVolume)); featureList.push_back(std::make_pair(prefix + "Sphericity (mesh based)",sphericity)); featureList.push_back(std::make_pair(prefix + "Sphericity (mesh, mesh based)", sphericityMesh)); featureList.push_back(std::make_pair(prefix + "Asphericity (mesh based)", asphericity)); featureList.push_back(std::make_pair(prefix + "Asphericity (mesh, mesh based)", asphericityMesh)); featureList.push_back(std::make_pair(prefix + "Compactness 1 (mesh based)", compactness3)); featureList.push_back(std::make_pair(prefix + "Compactness 1 old (mesh based)" ,compactness1)); featureList.push_back(std::make_pair(prefix + "Compactness 2 (mesh based)",compactness2)); featureList.push_back(std::make_pair(prefix + "Compactness 1 (mesh, mesh based)", compactness3MeshMesh)); featureList.push_back(std::make_pair(prefix + "Compactness 2 (mesh, mesh based)", compactness2MeshMesh)); featureList.push_back(std::make_pair(prefix + "Spherical disproportion (mesh based)", sphericalDisproportion)); featureList.push_back(std::make_pair(prefix + "Spherical disproportion (mesh, mesh based)", sphericalDisproportionMesh)); featureList.push_back(std::make_pair(prefix + "Surface to volume ratio (voxel based)", surfaceToVolumePixel)); featureList.push_back(std::make_pair(prefix + "Sphericity (voxel based)", sphericityPixel)); featureList.push_back(std::make_pair(prefix + "Asphericity (voxel based)", asphericityPixel)); featureList.push_back(std::make_pair(prefix + "Compactness 1 (voxel based)", compactness3Pixel)); featureList.push_back(std::make_pair(prefix + "Compactness 1 old (voxel based)", compactness1Pixel)); featureList.push_back(std::make_pair(prefix + "Compactness 2 (voxel based)", compactness2Pixel)); featureList.push_back(std::make_pair(prefix + "Spherical disproportion (voxel based)", sphericalDisproportionPixel)); featureList.push_back(std::make_pair(prefix + "PCA Major axis length",major)); featureList.push_back(std::make_pair(prefix + "PCA Minor axis length",minor)); featureList.push_back(std::make_pair(prefix + "PCA Least axis length",least)); featureList.push_back(std::make_pair(prefix + "PCA Elongation",elongation)); featureList.push_back(std::make_pair(prefix + "PCA Flatness",flatness)); featureList.push_back(std::make_pair(prefix + "PCA Major axis length (uncorrected)", majorUC)); featureList.push_back(std::make_pair(prefix + "PCA Minor axis length (uncorrected)", minorUC)); featureList.push_back(std::make_pair(prefix + "PCA Least axis length (uncorrected)", leastUC)); featureList.push_back(std::make_pair(prefix + "PCA Elongation (uncorrected)", elongationUC)); featureList.push_back(std::make_pair(prefix + "PCA Flatness (uncorrected)", flatnessUC)); return featureList; }