void mitk::GeometryClipImageFilter::GenerateData() { Image::ConstPointer input = this->GetInput(); Image::Pointer output = this->GetOutput(); if((output->IsInitialized()==false) || (m_ClippingGeometry.IsNull())) return; const Geometry2D * clippingGeometryOfCurrentTimeStep = NULL; if(m_TimeSlicedClippingGeometry.IsNull()) { clippingGeometryOfCurrentTimeStep = dynamic_cast<const Geometry2D*>(m_ClippingGeometry.GetPointer()); } else { clippingGeometryOfCurrentTimeStep = dynamic_cast<const Geometry2D*>(m_TimeSlicedClippingGeometry->GetGeometry3D(0)); } if(clippingGeometryOfCurrentTimeStep == NULL) return; m_InputTimeSelector->SetInput(input); m_OutputTimeSelector->SetInput(this->GetOutput()); mitk::Image::RegionType outputRegion = output->GetRequestedRegion(); const mitk::TimeSlicedGeometry *outputTimeGeometry = output->GetTimeSlicedGeometry(); const mitk::TimeSlicedGeometry *inputTimeGeometry = input->GetTimeSlicedGeometry(); ScalarType timeInMS; int timestep=0; int tstart=outputRegion.GetIndex(3); int tmax=tstart+outputRegion.GetSize(3); int t; for(t=tstart;t<tmax;++t) { timeInMS = outputTimeGeometry->TimeStepToMS( t ); timestep = inputTimeGeometry->MSToTimeStep( timeInMS ); m_InputTimeSelector->SetTimeNr(timestep); m_InputTimeSelector->UpdateLargestPossibleRegion(); m_OutputTimeSelector->SetTimeNr(t); m_OutputTimeSelector->UpdateLargestPossibleRegion(); if(m_TimeSlicedClippingGeometry.IsNotNull()) { timestep = m_TimeSlicedClippingGeometry->MSToTimeStep( timeInMS ); if(m_TimeSlicedClippingGeometry->IsValidTime(timestep) == false) continue; clippingGeometryOfCurrentTimeStep = dynamic_cast<const Geometry2D*>(m_TimeSlicedClippingGeometry->GetGeometry3D(timestep)); } AccessByItk_2(m_InputTimeSelector->GetOutput(),_InternalComputeClippedImage,this,clippingGeometryOfCurrentTimeStep); } m_TimeOfHeaderInitialization.Modified(); }
void mitk::PicFileReader::GenerateOutputInformation() { Image::Pointer output = this->GetOutput(); if ((output->IsInitialized()) && (this->GetMTime() <= m_ReadHeaderTime.GetMTime())) return; itkDebugMacro(<<"Reading file for GenerateOutputInformation()" << m_FileName); // 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* header=mitkIpPicGetHeader(const_cast<char *>(m_FileName.c_str()), NULL); if ( !header ) { throw itk::ImageFileReaderException(__FILE__, __LINE__, "File could not be read."); } header=MITKipPicGetTags(const_cast<char *>(m_FileName.c_str()), header); int channels = 1; mitkIpPicTSV_t *tsv; if ( (tsv = mitkIpPicQueryTag( header, "SOURCE HEADER" )) != NULL) { if(tsv->n[0]>1e+06) { mitkIpPicTSV_t *tsvSH; tsvSH = mitkIpPicDelTag( header, "SOURCE HEADER" ); mitkIpPicFreeTag(tsvSH); } } if ( (tsv = mitkIpPicQueryTag( header, "ICON80x80" )) != NULL) { mitkIpPicTSV_t *tsvSH; tsvSH = mitkIpPicDelTag( header, "ICON80x80" ); mitkIpPicFreeTag(tsvSH); } if ( (tsv = mitkIpPicQueryTag( header, "VELOCITY" )) != NULL) { ++channels; mitkIpPicDelTag( header, "VELOCITY" ); } if( header == NULL || header->bpe == 0) { itk::ImageFileReaderException e(__FILE__, __LINE__); itk::OStringStream msg; msg << " Could not read file " << m_FileName.c_str(); e.SetDescription(msg.str().c_str()); throw e; return; } // First initialize the geometry of the output image by the pic-header SlicedGeometry3D::Pointer slicedGeometry = mitk::SlicedGeometry3D::New(); PicHelper::InitializeEvenlySpaced(header, header->n[2], slicedGeometry); // if pic image only 3D, the n[3] value is not initialized unsigned int timesteps = 1; if( header->dim > 3 ) timesteps = header->n[3]; TimeSlicedGeometry::Pointer timeSliceGeometry = TimeSlicedGeometry::New(); timeSliceGeometry->InitializeEvenlyTimed(slicedGeometry, timesteps); timeSliceGeometry->ImageGeometryOn(); // Cast the pic descriptor to ImageDescriptor and initialize the output output->Initialize( CastToImageDescriptor(header)); output->SetGeometry( timeSliceGeometry ); mitkIpPicFree ( header ); } else { int numberOfImages=0; m_StartFileIndex=0; mitkIpPicDescriptor* header=NULL; char fullName[1024]; while(m_StartFileIndex<10) { sprintf(fullName, m_FilePattern.c_str(), m_FilePrefix.c_str(), m_StartFileIndex+numberOfImages); FILE * f=fopen(fullName,"r"); if(f==NULL) { //already found an image? if(numberOfImages>0) break; //no? let's increase start ++m_StartFileIndex; } else { fclose(f); //only open the header of the first file found, //@warning what to do when images do not have the same size?? if(header==NULL) { header=mitkIpPicGetHeader(fullName, NULL); header=MITKipPicGetTags(fullName, header); } ++numberOfImages; } } printf("\n numberofimages %d\n",numberOfImages); if(numberOfImages==0) { itk::ImageFileReaderException e(__FILE__, __LINE__); itk::OStringStream msg; msg << "no images found"; e.SetDescription(msg.str().c_str()); throw e; return; } //@FIXME: was ist, wenn die Bilder nicht alle gleich gross sind? if(numberOfImages>1) { printf("\n numberofimages %d > 1\n",numberOfImages); header->dim=3; header->n[2]=numberOfImages; } printf(" \ninitialisize output\n"); output->Initialize( CastToImageDescriptor(header) ); mitkIpPicFree ( header ); } m_ReadHeaderTime.Modified(); }