diff --git a/Modules/IpPicSupport/mitkPicFileReader.cpp b/Modules/IpPicSupport/mitkPicFileReader.cpp index e841ad852d..3ba42ae077 100644 --- a/Modules/IpPicSupport/mitkPicFileReader.cpp +++ b/Modules/IpPicSupport/mitkPicFileReader.cpp @@ -1,373 +1,375 @@ /*=================================================================== 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 "mitkPicFileReader.h" #include "mitkPicHelper.h" #include +#include "mitkImageWriteAccessor.h" extern "C" { mitkIpPicDescriptor * MITKipPicGet( char *infile_name, mitkIpPicDescriptor *pic ); mitkIpPicDescriptor * MITKipPicGetTags( char *infile_name, mitkIpPicDescriptor *pic ); } 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(m_FileName.c_str()), NULL); if ( !header ) { throw itk::ImageFileReaderException(__FILE__, __LINE__, "File could not be read."); } header=MITKipPicGetTags(const_cast(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__); std::ostringstream msg; msg << " Could not read file " << m_FileName.c_str(); e.SetDescription(msg.str().c_str()); throw e; return; } // if pic image only 2D, the n[2] value is not initialized unsigned int slices = 1; if( header->dim == 2 ) header->n[2] = slices; // 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__); std::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(); } void mitk::PicFileReader::ConvertHandedness(mitkIpPicDescriptor* pic) { //left to right handed conversion if(pic->dim>=3) { mitkIpPicDescriptor* slice=mitkIpPicCopyHeader(pic, NULL); slice->dim=2; size_t size=_mitkIpPicSize(slice); slice->data=malloc(size); size_t v, volumes = (pic->dim>3? pic->n[3] : 1); size_t volume_size = size*pic->n[2]; for(v=0; vdata; unsigned char *p_last=(unsigned char *)pic->data; p_first+=v*volume_size; p_last+=size*(pic->n[2]-1)+v*volume_size; size_t i, smid=pic->n[2]/2; for(i=0; idata, p_last, size); memcpy(p_last, p_first, size); memcpy(p_first, slice->data, size); } } mitkIpPicFree(slice); } } 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); + mitk::ImageWriteAccessor imageAccess(output); + outputPic = CastToIpPicDescriptor(output, &imageAccess, outputPic); mitkIpPicDescriptor* pic=MITKipPicGet(const_cast(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(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); } } void mitk::PicFileReader::EnlargeOutputRequestedRegion(itk::DataObject *output) { output->SetRequestedRegionToLargestPossibleRegion(); } bool mitk::PicFileReader::CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern) { // First check the extension if( filename == "" ) { //MITK_INFO<<"No filename specified."<SetNumberOfRequiredInputs( 1 ); } mitk::PicFileWriter::~PicFileWriter() { } void mitk::PicFileWriter::GenerateData() { if ( m_FileName == "" ) { itkWarningMacro( << "Sorry, filename has not been set!" ); return ; } std::ofstream testfilehandle( m_FileName.c_str(), std::ios::out); if (!testfilehandle.good()) { testfilehandle.close(); itkExceptionMacro(<<"File location '" << m_FileName << "' not writeable"); } else { testfilehandle.close(); } Image::Pointer input = const_cast(this->GetInput()); if ( input.IsNull() ) { itkExceptionMacro(<< "Nothing to write: Input is NULL." ); } if( input->GetNumberOfChannels() > 1) { std::cout << "Multiple channel. Cannot write. Will throw..."; itkExceptionMacro(<< "The PicFileWriter does not support multiple channel data. Nothing will be written." ); } mitkIpPicDescriptor * picImage = mitkIpPicNew(); - picImage = CastToIpPicDescriptor(input, picImage); + mitk::ImageWriteAccessor imageAccess(input); + picImage = CastToIpPicDescriptor(input, &imageAccess, picImage); SlicedGeometry3D* slicedGeometry = input->GetSlicedGeometry(); if (slicedGeometry != NULL) { //set tag "REAL PIXEL SIZE" const Vector3D & spacing = slicedGeometry->GetSpacing(); mitkIpPicTSV_t *pixelSizeTag; pixelSizeTag = mitkIpPicQueryTag( picImage, "REAL PIXEL SIZE" ); if (!pixelSizeTag) { pixelSizeTag = (mitkIpPicTSV_t *) malloc( sizeof(mitkIpPicTSV_t) ); pixelSizeTag->type = mitkIpPicFloat; pixelSizeTag->bpe = 32; strcpy(pixelSizeTag->tag, "REAL PIXEL SIZE"); pixelSizeTag->dim = 1; pixelSizeTag->n[0] = 3; pixelSizeTag->value = malloc( sizeof(float) * 3 ); mitkIpPicAddTag (picImage, pixelSizeTag); } ((float*)pixelSizeTag->value)[0] = spacing[0]; ((float*)pixelSizeTag->value)[1] = spacing[1]; ((float*)pixelSizeTag->value)[2] = spacing[2]; //set tag "ISG" //ISG == offset/origin transformation matrix(matrix) spancings //ISG == offset0 offset1 offset2 spalte0_0 spalte0_1 spalte0_2 spalte1_0 spalte1_1 spalte1_2 spalte2_0 spalte2_1 spalte2_2 spacing0 spacing1 spacing2 mitkIpPicTSV_t *geometryTag; geometryTag = mitkIpPicQueryTag( picImage, "ISG" ); if (!geometryTag) { geometryTag = (mitkIpPicTSV_t *) malloc( sizeof(mitkIpPicTSV_t) ); geometryTag->type = mitkIpPicFloat; geometryTag->bpe = 32; strcpy(geometryTag->tag, "ISG"); geometryTag->dim = 2; geometryTag->n[0] = 3; geometryTag->n[1] = 4; geometryTag->value = malloc( sizeof(float) * 3 * 4 ); mitkIpPicAddTag (picImage, geometryTag); } const AffineTransform3D::OffsetType& offset = slicedGeometry->GetIndexToWorldTransform()->GetOffset(); ((float*)geometryTag->value)[0] = offset[0]; ((float*)geometryTag->value)[1] = offset[1]; ((float*)geometryTag->value)[2] = offset[2]; const AffineTransform3D::MatrixType& matrix = slicedGeometry->GetIndexToWorldTransform()->GetMatrix(); const AffineTransform3D::MatrixType::ValueType* row0 = matrix[0]; const AffineTransform3D::MatrixType::ValueType* row1 = matrix[1]; const AffineTransform3D::MatrixType::ValueType* row2 = matrix[2]; Vector3D v; FillVector3D(v, row0[0], row1[0], row2[0]); v.Normalize(); ((float*)geometryTag->value)[3] = v[0]; ((float*)geometryTag->value)[4] = v[1]; ((float*)geometryTag->value)[5] = v[2]; FillVector3D(v, row0[1], row1[1], row2[1]); v.Normalize(); ((float*)geometryTag->value)[6] = v[0]; ((float*)geometryTag->value)[7] = v[1]; ((float*)geometryTag->value)[8] = v[2]; ((float*)geometryTag->value)[9] = spacing[0]; ((float*)geometryTag->value)[10] = spacing[1]; ((float*)geometryTag->value)[11] = spacing[2]; } PicFileReader::ConvertHandedness(picImage); // flip upside-down in MITK coordinates // Following line added to detect write errors. If saving .pic files from the plugin is broken again, // please report a bug, don't just remove this line! int ret = MITKIpPicPut((char*)(m_FileName.c_str()), picImage); if (ret != 0) { PicFileReader::ConvertHandedness(picImage); // flip back from upside-down state throw std::ios_base::failure("Error during .pic file writing in "__FILE__); } PicFileReader::ConvertHandedness(picImage); // flip back from upside-down state } void mitk::PicFileWriter::SetInputImage( Image* image ) { this->ProcessObject::SetNthInput( 0, image ); } const mitk::Image* mitk::PicFileWriter::GetInput() { if ( this->GetNumberOfInputs() < 1 ) { MITK_ERROR << "No input image present."; return NULL; } else { return static_cast< const Image * >( this->ProcessObject::GetInput( 0 ) ); } } int mitk::PicFileWriter::MITKIpPicPut( char *outfile_name, mitkIpPicDescriptor *pic ) { FILE* outfile; mitkIpUInt4_t len; mitkIpUInt4_t tags_len; if( pic->info->write_protect ) { fprintf( stderr, "mitkIpPicPut: sorry, can't write (missing tags !!!)\n" ); //return( -1 ); } if( mitkIpPicEncryptionType(pic) != ' ' ) { fprintf( stderr, "mitkIpPicPut: warning: was encrypted !!!\n" ); } if( outfile_name == NULL ) outfile = stdout; else if( strcmp(outfile_name, "stdout") == 0 ) outfile = stdout; else { mitkIpPicRemoveFile( outfile_name ); // Removed due to linker problems when compiling // an mitk chili plugin using msvc: there appear // unresolved external symbol errors to function // _ipPicGetWriteCompression() /* if( mitkIpPicGetWriteCompression() ) { char buff[1024]; sprintf( buff, "%s.gz", outfile_name ); outfile = (FILE*) mitkIpPicFOpen( buff, "wb" ); // cast to prevent warning. } else */ outfile = fopen( outfile_name, "wb" ); } if( outfile == NULL ) { fprintf( stderr, "mitkIpPicPut: sorry, error opening outfile\n" ); return( -1 ); } tags_len = _mitkIpPicTagsSize( pic->info->tags_head ); len = tags_len + 3 * sizeof(mitkIpUInt4_t) + pic->dim * sizeof(mitkIpUInt4_t); /* write oufile */ if( mitkIpPicEncryptionType(pic) == ' ' ) mitkIpPicFWrite( mitkIpPicVERSION, 1, sizeof(mitkIpPicTag_t), outfile ); else mitkIpPicFWrite( pic->info->version, 1, sizeof(mitkIpPicTag_t), outfile ); mitkIpPicFWriteLE( &len, sizeof(mitkIpUInt4_t), 1, outfile ); mitkIpPicFWriteLE( &(pic->type), sizeof(mitkIpUInt4_t), 1, outfile ); mitkIpPicFWriteLE( &(pic->bpe), sizeof(mitkIpUInt4_t), 1, outfile ); mitkIpPicFWriteLE( &(pic->dim), sizeof(mitkIpUInt4_t), 1, outfile ); mitkIpPicFWriteLE( pic->n, sizeof(mitkIpUInt4_t), pic->dim, outfile ); _mitkIpPicWriteTags( pic->info->tags_head, outfile, mitkIpPicEncryptionType(pic) ); // Removed due to linker problems when compiling // an mitk chili plugin using msvc: there appear // unresolved external symbol errors to function // _ipPicGetWriteCompression() /* if( mitkIpPicGetWriteCompression() ) pic->info->pixel_start_in_file = mitkIpPicFTell( outfile ); else */ pic->info->pixel_start_in_file = ftell( outfile ); if( pic->data ) { size_t number_of_elements = _mitkIpPicElements(pic); size_t bytes_per_element = pic->bpe / 8; size_t number_of_bytes = number_of_elements * bytes_per_element; size_t block_size = 1024*1024; /* Use 1 MB blocks. Make sure that block size is smaller than 2^31 */ size_t number_of_blocks = number_of_bytes / block_size; size_t remaining_bytes = number_of_bytes % block_size; size_t bytes_written = 0; size_t block_nr = 0; mitkIpUInt1_t* data = (mitkIpUInt1_t*) pic->data; assert( data != NULL ); if( pic->type == mitkIpPicNonUniform ) { for ( block_nr = 0 ; block_nr < number_of_blocks ; ++block_nr ) bytes_written += mitkIpPicFWrite( data + ( block_nr * block_size ), 1, block_size, outfile ); bytes_written += mitkIpPicFWrite( data + ( number_of_blocks * block_size ), 1, remaining_bytes, outfile ); } else { for ( block_nr = 0 ; block_nr < number_of_blocks ; ++block_nr ) bytes_written += mitkIpPicFWriteLE( data + ( block_nr * block_size ), 1, block_size, outfile ); bytes_written += mitkIpPicFWriteLE( data + ( number_of_blocks * block_size ), 1, remaining_bytes, outfile ); } if ( bytes_written != number_of_bytes ) { fprintf( stderr, "Error while writing (ferror indicates %u), only %u bytes were written! Eof indicator is %u.\n", ferror(outfile), ( (unsigned int) ( bytes_written ) ), feof(outfile) ); fclose( outfile ); return( -1 ); } } if( outfile != stdout ) { // Removed due to linker problems when compiling // an mitk chili plugin using msvc: there appear // unresolved external symbol errors to function // _ipPicGetWriteCompression() /* if( mitkIpPicGetWriteCompression() ) mitkIpPicFClose( outfile ); else */ fclose( outfile ); } return( 0 ); } std::vector mitk::PicFileWriter::GetPossibleFileExtensions() { std::vector possibleFileExtensions; possibleFileExtensions.push_back(".pic"); return possibleFileExtensions; } diff --git a/Modules/MitkExt/Algorithms/mitkCylindricToCartesianFilter.cpp b/Modules/MitkExt/Algorithms/mitkCylindricToCartesianFilter.cpp index 014e390b20..78defa2e6b 100644 --- a/Modules/MitkExt/Algorithms/mitkCylindricToCartesianFilter.cpp +++ b/Modules/MitkExt/Algorithms/mitkCylindricToCartesianFilter.cpp @@ -1,497 +1,498 @@ /*=================================================================== 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 "mitkCylindricToCartesianFilter.h" #include "mitkImageTimeSelector.h" #include "mitkSlicedGeometry3D.h" #include "mitkPlaneGeometry.h" #include "mitkProperties.h" #include "mitkLegacyAdaptors.h" #include template void _transform(mitkIpPicDescriptor *pic, mitkIpPicDescriptor *dest, float _outsideValue, float *fr, float *fphi, float *fz, short *rt, unsigned int *phit, unsigned int *zt, mitkIpPicDescriptor *coneCutOff_pic) //...t=truncated { T outsideValue = static_cast(_outsideValue); register float f, ft, f0, f1, f2, f3; mitkIpInt2_t ox_size; mitkIpInt2_t nx_size, ny_size, nz_size; int oxy_size, nxy_size; T* orig, *dp, *dest_start; mitkIpInt2_t* coneCutOff=(mitkIpInt2_t*)coneCutOff_pic->data; orig=(T*)pic->data; ox_size=pic->n[0]; oxy_size=ox_size*pic->n[1]; nx_size=dest->n[0]; ny_size=dest->n[1]; nxy_size=nx_size*ny_size; nz_size=dest->n[2]; /*nx_size=360; ny_size=360; nxy_size=nx_size*ny_size; nz_size=256;*/ dest_start=dp=((T*)dest->data)+nxy_size*(nz_size-1); mitkIpInt2_t y; // int size=_mitkIpPicElements(pic); register mitkIpInt2_t x,z; for(y=0;y=0) { x_start=0; x_end=nx_size; } else { x_start=-r0plusphi0; x_end=nx_size+r0plusphi0; for(z=0;ztype=mitkIpPicInt; rt_pic->bpe=16; rt_pic->dim=2; rt_pic->n[0]=rt_pic->n[1]=new_xsize; rt_pic->data=malloc(_mitkIpPicSize(rt_pic)); phit_pic=mitkIpPicNew(); phit_pic->type=mitkIpPicUInt; phit_pic->bpe=32; phit_pic->dim=2; phit_pic->n[0]=phit_pic->n[1]=new_xsize; phit_pic->data=malloc(_mitkIpPicSize(phit_pic)); fr_pic=mitkIpPicNew(); fr_pic->type=mitkIpPicFloat; fr_pic->bpe=32; fr_pic->dim=2; fr_pic->n[0]=fr_pic->n[1]=new_xsize; fr_pic->data=malloc(_mitkIpPicSize(fr_pic)); fphi_pic=mitkIpPicNew(); fphi_pic->type=mitkIpPicFloat; fphi_pic->bpe=32; fphi_pic->dim=2; fphi_pic->n[0]=fphi_pic->n[1]=new_xsize; fphi_pic->data=malloc(_mitkIpPicSize(fphi_pic)); mitkIpInt2_t *rtp=(mitkIpInt2_t*)rt_pic->data, *rt_xzero, rt, phit; mitkIpUInt4_t *phitp=(mitkIpUInt4_t*)phit_pic->data; mitkIpFloat4_t *fr=(mitkIpFloat4_t *)fr_pic->data; mitkIpFloat4_t *fphi=(mitkIpFloat4_t *)fphi_pic->data; mitkIpFloat4_t r, phi, scale=(double)orig_xsize/(double)new_xsize; int x,y,xy0,xy0_orig, oxy_size, new_zsize; oxy_size=orig_xsize*orig_ysize; xy0=(int)(((double)new_xsize)/2+0.5); xy0_orig=(int)(((double)orig_xsize)/2+0.5); new_zsize=(int)(orig_ysize/scale); // \bug y compared to x for(y=0;yanfangen bei -rt+1!*/ // if((x>=-rt) && (xxy0?1.0:-1.0)*scale+xy0_orig; else r=r*(x>xy0?-1.0:1.0)*scale+xy0_orig; rt=(mitkIpInt2_t)r; int xtmp=x; if(x>xy0) xtmp=new_xsize-x; if(rt<0) { r=rt=0; if(xtmp>-*rt_xzero) *rt_xzero=-xtmp; *fr=0; } else if(rt>orig_xsize-1) { r=rt=orig_xsize-1; if(xtmp>-*rt_xzero) *rt_xzero=-xtmp; *fr=0; } else *fr=r-rt; if(*fr<0) *fr=0; } // else // *fr=0; phi=orig_zsize-(yq==0?1:-atan((float)xq/yq)/M_PI+0.5)*orig_zsize; phit=(mitkIpUInt4_t)phi; *fphi=phi-phit; *rtp=rt; *phitp=phit*oxy_size; } } zt=(unsigned int *)malloc(sizeof(unsigned int)*new_zsize); fz=(float *)malloc(sizeof(float)*new_zsize); float *fzp=fz; unsigned int *ztp=zt; int z; float z_step=orig_ysize/(orig_ysize*((float)new_xsize)/orig_xsize); for(z=0;ztype=mitkIpPicInt; coneCutOff_pic->bpe=16; coneCutOff_pic->dim=2; coneCutOff_pic->n[0]=coneCutOff_pic->n[1]=rt_pic->n[0]; coneCutOff_pic->data=malloc(_mitkIpPicSize(coneCutOff_pic)); int i, size=_mitkIpPicElements(rt_pic); mitkIpInt2_t *rt, *ccop, ohx_size, nz_size; mitkIpFloat4_t *fr; a*=(float)rt_pic->n[0]/orig_xsize; b*=(float)rt_pic->n[0]/orig_xsize; ohx_size=orig_xsize/2; nz_size=orig_ysize*rt_pic->n[0]/orig_xsize; rt=(mitkIpInt2_t *)rt_pic->data; fr=(mitkIpFloat4_t*)fr_pic->data; ccop=(mitkIpInt2_t *)coneCutOff_pic->data; for(i=0; i=nz_size) cco=nz_size; *ccop=cco; } } void mitk::CylindricToCartesianFilter::GenerateOutputInformation() { mitk::Image::Pointer output = this->GetOutput(); if ((output->IsInitialized()) && (output->GetPipelineMTime() <= m_TimeOfHeaderInitialization.GetMTime())) return; mitk::Image::ConstPointer input = this->GetInput(); itkDebugMacro(<<"GenerateOutputInformation()"); unsigned int i, *tmpDimensions=new unsigned int[std::max(3u,input->GetDimension())]; tmpDimensions[0]=m_TargetXSize; if(tmpDimensions[0]==0) tmpDimensions[0] = input->GetDimension(0); float scale=((float)tmpDimensions[0])/input->GetDimension(0); tmpDimensions[1] = tmpDimensions[0]; tmpDimensions[2] = (unsigned int)(scale*input->GetDimension(1)); for(i=3;iGetDimension();++i) tmpDimensions[i]=input->GetDimension(i); output->Initialize(input->GetPixelType(), input->GetDimension(), tmpDimensions, input->GetNumberOfChannels()); // initialize the spacing of the output Vector3D spacing = input->GetSlicedGeometry()->GetSpacing(); if(input->GetDimension()>=2) spacing[2]=spacing[1]; else spacing[2] = 1.0; spacing[1] = spacing[0]; spacing *= 1.0/scale; output->GetSlicedGeometry()->SetSpacing(spacing); mitk::Point3iProperty::Pointer pointProp; pointProp = dynamic_cast(input->GetProperty("ORIGIN").GetPointer()); if (pointProp.IsNotNull() ) { itk::Point tp = pointProp->GetValue(); tp[2] = (int)(tmpDimensions[2]-tp[1] * scale-1); tp[0] = tmpDimensions[0]/2; tp[1] = tmpDimensions[0]/2; mitk::Point3iProperty::Pointer pointProp = mitk::Point3iProperty::New(tp); output->SetProperty("ORIGIN", pointProp); } delete [] tmpDimensions; //output->GetSlicedGeometry()->SetGeometry2D(mitk::Image::BuildStandardPlaneGeometry2D(output->GetSlicedGeometry(), tmpDimensions).GetPointer(), 0); //set the timebounds - after SetGeometry2D, so that the already created PlaneGeometry will also receive this timebounds. //@fixme!!! will not work for not evenly timed data! output->GetSlicedGeometry()->SetTimeBounds(input->GetSlicedGeometry()->GetTimeBounds()); output->GetTimeSlicedGeometry()->InitializeEvenlyTimed(output->GetSlicedGeometry(), output->GetTimeSlicedGeometry()->GetTimeSteps()); output->SetPropertyList(input->GetPropertyList()->Clone()); m_TimeOfHeaderInitialization.Modified(); } void mitk::CylindricToCartesianFilter::GenerateData() { mitk::Image::ConstPointer input = this->GetInput(); mitk::Image::Pointer output = this->GetOutput(); mitk::ImageTimeSelector::Pointer timeSelector=mitk::ImageTimeSelector::New(); timeSelector->SetInput(input); mitkIpPicDescriptor* pic_transformed=NULL; pic_transformed = mitkIpPicNew(); pic_transformed->dim=3; pic_transformed->bpe = output->GetPixelType().GetBpe(); //pic_transformed->type = output->GetPixelType().GetType(); pic_transformed->n[0] = output->GetDimension(0); pic_transformed->n[1] = output->GetDimension(1); pic_transformed->n[2] = output->GetDimension(2); pic_transformed->data=malloc(_mitkIpPicSize(pic_transformed)); int nstart, nmax; int tstart, tmax; tstart=output->GetRequestedRegion().GetIndex(3); nstart=output->GetRequestedRegion().GetIndex(4); tmax=tstart+output->GetRequestedRegion().GetSize(3); nmax=nstart+output->GetRequestedRegion().GetSize(4); if(zt==NULL) { timeSelector->SetChannelNr(nstart); timeSelector->SetTimeNr(tstart); buildTransformShortCuts(input->GetDimension(0),input->GetDimension(1), input->GetDimension(2), output->GetDimension(0), rt_pic, phit_pic, fr_pic, fphi_pic, zt, fz); // query the line limiting the sector a=b=0; mitk::FloatProperty::Pointer prop; prop = dynamic_cast(input->GetProperty("SECTOR LIMITING LINE SLOPE").GetPointer()); if (prop.IsNotNull() ) a = prop->GetValue(); prop = dynamic_cast(input->GetProperty("SECTOR LIMITING LINE OFFSET").GetPointer()); if (prop.IsNotNull() ) b = prop->GetValue(); buildConeCutOffShortCut(input->GetDimension(0),input->GetDimension(1), rt_pic, fr_pic, a, b, coneCutOff_pic); // mitkIpPicPut("C:\\temp\\rt_90.pic",rt_pic); //mitkIpPicPut("C:\\temp\\coneCutOff.pic", coneCutOff_pic); } int n,t; for(n=nstart;nGetNumberOfChannels();++n) { timeSelector->SetChannelNr(n); for(t=tstart;tSetTimeNr(t); timeSelector->Update(); // Cast to pic descriptor for the timeSelector image mitkIpPicDescriptor* timeSelectorPic = mitkIpPicNew(); - CastToIpPicDescriptor( timeSelector->GetOutput(), timeSelectorPic ); + mitk::ImageWriteAccessor imageAccess(timeSelector->GetOutput()); + CastToIpPicDescriptor( timeSelector->GetOutput(), &imageAccess, timeSelectorPic ); _mitkIpPicFreeTags(pic_transformed->info->tags_head); pic_transformed->info->tags_head = _mitkIpPicCloneTags(timeSelectorPic->info->tags_head); if(input->GetDimension(2)>1) { mitkIpPicTypeMultiplex9(_transform, timeSelectorPic , pic_transformed, m_OutsideValue, (float*)fr_pic->data, (float*)fphi_pic->data, fz, (short *)rt_pic->data, (unsigned int *)phit_pic->data, zt, coneCutOff_pic); // mitkIpPicPut("1trf.pic",pic_transformed); } else { mitkIpPicDescriptor *doubleSlice = mitkIpPicCopyHeader( timeSelectorPic , NULL); doubleSlice->dim=3; doubleSlice->n[2]=2; doubleSlice->data=malloc(_mitkIpPicSize(doubleSlice)); memcpy(doubleSlice->data, timeSelectorPic->data, _mitkIpPicSize(doubleSlice)/2); mitkIpPicTypeMultiplex9(_transform, doubleSlice, pic_transformed, m_OutsideValue, (float*)fr_pic->data, (float*)fphi_pic->data, fz, (short *)rt_pic->data, (unsigned int *)phit_pic->data, zt, coneCutOff_pic); mitkIpPicFree(doubleSlice); } output->SetVolume(pic_transformed->data, t, n); } } //mitkIpPicPut("outzzzzzzzz.pic",pic_transformed); mitkIpPicFree(pic_transformed); m_TimeOfHeaderInitialization.Modified(); } mitk::CylindricToCartesianFilter::CylindricToCartesianFilter() : m_OutsideValue(0.0), m_TargetXSize(0) { rt_pic = NULL; phit_pic = NULL; fr_pic = NULL; fphi_pic = NULL; coneCutOff_pic = NULL; zt = NULL; fz = NULL; a=b=0.0; } mitk::CylindricToCartesianFilter::~CylindricToCartesianFilter() { if(rt_pic!=NULL) mitkIpPicFree(rt_pic); if(phit_pic!=NULL) mitkIpPicFree(phit_pic); if(fr_pic!=NULL) mitkIpPicFree(fr_pic); if(fphi_pic!=NULL) mitkIpPicFree(fphi_pic); if(coneCutOff_pic!=NULL) mitkIpPicFree(coneCutOff_pic); if(zt != NULL) free(zt); if(fz != NULL) free (fz); } void mitk::CylindricToCartesianFilter::GenerateInputRequestedRegion() { Superclass::GenerateInputRequestedRegion(); mitk::ImageToImageFilter::InputImagePointer input = const_cast< mitk::ImageToImageFilter::InputImageType * > ( this->GetInput() ); mitk::Image::Pointer output = this->GetOutput(); Image::RegionType requestedRegion; requestedRegion = output->GetRequestedRegion(); requestedRegion.SetIndex(0, 0); requestedRegion.SetIndex(1, 0); requestedRegion.SetIndex(2, 0); requestedRegion.SetSize(0, input->GetDimension(0)); requestedRegion.SetSize(1, input->GetDimension(1)); requestedRegion.SetSize(2, input->GetDimension(2)); input->SetRequestedRegion( & requestedRegion ); } diff --git a/Modules/MitkExt/Algorithms/mitkDopplerToStrainRateFilter.cpp b/Modules/MitkExt/Algorithms/mitkDopplerToStrainRateFilter.cpp index 361995c59d..05be5f7a25 100644 --- a/Modules/MitkExt/Algorithms/mitkDopplerToStrainRateFilter.cpp +++ b/Modules/MitkExt/Algorithms/mitkDopplerToStrainRateFilter.cpp @@ -1,384 +1,386 @@ /*=================================================================== 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 "mitkDopplerToStrainRateFilter.h" #include "mitkImageTimeSelector.h" #include "mitkProperties.h" #include "mitkPlaneGeometry.h" #include "mitkLegacyAdaptors.h" #include #include #include void mitk::DopplerToStrainRateFilter::GenerateOutputInformation() { mitk::Image::ConstPointer input = this->GetInput(); mitk::Image::Pointer output = this->GetOutput(); if ((output->IsInitialized()) && (this->GetMTime() <= m_TimeOfHeaderInitialization.GetMTime())) return; itkDebugMacro(<<"GenerateOutputInformation()"); unsigned int i; unsigned int *tmpDimensions = new unsigned int[input->GetDimension()]; for(i=0;iGetDimension();++i) tmpDimensions[i]=input->GetDimension(i); //@todo maybe we should shift the following somehow in ImageToImageFilter output->Initialize(input->GetPixelType(), input->GetDimension(), tmpDimensions, input->GetNumberOfChannels()); output->GetSlicedGeometry()->SetSpacing(input->GetSlicedGeometry()->GetSpacing()); //output->GetSlicedGeometry()->SetGeometry2D(mitk::Image::BuildStandardPlaneGeometry2D(output->GetSlicedGeometry(), tmpDimensions).GetPointer(), 0); //output->GetSlicedGeometry()->SetEvenlySpaced(); //set the timebounds - after SetGeometry2D, so that the already created PlaneGeometry will also receive this timebounds. output->GetSlicedGeometry()->SetTimeBounds(input->GetSlicedGeometry()->GetTimeBounds()); output->SetPropertyList(input->GetPropertyList()->Clone()); delete [] tmpDimensions; m_TimeOfHeaderInitialization.Modified(); } void mitk::DopplerToStrainRateFilter::GenerateData() { mitk::Image::ConstPointer input = this->GetInput(); mitk::Image::Pointer output = this->GetOutput(); mitk::Point3iProperty::Pointer pointProp; pointProp = dynamic_cast(input->GetProperty("ORIGIN").GetPointer()); if (pointProp.IsNotNull() ) { m_Origin = pointProp->GetValue(); } MITK_INFO << "compute Strain Rate Image .... " << std::endl << " origin[0]=" << m_Origin[0] << " origin[1]=" << m_Origin[1] << " origin[2]=" << m_Origin[2] << std::endl << " distance=" << m_Distance << std::endl << " NoStrainIntervall=" << m_NoStrainInterval << std::endl; const Vector3D & spacing = input->GetSlicedGeometry()->GetSpacing(); // MITK_INFO << " in: xres=" << spacing[0] << " yres=" << spacing[1] << " zres=" << spacing[2] << std::endl; mitk::ImageTimeSelector::Pointer timeSelector=mitk::ImageTimeSelector::New(); timeSelector->SetInput(input); mitkIpPicDescriptor* picStrainRate; picStrainRate = mitkIpPicNew(); picStrainRate->dim=3; picStrainRate->bpe = output->GetPixelType().GetBpe(); //picStrainRate->type = output->GetPixelType().GetType(); picStrainRate->n[0] = output->GetDimension(0); picStrainRate->n[1] = output->GetDimension(1); picStrainRate->n[2] = output->GetDimension(2); picStrainRate->data=malloc(_mitkIpPicSize(picStrainRate)); int xDim = picStrainRate->n[0]; int yDim = picStrainRate->n[1]; int zDim = picStrainRate->n[2]; long slice_size = xDim*yDim; long vol_size = slice_size*zDim; mitkIpPicDescriptor *picDoppler; int x,y,z;//,time; // loop-counter int strainRate; // the computed Strain Rate int v1,v2; // velocity and Point p1 and p2 float alpha; // the beam-angle, angle betwen current point and beam-point float dx=0, dy=0; // projection of this->distance to x- and y-axis int x1; // a square, where the velocity v1 lies in int y1; // the points are used for interpolation int minStrainRate=128, maxStrainRate=128; int n, nmax; int t, tmax; t = output->GetRequestedRegion().GetIndex(3); n = output->GetRequestedRegion().GetIndex(4); MITK_INFO << "t = " <data)[y*xDim + x] = (int) ( (alpha/1.6)*128); if (!isAnglePicWritten) ((mitkIpInt1_t *)anglePic->data)[y*xDim + x] = (int) ( dx); #endif } // x } // y //isAnglePicWritten = mitkIpTrue; } // z //isStrainComputed = mitkIpTrue; std::string filenameD; filenameD ="doppler.pic"; mitkIpPicPut(const_cast(filenameD.c_str()),picDoppler); #define WRITE_STRAIN_PIC #ifdef WRITE_STRAIN_PIC char tmpfilename[100]; sprintf(tmpfilename,"strain%d.pic",t);; mitkIpPicPut(tmpfilename,picStrainRate); #endif #ifdef WRITE_ANGLE_PIC std::string filename2; filename2="angle.pic"; mitkIpPicPut(const_cast(filename2.c_str()),anglePic); #endif ((mitkIpUInt1_t *)picStrainRate->data)[0]=0; ((mitkIpUInt1_t *)picStrainRate->data)[1]=255; output->SetVolume(picStrainRate->data, t, n); } } mitkIpPicFree(picStrainRate); #define WRITE_STRAIN_PIC #ifdef WRITE_STRAIN_PIC // Get the StrainRate ipPic descriptor picStrainRate = mitkIpPicNew(); - CastToIpPicDescriptor( output, picStrainRate ); + ImageWriteAccessor imageAccess(output); + CastToIpPicDescriptor( output, &imageAccess, picStrainRate ); std::string filename; filename ="strain.pic"; mitkIpPicPut(const_cast(filename.c_str()),picStrainRate); #endif MITK_INFO << "Strain Rate Image computed.... " << std::endl << " minStrainRate: " << minStrainRate << std::endl << " maxStrainRate: " << maxStrainRate << std::endl; } mitk::DopplerToStrainRateFilter::DopplerToStrainRateFilter() : m_Distance(10), m_NoStrainInterval(2) { m_Origin[0] = 0; m_Origin[1] = 0; m_Origin[2] = 0; } float mitk::DopplerToStrainRateFilter::GetLimit() { return (128/m_Distance); } mitk::DopplerToStrainRateFilter::~DopplerToStrainRateFilter() { } void mitk::DopplerToStrainRateFilter::GenerateInputRequestedRegion() { Superclass::GenerateInputRequestedRegion(); mitk::ImageToImageFilter::InputImagePointer input = const_cast< mitk::ImageToImageFilter::InputImageType * > ( this->GetInput() ); mitk::Image::Pointer output = this->GetOutput(); Image::RegionType requestedRegion; requestedRegion = output->GetRequestedRegion(); requestedRegion.SetIndex(0, 0); requestedRegion.SetIndex(1, 0); requestedRegion.SetIndex(2, 0); //requestedRegion.SetIndex(3, 0); //requestedRegion.SetIndex(4, 0); requestedRegion.SetSize(0, input->GetDimension(0)); requestedRegion.SetSize(1, input->GetDimension(1)); requestedRegion.SetSize(2, input->GetDimension(2)); //requestedRegion.SetSize(3, output->GetDimension(3)); //requestedRegion.SetSize(4, output->GetNumberOfChannels()); input->SetRequestedRegion( & requestedRegion ); }