X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=vtk%2FvtkGdcmReader.cxx;h=02f05672b4f7c49687c54acba1ff250152386a69;hb=c34ecaa3bf4a10a611d4324686a8c25e93d805b8;hp=eaba22fe655e3b7cbf7a4ce250da8e55aa3e8488;hpb=90a2b8eeadb9d5afb2bc165b080f8a4622f5deb4;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index eaba22fe..02f05672 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,9 +1,9 @@ -// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.1 2003/05/05 14:13:59 frog Exp $ -#include "vtkGdcmReader.h" -#include "vtkByteSwap.h" +// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.15 2003/07/07 09:10:33 regrain Exp $ #include -#include "vtkObjectFactory.h" -#include "vtkImageFlip.h" +#include +#include +#include +#include "vtkGdcmReader.h" #include "gdcm.h" vtkGdcmReader::vtkGdcmReader() @@ -15,12 +15,281 @@ vtkGdcmReader::vtkGdcmReader() vtkGdcmReader::~vtkGdcmReader() { // FIXME free memory + this->RemoveAllFileName(); + this->InternalFileNameList.clear(); +} + +//---------------------------------------------------------------------------- +// Remove all files from the list of images to read. +void vtkGdcmReader::RemoveAllFileName(void) +{ + this->FileNameList.clear(); +} + +//---------------------------------------------------------------------------- +// Adds a file name to the list of images to read. +void vtkGdcmReader::AddFileName(const char* name) +{ + // We need to bypass the const pointer [since list<>.push_bash() only + // takes a char* (but not a const char*)] by making a local copy: + char * LocalName = new char[strlen(name) + 1]; + strcpy(LocalName, name); + this->FileNameList.push_back(LocalName); + this->Modified(); + delete[] LocalName; +} + +//---------------------------------------------------------------------------- +// Sets up a filename to be read. +void vtkGdcmReader::SetFileName(const char *name) { + vtkImageReader2::SetFileName(name); + // Since we maintain a list of filenames, when building a volume, + // (see vtkGdcmReader::AddFileName), we additionaly need to purge + // this list when we manually positionate the filename. + this->FileNameList.clear(); + this->Modified(); +} + +//---------------------------------------------------------------------------- +// Adds a file name to the internal list of images to read. +void vtkGdcmReader::RemoveAllInternalFileName(void) +{ + this->InternalFileNameList.clear(); +} + +//---------------------------------------------------------------------------- +// Adds a file name to the internal list of images to read. +void vtkGdcmReader::AddInternalFileName(const char* name) +{ + char * LocalName = new char[strlen(name) + 1]; + strcpy(LocalName, name); + this->InternalFileNameList.push_back(LocalName); + delete[] LocalName; +} + +//---------------------------------------------------------------------------- +// vtkGdcmReader can have the file names specified through two ways: +// (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and +// SetFilePattern() +// (2) By successive calls to vtkGdcmReader::AddFileName() +// When the first method was used by caller we need to update the local +// filename list +void vtkGdcmReader::BuildFileListFromPattern() +{ + if ((! this->FileNameList.empty()) && this->FileName ) + { + vtkErrorMacro("Both file patterns and AddFileName schemes were used"); + vtkErrorMacro("Only the files specified with AddFileName shall be used"); + return; + } + + if (! this->FileNameList.empty() ) + { + vtkDebugMacro("Using the AddFileName specified files"); + this->InternalFileNameList=this->FileNameList; + return; + } + + if (!this->FileName && !this->FilePattern) + { + vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); + vtkErrorMacro("specify a FileName or FilePattern."); + return; + } + + this->RemoveAllInternalFileName(); + for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) + { + this->ComputeInternalFileName(idx); + vtkDebugMacro("Adding file " << this->InternalFileName); + this->AddInternalFileName(this->InternalFileName); + } +} + +//---------------------------------------------------------------------------- +// When more than one filename is specified (i.e. we expect loading +// a stack or volume) we need to check that the corresponding images/volumes +// to be loaded are coherent i.e. to make sure: +// - they all share the same X dimensions +// - they all share the same Y dimensions +// - they all share the same ImageType ( 8 bit signed, or unsigned...) +// +// Eventually, we emit a warning when all the files do NOT share the +// Z dimension, since we can still build a stack but the +// files are not coherent in Z, which is probably a source a trouble... +// When files are not readable (either the file cannot be opened or +// because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE". +// This method returns the total number of planar images to be loaded +// (i.e. an image represents one plane, but a volume represents many planes) +int vtkGdcmReader::CheckFileCoherence() +{ + int ReturnedTotalNumberOfPlanes = 0; // The returned value. + + this->BuildFileListFromPattern(); + if (this->InternalFileNameList.empty()) + { + vtkErrorMacro("FileNames are not set."); + return 0; + } + + bool FoundReferenceFile = false; + int ReferenceNZ = 0; + + // Loop on the filenames: + // - check for their existence and gdcm "parasability" + // - get the coherence check done: + for (std::list::iterator FileName = InternalFileNameList.begin(); + FileName != InternalFileNameList.end(); + ++FileName) + { + // The file is always added in the number of planes + // - If file doesn't exist, it will be replaced by a black place in the + // ExecuteData method + // - If file has more than 1 plane, other planes will be added later to + // to the ReturnedTotalNumberOfPlanes variable counter + ReturnedTotalNumberOfPlanes += 1; + + /////// Stage 0: check for file name: + if(*FileName==std::string("GDCM_UNREADABLE")) + continue; + + /////// Stage 1: check for file readability: + // Stage 1.1: check for file existence. + FILE *fp; + fp = fopen(FileName->c_str(),"rb"); + if (!fp) + { + vtkErrorMacro("Unable to open file " << FileName->c_str()); + vtkErrorMacro("Removing this file from readed files " + << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; + continue; + } + fclose(fp); + + // Stage 1.2: check for Gdcm parsability + gdcmHeader GdcmHeader(FileName->c_str()); + if (!GdcmHeader.IsReadable()) + { + vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str()); + vtkErrorMacro("Removing this file from readed files " + << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; + continue; + } + + // Stage 1.3: further gdcm compatibility on PixelType + std::string type = GdcmHeader.GetPixelType(); + if ( (type != "8U") && (type != "8S") + && (type != "16U") && (type != "16S") + && (type != "32U") && (type != "32S") ) + { + vtkErrorMacro("Bad File Type for file" << FileName->c_str()); + vtkErrorMacro("Removing this file from readed files " + << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; + continue; + } + + /////// Stage 2: check coherence of the set of files + int NX = GdcmHeader.GetXSize(); + int NY = GdcmHeader.GetYSize(); + int NZ = GdcmHeader.GetZSize(); + if (FoundReferenceFile) + { + + // Stage 2.1: mandatory coherence stage: + if ( ( NX != this->NumColumns ) + || ( NY != this->NumLines ) + || ( type != this->ImageType ) ) + { + vtkErrorMacro("This file is not coherent with previous ones" + << FileName->c_str()); + vtkErrorMacro("Removing this file from readed files " + << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; + continue; + } + + // Stage 2.2: optional coherence stage + if ( NZ != ReferenceNZ ) + { + vtkErrorMacro("File is not coherent in Z with previous ones" + << FileName->c_str()); + } + else + { + vtkDebugMacro("File is coherent with previous ones" + << FileName->c_str()); + } + + // Stage 2.3: when the file contains a volume (as opposed to an image), + // notify the caller. + if (NZ > 1) + { + vtkErrorMacro("This file contains multiple planes (images)" + << FileName->c_str()); + } + + // Eventually, this file can be added on the stack. Update the + // full size of the stack + vtkDebugMacro("Number of planes added to the stack: " << NZ); + ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added + continue; + + } else { + // We didn't have a workable reference file yet. Set this one + // as the reference. + FoundReferenceFile = true; + vtkDebugMacro("This file taken as coherence reference:" + << FileName->c_str()); + vtkDebugMacro("Image dimension of reference file as read from Gdcm:" << + NX << " " << NY << " " << NZ); + vtkDebugMacro("Number of planes added to the stack: " << NZ); + // Set aside the size of the image + this->NumColumns = NX; + this->NumLines = NY; + ReferenceNZ = NZ; + ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added + this->ImageType = type; + this->PixelSize = GdcmHeader.GetPixelSize(); + } + } // End of loop on FileName + + ///////// The files we CANNOT load are flaged. On debugging purposes + // count the loadable number of files and display thir number: + int NumberCoherentFiles = 0; + for (std::list::iterator Filename = InternalFileNameList.begin(); + Filename != InternalFileNameList.end(); + ++Filename) + { + if (*Filename != "GDCM_UNREADABLE") + NumberCoherentFiles++; + } + vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles); + + if (ReturnedTotalNumberOfPlanes == 0) + { + vtkErrorMacro("No loadable file."); + } + + vtkDebugMacro("Total number of planes on the stack: " + << ReturnedTotalNumberOfPlanes); + + return ReturnedTotalNumberOfPlanes; } +//---------------------------------------------------------------------------- // Configure the output e.g. WholeExtent, spacing, origin, scalar type... void vtkGdcmReader::ExecuteInformation() { - //FIXME free any old memory + //FIXME free any old memory + this->TotalNumberOfPlanes = this->CheckFileCoherence(); + if ( this->TotalNumberOfPlanes == 0) + { + vtkErrorMacro("File set is not coherent. Exiting..."); + return; + } // if the user has not set the extent, but has set the VOI // set the zaxis extent to the VOI z axis @@ -31,161 +300,217 @@ void vtkGdcmReader::ExecuteInformation() this->DataExtent[5] = this->DataVOI[5]; } - this->ComputeInternalFileName(this->DataExtent[4]); - - // Check for file existence. - FILE *fp; - fp = fopen(this->InternalFileName,"rb"); - if (!fp) - { - vtkErrorMacro("Unable to open file " << this->InternalFileName); - return; - } - fclose(fp); - - // Check for Gdcm parsability - gdcmHeader GdcmHeader(this->InternalFileName); - if (!GdcmHeader.IsReadable()) - { - vtkErrorMacro("Gdcm cannot parse file " << this->InternalFileName); - return; - } - - int NX = GdcmHeader.GetXSize(); - int NY = GdcmHeader.GetYSize(); - int NZ = GdcmHeader.GetZSize(); - vtkDebugMacro("Image dimension as read from Gdcm:" << - NX << " " << NY << " " << NZ); - - if(NZ>1) this->SetFileDimensionality(3); - // When the user has set the VOI, check it's coherence with the file content. if (this->DataVOI[0] || this->DataVOI[1] || this->DataVOI[2] || this->DataVOI[3] || this->DataVOI[4] || this->DataVOI[5]) { if ((this->DataVOI[0] < 0) || - (this->DataVOI[1] >= NX) || + (this->DataVOI[1] >= this->NumColumns) || (this->DataVOI[2] < 0) || - (this->DataVOI[3] >= NY) || + (this->DataVOI[3] >= this->NumLines) || (this->DataVOI[4] < 0) || - (this->DataVOI[5] >= NZ)) + (this->DataVOI[5] >= this->TotalNumberOfPlanes )) { - vtkWarningMacro("The requested VOI is larger than the file's (" - << this->InternalFileName << ") extent "); + vtkWarningMacro("The requested VOI is larger than expected extent."); this->DataVOI[0] = 0; - this->DataVOI[1] = NX - 1; + this->DataVOI[1] = this->NumColumns - 1; this->DataVOI[2] = 0; - this->DataVOI[3] = NY - 1; + this->DataVOI[3] = this->NumLines - 1; this->DataVOI[4] = 0; - this->DataVOI[5] = NZ - 1; + this->DataVOI[5] = this->TotalNumberOfPlanes - 1; } } // Positionate the Extent. this->DataExtent[0] = 0; - this->DataExtent[1] = NX - 1; + this->DataExtent[1] = this->NumColumns - 1; this->DataExtent[2] = 0; - this->DataExtent[3] = NY - 1; - if(this->GetFileDimensionality()==3) + this->DataExtent[3] = this->NumLines - 1; + if(this->InternalFileNameList.size() > 1) { - this->DataExtent[4] = 0; - this->DataExtent[5] = NZ - 1; + this->DataExtent[4] = 0; + this->DataExtent[5] = this->TotalNumberOfPlanes - 1; } // We don't need to positionate the Endian related stuff (by using // this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian() - // since the // reading of the file is done by gdcm - - // But we need to set up the data type for downstream filters: - string type = GdcmHeader.GetPixelType(); - if ( type == "8U" ) + // since the reading of the file is done by gdcm. + // But we do need to set up the data type for downstream filters: + if ( ImageType == "8U" ) { vtkDebugMacro("8 bits unsigned image"); this->SetDataScalarTypeToUnsignedChar(); } - else if ( type == "8S" ) + else if ( ImageType == "8S" ) { vtkErrorMacro("Cannot handle 8 bit signed files"); return; } - else if ( type == "16U" ) + else if ( ImageType == "16U" ) { vtkDebugMacro("16 bits unsigned image"); this->SetDataScalarTypeToUnsignedShort(); } - else if ( type == "16S" ) + else if ( ImageType == "16S" ) { vtkDebugMacro("16 bits signed image"); this->SetDataScalarTypeToShort(); //vtkErrorMacro("Cannot handle 16 bit signed files"); } - else if ( type == "32U" ) + else if ( ImageType == "32U" ) { vtkDebugMacro("32 bits unsigned image"); vtkDebugMacro("WARNING: forced to signed int !"); this->SetDataScalarTypeToInt(); } - else if ( type == "32S" ) + else if ( ImageType == "32S" ) { vtkDebugMacro("32 bits signed image"); this->SetDataScalarTypeToInt(); } - else - { - vtkErrorMacro("Bad File Type " << this->InternalFileName - << "Type " << type); - return; - } vtkImageReader::ExecuteInformation(); } -// Update -> UpdateData -> Execute -> ExecuteData (see vtkSource.cxx for -// last step. +//---------------------------------------------------------------------------- +// Loads the contents of the image/volume contained by Filename at +// the Dest memory address. Returns the size of the data loaded. +size_t vtkGdcmReader::LoadImageInMemory( + std::string FileName, + unsigned char * Dest, + const unsigned long UpdateProgressTarget, + unsigned long & UpdateProgressCount) +{ + vtkDebugMacro("Copying to memmory image" << FileName.c_str()); + gdcmFile GdcmFile(FileName.c_str()); + size_t size = GdcmFile.GetImageDataSize(); + + // If the data structure of vtk for image/volume representation + // were straigthforwards the following would suffice: + // GdcmFile.GetImageDataIntoVector((void*)Dest, size); + // But vtk chose to invert the lines of an image, that is the last + // line comes first (for some axis related reasons?). Hence we need + // to load the image line by line, starting from the end: + int NumColumns = GdcmFile.GetXSize(); + int NumLines = GdcmFile.GetYSize(); + int NumPlanes = GdcmFile.GetZSize(); + int LineSize = NumColumns * GdcmFile.GetPixelSize(); + unsigned char * Source = (unsigned char*)GdcmFile.GetImageData(); + unsigned char * Destination = Dest + size - LineSize; + + for (int plane = 0; plane < NumPlanes; plane++) + { + for (int line = 0; line < NumLines; line++) + { + // Copy one line at proper destination: + memcpy((void*)Destination, (void*)Source, LineSize); + Source += LineSize; + Destination -= LineSize; + // Update progress related: + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } + UpdateProgressCount++; + } + } + return size; +} + +//---------------------------------------------------------------------------- +// Update => ouput->Update => UpdateData => Execute => ExecuteData +// (see vtkSource.cxx for last step). // This function (redefinition of vtkImageReader::ExecuteData, see // VTK/IO/vtkImageReader.cxx) reads a data from a file. The datas // extent/axes are assumed to be the // same as the file extent/order. void vtkGdcmReader::ExecuteData(vtkDataObject *output) { - if (!this->FileName) + if (this->InternalFileNameList.empty()) { - vtkErrorMacro("A valid FileName must be specified."); + vtkErrorMacro("A least a valid FileName must be specified."); return; } + // FIXME : the bad parse of header is made when allocating OuputData vtkImageData *data = this->AllocateOutputData(output); data->SetExtent(this->DataExtent); - data->GetPointData()->GetScalars()->SetName("ImageFile"); - - int size = - (this->DataExtent[1] - this->DataExtent[0]+1) * - (this->DataExtent[3] - this->DataExtent[2]+1) * - (this->DataExtent[5] - this->DataExtent[4]+1) * - 2; - gdcmFile GdcmFile(this->InternalFileName); - size = GdcmFile.GetImageDataSize(); - unsigned char *mem = new unsigned char [size]; - if ( size != GdcmFile.GetImageDataSize() ) + data->GetPointData()->GetScalars()->SetName("DicomImage-Volume"); + + // Test if output has valid extent + // Prevent memory errors + if((this->DataExtent[1]-this->DataExtent[0]>0) && + (this->DataExtent[3]-this->DataExtent[2]>0) && + (this->DataExtent[5]-this->DataExtent[4]>0)) { - vtkDebugMacro("Inconsistency with GetImageDataSize"); - vtkDebugMacro("Number of scalar components" - << this->NumberOfScalarComponents); - } - GdcmFile.GetImageDataIntoVector((void*)mem, size); - data->GetPointData()->GetScalars()->SetVoidArray(mem, size, 0); - //vtkImageFlip * Flip = vtkImageFlip::New(); - //Flip->SetInput(data); - //Flip->Update(); - //data = Flip->GetOutput(); - //Flip->SetInput(NULL); - this->Modified(); + // The memory size for a full stack of images of course depends + // on the number of planes and the size of each image: + size_t StackNumPixels = this->NumColumns * this->NumLines + * this->TotalNumberOfPlanes; + size_t stack_size = StackNumPixels * this->PixelSize; + // Allocate pixel data space itself. + unsigned char *mem = new unsigned char [stack_size]; + + // Variables for the UpdateProgress. We shall use 50 steps to signify + // the advance of the process: + unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines + * this->TotalNumberOfPlanes + / 50.0); + // The actual advance measure: + unsigned long UpdateProgressCount = 0; + + // Feeling the allocated memory space with each image/volume: + unsigned char * Dest = mem; + for (std::list::iterator FileName = InternalFileNameList.begin(); + FileName != InternalFileNameList.end(); + ++FileName) + { + // Images that were tagged as unreadable in CheckFileCoherence() + // are substituted with a black image to let the caller visually + // notice something wrong is going on: + if (*FileName != "GDCM_UNREADABLE") + { + // Update progress related for good files is made in LoadImageInMemory + Dest += this->LoadImageInMemory(*FileName, Dest, + UpdateProgressTarget, + UpdateProgressCount); + } else { + // We insert a black image in the stack for the user to be aware that + // this image/volume couldn't be loaded. We simply skip one image + // size: + Dest += this->NumColumns * this->NumLines * this->PixelSize; + + // Update progress related for bad files: + UpdateProgressCount += this->NumLines; + if (UpdateProgressTarget > 0) + { + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } + } + } // Else, file not loadable + } // Loop on files + + // The "size" of the vtkScalars data is expressed in number of points, + // and is not the memory size representing those points: + data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0); + this->Modified(); + } } +//---------------------------------------------------------------------------- void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) { vtkImageReader::PrintSelf(os,indent); - //CLEANME os << indent << "TypeSize: " << this->TypeSize << "\n"; + os << indent << "Filenames : " << endl; + vtkIndent nextIndent = indent.GetNextIndent(); + for (std::list::iterator FileName = FileNameList.begin(); + FileName != FileNameList.end(); + ++FileName) + { + os << nextIndent << FileName->c_str() << endl ; + } }