vtkGdcmReader Class Reference

#include <vtkGdcmReader.h>

List of all members.

Public Member Functions
	vtkTypeRevisionMacro (vtkGdcmReader, vtkImageReader)
void	PrintSelf (ostream &os, vtkIndent indent)
virtual void	RemoveAllFileName (void)
virtual void	AddFileName (const char *name)
virtual void	SetFileName (const char *name)
	vtkSetMacro (AllowLookupTable, int)
	vtkGetMacro (AllowLookupTable, int)
	vtkBooleanMacro (AllowLookupTable, int)
	vtkGetObjectMacro (LookupTable, vtkLookupTable)
Static Public Member Functions
vtkGdcmReader *	New ()
Protected Member Functions
	vtkGdcmReader ()
	~vtkGdcmReader ()
virtual void	ExecuteInformation ()
virtual void	ExecuteData (vtkDataObject *output)
virtual void	BuildFileListFromPattern ()
virtual int	CheckFileCoherence ()
Private Member Functions
void	RemoveAllInternalFileName (void)
void	AddInternalFileName (const char *name)
size_t	LoadImageInMemory (std::string FileName, unsigned char *Dest, const unsigned long UpdateProgressTarget, unsigned long &UpdateProgressCount)
Private Attributes
vtkLookupTable *	LookupTable
vtkTimeStamp	fileTime
int	AllowLookupTable
int	NumColumns
int	NumLines
int	TotalNumberOfPlanes
int	NumComponents
std::string	ImageType
size_t	PixelSize
std::list< std::string >	FileNameList
std::list< std::string >	InternalFileNameList

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Constructor & Destructor Documentation

vtkGdcmReader::vtkGdcmReader (   )  [protected]

Definition at line 83 of file vtkGdcmReader.cxx. References AllowLookupTable, and LookupTable. { this->LookupTable = NULL; this->AllowLookupTable = 0; }

vtkGdcmReader::~vtkGdcmReader (   )  [protected]

Definition at line 89 of file vtkGdcmReader.cxx. References InternalFileNameList, LookupTable, and RemoveAllFileName(). { this->RemoveAllFileName(); this->InternalFileNameList.clear(); if(this->LookupTable) this->LookupTable->Delete(); }

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Member Function Documentation

void vtkGdcmReader::AddFileName (  const char *  name  )  [virtual]

Definition at line 126 of file vtkGdcmReader.cxx. References FileNameList. Referenced by main(). { // 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); delete[] LocalName; this->Modified(); }

void vtkGdcmReader::AddInternalFileName (  const char *  name  )  [private]

Definition at line 613 of file vtkGdcmReader.cxx. References InternalFileNameList. Referenced by BuildFileListFromPattern(). { char * LocalName = new char[strlen(name) + 1]; strcpy(LocalName, name); this->InternalFileNameList.push_back(LocalName); delete[] LocalName; }

void vtkGdcmReader::BuildFileListFromPattern (   )  [protected, virtual]

Definition at line 342 of file vtkGdcmReader.cxx. References AddInternalFileName(), FileNameList, InternalFileNameList, and RemoveAllInternalFileName(). Referenced by CheckFileCoherence(). { this->RemoveAllInternalFileName(); if ((! this->FileNameList.empty()) && this->FileName ) { vtkErrorMacro(<< "Both AddFileName and SetFileName schemes were used"); vtkErrorMacro(<< "No images loaded ! "); return; } if ((! this->FileNameList.empty()) && this->FilePrefix ) { vtkErrorMacro(<< "Both AddFileName and SetFilePrefix schemes were used"); vtkErrorMacro(<< "No images loaded ! "); return; } if (this->FileName && this->FilePrefix) { vtkErrorMacro(<< "Both SetFileName and SetFilePrefix schemes were used"); vtkErrorMacro(<< "No images loaded ! "); return; } if (! this->FileNameList.empty() ) { vtkDebugMacro(<< "Using the AddFileName specified files"); this->InternalFileNameList=this->FileNameList; return; } if (!this->FileName && !this->FilePrefix) { vtkErrorMacro(<< "FileNames are not set. Either use AddFileName() or"); vtkErrorMacro(<< "specify a FileName or FilePrefix."); return; } if( this->FileName ) { // Single file loading (as given with ::SetFileName()): // Case of multi-frame file considered here this->ComputeInternalFileName(this->DataExtent[4]); vtkDebugMacro(<< "Adding file " << this->InternalFileName); this->AddInternalFileName(this->InternalFileName); } else { // Multi file loading (as given with ::SetFilePattern()): for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) { this->ComputeInternalFileName(idx); vtkDebugMacro(<< "Adding file " << this->InternalFileName); this->AddInternalFileName(this->InternalFileName); } } }

int vtkGdcmReader::CheckFileCoherence (   )  [protected, virtual]

Definition at line 417 of file vtkGdcmReader.cxx. References AllowLookupTable, BuildFileListFromPattern(), gdcm::File::GetNumberOfScalarComponents(), gdcm::File::GetNumberOfScalarComponentsRaw(), gdcm::File::GetPixelSize(), gdcm::File::GetPixelType(), gdcm::File::GetXSize(), gdcm::File::GetXSpacing(), gdcm::File::GetYSize(), gdcm::File::GetYSpacing(), gdcm::File::GetZSize(), gdcm::File::GetZSpacing(), gdcm::File::HasLUT(), ImageType, InternalFileNameList, gdcm::File::IsReadable(), NumColumns, NumComponents, and NumLines. Referenced by ExecuteInformation(). { 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 "parsability" // - get the coherence check done: for (std::list<std::string>::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 plane 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; if(*filename == std::string("GDCM_UNREADABLE")) continue; // 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 gdcm::File GdcmFile(filename->c_str() ); if (!GdcmFile.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 = GdcmFile.GetPixelType(); if ( (type != "8U") && (type != "8S") && (type != "16U") && (type != "16S") && (type != "32U") && (type != "32S") ) { vtkErrorMacro(<< "Bad File Type for file " << filename->c_str() << "\n" << " File type found : " << type.c_str() << " (might be 8U, 8S, 16U, 16S, 32U, 32S) \n" << " Removing this file from readed files"); *filename = "GDCM_UNREADABLE"; continue; } // Stage 2: check coherence of the set of files int NX = GdcmFile.GetXSize(); int NY = GdcmFile.GetYSize(); int NZ = GdcmFile.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 = GdcmFile.GetPixelSize(); if( GdcmFile.HasLUT() && this->AllowLookupTable ) { // I could raise an error is AllowLookupTable is on and HasLUT() off this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw(); } else { this->NumComponents = GdcmFile.GetNumberOfScalarComponents(); //rgb or mono } //Set image spacing this->DataSpacing[0] = GdcmFile.GetXSpacing(); this->DataSpacing[1] = GdcmFile.GetYSpacing(); this->DataSpacing[2] = GdcmFile.GetZSpacing(); //Set image origin //this->DataOrigin[0] = GdcmFile.GetXOrigin(); //this->DataOrigin[1] = GdcmFile.GetYOrigin(); //this->DataOrigin[2] = GdcmFile.GetZOrigin(); } } // End of loop on filename // count the loadable number of files and display their number: int NumberCoherentFiles = 0; for (std::list<std::string>::iterator it = InternalFileNameList.begin(); it != InternalFileNameList.end(); ++it) { if (*it != "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; }

void vtkGdcmReader::ExecuteData (  vtkDataObject *  output  )  [protected, virtual]

Definition at line 263 of file vtkGdcmReader.cxx. References InternalFileNameList, LoadImageInMemory(), NumColumns, and NumLines. { if (this->InternalFileNameList.empty()) { vtkErrorMacro(<< "A least a valid FileName must be specified."); return; } // FIXME : extraneous parsing of header is made when allocating OuputData vtkImageData *data = this->AllocateOutputData(output); data->SetExtent(this->DataExtent); 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)) { // 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 * this->NumComponents; //size_t stack_size = StackNumPixels * this->PixelSize; //not used // Allocate pixel data space itself. // 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 = (unsigned char *)data->GetScalarPointer(); for (std::list<std::string>::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 } }

void vtkGdcmReader::ExecuteInformation (   )  [protected, virtual]

Definition at line 156 of file vtkGdcmReader.cxx. References CheckFileCoherence(), fileTime, ImageType, NumColumns, NumLines, and TotalNumberOfPlanes. { if(this->MTime>this->fileTime) { 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 z axis extent to the VOI z axis if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 && (this->DataVOI[4] || this->DataVOI[5])) { this->DataExtent[4] = this->DataVOI[4]; this->DataExtent[5] = this->DataVOI[5]; } // 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] >= this->NumColumns) || (this->DataVOI[2] < 0) || (this->DataVOI[3] >= this->NumLines) || (this->DataVOI[4] < 0) || (this->DataVOI[5] >= this->TotalNumberOfPlanes )) { vtkWarningMacro(<< "The requested VOI is larger than expected extent."); this->DataVOI[0] = 0; this->DataVOI[1] = this->NumColumns - 1; this->DataVOI[2] = 0; this->DataVOI[3] = this->NumLines - 1; this->DataVOI[4] = 0; this->DataVOI[5] = this->TotalNumberOfPlanes - 1; } } // Positionate the Extent. this->DataExtent[0] = 0; this->DataExtent[1] = this->NumColumns - 1; this->DataExtent[2] = 0; this->DataExtent[3] = this->NumLines - 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 do need to set up the data type for downstream filters: if ( ImageType == "8U" ) { vtkDebugMacro(<< "8 bits unsigned image"); this->SetDataScalarTypeToUnsignedChar(); } else if ( ImageType == "8S" ) { vtkErrorMacro(<< "Cannot handle 8 bit signed files"); return; } else if ( ImageType == "16U" ) { vtkDebugMacro(<< "16 bits unsigned image"); this->SetDataScalarTypeToUnsignedShort(); } else if ( ImageType == "16S" ) { vtkDebugMacro(<< "16 bits signed image"); this->SetDataScalarTypeToShort(); //vtkErrorMacro(<< "Cannot handle 16 bit signed files"); } else if ( ImageType == "32U" ) { vtkDebugMacro(<< "32 bits unsigned image"); vtkDebugMacro(<< "WARNING: forced to signed int !"); this->SetDataScalarTypeToInt(); } else if ( ImageType == "32S" ) { vtkDebugMacro(<< "32 bits signed image"); this->SetDataScalarTypeToInt(); } else if ( ImageType == "FD" ) { vtkDebugMacro(<< "64 bits Double image"); this->SetDataScalarTypeToDouble(); } //Set number of scalar components: this->SetNumberOfScalarComponents(this->NumComponents); this->fileTime=this->MTime; } this->Superclass::ExecuteInformation(); }

size_t vtkGdcmReader::LoadImageInMemory (  std::string  FileName, unsigned char *  Dest, const unsigned long  UpdateProgressTarget, unsigned long &  UpdateProgressCount )  [private]

Definition at line 625 of file vtkGdcmReader.cxx. References AllowLookupTable, gdcm::FileHelper::GetFile(), gdcm::FileHelper::GetImageData(), gdcm::FileHelper::GetImageDataRaw(), gdcm::FileHelper::GetImageDataSize(), gdcm::FileHelper::GetLutRGBA(), LookupTable, and NumComponents. Referenced by ExecuteData(). { vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]"); gdcm::FileHelper file( fileName.c_str() ); size_t size; // If the data structure of vtk for image/volume representation // were straigthforwards the following would be enough: // GdcmFile.GetImageDataIntoVector((void*)Dest, size); // But vtk chooses 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 = file.GetFile()->GetXSize(); int numLines = file.GetFile()->GetYSize(); int numPlanes = file.GetFile()->GetZSize(); int lineSize = NumComponents * numColumns * file.GetFile()->GetPixelSize(); int planeSize = lineSize * numLines; unsigned char *src; if( file.GetFile()->HasLUT() && AllowLookupTable ) { size = file.GetImageDataSize(); src = (unsigned char*) file.GetImageDataRaw(); unsigned char *lut = (unsigned char*) file.GetLutRGBA(); if(!this->LookupTable) { this->LookupTable = vtkLookupTable::New(); } this->LookupTable->SetNumberOfTableValues(256); for (int tmp=0; tmp<256; tmp++) { this->LookupTable->SetTableValue(tmp, (float)lut[4*tmp+0]/255.0, (float)lut[4*tmp+1]/255.0, (float)lut[4*tmp+2]/255.0, 1); } this->LookupTable->SetRange(0,255); vtkDataSetAttributes *a = this->GetOutput()->GetPointData(); a->GetScalars()->SetLookupTable(this->LookupTable); free(lut); } else { size = file.GetImageDataSize(); src = (unsigned char*)file.GetImageData(); } unsigned char *dst = dest + planeSize - lineSize; for (int plane = 0; plane < numPlanes; plane++) { for (int line = 0; line < numLines; line++) { // Copy one line at proper destination: memcpy((void*)dst, (void*)src, lineSize); src += lineSize; dst -= lineSize; // Update progress related: if (!(updateProgressCount%updateProgressTarget)) { this->UpdateProgress(updateProgressCount/(50.0*updateProgressTarget)); } updateProgressCount++; } dst += 2 * planeSize; } return size; }

vtkGdcmReader* vtkGdcmReader::New (   )  [static]

Referenced by main().

void vtkGdcmReader::PrintSelf (  ostream &  os, vtkIndent  indent )

Definition at line 99 of file vtkGdcmReader.cxx. References FileNameList. { this->Superclass::PrintSelf(os,indent); os << indent << "Filenames : " << endl; vtkIndent nextIndent = indent.GetNextIndent(); for (std::list<std::string>::iterator it = FileNameList.begin(); it != FileNameList.end(); ++it) { os << nextIndent << it->c_str() << endl ; } }

void vtkGdcmReader::RemoveAllFileName (  void   )  [virtual]

Definition at line 117 of file vtkGdcmReader.cxx. References FileNameList. Referenced by ~vtkGdcmReader(). { this->FileNameList.clear(); this->Modified(); }

void vtkGdcmReader::RemoveAllInternalFileName (  void   )  [private]

Definition at line 605 of file vtkGdcmReader.cxx. References InternalFileNameList. Referenced by BuildFileListFromPattern(). { this->InternalFileNameList.clear(); }

void vtkGdcmReader::SetFileName (  const char *  name  )  [virtual]

Definition at line 140 of file vtkGdcmReader.cxx. References FileNameList. Referenced by main(). { 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. vtkDebugMacro(<< "Clearing all files given with AddFileName"); this->FileNameList.clear(); this->Modified(); }

vtkGdcmReader::vtkBooleanMacro (  AllowLookupTable  , int  )

vtkGdcmReader::vtkGetMacro (  AllowLookupTable  , int  )

vtkGdcmReader::vtkGetObjectMacro (  LookupTable  , vtkLookupTable  )

vtkGdcmReader::vtkSetMacro (  AllowLookupTable  , int  )

vtkGdcmReader::vtkTypeRevisionMacro (  vtkGdcmReader  , vtkImageReader  )

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Member Data Documentation

int vtkGdcmReader::AllowLookupTable [private]

Definition at line 75 of file vtkGdcmReader.h. Referenced by CheckFileCoherence(), LoadImageInMemory(), and vtkGdcmReader().

std::list<std::string> vtkGdcmReader::FileNameList [private]

Definition at line 92 of file vtkGdcmReader.h. Referenced by AddFileName(), BuildFileListFromPattern(), PrintSelf(), RemoveAllFileName(), and SetFileName().

vtkTimeStamp vtkGdcmReader::fileTime [private]

Definition at line 74 of file vtkGdcmReader.h. Referenced by ExecuteInformation().

std::string vtkGdcmReader::ImageType [private]

Definition at line 87 of file vtkGdcmReader.h. Referenced by CheckFileCoherence(), and ExecuteInformation().

std::list<std::string> vtkGdcmReader::InternalFileNameList [private]

Definition at line 100 of file vtkGdcmReader.h. Referenced by AddInternalFileName(), BuildFileListFromPattern(), CheckFileCoherence(), ExecuteData(), RemoveAllInternalFileName(), and ~vtkGdcmReader().

vtkLookupTable* vtkGdcmReader::LookupTable [private]

Definition at line 73 of file vtkGdcmReader.h. Referenced by LoadImageInMemory(), vtkGdcmReader(), and ~vtkGdcmReader().

int vtkGdcmReader::NumColumns [private]

Definition at line 79 of file vtkGdcmReader.h. Referenced by CheckFileCoherence(), ExecuteData(), and ExecuteInformation().

int vtkGdcmReader::NumComponents [private]

Definition at line 85 of file vtkGdcmReader.h. Referenced by CheckFileCoherence(), and LoadImageInMemory().

int vtkGdcmReader::NumLines [private]

Definition at line 81 of file vtkGdcmReader.h. Referenced by CheckFileCoherence(), ExecuteData(), and ExecuteInformation().

size_t vtkGdcmReader::PixelSize [private]

Definition at line 89 of file vtkGdcmReader.h.

int vtkGdcmReader::TotalNumberOfPlanes [private]

Definition at line 83 of file vtkGdcmReader.h. Referenced by ExecuteInformation().

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The documentation for this class was generated from the following files:

• vtkGdcmReader.h
• vtkGdcmReader.cxx

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