X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=035e25c3d5935b736cd172d9be5fe46558427c41;hb=75fe55c7b72932dac378a24e7315071bc0ac9af6;hp=cb69387531a50ab4b7529af62f59cc5c4ecbdb94;hpb=51b61705e90b352de08519835fa1c63b81bca616;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index cb693875..035e25c3 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,7 +1,802 @@ -#include "gdcm.h" + /*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/11/30 14:17:52 $ + Version: $Revision: 1.167 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ -gdcmFile::gdcmFile(string & filename) - :gdcmHeader(filename.c_str()) +#include "gdcmFile.h" +#include "gdcmDocument.h" +#include "gdcmDebug.h" +#include "gdcmUtil.h" +#include "gdcmBinEntry.h" +#include + +namespace gdcm +{ +typedef std::pair IterHT; + +//------------------------------------------------------------------------- +// Constructor / Destructor +/** + * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * file (Header only deals with the ... header) + * Opens (in read only and when possible) an existing file and checks + * for DICOM compliance. Returns NULL on failure. + * It will be up to the user to load the pixels into memory + * (see GetImageData, GetImageDataRaw) + * \note the in-memory representation of all available tags found in + * the DICOM header is post-poned to first header information access. + * This avoid a double parsing of public part of the header when + * user sets an a posteriori shadow dictionary (efficiency can be + * seen as a side effect). + * @param header already built Header + */ +File::File(Header *header) +{ + HeaderInternal = header; + SelfHeader = false; + Initialise(); +} + +/** + * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * file (Header only deals with the ... header) + * Opens (in read only and when possible) an existing file and checks + * for DICOM compliance. Returns NULL on failure. + * It will be up to the user to load the pixels into memory + * (see GetImageData, GetImageDataRaw) + * \note the in-memory representation of all available tags found in + * the DICOM header is post-poned to first header information access. + * This avoid a double parsing of public part of the header when + * one sets an a posteriori shadow dictionary (efficiency can be + * seen as a side effect). + * @param filename file to be opened for parsing + */ +File::File(std::string const & filename ) +{ + HeaderInternal = new Header( filename ); + SelfHeader = true; + Initialise(); +} + +/** + * \brief Factorization for various forms of constructors. + */ +void File::Initialise() +{ + WriteMode = WMODE_DECOMPRESSED; + WriteType = WTYPE_IMPL_VR; + + PixelConverter = new PixelConvert; + Archive = new DocEntryArchive( HeaderInternal ); + + if ( HeaderInternal->IsReadable() ) + { + PixelConverter->GrabInformationsFromHeader( HeaderInternal ); + } + + Pixel_Data = 0; + ImageDataSize = 0; +} + +/** + * \brief canonical destructor + * \note If the Header was created by the File constructor, + * it is destroyed by the File + */ +File::~File() +{ + if( PixelConverter ) + { + delete PixelConverter; + } + if( Archive ) + { + delete Archive; + } + + if( SelfHeader ) + { + delete HeaderInternal; + } + HeaderInternal = 0; +} + +//----------------------------------------------------------------------------- +// Print + +//----------------------------------------------------------------------------- +// Public +/** + * \brief Get the size of the image data + * + * If the image can be RGB (with a lut or by default), the size + * corresponds to the RGB image + * @return The image size + */ +size_t File::GetImageDataSize() +{ + return PixelConverter->GetRGBSize(); +} + +/** + * \brief Get the size of the image data + * + * If the image can be RGB by transformation in a LUT, this + * transformation isn't considered + * @return The raw image size + */ +size_t File::GetImageDataRawSize() +{ + return PixelConverter->GetDecompressedSize(); +} + +/** + * \brief - Allocates necessary memory, + * - Reads the pixels from disk (uncompress if necessary), + * - Transforms YBR pixels, if any, into RGB pixels + * - Transforms 3 planes R, G, B, if any, into a single RGB Plane + * - Transforms single Grey plane + 3 Palettes into a RGB Plane + * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone. + * @return Pointer to newly allocated pixel data. + * NULL if alloc fails + */ +uint8_t* File::GetImageData() +{ + if ( ! GetDecompressed() ) + { + // If the decompression failed nothing can be done. + return 0; + } + + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + return PixelConverter->GetRGB(); + } + else + { + // When no LUT or LUT conversion fails, return the decompressed + return PixelConverter->GetDecompressed(); + } +} + +/** + * \brief + * Read the pixels from disk (uncompress if necessary), + * Transforms YBR pixels, if any, into RGB pixels + * Transforms 3 planes R, G, B, if any, into a single RGB Plane + * Transforms single Grey plane + 3 Palettes into a RGB Plane + * Copies at most MaxSize bytes of pixel data to caller allocated + * memory space. + * \warning This function allows people that want to build a volume + * from an image stack *not to* have, first to get the image pixels, + * and then move them to the volume area. + * It's absolutely useless for any VTK user since vtk chooses + * to invert the lines of an image, that is the last line comes first + * (for some axis related reasons?). Hence he will have + * to load the image line by line, starting from the end. + * VTK users have to call GetImageData + * + * @param destination Address (in caller's memory space) at which the + * pixel data should be copied + * @param maxSize Maximum number of bytes to be copied. When MaxSize + * is not sufficient to hold the pixel data the copy is not + * executed (i.e. no partial copy). + * @return On success, the number of bytes actually copied. Zero on + * failure e.g. MaxSize is lower than necessary. + */ +size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) +{ + if ( ! GetDecompressed() ) + { + // If the decompression failed nothing can be done. + return 0; + } + + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + { + if ( PixelConverter->GetRGBSize() > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; + } + memcpy( destination, + (void*)PixelConverter->GetRGB(), + PixelConverter->GetRGBSize() ); + return PixelConverter->GetRGBSize(); + } + + // Either no LUT conversion necessary or LUT conversion failed + if ( PixelConverter->GetDecompressedSize() > maxSize ) + { + dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" + "than caller's expected MaxSize"); + return 0; + } + memcpy( destination, + (void*)PixelConverter->GetDecompressed(), + PixelConverter->GetDecompressedSize() ); + return PixelConverter->GetDecompressedSize(); +} + +/** + * \brief Allocates necessary memory, + * Transforms YBR pixels (if any) into RGB pixels + * Transforms 3 planes R, G, B (if any) into a single RGB Plane + * Copies the pixel data (image[s]/volume[s]) to newly allocated zone. + * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane + * @return Pointer to newly allocated pixel data. + * \ NULL if alloc fails + */ +uint8_t* File::GetImageDataRaw () +{ + return GetDecompressed(); +} + +uint8_t* File::GetDecompressed() +{ + uint8_t* decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) + { + // The decompressed image migth not be loaded yet: + std::ifstream* fp = HeaderInternal->OpenFile(); + PixelConverter->ReadAndDecompressPixelData( fp ); + if(fp) + HeaderInternal->CloseFile(); + + decompressed = PixelConverter->GetDecompressed(); + if ( ! decompressed ) + { + dbg.Verbose(0, "File::GetDecompressed: read/decompress of " + "pixel data apparently went wrong."); + return 0; + } + } + + return decompressed; +} + +/** + * \brief Points the internal Pixel_Data pointer to the callers inData + * image representation, BUT WITHOUT COPYING THE DATA. + * 'image' Pixels are presented as C-like 2D arrays : line per line. + * 'volume'Pixels are presented as C-like 3D arrays : plane per plane + * \warning Since the pixels are not copied, it is the caller's responsability + * not to deallocate it's data before gdcm uses them (e.g. with + * the Write() method. + * @param inData user supplied pixel area + * @param expectedSize total image size, in Bytes + * + * @return boolean + */ +bool File::SetImageData(uint8_t* inData, size_t expectedSize) +{ +// FIXME : if already allocated, memory leak ! + Pixel_Data = inData; + ImageDataSize = expectedSize; +// FIXME : 7fe0, 0010 IS NOT set ... + return true; +} + +/** + * \brief Writes on disk A SINGLE Dicom file + * NO test is performed on processor "Endiannity". + * It's up to the user to call his Reader properly + * @param fileName name of the file to be created + * (any already existing file is over written) + * @return false if write fails + */ + +bool File::WriteRawData(std::string const & fileName) +{ + std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); + if (!fp1) + { + dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str()); + return false; + } + fp1.write((char*)Pixel_Data, ImageDataSize); + fp1.close(); + + return true; +} + +/** + * \brief Writes on disk A SINGLE Dicom file, + * using the Implicit Value Representation convention + * NO test is performed on processor "Endiannity". + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails + */ + +bool File::WriteDcmImplVR (std::string const & fileName) +{ + SetWriteTypeToDcmImplVR(); + return Write(fileName); +} + +/** +* \brief Writes on disk A SINGLE Dicom file, + * using the Explicit Value Representation convention + * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails + */ + +bool File::WriteDcmExplVR (std::string const & fileName) +{ + SetWriteTypeToDcmExplVR(); + return Write(fileName); +} + +/** + * \brief Writes on disk A SINGLE Dicom file, + * using the ACR-NEMA convention + * NO test is performed on processor "Endiannity". + * (a l'attention des logiciels cliniques + * qui ne prennent en entrée QUE des images ACR ... + * \warning if a DICOM_V3 header is supplied, + * groups < 0x0008 and shadow groups are ignored + * \warning NO TEST is performed on processor "Endiannity". + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails + */ + +bool File::WriteAcr (std::string const & fileName) +{ + SetWriteTypeToAcr(); + return Write(fileName); +} + +bool File::Write(std::string const& fileName) +{ + switch(WriteType) + { + case WTYPE_IMPL_VR: + return WriteBase(fileName,ImplicitVR); + case WTYPE_EXPL_VR: + return WriteBase(fileName,ExplicitVR); + case WTYPE_ACR: + return WriteBase(fileName,ACR); + } + return(false); +} + +/** + * \brief Access to the underlying \ref PixelConverter RGBA LUT + */ +uint8_t* File::GetLutRGBA() +{ + return PixelConverter->GetLutRGBA(); +} + +//----------------------------------------------------------------------------- +// Protected +/** + * \brief NOT a end user inteded function + * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @param type file type (ExplicitVR, ImplicitVR, ...) + * @return false if write fails + */ +bool File::WriteBase (std::string const & fileName, FileType type) +{ + switch(type) + { + case ImplicitVR: + SetWriteFileTypeToImplicitVR(); + break; + case ExplicitVR: + SetWriteFileTypeToExplicitVR(); + break; + case ACR: + case ACR_LIBIDO: + SetWriteFileTypeToACR(); + break; + default: + SetWriteFileTypeToExplicitVR(); + } + + if( type == ACR_LIBIDO ) + { + SetWriteToLibido(); + } + else + { + SetWriteToNoLibido(); + } + + switch(WriteMode) + { + case WMODE_NATIVE : + SetWriteToNative(); + break; + case WMODE_DECOMPRESSED : + SetWriteToDecompressed(); + break; + case WMODE_RGB : + SetWriteToRGB(); + break; + } + + // -------------------------------------------------------------- + // Special Patch to allow gdcm to re-write ACR-LibIDO formated images + // + // if recognition code tells us we dealt with a LibIDO image + // we reproduce on disk the switch between lineNumber and columnNumber + // just before writting ... + /// \todo the best trick would be *change* the recognition code + /// but pb expected if user deals with, e.g. COMPLEX images +/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO) + { + SetWriteToLibido(); + }*/ + // ----------------- End of Special Patch ---------------- + + bool check = CheckWriteIntegrity(); + if(check) + { + check = HeaderInternal->Write(fileName,type); + } + + // -------------------------------------------------------------- + // Special Patch to allow gdcm to re-write ACR-LibIDO formated images + // + // ...and we restore the Header to be Dicom Compliant again + // just after writting +/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO ) + { + RestoreWriteFromLibido(); + }*/ + // ----------------- End of Special Patch ---------------- + + RestoreWrite(); + RestoreWriteFileType(); + RestoreWriteOfLibido(); + + return check; +} + +/** + * \brief Check the write integrity + * + * The tests made are : + * - verify the size of the image to write with the possible write + * when the user set an image data + * @return true if the check successfulls + */ +bool File::CheckWriteIntegrity() +{ + if(Pixel_Data) + { + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) + { + numberBitsAllocated = 16; + } + + size_t decSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); + size_t rgbSize = decSize; + if( HeaderInternal->HasLUT() ) + rgbSize = decSize * 3; + + switch(WriteMode) + { + case WMODE_NATIVE : + break; + case WMODE_DECOMPRESSED : + if( decSize!=ImageDataSize ) + { + dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect"); + //std::cerr<<"Dec : "<GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(Pixel_Data,false); + pixel->SetLength(ImageDataSize); + + Archive->Push(pixel); + } +} + +void File::SetWriteToDecompressed() +{ + if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) + { + SetWriteToRGB(); + } + else + { + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + if(HeaderInternal->HasLUT()) + { + photInt->SetValue("PALETTE COLOR "); + photInt->SetLength(14); + } + else + { + photInt->SetValue("MONOCHROME1 "); + photInt->SetLength(12); + } + + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + if(Pixel_Data) + { + pixel->SetBinArea(Pixel_Data,false); + pixel->SetLength(ImageDataSize); + } + else + { + pixel->SetBinArea(PixelConverter->GetDecompressed(),false); + pixel->SetLength(PixelConverter->GetDecompressedSize()); + } + + Archive->Push(photInt); + Archive->Push(pixel); + } +} + +void File::SetWriteToRGB() +{ + if(HeaderInternal->GetNumberOfScalarComponents()==3) + { + PixelConverter->BuildRGBImage(); + + ValEntry* spp = CopyValEntry(0x0028,0x0002); + spp->SetValue("3 "); + spp->SetLength(2); + + ValEntry* planConfig = CopyValEntry(0x0028,0x0006); + planConfig->SetValue("0 "); + planConfig->SetLength(2); + + ValEntry* photInt = CopyValEntry(0x0028,0x0004); + photInt->SetValue("RGB "); + photInt->SetLength(4); + + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + if(Pixel_Data) + { + pixel->SetBinArea(Pixel_Data,false); + pixel->SetLength(ImageDataSize); + } + else if(PixelConverter->GetRGB()) + { + pixel->SetBinArea(PixelConverter->GetRGB(),false); + pixel->SetLength(PixelConverter->GetRGBSize()); + } + else // Decompressed data + { + pixel->SetBinArea(PixelConverter->GetDecompressed(),false); + pixel->SetLength(PixelConverter->GetDecompressedSize()); + } + + Archive->Push(spp); + Archive->Push(planConfig); + Archive->Push(photInt); + Archive->Push(pixel); + + // Remove any LUT + Archive->Push(0x0028,0x1101); + Archive->Push(0x0028,0x1102); + Archive->Push(0x0028,0x1103); + Archive->Push(0x0028,0x1201); + Archive->Push(0x0028,0x1202); + Archive->Push(0x0028,0x1203); + + // For old ACR-NEMA + // Thus, we have a RGB image and the bits allocated = 24 and + // samples per pixels = 1 (in the read file) + if(HeaderInternal->GetBitsAllocated()==24) + { + ValEntry* bitsAlloc = CopyValEntry(0x0028,0x0100); + bitsAlloc->SetValue("8 "); + bitsAlloc->SetLength(2); + + ValEntry* bitsStored = CopyValEntry(0x0028,0x0101); + bitsStored->SetValue("8 "); + bitsStored->SetLength(2); + + ValEntry* highBit = CopyValEntry(0x0028,0x0102); + highBit->SetValue("7 "); + highBit->SetLength(2); + + Archive->Push(bitsAlloc); + Archive->Push(bitsStored); + Archive->Push(highBit); + } + } + else + { + SetWriteToDecompressed(); + } +} + +void File::RestoreWrite() +{ + Archive->Restore(0x0028,0x0002); + Archive->Restore(0x0028,0x0004); + Archive->Restore(0x0028,0x0006); + Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + + // For old ACR-NEMA (24 bits problem) + Archive->Restore(0x0028,0x0100); + Archive->Restore(0x0028,0x0101); + Archive->Restore(0x0028,0x0102); + + // For the LUT + Archive->Restore(0x0028,0x1101); + Archive->Restore(0x0028,0x1102); + Archive->Restore(0x0028,0x1103); + Archive->Restore(0x0028,0x1201); + Archive->Restore(0x0028,0x1202); + Archive->Restore(0x0028,0x1203); +} + +void File::SetWriteFileTypeToACR() +{ + Archive->Push(0x0002,0x0010); +} + +void File::SetWriteFileTypeToExplicitVR() { - + std::string ts = Util::DicomString( + Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() ); + + ValEntry* tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); + tss->SetLength(ts.length()); + + Archive->Push(tss); +} + +void File::SetWriteFileTypeToImplicitVR() +{ + std::string ts = Util::DicomString( + Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() ); + + ValEntry* tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); + tss->SetLength(ts.length()); } + +void File::RestoreWriteFileType() +{ + Archive->Restore(0x0002,0x0010); +} + +void File::SetWriteToLibido() +{ + ValEntry *oldRow = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); + ValEntry *oldCol = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); + + if( oldRow && oldCol ) + { + std::string rows, columns; + + ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); + ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); + + newRow->Copy(oldCol); + newCol->Copy(oldRow); + + newRow->SetValue(oldCol->GetValue()); + newCol->SetValue(oldRow->GetValue()); + + Archive->Push(newRow); + Archive->Push(newCol); + } + + ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); + libidoCode->SetValue("ACRNEMA_LIBIDO_1.1"); + libidoCode->SetLength(10); + Archive->Push(libidoCode); +} + +void File::SetWriteToNoLibido() +{ + ValEntry *recCode = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0008,0x0010)); + if( recCode ) + { + if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) + { + ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); + libidoCode->SetValue(""); + libidoCode->SetLength(0); + Archive->Push(libidoCode); + } + } +} + +void File::RestoreWriteOfLibido() +{ + Archive->Restore(0x0028,0x0010); + Archive->Restore(0x0028,0x0011); + Archive->Restore(0x0008,0x0010); +} + +ValEntry* File::CopyValEntry(uint16_t group,uint16_t element) +{ + DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); + ValEntry* newE; + + if(oldE) + { + newE = new ValEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else + { + newE = GetHeader()->NewValEntryByNumber(group,element); + } + + return(newE); +} + +BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) +{ + DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); + BinEntry* newE; + + if(oldE) + { + newE = new BinEntry(oldE->GetDictEntry()); + newE->Copy(oldE); + } + else + { + newE = GetHeader()->NewBinEntryByNumber(group,element); + } + + + return(newE); +} + +//----------------------------------------------------------------------------- +// Private + +//----------------------------------------------------------------------------- +} // end namespace gdcm +