X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=cd6ec36b48bc77078dffe8723c58d6c785a33137;hb=327dfe7647e3720b0f3125f9b19397cb9afc0ed3;hp=837df465e8139d9a30e94288c38bbb71e6ec6dc0;hpb=bac2910466f502dec4c1842527aa81a8f83f04b8;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 837df465..cd6ec36b 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/11/16 16:20:23 $ - Version: $Revision: 1.157 $ + Date: $Date: 2005/01/06 20:03:27 $ + Version: $Revision: 1.183 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -17,9 +17,15 @@ =========================================================================*/ #include "gdcmFile.h" +#include "gdcmDocument.h" #include "gdcmDebug.h" #include "gdcmUtil.h" #include "gdcmBinEntry.h" +#include "gdcmHeader.h" +#include "gdcmPixelReadConvert.h" +#include "gdcmPixelWriteConvert.h" +#include "gdcmDocEntryArchive.h" + #include namespace gdcm @@ -28,6 +34,26 @@ 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 + * one sets an a posteriori shadow dictionary (efficiency can be + * seen as a side effect). + */ +File::File( ) +{ + HeaderInternal = new Header( ); + SelfHeader = true; + Initialise(); +} + /** * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 * file (Header only deals with the ... header) @@ -70,30 +96,6 @@ File::File(std::string const & filename ) Initialise(); } -/** - * \brief Factorization for various forms of constructors. - */ -void File::Initialise() -{ - PixelConverter = NULL; //just in case - if ( HeaderInternal->IsReadable() ) - { - ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); - if ( HeaderInternal->HasLUT() ) - { - ImageDataSize = 3 * ImageDataSizeRaw; - } - else - { - ImageDataSize = ImageDataSizeRaw; - } - - PixelConverter = new PixelConvert; - PixelConverter->GrabInformationsFromHeader( HeaderInternal ); - } - SaveInitialValues(); -} - /** * \brief canonical destructor * \note If the Header was created by the File constructor, @@ -101,199 +103,71 @@ void File::Initialise() */ File::~File() { - if( SelfHeader ) + if( PixelReadConverter ) { - delete HeaderInternal; + delete PixelReadConverter; } - HeaderInternal = 0; - - DeleteInitialValues(); - if( PixelConverter ) + if( PixelWriteConverter ) { - delete PixelConverter; + delete PixelWriteConverter; } -} - -/** - * \brief Sets some initial values for the Constructor - * \warning not end user intended - */ -void File::SaveInitialValues() -{ - - PixelRead = -1; // no ImageData read yet. - LastAllocatedPixelDataLength = 0; - Pixel_Data = 0; - - InitialSpp = ""; - InitialPhotInt = ""; - InitialPlanConfig = ""; - InitialBitsAllocated = ""; - InitialHighBit = ""; - - InitialRedLUTDescr = 0; - InitialGreenLUTDescr = 0; - InitialBlueLUTDescr = 0; - InitialRedLUTData = 0; - InitialGreenLUTData = 0; - InitialBlueLUTData = 0; - - if ( HeaderInternal->IsReadable() ) + if( Archive ) { - // the following values *may* be modified - // by File::GetImageDataIntoVectorRaw - // we save their initial value. - InitialSpp = HeaderInternal->GetEntryByNumber(0x0028,0x0002); - InitialPhotInt = HeaderInternal->GetEntryByNumber(0x0028,0x0004); - InitialPlanConfig = HeaderInternal->GetEntryByNumber(0x0028,0x0006); - - InitialBitsAllocated = HeaderInternal->GetEntryByNumber(0x0028,0x0100); - InitialHighBit = HeaderInternal->GetEntryByNumber(0x0028,0x0102); - - // the following entries *may* be removed from the H table - // (NOT deleted ...) by File::GetImageDataIntoVectorRaw - // we keep a pointer on them. - InitialRedLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1101); - InitialGreenLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1102); - InitialBlueLUTDescr = HeaderInternal->GetDocEntryByNumber(0x0028,0x1103); - - InitialRedLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1201); - InitialGreenLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1202); - InitialBlueLUTData = HeaderInternal->GetDocEntryByNumber(0x0028,0x1203); + delete Archive; } -} -/** - * \brief restores some initial values - * \warning not end user intended - */ -void File::RestoreInitialValues() -{ - if ( HeaderInternal->IsReadable() ) - { - // the following values *may* have been modified - // by File::GetImageDataIntoVectorRaw - // we restore their initial value. - if ( InitialSpp != "") - HeaderInternal->SetEntryByNumber(InitialSpp,0x0028,0x0002); - if ( InitialPhotInt != "") - HeaderInternal->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); - if ( InitialPlanConfig != "") - - HeaderInternal->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); - if ( InitialBitsAllocated != "") - HeaderInternal->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); - if ( InitialHighBit != "") - HeaderInternal->SetEntryByNumber(InitialHighBit,0x0028,0x0102); - - // the following entries *may* be have been removed from the H table - // (NOT deleted ...) by File::GetImageDataIntoVectorRaw - // we restore them. - - if (InitialRedLUTDescr) - HeaderInternal->AddEntry(InitialRedLUTDescr); - if (InitialGreenLUTDescr) - HeaderInternal->AddEntry(InitialGreenLUTDescr); - if (InitialBlueLUTDescr) - HeaderInternal->AddEntry(InitialBlueLUTDescr); - - if (InitialRedLUTData) - HeaderInternal->AddEntry(InitialBlueLUTDescr); - if (InitialGreenLUTData) - HeaderInternal->AddEntry(InitialGreenLUTData); - if (InitialBlueLUTData) - HeaderInternal->AddEntry(InitialBlueLUTData); + if( SelfHeader ) + { + delete HeaderInternal; } -} - -/** - * \brief delete initial values (il they were saved) - * of InitialLutDescriptors and InitialLutData - */ -void File::DeleteInitialValues() -{ -// InitialLutDescriptors and InitialLutData -// will have to be deleted if the don't belong any longer -// to the Header H table when the header is deleted... - -// FIXME -// We don't know if the InitialLutData are still in the header or not ! -/* if ( InitialRedLUTDescr ) - delete InitialRedLUTDescr; - - if ( InitialGreenLUTDescr ) - delete InitialGreenLUTDescr; - - if ( InitialBlueLUTDescr ) - delete InitialBlueLUTDescr; - - if ( InitialRedLUTData ) - delete InitialRedLUTData; - - if ( InitialGreenLUTData ) - delete InitialGreenLUTData; - - if ( InitialBlueLUTData ) - delete InitialBlueLUTData;*/ + HeaderInternal = 0; } //----------------------------------------------------------------------------- // Print +void File::Print(std::ostream &os) +{ + HeaderInternal->SetPrintLevel(PrintLevel); + HeaderInternal->Print(os); + + PixelReadConverter->SetPrintLevel(PrintLevel); + PixelReadConverter->Print(os); +} //----------------------------------------------------------------------------- // 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() +{ + if ( PixelWriteConverter->GetUserData() ) + { + return PixelWriteConverter->GetUserDataSize(); + } + + return PixelReadConverter->GetRGBSize(); +} /** - * \brief computes the length (in bytes) we must ALLOCATE to receive the - * image(s) pixels (multiframes taken into account) - * \warning : it is NOT the group 7FE0 length - * (no interest for compressed images). + * \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 */ -int File::ComputeDecompressedPixelDataSizeFromHeader() +size_t File::GetImageDataRawSize() { - // see PS 3.3-2003 : C.7.6.3.2.1 - // - // MONOCHROME1 - // MONOCHROME2 - // PALETTE COLOR - // RGB - // HSV (Retired) - // ARGB (Retired) - // CMYK (Retired) - // YBR_FULL - // YBR_FULL_422 (no LUT, no Palette) - // YBR_PARTIAL_422 - // YBR_ICT - // YBR_RCT - - // LUT's - // ex : gdcm-US-ALOKA-16.dcm - // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data] - // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data] - // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data] - - // ex : OT-PAL-8-face.dcm - // 0028|1201 [US] [Red Palette Color Lookup Table Data] - // 0028|1202 [US] [Green Palette Color Lookup Table Data] - // 0028|1203 [US] [Blue Palette Color Lookup Table Data] - - int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); - // Number of "Bits Allocated" is fixed to 16 when: - // - it is not defined (i.e. it's value is 0) - // - it's 12, since we will expand the image to 16 bits (see - // PixelConvert::ConvertDecompress12BitsTo16Bits() ) - if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) - { - numberBitsAllocated = 16; - } + if ( PixelWriteConverter->GetUserData() ) + { + return PixelWriteConverter->GetUserDataSize(); + } - int DecompressedSize = HeaderInternal->GetXSize() - * HeaderInternal->GetYSize() - * HeaderInternal->GetZSize() - * ( numberBitsAllocated / 8 ) - * HeaderInternal->GetSamplesPerPixel(); - - return DecompressedSize; + return PixelReadConverter->GetRawSize(); } /** @@ -306,83 +180,42 @@ int File::ComputeDecompressedPixelDataSizeFromHeader() * @return Pointer to newly allocated pixel data. * NULL if alloc fails */ -uint8_t* File::GetImageData() +uint8_t *File::GetImageData() { - if ( ! GetDecompressed() ) + if ( PixelWriteConverter->GetUserData() ) { - // If the decompression failed nothing can be done. - return 0; + return PixelWriteConverter->GetUserData(); } - - uint8_t* pixelData; - if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) - { - pixelData = PixelConverter->GetRGB(); - } - else + + if ( ! GetRaw() ) { - // When no LUT or LUT conversion fails, return the decompressed - pixelData = PixelConverter->GetDecompressed(); + // If the decompression failed nothing can be done. + return 0; } -// PIXELCONVERT CLEANME - // Restore the header in a disk-consistent state - // (if user asks twice to get the pixels from disk) - if ( PixelRead != -1 ) // File was "read" before + if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) { - RestoreInitialValues(); - } - if ( PixelConverter->GetRGB() ) - { - // now, it's an RGB image - // Lets's write it in the Header - std::string spp = "3"; // Samples Per Pixel - HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); - std::string rgb = "RGB "; // Photometric Interpretation - HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004); - std::string planConfig = "0"; // Planar Configuration - HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); - PixelRead = 0; // no PixelRaw + return PixelReadConverter->GetRGB(); } else { - if ( HeaderInternal->HasLUT() ) - { - // The LUT interpretation failed - std::string photometricInterpretation = Util::DicomString("MONOCHROME1"); - HeaderInternal->SetEntryByNumber( photometricInterpretation, - 0x0028, 0x0004 ); - PixelRead = 0; // no PixelRaw - } - else - { - if ( PixelConverter->IsDecompressedRGB() ) - { - /////////////////////////////////////////////////// - // now, it's an RGB image - // Lets's write it in the Header - // Droping Palette Color out of the Header - // has been moved to the Write process. - // TODO : move 'values' modification to the write process - // : save also (in order to be able to restore) - // : 'high bit' -when not equal to 'bits stored' + 1 - // : 'bits allocated', when it's equal to 12 ?! - std::string spp = "3"; // Samples Per Pixel - std::string photInt = "RGB "; // Photometric Interpretation - std::string planConfig = "0"; // Planar Configuration - HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); - HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004); - HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); - } - PixelRead = 1; // PixelRaw - } + // When no LUT or LUT conversion fails, return the Raw + return PixelReadConverter->GetRaw(); } +} - // We say the value *is* loaded. - SetPixelData(pixelData); -// END PIXELCONVERT CLEANME - - return pixelData; +/** + * \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 GetRaw(); } /** @@ -410,142 +243,120 @@ uint8_t* File::GetImageData() * @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) +size_t File::GetImageDataIntoVector (void *destination, size_t maxSize) { - if ( ! GetDecompressed() ) + if ( ! GetRaw() ) { // If the decompression failed nothing can be done. return 0; } - if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) { - if ( PixelConverter->GetRGBSize() > maxSize ) + if ( PixelReadConverter->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(); + (void*)PixelReadConverter->GetRGB(), + PixelReadConverter->GetRGBSize() ); + return PixelReadConverter->GetRGBSize(); } // Either no LUT conversion necessary or LUT conversion failed - if ( PixelConverter->GetDecompressedSize() > maxSize ) + if ( PixelReadConverter->GetRawSize() > 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(); + (void*)PixelReadConverter->GetRaw(), + PixelReadConverter->GetRawSize() ); + return PixelReadConverter->GetRawSize(); } /** - * \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 + * \brief Points the internal 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 */ -uint8_t* File::GetImageDataRaw () +void File::SetImageData(uint8_t *inData, size_t expectedSize) { - uint8_t* decompressed = GetDecompressed(); - if ( ! decompressed ) - { - return 0; - } + SetUserData(inData,expectedSize); +} -// PIXELCONVERT CLEANME - // Restore the header in a disk-consistent state - // (if user asks twice to get the pixels from disk) - if ( PixelRead != -1 ) // File was "read" before - { - RestoreInitialValues(); - } - if ( PixelConverter->IsDecompressedRGB() ) - { - /////////////////////////////////////////////////// - // now, it's an RGB image - // Lets's write it in the Header - // Droping Palette Color out of the Header - // has been moved to the Write process. - // TODO : move 'values' modification to the write process - // : save also (in order to be able to restore) - // : 'high bit' -when not equal to 'bits stored' + 1 - // : 'bits allocated', when it's equal to 12 ?! - std::string spp = "3"; // Samples Per Pixel - std::string photInt = "RGB "; // Photometric Interpretation - std::string planConfig = "0"; // Planar Configuration - HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002); - HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004); - HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006); - } +/** + * \brief Set the image datas defined by the user + * \warning When writting the file, this datas are get as default datas to write + */ +void File::SetUserData(uint8_t *data, size_t expectedSize) +{ + PixelWriteConverter->SetUserData(data,expectedSize); +} - // We say the value *is* loaded. -/* GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - - // will be 7fe0, 0010 in standard cases - GetHeader()->SetEntryBinAreaByNumber( decompressed, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());*/ - SetPixelData(decompressed); - - PixelRead = 1; // PixelRaw -// END PIXELCONVERT CLEANME +/** + * \brief Get the image datas defined by the user + * \warning When writting the file, this datas are get as default data to write + */ +uint8_t *File::GetUserData() +{ + return PixelWriteConverter->GetUserData(); +} - return decompressed; +/** + * \brief Get the image data size defined by the user + * \warning When writting the file, this datas are get as default data to write + */ +size_t File::GetUserDataSize() +{ + return PixelWriteConverter->GetUserDataSize(); } -uint8_t* File::GetDecompressed() +/** + * \brief Get the image datas from the file. + * If a LUT is found, the data are expanded to be RGB + */ +uint8_t *File::GetRGBData() { - 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 PixelReadConverter->GetRGB(); +} - return decompressed; +/** + * \brief Get the image data size from the file. + * If a LUT is found, the data are expanded to be RGB + */ +size_t File::GetRGBDataSize() +{ + return PixelReadConverter->GetRGBSize(); } /** - * \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 + * \brief Get the image datas from the file. + * If a LUT is found, the datas are not expanded ! */ -bool File::SetImageData(uint8_t* inData, size_t expectedSize) -{ - HeaderInternal->SetImageDataSize( expectedSize ); -// FIXME : if already allocated, memory leak ! - Pixel_Data = inData; - ImageDataSize = ImageDataSizeRaw = expectedSize; - PixelRead = 1; -// FIXME : 7fe0, 0010 IS NOT set ... - return true; +uint8_t *File::GetRawData() +{ + return PixelReadConverter->GetRaw(); +} + +/** + * \brief Get the image data size from the file. + * If a LUT is found, the data are not expanded ! + */ +size_t File::GetRawDataSize() +{ + return PixelReadConverter->GetRawSize(); } /** @@ -557,7 +368,7 @@ bool File::SetImageData(uint8_t* inData, size_t expectedSize) * @return false if write fails */ -bool File::WriteRawData(std::string const & fileName) +bool File::WriteRawData(std::string const &fileName) { std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); if (!fp1) @@ -565,7 +376,14 @@ bool File::WriteRawData(std::string const & fileName) dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str()); return false; } - fp1.write((char*)Pixel_Data, ImageDataSize); + + if(PixelWriteConverter->GetUserData()) + fp1.write((char*)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize()); + else if(PixelReadConverter->GetRGB()) + fp1.write((char*)PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); + else if(PixelReadConverter->GetRaw()) + fp1.write((char*)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); + fp1.close(); return true; @@ -580,22 +398,25 @@ bool File::WriteRawData(std::string const & fileName) * @return false if write fails */ -bool File::WriteDcmImplVR (std::string const & fileName) +bool File::WriteDcmImplVR (std::string const &fileName) { - return WriteBase(fileName, ImplicitVR); + 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 + * 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) +bool File::WriteDcmExplVR (std::string const &fileName) { - return WriteBase(fileName, ExplicitVR); + SetWriteTypeToDcmExplVR(); + return Write(fileName); } /** @@ -612,43 +433,34 @@ bool File::WriteDcmExplVR (std::string const & fileName) * @return false if write fails */ -bool File::WriteAcr (std::string const & fileName) +bool File::WriteAcr (std::string const &fileName) { - return WriteBase(fileName, ACR); + SetWriteTypeToAcr(); + return Write(fileName); } -//----------------------------------------------------------------------------- -// Protected /** - * \brief NOT a end user inteded function - * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) + * \brief Writes on disk A SINGLE Dicom file, * @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) +bool File::Write(std::string const &fileName) { - if ( PixelRead == -1 && type != ExplicitVR) - { - return false; - } - - std::ofstream* fp1 = new std::ofstream(fileName.c_str(), - std::ios::out | std::ios::binary); - if (fp1 == NULL) - { - dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); - return false; - } - - if ( type == ImplicitVR || type == ExplicitVR ) + switch(WriteType) { - // writing Dicom File Preamble - char filePreamble[128]; - memset(filePreamble, 0, 128); - fp1->write(filePreamble, 128); - fp1->write("DICM", 4); + case ImplicitVR: + SetWriteFileTypeToImplicitVR(); + break; + case ExplicitVR: + SetWriteFileTypeToExplicitVR(); + break; + case ACR: + case ACR_LIBIDO: + SetWriteFileTypeToACR(); + break; + default: + SetWriteFileTypeToExplicitVR(); } // -------------------------------------------------------------- @@ -657,83 +469,459 @@ bool File::WriteBase (std::string const & fileName, FileType type) // 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 - - std::string rows, columns; - if ( HeaderInternal->GetFileType() == ACR_LIBIDO) + if( WriteType == ACR_LIBIDO ) { - rows = HeaderInternal->GetEntryByNumber(0x0028, 0x0010); - columns = HeaderInternal->GetEntryByNumber(0x0028, 0x0011); - - HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0010); - HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0011); + SetWriteToLibido(); + } + else + { + SetWriteToNoLibido(); } // ----------------- End of Special Patch ---------------- - - uint16_t grPixel = HeaderInternal->GetGrPixel(); - uint16_t numPixel = HeaderInternal->GetNumPixel();; - - DocEntry* PixelElement = - GetHeader()->GetDocEntryByNumber(grPixel, numPixel); - - if ( PixelRead == 1 ) - { - // we read pixel 'as is' (no tranformation LUT -> RGB) - PixelElement->SetLength( ImageDataSizeRaw ); + + switch(WriteMode) + { + case WMODE_RAW : + SetWriteToRaw(); + break; + case WMODE_RGB : + SetWriteToRGB(); + break; } - else if ( PixelRead == 0 ) + + bool check = CheckWriteIntegrity(); + if(check) { - // we tranformed GrayLevel pixels + LUT into RGB Pixel - PixelElement->SetLength( ImageDataSize ); + check = HeaderInternal->Write(fileName,WriteType); } - - HeaderInternal->Write(fp1, type); + + RestoreWrite(); + RestoreWriteFileType(); // -------------------------------------------------------------- // 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 ) - { - HeaderInternal->SetEntryByNumber(rows , 0x0028, 0x0010); - HeaderInternal->SetEntryByNumber(columns, 0x0028, 0x0011); - } + RestoreWriteOfLibido(); // ----------------- End of Special Patch ---------------- - fp1->close (); - delete fp1; - return true; + return check; } /** - * \brief Access to the underlying \ref PixelConverter RGBA LUT + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) + * through it's (group, element) and modifies it's content with + * the given value. + * @param content new value (string) to substitute with + * @param group group number of the Dicom Element to modify + * @param element element number of the Dicom Element to modify + */ +bool File::SetEntryByNumber(std::string const &content, + uint16_t group, uint16_t element) +{ + return HeaderInternal->SetEntryByNumber(content,group,element); +} + + +/** + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) + * through it's (group, element) and modifies it's content with + * the given value. + * @param content new value (void* -> uint8_t*) to substitute with + * @param lgth new value length + * @param group group number of the Dicom Element to modify + * @param element element number of the Dicom Element to modify + */ +bool File::SetEntryByNumber(uint8_t *content, int lgth, + uint16_t group, uint16_t element) +{ + return HeaderInternal->SetEntryByNumber(content,lgth,group,element); +} + +/** + * \brief Modifies the value of a given Doc Entry (Dicom Element) + * when it exists. Create it with the given value when unexistant. + * @param content (string) Value to be set + * @param group Group number of the Entry + * @param element Element number of the Entry + * \return pointer to the modified/created Header Entry (NULL when creation + * failed). + */ +bool File::ReplaceOrCreateByNumber(std::string const &content, + uint16_t group, uint16_t element) +{ + return HeaderInternal->ReplaceOrCreateByNumber(content,group,element) != NULL; +} + +/* + * \brief Modifies the value of a given Header Entry (Dicom Element) + * when it exists. Create it with the given value when unexistant. + * A copy of the binArea is made to be kept in the Document. + * @param binArea (binary) value to be set + * @param group Group number of the Entry + * @param element Element number of the Entry + * \return pointer to the modified/created Header Entry (NULL when creation + * failed). + */ +bool File::ReplaceOrCreateByNumber(uint8_t *binArea, int lgth, + uint16_t group, uint16_t element) +{ + return HeaderInternal->ReplaceOrCreateByNumber(binArea,lgth,group,element) != NULL; +} + +/** + * \brief Access to the underlying \ref PixelReadConverter RGBA LUT */ uint8_t* File::GetLutRGBA() { - return PixelConverter->GetLutRGBA(); + return PixelReadConverter->GetLutRGBA(); } //----------------------------------------------------------------------------- -// Private -void File::SetPixelData(uint8_t* data) +// Protected + +/** + * \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(PixelWriteConverter->GetUserData()) + { + 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_RAW : + if( decSize!=PixelWriteConverter->GetUserDataSize() ) + { + dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (Raw)"); + //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (Raw)\n" + // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n"; + return false; + } + break; + case WMODE_RGB : + if( rgbSize!=PixelWriteConverter->GetUserDataSize() ) + { + dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (RGB)"); + //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (RGB)\n" + // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n"; + return false; + } + break; + } + } + + return true; +} + +void File::SetWriteToRaw() +{ + if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) + { + SetWriteToRGB(); + } + else + { + ValEntry *photInt = CopyValEntry(0x0028,0x0004); + if(HeaderInternal->HasLUT()) + { + photInt->SetValue("PALETTE COLOR "); + } + else + { + photInt->SetValue("MONOCHROME1 "); + } + + PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), + PixelReadConverter->GetRawSize()); + + BinEntry *pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(PixelWriteConverter->GetData(),false); + pixel->SetLength(PixelWriteConverter->GetDataSize()); + + Archive->Push(photInt); + Archive->Push(pixel); + } +} + +void File::SetWriteToRGB() +{ + if(HeaderInternal->GetNumberOfScalarComponents()==3) + { + PixelReadConverter->BuildRGBImage(); + + ValEntry *spp = CopyValEntry(0x0028,0x0002); + spp->SetValue("3 "); + + ValEntry *planConfig = CopyValEntry(0x0028,0x0006); + planConfig->SetValue("0 "); + + ValEntry *photInt = CopyValEntry(0x0028,0x0004); + photInt->SetValue("RGB "); + + if(PixelReadConverter->GetRGB()) + { + PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), + PixelReadConverter->GetRGBSize()); + } + else // Raw data + { + PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), + PixelReadConverter->GetRawSize()); + } + + BinEntry *pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); + pixel->SetValue(GDCM_BINLOADED); + pixel->SetBinArea(PixelWriteConverter->GetData(),false); + pixel->SetLength(PixelWriteConverter->GetDataSize()); + + 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 "); + + ValEntry *bitsStored = CopyValEntry(0x0028,0x0101); + bitsStored->SetValue("8 "); + + ValEntry *highBit = CopyValEntry(0x0028,0x0102); + highBit->SetValue("7 "); + + Archive->Push(bitsAlloc); + Archive->Push(bitsStored); + Archive->Push(highBit); + } + } + else + { + SetWriteToRaw(); + } +} + +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() { - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + 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); + + Archive->Push(tss); +} + +void File::SetWriteFileTypeToImplicitVR() +{ + std::string ts = Util::DicomString( + Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() ); + + ValEntry *tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); + + Archive->Push(tss); +} - // Will be 7fe0, 0010 in standard case - DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - if ( currentEntry ) +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"); + Archive->Push(libidoCode); +} + +void File::SetWriteToNoLibido() +{ + ValEntry *recCode = dynamic_cast + (HeaderInternal->GetDocEntryByNumber(0x0008,0x0010)); + if( recCode ) { - if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) - // Flag is to false because datas are kept in the gdcmPixelConvert - binEntry->SetBinArea( data, false ); + if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) + { + ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); + libidoCode->SetValue(""); + 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); +} + +//----------------------------------------------------------------------------- +// Protected +/** + * \brief Factorization for various forms of constructors. + */ +void File::Initialise() +{ + WriteMode = WMODE_RAW; + WriteType = ExplicitVR; + + PixelReadConverter = new PixelReadConvert; + PixelWriteConverter = new PixelWriteConvert; + Archive = new DocEntryArchive( HeaderInternal ); + + if ( HeaderInternal->IsReadable() ) + { + PixelReadConverter->GrabInformationsFromHeader( HeaderInternal ); + } +} + +uint8_t *File::GetRaw() +{ + uint8_t *raw = PixelReadConverter->GetRaw(); + if ( ! raw ) + { + // The Raw image migth not be loaded yet: + std::ifstream *fp = HeaderInternal->OpenFile(); + PixelReadConverter->ReadAndDecompressPixelData( fp ); + if(fp) + HeaderInternal->CloseFile(); + + raw = PixelReadConverter->GetRaw(); + if ( ! raw ) + { + dbg.Verbose(0, "File::GetRaw: read/decompress of " + "pixel data apparently went wrong."); + return 0; + } + } + + return raw; +} + +//----------------------------------------------------------------------------- +// Private + //----------------------------------------------------------------------------- } // end namespace gdcm