X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmFile.cxx;h=43804b36618688ba894e783abefa4f94850b8ea6;hb=d31dacbd4792e49cccecc51ffd9d93fd71541561;hp=46e1f4c07a03933065249c079d659805c01e5666;hpb=c852120fdb6d542d84f74440b68414fdb52178d7;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 46e1f4c0..43804b36 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/11/24 16:39:18 $ - Version: $Revision: 1.162 $ + Date: $Date: 2004/12/07 13:39:33 $ + Version: $Revision: 1.173 $ 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 @@ -76,27 +82,16 @@ File::File(std::string const & filename ) void File::Initialise() { WriteMode = WMODE_DECOMPRESSED; - WriteType = WTYPE_IMPL_VR; + WriteType = ImplicitVR; - PixelConverter = new PixelConvert; + PixelReadConverter = new PixelReadConvert; + PixelWriteConverter = new PixelWriteConvert; Archive = new DocEntryArchive( HeaderInternal ); if ( HeaderInternal->IsReadable() ) { - ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); - if ( HeaderInternal->HasLUT() ) - { - ImageDataSize = 3 * ImageDataSizeRaw; - } - else - { - ImageDataSize = ImageDataSizeRaw; - } - - PixelConverter->GrabInformationsFromHeader( HeaderInternal ); + PixelReadConverter->GrabInformationsFromHeader( HeaderInternal ); } - - SaveInitialValues(); } /** @@ -106,9 +101,13 @@ void File::Initialise() */ File::~File() { - if( PixelConverter ) + if( PixelReadConverter ) { - delete PixelConverter; + delete PixelReadConverter; + } + if( PixelWriteConverter ) + { + delete PixelWriteConverter; } if( Archive ) { @@ -122,104 +121,33 @@ File::~File() HeaderInternal = 0; } -/** - * \brief Sets some initial values for the Constructor - * \warning not end user intended - */ -void File::SaveInitialValues() -{ - PixelRead = -1; // no ImageData read yet. - Pixel_Data = 0; -} - //----------------------------------------------------------------------------- // Print //----------------------------------------------------------------------------- // Public - /** - * \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 (with a lut or by default), the size + * corresponds to the RGB image + * @return The image size */ -int File::ComputeDecompressedPixelDataSizeFromHeader() -{ - // 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; - } - - int DecompressedSize = HeaderInternal->GetXSize() - * HeaderInternal->GetYSize() - * HeaderInternal->GetZSize() - * ( numberBitsAllocated / 8 ) - * HeaderInternal->GetSamplesPerPixel(); - - return DecompressedSize; -} - -/// Accessor to \ref ImageDataSize size_t File::GetImageDataSize() { - if ( ! GetDecompressed() ) - { - // If the decompression failed nothing can be done. - return 0; - } - - if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) - { - return PixelConverter->GetRGBSize(); - } - else - { - // When no LUT or LUT conversion fails, return the decompressed - return PixelConverter->GetDecompressedSize(); - } + return PixelReadConverter->GetRGBSize(); } -/// Accessor to \ref ImageDataSizeRaw -size_t File::GetImageDataSizeRaw() +/** + * \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() { - if ( ! GetDecompressed() ) - { - // If the decompression failed nothing can be done. - return 0; - } - return PixelConverter->GetDecompressedSize(); + return PixelReadConverter->GetDecompressedSize(); } /** @@ -239,15 +167,15 @@ uint8_t* File::GetImageData() // If the decompression failed nothing can be done. return 0; } - - if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + + if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) { - return PixelConverter->GetRGB(); + return PixelReadConverter->GetRGB(); } else { // When no LUT or LUT conversion fails, return the decompressed - return PixelConverter->GetDecompressed(); + return PixelReadConverter->GetDecompressed(); } } @@ -284,31 +212,31 @@ size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) 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->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(); + (void*)PixelReadConverter->GetDecompressed(), + PixelReadConverter->GetDecompressedSize() ); + return PixelReadConverter->GetDecompressedSize(); } /** @@ -327,18 +255,20 @@ uint8_t* File::GetImageDataRaw () uint8_t* File::GetDecompressed() { - uint8_t* decompressed = PixelConverter->GetDecompressed(); + uint8_t* decompressed = PixelReadConverter->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(); + PixelReadConverter->ReadAndDecompressPixelData( fp ); + if(fp) + HeaderInternal->CloseFile(); + + decompressed = PixelReadConverter->GetDecompressed(); if ( ! decompressed ) { - dbg.Verbose(0, "File::GetDecompressed: read/decompress of " - "pixel data apparently went wrong."); + dbg.Verbose(0, "File::GetDecompressed: read/decompress of " + "pixel data apparently went wrong."); return 0; } } @@ -347,7 +277,7 @@ uint8_t* File::GetDecompressed() } /** - * \brief Points the internal Pixel_Data pointer to the callers inData + * \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 @@ -361,12 +291,8 @@ uint8_t* File::GetDecompressed() */ 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 ... + PixelWriteConverter->SetUserData(inData,expectedSize); + return true; } @@ -387,7 +313,14 @@ 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->GetDecompressed()) + fp1.write((char*)PixelReadConverter->GetDecompressed(), PixelReadConverter->GetDecompressedSize()); + fp1.close(); return true; @@ -444,16 +377,22 @@ bool File::WriteAcr (std::string const & 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); + return WriteBase(fileName); +} + +bool File::SetEntryByNumber(std::string const& content, + uint16_t group, uint16_t element) +{ + HeaderInternal->SetEntryByNumber(content,group,element); + return true; +} + +/** + * \brief Access to the underlying \ref PixelReadConverter RGBA LUT + */ +uint8_t* File::GetLutRGBA() +{ + return PixelReadConverter->GetLutRGBA(); } //----------------------------------------------------------------------------- @@ -466,32 +405,22 @@ bool File::Write(std::string const& fileName) * @param type file type (ExplicitVR, ImplicitVR, ...) * @return false if write fails */ -bool File::WriteBase (std::string const & fileName, FileType type) +bool File::WriteBase (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; - } - - switch(WriteMode) + switch(WriteType) { - case WMODE_NATIVE : - SetWriteToNative(); + case ImplicitVR: + SetWriteFileTypeToImplicitVR(); break; - case WMODE_DECOMPRESSED : - SetWriteToDecompressed(); + case ExplicitVR: + SetWriteFileTypeToExplicitVR(); break; - case WMODE_RGB : - SetWriteToRGB(); + case ACR: + case ACR_LIBIDO: + SetWriteFileTypeToACR(); break; + default: + SetWriteFileTypeToExplicitVR(); } // -------------------------------------------------------------- @@ -502,65 +431,93 @@ bool File::WriteBase (std::string const & fileName, FileType type) // 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) + if( WriteType == ACR_LIBIDO ) { SetWriteToLibido(); - }*/ + } + else + { + SetWriteToNoLibido(); + } // ----------------- End of Special Patch ---------------- - - HeaderInternal->Write(fp1, type); + + switch(WriteMode) + { + case WMODE_DECOMPRESSED : + SetWriteToDecompressed(); + break; + case WMODE_RGB : + SetWriteToRGB(); + break; + } + + bool check = CheckWriteIntegrity(); + if(check) + { + check = HeaderInternal->Write(fileName,WriteType); + } + + 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 ) - { - RestoreWriteFromLibido(); - }*/ + RestoreWriteOfLibido(); // ----------------- End of Special Patch ---------------- - RestoreWrite(); - - - fp1->close (); - delete fp1; - - return true; + return check; } /** - * \brief Access to the underlying \ref PixelConverter RGBA LUT + * \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 */ -uint8_t* File::GetLutRGBA() +bool File::CheckWriteIntegrity() { - return PixelConverter->GetLutRGBA(); -} + if(PixelWriteConverter->GetUserData()) + { + int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); + if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) + { + numberBitsAllocated = 16; + } -//----------------------------------------------------------------------------- -// Private -/** - * \brief Set the pixel datas in the good entry of the Header - */ -void File::SetPixelData(uint8_t* data) -{ - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + size_t decSize = HeaderInternal->GetXSize() + * HeaderInternal->GetYSize() + * HeaderInternal->GetZSize() + * ( numberBitsAllocated / 8 ) + * HeaderInternal->GetSamplesPerPixel(); + size_t rgbSize = decSize; + if( HeaderInternal->HasLUT() ) + rgbSize = decSize * 3; - // Will be 7fe0, 0010 in standard case - DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - if ( currentEntry ) - { - if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) - // Flag is to false because datas are kept in the gdcmPixelConvert - binEntry->SetBinArea( data, false ); + switch(WriteMode) + { + case WMODE_DECOMPRESSED : + if( decSize!=PixelWriteConverter->GetUserDataSize() ) + { + dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect"); + return false; + } + break; + case WMODE_RGB : + if( rgbSize!=PixelWriteConverter->GetUserDataSize() ) + { + dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect"); + return false; + } + break; + } } -} - -void File::SetWriteToNative() -{ -// Nothing to do + + return true; } void File::SetWriteToDecompressed() @@ -575,26 +532,19 @@ void File::SetWriteToDecompressed() if(HeaderInternal->HasLUT()) { photInt->SetValue("PALETTE COLOR "); - photInt->SetLength(14); } else { photInt->SetValue("MONOCHROME1 "); - photInt->SetLength(12); } + PixelWriteConverter->SetReadData(PixelReadConverter->GetDecompressed(), + PixelReadConverter->GetDecompressedSize()); + 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()); - } + pixel->SetBinArea(PixelWriteConverter->GetData(),false); + pixel->SetLength(PixelWriteConverter->GetDataSize()); Archive->Push(photInt); Archive->Push(pixel); @@ -603,45 +553,48 @@ void File::SetWriteToDecompressed() void File::SetWriteToRGB() { - if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) + if(HeaderInternal->GetNumberOfScalarComponents()==3) { - PixelConverter->BuildRGBImage(); + PixelReadConverter->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()) + if(PixelReadConverter->GetRGB()) { - pixel->SetBinArea(PixelConverter->GetRGB(),false); - pixel->SetLength(PixelConverter->GetRGBSize()); + PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), + PixelReadConverter->GetRGBSize()); } else // Decompressed data { - pixel->SetBinArea(PixelConverter->GetDecompressed(),false); - pixel->SetLength(PixelConverter->GetDecompressedSize()); + PixelWriteConverter->SetReadData(PixelReadConverter->GetDecompressed(), + PixelReadConverter->GetDecompressedSize()); } + 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) @@ -649,15 +602,12 @@ void File::SetWriteToRGB() { 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); @@ -681,6 +631,44 @@ void File::RestoreWrite() 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); + + Archive->Push(tss); +} + +void File::SetWriteFileTypeToImplicitVR() +{ + std::string ts = Util::DicomString( + Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() ); + + ValEntry* tss = CopyValEntry(0x0002,0x0010); + tss->SetValue(ts); +} + +void File::RestoreWriteFileType() +{ + Archive->Restore(0x0002,0x0010); } void File::SetWriteToLibido() @@ -704,12 +692,31 @@ void File::SetWriteToLibido() 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( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) + { + ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); + libidoCode->SetValue(""); + Archive->Push(libidoCode); + } + } } -void File::RestoreWriteFromLibido() +void File::RestoreWriteOfLibido() { Archive->Restore(0x0028,0x0010); Archive->Restore(0x0028,0x0011); + Archive->Restore(0x0008,0x0010); } ValEntry* File::CopyValEntry(uint16_t group,uint16_t element) @@ -745,10 +752,12 @@ BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) newE = GetHeader()->NewBinEntryByNumber(group,element); } - return(newE); } +//----------------------------------------------------------------------------- +// Private + //----------------------------------------------------------------------------- } // end namespace gdcm