X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=035e25c3d5935b736cd172d9be5fe46558427c41;hb=75fe55c7b72932dac378a24e7315071bc0ac9af6;hp=c5219ed2f919cbfc2001a8961aef4024931fe7c5;hpb=c42ce41966ee7a572752d7f45ddff25b90515119;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index c5219ed2..035e25c3 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 10:23:47 $ - Version: $Revision: 1.160 $ + 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 @@ -17,6 +17,7 @@ =========================================================================*/ #include "gdcmFile.h" +#include "gdcmDocument.h" #include "gdcmDebug.h" #include "gdcmUtil.h" #include "gdcmBinEntry.h" @@ -75,7 +76,7 @@ File::File(std::string const & filename ) */ void File::Initialise() { - WriteMode = WMODE_RGB; + WriteMode = WMODE_DECOMPRESSED; WriteType = WTYPE_IMPL_VR; PixelConverter = new PixelConvert; @@ -83,20 +84,11 @@ void File::Initialise() if ( HeaderInternal->IsReadable() ) { - ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); - if ( HeaderInternal->HasLUT() ) - { - ImageDataSize = 3 * ImageDataSizeRaw; - } - else - { - ImageDataSize = ImageDataSizeRaw; - } - PixelConverter->GrabInformationsFromHeader( HeaderInternal ); } - SaveInitialValues(); + Pixel_Data = 0; + ImageDataSize = 0; } /** @@ -122,73 +114,33 @@ 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() +size_t File::GetImageDataSize() { - // 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; - } + return PixelConverter->GetRGBSize(); +} - int DecompressedSize = HeaderInternal->GetXSize() - * HeaderInternal->GetYSize() - * HeaderInternal->GetZSize() - * ( numberBitsAllocated / 8 ) - * HeaderInternal->GetSamplesPerPixel(); - - return DecompressedSize; +/** + * \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(); } /** @@ -208,76 +160,16 @@ uint8_t* File::GetImageData() // If the decompression failed nothing can be done. return 0; } - - uint8_t* pixelData; + if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) { - pixelData = PixelConverter->GetRGB(); + return PixelConverter->GetRGB(); } else { // When no LUT or LUT conversion fails, return the decompressed - pixelData = PixelConverter->GetDecompressed(); - } - -/*// 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->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 PixelConverter->GetDecompressed(); } - 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 - } - } - - // We say the value *is* loaded. - SetPixelData(pixelData); -// END PIXELCONVERT CLEANME*/ - - return pixelData; } /** @@ -351,45 +243,7 @@ size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) */ uint8_t* File::GetImageDataRaw () { - uint8_t* decompressed = GetDecompressed(); - if ( ! decompressed ) - { - 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 - { - 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); - } - - // We say the value *is* loaded. - SetPixelData(decompressed); - - PixelRead = 1; // PixelRaw -// END PIXELCONVERT CLEANME*/ - - return decompressed; + return GetDecompressed(); } uint8_t* File::GetDecompressed() @@ -400,12 +254,14 @@ uint8_t* File::GetDecompressed() // The decompressed image migth not be loaded yet: std::ifstream* fp = HeaderInternal->OpenFile(); PixelConverter->ReadAndDecompressPixelData( fp ); - if(fp) HeaderInternal->CloseFile(); + if(fp) + HeaderInternal->CloseFile(); + decompressed = PixelConverter->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; } } @@ -428,11 +284,9 @@ 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; + ImageDataSize = expectedSize; // FIXME : 7fe0, 0010 IS NOT set ... return true; } @@ -523,6 +377,14 @@ bool File::Write(std::string const& fileName) return(false); } +/** + * \brief Access to the underlying \ref PixelConverter RGBA LUT + */ +uint8_t* File::GetLutRGBA() +{ + return PixelConverter->GetLutRGBA(); +} + //----------------------------------------------------------------------------- // Protected /** @@ -535,28 +397,31 @@ bool File::Write(std::string const& fileName) */ bool File::WriteBase (std::string const & fileName, FileType type) { -/* if ( PixelRead == -1 && type != ExplicitVR) + switch(type) { - return false; - }*/ + case ImplicitVR: + SetWriteFileTypeToImplicitVR(); + break; + case ExplicitVR: + SetWriteFileTypeToExplicitVR(); + break; + case ACR: + case ACR_LIBIDO: + SetWriteFileTypeToACR(); + break; + default: + SetWriteFileTypeToExplicitVR(); + } - std::ofstream* fp1 = new std::ofstream(fileName.c_str(), - std::ios::out | std::ios::binary); - if (fp1 == NULL) + if( type == ACR_LIBIDO ) { - dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); - return false; + SetWriteToLibido(); } - - if ( type == ImplicitVR || type == ExplicitVR ) + else { - // writing Dicom File Preamble - char filePreamble[128]; - memset(filePreamble, 0, 128); - fp1->write(filePreamble, 128); - fp1->write("DICM", 4); + SetWriteToNoLibido(); } - + switch(WriteMode) { case WMODE_NATIVE : @@ -576,142 +441,212 @@ 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 ( HeaderInternal->GetFileType() == ACR_LIBIDO) { SetWriteToLibido(); - } + }*/ // ----------------- 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 ); - } - else if ( PixelRead == 0 ) + + bool check = CheckWriteIntegrity(); + if(check) { - // we tranformed GrayLevel pixels + LUT into RGB Pixel - PixelElement->SetLength( ImageDataSize ); - }*/ - - HeaderInternal->Write(fp1, type); + 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 ) +/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO ) { RestoreWriteFromLibido(); - } + }*/ // ----------------- End of Special Patch ---------------- RestoreWrite(); + RestoreWriteFileType(); + RestoreWriteOfLibido(); - - 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(Pixel_Data) + { + 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_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->HasLUT() ) || (!PixelConverter->BuildRGBImage())) - if(HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage()) + if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) { SetWriteToRGB(); } else { ValEntry* photInt = CopyValEntry(0x0028,0x0004); - photInt->SetValue("MONOCHROME1 "); - photInt->SetLength(12); + 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); - pixel->SetBinArea(PixelConverter->GetDecompressed(),false); - pixel->SetLength(PixelConverter->GetDecompressedSize()); + 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); } -/* else - { - SetWriteToRGB(); - } */ } void File::SetWriteToRGB() { - if(PixelConverter->BuildRGBImage()) + if(HeaderInternal->GetNumberOfScalarComponents()==3) { + PixelConverter->BuildRGBImage(); + ValEntry* spp = CopyValEntry(0x0028,0x0002); spp->SetValue("3 "); spp->SetLength(2); - ValEntry* photInt = CopyValEntry(0x0028,0x0004); - photInt->SetValue("RGB "); - photInt->SetLength(4); - 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); - pixel->SetBinArea(PixelConverter->GetRGB(),false); - pixel->SetLength(PixelConverter->GetRGBSize()); + 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(photInt); 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 { @@ -725,6 +660,51 @@ void File::RestoreWrite() 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() @@ -748,12 +728,33 @@ void File::SetWriteToLibido() 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::RestoreWriteFromLibido() +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) @@ -793,6 +794,9 @@ BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) return(newE); } +//----------------------------------------------------------------------------- +// Private + //----------------------------------------------------------------------------- } // end namespace gdcm