X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=395f8bd2fff40130a54929959188ed82ce472519;hb=4beda181275414e5cba990113f8d16424b2c09e6;hp=c7f72f23ee4e4ba4f4f422874feabce4a27ab43f;hpb=ba78e6c6d47d6db1528e8e88e5ebde7296a26692;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index c7f72f23..395f8bd2 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/12/03 20:16:58 $ - Version: $Revision: 1.171 $ + Date: $Date: 2005/01/06 14:49:16 $ + Version: $Revision: 1.181 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -34,6 +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) @@ -76,24 +96,6 @@ File::File(std::string const & filename ) Initialise(); } -/** - * \brief Factorization for various forms of constructors. - */ -void File::Initialise() -{ - WriteMode = WMODE_DECOMPRESSED; - WriteType = ImplicitVR; - - PixelReadConverter = new PixelReadConvert; - PixelWriteConverter = new PixelWriteConvert; - Archive = new DocEntryArchive( HeaderInternal ); - - if ( HeaderInternal->IsReadable() ) - { - PixelReadConverter->GrabInformationsFromHeader( HeaderInternal ); - } -} - /** * \brief canonical destructor * \note If the Header was created by the File constructor, @@ -123,6 +125,14 @@ File::~File() //----------------------------------------------------------------------------- // Print +void File::Print(std::ostream &os) +{ + HeaderInternal->SetPrintLevel(PrintLevel); + HeaderInternal->Print(os); + + PixelReadConverter->SetPrintLevel(PrintLevel); + PixelReadConverter->Print(os); +} //----------------------------------------------------------------------------- // Public @@ -135,6 +145,11 @@ File::~File() */ size_t File::GetImageDataSize() { + if ( PixelWriteConverter->GetUserData() ) + { + return PixelWriteConverter->GetUserDataSize(); + } + return PixelReadConverter->GetRGBSize(); } @@ -147,7 +162,12 @@ size_t File::GetImageDataSize() */ size_t File::GetImageDataRawSize() { - return PixelReadConverter->GetDecompressedSize(); + if ( PixelWriteConverter->GetUserData() ) + { + return PixelWriteConverter->GetUserDataSize(); + } + + return PixelReadConverter->GetRawSize(); } /** @@ -162,7 +182,12 @@ size_t File::GetImageDataRawSize() */ uint8_t* File::GetImageData() { - if ( ! GetDecompressed() ) + if ( PixelWriteConverter->GetUserData() ) + { + return PixelWriteConverter->GetUserData(); + } + + if ( ! GetRaw() ) { // If the decompression failed nothing can be done. return 0; @@ -174,11 +199,25 @@ uint8_t* File::GetImageData() } else { - // When no LUT or LUT conversion fails, return the decompressed - return PixelReadConverter->GetDecompressed(); + // When no LUT or LUT conversion fails, return the Raw + return PixelReadConverter->GetRaw(); } } +/** + * \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(); +} + /** * \brief * Read the pixels from disk (uncompress if necessary), @@ -206,7 +245,7 @@ uint8_t* File::GetImageData() */ size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) { - if ( ! GetDecompressed() ) + if ( ! GetRaw() ) { // If the decompression failed nothing can be done. return 0; @@ -227,53 +266,16 @@ size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) } // Either no LUT conversion necessary or LUT conversion failed - if ( PixelReadConverter->GetDecompressedSize() > maxSize ) + if ( PixelReadConverter->GetRawSize() > maxSize ) { dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" "than caller's expected MaxSize"); return 0; } memcpy( destination, - (void*)PixelReadConverter->GetDecompressed(), - PixelReadConverter->GetDecompressedSize() ); - return PixelReadConverter->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 = PixelReadConverter->GetDecompressed(); - if ( ! decompressed ) - { - // The decompressed image migth not be loaded yet: - std::ifstream* fp = HeaderInternal->OpenFile(); - 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."); - return 0; - } - } - - return decompressed; + (void*)PixelReadConverter->GetRaw(), + PixelReadConverter->GetRawSize() ); + return PixelReadConverter->GetRawSize(); } /** @@ -289,11 +291,72 @@ uint8_t* File::GetDecompressed() * * @return boolean */ -bool File::SetImageData(uint8_t* inData, size_t expectedSize) +void File::SetImageData(uint8_t* inData, size_t expectedSize) { - PixelWriteConverter->SetUserData(inData,expectedSize); + SetUserData(inData,expectedSize); +} - return true; +/** + * \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); +} + +/** + * \brief Get the image datas defined by the user + * \warning When writting the file, this datas are get as default datas to write + */ +uint8_t* File::GetUserData() +{ + return PixelWriteConverter->GetUserData(); +} + +/** + * \brief Get the image data size defined by the user + * \warning When writting the file, this datas are get as default datas to write + */ +size_t File::GetUserDataSize() +{ + return PixelWriteConverter->GetUserDataSize(); +} + +/** + * \brief Get the image datas from the file. + * If a LUT is found, the datas are expanded to be RGB + */ +uint8_t* File::GetRGBData() +{ + return PixelReadConverter->GetRGB(); +} + +/** + * \brief Get the image data size from the file. + * If a LUT is found, the datas are expanded to be RGB + */ +size_t File::GetRGBDataSize() +{ + return PixelReadConverter->GetRGBSize(); +} + +/** + * \brief Get the image datas from the file. + * If a LUT is found, the datas are not expanded ! + */ +uint8_t* File::GetRawData() +{ + return PixelReadConverter->GetRaw(); +} + +/** + * \brief Get the image data size from the file. + * If a LUT is found, the datas are not expanded ! + */ +size_t File::GetRawDataSize() +{ + return PixelReadConverter->GetRawSize(); } /** @@ -318,8 +381,8 @@ bool File::WriteRawData(std::string const & fileName) 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()); + else if(PixelReadConverter->GetRaw()) + fp1.write((char*)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); fp1.close(); @@ -344,7 +407,8 @@ bool File::WriteDcmImplVR (std::string const & 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 */ @@ -375,37 +439,13 @@ bool File::WriteAcr (std::string const & fileName) return Write(fileName); } -bool File::Write(std::string const& fileName) -{ - 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(); -} - -//----------------------------------------------------------------------------- -// 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) +bool File::Write(std::string const& fileName) { switch(WriteType) { @@ -443,8 +483,8 @@ bool File::WriteBase (std::string const & fileName) switch(WriteMode) { - case WMODE_DECOMPRESSED : - SetWriteToDecompressed(); + case WMODE_RAW : + SetWriteToRaw(); break; case WMODE_RGB : SetWriteToRGB(); @@ -471,6 +511,78 @@ bool File::WriteBase (std::string const & fileName) return check; } +/** + * \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 value (string) Value to be set + * @param group Group number of the Entry + * @param elem 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 Elem 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 PixelReadConverter->GetLutRGBA(); +} + +//----------------------------------------------------------------------------- +// Protected + /** * \brief Check the write integrity * @@ -500,17 +612,21 @@ bool File::CheckWriteIntegrity() switch(WriteMode) { - case WMODE_DECOMPRESSED : + case WMODE_RAW : if( decSize!=PixelWriteConverter->GetUserDataSize() ) { - dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect"); + 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"); + 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; @@ -520,7 +636,7 @@ bool File::CheckWriteIntegrity() return true; } -void File::SetWriteToDecompressed() +void File::SetWriteToRaw() { if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) { @@ -532,26 +648,19 @@ void File::SetWriteToDecompressed() if(HeaderInternal->HasLUT()) { photInt->SetValue("PALETTE COLOR "); - photInt->SetLength(14); } else { photInt->SetValue("MONOCHROME1 "); - photInt->SetLength(12); } + PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), + PixelReadConverter->GetRawSize()); + BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); pixel->SetValue(GDCM_BINLOADED); - if(PixelWriteConverter->GetUserData()) - { - pixel->SetBinArea(PixelWriteConverter->GetUserData(),false); - pixel->SetLength(PixelWriteConverter->GetUserDataSize()); - } - else - { - pixel->SetBinArea(PixelReadConverter->GetDecompressed(),false); - pixel->SetLength(PixelReadConverter->GetDecompressedSize()); - } + pixel->SetBinArea(PixelWriteConverter->GetData(),false); + pixel->SetLength(PixelWriteConverter->GetDataSize()); Archive->Push(photInt); Archive->Push(pixel); @@ -566,34 +675,29 @@ void File::SetWriteToRGB() 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(PixelWriteConverter->GetUserData()) - { - pixel->SetBinArea(PixelWriteConverter->GetUserData(),false); - pixel->SetLength(PixelWriteConverter->GetUserDataSize()); - } - else if(PixelReadConverter->GetRGB()) + if(PixelReadConverter->GetRGB()) { - pixel->SetBinArea(PixelReadConverter->GetRGB(),false); - pixel->SetLength(PixelReadConverter->GetRGBSize()); + PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), + PixelReadConverter->GetRGBSize()); } - else // Decompressed data + else // Raw data { - pixel->SetBinArea(PixelReadConverter->GetDecompressed(),false); - pixel->SetLength(PixelReadConverter->GetDecompressedSize()); + 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); @@ -614,15 +718,12 @@ 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); @@ -631,7 +732,7 @@ void File::SetWriteToRGB() } else { - SetWriteToDecompressed(); + SetWriteToRaw(); } } @@ -668,7 +769,6 @@ void File::SetWriteFileTypeToExplicitVR() ValEntry* tss = CopyValEntry(0x0002,0x0010); tss->SetValue(ts); - tss->SetLength(ts.length()); Archive->Push(tss); } @@ -680,7 +780,8 @@ void File::SetWriteFileTypeToImplicitVR() ValEntry* tss = CopyValEntry(0x0002,0x0010); tss->SetValue(ts); - tss->SetLength(ts.length()); + + Archive->Push(tss); } void File::RestoreWriteFileType() @@ -690,8 +791,10 @@ void File::RestoreWriteFileType() void File::SetWriteToLibido() { - ValEntry *oldRow = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); - ValEntry *oldCol = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); + ValEntry *oldRow = dynamic_cast + (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); + ValEntry *oldCol = dynamic_cast + (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); if( oldRow && oldCol ) { @@ -712,20 +815,19 @@ void File::SetWriteToLibido() 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)); + 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); } } @@ -774,6 +876,49 @@ BinEntry* File::CopyBinEntry(uint16_t group,uint16_t 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