X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=62051158b1acc18cb5bebfd277f9a013b749acb1;hb=689f929ff0f35aabd30d81ffa75eb66fdf1a3c16;hp=8c3cb2796cfa1c0f98e232571c47caffcd74e807;hpb=2e885708cc267161a461c9921564475fbd7d514e;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 8c3cb279..62051158 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/09/27 08:39:07 $ - Version: $Revision: 1.131 $ + Date: $Date: 2004/09/29 17:33:17 $ + Version: $Revision: 1.132 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -25,7 +25,6 @@ typedef std::pair IterHT; //------------------------------------------------------------------------- // Constructor / Destructor /** - * \ingroup gdcmFile * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 * file (gdcmHeader only deals with the ... header) * Opens (in read only and when possible) an existing file and checks @@ -43,11 +42,10 @@ gdcmFile::gdcmFile(gdcmHeader *header) { Header = header; SelfHeader = false; - SaveInitialValues(); + Initialise(); } /** - * \ingroup gdcmFile * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 * file (gdcmHeader only deals with the ... header) * Opens (in read only and when possible) an existing file and checks @@ -65,11 +63,30 @@ gdcmFile::gdcmFile(std::string const & filename ) { Header = new gdcmHeader( filename ); SelfHeader = true; + Initialise(); +} + +/** + * \brief Factorization for various forms of constructors. + */ +void gdcmFile::Initialise() +{ + if ( Header->IsReadable() ) + { + ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader(); + if ( Header->HasLUT() ) + { + ImageDataSize = 3 * ImageDataSizeRaw; + } + else + { + ImageDataSize = ImageDataSizeRaw; + } + } SaveInitialValues(); } /** - * \ingroup gdcmFile * \brief canonical destructor * \note If the gdcmHeader was created by the gdcmFile constructor, * it is destroyed by the gdcmFile @@ -86,7 +103,6 @@ gdcmFile::~gdcmFile() } /** - * \ingroup gdcmFile * \brief Sets some initial values for the Constructor * \warning not end user intended */ @@ -112,8 +128,6 @@ void gdcmFile::SaveInitialValues() if ( Header->IsReadable() ) { - SetPixelDataSizeFromHeader(); - // the following values *may* be modified // by gdcmFile::GetImageDataIntoVectorRaw // we save their initial value. @@ -138,7 +152,6 @@ void gdcmFile::SaveInitialValues() } /** - * \ingroup gdcmFile * \brief restores some initial values * \warning not end user intended */ @@ -182,7 +195,6 @@ void gdcmFile::RestoreInitialValues() } /** - * \ingroup gdcmFile * \brief delete initial values (il they were saved) * of InitialLutDescriptors and InitialLutData */ @@ -212,62 +224,6 @@ void gdcmFile::DeleteInitialValues() delete InitialBlueLUTData; } -/** - * \ingroup gdcmFile - * \brief drop palette related initial values -if any- - * (InitialLutDescriptors and InitialLutData) - * out of header, to make it consistent with the Pixel_Data - * as it's loaded in memory - */ - -//FIXME : Should be nice, if we could let it here. -// will be moved to PixelData class -// Now, the job is done in gdcmHeader.cxx - - /* -void gdcmFile::DropInitialValues() -{ - gdcmHeader* h=GetHeader(); - if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' ) - { - // if SamplesPerPixel = 3, sure we don't need any LUT ! - // Drop 0028|1101, 0028|1102, 0028|1103 - // Drop 0028|1201, 0028|1202, 0028|1203 - - gdcmDocEntry* e = h->GetDocEntryByNumber(0x0028,0x01101); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x1102); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x1103); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x01201); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x1202); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - e = h->GetDocEntryByNumber(0x0028,0x1203); - if (e) - { - h->RemoveEntryNoDestroy(e); - } - } -} -*/ - //----------------------------------------------------------------------------- // Print @@ -275,14 +231,12 @@ void gdcmFile::DropInitialValues() // Public /** - * \ingroup gdcmFile * \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). - * \warning : not end user intended ? */ -void gdcmFile::SetPixelDataSizeFromHeader() +int gdcmFile::ComputeDecompressedPixelDataSizeFromHeader() { // see PS 3.3-2003 : C.7.6.3.2.1 // @@ -311,38 +265,22 @@ void gdcmFile::SetPixelDataSizeFromHeader() // 0028|1203 [US] [Blue Palette Color Lookup Table Data] // Number of "Bits Allocated" - int nb; - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - - if ( str_nb == GDCM_UNFOUND ) + int numberBitsAllocated = Header->GetBitsAllocated(); + if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) { - nb = 16; + numberBitsAllocated = 16; } - else - { - nb = atoi( str_nb.c_str() ); - if (nb == 12) - { - nb =16; - } - } - ImageDataSize = - ImageDataSizeRaw = Header->GetXSize() * Header->GetYSize() - * Header->GetZSize() * (nb/8) * Header->GetSamplesPerPixel(); - std::string str_PhotometricInterpretation = - Header->GetEntryByNumber(0x0028,0x0004); - - // if ( str_PhotometricInterpretation == "PALETTE COLOR " ), - // pb when undealt Segmented Palette Color + + int DecompressedSize = Header->GetXSize() + * Header->GetYSize() + * Header->GetZSize() + * ( numberBitsAllocated / 8 ) + * Header->GetSamplesPerPixel(); - if ( Header->HasLUT() ) - { - ImageDataSize *= 3; - } + return DecompressedSize; } /** - * \ingroup gdcmFile * \brief - Allocates necessary memory, * - Reads the pixels from disk (uncompress if necessary), * - Transforms YBR pixels, if any, into RGB pixels @@ -384,7 +322,6 @@ uint8_t* gdcmFile::GetImageData() } /** - * \ingroup gdcmFile * \brief * Read the pixels from disk (uncompress if necessary), * Transforms YBR pixels, if any, into RGB pixels @@ -468,7 +405,6 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) } /** - * \ingroup gdcmFile * \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 @@ -516,7 +452,6 @@ uint8_t* gdcmFile::GetImageDataRaw () } /** - * \ingroup gdcmFile * \brief Copies at most MaxSize bytes of pixel data to caller's * memory space. * \warning This function was designed to avoid people that want to build @@ -541,8 +476,6 @@ uint8_t* gdcmFile::GetImageDataRaw () */ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) { - int nb, nbu, highBit, sign; - // we save the initial values of the following // in order to be able to restore the header in a disk-consistent state // (if user asks twice to get the pixels from disk) @@ -564,64 +497,43 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) ReadPixelData( destination ); // Number of Bits Allocated for storing a Pixel - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) + int numberBitsAllocated = Header->GetBitsAllocated(); + if ( numberBitsAllocated == 0 ) { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - // FIXME - // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated - // separately, correct ? + numberBitsAllocated = 16; } // Number of Bits actually used - std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101); - if ( str_nbu == GDCM_UNFOUND ) + int numberBitsStored = Header->GetBitsStored(); + if ( numberBitsStored == 0 ) { - nbu = nb; - } - else - { - nbu = atoi( str_nbu.c_str() ); + numberBitsStored = numberBitsAllocated; } // High Bit Position - std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102); - if ( str_highBit == GDCM_UNFOUND ) + int highBitPosition = Header->GetHighBitPosition(); + if ( highBitPosition == 0 ) { - highBit = nb - 1; + highBitPosition = numberBitsAllocated - 1; } - else - { - highBit = atoi( str_highBit.c_str() ); - } - // Pixel sign - // 0 = Unsigned - // 1 = Signed - std::string str_sign = Header->GetEntryByNumber(0x0028,0x0103); - if ( str_sign == GDCM_UNFOUND ) - { - sign = 0; // default is unsigned - } - else - { - sign = atoi( str_sign.c_str() ); - } + bool signedPixel = Header->IsSignedPixelData(); - // re arange bytes inside the integer (processor endianity) - if ( nb != 8 ) +// SPLIT ME +//////////////////////////////////////////////////////// +// ENDIANITY SECTION: re-arange bytes inside the integer + if ( numberBitsAllocated != 8 ) { - SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb); + SwapZone( destination, Header->GetSwapCode(), ImageDataSize, + numberBitsAllocated ); } // to avoid pb with some xmedcon breakers images - if ( nb == 16 && nbu < nb && sign == 0) + if ( ( numberBitsAllocated == 16 ) + && ( numberBitsStored < numberBitsAllocated ) + && ( ! signedPixel ) ) { - int l = (int)(ImageDataSize / (nb/8)); + int l = (int)(ImageDataSize / (numberBitsAllocated/8)); uint16_t *deb = (uint16_t *)destination; for(int i = 0; i> (nb-nbu); + mask = mask >> ( numberBitsAllocated - numberBitsStored ); uint16_t *deb = (uint16_t *)destination; for(int i = 0; i> (nbu - highBit - 1)) & mask; + *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask; deb++; } } - else if ( nb == 32 ) + else if ( numberBitsAllocated == 32 ) { uint32_t mask = 0xffffffff; - mask = mask >> (nb - nbu); + mask = mask >> ( numberBitsAllocated - numberBitsStored ); uint32_t *deb = (uint32_t *)destination; for(int i = 0; i> (nbu - highBit - 1)) & mask; + *deb = (*deb >> (numberBitsStored - highBitPosition - 1)) & mask; deb++; } } @@ -665,24 +579,22 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) return 0; } } -/// \todo -/// DO NOT remove this code commented out. -/// Nobody knows what's expecting you ... -/// Just to 'see' what was actually read on disk :-( -/// -/// FILE* f2; -/// f2 = fopen("SpuriousFile.RAW","wb"); -/// fwrite(destination,ImageDataSize,1,f2); -/// fclose(f2); - - // Deal with the color - // ------------------- - - std::string str_PhotometricInterpretation = - Header->GetEntryByNumber(0x0028,0x0004); - if ( str_PhotometricInterpretation == "MONOCHROME1 " - || str_PhotometricInterpretation == "MONOCHROME2 " ) +#ifdef GDCM_DEBUG + FILE* DebugFile; + DebugFile = fopen( "SpuriousFile.RAW", "wb" ); + fwrite( PixelConvertor.GetUncompressed(), + PixelConvertor.GetUncompressedsSize(), + 1, DebugFile ); + fclose( DebugFile ); +#endif //GDCM_DEBUG + +// SPLIT ME +////////////////////////////////// +// Deal with the color + + // Monochrome pictures don't require color intervention + if ( Header->IsMonochrome() ) { return ImageDataSize; } @@ -700,7 +612,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) // Whatever Planar Configuration is, // "PALETTE COLOR " implies that we deal with the palette. - if ( str_PhotometricInterpretation == "PALETTE COLOR ") + if ( Header->IsPaletteColor() ) { planConf = 2; } @@ -711,7 +623,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) // Pixels are already RGB break; case 1: - if (str_PhotometricInterpretation == "YBR_FULL") + if ( Header->IsYBRFull() ) { // Warning : YBR_FULL_422 acts as RGB // : we need to make RGB Pixels from Planes Y,cB,cR @@ -811,12 +723,13 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t maxSize) } /** - * \ingroup gdcmFile - * \brief performs a shalow copy (not a deep copy) of the user given - * pixel area. - * '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 user is kindly requested NOT TO 'free' the Pixel area + * \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 * @@ -834,7 +747,6 @@ bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize) } /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file * NO test is performed on processor "Endiannity". * It's up to the user to call his Reader properly @@ -858,7 +770,6 @@ bool gdcmFile::WriteRawData(std::string const & fileName) } /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the Implicit Value Representation convention * NO test is performed on processor "Endiannity". @@ -873,7 +784,6 @@ bool gdcmFile::WriteDcmImplVR (std::string const & fileName) } /** - * \ingroup gdcmFile * \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 @@ -887,7 +797,6 @@ bool gdcmFile::WriteDcmExplVR (std::string const & fileName) } /** - * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file, * using the ACR-NEMA convention * NO test is performed on processor "Endiannity". @@ -909,7 +818,6 @@ bool gdcmFile::WriteAcr (std::string const & fileName) //----------------------------------------------------------------------------- // Protected /** - * \ingroup gdcmFile * \brief NOT a end user inteded function * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) * @param fileName name of the file to be created @@ -1004,7 +912,6 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) //----------------------------------------------------------------------------- // Private /** - * \ingroup gdcmFile * \brief Swap the bytes, according to swap code. * \warning not end user intended * @param im area to deal with @@ -1088,7 +995,6 @@ void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) } /** - * \ingroup gdcmFile * \brief Read pixel data from disk (optionaly decompressing) into the * caller specified memory location. * @param destination where the pixel data should be stored.