X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=2defabdaebfcadf3c4ec6046467059cda33038c6;hb=00e89cde772e18e4f2baab2b01680330af909d59;hp=75bdc905d5c1caf5b6d7d007a4ff8e269122e5d8;hpb=692f863c018c259a380e664d3608a46ec0c8bb3e;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 75bdc905..2defabda 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/09/23 09:40:30 $ - Version: $Revision: 1.127 $ + Date: $Date: 2004/10/08 17:24:54 $ + Version: $Revision: 1.137 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -18,6 +18,7 @@ #include "gdcmFile.h" #include "gdcmDebug.h" +#include "gdcmPixelConvert.h" #include "jpeg/ljpg/jpegless.h" typedef std::pair IterHT; @@ -25,7 +26,6 @@ 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 +43,10 @@ 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 +64,30 @@ 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 +104,6 @@ gdcmFile::~gdcmFile() } /** - * \ingroup gdcmFile * \brief Sets some initial values for the Constructor * \warning not end user intended */ @@ -112,8 +129,6 @@ void gdcmFile::SaveInitialValues() if ( Header->IsReadable() ) { - SetPixelDataSizeFromHeader(); - // the following values *may* be modified // by gdcmFile::GetImageDataIntoVectorRaw // we save their initial value. @@ -138,7 +153,6 @@ void gdcmFile::SaveInitialValues() } /** - * \ingroup gdcmFile * \brief restores some initial values * \warning not end user intended */ @@ -182,7 +196,6 @@ void gdcmFile::RestoreInitialValues() } /** - * \ingroup gdcmFile * \brief delete initial values (il they were saved) * of InitialLutDescriptors and InitialLutData */ @@ -212,62 +225,6 @@ 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 +232,12 @@ 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 +266,22 @@ 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 @@ -375,7 +314,7 @@ uint8_t* gdcmFile::GetImageData() GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); // Will be 7fe0, 0010 in standard case - GetHeader()->SetEntryVoidAreaByNumber( Pixel_Data, + GetHeader()->SetEntryBinAreaByNumber( Pixel_Data, GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); } PixelRead = 0; // no PixelRaw @@ -384,7 +323,6 @@ 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 +406,6 @@ 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 @@ -507,7 +444,7 @@ uint8_t* gdcmFile::GetImageDataRaw () GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); // will be 7fe0, 0010 in standard cases - GetHeader()->SetEntryVoidAreaByNumber(Pixel_Data, + GetHeader()->SetEntryBinAreaByNumber(Pixel_Data, GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); } PixelRead = 1; // PixelRaw @@ -516,7 +453,6 @@ 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 @@ -539,10 +475,8 @@ uint8_t* gdcmFile::GetImageDataRaw () * @return On success, the number of bytes actually copied. Zero on * failure e.g. MaxSize is lower than necessary. */ -size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t maxSize) +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) @@ -564,124 +498,57 @@ 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 ) - { - nb = 16; - } - else + int numberBitsAllocated = Header->GetBitsAllocated(); + if ( numberBitsAllocated == 0 ) { - 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 ) - { - nbu = nb; - } - else + int numberBitsStored = Header->GetBitsStored(); + if ( numberBitsStored == 0 ) { - nbu = atoi( str_nbu.c_str() ); + numberBitsStored = numberBitsAllocated; } // High Bit Position - std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102); - if ( str_highBit == GDCM_UNFOUND ) - { - highBit = nb - 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() ); - } - - // re arange bytes inside the integer (processor endianity) - if ( nb != 8 ) - { - SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb); - } - - // to avoid pb with some xmedcon breakers images - if ( nb == 16 && nbu < nb && sign == 0) - { - int l = (int)(ImageDataSize / (nb/8)); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; iGetHighBitPosition(); + if ( highBitPosition == 0 ) { - int l = (int)(ImageDataSize / (nb/8)); - if ( nb == 16 ) - { - uint16_t mask = 0xffff; - mask = mask >> (nb-nbu); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; i> (nbu - highBit - 1)) & mask; - deb++; - } - } - else if ( nb == 32 ) - { - uint32_t mask = 0xffffffff; - mask = mask >> (nb - nbu); - uint32_t *deb = (uint32_t *)destination; - for(int i = 0; i> (nbu - highBit - 1)) & mask; - deb++; - } - } - else - { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); - return 0; - } + highBitPosition = numberBitsAllocated - 1; } -// 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 - // ------------------- + bool signedPixel = Header->IsSignedPixelData(); + + gdcmPixelConvert::ConvertReorderEndianity( + (uint8_t*) destination, + ImageDataSize, + numberBitsStored, + numberBitsAllocated, + Header->GetSwapCode(), + signedPixel ); + + ConvertReArrangeBits( (uint8_t*) destination, + ImageDataSize, + numberBitsStored, + numberBitsAllocated, + highBitPosition ); + +#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 - std::string str_PhotometricInterpretation = - Header->GetEntryByNumber(0x0028,0x0004); - - if ( str_PhotometricInterpretation == "MONOCHROME1 " - || str_PhotometricInterpretation == "MONOCHROME2 " ) + // Monochrome pictures don't require color intervention + if ( Header->IsMonochrome() ) { return ImageDataSize; } @@ -695,98 +562,36 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t maxSize) // PhotometricInterpretation=PALETTE COLOR // and heuristic has to be found :-( - int planConf = Header->GetPlanarConfiguration(); // 0028,0006 + int planConf = Header->GetPlanarConfiguration(); - // Whatever Planar Configuration is, - // "PALETTE COLOR " implies that we deal with the palette. - if ( str_PhotometricInterpretation == "PALETTE COLOR ") + // Planar configuration = 2 ==> 1 gray Plane + 3 LUT + // ...and... + // whatever the Planar Configuration might be, "PALETTE COLOR " + // implies that we deal with the palette. + if ( ( planConf == 2 ) || Header->IsPaletteColor() ) { - planConf = 2; + return ImageDataSize; } - switch ( planConf ) + // When planConf is 0, pixels are allready in RGB + + if ( planConf == 1 ) { - case 0: - // Pixels are already RGB - break; - case 1: - if (str_PhotometricInterpretation == "YBR_FULL") - { - // Warning : YBR_FULL_422 acts as RGB - // : we need to make RGB Pixels from Planes Y,cB,cR - - // to see the tricks about YBR_FULL, YBR_FULL_422, - // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : - // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf - // and be *very* affraid - // - int l = Header->GetXSize() * Header->GetYSize(); - int nbFrames = Header->GetZSize(); - - uint8_t* newDest = new uint8_t[ImageDataSize]; - uint8_t* x = newDest; - uint8_t* a = (uint8_t*)destination; - uint8_t* b = a + l; - uint8_t* c = b + l; - double R,G,B; - - /// \todo : Replace by the 'well known' integer computation - /// counterpart - /// see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - /// for code optimisation - - for (int i = 0; i < nbFrames; i++) - { - for (int j = 0; j < l; j++) - { - R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; - G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; - B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; - - if (R < 0.0) R = 0.0; - if (G < 0.0) G = 0.0; - if (B < 0.0) B = 0.0; - if (R > 255.0) R = 255.0; - if (G > 255.0) G = 255.0; - if (B > 255.0) B = 255.0; - - *(x++) = (uint8_t)R; - *(x++) = (uint8_t)G; - *(x++) = (uint8_t)B; - a++; b++; c++; - } - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - else - { - // need to make RGB Pixels from R,G,B Planes - // (all the Frames at a time) - - int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); - - uint8_t *newDest = new uint8_t[ImageDataSize]; - uint8_t *x = newDest; - uint8_t *a = (uint8_t *)destination; - uint8_t *b = a + l; - uint8_t *c = b + l; - - for (int j = 0; j < l; j++) - { - *(x++) = *(a++); - *(x++) = *(b++); - *(x++) = *(c++); - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - break; - case 2: - // Palettes were found - // Let the user deal with them ! - return ImageDataSize; + uint8_t* newDest = new uint8_t[ImageDataSize]; + // Warning : YBR_FULL_422 acts as RGB + if ( Header->IsYBRFull() ) + { + ConvertYcBcRPlanesToRGBPixels((uint8_t*)destination, newDest); + } + else + { + ConvertRGBPlanesToRGBPixels((uint8_t*)destination, newDest); + } + memmove(destination, newDest, ImageDataSize); + delete[] newDest; } + +/////////////////////////////////////////////////// // now, it's an RGB image // Lets's write it in the Header @@ -810,12 +615,128 @@ 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 Re-arrange the bits within the bytes. + */ +void gdcmFile::ConvertReArrangeBits( uint8_t* pixelZone, + size_t imageDataSize, + int numberBitsStored, + int numberBitsAllocated, + int highBitPosition) + throw ( gdcmFormatError ) +{ + if ( numberBitsStored != numberBitsAllocated ) + { + int l = (int)(imageDataSize / (numberBitsAllocated/8)); + if ( numberBitsAllocated == 16 ) + { + uint16_t mask = 0xffff; + mask = mask >> ( numberBitsAllocated - numberBitsStored ); + uint16_t* deb = (uint16_t*)pixelZone; + for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; + deb++; + } + } + else if ( numberBitsAllocated == 32 ) + { + uint32_t mask = 0xffffffff; + mask = mask >> ( numberBitsAllocated - numberBitsStored ); + uint32_t* deb = (uint32_t*)pixelZone; + for(int i = 0; i> (numberBitsStored - highBitPosition - 1)) & mask; + deb++; + } + } + else + { + dbg.Verbose(0, "gdcmFile::ConvertReArrangeBits: weird image"); + throw gdcmFormatError( "gdcmFile::ConvertReArrangeBits()", + "weird image !?" ); + } + } +} + +/** + * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels + * \warning Works on all the frames at a time + */ +void gdcmFile::ConvertYcBcRPlanesToRGBPixels(uint8_t* source, + uint8_t* destination) +{ + // to see the tricks about YBR_FULL, YBR_FULL_422, + // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : + // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf + // and be *very* affraid + // + int l = Header->GetXSize() * Header->GetYSize(); + int nbFrames = Header->GetZSize(); + + uint8_t* a = source; + uint8_t* b = source + l; + uint8_t* c = source + l + l; + double R, G, B; + + /// \todo : Replace by the 'well known' integer computation + /// counterpart. Refer to + /// http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf + /// for code optimisation. + + for (int i = 0; i < nbFrames; i++) + { + for (int j = 0; j < l; j++) + { + R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; + G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; + B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; + + if (R < 0.0) R = 0.0; + if (G < 0.0) G = 0.0; + if (B < 0.0) B = 0.0; + if (R > 255.0) R = 255.0; + if (G > 255.0) G = 255.0; + if (B > 255.0) B = 255.0; + + *(destination++) = (uint8_t)R; + *(destination++) = (uint8_t)G; + *(destination++) = (uint8_t)B; + a++; + b++; + c++; + } + } +} + +/** + * \brief Convert (Red plane, Green plane, Blue plane) to RGB pixels + * \warning Works on all the frames at a time + */ +void gdcmFile::ConvertRGBPlanesToRGBPixels(uint8_t* source, + uint8_t* destination) +{ + int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); + + uint8_t* a = source; + uint8_t* b = source + l; + uint8_t* c = source + l + l; + + for (int j = 0; j < l; j++) + { + *(destination++) = *(a++); + *(destination++) = *(b++); + *(destination++) = *(c++); + } +} + +/** + * \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 * @@ -833,7 +754,6 @@ 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 @@ -844,7 +764,7 @@ bool gdcmFile::SetImageData(uint8_t* inData, size_t expectedSize) bool gdcmFile::WriteRawData(std::string const & fileName) { - FILE *fp1 = fopen(fileName.c_str(), "wb"); + FILE* fp1 = fopen(fileName.c_str(), "wb"); if (fp1 == NULL) { printf("Fail to open (write) file [%s] \n", fileName.c_str()); @@ -857,7 +777,6 @@ 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". @@ -872,7 +791,6 @@ 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 @@ -886,7 +804,6 @@ 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". @@ -908,7 +825,6 @@ 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 @@ -923,7 +839,7 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) return false; } - FILE *fp1 = fopen(fileName.c_str(), "wb"); + FILE* fp1 = fopen(fileName.c_str(), "wb"); if (fp1 == NULL) { printf("Failed to open (write) File [%s] \n", fileName.c_str()); @@ -1003,99 +919,14 @@ 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 - * @param swap swap code - * @param lgr Area Length - * @param nb Pixels Bit number - */ -void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) -{ - int i; - - if( nb == 16 ) - { - uint16_t* im16 = (uint16_t*)im; - switch( swap ) - { - case 0: - case 12: - case 1234: - break; - case 21: - case 3412: - case 2143: - case 4321: - for(i=0; i < lgr/2; i++) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - break; - default: - std::cout << "SWAP value (16 bits) not allowed :i" << swap << - std::endl; - } - } - else if( nb == 32 ) - { - uint32_t s32; - uint16_t fort, faible; - uint32_t* im32 = (uint32_t*)im; - switch ( swap ) - { - case 0: - case 1234: - break; - case 4321: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 4321 - fort = im32[i] >> 16; - fort = ( fort >> 8 ) | ( fort << 8 ); - faible = ( faible >> 8 ) | ( faible << 8); - s32 = faible; - im32[i] = ( s32 << 16 ) | fort; - } - break; - case 2143: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 2143 - fort = im32[i] >> 16; - fort = ( fort >> 8 ) | ( fort << 8 ); - faible = ( faible >> 8) | ( faible << 8); - s32 = fort; - im32[i] = ( s32 << 16 ) | faible; - } - break; - case 3412: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 3412 - fort = im32[i] >> 16; - s32 = faible; - im32[i] = ( s32 << 16 ) | fort; - } - break; - default: - std::cout << "SWAP value (32 bits) not allowed : " << swap << - std::endl; - } - } -} - -/** - * \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. * */ -bool gdcmFile::ReadPixelData(void *destination) +bool gdcmFile::ReadPixelData(void* destination) { - FILE *fp = Header->OpenFile(); + FILE* fp = Header->OpenFile(); if ( !fp ) { @@ -1107,32 +938,13 @@ bool gdcmFile::ReadPixelData(void *destination) return false; } - // ---------------------- Compacted File (12 Bits Per Pixel) - // unpack 12 Bits pixels into 16 Bits pixels - // 2 pixels 12bit = [0xABCDEF] - // 2 pixels 16bit = [0x0ABD] + [0x0FCE] - if ( Header->GetBitsAllocated() == 12 ) { - int nbPixels = Header->GetXSize() * Header->GetYSize(); - uint8_t b0, b1, b2; - - uint16_t* pdestination = (uint16_t*)destination; - for(int p = 0; p < nbPixels; p += 2 ) - { - fread(&b0,1,1,fp); - fread(&b1,1,1,fp); - fread(&b2,1,1,fp); - - //Two steps is necessary to please VC++ - *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - // A B D - *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - // F C E - - // Troubles expected on Big-Endian processors ? - } - + gdcmPixelConvert::ConvertDecompress12BitsTo16Bits( + (uint8_t*)destination, + Header->GetXSize(), + Header->GetYSize(), + fp); Header->CloseFile(); return true; } @@ -1159,28 +971,25 @@ bool gdcmFile::ReadPixelData(void *destination) // ---------------------- Run Length Encoding if ( Header->IsRLELossLessTransferSyntax() ) { - bool res = gdcm_read_RLE_file (fp,destination); + bool res = gdcmPixelConvert::gdcm_read_RLE_file ( destination, + Header->GetXSize(), + Header->GetYSize(), + Header->GetZSize(), + Header->GetBitsAllocated(), + &(Header->RLEInfo), + fp ); Header->CloseFile(); return res; } // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - int nb; - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) - { - nb = 16; - } - else + int numberBitsAllocated = Header->GetBitsAllocated(); + if ( ( numberBitsAllocated == 0 ) || ( numberBitsAllocated == 12 ) ) { - nb = atoi( str_nb.c_str() ); - if ( nb == 12 ) - { - nb = 16; // ?? 12 should be ACR-NEMA only - } + numberBitsAllocated = 16; } - int nBytes= nb/8; + int nBytes= numberBitsAllocated/8; int taille = Header->GetXSize() * Header->GetYSize() * Header->GetSamplesPerPixel(); long fragmentBegining; // for ftell, fseek @@ -1259,11 +1068,17 @@ bool gdcmFile::ReadPixelData(void *destination) // Reading Fragment pixels res = gdcm_read_JPEG_file (fp,destination); } - else + else if ( Header->GetBitsStored() == 12) { // Reading Fragment pixels res = gdcm_read_JPEG_file12 (fp,destination); } + else + { + // other JPEG lossy not supported + dbg.Error(" gdcmFile::ReadPixelData : unknown jpeg lossy compression"); + return 0; + } // ------------------------------------- endif (JPEGLossy) } @@ -1293,4 +1108,4 @@ bool gdcmFile::ReadPixelData(void *destination) Header->CloseFile(); return res; } -//----------------------------------------------------------------------------- +