X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=484cc6909b771923839065f92c52f157918b63ee;hb=3fd520b58c8d1939994de2c63cc038c3e7ac9522;hp=6dfb630cf92002c072039c36509d3b5d9eb1fc8a;hpb=45bf98d79625d7efdb227b07c8746a918b49568b;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 6dfb630c..484cc690 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,10 +1,28 @@ -// gdcmFile.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/08/26 15:29:53 $ + Version: $Revision: 1.121 $ + + 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. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + #include "gdcmFile.h" -#include "gdcmUtil.h" +#include "gdcmDebug.h" #include "jpeg/ljpg/jpegless.h" -//----------------------------------------------------------------------------- +typedef std::pair IterHT; + +//------------------------------------------------------------------------- // Constructor / Destructor /** * \ingroup gdcmFile @@ -12,23 +30,24 @@ * file (see SetFileName, SetDcmTag and Write) * Opens (in read only and when possible) an existing file and checks * for DICOM compliance. Returns NULL on failure. - * \Note the in-memory representation of all available tags found in + * \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). - * * @param header file to be opened for reading datas - * - * @return + * @return */ - -gdcmFile::gdcmFile(gdcmHeader *header) { - Header=header; - SelfHeader=false; +gdcmFile::gdcmFile(gdcmHeader *header) +{ + Header = header; + SelfHeader = false; + PixelRead = -1; // no ImageData read yet. if (Header->IsReadable()) + { SetPixelDataSizeFromHeader(); + } } /** @@ -37,40 +56,38 @@ gdcmFile::gdcmFile(gdcmHeader *header) { * file (see SetFileName, SetDcmTag and Write) * Opens (in read only and when possible) an existing file and checks * for DICOM compliance. Returns NULL on failure. - * \Note the in-memory representation of all available tags found in + * \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). * @param filename file to be opened for parsing - * @return */ -gdcmFile::gdcmFile(std::string & filename) { - Header=new gdcmHeader(filename.c_str()); - SelfHeader=true; - - if (Header->IsReadable()) - SetPixelDataSizeFromHeader(); -} - -gdcmFile::gdcmFile(const char * filename) { - Header=new gdcmHeader(filename); - SelfHeader=true; - - if (Header->IsReadable()) +gdcmFile::gdcmFile(std::string const & filename ) +{ + Header = new gdcmHeader( filename ); + SelfHeader = true; + PixelRead = -1; // no ImageData read yet. + + if ( Header->IsReadable() ) + { SetPixelDataSizeFromHeader(); + } } /** * \ingroup gdcmFile * \brief canonical destructor - * \Note If the gdcmHeader is created by the gdcmFile, it is destroyed + * \note If the gdcmHeader is created by the gdcmFile, it is destroyed * by the gdcmFile */ -gdcmFile::~gdcmFile(void) { - if(SelfHeader) +gdcmFile::~gdcmFile() +{ + if( SelfHeader ) + { delete Header; - Header=NULL; + } + Header = 0; } //----------------------------------------------------------------------------- @@ -78,24 +95,17 @@ gdcmFile::~gdcmFile(void) { //----------------------------------------------------------------------------- // Public -/** - * \ingroup gdcmFile - * \brief - * @return - */ -gdcmHeader *gdcmFile::GetHeader(void) { - return(Header); -} /** * \ingroup gdcmFile * \brief computes the length (in bytes) to ALLOCATE to receive the - * image(s) pixels (multiframes taken into account) + * image(s) pixels (multiframes taken into account) * \warning : it is NOT the group 7FE0 length * (no interest for compressed images). * @return length to allocate */ -void gdcmFile::SetPixelDataSizeFromHeader(void) { +void gdcmFile::SetPixelDataSizeFromHeader() +{ // see PS 3.3-2003 : C.7.6.3.2.1 // // MONOCHROME1 @@ -122,25 +132,33 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { // 0028|1202 [US] [Green Palette Color Lookup Table Data] // 0028|1203 [US] [Blue Palette Color Lookup Table Data] + // Number of "Bits Allocated" int nb; - std::string str_nb; - str_nb=Header->GetEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { + std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); + + if ( str_nb == GDCM_UNFOUND ) + { nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; + } + else + { + nb = atoi( str_nb.c_str() ); + if (nb == 12) + { + nb =16; + } } - lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize() - * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel(); + 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 " )*/ + + // if ( str_PhotometricInterpretation == "PALETTE COLOR " ) // pb when undealt Segmented Palette Color - if (Header->HasLUT()) { - lgrTotale*=3; + if ( Header->HasLUT() ) + { + ImageDataSize *= 3; } } @@ -150,21 +168,23 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { * the pixel data represented in this file. * @return The size of pixel data in bytes. */ -size_t gdcmFile::GetImageDataSize(void) { - return (lgrTotale); +size_t gdcmFile::GetImageDataSize() +{ + return ImageDataSize; } /** * \ingroup gdcmFile * \brief Returns the size (in bytes) of required memory to hold - * \ the pixel data represented in this file, when user DOESN'T want - * \ to get RGB pixels image when it's stored as a PALETTE COLOR image - * \ - the (vtk) user is supposed to know how deal with LUTs - + * the pixel data represented in this file, when user DOESN'T want + * to get RGB pixels image when it's stored as a PALETTE COLOR image + * -the (vtk) user is supposed to know how deal with LUTs- * \warning to be used with GetImagePixelsRaw() * @return The size of pixel data in bytes. */ -size_t gdcmFile::GetImageDataSizeRaw(void) { - return (lgrTotaleRaw); +size_t gdcmFile::GetImageDataSizeRaw() +{ + return ImageDataSizeRaw; } /** @@ -175,13 +195,22 @@ size_t gdcmFile::GetImageDataSizeRaw(void) { * Transforms 3 planes R, G, B into a single RGB Plane * Transforms single Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. - * \ NULL if alloc fails + * NULL if alloc fails */ -void * gdcmFile::GetImageData (void) { - PixelData = (void *) malloc(lgrTotale); - if (PixelData) - GetImageDataIntoVector(PixelData, lgrTotale); - return(PixelData); +void *gdcmFile::GetImageData() +{ + // FIXME + // I need to deallocate PixelData before doing any allocation: + PixelData = new uint8_t[ImageDataSize]; + if ( PixelData ) + { + GetImageDataIntoVector(PixelData, ImageDataSize); + GetHeader()->SetEntryVoidAreaByNumber( PixelData, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + } + PixelRead = 0; // no PixelRaw + + return PixelData; } /** @@ -199,62 +228,74 @@ void * gdcmFile::GetImageData (void) { * * @param destination Address (in caller's memory space) at which the * pixel data should be copied - * @param MaxSize Maximum number of bytes to be copied. When MaxSize + * @param maxSize Maximum number of bytes to be copied. When MaxSize * is not sufficient to hold the pixel data the copy is not * executed (i.e. no partial copy). * @return On success, the number of bytes actually copied. Zero on * failure e.g. MaxSize is lower than necessary. */ -size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { - size_t l = GetImageDataIntoVectorRaw (destination, MaxSize); - - if (!Header->HasLUT()) - return lgrTotale; +size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) +{ + //size_t l = GetImageDataIntoVectorRaw (destination, maxSize); + GetImageDataIntoVectorRaw (destination, maxSize); + PixelRead = 0 ; // no PixelRaw + if ( !Header->HasLUT() ) + { + return ImageDataSize; + } // from Lut R + Lut G + Lut B - unsigned char * newDest = (unsigned char *)malloc(lgrTotale); - unsigned char * a = (unsigned char *)destination; - unsigned char * lutRGBA = Header->GetLUTRGBA(); - if (lutRGBA) { - int l = lgrTotaleRaw; - memmove(newDest, destination, l);// move Gray pixels to temp area - int j; - for (int i=0;iGetLUTRGBA(); + + if ( lutRGBA ) + { + int j; + //int l = ImageDataSizeRaw; //loss of precision + // move Gray pixels to temp area + memmove(newDest, destination, ImageDataSizeRaw); + for (size_t i=0; iSetEntryByNumber(spp,0x0028,0x0002); - std::string rgb= "RGB "; // Photometric Interpretation + std::string rgb = "RGB "; // Photometric Interpretation Header->SetEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration Header->SetEntryByNumber(planConfig,0x0028,0x0006); - } else { - // need to make RGB Pixels (?) - // from grey Pixels (?!) - // and Gray Lut (!?!) - // or Segmented xxx Palette Color Lookup Table Data and so on - - // Oops! I get one (gdcm-US-ALOKA-16.dcm) - // No idea how to manage such an image - // It seems that *no Dicom Viewer* has any idea :-( - // Segmented xxx Palette Color are *more* than 65535 long ?!? - - std::string rgb= "MONOCHROME1 "; // Photometric Interpretation - Header->SetEntryByNumber(rgb,0x0028,0x0004); - } - // TODO : Drop Palette Color out of the Header? - return lgrTotale; + } + else //why is there a 'else' when an allocation failed ? + { + // need to make RGB Pixels (?) + // from grey Pixels (?!) + // and Gray Lut (!?!) + // or Segmented xxx Palette Color Lookup Table Data and so on + + // Oops! I get one (gdcm-US-ALOKA-16.dcm) + // No idea how to manage such an image + // It seems that *no Dicom Viewer* has any idea :-( + // Segmented xxx Palette Color are *more* than 65535 long ?!? + + std::string rgb = "MONOCHROME1 "; // Photometric Interpretation + Header->SetEntryByNumber(rgb,0x0028,0x0004); + } + + /// \todo Drop Palette Color out of the Header? + return ImageDataSize; } /** @@ -263,19 +304,31 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { * (image[s]/volume[s]) to newly allocated zone. * Transforms YBR pixels into RGB pixels if any * Transforms 3 planes R, G, B into a single RGB Plane - * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane + * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ -void * gdcmFile::GetImageDataRaw (void) { - if (Header->HasLUT()) - lgrTotale /= 3; // TODO Let gdcmHeadar user a chance - // to get the right value - // Create a member lgrTotaleRaw ??? - PixelData = (void *) malloc(lgrTotale); - if (PixelData) - GetImageDataIntoVectorRaw(PixelData, lgrTotale); - return(PixelData); +void * gdcmFile::GetImageDataRaw () +{ + size_t imgDataSize = ImageDataSize; + if ( Header->HasLUT() ) + { + /// \todo Let gdcmHeader user a chance to get the right value + imgDataSize = ImageDataSizeRaw; + } + + // FIXME + // I need to deallocate PixelData before doing any allocation: + PixelData = new uint8_t[imgDataSize]; + if ( PixelData ) + { + GetImageDataIntoVectorRaw(PixelData, ImageDataSize); + GetHeader()->SetEntryVoidAreaByNumber(PixelData, + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); + } + PixelRead = 1; // PixelRaw + + return PixelData; } /** @@ -296,114 +349,148 @@ void * gdcmFile::GetImageDataRaw (void) { * * @param destination Address (in caller's memory space) at which the * pixel data should be copied - * @param MaxSize Maximum number of bytes to be copied. When MaxSize + * @param maxSize Maximum number of bytes to be copied. When MaxSize * is not sufficient to hold the pixel data the copy is not * executed (i.e. no partial copy). * @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) { - - int nb, nbu, highBit, signe; - std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; +size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t maxSize) +{ + int nb, nbu, highBit, sign; + PixelRead = 1 ; // PixelRaw - if ( lgrTotale > MaxSize ) { + if ( ImageDataSize > maxSize ) + { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" "than caller's expected MaxSize"); - return (size_t)0; - } - - (void)ReadPixelData(destination); - - // Number of Bits Allocated for storing a Pixel - str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { + return (size_t)0; + } + + 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 { - nb = atoi(str_nb.c_str() ); - } - // Number of Bits actually used - str_nbu=Header->GetEntryByNumber(0x0028,0x0101); - if (str_nbu == GDCM_UNFOUND ) { + } + else + { + nb = atoi( str_nb.c_str() ); + // FIXME + // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated + // separately, correct ? + } + + // Number of Bits actually used + std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101); + if ( str_nbu == GDCM_UNFOUND ) + { nbu = nb; - } else { - nbu = atoi(str_nbu.c_str() ); - } - // High Bit Position - str_highBit=Header->GetEntryByNumber(0x0028,0x0102); - if (str_highBit == GDCM_UNFOUND ) { + } + else + { + nbu = atoi( str_nbu.c_str() ); + } + + // 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 - str_signe=Header->GetEntryByNumber(0x0028,0x0103); - if (str_signe == GDCM_UNFOUND ) { - signe = 0; // default is unsigned - } else { - signe = atoi(str_signe.c_str() ); + } + 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(), lgrTotale, nb); + if ( nb != 8 ) + { + SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb); + } // to avoid pb with some xmedcon breakers images - if (nb==16 && nbu> (nb-nbu); - guint16 *deb = (guint16 *)destination; - for(int i = 0; i> (nbu-highBit-1)) & mask; - deb ++; + uint16_t *deb = (uint16_t *)destination; + for(int i = 0; i> (nbu - highBit - 1)) & mask; + deb++; } - } else if (nb == 32 ) { - guint32 mask = 0xffffffff; - mask = mask >> (nb-nbu); - guint32 *deb = (guint32 *)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: wierd image"); - return (size_t)0; } - } + else + { + dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); + return 0; + } + } // 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,lgrTotale,1,f2); +// 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 ") ) { - return lgrTotale; - } + std::string str_PhotometricInterpretation = + Header->GetEntryByNumber(0x0028,0x0004); + + if ( str_PhotometricInterpretation == "MONOCHROME1 " + || str_PhotometricInterpretation == "MONOCHROME2 " ) + { + return ImageDataSize; + } // Planar configuration = 0 : Pixels are already RGB // Planar configuration = 1 : 3 planes : R, G, B @@ -414,239 +501,244 @@ 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(); // 0028,0006 - // Whatever Planar Configuration is, - // "PALETTE COLOR " implies that we deal with the palette. - if (str_PhotometricInterpretation == "PALETTE COLOR ") - planConf=2; + // Whatever Planar Configuration is, + // "PALETTE COLOR " implies that we deal with the palette. + if ( str_PhotometricInterpretation == "PALETTE COLOR ") + { + planConf = 2; + } - switch (planConf) { - case 0: - // Pixels are already RGB + switch ( planConf ) + { + case 0: + // Pixels are already RGB break; - case 1: - + if (str_PhotometricInterpretation == "YBR_FULL") { - 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(); + // 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(); - unsigned char * newDest = (unsigned char*) malloc(lgrTotale); - unsigned char *x = newDest; - unsigned char * a = (unsigned char *)destination; - unsigned char * b = a + l; - unsigned char * c = b + l; + 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;i255.0) R=255.0; - if (G>255.0) G=255.0; - if (B>255.0) B=255.0; - - *(x++) = (unsigned char)R; - *(x++) = (unsigned char)G; - *(x++) = (unsigned char)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,lgrTotale); - free(newDest); - - } else { - - // need to make RGB Pixels from R,G,B Planes - // (all the Frames at a time) + } + 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(); + int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); - char * newDest = (char*) malloc(lgrTotale); - char * x = newDest; - char * a = (char *)destination; - char * b = a + l; - char * c = b + l; + 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;jSetEntryByNumber(spp,0x0028,0x0002); - std::string rgb="RGB "; // Photometric Interpretation Header->SetEntryByNumber(rgb,0x0028,0x0004); - - std::string planConfig = "0"; // Planar Configuration Header->SetEntryByNumber(planConfig,0x0028,0x0006); - - // TODO : Drop Palette Color out of the Header? - return lgrTotale; + + /// \todo Drop Palette Color out of the Header? + return ImageDataSize; } /** * \ingroup gdcmFile - * \brief TODO JPR - * \warning doit-etre etre publique ? - * TODO : y a-t-il un inconvenient à fusioner ces 2 fonctions - * - * @param inData - * @param ExpectedSize + * \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 : lane per plane + * \warning user is kindly requested NOT TO 'free' the Pixel area + * @param inData user supplied pixel area + * @param expectedSize total image size, in Bytes * - * @return boolean + * @return boolean */ -bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { - Header->SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - return(true); +bool gdcmFile::SetImageData(void *inData, size_t expectedSize) +{ + Header->SetImageDataSize( expectedSize ); + PixelData = inData; + ImageDataSize = expectedSize; + PixelRead = 1; + + return true; } /** * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file * NO test is performed on processor "Endiannity". - * Ca sera à l'utilisateur d'appeler son Reader correctement - * (Equivalent a IdImaWriteRawFile) - * + * It's up to the user to call his Reader properly * @param fileName name of the file to be created * (any already existing file is over written) - * @return false if write fails + * @return false if write fails */ -bool gdcmFile::WriteRawData (std::string fileName) { - FILE * fp1; - fp1 = fopen(fileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); - return (false); - } - fwrite (PixelData,lgrTotale, 1, fp1); +bool gdcmFile::WriteRawData(std::string const & fileName) +{ + FILE *fp1 = fopen(fileName.c_str(), "wb"); + if (fp1 == NULL) + { + printf("Fail to open (write) file [%s] \n", fileName.c_str()); + return false; + } + fwrite (PixelData, ImageDataSize, 1, fp1); fclose (fp1); - return(true); + + return true; } /** * \ingroup gdcmFile - * \brief Writes on disk A SINGLE Dicom file + * \brief Writes on disk A SINGLE Dicom file, + * using the Implicit Value Representation convention * 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 + * @return false if write fails */ -bool gdcmFile::WriteDcmImplVR (std::string fileName) { - return WriteBase(fileName, ImplicitVR); +bool gdcmFile::WriteDcmImplVR (std::string const & fileName) +{ + return WriteBase(fileName, gdcmImplicitVR); } /** * \ingroup gdcmFile - * \brief - * @param fileName name of the file to be created - * (any already existing file is overwritten) - * @return false if write fails - */ - -bool gdcmFile::WriteDcmImplVR (const char* fileName) { - return WriteDcmImplVR (std::string (fileName)); -} - -/** - * \ingroup gdcmFile - * \brief - * @param fileName name of the file to be created +* \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 * (any already existing file is overwritten) - * @return false if write fails + * @return false if write fails */ -bool gdcmFile::WriteDcmExplVR (std::string fileName) { - return WriteBase(fileName, ExplicitVR); +bool gdcmFile::WriteDcmExplVR (std::string const & fileName) +{ + return WriteBase(fileName, gdcmExplicitVR); } - + /** * \ingroup gdcmFile - * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels + * \brief Writes on disk A SINGLE Dicom file, + * using the ACR-NEMA convention + * NO test is performed on processor "Endiannity". * (a l'attention des logiciels cliniques * qui ne prennent en entrée QUE des images ACR ... * \warning if a DICOM_V3 header is supplied, - * groups < 0x0008 and shadow groups are ignored) + * groups < 0x0008 and shadow groups are ignored * \warning NO TEST is performed on processor "Endiannity". - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * * @param fileName name of the file to be created * (any already existing file is overwritten) - * @return false if write fails + * @return false if write fails */ -bool gdcmFile::WriteAcr (std::string fileName) { - return WriteBase(fileName, ACR); +bool gdcmFile::WriteAcr (std::string const & fileName) +{ + return WriteBase(fileName, gdcmACR); } //----------------------------------------------------------------------------- // Protected /** * \ingroup gdcmFile - * -* @param fileName name of the file to be created + * \brief NOT a end user inteded function + * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) + * @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 + * @return false if write fails */ -bool gdcmFile::WriteBase (std::string fileName, FileType type) { +bool gdcmFile::WriteBase (std::string const & fileName, FileType type) +{ + if ( PixelRead == -1 && type != gdcmExplicitVR) + { + return false; + } - FILE * fp1; - fp1 = fopen(fileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Failed to open (write) File [%s] \n",fileName.c_str()); - return (false); + FILE *fp1 = fopen(fileName.c_str(), "wb"); + if (fp1 == NULL) + { + printf("Failed to open (write) File [%s] \n", fileName.c_str()); + return false; } - if ( (type == ImplicitVR) || (type == ExplicitVR) ) { - char * filePreamble; + if ( type == gdcmImplicitVR || type == gdcmExplicitVR ) + { // writing Dicom File Preamble - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - free (filePreamble); + uint8_t* filePreamble = new uint8_t[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble, 128, 1, fp1); + fwrite("DICM", 4, 1, fp1); + + delete[] filePreamble; } // -------------------------------------------------------------- @@ -655,16 +747,38 @@ bool gdcmFile::WriteBase (std::string 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 ( Header->GetFileType() == ACR_LIBIDO){ - rows = Header->GetEntryByNumber(0x0028, 0x0010); - columns = Header->GetEntryByNumber(0x0028, 0x0011); - Header->SetEntryByNumber(columns, 0x0028, 0x0010); - Header->SetEntryByNumber(rows , 0x0028, 0x0011); - } - // ----------------- End of Special Patch ---------------- + if ( Header->GetFileType() == gdcmACR_LIBIDO) + { + rows = Header->GetEntryByNumber(0x0028, 0x0010); + columns = Header->GetEntryByNumber(0x0028, 0x0011); + Header->SetEntryByNumber(columns, 0x0028, 0x0010); + Header->SetEntryByNumber(rows , 0x0028, 0x0011); + } + // ----------------- End of Special Patch ---------------- + + uint16_t grPixel = Header->GetGrPixel(); + uint16_t numPixel = Header->GetNumPixel();; + + gdcmDocEntry* PixelElement = + GetHeader()->GetDocEntryByNumber(grPixel, numPixel); + + if ( PixelRead == 1 ) + { + // we read pixel 'as is' (no tranformation LUT -> RGB) + PixelElement->SetLength( ImageDataSizeRaw ); + } + else if ( PixelRead == 0 ) + { + // we tranformed GrayLevel pixels + LUT into RGB Pixel + PixelElement->SetLength( ImageDataSize ); + } + Header->Write(fp1, type); // -------------------------------------------------------------- @@ -673,15 +787,17 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { // ...and we restore the Header to be Dicom Compliant again // just after writting - if (Header->GetFileType() == ACR_LIBIDO){ - Header->SetEntryByNumber(rows , 0x0028, 0x0010); - Header->SetEntryByNumber(columns, 0x0028, 0x0011); - } + if ( Header->GetFileType() == gdcmACR_LIBIDO ) + { + Header->SetEntryByNumber(rows , 0x0028, 0x0010); + Header->SetEntryByNumber(columns, 0x0028, 0x0011); + } // ----------------- End of Special Patch ---------------- - - fwrite(PixelData, lgrTotale, 1, fp1); + + // fwrite(PixelData, ImageDataSize, 1, fp1); // should be useless, now fclose (fp1); - return(true); + + return true; } //----------------------------------------------------------------------------- @@ -695,73 +811,79 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { * @param lgr Area Length * @param nb Pixels Bit number */ -void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) { -guint32 s32; -guint16 fort,faible; -int i; - -if(nb == 16) - switch(swap) { - case 0: - case 12: - case 1234: - break; - - case 21: - case 3412: - case 2143: - case 4321: - - for(i=0;i>8) - | ((((unsigned short int*)im)[i])<<8); - break; - - default: - printf("SWAP value (16 bits) not allowed : %d\n", swap); - } - -if( nb == 32 ) - switch (swap) { - case 0: - case 1234: - break; - - case 4321: - for(i=0;i>16; - fort= (fort>>8) | (fort<<8); - faible=(faible>>8) | (faible<<8); - s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; - } - break; - - case 2143: - for(i=0;i>16; - fort= (fort>>8) | (fort<<8); - faible=(faible>>8) | (faible<<8); - s32=fort; - ((unsigned long int*)im)[i]=(s32<<16)|faible; - } - break; - - case 3412: - for(i=0;i>16; - s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; - } - break; - - default: - printf("SWAP value (32 bits) not allowed : %d\n", swap); - } -return; +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; + } + } } /** @@ -771,169 +893,203 @@ return; * @param destination where the pixel data should be stored. * */ -bool gdcmFile::ReadPixelData(void* destination) { - - FILE *fp; +bool gdcmFile::ReadPixelData(void *destination) +{ + FILE *fp = Header->OpenFile(); - if ( !(fp=Header->OpenFile())) + if ( !fp ) + { return false; - if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) { + } + if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) + { Header->CloseFile(); 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] */ + // unpack 12 Bits pixels into 16 Bits pixels + // 2 pixels 12bit = [0xABCDEF] + // 2 pixels 16bit = [0x0ABD] + [0x0FCE] - if (Header->GetBitsAllocated()==12) { + if ( Header->GetBitsAllocated() == 12 ) + { int nbPixels = Header->GetXSize() * Header->GetYSize(); - unsigned char b0, b1, b2; + uint8_t b0, b1, b2; - unsigned short int* pdestination = (unsigned short int*)destination; - for(int p=0;p> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - /* A */ /* B */ /* D */ + // A B D *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - /* F */ /* C */ /* E */ - - // Troubles expected on Big-Endian processors ? + // F C E + + // Troubles expected on Big-Endian processors ? } Header->CloseFile(); - return(true); - } + return true; + } // ---------------------- Uncompressed File if ( !Header->IsDicomV3() || Header->IsImplicitVRLittleEndianTransferSyntax() || Header->IsExplicitVRLittleEndianTransferSyntax() || Header->IsExplicitVRBigEndianTransferSyntax() || - Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - + Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) + { size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - if ( ItemRead != 1 ) { - Header->CloseFile(); + Header->CloseFile(); + if ( ItemRead != 1 ) + { return false; - } else { - Header->CloseFile(); + } + else + { return true; } - } + } // ---------------------- Run Length Encoding - if (Header->IsRLELossLessTransferSyntax()) { - bool res = (bool)gdcm_read_RLE_file (fp,destination); + if ( Header->IsRLELossLessTransferSyntax() ) + { + bool res = gdcm_read_RLE_file (fp,destination); 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 ) { + std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); + if ( str_nb == GDCM_UNFOUND ) + { nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ? + } + else + { + nb = atoi( str_nb.c_str() ); + if ( nb == 12 ) + { + nb = 16; // ?? 12 should be ACR-NEMA only + } } int nBytes= nb/8; - int taille = Header->GetXSize() * Header->GetYSize() - * Header->GetSamplesPerPixel(); + * Header->GetSamplesPerPixel(); long fragmentBegining; // for ftell, fseek - bool jpg2000 = Header->IsJPEG2000(); + bool jpg2000 = Header->IsJPEG2000(); bool jpgLossless = Header->IsJPEGLossless(); - + bool res = true; - guint16 ItemTagGr,ItemTagEl; + uint16_t ItemTagGr, ItemTagEl; int ln; // Position on begining of Jpeg Pixels fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) { - ItemTagGr=Header->SwapShort(ItemTagGr); - ItemTagEl=Header->SwapShort(ItemTagEl); + if(Header->GetSwapCode()) + { + ItemTagGr = Header->SwapShort(ItemTagGr); + ItemTagEl = Header->SwapShort(ItemTagEl); } - fread(&ln,4,1,fp); - if(Header->GetSwapCode()) - ln=Header->SwapLong(ln); // Basic Offset Table Item length - - if (ln != 0) { + + fread(&ln,4,1,fp); + if( Header->GetSwapCode() ) + { + ln = Header->SwapLong( ln ); // Basic Offset Table Item length + } + + if ( ln != 0 ) + { // What is it used for ?!? - char *BasicOffsetTableItemValue = (char *)malloc(ln+1); - fread(BasicOffsetTableItemValue,ln,1,fp); + uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1]; + fread(BasicOffsetTableItemValue,ln,1,fp); + //delete[] BasicOffsetTableItemValue; } - + // first Fragment initialisation fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) { - ItemTagGr=Header->SwapShort(ItemTagGr); - ItemTagEl=Header->SwapShort(ItemTagEl); + if( Header->GetSwapCode() ) + { + ItemTagGr = Header->SwapShort( ItemTagGr ); + ItemTagEl = Header->SwapShort( ItemTagEl ); } - + // parsing fragments until Sequence Delim. Tag found - while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { + while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd ) + { // --- for each Fragment + fread(&ln,4,1,fp); + if( Header->GetSwapCode() ) + { + ln = Header->SwapLong(ln); // Fragment Item length + } + fragmentBegining = ftell( fp ); - fread(&ln,4,1,fp); - if(Header->GetSwapCode()) - ln=Header->SwapLong(ln); // Fragment Item length - - fragmentBegining=ftell(fp); - - if (jpg2000) { // JPEG 2000 : call to ??? - - res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written - - } // ------------------------------------- endif (JPEG2000) - - else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG - - JPEGLosslessDecodeImage (fp, // Reading Fragment pixels - (unsigned short *)destination, - Header->GetPixelSize()*8* Header->GetSamplesPerPixel(), - ln); - res=1; // in order not to break the loop + if ( jpg2000 ) + { + // JPEG 2000 : call to ??? + res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written + // ------------------------------------- endif (JPEG2000) + } + else if (jpgLossless) + { + // JPEG LossLess : call to xmedcom Lossless JPEG + // Reading Fragment pixels + JPEGLosslessDecodeImage (fp, (uint16_t*)destination, + Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), ln); + res = 1; // in order not to break the loop } // ------------------------------------- endif (JPEGLossless) + else + { + // JPEG Lossy : call to IJG 6b + if ( Header->GetBitsStored() == 8) + { + // Reading Fragment pixels + res = gdcm_read_JPEG_file (fp,destination); + } + else + { + // Reading Fragment pixels + res = gdcm_read_JPEG_file12 (fp,destination); + } + // ------------------------------------- endif (JPEGLossy) + } + + if ( !res ) + { + break; + } - else { // JPEG Lossy : call to IJG 6b - - if (Header->GetBitsStored() == 8) { - res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels - } else { - res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels - } - } // ------------------------------------- endif (JPEGLossy) - - if (!res) break; - - destination = (char *)destination + taille * nBytes; // location in user's memory - // for next fragment (if any) - - fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start - fseek(fp,ln,SEEK_CUR); // at the begining of next fragment + // location in user's memory + // for next fragment (if any) + destination = (uint8_t*)destination + taille * nBytes; + + fseek(fp,fragmentBegining, SEEK_SET); // To be sure we start + fseek(fp,ln,SEEK_CUR); // at the begining of next fragment - ItemTagGr = ItemTagEl =0; + ItemTagGr = ItemTagEl = 0; fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) { - ItemTagGr=Header->SwapShort(ItemTagGr); - ItemTagEl=Header->SwapShort(ItemTagEl); - } - - } // endWhile parsing fragments until Sequence Delim. Tag found - + if( Header->GetSwapCode() ) + { + ItemTagGr = Header->SwapShort( ItemTagGr ); + ItemTagEl = Header->SwapShort( ItemTagEl ); + } + } + // endWhile parsing fragments until Sequence Delim. Tag found + Header->CloseFile(); return res; }