From 00b6e0ddcbdbd41252e03732783f65efe5f52526 Mon Sep 17 00:00:00 2001 From: malaterre Date: Sat, 26 Jun 2004 04:09:32 +0000 Subject: [PATCH] ENH: Some cosmetic cleanup of gdcmFile, main changes are: lgrTotal -> ImageDataSize / lgrTotaleRaw -> ImageDataSizeRaw, it matches then there accessors (simple et de bon gout in french). * I also marked some lines as dangerous (mem leaks), and a comment for 12 bits images * Added conversion table in DEVELOPPERS * Also untabify, checkTabs is working :P --- DEVELOPPER | 13 +- src/gdcmFile.cxx | 964 +++++++++++++++++++++++++++-------------------- src/gdcmFile.h | 28 +- src/gdcmRLE.cxx | 8 +- 4 files changed, 578 insertions(+), 435 deletions(-) diff --git a/DEVELOPPER b/DEVELOPPER index 03e858b4..fd8a6796 100644 --- a/DEVELOPPER +++ b/DEVELOPPER @@ -343,12 +343,23 @@ gdcm coding style and religious/agnostic beliefs (proposition) typedef Header* HeaderPointer; HeaderPointer MyHeaderPointer; - One notorious counter example for non using C style inclusion concerns - exact-width intergers (since there seem to be no equivalent for C++). + exact-width integers (since there seem to be no equivalent for C++). When using exact-width integers use the typedef names defined by the Basic ISO C99: 7.18 Integer types i.e. int8_t int16_t int32_t int64_t (signed integers) and uint8_t uint16_t uint32_t uint64_t (unsigned integers). + Conversion table is then: + unsigned char -> uint8_t; + unsigned short -> uint16_t; + unsigned int -> uint32_t; + unsigned long -> uint32_t; + unsigned long long -> uint64_t; + (signed) char -> int8_t; + short -> int16_t; + int -> int32_t; + long -> int32_t; + long long -> int64_t; Hence do not use declarations like "unsigned int". With g++, accessing those typedef is achieved by the following #include diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 44579afa..c7a8b5d1 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/06/25 17:48:45 $ - Version: $Revision: 1.110 $ + Date: $Date: 2004/06/26 04:09:33 $ + Version: $Revision: 1.111 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -38,13 +38,16 @@ typedef std::pair IterHT; * @param header file to be opened for reading datas * @return */ -gdcmFile::gdcmFile(gdcmHeader *header) { - Header=header; - SelfHeader=false; - PixelRead=-1; // no ImageData read yet. +gdcmFile::gdcmFile(gdcmHeader *header) +{ + Header = header; + SelfHeader = false; + PixelRead = -1; // no ImageData read yet. if (Header->IsReadable()) + { SetPixelDataSizeFromHeader(); + } } /** @@ -73,16 +76,19 @@ gdcmFile::gdcmFile(gdcmHeader *header) { gdcmFile::gdcmFile(std::string const & filename, bool exception_on_error, bool enable_sequences, - bool ignore_shadow) { - Header=new gdcmHeader(filename.c_str(), - exception_on_error, - enable_sequences, - ignore_shadow); - SelfHeader=true; - PixelRead=-1; // no ImageData read yet. - - if (Header->IsReadable()) + bool ignore_shadow) +{ + Header = new gdcmHeader( filename, + exception_on_error, + enable_sequences, + ignore_shadow ); + SelfHeader = true; + PixelRead = -1; // no ImageData read yet. + + if ( Header->IsReadable() ) + { SetPixelDataSizeFromHeader(); + } } /** @@ -91,10 +97,13 @@ gdcmFile::gdcmFile(std::string const & filename, * \note If the gdcmHeader is created by the gdcmFile, it is destroyed * by the gdcmFile */ -gdcmFile::~gdcmFile() { - if(SelfHeader) +gdcmFile::~gdcmFile() +{ + if( SelfHeader ) + { delete Header; - Header=NULL; + } + Header = 0; } //----------------------------------------------------------------------------- @@ -111,7 +120,8 @@ gdcmFile::~gdcmFile() { * (no interest for compressed images). * @return length to allocate */ -void gdcmFile::SetPixelDataSizeFromHeader() { +void gdcmFile::SetPixelDataSizeFromHeader() +{ // see PS 3.3-2003 : C.7.6.3.2.1 // // MONOCHROME1 @@ -138,25 +148,33 @@ void gdcmFile::SetPixelDataSizeFromHeader() { // 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 " )*/ // pb when undealt Segmented Palette Color - if (Header->HasLUT()) { - lgrTotale*=3; + if ( Header->HasLUT() ) + { + ImageDataSize *= 3; } } @@ -166,8 +184,9 @@ void gdcmFile::SetPixelDataSizeFromHeader() { * the pixel data represented in this file. * @return The size of pixel data in bytes. */ -size_t gdcmFile::GetImageDataSize() { - return lgrTotale; +size_t gdcmFile::GetImageDataSize() +{ + return ImageDataSize; } /** @@ -179,8 +198,9 @@ size_t gdcmFile::GetImageDataSize() { * \warning to be used with GetImagePixelsRaw() * @return The size of pixel data in bytes. */ -size_t gdcmFile::GetImageDataSizeRaw() { - return lgrTotaleRaw; +size_t gdcmFile::GetImageDataSizeRaw() +{ + return ImageDataSizeRaw; } /** @@ -193,15 +213,18 @@ size_t gdcmFile::GetImageDataSizeRaw() { * @return Pointer to newly allocated pixel data. * NULL if alloc fails */ -void * gdcmFile::GetImageData () { - PixelData = new unsigned char[lgrTotale]; //consistant with GetImageDataIntoVector - if (PixelData) { - GetImageDataIntoVector(PixelData, lgrTotale); - GetHeader()->SetEntryVoidAreaByNumber(PixelData, - GetHeader()->GetGrPixel(), - GetHeader()->GetNumPixel()); +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 + PixelRead = 0; // no PixelRaw return PixelData; } @@ -227,25 +250,32 @@ void * gdcmFile::GetImageData () { * @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); - GetImageDataIntoVectorRaw (destination, MaxSize); - PixelRead=0 ; // no PixelRaw - 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 = new unsigned char[lgrTotale]; - unsigned char *a = (unsigned char *)destination; - unsigned char *lutRGBA = Header->GetLUTRGBA(); + uint8_t *newDest = new uint8_t[ImageDataSize]; + uint8_t *a = (uint8_t *)destination; + uint8_t *lutRGBA = Header->GetLUTRGBA(); - if (lutRGBA) { - int l = lgrTotaleRaw; - memmove(newDest, destination, l);// move Gray pixels to temp area + if ( lutRGBA ) + { int j; - for (int i=0;iSetEntryByNumber(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 + } + 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 ?!? + // 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 + std::string rgb = "MONOCHROME1 "; // Photometric Interpretation Header->SetEntryByNumber(rgb,0x0028,0x0004); } + /// \todo Drop Palette Color out of the Header? - return lgrTotale; + return ImageDataSize; } /** @@ -291,20 +324,26 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ -void * gdcmFile::GetImageDataRaw () { - if (Header->HasLUT()) +void * gdcmFile::GetImageDataRaw () +{ + size_t imgDataSize; + if ( Header->HasLUT() ) + { /// \todo Let gdcmHeader user a chance to get the right value - /// Create a member lgrTotaleRaw ??? - lgrTotale /= 3; - PixelData = new unsigned char[lgrTotale]; + // ImageDataSize /= 3; //dangerous + imgDataSize = ImageDataSizeRaw; + } - if (PixelData) { - GetImageDataIntoVectorRaw(PixelData, lgrTotale); + // 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()); + GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); } - PixelRead=1; // PixelRaw + PixelRead = 1; // PixelRaw return PixelData; } @@ -333,108 +372,142 @@ void * 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) { - - int nb, nbu, highBit, signe; - std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; - PixelRead=1 ; // PixelRaw +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; + return (size_t)0; } - ReadPixelData(destination); + ReadPixelData( destination ); // Number of Bits Allocated for storing a Pixel - 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() ); - } - // 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() ); + } + else + { + nbu = atoi( str_nbu.c_str() ); } + // High Bit Position - str_highBit=Header->GetEntryByNumber(0x0028,0x0102); - if (str_highBit == GDCM_UNFOUND ) { + std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102); + if ( str_highBit == GDCM_UNFOUND ) + { highBit = nb - 1; - } else { - highBit = atoi(str_highBit.c_str() ); + } + 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() ); + 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 ) { + } + else if ( nb == 32 ) + { guint32 mask = 0xffffffff; - mask = mask >> (nb-nbu); + mask = mask >> (nb - nbu); guint32 *deb = (guint32 *)destination; - for(int i = 0; i> (nbu-highBit-1)) & mask; - deb ++; + for(int i = 0; i> (nbu - highBit - 1)) & mask; + deb++; } - } else { + } + else + { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); return 0; } - } -// DO NOT remove this commented out code . + } +// 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); + std::string str_PhotometricInterpretation = + Header->GetEntryByNumber(0x0028,0x0004); - if ( (str_PhotometricInterpretation == "MONOCHROME1 ") - || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { - return lgrTotale; - } + if ( str_PhotometricInterpretation == "MONOCHROME1 " + || str_PhotometricInterpretation == "MONOCHROME2 " ) + { + return ImageDataSize; + } // Planar configuration = 0 : Pixels are already RGB // Planar configuration = 1 : 3 planes : R, G, B @@ -445,39 +518,39 @@ 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 = new unsigned char[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 @@ -485,71 +558,73 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) { /// 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; + 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); + } + memmove(destination, newDest, ImageDataSize); delete[] newDest; + } + else + { + // need to make RGB Pixels from R,G,B Planes + // (all the Frames at a time) - } 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 = new char[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; } /** @@ -564,11 +639,12 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) { * * @return boolean */ -bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) { - Header->SetImageDataSize(ExpectedSize); - PixelData = inData; - lgrTotale = ExpectedSize; - PixelRead = 1; +bool gdcmFile::SetImageData(void *inData, size_t expectedSize) +{ + Header->SetImageDataSize( expectedSize ); + PixelData = inData; + ImageDataSize = expectedSize; + PixelRead = 1; return true; } @@ -583,14 +659,16 @@ bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) { * @return false if write fails */ -bool gdcmFile::WriteRawData (std::string const & fileName) { +bool gdcmFile::WriteRawData(std::string const & fileName) +{ FILE *fp1; - fp1 = fopen(fileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Fail to open (write) file [%s] \n",fileName.c_str()); + fp1 = fopen(fileName.c_str(), "wb"); + if (fp1 == NULL) + { + printf("Fail to open (write) file [%s] \n", fileName.c_str()); return false; } - fwrite (PixelData,lgrTotale, 1, fp1); + fwrite (PixelData,ImageDataSize, 1, fp1); fclose (fp1); return true; @@ -606,7 +684,8 @@ bool gdcmFile::WriteRawData (std::string const & fileName) { * @return false if write fails */ -bool gdcmFile::WriteDcmImplVR (std::string const & fileName) { +bool gdcmFile::WriteDcmImplVR (std::string const & fileName) +{ return WriteBase(fileName, gdcmImplicitVR); } @@ -619,7 +698,8 @@ bool gdcmFile::WriteDcmImplVR (std::string const & fileName) { * @return false if write fails */ -bool gdcmFile::WriteDcmExplVR (std::string const & fileName) { +bool gdcmFile::WriteDcmExplVR (std::string const & fileName) +{ return WriteBase(fileName, gdcmExplicitVR); } @@ -638,7 +718,8 @@ bool gdcmFile::WriteDcmExplVR (std::string const & fileName) { * @return false if write fails */ -bool gdcmFile::WriteAcr (std::string const & fileName) { +bool gdcmFile::WriteAcr (std::string const & fileName) +{ return WriteBase(fileName, gdcmACR); } @@ -653,27 +734,30 @@ bool gdcmFile::WriteAcr (std::string const & fileName) { * @param type file type (ExplicitVR, ImplicitVR, ...) * @return false if write fails */ -bool gdcmFile::WriteBase (std::string const & fileName, FileType type) { - +bool gdcmFile::WriteBase (std::string const & fileName, FileType type) +{ FILE *fp1; - - if (PixelRead==-1 && type != gdcmExplicitVR) { + + if ( PixelRead == -1 && type != gdcmExplicitVR) + { return false; } - fp1 = fopen(fileName.c_str(),"wb"); - if (fp1 == NULL) { - printf("Failed to open (write) File [%s] \n",fileName.c_str()); - return (false); + fp1 = fopen(fileName.c_str(), "wb"); + if (fp1 == NULL) + { + printf("Failed to open (write) File [%s] \n", fileName.c_str()); + return false; } - if ( (type == gdcmImplicitVR) || (type == gdcmExplicitVR) ) { - char *filePreamble; + if ( type == gdcmImplicitVR || type == gdcmExplicitVR ) + { // writing Dicom File Preamble - filePreamble=new char[128]; - memset(filePreamble,0,128); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); + uint8_t* filePreamble = new uint8_t[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble, 128, 1, fp1); + fwrite("DICM", 4, 1, fp1); + delete[] filePreamble; } @@ -688,41 +772,51 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) { /// but pb expected if user deals with, e.g. COMPLEX images std::string rows, columns; - 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); + 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 ---------------- /// \todo get the grPixel, numPixel values (for some ACR-NEMA images only) - guint16 grPixel =Header->GetGrPixel(); - guint16 numPixel=Header->GetNumPixel();; + uint16_t grPixel = Header->GetGrPixel(); + uint16_t numPixel = Header->GetNumPixel();; // Update Pixel Data Length // the *last* of the (GrPixel, NumPixel), if many. TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel); TagDocEntryHT::iterator p2; - gdcmDocEntry *PixelElement; + gdcmDocEntry* PixelElement; - IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym + IterHT it = Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym - if (Header->GetEntry().count(key) == 1) // only the first is significant - p2=it.first; // iterator on the first (unique) synonym + if ( Header->GetEntry().count(key) == 1 ) // only the first is significant + { + p2 = it.first; // iterator on the first (unique) synonym + } else - p2=it.second;// iterator on the last synonym + { + p2 = it.second;// iterator on the last synonym + } - PixelElement=p2->second; // H Table target column (2-nd col) + PixelElement = p2->second; // H Table target column (2-nd col) // PixelElement->SetPrintLevel(2); // PixelElement->Print(); - if (PixelRead==1) - PixelElement->SetLength(lgrTotaleRaw); - else if (PixelRead==0) - PixelElement->SetLength(lgrTotale); + if ( PixelRead == 1 ) + { + PixelElement->SetLength( ImageDataSizeRaw ); + } + else if ( PixelRead == 0 ) + { + PixelElement->SetLength( ImageDataSize ); + } //PixelElement->SetPrintLevel(2); //PixelElement->Print(); @@ -734,13 +828,14 @@ bool gdcmFile::WriteBase (std::string const & fileName, FileType type) { // ...and we restore the Header to be Dicom Compliant again // just after writting - if (Header->GetFileType() == gdcmACR_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); // should be useless, now + // fwrite(PixelData, ImageDataSize, 1, fp1); // should be useless, now fclose (fp1); return true; @@ -757,73 +852,79 @@ bool gdcmFile::WriteBase (std::string const & 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: - std::cout << "SWAP value (16 bits) not allowed :i" << swap << std::endl; - } - - 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: - std::cout << "SWAP value (32 bits) not allowed : " << swap << std::endl; - } +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; + } + } } /** @@ -833,62 +934,72 @@ void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) { * @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; - - 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 */ + // F C E - // Troubles expected on Big-Endian processors ? + // Troubles expected on Big-Endian processors ? } Header->CloseFile(); 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()) { + if ( Header->IsRLELossLessTransferSyntax() ) + { bool res = (bool)gdcm_read_RLE_file (fp,destination); Header->CloseFile(); return res; @@ -896,105 +1007,130 @@ bool gdcmFile::ReadPixelData(void *destination) { // --------------- 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 = new char[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 = (bool)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 = (bool)gdcm_read_JPEG_file (fp,destination); + } + else + { + // Reading Fragment pixels + res = (bool)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; } diff --git a/src/gdcmFile.h b/src/gdcmFile.h index 5b2be693..c824a342 100644 --- a/src/gdcmFile.h +++ b/src/gdcmFile.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.h,v $ Language: C++ - Date: $Date: 2004/06/23 16:22:21 $ - Version: $Revision: 1.35 $ + Date: $Date: 2004/06/26 04:09:33 $ + Version: $Revision: 1.36 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -38,9 +38,9 @@ public: bool skip_shadow = false); virtual ~gdcmFile(); - - /// \brief returns the gdcmHeader *Header - inline gdcmHeader *GetHeader() { return Header;}; + + /// \brief returns the gdcmHeader *Header + inline gdcmHeader *GetHeader() { return Header; } // For promotion (performs a deepcopy of pointed header object) // TODO Swig gdcmFile(gdcmHeader* header); @@ -83,16 +83,15 @@ public: bool WriteAcr (std::string const & fileName); // Don't look any longer for the code : - // It's in file gdcmParsePixels.cxx + // It's in file gdcmParsePixels.cxx bool ParsePixelData(); inline virtual bool SetEntryByNumber(std::string const & content, guint16 group, guint16 element) - { - GetHeader()->SetEntryByNumber(content,group,element); - return true; //default behavior ? - } - + { + GetHeader()->SetEntryByNumber(content,group,element); + return true; //default behavior ? + } protected: bool WriteBase(std::string const & FileName, FileType type); @@ -128,11 +127,11 @@ private: void* PixelData; /// \brief Area length to receive the pixels - size_t lgrTotaleRaw; + size_t ImageDataSizeRaw; /// \brief Area length to receive the RGB pixels /// from Grey Plane + Palette Color - size_t lgrTotale; + size_t ImageDataSize; /// \brief ==1 if GetImageDataRaw was used /// ==0 if GetImageData was used @@ -141,9 +140,6 @@ private: /// wether already parsed int Parsed; - - /// To avoid file overwrite - std::string OrigFileName; }; //----------------------------------------------------------------------------- diff --git a/src/gdcmRLE.cxx b/src/gdcmRLE.cxx index 72cf3340..45f29895 100644 --- a/src/gdcmRLE.cxx +++ b/src/gdcmRLE.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmRLE.cxx,v $ Language: C++ - Date: $Date: 2004/06/23 03:36:24 $ - Version: $Revision: 1.19 $ + Date: $Date: 2004/06/26 04:09:33 $ + Version: $Revision: 1.20 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -141,7 +141,7 @@ bool gdcmFile::gdcm_read_RLE_file (FILE *fp,void * image_buffer) { *(x++) = *(b++); } } - memmove(image_buffer,newDest,lgrTotale); + memmove(image_buffer,newDest,ImageDataSize); delete[] newDest; } @@ -153,7 +153,7 @@ bool gdcmFile::gdcm_read_RLE_file (FILE *fp,void * image_buffer) { // RLE LossLess Fragment int gdcmFile::gdcm_read_RLE_fragment(char **areaToRead, long lengthToDecode, long uncompressedSegmentSize, FILE *fp) { - (void)lengthToDecode; //FIXME + (void)lengthToDecode; //FIXME long ftellRes; int count; long numberOfOutputBytes=0; -- 2.45.1