X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=fa98cf0d5d56175ecafbf36fa0d833dcbaafea21;hb=05f9a9731209a5c98895a57c6abca609f8e9b312;hp=607c37ae1bfd2b1e4c0654c4337786b9981324ce;hpb=7d8572bf6b911f746d4dc5389bb3270868957373;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 607c37ae..fa98cf0d 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,10 +1,26 @@ -// gdcmFile.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/06/23 16:22:21 $ + Version: $Revision: 1.109 $ + + 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 "gdcmDebug.h" #include "jpeg/ljpg/jpegless.h" -typedef std::pair IterHT; +typedef std::pair IterHT; //----------------------------------------------------------------------------- // Constructor / Destructor @@ -20,7 +36,7 @@ typedef std::pair IterHT; * 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; @@ -54,7 +70,7 @@ gdcmFile::gdcmFile(gdcmHeader *header) { * with a FALSE value for the 'enable_sequence' param. * ('public elements' may be embedded in 'shadow Sequences') */ -gdcmFile::gdcmFile(std::string & filename, +gdcmFile::gdcmFile(std::string const & filename, bool exception_on_error, bool enable_sequences, bool ignore_shadow) { @@ -69,51 +85,13 @@ gdcmFile::gdcmFile(std::string & filename, SetPixelDataSizeFromHeader(); } -/** - * \ingroup gdcmFile - * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant - * 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 - * 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 - * @param exception_on_error whether we throw an exception or not - * @param enable_sequences = true to allow the header - * to be parsed *inside* the SeQuences, - * when they have an actual length - * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files - * @param ignore_shadow to allow skipping the shadow elements, - * to save memory space. - * \warning The TRUE value for this param has to be used - * with a FALSE value for the 'enable_sequence' param. - * ('public elements' may be embedded in 'shadow Sequences') - */ - gdcmFile::gdcmFile(const char *filename, - bool exception_on_error, - bool enable_sequences, - 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(); -} - /** * \ingroup gdcmFile * \brief canonical destructor * \note If the gdcmHeader is created by the gdcmFile, it is destroyed * by the gdcmFile */ -gdcmFile::~gdcmFile(void) { +gdcmFile::~gdcmFile() { if(SelfHeader) delete Header; Header=NULL; @@ -124,24 +102,16 @@ gdcmFile::~gdcmFile(void) { //----------------------------------------------------------------------------- // Public -/** - * \ingroup gdcmFile - * \brief returns the gdcmHeader *Header - * @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 @@ -181,7 +151,7 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { * 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 @@ -196,8 +166,8 @@ 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 lgrTotale; } /** @@ -209,8 +179,8 @@ size_t gdcmFile::GetImageDataSize(void) { * \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 lgrTotaleRaw; } /** @@ -223,13 +193,17 @@ size_t gdcmFile::GetImageDataSizeRaw(void) { * @return Pointer to newly allocated pixel data. * NULL if alloc fails */ -void * gdcmFile::GetImageData (void) { - PixelData = new char[lgrTotale]; - if (PixelData) +void * gdcmFile::GetImageData () { + PixelData = new unsigned char[lgrTotale]; //consistant with GetImageDataIntoVector + if (PixelData) { GetImageDataIntoVector(PixelData, lgrTotale); - + GetHeader()->SetEntryVoidAreaByNumber(PixelData, + GetHeader()->GetGrPixel(), + GetHeader()->GetNumPixel()); + } PixelRead=0; // no PixelRaw - return(PixelData); + + return PixelData; } /** @@ -255,19 +229,20 @@ void * gdcmFile::GetImageData (void) { */ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { //size_t l = GetImageDataIntoVectorRaw (destination, MaxSize); - GetImageDataIntoVectorRaw (destination, MaxSize); + GetImageDataIntoVectorRaw (destination, MaxSize); PixelRead=0 ; // no PixelRaw if (!Header->HasLUT()) return lgrTotale; // 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(); - if (lutRGBA) { + 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; + memmove(newDest, destination, l);// move Gray pixels to temp area + int j; for (int i=0;iSetEntryByNumber(spp,0x0028,0x0002); std::string rgb= "RGB "; // Photometric Interpretation @@ -289,20 +264,20 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { 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 - + // 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? + Header->SetEntryByNumber(rgb,0x0028,0x0004); + } + /// \todo Drop Palette Color out of the Header? return lgrTotale; } @@ -312,20 +287,26 @@ 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) { +void * gdcmFile::GetImageDataRaw () { if (Header->HasLUT()) /// \todo Let gdcmHeadar user a chance to get the right value - /// Create a member lgrTotaleRaw ??? + /// Create a member lgrTotaleRaw ??? lgrTotale /= 3; - PixelData = new char[lgrTotale]; - if (PixelData) + PixelData = new unsigned char[lgrTotale]; + + if (PixelData) { GetImageDataIntoVectorRaw(PixelData, lgrTotale); + GetHeader()->SetEntryVoidAreaByNumber(PixelData, + GetHeader()->GetGrPixel(), + GetHeader()->GetNumPixel()); + } PixelRead=1; // PixelRaw - return(PixelData); + + return PixelData; } /** @@ -363,33 +344,33 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) { "than caller's expected MaxSize"); return (size_t)0; } - - (void)ReadPixelData(destination); - - // Number of Bits Allocated for storing a Pixel + + ReadPixelData(destination); + + // Number of Bits Allocated for storing a Pixel 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 + } + // Number of Bits actually used str_nbu=Header->GetEntryByNumber(0x0028,0x0101); if (str_nbu == GDCM_UNFOUND ) { nbu = nb; } else { nbu = atoi(str_nbu.c_str() ); - } - // High Bit Position + } + // High Bit Position 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 + } + // Pixel sign + // 0 = Unsigned + // 1 = Signed str_signe=Header->GetEntryByNumber(0x0028,0x0103); if (str_signe == GDCM_UNFOUND ) { signe = 0; // default is unsigned @@ -407,8 +388,8 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) { guint16 *deb = (guint16 *)destination; for(int i = 0; iGetEntryByNumber(0x0028,0x0004); - + if ( (str_PhotometricInterpretation == "MONOCHROME1 ") || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { return lgrTotale; @@ -480,15 +461,15 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) { { 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 - // + + // 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(); @@ -501,9 +482,9 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) { /// \todo : Replace by the 'well known' integer computation /// counterpart - /// see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf + /// see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf /// for code optimisation - + for (int i=0;iSetEntryByNumber(planConfig,0x0028,0x0006); - - /// \todo Drop Palette Color out of the Header? + + /// \todo Drop Palette Color out of the Header? return lgrTotale; } /** * \ingroup gdcmFile - * \brief performs a shadow copy (not a deep copy) of the user given + * \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 @@ -581,13 +562,15 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) { * @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); + PixelRead = 1; + + return true; } /** @@ -597,19 +580,20 @@ bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) { * 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) { +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()); - return (false); - } + return false; + } fwrite (PixelData,lgrTotale, 1, fp1); fclose (fp1); - return(true); + + return true; } /** @@ -619,39 +603,26 @@ bool gdcmFile::WriteRawData (std::string fileName) { * 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 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 - */ - -bool gdcmFile::WriteDcmImplVR (const char *fileName) { - return WriteDcmImplVR (std::string (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 * (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 Writes on disk A SINGLE Dicom file, @@ -664,11 +635,11 @@ bool gdcmFile::WriteDcmExplVR (std::string fileName) { * \warning 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::WriteAcr (std::string fileName) { - return WriteBase(fileName, ACR); +bool gdcmFile::WriteAcr (std::string const & fileName) { + return WriteBase(fileName, gdcmACR); } //----------------------------------------------------------------------------- @@ -680,14 +651,14 @@ bool gdcmFile::WriteAcr (std::string fileName) { * @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) { FILE *fp1; - if (PixelRead==-1 && type != ExplicitVR) { - return false; + if (PixelRead==-1 && type != gdcmExplicitVR) { + return false; } fp1 = fopen(fileName.c_str(),"wb"); @@ -696,7 +667,7 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { return (false); } - if ( (type == ImplicitVR) || (type == ExplicitVR) ) { + if ( (type == gdcmImplicitVR) || (type == gdcmExplicitVR) ) { char *filePreamble; // writing Dicom File Preamble filePreamble=new char[128]; @@ -717,12 +688,12 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { /// but pb expected if user deals with, e.g. COMPLEX images std::string rows, columns; - if ( Header->GetFileType() == ACR_LIBIDO){ + 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) @@ -734,8 +705,8 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { // the *last* of the (GrPixel, NumPixel), if many. TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel); - TagHeaderEntryHT::iterator p2; - gdcmHeaderEntry *PixelElement; + TagDocEntryHT::iterator p2; + gdcmDocEntry *PixelElement; IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym @@ -763,15 +734,16 @@ 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){ + 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, lgrTotale, 1, fp1); // should be useless, now fclose (fp1); - return(true); + + return true; } //----------------------------------------------------------------------------- @@ -786,17 +758,17 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { * @param nb Pixels Bit number */ void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) { -guint32 s32; -guint16 fort,faible; -int i; + guint32 s32; + guint16 fort,faible; + int i; -if(nb == 16) - switch(swap) { + if(nb == 16) + switch(swap) { case 0: case 12: case 1234: break; - + case 21: case 3412: case 2143: @@ -805,15 +777,15 @@ if(nb == 16) for(i=0;i>8) | ((((unsigned short int *)im)[i])<<8); - } + } break; - + default: - printf("SWAP value (16 bits) not allowed : %d\n", swap); + std::cout << "SWAP value (16 bits) not allowed :i" << swap << std::endl; } -if( nb == 32 ) - switch (swap) { + if( nb == 32 ) + switch (swap) { case 0: case 1234: break; @@ -848,11 +820,10 @@ if( nb == 32 ) ((unsigned long int *)im)[i]=(s32<<16)|fort; } break; - + default: - printf("SWAP value (32 bits) not allowed : %d\n", swap); + std::cout << "SWAP value (32 bits) not allowed : " << swap << std::endl; } -return; } /** @@ -891,12 +862,12 @@ bool gdcmFile::ReadPixelData(void *destination) { /* A */ /* B */ /* D */ *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); /* F */ /* C */ /* E */ - - // Troubles expected on Big-Endian processors ? + + // Troubles expected on Big-Endian processors ? } Header->CloseFile(); - return(true); + return true; } // ---------------------- Uncompressed File @@ -941,7 +912,7 @@ bool gdcmFile::ReadPixelData(void *destination) { bool jpg2000 = Header->IsJPEG2000(); bool jpgLossless = Header->IsJPEGLossless(); - + bool res = true; guint16 ItemTagGr,ItemTagEl; int ln; @@ -987,13 +958,12 @@ bool gdcmFile::ReadPixelData(void *destination) { 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); + (unsigned short *)destination, + Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), + ln); res=1; // in order not to break the loop } // ------------------------------------- endif (JPEGLossless)