X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=bd35f100dc44b0df4eb8eb4874f0fdf6bdc0c559;hb=45a9005ae5c1975bbe932e43c8080a83c9daf29e;hp=4ead10ad6f3e742d1e0c4552dded5c23ca4d011a;hpb=e3a31fcb86b0e19229473ad24788e5e9df423faa;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 4ead10ad..bd35f100 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,9 +1,27 @@ -// gdcmFile.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmFile.cxx,v $ + Language: C++ + Date: $Date: 2004/06/23 09:30:22 $ + Version: $Revision: 1.108 $ + + 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 /** @@ -12,20 +30,18 @@ * 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; + PixelRead=-1; // no ImageData read yet. if (Header->IsReadable()) SetPixelDataSizeFromHeader(); @@ -37,27 +53,33 @@ 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 + * @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(std::string & filename) { - Header=new gdcmHeader(filename.c_str()); - SelfHeader=true; - - if (Header->IsReadable()) - SetPixelDataSizeFromHeader(); -} - -gdcmFile::gdcmFile(const char * filename) { - Header=new gdcmHeader(filename); +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()) SetPixelDataSizeFromHeader(); @@ -65,13 +87,11 @@ gdcmFile::gdcmFile(const char * filename) { /** * \ingroup gdcmFile - * \brief Destructor dedicated to writing a new DICOMV3 part10 compliant - * file (see SetFileName, SetDcmTag and Write) - * \Note If the gdcmHeader is created by the gdcmFile, it is destroyed + * \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; @@ -82,26 +102,16 @@ gdcmFile::~gdcmFile(void) { //----------------------------------------------------------------------------- // Public -/** - * \ingroup gdcmFile - * \brief - * @return - */ -gdcmHeader *gdcmFile::GetHeader(void) { - return(Header); -} /** * \ingroup gdcmFile - * \brief calcule la longueur (in bytes) A ALLOUER pour recevoir les - * pixels de l'image ou DES images dans le cas d'un multiframe - * - * ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels - * (dans le cas d'images compressees, elle n'a pas de sens). - * - * @return longueur a allouer + * \brief computes the length (in bytes) to ALLOCATE to receive the + * 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 @@ -130,7 +140,7 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { int nb; std::string str_nb; - str_nb=Header->GetPubEntryByNumber(0x0028,0x0100); + str_nb=Header->GetEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { @@ -140,8 +150,8 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize() * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel(); std::string str_PhotometricInterpretation = - Header->GetPubEntryByNumber(0x0028,0x0004); - + Header->GetEntryByNumber(0x0028,0x0004); + /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/ // pb when undealt Segmented Palette Color @@ -156,21 +166,21 @@ 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; } /** * \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 - - * \ warning to be used with GetImagePixelsRaw() + * 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 lgrTotaleRaw; } /** @@ -178,16 +188,22 @@ size_t gdcmFile::GetImageDataSizeRaw(void) { * \brief Allocates necessary memory, copies the pixel data * (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 - Transforms single Grey plane + 3 Palettes into a RGB Plane + * 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) +void * gdcmFile::GetImageData () { + PixelData = new unsigned char[lgrTotale]; //consistant with GetImageDataIntoVector + if (PixelData) { GetImageDataIntoVector(PixelData, lgrTotale); - return(PixelData); + GetHeader()->SetEntryVoidAreaByNumber(PixelData, + GetHeader()->GetGrPixel(), + GetHeader()->GetNumPixel()); + } + PixelRead=0; // no PixelRaw + + return PixelData; } /** @@ -212,15 +228,17 @@ void * gdcmFile::GetImageData (void) { * failure e.g. MaxSize is lower than necessary. */ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { - size_t l = GetImageDataIntoVectorRaw (destination, MaxSize); - + //size_t l = 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 = (unsigned char *)malloc(lgrTotale); - unsigned char * a = (unsigned char *)destination; - unsigned char * lutRGBA = Header->GetLUTRGBA(); + unsigned char *newDest = new unsigned char[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 @@ -231,7 +249,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { *a++ = lutRGBA[j+1]; *a++ = lutRGBA[j+2]; } - free(newDest); + delete[] newDest; // now, it's an RGB image // Lets's write it in the Header @@ -239,31 +257,27 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // CreateOrReplaceIfExist ? std::string spp = "3"; // Samples Per Pixel - Header->SetPubEntryByNumber(spp,0x0028,0x0002); + Header->SetEntryByNumber(spp,0x0028,0x0002); std::string rgb= "RGB "; // Photometric Interpretation - Header->SetPubEntryByNumber(rgb,0x0028,0x0004); + Header->SetEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration - Header->SetPubEntryByNumber(planConfig,0x0028,0x0006); + Header->SetEntryByNumber(planConfig,0x0028,0x0006); } else { // need to make RGB Pixels (?) - // from grey Pixels (?!) - // and Gray Lut (!?!) + // from grey Pixels (?!) + // and Gray Lut (!?!) // or Segmented xxx Palette Color Lookup Table Data and so on - - // Well . I'll wait till I find such an image - - // Oops! I get one (gdcm-US-ALOKA-16.dcm) - // No idea how to manage it - // 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 - Header->SetPubEntryByNumber(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; } @@ -272,20 +286,27 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { * \brief Allocates necessary memory, copies the pixel data * (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 + * Transforms 3 planes R, G, B into a single 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()) - lgrTotale /= 3; // TODO Let gdcmHeadar user a chance - // to get the right value - // Create a member lgrTotaleRaw ??? - PixelData = (void *) malloc(lgrTotale); - if (PixelData) + /// \todo Let gdcmHeadar user a chance to get the right value + /// Create a member lgrTotaleRaw ??? + lgrTotale /= 3; + PixelData = new unsigned char[lgrTotale]; + + if (PixelData) { GetImageDataIntoVectorRaw(PixelData, lgrTotale); - return(PixelData); + GetHeader()->SetEntryVoidAreaByNumber(PixelData, + GetHeader()->GetGrPixel(), + GetHeader()->GetNumPixel()); + } + PixelRead=1; // PixelRaw + + return PixelData; } /** @@ -312,10 +333,11 @@ void * gdcmFile::GetImageDataRaw (void) { * @return On success, the number of bytes actually copied. Zero on * failure e.g. MaxSize is lower than necessary. */ -size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { +size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t MaxSize) { int nb, nbu, highBit, signe; std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; + PixelRead=1 ; // PixelRaw if ( lgrTotale > MaxSize ) { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" @@ -323,26 +345,24 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { return (size_t)0; } - (void)ReadPixelData(destination); - - // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb = Header->GetPubEntryByNumber(0x0028,0x0100); + 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() ); - } - - // Nombre de Bits Utilises - str_nbu=Header->GetPubEntryByNumber(0x0028,0x0101); + } + // 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() ); - } - - // Position du Bit de Poids Fort - str_highBit=Header->GetPubEntryByNumber(0x0028,0x0102); + } + // High Bit Position + str_highBit=Header->GetEntryByNumber(0x0028,0x0102); if (str_highBit == GDCM_UNFOUND ) { highBit = nb - 1; } else { @@ -351,14 +371,14 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // Pixel sign // 0 = Unsigned // 1 = Signed - str_signe=Header->GetPubEntryByNumber(0x0028,0x0103); + str_signe=Header->GetEntryByNumber(0x0028,0x0103); if (str_signe == GDCM_UNFOUND ) { signe = 0; // default is unsigned } else { signe = atoi(str_signe.c_str() ); } - // re arange bytes inside the integer + // re arange bytes inside the integer (processor endianity) if (nb != 8) SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb); @@ -372,7 +392,6 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { deb++; } } - // re arange bits inside the bytes if (nbu != nb){ int l = (int)lgrTotale / (nb/8); @@ -393,15 +412,16 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { deb ++; } } else { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image"); - return (size_t)0; + dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); + return 0; } } - +// DO NOT remove this commented out code . +// Nobody knows what's expecting you ... // Just to 'see' what was actually read on disk :-( -// Some troubles expected + // FILE * f2; -// f2 = fopen("SpuriousFile.raw","wb"); +// f2 = fopen("SpuriousFile.RAW","wb"); // fwrite(destination,lgrTotale,1,f2); // fclose(f2); @@ -409,7 +429,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // ------------------- std::string str_PhotometricInterpretation = - Header->GetPubEntryByNumber(0x0028,0x0004); + Header->GetEntryByNumber(0x0028,0x0004); if ( (str_PhotometricInterpretation == "MONOCHROME1 ") || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { @@ -444,27 +464,27 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // Warning : YBR_FULL_422 acts as RGB // : we need to make RGB Pixels from Planes Y,cB,cR - // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - // for code optimisation // to see the tricks about YBR_FULL, YBR_FULL_422, - // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : + // 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; - + 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; double R,G,B; - // TODO : Replace by the 'well known' - // integer computation counterpart + /// \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;iGetXSize()*Header->GetYSize()*Header->GetZSize(); - char * newDest = (char*) malloc(lgrTotale); - char * x = newDest; - char * a = (char *)destination; - char * b = a + l; - char * c = b + l; + char *newDest = new char[lgrTotale]; + char *x = newDest; + char *a = (char *)destination; + char *b = a + l; + char *c = b + l; for (int j=0;jSetPubEntryByNumber(spp,0x0028,0x0002); + Header->SetEntryByNumber(spp,0x0028,0x0002); std::string rgb="RGB "; // Photometric Interpretation - Header->SetPubEntryByNumber(rgb,0x0028,0x0004); + Header->SetEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration - Header->SetPubEntryByNumber(planConfig,0x0028,0x0006); + Header->SetEntryByNumber(planConfig,0x0028,0x0006); - // TODO : Drop Palette Color out of the Header? + /// \todo Drop Palette Color out of the Header? return lgrTotale; } /** * \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 shadow 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 integer acts as a boolean + * @return boolean */ -bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { +bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) { Header->SetImageDataSize(ExpectedSize); PixelData = inData; lgrTotale = ExpectedSize; - return(true); + PixelRead = 1; + + return true; } /** * \ingroup gdcmFile - * \brief Ecrit sur disque les pixels d'UNE image - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca sera à l'utilisateur d'appeler son Reader correctement - * (Equivalent a IdImaWriteRawFile) - * - * @param fileName - * @return + * \brief Writes on disk A SINGLE Dicom file + * NO test is performed on processor "Endiannity". + * It's up to the user to call his Reader properly + * @param fileName name of the file to be created + * (any already existing file is over written) + * @return false if write fails */ -bool gdcmFile::WriteRawData (std::string fileName) { - FILE * fp1; +bool gdcmFile::WriteRawData (std::string const & fileName) { + FILE *fp1; fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); - return (false); + printf("Fail to open (write) file [%s] \n",fileName.c_str()); + return false; } fwrite (PixelData,lgrTotale, 1, fp1); fclose (fp1); - return(true); + + return true; } /** * \ingroup gdcmFile - * \brief Ecrit sur disque UNE image Dicom - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * - * @param fileName - * @return int acts as a boolean + * \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 (std::string fileName) { - return WriteBase(fileName, ImplicitVR); +bool gdcmFile::WriteDcmImplVR (std::string const & fileName) { + return WriteBase(fileName, gdcmImplicitVR); } /** * \ingroup gdcmFile - * \brief - * @param fileName - * @return int acts as a boolean - */ - -bool gdcmFile::WriteDcmImplVR (const char* fileName) { - return WriteDcmImplVR (std::string (fileName)); -} - -/** - * \ingroup gdcmFile - * \brief - * @param fileName - * @return int acts as a boolean +* \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 */ -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 si un header DICOM est fourni en entree, - * les groupes < 0x0008 et les groupes impairs sont ignores) - * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * - * @param fileName - * @return int acts as a boolean + * \warning if a DICOM_V3 header is supplied, + * groups < 0x0008 and shadow groups are ignored + * \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 */ -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 - * @param type - * - * @return int acts as a boolean + * \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 */ -bool gdcmFile::WriteBase (std::string FileName, FileType type) { +bool gdcmFile::WriteBase (std::string const & fileName, FileType type) { + + FILE *fp1; + + if (PixelRead==-1 && type != gdcmExplicitVR) { + return false; + } - FILE * fp1; - fp1 = fopen(FileName.c_str(),"wb"); + fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); + 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) ) { + char *filePreamble; // writing Dicom File Preamble - filePreamble=(char*)calloc(128,1); + filePreamble=new char[128]; + memset(filePreamble,0,128); fwrite(filePreamble,128,1,fp1); fwrite("DICM",4,1,fp1); + delete[] filePreamble; } // -------------------------------------------------------------- @@ -665,16 +683,49 @@ 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->GetPubEntryByNumber(0x0028, 0x0010); - columns = Header->GetPubEntryByNumber(0x0028, 0x0011); - Header->SetPubEntryByNumber(columns, 0x0028, 0x0010); - Header->SetPubEntryByNumber(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();; + + // Update Pixel Data Length + // the *last* of the (GrPixel, NumPixel), if many. + + TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel); + TagDocEntryHT::iterator p2; + gdcmDocEntry *PixelElement; + + 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 + else + p2=it.second;// iterator on the last synonym + + 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); + + //PixelElement->SetPrintLevel(2); + //PixelElement->Print(); Header->Write(fp1, type); // -------------------------------------------------------------- @@ -683,15 +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){ - Header->SetPubEntryByNumber(rows , 0x0028, 0x0010); - Header->SetPubEntryByNumber(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, lgrTotale, 1, fp1); // should be useless, now fclose (fp1); - return(true); + + return true; } //----------------------------------------------------------------------------- @@ -705,13 +757,13 @@ 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; +void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) { + guint32 s32; + guint16 fort,faible; + int i; -if(nb == 16) - switch(swap) { + if(nb == 16) + switch(swap) { case 0: case 12: case 1234: @@ -722,56 +774,56 @@ if(nb == 16) case 2143: case 4321: - for(i=0;i>8) - | ((((unsigned short int*)im)[i])<<8); + for(i=0;i>8) + | ((((unsigned short int *)im)[i])<<8); + } break; default: - printf("valeur de SWAP (16 bits) not allowed : %d\n", swap); + printf("SWAP value (16 bits) not allowed : %d\n", swap); } -if( nb == 32 ) - switch (swap) { + if( nb == 32 ) + switch (swap) { case 0: case 1234: break; case 4321: - for(i=0;i>16; + 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; + ((unsigned long int *)im)[i]=(s32<<16)|fort; } break; case 2143: - for(i=0;i>16; + 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; + ((unsigned long int *)im)[i]=(s32<<16)|faible; } break; case 3412: - for(i=0;i>16; + for(i=0;i>16; s32=faible; - ((unsigned long int*)im)[i]=(s32<<16)|fort; + ((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; } /** @@ -781,41 +833,41 @@ return; * @param destination where the pixel data should be stored. * */ -bool gdcmFile::ReadPixelData(void* destination) { +bool gdcmFile::ReadPixelData(void *destination) { FILE *fp; if ( !(fp=Header->OpenFile())) return false; - 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] */ + if (Header->GetBitsAllocated()==12) { int nbPixels = Header->GetXSize() * Header->GetYSize(); unsigned char b0, b1, b2; - unsigned short int* pdestination = (unsigned short int*)destination; + 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 ? } - return(true); + + Header->CloseFile(); + return true; } // ---------------------- Uncompressed File @@ -826,7 +878,6 @@ bool gdcmFile::ReadPixelData(void* destination) { Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - if ( ItemRead != 1 ) { Header->CloseFile(); return false; @@ -838,13 +889,14 @@ bool gdcmFile::ReadPixelData(void* destination) { // ---------------------- Run Length Encoding if (Header->IsRLELossLessTransferSyntax()) { - bool res = (bool)gdcm_read_RLE_file (fp,destination); - return res; + bool res = (bool)gdcm_read_RLE_file (fp,destination); + Header->CloseFile(); + return res; } // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 int nb; - std::string str_nb=Header->GetPubEntryByNumber(0x0028,0x0100); + std::string str_nb=Header->GetEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { @@ -857,15 +909,15 @@ bool gdcmFile::ReadPixelData(void* destination) { int taille = Header->GetXSize() * Header->GetYSize() * Header->GetSamplesPerPixel(); long fragmentBegining; // for ftell, fseek - + bool jpg2000 = Header->IsJPEG2000(); bool jpgLossless = Header->IsJPEGLossless(); - + bool res = true; guint16 ItemTagGr,ItemTagEl; int ln; - // Position on begining of Jpeg Pixels + // 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 @@ -879,7 +931,7 @@ bool gdcmFile::ReadPixelData(void* destination) { if (ln != 0) { // What is it used for ?!? - char *BasicOffsetTableItemValue = (char *)malloc(ln+1); + char *BasicOffsetTableItemValue = new char[ln+1]; fread(BasicOffsetTableItemValue,ln,1,fp); } @@ -892,7 +944,7 @@ bool gdcmFile::ReadPixelData(void* destination) { } // 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); @@ -908,10 +960,9 @@ bool gdcmFile::ReadPixelData(void* destination) { } // ------------------------------------- endif (JPEG2000) else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG - JPEGLosslessDecodeImage (fp, // Reading Fragment pixels (unsigned short *)destination, - Header->GetPixelSize()*8* Header->GetSamplesPerPixel(), + Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), ln); res=1; // in order not to break the loop