X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=0777c3d7c07c80cc721218171f4a2384b57ce781;hb=90af79e0712a2b807b2388456d13d94c50e8f0ca;hp=328845eaebdb129d2aaa08c969ff110f6645fd20;hpb=b1cbd2d3c12ccac8b257901236fe8eb27a20b117;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 328845ea..0777c3d7 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,9 +1,11 @@ // gdcmFile.cxx //----------------------------------------------------------------------------- #include "gdcmFile.h" -#include "gdcmUtil.h" +#include "gdcmDebug.h" #include "jpeg/ljpg/jpegless.h" +typedef std::pair IterHT; + //----------------------------------------------------------------------------- // Constructor / Destructor /** @@ -12,20 +14,18 @@ * 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 */ - gdcmFile::gdcmFile(gdcmHeader *header) { Header=header; SelfHeader=false; + PixelRead=-1; // no ImageData read yet. if (Header->IsReadable()) SetPixelDataSizeFromHeader(); @@ -37,25 +37,71 @@ 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()); +gdcmFile::gdcmFile(std::string & 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(); } -gdcmFile::gdcmFile(const char * filename) { - Header=new gdcmHeader(filename); +/** + * \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(); @@ -64,7 +110,7 @@ gdcmFile::gdcmFile(const char * filename) { /** * \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) { @@ -80,7 +126,7 @@ gdcmFile::~gdcmFile(void) { // Public /** * \ingroup gdcmFile - * \brief + * \brief returns the gdcmHeader *Header * @return */ gdcmHeader *gdcmFile::GetHeader(void) { @@ -157,9 +203,9 @@ size_t gdcmFile::GetImageDataSize(void) { /** * \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. */ @@ -175,12 +221,14 @@ 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); + PixelData = new char[lgrTotale]; if (PixelData) GetImageDataIntoVector(PixelData, lgrTotale); + + PixelRead=0; // no PixelRaw return(PixelData); } @@ -206,15 +254,16 @@ 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 @@ -225,7 +274,7 @@ 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 @@ -253,7 +302,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { std::string rgb= "MONOCHROME1 "; // Photometric Interpretation Header->SetEntryByNumber(rgb,0x0028,0x0004); } - // TODO : Drop Palette Color out of the Header? + /// \todo Drop Palette Color out of the Header? return lgrTotale; } @@ -269,12 +318,13 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { */ 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); + /// \todo Let gdcmHeadar user a chance to get the right value + /// Create a member lgrTotaleRaw ??? + lgrTotale /= 3; + PixelData = new char[lgrTotale]; if (PixelData) GetImageDataIntoVectorRaw(PixelData, lgrTotale); + PixelRead=1; // PixelRaw return(PixelData); } @@ -302,10 +352,11 @@ 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" @@ -314,7 +365,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { } (void)ReadPixelData(destination); - + // Number of Bits Allocated for storing a Pixel str_nb = Header->GetEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { @@ -360,7 +411,6 @@ 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); @@ -385,11 +435,12 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { return (size_t)0; } } -// DO NOT remove this code commented out. +// DO NOT remove this commented out code . // Nobody knows what's expecting you ... // Just to 'see' what was actually read on disk :-( + // FILE * f2; -// f2 = fopen("SpuriousFile.raw","wb"); +// f2 = fopen("SpuriousFile.RAW","wb"); // fwrite(destination,lgrTotale,1,f2); // fclose(f2); @@ -441,17 +492,17 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { 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 - // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - // for code optimisation + /// \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;jSetEntryByNumber(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 boolean */ -bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { +bool gdcmFile::SetImageData(void *inData, size_t ExpectedSize) { Header->SetImageDataSize(ExpectedSize); PixelData = inData; lgrTotale = ExpectedSize; + 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) - * + * \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; + FILE *fp1; fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); + printf("Fail to open (write) file [%s] \n",fileName.c_str()); return (false); } fwrite (PixelData,lgrTotale, 1, fp1); @@ -564,89 +615,96 @@ bool gdcmFile::WriteRawData (std::string fileName) { /** * \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) - * + * \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); + return WriteBase(fileName, gdcmImplicitVR); } /** * \ingroup gdcmFile - * \brief - * @param fileName name of the file to be created + * \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) { +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 */ bool gdcmFile::WriteDcmExplVR (std::string fileName) { - return WriteBase(fileName, ExplicitVR); + 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 */ bool gdcmFile::WriteAcr (std::string fileName) { - return WriteBase(fileName, ACR); + 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 */ bool gdcmFile::WriteBase (std::string fileName, FileType type) { - FILE * fp1; + FILE *fp1; + + if (PixelRead==-1 && type != gdcmExplicitVR) { + return false; + } + 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; } // -------------------------------------------------------------- @@ -655,16 +713,49 @@ 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){ + 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); + TagHeaderEntryHT::iterator p2; + gdcmHeaderEntry *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); // -------------------------------------------------------------- @@ -673,12 +764,12 @@ 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); fclose (fp1); return(true); @@ -695,7 +786,7 @@ 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) { +void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) { guint32 s32; guint16 fort,faible; int i; @@ -712,9 +803,10 @@ 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: @@ -728,33 +820,33 @@ if( nb == 32 ) 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; @@ -771,28 +863,26 @@ 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;pGetPixelSize()*8* Header->GetSamplesPerPixel(), + Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), ln); res=1; // in order not to break the loop