X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=e13944b2a10be1c6cd2d270e3fa7c568ecf75a95;hb=d25c25666b3d84678bbb8c178000a583c71a2db4;hp=2442edf0125d90c276e1b00dc657661ebab304d0;hpb=001ea156121341aef6d2445842e5a68ee9723252;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 2442edf0..e13944b2 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: 2004/06/21 04:52:08 $ + Version: $Revision: 1.104 $ + + 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; +typedef std::pair IterHT; //----------------------------------------------------------------------------- // Constructor / Destructor @@ -22,7 +38,6 @@ typedef std::pair IterHT; * @param header file to be opened for reading datas * @return */ - gdcmFile::gdcmFile(gdcmHeader *header) { Header=header; SelfHeader=false; @@ -44,31 +59,25 @@ gdcmFile::gdcmFile(gdcmHeader *header) { * 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(std::string & filename) { - Header=new gdcmHeader(filename.c_str()); - SelfHeader=true; - PixelRead=-1; // no ImageData read yet. - - if (Header->IsReadable()) - 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 - */ - 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. @@ -79,7 +88,7 @@ gdcmFile::gdcmFile(std::string & 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) { @@ -95,7 +104,7 @@ gdcmFile::~gdcmFile(void) { // Public /** * \ingroup gdcmFile - * \brief + * \brief returns the gdcmHeader *Header * @return */ gdcmHeader *gdcmFile::GetHeader(void) { @@ -193,10 +202,15 @@ size_t gdcmFile::GetImageDataSizeRaw(void) { * NULL if alloc fails */ void * gdcmFile::GetImageData (void) { - PixelData = (void *) malloc(lgrTotale); - if (PixelData) + PixelData = new char[lgrTotale]; + if (PixelData) { GetImageDataIntoVector(PixelData, lgrTotale); + GetHeader()->SetEntryVoidAreaByNumber(PixelData, + GetHeader()->GetGrPixel(), + GetHeader()->GetNumPixel()); + } PixelRead=0; // no PixelRaw + return(PixelData); } @@ -222,15 +236,16 @@ 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 @@ -241,7 +256,7 @@ 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 @@ -269,7 +284,7 @@ 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; } @@ -285,12 +300,17 @@ 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); - if (PixelData) + /// \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); + GetHeader()->SetEntryVoidAreaByNumber(PixelData, + GetHeader()->GetGrPixel(), + GetHeader()->GetNumPixel()); + } PixelRead=1; // PixelRaw return(PixelData); } @@ -319,7 +339,7 @@ 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; @@ -332,7 +352,7 @@ 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 ) { @@ -378,7 +398,6 @@ 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); @@ -403,7 +422,7 @@ 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 :-( @@ -460,17 +479,17 @@ 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 ? - * \toto : 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); } @@ -568,7 +589,7 @@ bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { */ bool gdcmFile::WriteRawData (std::string fileName) { - FILE * fp1; + FILE *fp1; fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { printf("Fail to open (write) file [%s] \n",fileName.c_str()); @@ -581,7 +602,8 @@ bool gdcmFile::WriteRawData (std::string fileName) { /** * \ingroup gdcmFile - * \brief Writes on disk A SINGLE Dicom file + * \brief Writes on disk A SINGLE Dicom file, + * using the Implicit Value Representation convention * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created * (any already existing file is overwritten) @@ -589,58 +611,60 @@ bool gdcmFile::WriteRawData (std::string fileName) { */ 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 - * + * \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, ...) @@ -648,11 +672,9 @@ bool gdcmFile::WriteAcr (std::string fileName) { */ bool gdcmFile::WriteBase (std::string fileName, FileType type) { - FILE * fp1; + FILE *fp1; - if (PixelRead==-1 && type != DICOMDIR) { -/* std::cout << "U never Read the pixels; U cannot write the file" - << std::endl;*/ + if (PixelRead==-1 && type != gdcmExplicitVR) { return false; } @@ -662,13 +684,14 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { 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); - free (filePreamble); + delete[] filePreamble; } // -------------------------------------------------------------- @@ -678,11 +701,11 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { // 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 + /// \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); @@ -690,7 +713,7 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { } // ----------------- End of Special Patch ---------------- - // TODO : get the grPixel, numPixel values (for some ACR-NEMA images only) + /// \todo get the grPixel, numPixel values (for some ACR-NEMA images only) guint16 grPixel =Header->GetGrPixel(); guint16 numPixel=Header->GetNumPixel();; @@ -699,8 +722,8 @@ 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 @@ -720,7 +743,6 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { //PixelElement->SetPrintLevel(2); //PixelElement->Print(); - Header->Write(fp1, type); // -------------------------------------------------------------- @@ -729,13 +751,13 @@ 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); } @@ -751,7 +773,7 @@ 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; @@ -768,9 +790,10 @@ 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: @@ -784,33 +807,33 @@ 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; @@ -827,7 +850,7 @@ return; * @param destination where the pixel data should be stored. * */ -bool gdcmFile::ReadPixelData(void* destination) { +bool gdcmFile::ReadPixelData(void *destination) { FILE *fp; @@ -846,7 +869,7 @@ bool gdcmFile::ReadPixelData(void* destination) { 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