X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=aa60bd7683b271c24715a09e712ccb35c61ba194;hb=c5618e6b8276e1b21bbea354fe8bcba3c78eb4bd;hp=2ae2bd0974f56f11139cbdb2f3928b8d42833701;hpb=81e328d78c2028a7c2ecb86e6cee04839f4d56b2;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 2ae2bd09..aa60bd76 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -43,9 +43,25 @@ 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()); +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. @@ -65,9 +81,25 @@ gdcmFile::gdcmFile(std::string & filename) { * 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) { - Header=new gdcmHeader(filename); + 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. @@ -192,7 +224,7 @@ size_t gdcmFile::GetImageDataSizeRaw(void) { * NULL if alloc fails */ void * gdcmFile::GetImageData (void) { - PixelData = (void *) malloc(lgrTotale); + PixelData = new char[lgrTotale]; if (PixelData) GetImageDataIntoVector(PixelData, lgrTotale); @@ -222,13 +254,14 @@ 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 * newDest = new (unsigned char)[lgrTotale]; unsigned char * a = (unsigned char *)destination; unsigned char * lutRGBA = Header->GetLUTRGBA(); if (lutRGBA) { @@ -241,7 +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 @@ -269,7 +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; } @@ -285,10 +318,10 @@ 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 @@ -459,17 +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 * 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 * newDest = new char[lgrTotale]; char * x = newDest; char * a = (char *)destination; char * b = a + l; @@ -512,7 +545,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { *(x++) = *(c++); } memmove(destination,newDest,lgrTotale); - free(newDest); + delete[] newDest; } break; } @@ -534,7 +567,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { std::string planConfig = "0"; // Planar Configuration Header->SetEntryByNumber(planConfig,0x0028,0x0006); - // TODO : Drop Palette Color out of the Header? + /// \todo Drop Palette Color out of the Header? return lgrTotale; } @@ -666,10 +699,10 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { if ( (type == ImplicitVR) || (type == ExplicitVR) ) { char * filePreamble; // writing Dicom File Preamble - filePreamble=(char*)calloc(128,1); + filePreamble=new char[128]; fwrite(filePreamble,128,1,fp1); fwrite("DICM",4,1,fp1); - free (filePreamble); + delete[] filePreamble; } // -------------------------------------------------------------- @@ -679,8 +712,8 @@ 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){ @@ -691,7 +724,7 @@ 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();; @@ -721,7 +754,6 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { //PixelElement->SetPrintLevel(2); //PixelElement->Print(); - Header->Write(fp1, type); // -------------------------------------------------------------- @@ -927,7 +959,7 @@ 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); }