X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=aa60bd7683b271c24715a09e712ccb35c61ba194;hb=1aad11d86fa8d683d4f1a38b6f0483444e67f217;hp=62e75550f9a5810e112f8f7deecca5a8f019d27e;hpb=72911a1e847536580a21f85f211c0a14cdcf944c;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 62e75550..aa60bd76 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,7 +1,7 @@ // gdcmFile.cxx //----------------------------------------------------------------------------- #include "gdcmFile.h" -#include "gdcmUtil.h" +#include "gdcmDebug.h" #include "jpeg/ljpg/jpegless.h" typedef std::pair IterHT; @@ -22,7 +22,6 @@ typedef std::pair IterHT; * @param header file to be opened for reading datas * @return */ - gdcmFile::gdcmFile(gdcmHeader *header) { Header=header; SelfHeader=false; @@ -44,9 +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. @@ -66,9 +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. @@ -79,7 +110,7 @@ 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) { @@ -193,7 +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); @@ -223,13 +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) { @@ -242,7 +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 @@ -270,7 +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; } @@ -286,10 +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 @@ -460,17 +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; @@ -513,7 +545,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { *(x++) = *(c++); } memmove(destination,newDest,lgrTotale); - free(newDest); + delete[] newDest; } break; } @@ -535,7 +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; } @@ -647,16 +679,14 @@ bool gdcmFile::WriteAcr (std::string fileName) { * (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, DICOMDIR, ...) + * @param type file type (ExplicitVR, ImplicitVR, ...) * @return false if write fails */ bool gdcmFile::WriteBase (std::string fileName, FileType type) { 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 != ExplicitVR) { return false; } @@ -669,10 +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; } // -------------------------------------------------------------- @@ -682,8 +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){ @@ -694,7 +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();; @@ -724,7 +754,6 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { //PixelElement->SetPrintLevel(2); //PixelElement->Print(); - Header->Write(fp1, type); // -------------------------------------------------------------- @@ -930,7 +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); }