X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=8e12ec3ac10e3d866f04fb814c02aff5bb97b138;hb=5285811a83dcd08d4e9364c74ebe1b163688f5bb;hp=f802dcb86ae9a4515f136e6c9998d89a8ce73e19;hpb=be70f5cdc8ac472bff8ad8a36637457fe49778bd;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index f802dcb8..8e12ec3a 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) { @@ -193,9 +224,10 @@ 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); + PixelRead=0; // no PixelRaw return(PixelData); } @@ -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 @@ -288,7 +321,7 @@ void * gdcmFile::GetImageDataRaw (void) { lgrTotale /= 3; // TODO Let gdcmHeadar user a chance // to get the right value // Create a member lgrTotaleRaw ??? - PixelData = (void *) malloc(lgrTotale); + PixelData = new char[lgrTotale]; if (PixelData) GetImageDataIntoVectorRaw(PixelData, lgrTotale); PixelRead=1; // PixelRaw @@ -332,7 +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 ) { @@ -378,7 +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); @@ -460,7 +492,7 @@ 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; @@ -492,7 +524,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { } } memmove(destination,newDest,lgrTotale); - free(newDest); + delete[] newDest; } else { @@ -501,7 +533,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { int l = Header->GetXSize()*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; } @@ -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; } // -------------------------------------------------------------- @@ -724,7 +754,6 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { //PixelElement->SetPrintLevel(2); //PixelElement->Print(); - Header->Write(fp1, type); // -------------------------------------------------------------- @@ -772,9 +801,10 @@ if(nb == 16) case 2143: case 4321: - for(i=0;i>8) | ((((unsigned short int*)im)[i])<<8); + } break; default: @@ -788,7 +818,7 @@ if( nb == 32 ) break; case 4321: - for(i=0;i>16; fort= (fort>>8) | (fort<<8); @@ -799,7 +829,7 @@ if( nb == 32 ) break; case 2143: - for(i=0;i>16; fort= (fort>>8) | (fort<<8); @@ -810,7 +840,7 @@ if( nb == 32 ) break; case 3412: - for(i=0;i>16; s32=faible; @@ -929,7 +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); }