X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=8e12ec3ac10e3d866f04fb814c02aff5bb97b138;hb=ce855abf19191d31dcd568ea0277cdc8e691b3c0;hp=2bb43980229a7a88af084b7f2ab16ac5d0884d41;hpb=27c61aa23c3f02def28d44dca855e54d9adb25a1;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 2bb43980..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; @@ -14,17 +14,14 @@ typedef std::pair IterHT; * 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; @@ -40,16 +37,31 @@ 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. @@ -57,8 +69,37 @@ gdcmFile::gdcmFile(std::string & filename) { 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. @@ -69,7 +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) { @@ -85,7 +126,7 @@ gdcmFile::~gdcmFile(void) { // Public /** * \ingroup gdcmFile - * \brief + * \brief returns the gdcmHeader *Header * @return */ gdcmHeader *gdcmFile::GetHeader(void) { @@ -162,9 +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. */ @@ -180,12 +221,13 @@ 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); } @@ -212,13 +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) { @@ -231,7 +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 @@ -278,7 +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 @@ -322,7 +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 ) { @@ -368,7 +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); @@ -393,7 +435,7 @@ 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 :-( @@ -450,7 +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; @@ -482,7 +524,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { } } memmove(destination,newDest,lgrTotale); - free(newDest); + delete[] newDest; } else { @@ -491,7 +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; @@ -503,7 +545,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { *(x++) = *(c++); } memmove(destination,newDest,lgrTotale); - free(newDest); + delete[] newDest; } break; } @@ -531,12 +573,13 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { /** * \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 */ @@ -551,9 +594,7 @@ bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { * \ingroup gdcmFile * \brief Writes on disk A SINGLE Dicom file * NO test is performed on processor "Endiannity". - * Ca sera à l'utilisateur d'appeler son Reader correctement - * (Equivalent a IdImaWriteRawFile) - * + * 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 @@ -573,9 +614,9 @@ 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) * @return false if write fails @@ -587,8 +628,9 @@ bool gdcmFile::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 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 */ @@ -599,8 +641,9 @@ bool gdcmFile::WriteDcmImplVR (const char* 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 */ @@ -611,15 +654,14 @@ bool gdcmFile::WriteDcmExplVR (std::string fileName) { /** * \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 @@ -633,8 +675,9 @@ bool gdcmFile::WriteAcr (std::string fileName) { // 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 @@ -643,9 +686,7 @@ 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; } @@ -658,10 +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; } // -------------------------------------------------------------- @@ -703,17 +744,16 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { p2=it.second;// iterator on the last synonym PixelElement=p2->second; // H Table target column (2-nd col) - PixelElement->SetPrintLevel(2); - PixelElement->Print(); + // PixelElement->SetPrintLevel(2); + // PixelElement->Print(); if (PixelRead==1) PixelElement->SetLength(lgrTotaleRaw); else if (PixelRead==0) PixelElement->SetLength(lgrTotale); - PixelElement->SetPrintLevel(2); - PixelElement->Print(); - + //PixelElement->SetPrintLevel(2); + //PixelElement->Print(); Header->Write(fp1, type); // -------------------------------------------------------------- @@ -761,9 +801,10 @@ if(nb == 16) case 2143: case 4321: - for(i=0;i>8) | ((((unsigned short int*)im)[i])<<8); + } break; default: @@ -777,7 +818,7 @@ if( nb == 32 ) break; case 4321: - for(i=0;i>16; fort= (fort>>8) | (fort<<8); @@ -788,7 +829,7 @@ if( nb == 32 ) break; case 2143: - for(i=0;i>16; fort= (fort>>8) | (fort<<8); @@ -799,7 +840,7 @@ if( nb == 32 ) break; case 3412: - for(i=0;i>16; s32=faible; @@ -918,7 +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); }