X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=feca29338c587a829360f4c154357b524403a6ff;hb=22f785a2627d1e7823701193bd7624739a3e033b;hp=581c5f4a4c0a1a926b3b55f857ec9cf04e971e16;hpb=226dc977654dc5150d279a7e72356f7790341040;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 581c5f4a..feca2933 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -4,6 +4,8 @@ #include "gdcmUtil.h" #include "jpeg/ljpg/jpegless.h" +typedef std::pair IterHT; + //----------------------------------------------------------------------------- // Constructor / Destructor /** @@ -12,20 +14,19 @@ * 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; + PixelRead=-1; // no ImageData read yet. if (Header->IsReadable()) SetPixelDataSizeFromHeader(); @@ -37,25 +38,39 @@ 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 */ gdcmFile::gdcmFile(std::string & filename) { Header=new gdcmHeader(filename.c_str()); SelfHeader=true; + PixelRead=-1; // no ImageData read yet. if (Header->IsReadable()) SetPixelDataSizeFromHeader(); } -gdcmFile::gdcmFile(const char * 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 + */ + gdcmFile::gdcmFile(const char * filename) { Header=new gdcmHeader(filename); SelfHeader=true; + PixelRead=-1; // no ImageData read yet. if (Header->IsReadable()) SetPixelDataSizeFromHeader(); @@ -157,9 +172,9 @@ 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. */ @@ -175,12 +190,13 @@ 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); if (PixelData) GetImageDataIntoVector(PixelData, lgrTotale); + PixelRead=0; // no PixelRaw return(PixelData); } @@ -207,7 +223,7 @@ void * gdcmFile::GetImageData (void) { */ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { size_t l = GetImageDataIntoVectorRaw (destination, MaxSize); - + PixelRead=0 ; // no PixelRaw if (!Header->HasLUT()) return lgrTotale; @@ -275,6 +291,7 @@ void * gdcmFile::GetImageDataRaw (void) { PixelData = (void *) malloc(lgrTotale); if (PixelData) GetImageDataIntoVectorRaw(PixelData, lgrTotale); + PixelRead=1; // PixelRaw return(PixelData); } @@ -306,6 +323,7 @@ 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; + PixelRead=1 ; // PixelRaw if ( lgrTotale > MaxSize ) { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" @@ -314,7 +332,7 @@ 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 ) { @@ -388,8 +406,9 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // DO NOT remove this code commented out. // Nobody knows what's expecting you ... // Just to 'see' what was actually read on disk :-( + // FILE * f2; -// f2 = fopen("SpuriousFile.raw","wb"); +// f2 = fopen("SpuriousFile.RAW","wb"); // fwrite(destination,lgrTotale,1,f2); // fclose(f2); @@ -522,12 +541,13 @@ 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 */ @@ -540,11 +560,9 @@ bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { /** * \ingroup gdcmFile - * \brief Ecrit sur disque les pixels d'UNE image - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca sera à l'utilisateur d'appeler son Reader correctement - * (Equivalent a IdImaWriteRawFile) - * + * \brief Writes on disk A SINGLE Dicom file + * NO test is performed on processor "Endiannity". + * 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 @@ -554,7 +572,7 @@ bool gdcmFile::WriteRawData (std::string fileName) { FILE * fp1; fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); + printf("Fail to open (write) file [%s] \n",fileName.c_str()); return (false); } fwrite (PixelData,lgrTotale, 1, fp1); @@ -564,11 +582,9 @@ bool gdcmFile::WriteRawData (std::string fileName) { /** * \ingroup gdcmFile - * \brief Ecrit sur disque UNE image Dicom - * Aucun test n'est fait sur l'"Endiannerie" du processeur. - * Ca fonctionnera correctement (?) sur processeur Intel - * (Equivalent a IdDcmWrite) - * + * \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 @@ -580,8 +596,9 @@ 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 */ @@ -592,8 +609,9 @@ 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 */ @@ -604,15 +622,14 @@ 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) * \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 @@ -626,18 +643,26 @@ 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, ...) + * @param type file type (ExplicitVR, ImplicitVR, DICOMDIR, ...) * @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;*/ + return false; + } + fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); + printf("Failed to open (write) File [%s] \n",fileName.c_str()); return (false); } @@ -647,6 +672,7 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { filePreamble=(char*)calloc(128,1); fwrite(filePreamble,128,1,fp1); fwrite("DICM",4,1,fp1); + free (filePreamble); } // -------------------------------------------------------------- @@ -655,6 +681,9 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { // if recognition code tells us we dealt with a LibIDO image // 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 std::string rows, columns; if ( Header->GetFileType() == ACR_LIBIDO){ @@ -664,7 +693,38 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { Header->SetEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- + + // TODO : get the grPixel, numPixel values (for some ACR-NEMA images only) + + guint16 grPixel =Header->GetGrPixel(); + guint16 numPixel=Header->GetNumPixel();; + + // Update Pixel Data Length + // the *last* of the (GrPixel, NumPixel), if many. + + TagKey key = gdcmDictEntry::TranslateToKey(grPixel, numPixel); + TagHeaderEntryHT::iterator p2; + gdcmHeaderEntry * PixelElement; + + IterHT it= Header->GetEntry().equal_range(key); // get a pair of iterators first-last synonym + if (Header->GetEntry().count(key) == 1) // only the first is significant + p2=it.first; // iterator on the first (unique) synonym + else + p2=it.second;// iterator on the last synonym + + PixelElement=p2->second; // H Table target column (2-nd col) + // PixelElement->SetPrintLevel(2); + // PixelElement->Print(); + + if (PixelRead==1) + PixelElement->SetLength(lgrTotaleRaw); + else if (PixelRead==0) + PixelElement->SetLength(lgrTotale); + + //PixelElement->SetPrintLevel(2); + //PixelElement->Print(); + Header->Write(fp1, type); // -------------------------------------------------------------- @@ -678,7 +738,7 @@ bool gdcmFile::WriteBase (std::string fileName, FileType type) { Header->SetEntryByNumber(columns, 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- - + fwrite(PixelData, lgrTotale, 1, fp1); fclose (fp1); return(true); @@ -777,17 +837,15 @@ bool gdcmFile::ReadPixelData(void* destination) { if ( !(fp=Header->OpenFile())) return false; - if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) { Header->CloseFile(); return false; } - - // ---------------------- Compacted File (12 Bits Per Pixel) /* unpack 12 Bits pixels into 16 Bits pixels */ /* 2 pixels 12bit = [0xABCDEF] */ /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */ + if (Header->GetBitsAllocated()==12) { int nbPixels = Header->GetXSize() * Header->GetYSize(); unsigned char b0, b1, b2; @@ -799,9 +857,9 @@ bool gdcmFile::ReadPixelData(void* destination) { fread(&b2,1,1,fp); //Two steps is necessary to please VC++ *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - /* A */ /* B */ /* D */ + /* A */ /* B */ /* D */ *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - /* F */ /* C */ /* E */ + /* F */ /* C */ /* E */ // Troubles expected on Big-Endian processors ? } @@ -818,7 +876,6 @@ bool gdcmFile::ReadPixelData(void* destination) { Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - if ( ItemRead != 1 ) { Header->CloseFile(); return false;