X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=858ee0cb358f30cbe2cc8b1e9ecbd2e5d9ff29aa;hb=bafdfafe6c1b30607035fc4018c0405169b348e8;hp=fb042163f66476c3d17f6457a19230f262d19a6a;hpb=06c1c583239fdf5196260e6ef83a78669c1bd17f;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index fb042163..858ee0cb 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -23,8 +23,7 @@ * @return */ -gdcmFile::gdcmFile(gdcmHeader *header) -{ +gdcmFile::gdcmFile(gdcmHeader *header) { Header=header; SelfHeader=false; @@ -43,13 +42,10 @@ gdcmFile::gdcmFile(gdcmHeader *header) * 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) -{ +gdcmFile::gdcmFile(std::string & filename) { Header=new gdcmHeader(filename.c_str()); SelfHeader=true; @@ -57,8 +53,7 @@ gdcmFile::gdcmFile(std::string & filename) SetPixelDataSizeFromHeader(); } -gdcmFile::gdcmFile(const char * filename) -{ +gdcmFile::gdcmFile(const char * filename) { Header=new gdcmHeader(filename); SelfHeader=true; @@ -68,16 +63,11 @@ gdcmFile::gdcmFile(const char * filename) /** * \ingroup gdcmFile - * \brief Destructor 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. + * \brief canonical destructor * \Note If the gdcmHeader is created by the gdcmFile, it is destroyed * by the gdcmFile - * * */ -gdcmFile::~gdcmFile(void) -{ +gdcmFile::~gdcmFile(void) { if(SelfHeader) delete Header; Header=NULL; @@ -93,20 +83,17 @@ gdcmFile::~gdcmFile(void) * \brief * @return */ -gdcmHeader *gdcmFile::GetHeader(void) -{ +gdcmHeader *gdcmFile::GetHeader(void) { return(Header); } /** * \ingroup gdcmFile - * \brief calcule la longueur (in bytes) A ALLOUER pour recevoir les - * pixels de l'image ou DES images dans le cas d'un multiframe - * - * ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels - * (dans le cas d'images compressees, elle n'a pas de sens). - * - * @return longueur a allouer + * \brief computes the length (in bytes) to ALLOCATE to receive the + * image(s) pixels (multiframes taken into account) + * \warning : it is NOT the group 7FE0 length + * (no interest for compressed images). + * @return length to allocate */ void gdcmFile::SetPixelDataSizeFromHeader(void) { // see PS 3.3-2003 : C.7.6.3.2.1 @@ -137,7 +124,7 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { int nb; std::string str_nb; - str_nb=Header->GetPubElValByNumber(0x0028,0x0100); + str_nb=Header->GetEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { @@ -147,7 +134,7 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize() * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel(); std::string str_PhotometricInterpretation = - Header->GetPubElValByNumber(0x0028,0x0004); + Header->GetEntryByNumber(0x0028,0x0004); /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/ // pb when undealt Segmented Palette Color @@ -173,7 +160,7 @@ size_t gdcmFile::GetImageDataSize(void) { * \ 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() + * \warning to be used with GetImagePixelsRaw() * @return The size of pixel data in bytes. */ size_t gdcmFile::GetImageDataSizeRaw(void) { @@ -185,8 +172,8 @@ size_t gdcmFile::GetImageDataSizeRaw(void) { * \brief Allocates necessary memory, copies the pixel data * (image[s]/volume[s]) to newly allocated zone. * Transforms YBR pixels into RGB pixels if any - Transforms 3 planes R, G, B into a single RGB Plane - Transforms single Grey plane + 3 Palettes into a RGB Plane + * 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 */ @@ -246,30 +233,26 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // CreateOrReplaceIfExist ? std::string spp = "3"; // Samples Per Pixel - Header->SetPubElValByNumber(spp,0x0028,0x0002); + Header->SetEntryByNumber(spp,0x0028,0x0002); std::string rgb= "RGB "; // Photometric Interpretation - Header->SetPubElValByNumber(rgb,0x0028,0x0004); + Header->SetEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration - Header->SetPubElValByNumber(planConfig,0x0028,0x0006); + Header->SetEntryByNumber(planConfig,0x0028,0x0006); } else { // need to make RGB Pixels (?) // from grey Pixels (?!) // and Gray Lut (!?!) // or Segmented xxx Palette Color Lookup Table Data and so on - - // Well . I'll wait till I find such an image - - // Oops! I get one (gdcm-US-ALOKA-16.dcm) - // No idea how to manage it - // It seems that *no Dicom Viewer* has any idea :-( - // Segmented xxx Palette Color are *more* than 65535 long ?!? + + // Oops! I get one (gdcm-US-ALOKA-16.dcm) + // No idea how to manage such an image + // It seems that *no Dicom Viewer* has any idea :-( + // Segmented xxx Palette Color are *more* than 65535 long ?!? std::string rgb= "MONOCHROME1 "; // Photometric Interpretation - Header->SetPubElValByNumber(rgb,0x0028,0x0004); - - } - + Header->SetEntryByNumber(rgb,0x0028,0x0004); + } // TODO : Drop Palette Color out of the Header? return lgrTotale; } @@ -279,8 +262,8 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { * \brief Allocates necessary memory, copies the pixel data * (image[s]/volume[s]) to newly allocated zone. * Transforms YBR pixels into RGB pixels if any - Transforms 3 planes R, G, B into a single RGB Plane - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane + * Transforms 3 planes R, G, B into a single RGB Plane + * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. * \ NULL if alloc fails */ @@ -332,24 +315,22 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { (void)ReadPixelData(destination); - // Nombre de Bits Alloues pour le stockage d'un Pixel - str_nb = Header->GetPubElValByNumber(0x0028,0x0100); + // Number of Bits Allocated for storing a Pixel + str_nb = Header->GetEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { nb = atoi(str_nb.c_str() ); - } - - // Nombre de Bits Utilises - str_nbu=Header->GetPubElValByNumber(0x0028,0x0101); + } + // Number of Bits actually used + str_nbu=Header->GetEntryByNumber(0x0028,0x0101); if (str_nbu == GDCM_UNFOUND ) { nbu = nb; } else { nbu = atoi(str_nbu.c_str() ); - } - - // Position du Bit de Poids Fort - str_highBit=Header->GetPubElValByNumber(0x0028,0x0102); + } + // High Bit Position + str_highBit=Header->GetEntryByNumber(0x0028,0x0102); if (str_highBit == GDCM_UNFOUND ) { highBit = nb - 1; } else { @@ -358,14 +339,14 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // Pixel sign // 0 = Unsigned // 1 = Signed - str_signe=Header->GetPubElValByNumber(0x0028,0x0103); + str_signe=Header->GetEntryByNumber(0x0028,0x0103); if (str_signe == GDCM_UNFOUND ) { signe = 0; // default is unsigned } else { signe = atoi(str_signe.c_str() ); } - // re arange bytes inside the integer + // re arange bytes inside the integer (processor endianity) if (nb != 8) SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb); @@ -404,9 +385,9 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { return (size_t)0; } } - +// DO NOT remove this code commented out. +// Nobody knows what's expecting you ... // Just to 'see' what was actually read on disk :-( -// Some troubles expected // FILE * f2; // f2 = fopen("SpuriousFile.raw","wb"); // fwrite(destination,lgrTotale,1,f2); @@ -416,7 +397,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // ------------------- std::string str_PhotometricInterpretation = - Header->GetPubElValByNumber(0x0028,0x0004); + Header->GetEntryByNumber(0x0028,0x0004); if ( (str_PhotometricInterpretation == "MONOCHROME1 ") || (str_PhotometricInterpretation == "MONOCHROME2 ") ) { @@ -451,11 +432,9 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { // Warning : YBR_FULL_422 acts as RGB // : we need to make RGB Pixels from Planes Y,cB,cR - // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - // for code optimisation // to see the tricks about YBR_FULL, YBR_FULL_422, - // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : + // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf // and be *very* affraid // @@ -467,11 +446,13 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { 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 + for (int i=0;iSetPubElValByNumber(spp,0x0028,0x0002); + Header->SetEntryByNumber(spp,0x0028,0x0002); std::string rgb="RGB "; // Photometric Interpretation - Header->SetPubElValByNumber(rgb,0x0028,0x0004); + Header->SetEntryByNumber(rgb,0x0028,0x0004); std::string planConfig = "0"; // Planar Configuration - Header->SetPubElValByNumber(planConfig,0x0028,0x0006); + Header->SetEntryByNumber(planConfig,0x0028,0x0006); // TODO : Drop Palette Color out of the Header? return lgrTotale; @@ -551,7 +529,7 @@ size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) { * @param inData * @param ExpectedSize * - * @return integer acts as a boolean + * @return boolean */ bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { Header->SetImageDataSize(ExpectedSize); @@ -567,8 +545,9 @@ bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { * Ca sera à l'utilisateur d'appeler son Reader correctement * (Equivalent a IdImaWriteRawFile) * - * @param fileName - * @return + * @param fileName name of the file to be created + * (any already existing file is over written) + * @return false if write fails */ bool gdcmFile::WriteRawData (std::string fileName) { @@ -590,8 +569,9 @@ bool gdcmFile::WriteRawData (std::string fileName) { * Ca fonctionnera correctement (?) sur processeur Intel * (Equivalent a IdDcmWrite) * - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ bool gdcmFile::WriteDcmImplVR (std::string fileName) { @@ -601,8 +581,9 @@ bool gdcmFile::WriteDcmImplVR (std::string fileName) { /** * \ingroup gdcmFile * \brief - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ bool gdcmFile::WriteDcmImplVR (const char* fileName) { @@ -612,8 +593,9 @@ bool gdcmFile::WriteDcmImplVR (const char* fileName) { /** * \ingroup gdcmFile * \brief - * @param fileName - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ bool gdcmFile::WriteDcmExplVR (std::string fileName) { @@ -625,14 +607,15 @@ bool gdcmFile::WriteDcmExplVR (std::string fileName) { * \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels * (a l'attention des logiciels cliniques * qui ne prennent en entrée QUE des images ACR ... - * \warning si un header DICOM est fourni en entree, - * les groupes < 0x0008 et les groupes impairs sont ignores) - * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur. + * \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 - * @return int acts as a boolean + * @param fileName name of the file to be created + * (any already existing file is overwritten) + * @return false if write fails */ bool gdcmFile::WriteAcr (std::string fileName) { @@ -644,17 +627,17 @@ bool gdcmFile::WriteAcr (std::string fileName) { /** * \ingroup gdcmFile * - * @param FileName - * @param type - * - * @return int acts as a boolean +* @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 */ -bool gdcmFile::WriteBase (std::string FileName, FileType type) { +bool gdcmFile::WriteBase (std::string fileName, FileType type) { FILE * fp1; - fp1 = fopen(FileName.c_str(),"wb"); + fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { - printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str()); + printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str()); return (false); } @@ -675,10 +658,10 @@ bool gdcmFile::WriteBase (std::string FileName, FileType type) { std::string rows, columns; if ( Header->GetFileType() == ACR_LIBIDO){ - rows = Header->GetPubElValByNumber(0x0028, 0x0010); - columns = Header->GetPubElValByNumber(0x0028, 0x0011); - Header->SetPubElValByNumber(columns, 0x0028, 0x0010); - Header->SetPubElValByNumber(rows , 0x0028, 0x0011); + rows = Header->GetEntryByNumber(0x0028, 0x0010); + columns = Header->GetEntryByNumber(0x0028, 0x0011); + Header->SetEntryByNumber(columns, 0x0028, 0x0010); + Header->SetEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- @@ -691,8 +674,8 @@ bool gdcmFile::WriteBase (std::string FileName, FileType type) { // just after writting if (Header->GetFileType() == ACR_LIBIDO){ - Header->SetPubElValByNumber(rows , 0x0028, 0x0010); - Header->SetPubElValByNumber(columns, 0x0028, 0x0011); + Header->SetEntryByNumber(rows , 0x0028, 0x0010); + Header->SetEntryByNumber(columns, 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- @@ -735,7 +718,7 @@ if(nb == 16) break; default: - printf("valeur de SWAP (16 bits) not allowed : %d\n", swap); + printf("SWAP value (16 bits) not allowed : %d\n", swap); } if( nb == 32 ) @@ -776,7 +759,7 @@ if( nb == 32 ) break; default: - printf(" SWAP value (32 bits) not allowed : %d\n", swap); + printf("SWAP value (32 bits) not allowed : %d\n", swap); } return; } @@ -816,9 +799,9 @@ 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 ? } @@ -851,7 +834,7 @@ bool gdcmFile::ReadPixelData(void* destination) { // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 int nb; - std::string str_nb=Header->GetPubElValByNumber(0x0028,0x0100); + std::string str_nb=Header->GetEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { @@ -864,7 +847,7 @@ bool gdcmFile::ReadPixelData(void* destination) { int taille = Header->GetXSize() * Header->GetYSize() * Header->GetSamplesPerPixel(); long fragmentBegining; // for ftell, fseek - + bool jpg2000 = Header->IsJPEG2000(); bool jpgLossless = Header->IsJPEGLossless();