X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmFile.cxx;h=a864ff554eb74eef882b267d643042419149b33c;hb=b950a88db3b779f409f548361bbc62882094b9fb;hp=58da7385690e835c033bb3325b8aaf6c9d19fb62;hpb=f58ef7f4b7e1e6c25c4fb7b78cd658e1b6efc639;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 58da7385..a864ff55 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -15,7 +15,6 @@ #include "gdcmFile.h" #include "gdcmUtil.h" #include "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess -using namespace std; #define str2num(str, typeNum) *((typeNum *)(str)) @@ -37,7 +36,7 @@ using namespace std; * @return */ -gdcmFile::gdcmFile(string & filename) +gdcmFile::gdcmFile(std::string & filename) :gdcmHeader(filename.c_str()) { SetPixelDataSizeFromHeader(); @@ -61,10 +60,10 @@ gdcmFile::gdcmFile(const char * filename) */ void gdcmFile::SetPixelDataSizeFromHeader(void) { int nb; - string str_nb; + std::string str_nb; str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { + if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { nb = atoi(str_nb.c_str() ); @@ -72,7 +71,7 @@ void gdcmFile::SetPixelDataSizeFromHeader(void) { } lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel(); - string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); + std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); if ( str_PhotometricInterpretation == "PALETTE COLOR " || str_PhotometricInterpretation == "YBR_FULL") { // --> some more to be added !! lgrTotale*=3; @@ -100,13 +99,14 @@ size_t gdcmFile::GetImageDataSize(void) { /** * \ingroup gdcmFile * \brief Parse pixel data from disk and *prints* the result - * \ For multi-fragment Jpeg files checking purpose *only* + * \ For multi-fragment Jpeg/Rle files checking purpose *only* * \ Allows to 'see' if the file *does* conform * \ (some of them do not) - * \ with Dicom Part 3, Annex A (PS 3.5-2003, page 58) + * \ with Dicom Part 3, Annex A (PS 3.5-2003, page 58, page 85) * */ bool gdcmFile::ParsePixelData(void) { + if ( !OpenFile()) return false; @@ -121,13 +121,13 @@ bool gdcmFile::ParsePixelData(void) { IsExplicitVRBigEndianTransferSyntax() || IsDeflatedExplicitVRLittleEndianTransferSyntax() ) { - printf ("gdcmFile::ParsePixelData : non JPEG File\n"); + printf ("gdcmFile::ParsePixelData : non JPEG/RLE File\n"); return 0; } int nb; - string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { + std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); + if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { nb = atoi(str_nb.c_str() ); @@ -140,11 +140,18 @@ bool gdcmFile::ParsePixelData(void) { printf ("Checking the Dicom-Jpeg/RLE Pixels\n"); - // ------------------------------- for Parsing : Position on begining of Jpeg Pixels - guint16 ItemTagGr,ItemTagEl; - int ln; - long ftellRes; - char * destination = NULL; + guint16 ItemTagGr,ItemTagEl; + int ln; + long ftellRes; + char * destination = NULL; + + // ------------------------------- for Parsing : Position on begining of Jpeg/RLE Pixels + + if( !IsRLELossLessTransferSyntax()) { + + // JPEG Image + + cout << "JPEG image" << std::endl; ftellRes=ftell(fp); fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Basic Offset Table Item Tag Gr fread(&ItemTagEl,2,1,fp); // Reading (e000) : Basic Offset Table Item Tag El @@ -190,13 +197,14 @@ bool gdcmFile::ParsePixelData(void) { printf(" at %x : fragment length %d x(%08x)\n", ftellRes, ln,ln); - destination += taille * nBytes; // location in user's memory - - printf (" Destination will be x(%x) = %d \n", - destination,destination ); - + // destination += taille * nBytes; // location in user's memory + //printf (" Destination will be x(%x) = %d \n", + // destination,destination ); + + // ------------------------ fseek(fp,ln,SEEK_CUR); // skipping (not reading) fragment pixels - + // ------------------------ + ftellRes=ftell(fp); fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El @@ -206,9 +214,114 @@ bool gdcmFile::ParsePixelData(void) { } printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n", ftellRes,ItemTagGr,ItemTagEl ); - + } + + } else { + + // RLE Image + + cout << "RLE image" << std::endl; + long RleSegmentLength[15],fragmentLength; + guint32 nbRleSegments; + guint32 RleSegmentOffsetTable[15]; + ftellRes=ftell(fp); + // Basic Offset Table with Item Value + // Item Tag + fread(&ItemTagGr,2,1,fp); // Reading (fffe):Basic Offset Table Item Tag Gr + fread(&ItemTagEl,2,1,fp); // Reading (e000):Basic Offset Table Item Tag El + if(GetSwapCode()) { + ItemTagGr=SwapShort(ItemTagGr); + ItemTagEl=SwapShort(ItemTagEl); + } + printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n", + ftellRes,ItemTagGr,ItemTagEl ); + // Item Length + ftellRes=ftell(fp); + fread(&ln,4,1,fp); + if(GetSwapCode()) + ln=SwapLong(ln); // Basic Offset Table Item Lentgh + printf("at %x : Basic Offset Table Item Lentgh (??) %d x(%08x)\n", + ftellRes,ln,ln); + if (ln != 0) { + // What is it used for ?? + char * BasicOffsetTableItemValue= (char *)malloc(ln+1); + fread(BasicOffsetTableItemValue,ln,1,fp); + guint32 a; + for (int i=0;i1) { + for(int k=1; k<=nbRleSegments-1; k++) { // skipping (not reading) RLE Segments + RleSegmentLength[k]=RleSegmentOffsetTable[k+1]-RleSegmentOffsetTable[k]; + ftellRes=ftell(fp); + printf (" Segment %d : Length = %d Start at %x\n", + k,RleSegmentLength[k], ftellRes); + fseek(fp,RleSegmentLength[k],SEEK_CUR); + } + } + RleSegmentLength[nbRleSegments] = fragmentLength - RleSegmentOffsetTable[nbRleSegments] ; + // TODO : Check the value + ftellRes=ftell(fp); + printf (" Segment %d : Length = %d Start at %x\n", + nbRleSegments,RleSegmentLength[nbRleSegments],ftellRes); + + fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR); + + // ------------------ end of scanning fragment pixels + ftellRes=ftell(fp); + fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr + fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El + if(GetSwapCode()) { + ItemTagGr=SwapShort(ItemTagGr); + ItemTagEl=SwapShort(ItemTagEl); + } + printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n", + ftellRes,ItemTagGr,ItemTagEl ); } + } return 1; } @@ -230,7 +343,7 @@ bool gdcmFile::ReadPixelData(void* destination) { return false; } -// ------------------------------- Uncompressed File +// ------------------------- Uncompressed File if ( !IsDicomV3() || IsImplicitVRLittleEndianTransferSyntax() || @@ -248,11 +361,11 @@ bool gdcmFile::ReadPixelData(void* destination) { } } - // ----------------------------- JPEG Compressed File . + // ------------------------ Compressed File . int nb; - string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { + std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100); + if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { nb = atoi(str_nb.c_str() ); @@ -308,17 +421,19 @@ bool gdcmFile::ReadPixelData(void* destination) { } _IdDcmJpegFree (jpg); return true; - } + } + // ------------------------------- RLE + + if (gdcmHeader::IsRLELossLessTransferSyntax()) { + int res = (bool)gdcm_read_RLE_file (destination); + return res; + } + // ------------------------------- JPEG Lossy : call to IJG 6b long fragmentBegining; // for ftell, fseek - - bool a=0, b=0; - - a = gdcmHeader::IsRLELossLessTransferSyntax(); - if (!a) - bool b = gdcmHeader::IsJPEG2000(); + bool b = gdcmHeader::IsJPEG2000(); bool res; guint16 ItemTagGr,ItemTagEl; @@ -359,9 +474,8 @@ bool gdcmFile::ReadPixelData(void* destination) { // FIXME : multi fragments fragmentBegining=ftell(fp); - if (a) - res = (bool)gdcm_read_RLE_file (destination); // Reading Fragment pixels - else if (b) + + if (b) res = (bool)gdcm_read_JPEG2000_file (destination); // Reading Fragment pixels else if (IsJPEGLossless()) { // ------------- call to LibIDO Jpeg for each Frame/fragment @@ -460,7 +574,7 @@ void * gdcmFile::GetImageData (void) { size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { int nb, nbu, highBit, signe; - string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; + std::string str_nbFrames, str_nb, str_nbu, str_highBit, str_signe; if ( lgrTotale > MaxSize ) { dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" @@ -472,7 +586,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // Nombre de Bits Alloues pour le stockage d'un Pixel str_nb = GetPubElValByNumber(0x0028,0x0100); - if (str_nb == "gdcm::Unfound" ) { + if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { nb = atoi(str_nb.c_str() ); @@ -480,7 +594,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // Nombre de Bits Utilises str_nbu=GetPubElValByNumber(0x0028,0x0101); - if (str_nbu == "gdcm::Unfound" ) { + if (str_nbu == GDCM_UNFOUND ) { nbu = nb; } else { nbu = atoi(str_nbu.c_str() ); @@ -488,7 +602,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // Position du Bit de Poids Fort str_highBit=GetPubElValByNumber(0x0028,0x0102); - if (str_highBit == "gdcm::Unfound" ) { + if (str_highBit == GDCM_UNFOUND ) { highBit = nb - 1; } else { highBit = atoi(str_highBit.c_str() ); @@ -496,7 +610,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // Signe des Pixels str_signe=GetPubElValByNumber(0x0028,0x0103); - if (str_signe == "gdcm::Unfound" ) { + if (str_signe == GDCM_UNFOUND ) { signe = 1; } else { signe = atoi(str_signe.c_str() ); @@ -534,7 +648,7 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { // Try to deal with the color // -------------------------- - string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); + std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004); if ( (str_PhotometricInterpretation == "MONOCHROME1 ") || (str_PhotometricInterpretation == "MONOCHROME2 ") @@ -567,9 +681,9 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { memmove(destination,newDest,lgrTotale); free(newDest); // now, it's an RGB image - string spp = "3"; + std::string spp = "3"; gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002); - string rgb="RGB"; + std::string rgb="RGB"; gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004); break; } @@ -604,9 +718,9 @@ size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) { free(newDest); // now, it's an RGB image - string spp = "3"; + std::string spp = "3"; gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002); - string rgb="RGB"; + std::string rgb="RGB"; gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004); } else { // need to make RGB Pixels (?) @@ -739,7 +853,7 @@ int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) { */ void gdcmFile::SetImageDataSize(size_t ImageDataSize) { - string content1; + std::string content1; char car[20]; // Assumes ElValue (0x7fe0, 0x0010) exists ... sprintf(car,"%d",ImageDataSize); @@ -766,7 +880,7 @@ void gdcmFile::SetImageDataSize(size_t ImageDataSize) { * @return */ -int gdcmFile::WriteRawData (string fileName) { +int gdcmFile::WriteRawData (std::string fileName) { FILE * fp1; fp1 = fopen(fileName.c_str(),"wb"); if (fp1 == NULL) { @@ -790,7 +904,7 @@ int gdcmFile::WriteRawData (string fileName) { * @return int acts as a boolean */ -int gdcmFile::WriteDcmImplVR (string fileName) { +int gdcmFile::WriteDcmImplVR (std::string fileName) { return WriteBase(fileName, ImplicitVR); } @@ -803,7 +917,7 @@ int gdcmFile::WriteDcmImplVR (string fileName) { */ int gdcmFile::WriteDcmImplVR (const char* fileName) { - return WriteDcmImplVR (string (fileName)); + return WriteDcmImplVR (std::string (fileName)); } ///////////////////////////////////////////////////////////////// @@ -814,7 +928,7 @@ int gdcmFile::WriteDcmImplVR (const char* fileName) { * @return int acts as a boolean */ -int gdcmFile::WriteDcmExplVR (string fileName) { +int gdcmFile::WriteDcmExplVR (std::string fileName) { return WriteBase(fileName, ExplicitVR); } @@ -834,7 +948,7 @@ int gdcmFile::WriteDcmExplVR (string fileName) { * @return int acts as a boolean */ -int gdcmFile::WriteAcr (string fileName) { +int gdcmFile::WriteAcr (std::string fileName) { return WriteBase(fileName, ACR); } @@ -847,7 +961,7 @@ int gdcmFile::WriteAcr (string fileName) { * * @return int acts as a boolean */ -int gdcmFile::WriteBase (string FileName, FileType type) { +int gdcmFile::WriteBase (std::string FileName, FileType type) { FILE * fp1; fp1 = fopen(FileName.c_str(),"wb");