// gdcmFile.cxx
-//This is needed when compiling in debug mode
-#ifdef _MSC_VER
-// 'type' : forcing value to bool 'true' or 'false' (performance warning)
-//#pragma warning ( disable : 4800 )
-// 'identifier' : class 'type' needs to have dll-interface to be used by
-// clients of class 'type2'
-#pragma warning ( disable : 4251 )
-// 'identifier' : identifier was truncated to 'number' characters in the
-// debug information
-#pragma warning ( disable : 4786 )
-#endif //_MSC_VER
-
#include "gdcmFile.h"
#include "gdcmUtil.h"
#include "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess
-#define str2num(str, typeNum) *((typeNum *)(str))
-
/////////////////////////////////////////////////////////////////
/**
* \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
+ * 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
if (nb == 12) nb =16;
}
lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();
-
std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
- if ( str_PhotometricInterpretation == "PALETTE COLOR "
- || str_PhotometricInterpretation == "YBR_FULL") { // --> some more to be added !!
+ if ( str_PhotometricInterpretation == "PALETTE COLOR " ) {
lgrTotale*=3;
}
-
- // remaining to check :
- // str_PhotometricInterpretation == "YBR_FULL"
- // str_PhotometricInterpretation == "YBR_FULL_422" (no LUT, no Palette)
- // -->and some more !!
}
+ // see PS 3.3-2003 : C.7.6.3.2.1
+ //
+ // MONOCHROME1
+ // MONOCHROME2
+ // PALETTE COLOR
+ // RGB
+ // HSV (Retired)
+ // ARGB (Retired)
+ // CMYK (Retired)
+ // YBR_FULL
+ // YBR_FULL_422 (no LUT, no Palette)
+ // YBR_PARTIAL_422
+ // YBR_ICT
+ // YBR_RCT
+
+ // LUT's
+ // ex : gdcm-US-ALOKA-16.dcm
+ // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
+ // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
+ // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
+
+ // ex : US-PAL-8-10x-echo.dcm, 8BitsRunLengthColor.dcm
+ // 0028|1201 [OW] [Red Palette Color Lookup Table Data]
+ // 0028|1202 [OW] [Green Palette Color Lookup Table Data]
+ // 0028|1203 [OW] [Blue Palette Color Lookup Table Data]
+
+ // ex : OT-PAL-8-face.dcm
+ // 0028|1201 [US] [Red Palette Color Lookup Table Data]
+ // 0028|1202 [US] [Green Palette Color Lookup Table Data]
+ // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
+
+
/////////////////////////////////////////////////////////////////
/**
* the pixel data represented in this file.
* @return The size of pixel data in bytes.
*/
+
size_t gdcmFile::GetImageDataSize(void) {
return (lgrTotale);
}
-/////////////////////////////////////////////////////////////////
-/**
- * \ingroup gdcmFile
- * \brief Parse pixel data from disk and *prints* the result
- * \ 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, page 85)
- *
- */
-bool gdcmFile::ParsePixelData(void) {
-
- if ( !OpenFile())
- return false;
-
- if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
- CloseFile();
- return false;
- }
-
- if ( !IsDicomV3() ||
- IsImplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRBigEndianTransferSyntax() ||
- IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
-
- printf ("gdcmFile::ParsePixelData : non JPEG/RLE File\n");
- return 0;
- }
-
- int nb;
- std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16;
- }
- int nBytes= nb/8;
-
- //int taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel();
- int taille = GetXSize() * GetYSize() * GetSamplesPerPixel();
-
- printf ("Checking the Dicom-Jpeg/RLE Pixels\n");
-
- 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" << 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
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
- ftellRes,ItemTagGr,ItemTagEl );
- 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;i<ln;i+=4){
- a=str2num(&BasicOffsetTableItemValue[i],guint32);
- printf(" x(%08x) %d\n",a,a);
- }
- }
-
- 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 );
-
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) { // Parse fragments
-
- ftellRes=ftell(fp);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // length
- 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 );
-
- // ------------------------
- 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
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
- ftellRes,ItemTagGr,ItemTagEl );
- }
-
- } else {
-
- // RLE Image
-
- cout << "RLE image" << 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;i<ln;i+=4){
- a=str2num(&BasicOffsetTableItemValue[i],guint32);
- printf(" x(%08x) %d\n",a,a);
- }
- }
-
- 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 );
-
- // while 'Sequence Delimiter Item' (fffe,e0dd) not found
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
- // Parse fragments of the current Fragment (Frame)
- ftellRes=ftell(fp);
- fread(&fragmentLength,4,1,fp);
- if(GetSwapCode())
- fragmentLength=SwapLong(fragmentLength); // length
- printf(" at %x : 'fragment' length %d x(%08x)\n",
- ftellRes, fragmentLength,fragmentLength);
-
-// destination += taille * nBytes; // location in user's memory
-// printf (" Destination will be x(%x) = %d \n",
-// destination,destination );
-
- //------------------ scanning (not reading) fragment pixels
-
- fread(&nbRleSegments,4,1,fp); // Reading : Number of RLE Segments
- if(GetSwapCode())
- nbRleSegments=SwapLong(nbRleSegments);
- printf(" Nb of RLE Segments : %d\n",nbRleSegments);
-
- for(int k=1; k<=15; k++) { // Reading RLE Segments Offset Table
- ftellRes=ftell(fp);
- fread(&RleSegmentOffsetTable[k],4,1,fp);
- if(GetSwapCode())
- RleSegmentOffsetTable[k]=SwapLong(RleSegmentOffsetTable[k]);
- printf(" at : %x Offset Segment %d : %d (%x)\n",
- ftellRes,k,RleSegmentOffsetTable[k],RleSegmentOffsetTable[k]);
- }
- if (nbRleSegments>1) {
- 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;
-}
-
/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
}
int nBytes= nb/8;
- //int taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel();
int taille = GetXSize() * GetYSize() * GetSamplesPerPixel();
if (b)
res = (bool)gdcm_read_JPEG2000_file (destination); // Reading Fragment pixels
- else if (IsJPEGLossless()) { // ------------- call to LibIDO Jpeg for each Frame/fragment
+ else if (IsJPEGLossless()) {
+ // ------------- call to LibIDO Jpeg for each Frame/fragment
- // Warning : Works only if there is one fragment per frame
- // (Or a single fragment for the multiframe file)
+ // Warning : Works only if there is one fragment per frame
+ // (Or a single fragment for the multiframe file)
ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
// (We use the LibIDO one :-(
if(jpg == NULL) {
}
//(char *) destination += taille * nBytes;
- //cout << "destination" << destination << "\n";
+ //std::cout << "destination" << destination << std::endl;
}
return res;
dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image");
return (size_t)0;
}
- }
-
- // Try to deal with the color
- // --------------------------
-
- std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
-
- if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
- || (str_PhotometricInterpretation == "MONOCHROME2 ")
- || (str_PhotometricInterpretation == "RGB")) {
- return lgrTotale;
- }
-
- switch ( GetPlanarConfiguration() ) {
- case 0:
- // Pixels are already RGB
- break;
+ }
+
+// Just to 'see' was was actually read on disk :-(
+// Some troubles expected
+
+FILE * fpSpurious;
+fpSpurious=fopen("SpuriousFile.raw","w");
+fwrite(destination,lgrTotale, 1,fpSpurious);
+fclose(fpSpurious);
+
+
+ // *Try* to deal with the color
+ // ----------------------------
+
+ // Planar configuration = 0 : Pixels are already RGB
+ // Planar configuration = 1 : 3 planes : R, G, B
+ // Planar configuration = 2 : 1 gray Plane + 3 LUT
+
+ // Well ... supposed to be !
+ // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,PhotometricInterpretation=PALETTE COLOR
+ // and heuristic has to be found :-(
+
+ std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
- case 1:
- // need to make RGB Pixels from Planes R,G,B
- {
- int l = lgrTotale/3 ;
-
- char * a = (char *)destination;
- char * b = a + l;
- char * c = b + l;
- char * newDest = (char*) malloc(lgrTotale);
- // TODO :
- // any trick not to have to allocate temporary buffer is welcome ...
- char *x = newDest;
- for (int j=0;j<l; j++) {
- *(x++) = *(a++);
- *(x++) = *(b++);
- *(x++) = *(c++);
- }
- memmove(destination,newDest,lgrTotale);
- free(newDest);
- // now, it's an RGB image
+ if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
+ || (str_PhotometricInterpretation == "MONOCHROME2 ")
+ || (str_PhotometricInterpretation == "RGB")) {
+ return lgrTotale;
+ }
+ int planConf=GetPlanarConfiguration();
+
+ switch (planConf) {
+ case 0:
+ // Pixels are already RGB
+ break;
+
+ case 1:
+
+ {
+ if (str_PhotometricInterpretation == "YBR_FULL") { // Warning : YBR_FULL_422 acts as RGB (?!)
+
+ // need to make RGB Pixels from Planes Y,cB,cR
+ // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ // for code optimisation
+
+ int l = GetXSize()*GetYSize();
+ int nbFrames = GetZSize();
+
+ unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
+ unsigned char *x = newDest;
+ 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
+ for (int i=0;i<nbFrames;i++) {
+ for (int j=0;j<l; j++) {
+ R= 1.164 *( *a-16) + 1.596 *( *c -128) + 0.5;
+ G= 1.164 *( *a-16) - 0.813 *( *c -128) - 0.392 *(*b -128) + 0.5;
+ B= 1.164 *( *a-16) + 2.017 *( *b -128) + 0.5;
+
+ if (R<0.0) R=0.0;
+ if (G<0.0) G=0.0;
+ if (B<0.0) B=0.0;
+ if (R>255.0) R=255.0;
+ if (G>255.0) G=255.0;
+ if (B>255.0) B=255.0;
+
+ *(x++) = (unsigned char)R;
+ *(x++) = (unsigned char)G;
+ *(x++) = (unsigned char)B;
+ a++; b++; c++;
+ }
+ }
+ memmove(destination,newDest,lgrTotale);
+ free(newDest);
+
+ } else {
+
+ // need to make RGB Pixels from Planes R,G,B
+
+ int l = GetXSize()*GetYSize();
+ int nbFrames = GetZSize();
+
+ char * newDest = (char*) malloc(lgrTotale);
+ char *x = newDest;
+ char * a = (char *)destination;
+ char * b = a + l;
+ char * c = b + l;
+
+ // TODO :
+ // any trick not to have to allocate temporary buffer is welcome ...
+
+ for (int i=0;i<nbFrames;i++) {
+ for (int j=0;j<l; j++) {
+ *(x++) = *(a++);
+ *(x++) = *(b++);
+ *(x++) = *(c++);
+ }
+ }
+ memmove(destination,newDest,lgrTotale);
+ free(newDest);
+ }
+
+ // now, it's an RGB image
+ // Lets's write it in the Header
std::string spp = "3";
gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
std::string rgb="RGB";
gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
break;
- }
-
- case 2:
- // from Lut R + Lut G + Lut B
+ }
+
+ case 2:
+ // from Lut R + Lut G + Lut B
- // we no longer use gdcmHeader::GetLUTRGB
- // since a lot of images have wrong info
- // in the Lookup Table Descriptors (0028,1101),...
- {
+ // we no longer use gdcmHeader::GetLUTRGB
+ // since a lot of images have strange info
+ // in the Lookup Table Descriptors (0028,1101),...
+ {
+ unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
+ unsigned char * a = (unsigned char *)destination;
+
unsigned char *lutR =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1201);
unsigned char *lutG =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1202);
unsigned char *lutB =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1203);
-
+
if (lutR && lutG && lutB ) { // need to make RGB Pixels
// from grey Pixels
// and Lut R,Lut G,Lut B
+
unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
int l = lgrTotale/3;
memmove(newDest, destination, l);// move Gray pixels to temp area
unsigned char * x = newDest;
- unsigned char * a = (unsigned char *)destination;
- int j;
- for (int i=0;i<l; i++) {
- j=newDest[i]*2; // Who can explain *why* we have to skip bytes
- *a++ = lutR[j];
- *a++ = lutG[j];
- *a++ = lutB[j];
- }
- free(newDest);
-
- // now, it's an RGB image
+
+ int j;
+ // See PS 3.3-2003 C.11.1.1.2 p 619
+ //
+ int mult;
+ if ( GetLUTNbits()==16 && nb==8) mult=2; // See PS 3.3
+ else mult=1;
+
+ for (int i=0;i<l; i++) {
+ j=newDest[i]*mult;
+ *a++ = lutR[j];
+ *a++ = lutG[j];
+ *a++ = lutB[j];
+ }
+
+ free(newDest);
+
+ // now, it's an RGB image
std::string spp = "3";
- gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+ gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
std::string rgb="RGB";
gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
-
+
} else { // need to make RGB Pixels (?)
- // from grey Pixels (?!)
- // and Gray Lut (!?!)
- unsigned char *lutGray =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1200);
- // Well . I'll wait till I find such an image
+ // from grey Pixels (?!)
+ // and Gray Lut (!?!)
+ unsigned char *lutGray =(unsigned char *)GetPubElValVoidAreaByNumber(0x0028,0x1200);
+ // Well . I'll wait till I find such an image
}
break;
- }
+ }
}
return lgrTotale;
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff