void gdcmFile::SetPixelDataSizeFromHeader(void) {
int nb;
std::string str_nb;
-
str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
if (str_nb == GDCM_UNFOUND ) {
nb = 16;
lgrTotale*=3;
}
}
+
// see PS 3.3-2003 : C.7.6.3.2.1
//
// MONOCHROME1
// 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]
CloseFile();
return false;
}
+
-// ------------------------- Compacted File (12 Bits Per Pixel)
+ // ---------------------- Compacted File (12 Bits Per Pixel)
/* unpack 12 Bits pixels into 16 Bits pixels */
/* 2 pixels 12bit = [0xABCDEF] */
int nbPixels = GetXSize()*GetYSize();
unsigned char b0, b1, b2;
+ unsigned short int* pdestination = (unsigned short int*)destination;
for(int p=0;p<nbPixels;p+=2) {
fread(&b0,1,1,fp);
fread(&b1,1,1,fp);
fread(&b2,1,1,fp);
- //Two steps is necessary to please VC++:
- unsigned short int* pdestination = (unsigned short int*)destination;
+ //Two steps is necessary to please VC++
*pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
/* A */ /* B */ /* D */
*pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
// Troubles expected on Big-Endian processors ?
}
return(true);
- }
-
+ }
-// ------------------------- Uncompressed File
+ // ---------------------- Uncompressed File
if ( !IsDicomV3() ||
IsImplicitVRLittleEndianTransferSyntax() ||
IsExplicitVRLittleEndianTransferSyntax() ||
IsExplicitVRBigEndianTransferSyntax() ||
IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
-
- size_t ItemRead = fread(destination, lgrTotale, 1, fp);
+
+ size_t ItemRead = fread(destination, GetPixelAreaLength(), 1, fp);
+
if ( ItemRead != 1 ) {
CloseFile();
return false;
}
}
-
-// ------------------------- Run Length Encoding
+ // ---------------------- Run Length Encoding
if (gdcmHeader::IsRLELossLessTransferSyntax()) {
int res = (bool)gdcm_read_RLE_file (destination);
return res;
}
-
-
-// ----------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
+ // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
int nb;
std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
* \ingroup gdcmFile
* \brief Copies at most MaxSize bytes of pixel data to caller's
* memory space.
+ * \warning This function was designed to avoid people that want to build
+ * a volume from an image stack to need first to get the image pixels
+ * and then move them to the volume area.
+ * It's absolutely useless for VTK users since vtk chooses
+ * to invert the lines of an image, that is the last line comes first
+ * (for some axis related reasons?). Hence he will have
+ * to load the image line by line, starting from the end.
+ * VTK users hace to call GetImageData
+ *
* @param destination Address (in caller's memory space) at which the
* pixel data should be copied
* @param MaxSize Maximum number of bytes to be copied. When MaxSize
highBit = nb - 1;
} else {
highBit = atoi(str_highBit.c_str() );
- }
-
- // Signe des Pixels
+ }
+ // Pixel sign
// 0 = Unsigned
// 1 = Signed
str_signe=GetPubElValByNumber(0x0028,0x0103);
}
}
-
-// Just to 'see' was was actually read on disk :-(
+// Just to 'see' what was actually read on disk :-(
// Some troubles expected
+// FILE * f2;
+// f2 = fopen("SpuriousFile.raw","wb");
+// fwrite(destination,lgrTotale,1,f2);
+// fclose(f2);
- // *Try* to deal with the color
- // ----------------------------
+ // Deal with the color
+ // -------------------
std::string str_PhotometricInterpretation =
gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
case 1:
{
- if (str_PhotometricInterpretation == "YBR_FULL") { // Warning : YBR_FULL_422 acts as RGB (?!)
-
+ 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
} else {
// need to make RGB Pixels from Planes R,G,B
+ // (all the Frames at a time)
- int l = GetXSize()*GetYSize();
- int nbFrames = GetZSize();
+ int l = GetXSize()*GetYSize()*GetZSize();
char * newDest = (char*) malloc(lgrTotale);
- char *x = newDest;
+ 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++);
- }
+ for (int j=0;j<l; j++) {
+ *(x++) = *(a++);
+ *(x++) = *(b++);
+ *(x++) = *(c++);
}
+
memmove(destination,newDest,lgrTotale);
free(newDest);
}
case 2:
// from Lut R + Lut G + Lut B
-
- // 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
-
- 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;
-
- // if we get a black image, let's just remove the '+1'
- // and check again
- // if it works, we shall have to check the 3 Palettes
- // to see which byte is ==0 (first one, or second one)
-
- for (int i=0;i<l; i++) {
- j=newDest[i]*mult +1;
- *a++ = lutR[j];
- *a++ = lutG[j];
- *a++ = lutB[j];
- }
+ {
+ unsigned char * newDest = (unsigned char *)malloc(lgrTotale);
+ unsigned char * a = (unsigned char *)destination;
+
+ unsigned char * lutRGBA = (unsigned char *) GetLUTRGBA();
+ if (lutRGBA) {
+
+ int l = lgrTotale/3;
+ memmove(newDest, destination, l);// move Gray pixels to temp area
+ int j;
+ for (int i=0;i<l; i++) { // Build RGB Pixels
+ j=newDest[i]*4;
+ *a++ = lutRGBA[j];
+ *a++ = lutRGBA[j+1];
+ *a++ = lutRGBA[j+2];
+ }
free(newDest);
} 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 (!?!)
+ // or Segmented Green Palette Color Lookup Table Data and so on
- // or Segmented Green Palette Color Lookup Table Data and so on
-
- // Oops! I get one (gdcm-US-ALOKA-16.dcm)
- // No idea how to manage it :-(
- // Segmented xxx Palette Color are *more* than 65535 long ?!?
+ // 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 ?!?
- // WARNING : quick and dirty trick to produce a single plane Grey image
+ // WARNING : quick and dirty trick to produce
+ // a single plane Grey image
// See also gdcmHeaderHelper::GetNumberOfScalarComponents()
lgrTotale /=3;
return lgrTotale;
break;
}
}
-
// now, it's an RGB image
// Lets's write it in the Header
std::string planConfig = "0"; // Planar Configuration
gdcmHeader::SetPubElValByNumber(planConfig,0x0028,0x0006);
- // + Drop Palette Color ?
+ // TODO : Drop Palette Color out of the Header?
return lgrTotale;
}
-//
-// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
-//
/**
* \ingroup gdcmFile
projects / gdcm.git / commitdiff