void gdcmFile::SetPixelDataSizeFromHeader(void) {
int nb;
std::string str_nb;
-
str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
if (str_nb == GDCM_UNFOUND ) {
nb = 16;
nb = atoi(str_nb.c_str() );
if (nb == 12) nb =16;
}
- lgrTotale = GetXSize() * GetYSize() * GetZSize()
+ lgrTotale = lgrTotaleRaw = GetXSize() * GetYSize() * GetZSize()
* (nb/8)* GetSamplesPerPixel();
std::string str_PhotometricInterpretation =
gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
- if ( str_PhotometricInterpretation == "PALETTE COLOR " ) {
+
+ /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/
+ // pb when undealt Segmented Palette Color
+
+ if (HasLUT()) {
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]
// 0028|1203 [US] [Blue Palette Color Lookup Table Data]
+/////////////////////////////////////////////////////////////////
+/**
+ * \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 -
+ * \ warning to be used with GetImagePixelsRaw()
+ * @return The size of pixel data in bytes.
+ */
+
+size_t gdcmFile::GetImageDataSizeRaw(void) {
+ return (lgrTotaleRaw);
+}
+
/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
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);
- *((unsigned short int*)destination)++ =
- ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ //Two steps is necessary to please VC++
+ *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
/* A */ /* B */ /* D */
- *((unsigned short int*)destination)++ =
- ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+ *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
/* F */ /* C */ /* E */
// 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);
+ IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
+
+ 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 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
* @return Pointer to newly allocated pixel data.
* \ NULL if alloc fails
*/
return(PixelData);
}
+/**
+ * \ingroup gdcmFile
+ * \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
+ * @return Pointer to newly allocated pixel data.
+ * \ NULL if alloc fails
+ */
+void * gdcmFile::GetImageDataRaw (void) {
+ if (HasLUT())
+ lgrTotale /= 3; // TODO Let gdcmHeadar user a chance
+ // to get the right value
+ // Create a member lgrTotaleRaw ???
+ PixelData = (void *) malloc(lgrTotale);
+ if (PixelData)
+ GetImageDataIntoVectorRaw(PixelData, lgrTotale);
+ return(PixelData);
+}
+
/**
* \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 any VTK user 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 have 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
size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
+ size_t l = GetImageDataIntoVectorRaw (destination, MaxSize);
+
+ if (!HasLUT())
+ return lgrTotale;
+
+ // from Lut R + Lut G + Lut B
+
+ unsigned char * newDest = (unsigned char *)malloc(lgrTotale);
+ unsigned char * a = (unsigned char *)destination;
+ unsigned char * lutRGBA = GetLUTRGBA();
+ if (lutRGBA) {
+ int l = lgrTotaleRaw;
+ 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);
+
+ // now, it's an RGB image
+ // Lets's write it in the Header
+
+ // CreateOrReplaceIfExist ?
+
+ std::string spp = "3"; // Samples Per Pixel
+ gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+ std::string rgb= "RGB "; // Photometric Interpretation
+ gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+ std::string planConfig = "0"; // Planar Configuration
+ gdcmHeader::SetPubElValByNumber(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 ?!?
+
+ std::string rgb= "MONOCHROME1 "; // Photometric Interpretation
+ gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+
+ }
+
+ // TODO : Drop Palette Color out of the Header?
+ return lgrTotale;
+}
+
+
+
+/**
+ * \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 any VTK user 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
+ * \warning DOES NOT transform the Grey Plane + Palette Color (if any)
+ * into a single RGB Pixels Plane
+ * the (VTK) user will manage the palettes
+ *
+ * @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
+ * is not sufficient to hold the pixel data the copy is not
+ * executed (i.e. no partial copy).
+ * @return On success, the number of bytes actually copied. Zero on
+ * failure e.g. MaxSize is lower than necessary.
+ */
+
+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;
highBit = nb - 1;
} else {
highBit = atoi(str_highBit.c_str() );
- }
-
- // Signe des Pixels
+ }
+ // Pixel sign
+ // 0 = Unsigned
+ // 1 = Signed
str_signe=GetPubElValByNumber(0x0028,0x0103);
if (str_signe == GDCM_UNFOUND ) {
- signe = 1;
+ signe = 0; // default is unsigned
} else {
signe = atoi(str_signe.c_str() );
}
// re arange bytes inside the integer
if (nb != 8)
SwapZone(destination, GetSwapCode(), lgrTotale, nb);
-
+
+ // to avoid pb with some xmedcon breakers images
+ if (nb==16 && nbu<nb && signe==0) {
+ int l = (int)lgrTotale / (nb/8);
+ guint16 *deb = (guint16 *)destination;
+ for(int i = 0; i<l; i++) {
+ if(*deb == 0xffff)
+ *deb=0;
+ deb++;
+ }
+ }
+
// re arange bits inside the bytes
if (nbu != nb){
int l = (int)lgrTotale / (nb/8);
}
}
-// 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 (?!)
-
- // need to make RGB Pixels from Planes Y,cB,cR
+ if (str_PhotometricInterpretation == "YBR_FULL") {
+
+ // 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 :
+ // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
+ // and be *very* affraid
+ //
int l = GetXSize()*GetYSize();
int nbFrames = GetZSize();
} else {
- // need to make RGB Pixels from Planes R,G,B
+ // need to make RGB Pixels from R,G,B Planes
+ // (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];
- }
-
- 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
-
- // 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 ?!?
-
- // WARNING : quick and dirty trick to produce a single plane Grey image
- // See also gdcmHeaderHelper::GetNumberOfScalarComponents()
- lgrTotale /=3;
- return lgrTotale;
- // end of dirty trick
- }
- break;
- }
+ // Palettes were found
+ // Let the user deal with them !
+ return lgrTotale;
}
-
// now, it's an RGB image
// Lets's write it in the Header
// CreateOrReplaceIfExist ?
+
+
std::string spp = "3"; // Samples Per Pixel
gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
- std::string rgb="RGB "; // Photometric Interpretation
+ std::string rgb="RGB "; // Photometric Interpretation
gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+
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
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff