#include "gdcmFile.h"
#include "gdcmUtil.h"
-#include "iddcmjpeg.h" // for the 'LibIDO' Jpeg LossLess
-using namespace std;
-
-#define str2num(str, typeNum) *((typeNum *)(str))
+#include "jpeg/ljpg/jpegless.h"
/////////////////////////////////////////////////////////////////
/**
* @return
*/
-gdcmFile::gdcmFile(string & filename)
+gdcmFile::gdcmFile(std::string & filename)
:gdcmHeader(filename.c_str())
{
- SetPixelDataSizeFromHeader();
+ if (IsReadable())
+ SetPixelDataSizeFromHeader();
}
gdcmFile::gdcmFile(const char * filename)
:gdcmHeader(filename)
{
- SetPixelDataSizeFromHeader();
+ if (IsReadable())
+ SetPixelDataSizeFromHeader();
}
/**
* \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).
+ * 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
*/
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() );
if (nb == 12) nb =16;
}
- lgrTotale = GetXSize() * GetYSize() * GetZSize() * (nb/8)* GetSamplesPerPixel();
+ lgrTotale = lgrTotaleRaw = GetXSize() * GetYSize() * GetZSize()
+ * (nb/8)* GetSamplesPerPixel();
+ std::string str_PhotometricInterpretation =
+ gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+
+ /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/
+ // pb when undealt Segmented Palette Color
- string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
- if ( str_PhotometricInterpretation == "PALETTE COLOR "
- || str_PhotometricInterpretation == "YBR_FULL") { // --> some more to be added !!
+ if (HasLUT()) {
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 : 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.
+ * \ 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::GetImageDataSize(void) {
- return (lgrTotale);
-}
+size_t gdcmFile::GetImageDataSizeRaw(void) {
+ return (lgrTotaleRaw);
+}
/////////////////////////////////////////////////////////////////
/**
- * \ingroup gdcmFile
- * \brief Parse pixel data from disk and *prints* the result
- * \ For multi-fragment Jpeg 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)
- *
+ * \ingroup gdcmFile
+ * \brief Returns the size (in bytes) of required memory to hold
+ * the pixel data represented in this file.
+ * @return The size of pixel data in bytes.
*/
-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 File\n");
- return 0;
- }
- int nb;
- 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");
-
- // ------------------------------- for Parsing : Position on begining of Jpeg Pixels
- guint16 ItemTagGr,ItemTagEl;
- int ln;
- long ftellRes;
- char * destination = NULL;
- 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 );
-
-
- }
- return 1;
+size_t gdcmFile::GetImageDataSize(void) {
+ return (lgrTotale);
}
+
/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
CloseFile();
return false;
- }
+ }
+
+
+ // ---------------------- Compacted File (12 Bits Per Pixel)
+
+ /* unpack 12 Bits pixels into 16 Bits pixels */
+ /* 2 pixels 12bit = [0xABCDEF] */
+ /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */
+
+ if (GetBitsAllocated()==12) {
+ 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++
+ *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ /* A */ /* B */ /* D */
+ *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;
return true;
}
}
+
+ // ---------------------- Run Length Encoding
+
+ if (gdcmHeader::IsRLELossLessTransferSyntax()) {
+ int res = (bool)gdcm_read_RLE_file (destination);
+ return res;
+ }
- // ----------------------------- JPEG Compressed File .
+ // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
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() );
- if (nb == 12) nb =16;
+ if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ?
}
int nBytes= nb/8;
- //int taille = GetXSize() * GetYSize() * GetZSize() * GetSamplesPerPixel();
- int taille = GetXSize() * GetYSize() * GetSamplesPerPixel();
-
-
- // ------------------------------- JPEG LossLess : call to Jpeg Libido
-
- if (IsJPEGLossless() && GetZSize() == 1) {
-
- int ln; // Position on begining of Jpeg Pixels
- fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : Basic Offset Table Item
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Item length
- fseek(fp,ln,SEEK_CUR); // skipping Basic Offset Table ('ln' bytes)
- fseek(fp,4,SEEK_CUR); // skipping (fffe,e000) : First fragment Item Tag
- fread(&ln,4,1,fp); // First fragment length (just to know)
- if(GetSwapCode())
- ln=SwapLong(ln);
-
- ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
- // (We use the LibIDO one :-(
- if(jpg == NULL) {
- CloseFile();
- return false;
- }
- int * dataJpg = jpg->DataImg;
-
- switch (nBytes) {
- case 1:
- {
- unsigned short *dest = (unsigned short *)destination;
- for (int i=0; i<taille; i++) {
- *((unsigned char *)dest+i) = *(dataJpg +i);
- }
- }
- break;
-
- case 2:
- {
- unsigned short *dest = (unsigned short *)destination;
- for (int i=0; i<taille; i++) {
- *((unsigned short *)dest+i) = *(dataJpg +i);
- }
- }
- break;
- }
- _IdDcmJpegFree (jpg);
- return true;
- }
-
- // ------------------------------- JPEG Lossy : call to IJG 6b
-
+ int taille = GetXSize() * GetYSize() * GetSamplesPerPixel();
long fragmentBegining; // for ftell, fseek
- bool a=0, b=0;
-
- a = gdcmHeader::IsRLELossLessTransferSyntax();
- if (!a)
- bool b = gdcmHeader::IsJPEG2000();
+ bool jpg2000 = IsJPEG2000();
+ bool jpgLossless = IsJPEGLossless();
- bool res;
+ bool res = true;
guint16 ItemTagGr,ItemTagEl;
- int ln; // Position on begining of Jpeg Pixels
+ int ln;
+
+ // Position on begining of Jpeg Pixels
fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
}
// parsing fragments until Sequence Delim. Tag found
- //unsigned short *dest = (unsigned short *)destination;
-
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+
+ while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+
+ // --- for each Fragment
+
fread(&ln,4,1,fp);
if(GetSwapCode())
ln=SwapLong(ln); // Fragment Item length
- // FIXME : multi fragments
- fragmentBegining=ftell(fp);
-
- if (a)
- res = (bool)gdcm_read_RLE_file (destination); // Reading Fragment pixels
- else if (b)
- res = (bool)gdcm_read_JPEG2000_file (destination); // Reading Fragment pixels
-
- 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)
- ClbJpeg* jpg = _IdDcmJpegRead(fp); // TODO : find a 'full' one.
- // (We use the LibIDO one :-(
- if(jpg == NULL) {
- CloseFile();
- return false;
- }
- int * dataJpg = jpg->DataImg;
- unsigned short *dest = (unsigned short *)destination;
- switch (nBytes) {
- case 1:
- {
- for (int i=0; i<taille; i++) {
- *((unsigned char *)dest+i) = *(dataJpg +i);
- }
- break;
- }
-
- case 2:
- {
- for (int i=0; i<taille; i++) {
- *((unsigned short *)dest+i) = *(dataJpg +i);
- }
- break;
- }
- }
- _IdDcmJpegFree (jpg);
+ fragmentBegining=ftell(fp);
+
+ if (jpg2000) { // JPEG 2000 : call to ???
+
+ res = (bool)gdcm_read_JPEG2000_file (destination); // Not Yet written
+
+ } // ------------------------------------- endif (JPEG2000)
+
+ else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
+
+ JPEGLosslessDecodeImage (fp, // Reading Fragment pixels
+ (unsigned short *)destination,
+ GetPixelSize()*8* GetSamplesPerPixel(),
+ ln);
+ res=1; // in order not to break the loop
- } // ------------------------------------- endif (IsJPEGLossless())
+ } // ------------------------------------- endif (JPEGLossless)
- else
+ else { // JPEG Lossy : call to IJG 6b
+
if (GetBitsStored() == 8) {
res = (bool)gdcm_read_JPEG_file (destination); // Reading Fragment pixels
} else {
res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels
- }
+ }
+ } // ------------------------------------- endif (JPEGLossy)
if (!res) break;
-
- // FIXME : will work only when each fragment corresponds to a Frame :-(
-
+
destination = (char *)destination + taille * nBytes; // location in user's memory
- // for next fragment (if any)
- // TODO : find a suitable file (multifragment/single Frame Jpeg file) to check
+ // for next fragment (if any)
fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start
fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
ItemTagGr=SwapShort(ItemTagGr);
ItemTagEl=SwapShort(ItemTagEl);
}
-
- //(char *) destination += taille * nBytes;
- //cout << "destination" << destination << "\n";
- }
-
+
+ } // endWhile parsing fragments until Sequence Delim. Tag found
+
return res;
}
* \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 = (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);
+
+ // 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;
- 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"
// 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() );
// 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() );
// 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() );
- }
-
- // Signe des Pixels
+ }
+ // Pixel sign
+ // 0 = Unsigned
+ // 1 = Signed
str_signe=GetPubElValByNumber(0x0028,0x0103);
- if (str_signe == "gdcm::Unfound" ) {
- signe = 1;
+ if (str_signe == GDCM_UNFOUND ) {
+ 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);
dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: wierd image");
return (size_t)0;
}
- }
-
- // Try to deal with the color
- // --------------------------
-
- 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' what was actually read on disk :-(
+// Some troubles expected
+// FILE * f2;
+// f2 = fopen("SpuriousFile.raw","wb");
+// fwrite(destination,lgrTotale,1,f2);
+// fclose(f2);
+
+ // Deal with the color
+ // -------------------
- 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
- string spp = "3";
- gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
- string rgb="RGB";
- gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
- break;
+ std::string str_PhotometricInterpretation =
+ gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+
+ if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
+ || (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
+ return lgrTotale;
}
- 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),...
- {
- 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
+ // 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 :-(
+
+ int planConf=GetPlanarConfiguration(); // 0028,0006
+
+ // Whatever Planar Configuration is,
+ // "PALETTE COLOR " implies that we deal with the palette.
+ if (str_PhotometricInterpretation == "PALETTE COLOR ")
+ planConf=2;
+
+ 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 * x = newDest;
+ unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
+ 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];
- }
+ 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 {
- // now, it's an RGB image
- string spp = "3";
- gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
- 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
- }
+ // need to make RGB Pixels from R,G,B Planes
+ // (all the Frames at a time)
+
+ int l = GetXSize()*GetYSize()*GetZSize();
+
+ char * newDest = (char*) malloc(lgrTotale);
+ char * x = newDest;
+ char * a = (char *)destination;
+ char * b = a + l;
+ char * c = b + l;
+
+ for (int j=0;j<l; j++) {
+ *(x++) = *(a++);
+ *(x++) = *(b++);
+ *(x++) = *(c++);
+ }
+
+ memmove(destination,newDest,lgrTotale);
+ free(newDest);
+ }
+
break;
- }
+ }
+
+ case 2:
+ // 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
+ gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+
+ std::string planConfig = "0"; // Planar Configuration
+ gdcmHeader::SetPubElValByNumber(planConfig,0x0028,0x0006);
+
+ // TODO : Drop Palette Color out of the Header?
+
return lgrTotale;
}
-//
-// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
-//
+
/**
* \ingroup gdcmFile
*/
void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
- string content1;
+ std::string content1;
char car[20];
// Assumes ElValue (0x7fe0, 0x0010) exists ...
sprintf(car,"%d",ImageDataSize);
* @return
*/
-int gdcmFile::WriteRawData (string fileName) {
+int gdcmFile::WriteRawData (std::string fileName) {
FILE * fp1;
fp1 = fopen(fileName.c_str(),"wb");
if (fp1 == NULL) {
* @return int acts as a boolean
*/
-int gdcmFile::WriteDcmImplVR (string fileName) {
+int gdcmFile::WriteDcmImplVR (std::string fileName) {
return WriteBase(fileName, ImplicitVR);
}
*/
int gdcmFile::WriteDcmImplVR (const char* fileName) {
- return WriteDcmImplVR (string (fileName));
+ return WriteDcmImplVR (std::string (fileName));
}
/////////////////////////////////////////////////////////////////
* @return int acts as a boolean
*/
-int gdcmFile::WriteDcmExplVR (string fileName) {
+int gdcmFile::WriteDcmExplVR (std::string fileName) {
return WriteBase(fileName, ExplicitVR);
}
* @return int acts as a boolean
*/
-int gdcmFile::WriteAcr (string fileName) {
+int gdcmFile::WriteAcr (std::string fileName) {
return WriteBase(fileName, ACR);
}
*
* @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");
fwrite("DICM",4,1,fp1);
}
+ // --------------------------------------------------------------
+ // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
+ //
+ // if recognition code tells us we dealt with a LibIDO image
+ // we reproduce on disk the switch between lineNumber and columnNumber
+ // just before writting ...
+
+ std::string rows, columns;
+ if ( filetype == ACR_LIBIDO){
+ rows = GetPubElValByNumber(0x0028, 0x0010);
+ columns = GetPubElValByNumber(0x0028, 0x0011);
+ SetPubElValByNumber(columns, 0x0028, 0x0010);
+ SetPubElValByNumber(rows , 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+
gdcmHeader::Write(fp1, type);
+
+ // --------------------------------------------------------------
+ // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
+ //
+ // ...and we restore the Header to be Dicom Compliant again
+ // just after writting
+
+ if (filetype == ACR_LIBIDO){
+ SetPubElValByNumber(rows , 0x0028, 0x0010);
+ SetPubElValByNumber(columns, 0x0028, 0x0011);
+ }
+ // ----------------- End of Special Patch ----------------
+
fwrite(PixelData, lgrTotale, 1, fp1);
fclose (fp1);
return(1);
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff