// 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
+#include "jpeg/ljpg/jpegless.h"
-#define str2num(str, typeNum) *((typeNum *)(str))
-
-/////////////////////////////////////////////////////////////////
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
/**
* \ingroup gdcmFile
* \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
* one sets an a posteriori shadow dictionary (efficiency can be
* seen as a side effect).
*
- * @param filename file to be opened for parsing
+ * @param header file to be opened for reading datas
*
* @return
*/
-gdcmFile::gdcmFile(std::string & filename)
- :gdcmHeader(filename.c_str())
-{
- SetPixelDataSizeFromHeader();
+gdcmFile::gdcmFile(gdcmHeader *header) {
+ Header=header;
+ SelfHeader=false;
+
+ if (Header->IsReadable())
+ SetPixelDataSizeFromHeader();
}
-gdcmFile::gdcmFile(const char * filename)
- :gdcmHeader(filename)
-{
- SetPixelDataSizeFromHeader();
+/**
+ * \ingroup gdcmFile
+ * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
+ * file (see SetFileName, SetDcmTag and Write)
+ * Opens (in read only and when possible) an existing file and checks
+ * for DICOM compliance. Returns NULL on failure.
+ * \Note the in-memory representation of all available tags found in
+ * the DICOM header is post-poned to first header information access.
+ * This avoid a double parsing of public part of the header when
+ * one sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ * @param filename file to be opened for parsing
+ * @return
+ */
+gdcmFile::gdcmFile(std::string & filename) {
+ Header=new gdcmHeader(filename.c_str());
+ SelfHeader=true;
+
+ if (Header->IsReadable())
+ SetPixelDataSizeFromHeader();
+}
+
+gdcmFile::gdcmFile(const char * filename) {
+ Header=new gdcmHeader(filename);
+ SelfHeader=true;
+
+ if (Header->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).
- *
- * @return longueur a allouer
+ * \brief canonical destructor
+ * \Note If the gdcmHeader is created by the gdcmFile, it is destroyed
+ * by the gdcmFile
+ */
+gdcmFile::~gdcmFile(void) {
+ if(SelfHeader)
+ delete Header;
+ Header=NULL;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+
+//-----------------------------------------------------------------------------
+// Public
+/**
+ * \ingroup gdcmFile
+ * \brief
+ * @return
+ */
+gdcmHeader *gdcmFile::GetHeader(void) {
+ return(Header);
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief computes the length (in bytes) to ALLOCATE to receive the
+ * image(s) pixels (multiframes taken into account)
+ * \warning : it is NOT the group 7FE0 length
+ * (no interest for compressed images).
+ * @return length to allocate
*/
void gdcmFile::SetPixelDataSizeFromHeader(void) {
+ // 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]
+
int nb;
std::string str_nb;
-
- str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
+ str_nb=Header->GetEntryByNumber(0x0028,0x0100);
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 = Header->GetXSize() * Header->GetYSize()
+ * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel();
+ std::string str_PhotometricInterpretation =
+ Header->GetEntryByNumber(0x0028,0x0004);
+
+ /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/
+ // pb when undealt Segmented Palette Color
- std::string str_PhotometricInterpretation = gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
- if ( str_PhotometricInterpretation == "PALETTE COLOR "
- || str_PhotometricInterpretation == "YBR_FULL") { // --> some more to be added !!
+ if (Header->HasLUT()) {
lgrTotale*=3;
}
-
- // remaining to check :
- // str_PhotometricInterpretation == "YBR_FULL"
- // str_PhotometricInterpretation == "YBR_FULL_422" (no LUT, no Palette)
- // -->and some more !!
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief Returns the size (in bytes) of required memory to hold
return (lgrTotale);
}
+/**
+ * \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
- * \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)
- *
+ * \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
*/
-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
-
- std::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
- 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
-
- std::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;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;
+void * gdcmFile::GetImageData (void) {
+ PixelData = (void *) malloc(lgrTotale);
+ if (PixelData)
+ GetImageDataIntoVector(PixelData, lgrTotale);
+ return(PixelData);
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
- * \brief Read pixel data from disk (optionaly decompressing) into the
- * caller specified memory location.
- * @param destination where the pixel data should be stored.
- *
+ * \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
+ * 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.
*/
-bool gdcmFile::ReadPixelData(void* destination) {
-
- if ( !OpenFile())
- return false;
-
- if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
- CloseFile();
- return false;
- }
-
-// ------------------------- Uncompressed File
-
- if ( !IsDicomV3() ||
- IsImplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRBigEndianTransferSyntax() ||
- IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
-
- size_t ItemRead = fread(destination, lgrTotale, 1, fp);
- if ( ItemRead != 1 ) {
- CloseFile();
- return false;
- } else {
- CloseFile();
- return true;
- }
- }
-
- // ------------------------ Compressed File .
-
- 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();
-
-
- // ------------------------------- JPEG LossLess : call to Jpeg Libido
-
- if (IsJPEGLossless() && GetZSize() == 1) {
+size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
+ size_t l = GetImageDataIntoVectorRaw (destination, MaxSize);
- 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;
- }
-
- // ------------------------------- RLE
-
- if (gdcmHeader::IsRLELossLessTransferSyntax()) {
- int res = (bool)gdcm_read_RLE_file (destination);
- return res;
+ if (!Header->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 = Header->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];
}
-
- // ------------------------------- JPEG Lossy : call to IJG 6b
+ free(newDest);
- long fragmentBegining; // for ftell, fseek
- bool b = gdcmHeader::IsJPEG2000();
-
- bool res;
- guint16 ItemTagGr,ItemTagEl;
- 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
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Basic Offset Table Item length
-
- if (ln != 0) {
- // What is it used for ?!?
- char *BasicOffsetTableItemValue = (char *)malloc(ln+1);
- fread(BasicOffsetTableItemValue,ln,1,fp);
- }
-
- // first Fragment initialisation
- 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);
- }
-
- // parsing fragments until Sequence Delim. Tag found
- //unsigned short *dest = (unsigned short *)destination;
-
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Fragment Item length
-
- // FIXME : multi fragments
- fragmentBegining=ftell(fp);
-
-
- 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);
-
- } // ------------------------------------- endif (IsJPEGLossless())
-
- else
- if (GetBitsStored() == 8) {
- res = (bool)gdcm_read_JPEG_file (destination); // Reading Fragment pixels
- } else {
- res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels
- }
-
- 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
-
- fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start
- fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
-
- ItemTagGr = ItemTagEl =0;
- 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);
- }
-
- //(char *) destination += taille * nBytes;
- //std::cout << "destination" << destination << std::endl;
- }
-
- return res;
-}
+ // now, it's an RGB image
+ // Lets's write it in the Header
+
+ // CreateOrReplaceIfExist ?
+
+ std::string spp = "3"; // Samples Per Pixel
+ Header->SetEntryByNumber(spp,0x0028,0x0002);
+ std::string rgb= "RGB "; // Photometric Interpretation
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
+ std::string planConfig = "0"; // Planar Configuration
+ Header->SetEntryByNumber(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
+
+ // Oops! I get one (gdcm-US-ALOKA-16.dcm)
+ // No idea how to manage such an image
+ // It seems that *no Dicom Viewer* has any idea :-(
+ // Segmented xxx Palette Color are *more* than 65535 long ?!?
+
+ std::string rgb= "MONOCHROME1 "; // Photometric Interpretation
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
+ }
+ // TODO : Drop Palette Color out of the Header?
+ return lgrTotale;
+}
/**
* \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::GetImageData (void) {
+void * gdcmFile::GetImageDataRaw (void) {
+ if (Header->HasLUT())
+ lgrTotale /= 3; // TODO Let gdcmHeadar user a chance
+ // to get the right value
+ // Create a member lgrTotaleRaw ???
PixelData = (void *) malloc(lgrTotale);
if (PixelData)
- GetImageDataIntoVector(PixelData, lgrTotale);
+ 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 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
* @return On success, the number of bytes actually copied. Zero on
* failure e.g. MaxSize is lower than necessary.
*/
-
-size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
+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;
(void)ReadPixelData(destination);
- // Nombre de Bits Alloues pour le stockage d'un Pixel
- str_nb = GetPubElValByNumber(0x0028,0x0100);
+ // Number of Bits Allocated for storing a Pixel
+ str_nb = Header->GetEntryByNumber(0x0028,0x0100);
if (str_nb == GDCM_UNFOUND ) {
nb = 16;
} else {
nb = atoi(str_nb.c_str() );
- }
-
- // Nombre de Bits Utilises
- str_nbu=GetPubElValByNumber(0x0028,0x0101);
+ }
+ // Number of Bits actually used
+ str_nbu=Header->GetEntryByNumber(0x0028,0x0101);
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);
+ }
+ // High Bit Position
+ str_highBit=Header->GetEntryByNumber(0x0028,0x0102);
if (str_highBit == GDCM_UNFOUND ) {
highBit = nb - 1;
} else {
highBit = atoi(str_highBit.c_str() );
- }
-
- // Signe des Pixels
- str_signe=GetPubElValByNumber(0x0028,0x0103);
+ }
+ // Pixel sign
+ // 0 = Unsigned
+ // 1 = Signed
+ str_signe=Header->GetEntryByNumber(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
+ // re arange bytes inside the integer (processor endianity)
if (nb != 8)
- SwapZone(destination, GetSwapCode(), lgrTotale, nb);
-
+ SwapZone(destination, Header->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
- // --------------------------
-
- 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;
+ }
+// DO NOT remove this code commented out.
+// Nobody knows what's expecting you ...
+// Just to 'see' what was actually read on disk :-(
+// 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
- std::string spp = "3";
- gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
- std::string rgb="RGB";
- gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
- break;
+ std::string str_PhotometricInterpretation =
+ Header->GetEntryByNumber(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
- 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
- std::string spp = "3";
- 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
- }
- break;
- }
- }
-
- return lgrTotale;
-}
+ // Well ... supposed to be !
+ // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0,
+ // PhotometricInterpretation=PALETTE COLOR
+ // and heuristic has to be found :-(
-//
-// Je laisse le code integral, au cas ça puisse etre reutilise ailleurs
-//
+ int planConf=Header->GetPlanarConfiguration(); // 0028,0006
-/**
- * \ingroup gdcmFile
- * \brief Swap the bytes, according to swap code.
- * \warning not end user intended
- * @param im area to deal with
- * @param swap swap code
- * @param lgr Area Length
- * @param nb Pixels Bit number
- */
+ // Whatever Planar Configuration is,
+ // "PALETTE COLOR " implies that we deal with the palette.
+ if (str_PhotometricInterpretation == "PALETTE COLOR ")
+ planConf=2;
-void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) {
-guint32 s32;
-guint16 fort,faible;
-int i;
-
-if(nb == 16)
- switch(swap) {
- case 0:
- case 12:
- case 1234:
+ switch (planConf) {
+ case 0:
+ // Pixels are already RGB
break;
-
- case 21:
- case 3412:
- case 2143:
- case 4321:
+
+ case 1:
- for(i=0;i<lgr;i++)
- ((unsigned short int*)im)[i]= ((((unsigned short int*)im)[i])>>8)
- | ((((unsigned short int*)im)[i])<<8);
- break;
-
- default:
- printf("valeur de SWAP (16 bits) not allowed : %d\n", swap);
- }
-
-if( nb == 32 )
- switch (swap) {
- case 0:
- case 1234:
- break;
+ {
+ if (str_PhotometricInterpretation == "YBR_FULL") {
+
+ // Warning : YBR_FULL_422 acts as RGB
+ // : we need to make RGB Pixels from Planes Y,cB,cR
+
+ // 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 = Header->GetXSize()*Header->GetYSize();
+ int nbFrames = Header->GetZSize();
- case 4321:
- for(i=0;i<lgr;i++) {
- faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 4321 */
- fort =((unsigned long int*)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=faible;
- ((unsigned long int*)im)[i]=(s32<<16)|fort;
- }
- break;
+ 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
+ // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ // for code optimisation
+
+ 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);
- case 2143:
- for(i=0;i<lgr;i++) {
- faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 2143 */
- fort=((unsigned long int*)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=fort;
- ((unsigned long int*)im)[i]=(s32<<16)|faible;
- }
+ } else {
+
+ // need to make RGB Pixels from R,G,B Planes
+ // (all the Frames at a time)
+
+ int l = Header->GetXSize()*Header->GetYSize()*Header->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 3412:
- for(i=0;i<lgr;i++) {
- faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 3412 */
- fort=((unsigned long int*)im)[i]>>16;
- s32=faible;
- ((unsigned long int*)im)[i]=(s32<<16)|fort;
- }
- break;
-
- default:
- printf(" SWAP value (32 bits) not allowed : %d\n", swap);
+ }
+ case 2:
+ // Palettes were found
+ // Let the user deal with them !
+ return lgrTotale;
}
-return;
+ // now, it's an RGB image
+ // Lets's write it in the Header
+
+ // CreateOrReplaceIfExist ?
+
+ std::string spp = "3"; // Samples Per Pixel
+ Header->SetEntryByNumber(spp,0x0028,0x0002);
+ std::string rgb="RGB "; // Photometric Interpretation
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
+
+ std::string planConfig = "0"; // Planar Configuration
+ Header->SetEntryByNumber(planConfig,0x0028,0x0006);
+
+ // TODO : Drop Palette Color out of the Header?
+ return lgrTotale;
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief TODO JPR
* @param inData
* @param ExpectedSize
*
- * @return integer acts as a boolean
+ * @return boolean
*/
-int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
- SetImageDataSize(ExpectedSize);
+bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
+ Header->SetImageDataSize(ExpectedSize);
PixelData = inData;
lgrTotale = ExpectedSize;
- return(1);
-}
-
-
-/////////////////////////////////////////////////////////////////
-/**
- * \ingroup gdcmFile
- * \brief Sets the Pixel Area size in the Header
- * --> not-for-rats function
- *
- * \warning WARNING doit-etre etre publique ?
- * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions
- *
- * @param ImageDataSize new Pixel Area Size
- * warning : nothing else is checked
- */
-
-void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
- std::string content1;
- char car[20];
- // Assumes ElValue (0x7fe0, 0x0010) exists ...
- sprintf(car,"%d",ImageDataSize);
-
- gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
- a->SetLength(ImageDataSize);
-
- ImageDataSize+=8;
- sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetPubElValByNumber(content1, 0x7fe0, 0x0000);
+ return(true);
}
-
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief Ecrit sur disque les pixels d'UNE image
* Ca sera à l'utilisateur d'appeler son Reader correctement
* (Equivalent a IdImaWriteRawFile)
*
- * @param fileName
- * @return
+ * @param fileName name of the file to be created
+ * (any already existing file is over written)
+ * @return false if write fails
*/
-int gdcmFile::WriteRawData (std::string fileName) {
+bool gdcmFile::WriteRawData (std::string fileName) {
FILE * fp1;
fp1 = fopen(fileName.c_str(),"wb");
if (fp1 == NULL) {
printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str());
- return (0);
+ return (false);
}
fwrite (PixelData,lgrTotale, 1, fp1);
fclose (fp1);
- return(1);
+ return(true);
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief Ecrit sur disque UNE image Dicom
* Ca fonctionnera correctement (?) sur processeur Intel
* (Equivalent a IdDcmWrite)
*
- * @param fileName
- * @return int acts as a boolean
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteDcmImplVR (std::string fileName) {
+bool gdcmFile::WriteDcmImplVR (std::string fileName) {
return WriteBase(fileName, ImplicitVR);
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief
- * @param fileName
- * @return int acts as a boolean
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteDcmImplVR (const char* fileName) {
+bool gdcmFile::WriteDcmImplVR (const char* fileName) {
return WriteDcmImplVR (std::string (fileName));
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief
- * @param fileName
- * @return int acts as a boolean
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteDcmExplVR (std::string fileName) {
+bool gdcmFile::WriteDcmExplVR (std::string fileName) {
return WriteBase(fileName, ExplicitVR);
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels
* (a l'attention des logiciels cliniques
* qui ne prennent en entrée QUE des images ACR ...
- * \warning si un header DICOM est fourni en entree,
- * les groupes < 0x0008 et les groupes impairs sont ignores)
- * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur.
+ * \warning if a DICOM_V3 header is supplied,
+ * groups < 0x0008 and shadow groups are ignored)
+ * \warning NO TEST is performed on processor "Endiannity".
* Ca fonctionnera correctement (?) sur processeur Intel
* (Equivalent a IdDcmWrite)
*
- * @param fileName
- * @return int acts as a boolean
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteAcr (std::string fileName) {
+bool gdcmFile::WriteAcr (std::string fileName) {
return WriteBase(fileName, ACR);
}
-/////////////////////////////////////////////////////////////////
+//-----------------------------------------------------------------------------
+// Protected
/**
* \ingroup gdcmFile
*
- * @param FileName
- * @param type
- *
- * @return int acts as a boolean
+* @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @param type file type (ExplicitVR, ImplicitVR, ...)
+ * @return false if write fails
*/
-int gdcmFile::WriteBase (std::string FileName, FileType type) {
+bool gdcmFile::WriteBase (std::string fileName, FileType type) {
FILE * fp1;
- fp1 = fopen(FileName.c_str(),"wb");
+ fp1 = fopen(fileName.c_str(),"wb");
if (fp1 == NULL) {
- printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str());
- return (0);
+ printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str());
+ return (false);
}
if ( (type == ImplicitVR) || (type == ExplicitVR) ) {
// 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);
+ if ( Header->GetFileType() == ACR_LIBIDO){
+ rows = Header->GetEntryByNumber(0x0028, 0x0010);
+ columns = Header->GetEntryByNumber(0x0028, 0x0011);
+ Header->SetEntryByNumber(columns, 0x0028, 0x0010);
+ Header->SetEntryByNumber(rows , 0x0028, 0x0011);
}
// ----------------- End of Special Patch ----------------
- gdcmHeader::Write(fp1, type);
+ Header->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);
+ if (Header->GetFileType() == ACR_LIBIDO){
+ Header->SetEntryByNumber(rows , 0x0028, 0x0010);
+ Header->SetEntryByNumber(columns, 0x0028, 0x0011);
}
// ----------------- End of Special Patch ----------------
fwrite(PixelData, lgrTotale, 1, fp1);
fclose (fp1);
- return(1);
+ return(true);
+}
+
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \ingroup gdcmFile
+ * \brief Swap the bytes, according to swap code.
+ * \warning not end user intended
+ * @param im area to deal with
+ * @param swap swap code
+ * @param lgr Area Length
+ * @param nb Pixels Bit number
+ */
+void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) {
+guint32 s32;
+guint16 fort,faible;
+int i;
+
+if(nb == 16)
+ switch(swap) {
+ case 0:
+ case 12:
+ case 1234:
+ break;
+
+ case 21:
+ case 3412:
+ case 2143:
+ case 4321:
+
+ for(i=0;i<lgr;i++)
+ ((unsigned short int*)im)[i]= ((((unsigned short int*)im)[i])>>8)
+ | ((((unsigned short int*)im)[i])<<8);
+ break;
+
+ default:
+ printf("SWAP value (16 bits) not allowed : %d\n", swap);
+ }
+
+if( nb == 32 )
+ switch (swap) {
+ case 0:
+ case 1234:
+ break;
+
+ case 4321:
+ for(i=0;i<lgr;i++) {
+ faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 4321 */
+ fort =((unsigned long int*)im)[i]>>16;
+ fort= (fort>>8) | (fort<<8);
+ faible=(faible>>8) | (faible<<8);
+ s32=faible;
+ ((unsigned long int*)im)[i]=(s32<<16)|fort;
+ }
+ break;
+
+ case 2143:
+ for(i=0;i<lgr;i++) {
+ faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 2143 */
+ fort=((unsigned long int*)im)[i]>>16;
+ fort= (fort>>8) | (fort<<8);
+ faible=(faible>>8) | (faible<<8);
+ s32=fort;
+ ((unsigned long int*)im)[i]=(s32<<16)|faible;
+ }
+ break;
+
+ case 3412:
+ for(i=0;i<lgr;i++) {
+ faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 3412 */
+ fort=((unsigned long int*)im)[i]>>16;
+ s32=faible;
+ ((unsigned long int*)im)[i]=(s32<<16)|fort;
+ }
+ break;
+
+ default:
+ printf("SWAP value (32 bits) not allowed : %d\n", swap);
+ }
+return;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Read pixel data from disk (optionaly decompressing) into the
+ * caller specified memory location.
+ * @param destination where the pixel data should be stored.
+ *
+ */
+bool gdcmFile::ReadPixelData(void* destination) {
+
+ FILE *fp;
+
+ if ( !(fp=Header->OpenFile()))
+ return false;
+
+ if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) {
+ Header->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 (Header->GetBitsAllocated()==12) {
+ int nbPixels = Header->GetXSize() * Header->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
+ if ( !Header->IsDicomV3() ||
+ Header->IsImplicitVRLittleEndianTransferSyntax() ||
+ Header->IsExplicitVRLittleEndianTransferSyntax() ||
+ Header->IsExplicitVRBigEndianTransferSyntax() ||
+ Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
+
+ size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
+
+ if ( ItemRead != 1 ) {
+ Header->CloseFile();
+ return false;
+ } else {
+ Header->CloseFile();
+ return true;
+ }
+ }
+
+ // ---------------------- Run Length Encoding
+ if (Header->IsRLELossLessTransferSyntax()) {
+ bool res = (bool)gdcm_read_RLE_file (fp,destination);
+ return res;
+ }
+
+ // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
+ int nb;
+ std::string str_nb=Header->GetEntryByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ?
+ }
+
+ int nBytes= nb/8;
+
+ int taille = Header->GetXSize() * Header->GetYSize()
+ * Header->GetSamplesPerPixel();
+ long fragmentBegining; // for ftell, fseek
+
+ bool jpg2000 = Header->IsJPEG2000();
+ bool jpgLossless = Header->IsJPEGLossless();
+
+ bool res = true;
+ guint16 ItemTagGr,ItemTagEl;
+ 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
+ if(Header->GetSwapCode()) {
+ ItemTagGr=Header->SwapShort(ItemTagGr);
+ ItemTagEl=Header->SwapShort(ItemTagEl);
+ }
+ fread(&ln,4,1,fp);
+ if(Header->GetSwapCode())
+ ln=Header->SwapLong(ln); // Basic Offset Table Item length
+
+ if (ln != 0) {
+ // What is it used for ?!?
+ char *BasicOffsetTableItemValue = (char *)malloc(ln+1);
+ fread(BasicOffsetTableItemValue,ln,1,fp);
+ }
+
+ // first Fragment initialisation
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(Header->GetSwapCode()) {
+ ItemTagGr=Header->SwapShort(ItemTagGr);
+ ItemTagEl=Header->SwapShort(ItemTagEl);
+ }
+
+ // parsing fragments until Sequence Delim. Tag found
+ while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+ // --- for each Fragment
+
+ fread(&ln,4,1,fp);
+ if(Header->GetSwapCode())
+ ln=Header->SwapLong(ln); // Fragment Item length
+
+ fragmentBegining=ftell(fp);
+
+ if (jpg2000) { // JPEG 2000 : call to ???
+
+ res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
+
+ } // ------------------------------------- endif (JPEG2000)
+
+ else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
+
+ JPEGLosslessDecodeImage (fp, // Reading Fragment pixels
+ (unsigned short *)destination,
+ Header->GetPixelSize()*8* Header->GetSamplesPerPixel(),
+ ln);
+ res=1; // in order not to break the loop
+
+ } // ------------------------------------- endif (JPEGLossless)
+
+ else { // JPEG Lossy : call to IJG 6b
+
+ if (Header->GetBitsStored() == 8) {
+ res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels
+ } else {
+ res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels
+ }
+ } // ------------------------------------- endif (JPEGLossy)
+
+ if (!res) break;
+
+ destination = (char *)destination + taille * nBytes; // location in user's memory
+ // 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 = ItemTagEl =0;
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(Header->GetSwapCode()) {
+ ItemTagGr=Header->SwapShort(ItemTagGr);
+ ItemTagEl=Header->SwapShort(ItemTagEl);
+ }
+
+ } // endWhile parsing fragments until Sequence Delim. Tag found
+
+ Header->CloseFile();
+ return res;
}
+//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff