-// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.99 2003/10/10 16:54:25 jpr Exp $
+// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.104 2003/10/30 17:04:21 jpr Exp $
#include "gdcmHeader.h"
Initialise();
if ( !OpenFile(exception_on_error))
return;
-
ParseHeader();
LoadElements();
CloseFile();
if(!fp)
throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)");
}
-// char *testEntete = new char[204];
- guint16 zero;
- fread(&zero, (size_t)2, (size_t)1, fp);
+
if ( fp ) {
- //ACR
- if( zero == 0x0008 || zero == 0x0800 )
+ guint16 zero;
+ fread(&zero, (size_t)2, (size_t)1, fp);
+
+ //ACR -- or DICOM with no Preamble
+ if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200)
return true;
//DICOM
fseek(fp, 126L, SEEK_CUR);
char dicm[4];
fread(dicm, (size_t)4, (size_t)1, fp);
- if( strncmp(dicm, "DICM", 4) == 0 )
+ if( memcmp(dicm, "DICM", 4) == 0 )
return true;
fclose(fp);
dbg.Verbose(0, "gdcmHeader::gdcmHeader not DICOM/ACR", filename.c_str());
// Fourth semantics:
//
-// ---> Warning : This fourth fiels is NOT part
+// ---> Warning : This fourth field is NOT part
// of the 'official' Dicom Dictionnary
// and should NOT be used.
// (Not defined for all the groups
void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) {
if ( FoundLength == 0xffffffff)
FoundLength = 0;
+
// Sorry for the patch!
// XMedCom did the trick to read some nasty GE images ...
- if (FoundLength == 13)
+ else if (FoundLength == 13) {
// The following 'if' will be removed when there is no more
- // images on Creatis HD with a 13 length for Manufacturer...
- if ( (ElVal->GetGroup() != 0x0008) || (ElVal->GetElement() ) )
+ // images on Creatis HDs with a 13 length for Manufacturer...
+ if ( (ElVal->GetGroup() != 0x0008) || (ElVal->GetElement() != 0x0070)) {
// end of remove area
FoundLength =10;
+ }
+ }
+ // to fix some garbage 'Leonardo' Siemens images
+ // May be commented out to avoid overhead
+ else if ( (ElVal->GetGroup() == 0x0009)
+ &&
+ ( (ElVal->GetElement() == 0x1113) || (ElVal->GetElement() == 0x1114) ) )
+ FoundLength =4;
ElVal->SetLength(FoundLength);
}
while ( ! FoundSequenceDelimiter) {
g = ReadInt16();
- n = ReadInt16();
-
- long l = ftell(fp);
-
+ n = ReadInt16();
if (errno == 1)
return 0;
TotalLength += 4; // We even have to decount the group and element
- if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ {
+ if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ {
char msg[100]; // for sprintf. Sorry
sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n);
dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg);
- long l = ftell(fp);
errno = 1;
return 0;
}
- if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */
+ if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */
FoundSequenceDelimiter = true;
else if ( n != 0xe000 ){
char msg[100]; // for sprintf. Sorry
}
ItemLength = ReadInt32();
TotalLength += ItemLength + 4; // We add 4 bytes since we just read
- // the ItemLength with ReadInt32
-
+ // the ItemLength with ReadInt32
SkipBytes(ItemLength);
}
fseek(fp, PositionOnEntry, SEEK_SET);
* \ingroup gdcmHeader
* \brief Swaps back the bytes of 4-byte long integer accordingly to
* processor order.
- *
- * @return The suggested integer.
+ * @return The properly swaped 32 bits integer.
*/
guint32 gdcmHeader::SwapLong(guint32 a) {
switch (sw) {
if( vr == "SQ" )
SkipLoad = true;
- // Heuristic : a sequence "contains" a set of tags (called items). It looks
- // like the last tag of a sequence (the one that terminates the sequence)
- // has a group of 0xfffe (with a dummy length).
- // Well ...
- // Actually (fffe e000) tells us an Element is beginning
+ // A sequence "contains" a set of Elements.
+ // (fffe e000) tells us an Element is beginning
// (fffe e00d) tells us an Element just ended
- // (fffe e0dd) tells us the current SEQuence just ended
+ // (fffe e0dd) tells us the current SQuence just ended
if( group == 0xfffe )
SkipLoad = true;
/**
* \ingroup gdcmHeader
* \brief Set a new value if the invoked element exists
+ * Seems to be useless !!!
* @param Value
* @param Group
* @param Elem
*/
int gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) {
- gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
+ //gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem);
std::string v = Value;
PubElValSet.SetElValueByNumber(v, Group, Elem);
return 1;
* @return The result of the heuristical predicate.
*/
bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) {
- guint16 group = ElVal->GetGroup();
guint16 element = ElVal->GetElement();
- std::string vr = ElVal->GetVR();
+ std::string vr = ElVal->GetVR();
guint32 length = ElVal->GetLength();
// When we have some semantics on the element we just read, and if we
return 0;
}
+/**
+ * \ingroup gdcmHeader
+ * \brief Recover the pixel area length (in Bytes) .
+ */
+size_t gdcmHeader::GetPixelAreaLength(void) {
+ // If this file complies with the norm we should encounter the
+ // "Image Location" tag (0x0028, 0x0200). This tag contains the
+ // the group that contains the pixel data (hence the "Pixel Data"
+ // is found by indirection through the "Image Location").
+ // Inside the group pointed by "Image Location" the searched element
+ // is conventionally the element 0x0010 (when the norm is respected).
+ // When the "Image Location" is absent we default to group 0x7fe0.
+ guint16 grPixel;
+ guint16 numPixel;
+ std::string ImageLocation = GetPubElValByName("Image Location");
+ if ( ImageLocation == GDCM_UNFOUND ) {
+ grPixel = 0x7fe0;
+ } else {
+ grPixel = (guint16) atoi( ImageLocation.c_str() );
+ }
+ if (grPixel != 0x7fe0)
+ // This is a kludge for old dirty Philips imager.
+ numPixel = 0x1010;
+ else
+ numPixel = 0x0010;
+
+ gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel,
+ numPixel);
+ if (PixelElement)
+ return PixelElement->GetLength();
+ else
+ return 0;
+}
+
/**
* \ingroup gdcmHeader
* \brief Searches both the public and the shadow dictionary (when they
/**
* \ingroup gdcmHeader
- * \brief
+ * \brief
* @return
*/
void gdcmHeader::PrintPubDict(std::ostream & os) {
/**
* \ingroup gdcmHeader
* \brief
- * @return
+ * @return integer, acts as a Boolean
*/
int gdcmHeader::Write(FILE * fp, FileType type) {
<< std::hex << Group << " " << Elem << std::endl;
return NULL;
}
- int res = PubElValSet.SetVoidAreaByNumber(a, Group, Elem);
+ /* int res = */ PubElValSet.SetVoidAreaByNumber(a, Group, Elem);
// TODO check the result
size_t l2 = fread(a, 1, l ,fp);
if(l != l2) {
<< std::hex << Group << " " << Elem << std::endl;
free(a);
return NULL;
- }
+ }
+ return a;
}
/**
return atoi(StrSize.c_str());
}
+/**
+ * \ingroup gdcmHeader
+ * \brief Retrieve the number of Bits Allocated
+ * (8, 12 -compacted ACR-NEMA files, 16, ...)
+ *
+ * @return The encountered number of Bits Allocated, 0 by default.
+ */
+int gdcmHeader::GetBitsAllocated(void) {
+ std::string StrSize = GetPubElValByNumber(0x0028,0x0100);
+ if (StrSize == GDCM_UNFOUND)
+ return 1;
+ return atoi(StrSize.c_str());
+}
/**
* \ingroup gdcmHeader
/**
* \ingroup gdcmHeader
- * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
- * \ else 0
- * @return Lookup Table Length
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * \brief tells us if LUT are used
+ * @return int acts as a Boolean
*/
-int gdcmHeader::GetLUTLength(void) {
- std::vector<std::string> tokens;
- int LutLength;
- //int LutDepth;
- //int LutNbits;
- // Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
- std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101);
- if (LutDescriptionR == GDCM_UNFOUND)
- return 0;
- std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102);
- if (LutDescriptionG == GDCM_UNFOUND)
+int gdcmHeader::HasLUT(void) {
+
+ // Just hope checking the presence of the LUT Descriptors is enough
+ if (GetPubElValByNumber(0x0028,0x1101) == GDCM_UNFOUND)
return 0;
- std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103);
- if (LutDescriptionB == GDCM_UNFOUND)
+ // LutDescriptorGreen
+ if (GetPubElValByNumber(0x0028,0x1102) == GDCM_UNFOUND)
return 0;
- if( (LutDescriptionR != LutDescriptionG) || (LutDescriptionR != LutDescriptionB) ) {
- dbg.Verbose(0, "gdcmHeader::GetLUTLength: The CLUT R,G,B are not equal");
- return 0;
- }
- std::cout << "Lut Description " << LutDescriptionR <<std::endl;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (LutDescriptionR, tokens, "\\");
- LutLength=atoi(tokens[0].c_str());
- //LutDepth=atoi(tokens[1].c_str());
- //LutNbits=atoi(tokens[2].c_str());
- tokens.clear();
- return LutLength;
+ // LutDescriptorBlue
+ if (GetPubElValByNumber(0x0028,0x1103) == GDCM_UNFOUND)
+ return 0;
+ return 1;
}
/**
tokens.clear();
return LutNbits;
}
-
-
-/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0028,1201 : Lookup Table Red
- * \ else 0
- * @return Lookup Table Red
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- */
-void * gdcmHeader::GetLUTRed(void) {
- return GetPubElValVoidAreaByNumber(0x0028,0x1201);
-}
/**
* \ingroup gdcmHeader
- * \brief gets the info from 0028,1202 : Lookup Table Green
- * \ else 0
- * @return Lookup Table Red
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- */
- void * gdcmHeader::GetLUTGreen(void) {
- return GetPubElValVoidAreaByNumber(0x0028,0x1202);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief gets the info from 0028,1202 : Lookup Table Blue
- * \ else 0
- * @return Lookup Table Blue
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- */
-void * gdcmHeader::GetLUTBlue(void) {
- return GetPubElValVoidAreaByNumber(0x0028,0x1203);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief
- * @return Lookup Table RGB
+ * \brief builts Red/Green/Blue/Alpha LUT from Header
* \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- * \ and (0028,1201),(0028,1202),(0028,1202) are found
- * \warning : hazardous ! Use better GetPubElValVoidAreaByNumber
+ * \ and (0028,1101),(0028,1102),(0028,1102)
+ * \ - xxx Palette Color Lookup Table Descriptor - are found
+ * \ and (0028,1201),(0028,1202),(0028,1202)
+ * \ - xxx Palette Color Lookup Table Data - are found
+ * \warning does NOT deal with :
+ * \ 0028 1100 Gray Lookup Table Descriptor (Retired)
+ * \ 0028 1221 Segmented Red Palette Color Lookup Table Data
+ * \ 0028 1222 Segmented Green Palette Color Lookup Table Data
+ * \ 0028 1223 Segmented Blue Palette Color Lookup Table Data
+ * \ no known Dicom reader deails with them :-(
+ * @return Lookup Table RGBA
*/
-void * gdcmHeader::GetLUTRGB(void) {
+
+void * gdcmHeader::GetLUTRGBA(void) {
// Not so easy : see
// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
// and OT-PAL-8-face.dcm
- if (GetPubElValByNumber(0x0028,0x0004) == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetLUTRGB: unfound Photometric Interpretation");
+// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
+
+ if (gdcmHeader::GetPubElValByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
return NULL;
}
+
void * LutR,*LutG,*LutB;
int l;
-
- // Maybe, some day we get an image
- // that respects the definition ...
- // Let's consider no ones does.
-
- l= GetLUTLength();
- if(l==0)
- return (NULL);
- int nBits=GetLUTNbits();
-
- // a virer quand on aura trouve UNE image
- // qui correspond VRAIMENT à la definition !
- std::cout << "l " << l << " nBits " << nBits;
+ int lengthR, debR, nbitsR;
+ int lengthG, debG, nbitsG;
+ int lengthB, debB, nbitsB;
- l= l/(nBits/8);
-
- LutR =GetPubElValVoidAreaByNumber(0x0028,0x1201);
- LutG =GetPubElValVoidAreaByNumber(0x0028,0x1202);
- LutB =GetPubElValVoidAreaByNumber(0x0028,0x1203);
+// Get info from Lut Descriptors
+// (the 3 LUT descriptors may be different)
- // Warning : Any value for nBits as to be considered as 8
- // Any value for Length as to be considered as 256
- // That's DICOM ...
+ std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101);
+ if (LutDescriptionR == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102);
+ if (LutDescriptionG == GDCM_UNFOUND)
+ return NULL;
+ std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103);
+ if (LutDescriptionB == GDCM_UNFOUND)
+ return NULL;
+
+ std::vector<std::string> tokens;
+
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionR, tokens, "\\");
+ lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes
+ debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value
+ nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits)
+ tokens.clear();
- // Just wait before removing the following code
- /*
- if (nBits == 16) {
- guint16 * LUTRGB, *rgb;
- LUTRGB = rgb = (guint16 *) malloc(3*l*sizeof( guint16));
- guint16 * r = (guint16 *)LutR;
- guint16 * g = (guint16 *)LutG;
- guint16 * b = (guint16 *)LutB;
- for(int i=0;i<l;i++) {
- *rgb++ = *r++;
- *rgb++ = *g++;
- *rgb++ = *b++;
- }
- return(LUTRGB);
- } else
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionG, tokens, "\\");
+ lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes
+ debG =atoi(tokens[1].c_str());
+ nbitsG =atoi(tokens[2].c_str());
+ tokens.clear();
+
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (LutDescriptionB, tokens, "\\");
+ lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes
+ debB =atoi(tokens[1].c_str());
+ nbitsB =atoi(tokens[2].c_str());
+ tokens.clear();
+
+// Load LUTs into memory, (as they were stored on disk)
+
+ unsigned char *lutR =(unsigned char *)
+ GetPubElValVoidAreaByNumber(0x0028,0x1201);
+ unsigned char *lutG =(unsigned char *)
+ GetPubElValVoidAreaByNumber(0x0028,0x1202);
+ unsigned char *lutB =(unsigned char *)
+ GetPubElValVoidAreaByNumber(0x0028,0x1203);
- */ { // we assume it's always 8 Bits
- l=256; // we assume ...
- unsigned char * LUTRGB, *rgb;
- LUTRGB = rgb = (unsigned char *) malloc(3*l*sizeof( char));
- unsigned char * r = (unsigned char *)LutR;
- unsigned char * g = (unsigned char *)LutG;
- unsigned char * b = (unsigned char *)LutB;
- for(int i=0;i<l;i++) {
- //std::cout << "lut16 " << i << " : " << *r << " " << *g << " " << *b
- // << std::endl;
- printf("lut 8 %d : %d %d %d \n",i,*r,*g,*b);
- *rgb++ = *r++;
- *rgb++ = *g++;
- *rgb++ = *b++;
- }
- free(LutR); free(LutB); free(LutG);
- return(LUTRGB);
+ if (!lutR || !lutG || !lutB ) {
+ return NULL;
}
+ // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
+
+ char *LUTRGBA = (char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha)
+ if (!LUTRGBA) {
+ return NULL;
+ }
+ // Bits Allocated
+ int nb;
+ std::string str_nb = GetPubElValByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ }
+ int mult;
+
+ if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size
+ mult=2; // high byte must be = low byte
+ else // See PS 3.3-2003 C.11.1.1.2 p 619
+ mult=1;
+
+
+ // if we get a black image, let's just remove the '+1'
+ // from 'i*mult+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)
+ // and fix the code
+ // We give up the checking to avoid some overhead
+ char *a;
+ a= LUTRGBA+debR;
+ for(int i=0;i<lengthR;i++) {
+ *a = lutR[i*mult+1];
+ a+=4;
+ }
+ a= LUTRGBA+debG;
+ for(int i=0;i<lengthG;i++) {
+ *(a+1) = lutG[i*mult+1];
+ a+=4;
+ }
+ a= LUTRGBA+debB;
+ for(int i=0;i<lengthB;i++) {
+ *(a+2) = lutB[i*mult+1];
+ a+=4;
+ }
+ for(int i=0;i<255;i++) {
+ *(a+3) = 1; // Alpha component
+ a+=4;
+ }
+
+for (int i=0;i<255;i++)
+ printf ( "%d %02x %02x %02x %02x \n",
+ i,(LUTRGBA+i*4)[0],(LUTRGBA+i*4)[1],(LUTRGBA+i*4)[2],(LUTRGBA+i*4)[3]);
+
+// WHY does it seg fault ?!?
+//free(LutR); free(LutB); free(LutG); printf ("libere\n");
-/* Sorry for the comments. The code will be moved in a fonction
-
- std::string x=GetPubElValByNumber(0x0028,0x1201);
- unsigned short int * lutR = (unsigned short int *)malloc((size_t)200*sizeof(short int));
- unsigned short int * lutG = (unsigned short int *)malloc((size_t)200*sizeof(short int));
- unsigned short int * lutB = (unsigned short int *)malloc((size_t)200*sizeof(short int));
-
- std::vector<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((const std::string)x, tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- lutR[i] = atoi(tokens[i].c_str());
- printf("%d (%x)\n",lutR[i],lutR[i]);
- }
-
- std::string y=GetPubElValByNumber(0x0028,0x1202);
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((const std::string)y, tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- lutG[i] = atoi(tokens[i].c_str());
- }
-
- std::string z=GetPubElValByNumber(0x0028,0x1203);
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((const std::string)z, tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- lutB[i] = atoi(tokens[i].c_str());
- }
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize ((const std::string)x, tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++) {
- lutB[i] = atoi(tokens[i].c_str());
- }
-
- */
-
-//int lgth=GetLUTLength();
-//cout << "lgth " << lgth << std::endl;;
-//for (int j=0;j<lgth;j++){
-//printf ("%d : %d (%x) %d (%x) %d (%x)\n",j,lutR[j],lutR[j],lutG[j],lutG[j],lutB[j],lutB[j]);
-//}
-
-
-}
+ return(LUTRGBA);
+}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff