// gdcmHeader.cxx
//-----------------------------------------------------------------------------
#include "gdcmHeader.h"
-
-#include <stdio.h>
-#include <cerrno>
-#include <cctype> // for isalpha
-
+#include "gdcmGlobal.h"
#include "gdcmUtil.h"
+#include "gdcmDebug.h"
#include "gdcmTS.h"
-//-----------------------------------------------------------------------------
-// Refer to gdcmHeader::CheckSwap()
-//const unsigned int gdcmHeader::HEADER_LENGTH_TO_READ = 256;
-
-// Refer to gdcmHeader::SetMaxSizeLoadEntry()
-//const unsigned int gdcmHeader::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
+#include <vector>
//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
- * \ingroup gdcmHeader
- * \brief
- * @param InFilename
- * @param exception_on_error
- * @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences,
- * when they have an actual length
- * @param ignore_shadow = true if user wants to skip shadow groups
- during parsing, to save memory space
- *\TODO : may be we need one more bool,
- * to allow skipping the private elements while parsing the header
- * in order to save space
+ * \brief Constructor
+ * @param InFilename name of the file whose header we want to analyze
+ * @param exception_on_error whether we want to throw an exception or not
+ * @param enable_sequences = true to allow the header
+ * to be parsed *inside* the SeQuences, when they have an actual length
+ * @param ignore_shadow = true if user wants to skip shadow groups
+ * during parsing, to save memory space
*/
gdcmHeader::gdcmHeader(const char *InFilename,
bool exception_on_error,
bool enable_sequences,
- bool ignore_shadow):
+ bool ignore_shadow):
gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow)
-{
+{
+
+ typedef struct {
+ guint32 totalSQlength;
+ guint32 alreadyParsedlength;
+ } pileElem;
+
+
+ // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
+ // We may encounter the 'RETired' (0x0028, 0x0200) tag
+ // (Image Location") . This Element contains the number of
+ // 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.
+
+ // This IS the right place for the code
+
+ std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
+ if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
+ GrPixel = 0x7fe0; // default value
+ } else {
+ GrPixel = (guint16) atoi( ImageLocation.c_str() );
+ }
+ if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow
+ GrPixel = 0x7fe0; // the supposed processor endianity.
+ // see gdcmData/cr172241.dcm
+ if (GrPixel != 0x7fe0)
+ // This is a kludge for old dirty Philips imager.
+ NumPixel = 0x1010;
+ else
+ NumPixel = 0x0010;
+
+ TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel);
+ countGrPixel = GetEntry().count(key);
+
+ // we set the SQ Depth of each Header Entry
+
+ int top =-1;
+ int countSQ = 0;
+ pileElem pile[100]; // Hope embedded sequence depth is no that long !
+
+ int currentParsedlength = 0;
+ int totalElementlength;
+ std::ostringstream tab;
+ tab << " ";
+
+ // GDCM_DEBUG
+ // Sorry; Dealing with e-film breaker images
+ // will (certainly) cause a lot of troubles ...
+ // I prefer keeping my 'trace' on .
+
+ for (ListTag::iterator i = listEntries.begin();
+ i != listEntries.end();
+ ++i) {
+ (*i)->SetSQDepthLevel(countSQ);
+ if ( (*i)->GetVR() == "SQ" && (*i)->GetReadLength() != 0) { // SQ found
+ countSQ++;
+ top ++;
+ if ( top >= 20) {
+#ifdef GDCM_DEBUG
+ std::cout << "Kaie ! Kaie! SQ Stack Overflow" << std::endl;
+#endif //GDCM_DEBUG
+ return;
+ }
+#ifdef GDCM_DEBUG
+ std::cout << "\n >>>>> empile niveau " << top
+ << "; Lgr SeQ: " << (*i)->GetReadLength()
+ << "\n" <<std::endl;
+#endif //GDCM_DEBUG
+
+ pile[top].totalSQlength = (*i)->GetReadLength();
+ pile[top].alreadyParsedlength = 0;
+ currentParsedlength = 0;
+
+ } else { // non SQ found
+ if (countSQ != 0) { // we are 'inside a SeQuence'
+ if ( (*i)->GetGroup()==0xfffe && (*i)->GetElement()==0xe0dd) {
+ // we just found 'end of SeQuence'
+
+#ifdef GDCM_DEBUG
+ std::cout << "fffe,e0dd : depile" << std::endl;
+#endif //GDCM_DEBUG
+
+ currentParsedlength += 8; // gr:2 elem:2 vr:2 lgt:2
+ countSQ --;
+ top --;
+ pile[top].alreadyParsedlength += currentParsedlength;
+ } else {
+ // we are on a 'standard' elem
+ // or a Zero-length SeQuence
+
+ totalElementlength = (*i)->GetFullLength();
+ currentParsedlength += totalElementlength;
+ pile[top].alreadyParsedlength += totalElementlength;
+
+ if (pile[top].totalSQlength == 0xffffffff) {
+#ifdef GDCM_DEBUG
+ std::cout << "totalSeQlength == 0xffffffff" << std::endl;
+#endif //GDCM_DEBUG
+ } else {
+#ifdef GDCM_DEBUG
+ std::cout << "alrdyPseLgt:"
+ << pile[top].alreadyParsedlength << " totSeQlgt: "
+ << pile[top].totalSQlength << " curPseLgt: "
+ << currentParsedlength
+ << std::endl;
+#endif //GDCM_DEBUG
+ while (pile[top].alreadyParsedlength==pile[top].totalSQlength) {
+#ifdef GDCM_DEBUG
+ std::cout << " \n<<<<<< On depile niveau " << top
+ << " \n" << std::endl;
+#endif //GDCM_DEBUG
+ (*i)->SetSQDepthLevel(countSQ);
+ currentParsedlength = pile[top].alreadyParsedlength;
+ countSQ --;
+ top --;
+ if (top >=0) {
+ pile[top].alreadyParsedlength += currentParsedlength +12;
+ // 12 : length of 'SQ embedded' SQ element
+ currentParsedlength += 8; // gr:2 elem:2 vr:2 lgt:2
+
+#ifdef GDCM_DEBUG
+ std::cout << pile[top].alreadyParsedlength << " "
+ << pile[top].totalSQlength << " "
+ << currentParsedlength
+ << std::endl;
+#endif //GDCM_DEBUG
+ }
+ if (top == -1) {
+ currentParsedlength = 0;
+ break;
+ }
+ }
+ }
+ }
+ } // end : 'inside a SeQuence'
+ }
+#ifdef GDCM_DEBUG
+ for (int k=0; k<(*i)->GetSQDepthLevel();k++) {
+ std::cout << tab;
+ }
+ (*i)->SetPrintLevel(2);
+ (*i)->Print();
+#endif //GDCM_DEBUG
+ } // end for
}
/**
- * \ingroup gdcmHeader
- * \brief
- * @param exception_on_error
+ * \brief Constructor
+ * @param exception_on_error whether we want to throw an exception or not
*/
gdcmHeader::gdcmHeader(bool exception_on_error) :
gdcmParser(exception_on_error)
//-----------------------------------------------------------------------------
// Print
+// see gdcmParser.cxx
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Prints the Header Entries (Dicom Elements)
+ * from the chained list
+ * and skips the elements belonging to a SeQuence
+ * @return
+ */
+void gdcmHeader::PrintEntryNoSQ(std::ostream & os) {
+
+ int depth;
+ for (ListTag::iterator i = listEntries.begin();
+ i != listEntries.end();
+ ++i)
+ {
+ depth= (*i)->GetSQDepthLevel();
+ if ( depth != 0 /*|| (*i)->GetVR() =="SQ" */){
+ continue;
+ }
+ (*i)->SetPrintLevel(printLevel);
+ (*i)->Print(os);
+ }
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Prints the Header Entries (Dicom Elements)
+ * from the chained list
+ * and indents the elements belonging to any SeQuence
+ * \warning : will be removed
+ * @return
+ */
+void gdcmHeader::PrintEntryNiceSQ(std::ostream & os) {
+ std::ostringstream tab;
+ tab << " ";
+
+ int depth;
+ for (ListTag::iterator i = listEntries.begin();
+ i != listEntries.end();
+ ++i) {
+ depth= (*i)->GetSQDepthLevel();
+ if (depth != 0) {
+ for (int k=0;k<depth;k++)
+ os << tab.str();
+ }
+ (*i)->SetPrintLevel(printLevel);
+ (*i)->Print(os);
+
+ } // end for
+}
+
//-----------------------------------------------------------------------------
// Public
+
/**
* \ingroup gdcmHeader
* \brief This predicate, based on hopefully reasonable heuristics,
* false otherwise.
*/
bool gdcmHeader::IsReadable(void) {
- if(!gdcmParser::IsReadable())
+ if(!gdcmParser::IsReadable()) {
return(false);
-
+ }
std::string res = GetEntryByNumber(0x0028, 0x0005);
if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
return false; // Image Dimensions
if ( !GetHeaderEntryByNumber(0x0028, 0x0102) )
return false; // "High Bit"
if ( !GetHeaderEntryByNumber(0x0028, 0x0103) )
- return false; // "Pixel Representation"
+ return false; // "Pixel Representation" i.e. 'Sign'
return true;
}
* \ingroup gdcmHeader
* \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a JPEGBaseLineProcess1 one.
- *
* @return True when JPEGBaseLineProcess1found. False in all other cases.
*/
bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) {
* \ingroup gdcmHeader
* \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a JPEGExtendedProcess2-4 one.
- *
* @return True when JPEGExtendedProcess2-4 found. False in all other cases.
*/
bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) {
* \ingroup gdcmHeader
* \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a JPEGExtendeProcess3-5 one.
- *
* @return True when JPEGExtendedProcess3-5 found. False in all other cases.
*/
bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) {
* \ingroup gdcmHeader
* \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a JPEGSpectralSelectionProcess6-8 one.
- *
* @return True when JPEGSpectralSelectionProcess6-8 found. False in all
* other cases.
*/
* \ingroup gdcmHeader
* \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a RLE Lossless one.
- *
* @return True when RLE Lossless found. False in all
* other cases.
*/
* \ingroup gdcmHeader
* \brief Determines if Transfer Syntax was already encountered
* and if it corresponds to a JPEG Lossless one.
- *
* @return True when RLE Lossless found. False in all
* other cases.
*/
/**
* \ingroup gdcmHeader
* \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a JPEG200 one.0
- *
+ * and if it corresponds to a JPEG2000 one
* @return True when JPEG2000 (Lossly or LossLess) found. False in all
* other cases.
*/
*/
bool gdcmHeader::IsDicomV3(void) {
// Checking if Transfert Syntax exists is enough
+ // Anyway, it's to late check if the 'Preamble' was found ...
+ // And ... would it be a rich idea to check ?
+ // (some 'no Preamble' DICOM images exist !)
return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL);
}
* \brief Retrieve the number of lines of image.
* \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
* @return The encountered size when found, 1 by default
- * (The file contains a Signal, not an Image).
+ * (The ACR-MEMA file contains a Signal, not an Image).
*/
int gdcmHeader::GetYSize(void) {
std::string StrSize = GetEntryByNumber(0x0028,0x0010);
* of frames of a multiframe.
* \warning When present we consider the "Number of Frames" as the third
* dimension. When absent we consider the third dimension as
- * being the "Planes" tag content.
+ * being the ACR-NEMA "Planes" tag content.
* @return The encountered size when found, 1 by default (single image).
*/
int gdcmHeader::GetZSize(void) {
if (StrSize != GDCM_UNFOUND)
return atoi(StrSize.c_str());
- // We then consider the "Planes" entry as the third dimension [we
- // cannot retrieve by name since "Planes tag is present both in
- // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary].
+ // We then consider the "Planes" entry as the third dimension
StrSize = GetEntryByNumber(0x0028,0x0012);
if (StrSize != GDCM_UNFOUND)
return atoi(StrSize.c_str());
* \ingroup gdcmHeader
* \brief Retrieve the number of Bits Stored (actually used)
* (as opposite to number of Bits Allocated)
- *
* @return The encountered number of Bits Stored, 0 by default.
* 0 means the file is NOT USABLE. The caller has to check it !
*/
-int gdcmHeader::GetBitsStored(void) {
+int gdcmHeader::GetBitsStored(void) {
std::string StrSize = GetEntryByNumber(0x0028,0x0101);
if (StrSize == GDCM_UNFOUND)
return 0; // It's supposed to be mandatory
* \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.
* 0 means the file is NOT USABLE. The caller has to check it !
*/
-int gdcmHeader::GetBitsAllocated(void) {
+int gdcmHeader::GetBitsAllocated(void) {
std::string StrSize = GetEntryByNumber(0x0028,0x0100);
if (StrSize == GDCM_UNFOUND)
return 0; // It's supposed to be mandatory
* \ingroup gdcmHeader
* \brief Retrieve the number of Samples Per Pixel
* (1 : gray level, 3 : RGB -1 or 3 Planes-)
- *
* @return The encountered number of Samples Per Pixel, 1 by default.
* (Gray level Pixels)
*/
-int gdcmHeader::GetSamplesPerPixel(void) {
+int gdcmHeader::GetSamplesPerPixel(void) {
std::string StrSize = GetEntryByNumber(0x0028,0x0002);
if (StrSize == GDCM_UNFOUND)
return 1; // Well, it's supposed to be mandatory ...
- // but sometimes it's missing : we assume Gray pixels
+ // but sometimes it's missing : *we* assume Gray pixels
return atoi(StrSize.c_str());
}
* \ingroup gdcmHeader
* \brief Retrieve the Planar Configuration for RGB images
* (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
- *
* @return The encountered Planar Configuration, 0 by default.
*/
-int gdcmHeader::GetPlanarConfiguration(void) {
+int gdcmHeader::GetPlanarConfiguration(void) {
std::string StrSize = GetEntryByNumber(0x0028,0x0006);
if (StrSize == GDCM_UNFOUND)
return 0;
return 2;
if (PixelType == "32U" || PixelType == "32S")
return 4;
+ if (PixelType == "FD")
+ return 8;
dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
return 0;
}
* - 16S signed 16 bit,
* - 32U unsigned 32 bit,
* - 32S signed 32 bit,
+ * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
* \warning 12 bit images appear as 16 bit.
- * \ 24 bit images appear as 8 bit
+ * 24 bit images appear as 8 bit
* @return 0S if nothing found. NOT USABLE file. The caller has to check
*/
-std::string gdcmHeader::GetPixelType(void) {
+std::string gdcmHeader::GetPixelType(void) {
std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
if (BitsAlloc == GDCM_UNFOUND) {
dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
BitsAlloc = std::string("16");
}
+ if (BitsAlloc == "64") // )
+ return ("FD");
if (BitsAlloc == "12") // It will be unpacked
BitsAlloc = std::string("16");
else if (BitsAlloc == "24") // (in order no to be messed up
return( BitsAlloc + Signed);
}
+
/**
* \ingroup gdcmHeader
* \brief Recover the offset (from the beginning of the file)
- * \ of *image* pixels (not *icone image* pixels, if any !)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
*/
-size_t gdcmHeader::GetPixelOffset(void) {
- // We may encounter the 'RETired' (0x0028, 0x0200) tag
- // (Image Location") . This Element contains the number of
- // 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.
+size_t gdcmHeader::GetPixelOffset(void) {
//
// If the element (0x0088,0x0200) 'icone image sequence' is found
// (grPixel,numPixel) is stored twice : the first one for the icon
// the second one for the image ...
// pb : sometimes , (0x0088,0x0200) exists, but doesn't contain *anything*
// see gdcmData/MxTwinLossLess.dcm ...
- guint16 grPixel;
- guint16 numPixel;
- std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
- if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
- grPixel = 0x7fe0; // default value
- } else {
- grPixel = (guint16) atoi( ImageLocation.c_str() );
- }
-
- if (grPixel == 0xe07f) // sometimes Image Location value doesn't follow
- grPixel = 0x7fe0; // the supposed processor endianity.
- // see gdcmData/cr172241.dcm
-
- if (grPixel != 0x7fe0)
- // This is a kludge for old dirty Philips imager.
- numPixel = 0x1010;
- else
- numPixel = 0x0010;
+ /**
+ * \todo Clean me
+ *std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence
+ */
- IterHT it = GetHeaderEntrySameNumber(grPixel,numPixel);
- //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence
- TagKey key = gdcmDictEntry::TranslateToKey(grPixel,numPixel);
+ IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
+ TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
gdcmHeaderEntry* PixelElement;
-
- if (tagHT.count(key) == 1)
+ if (countGrPixel == 1)
PixelElement = (it.first)->second;
- else
- PixelElement = (++it.first)->second;
-
+ else {
+ PixelElement = (++it.first)->second; // hope there are no more than 2 !
+ }
if (PixelElement) {
return PixelElement->GetOffset();
- }
- else
+ } else {
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
return 0;
+ }
}
// TODO : unify those two (previous one and next one)
/**
* \ingroup gdcmHeader
* \brief Recover the pixel area length (in Bytes)
- * @return 0 by default. NOT USABLE file. The caller has to check.
+ * @return Pixel Element Length, as stored in the header
+ * (NOT the memory space necessary to hold the Pixels
+ * -in case of embeded compressed image-)
+ * 0 : NOT USABLE file. The caller has to check.
*/
-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 = GetEntryByNumber(0x0028, 0x0200);
- if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
- grPixel = 0x7fe0; // default value
- } else {
- grPixel = (guint16) atoi( ImageLocation.c_str() );
- }
- if (grPixel == 0xe07f) // sometimes group doesn't follow
- grPixel = 0x7fe0; // the supposed processor endianity. see cr172241.dcm
-
- if (grPixel != 0x7fe0)
- // This is a kludge for old dirty Philips imager.
- numPixel = 0x1010;
- else
- numPixel = 0x0010;
-
- IterHT it = GetHeaderEntrySameNumber(grPixel,numPixel);
- //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence
- TagKey key = gdcmDictEntry::TranslateToKey(grPixel,numPixel);
+size_t gdcmHeader::GetPixelAreaLength(void) {
+
+ IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel);
+ TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel);
gdcmHeaderEntry* PixelElement;
- if (tagHT.count(key) == 1)
+ if (countGrPixel==1)
PixelElement = (it.first)->second;
else
PixelElement = (++it.first)->second;
-
- if (PixelElement)
+
+ if (PixelElement) {
return PixelElement->GetLength();
- else {
+ } else {
+#ifdef GDCM_DEBUG
std::cout << "Big trouble : Pixel Element ("
- << std::hex << grPixel<<","<< numPixel<< ") NOT found"
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
<< std::endl;
+#endif //GDCM_DEBUG
return 0;
}
}
* \ingroup gdcmHeader
* \brief tells us if LUT are used
* \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
- * \ are NOT considered as LUT, since nobody knows
- * \ how to deal with them
- * @return a Boolean
+ * are NOT considered as LUT, since nobody knows
+ * how to deal with them
+ * Please warn me if you know sbdy that *does* know ... jprx
+ * @return true if LUT Descriptors and LUT Tables were found
*/
bool gdcmHeader::HasLUT(void) {
- // Check the presence of the LUT Descriptors
-
+ // Check the presence of the LUT Descriptors, and LUT Tables
// LutDescriptorRed
if ( !GetHeaderEntryByNumber(0x0028,0x1101) )
return false;
return false;
// LutDescriptorBlue
if ( !GetHeaderEntryByNumber(0x0028,0x1103) )
- return false;
-
- // It is not enough :
- // we check also
-
+ return false;
// Red Palette Color Lookup Table Data
if ( !GetHeaderEntryByNumber(0x0028,0x1201) )
return false;
return false;
// Blue Palette Color Lookup Table Data
if ( !GetHeaderEntryByNumber(0x0028,0x1203) )
- return false;
+ return false;
+ // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
+ // NOT taken into account, but we don't know how to use it ...
return true;
}
/**
* \ingroup gdcmHeader
* \brief gets the info from 0028,1101 : Lookup Table Desc-Red
- * \ else 0
+ * else 0
* @return Lookup Table number of Bits , 0 by default
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * @ return bit number of each LUT item
*/
int gdcmHeader::GetLUTNbits(void) {
std::vector<std::string> tokens;
/**
* \ingroup gdcmHeader
* \brief builts Red/Green/Blue/Alpha LUT from Header
- * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
- * \ 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
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * 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 deals with them :-(
+ * 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 deals with them :-(
* @return a RGBA Lookup Table
*/
unsigned char * gdcmHeader::GetLUTRGBA(void) {
// if Photometric Interpretation # PALETTE COLOR, no LUT to be done
if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
- return NULL;
+ return NULL;
}
int lengthR, debR, nbitsR;
int lengthG, debG, nbitsG;
GetEntryVoidAreaByNumber(0x0028,0x1203);
if (!lutR || !lutG || !lutB ) {
- return NULL;
+ return NULL;
}
// forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
- unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha)
+ unsigned char *LUTRGBA = new (unsigned char)[1024]; // 256 * 4 (R, G, B, Alpha)
if (!LUTRGBA) {
return NULL;
}
memset(LUTRGBA, 0, 1024);
- // Bits Allocated
+ // Bits Allocated
int nb;
std::string str_nb = GetEntryByNumber(0x0028,0x0100);
if (str_nb == GDCM_UNFOUND ) {
/**
* \ingroup gdcmHeader
- * \brief gets the info from 0002,0010 : Transfert Syntax
- * \ else 1.
- * @return Transfert Syntax Name (as oposite to Transfert Syntax UID)
+ * \brief gets the info from 0002,0010 : Transfert Syntax and gdcmTS
+ * else 1.
+ * @return the full Transfert Syntax Name (as oposite to Transfert Syntax UID)
*/
std::string gdcmHeader::GetTransfertSyntaxName(void) {
// use the gdcmTS (TS : Transfert Syntax)
}
/**
- * \ingroup gdcmFile
+ * \ingroup gdcmHeader
* \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 gdcmHeader::SetImageDataSize(size_t ImageDataSize) {
std::string content1;
- char car[20];
- // Assumes HeaderEntry (0x7fe0, 0x0010) exists ...
- // TODO define private members PixelGroupNumber, PicxelElementNumber
- // update them, use them (only necessary for ACR-NEMA, not DICOM)
+ char car[20];
+
+ // Assumes HeaderEntry (GrPixel, NumPixel) is unique ...
+ //\todo deal with multiplicity (see gdcmData/icone.dcm)
sprintf(car,"%d",ImageDataSize);
- gdcmHeaderEntry *a = GetHeaderEntryByNumber(0x7fe0, 0x0010);
+ gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel);
a->SetLength(ImageDataSize);
-
+
ImageDataSize+=8;
sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetEntryByNumber(content1, 0x7fe0, 0x0000);
+ content1=car;
+ SetEntryByNumber(content1, GrPixel, NumPixel);
+}
+
+
+/**
+ * \ingroup gdcmHeader
+ * \brief compares 2 Headers, according to DICOMDIR rules
+ * --> not-for-rats function
+ * \warning does NOT work with ACR-NEMA files
+ * \todo find a trick to solve the pb (use RET fields ?)
+ * @param header
+ * @return true if 'smaller'
+ */
+ bool gdcmHeader::operator<(gdcmHeader &header){
+ std::string s1,s2;
+
+ // Patient Name
+ s1=this->GetEntryByNumber(0x0010,0x0010);
+ s2=header.GetEntryByNumber(0x0010,0x0010);
+ if(s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ else
+ {
+ // Patient ID
+ s1=this->GetEntryByNumber(0x0010,0x0020);
+ s2=header.GetEntryByNumber(0x0010,0x0020);
+ if (s1 < s2)
+ return(true);
+ else if (s1 > s2)
+ return(1);
+ else
+ {
+ // Study Instance UID
+ s1=this->GetEntryByNumber(0x0020,0x000d);
+ s2=header.GetEntryByNumber(0x0020,0x000d);
+ if (s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ else
+ {
+ // Serie Instance UID
+ s1=this->GetEntryByNumber(0x0020,0x000e);
+ s2=header.GetEntryByNumber(0x0020,0x000e);
+ if (s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ }
+ }
+ }
+ return(false);
+}
+
+bool gdcmHeader::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
+{
+ guint32 length = tag->GetLength();
+
+ // The value of a tag MUST (see the DICOM norm) be an odd number of
+ // bytes. When this is not the case, pad with an additional byte:
+ if(length%2==1)
+ {
+ tag->SetValue(tag->GetValue()+"\0");
+ tag->SetLength(tag->GetReadLength()+1);
+ }
+
+ WriteEntryTagVRLength(tag, _fp, type);
+
+ // Pixels are never loaded in the element !
+ // we stop writting when Pixel are processed
+ // FIX : we loose trailing elements (RAB, right now)
+ guint16 el = tag->GetElement();
+ guint16 group = tag->GetGroup();
+ int compte =0;
+ if ((group == GrPixel) && (el == NumPixel) ) {
+ compte++;
+ if (compte == countGrPixel) {// we passed *all* the GrPixel,NumPixel
+ return false;
+ }
+ }
+ WriteEntryValue(tag, _fp, type);
+ return true;
}
//-----------------------------------------------------------------------------
// Protected
+/**
+ * \ingroup gdcmHeader
+ * \brief anonymize a Header (removes Patient's personal info)
+ * (read the code to see which ones ...)
+ */
+bool gdcmHeader::anonymizeHeader() {
+
+ gdcmHeaderEntry *patientNameHE = GetHeaderEntryByNumber (0x0010, 0x0010);
+ // gdcmHeaderEntry *patientIDHE = GetHeaderEntryByNumber (0x0010, 0x0020);
+
+ ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone
+ ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress
+ ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID
+
+ if (patientNameHE) {
+ std::string StudyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
+ if (StudyInstanceUID !=GDCM_UNFOUND)
+ ReplaceOrCreateByNumber(StudyInstanceUID, 0x0010, 0x0010);
+ else
+ ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010);
+ }
+
+ // Just for fun :-(
+ // (if any) remove or replace all the stuff that contains a Date
+
+//0008 0012 DA ID Instance Creation Date
+//0008 0020 DA ID Study Date
+//0008 0021 DA ID Series Date
+//0008 0022 DA ID Acquisition Date
+//0008 0023 DA ID Content Date
+//0008 0024 DA ID Overlay Date
+//0008 0025 DA ID Curve Date
+//0008 002a DT ID Acquisition Datetime
+//0018 9074 DT ACQ Frame Acquisition Datetime
+//0018 9151 DT ACQ Frame Reference Datetime
+//0018 a002 DT ACQ Contribution Date Time
+//0020 3403 SH REL Modified Image Date (RET)
+//0032 0032 DA SDY Study Verified Date
+//0032 0034 DA SDY Study Read Date
+//0032 1000 DA SDY Scheduled Study Start Date
+//0032 1010 DA SDY Scheduled Study Stop Date
+//0032 1040 DA SDY Study Arrival Date
+//0032 1050 DA SDY Study Completion Date
+//0038 001a DA VIS Scheduled Admission Date
+//0038 001c DA VIS Scheduled Discharge Date
+//0038 0020 DA VIS Admitting Date
+//0038 0030 DA VIS Discharge Date
+//0040 0002 DA PRC Scheduled Procedure Step Start Date
+//0040 0004 DA PRC Scheduled Procedure Step End Date
+//0040 0244 DA PRC Performed Procedure Step Start Date
+//0040 0250 DA PRC Performed Procedure Step End Date
+//0040 2004 DA PRC Issue Date of Imaging Service Request
+//0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
+//0040 4011 DT PRC Expected Completion Date and Time
+//0040 a030 DT PRC Verification Date Time
+//0040 a032 DT PRC Observation Date Time
+//0040 a120 DT PRC DateTime
+//0040 a121 DA PRC Date
+//0040 a13a DT PRC Referenced Datetime
+//0070 0082 DA ??? Presentation Creation Date
+//0100 0420 DT ??? SOP Autorization Date and Time
+//0400 0105 DT ??? Digital Signature DateTime
+//2100 0040 DA PJ Creation Date
+//3006 0008 DA SSET Structure Set Date
+//3008 0024 DA ??? Treatment Control Point Date
+//3008 0054 DA ??? First Treatment Date
+//3008 0056 DA ??? Most Recent Treatment Date
+//3008 0162 DA ??? Safe Position Exit Date
+//3008 0166 DA ??? Safe Position Return Date
+//3008 0250 DA ??? Treatment Date
+//300a 0006 DA RT RT Plan Date
+//300a 022c DA RT Air Kerma Rate Reference Date
+//300e 0004 DA RT Review Date
+ return true;
+}
//-----------------------------------------------------------------------------
// Private
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff