1 /*=========================================================================
4 Module: $RCSfile: gdcmHeader.cxx,v $
6 Date: $Date: 2005/01/07 22:19:48 $
7 Version: $Revision: 1.226 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
19 #include "gdcmHeader.h"
20 #include "gdcmGlobal.h"
22 #include "gdcmDebug.h"
24 #include "gdcmValEntry.h"
25 #include <stdio.h> //sscanf
31 //-----------------------------------------------------------------------------
32 // Constructor / Destructor
35 * @param filename name of the file whose header we want to analyze
37 Header::Header( std::string const &filename ):
40 // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
41 // We may encounter the 'RETired' (0x0028, 0x0200) tag
42 // (Image Location") . This Element contains the number of
43 // the group that contains the pixel data (hence the "Pixel Data"
44 // is found by indirection through the "Image Location").
45 // Inside the group pointed by "Image Location" the searched element
46 // is conventionally the element 0x0010 (when the norm is respected).
47 // When the "Image Location" is absent we default to group 0x7fe0.
48 // Note: this IS the right place for the code
51 const std::string &imgLocation = GetEntryByNumber(0x0028, 0x0200);
52 if ( imgLocation == GDCM_UNFOUND )
59 GrPixel = (uint16_t) atoi( imgLocation.c_str() );
62 // sometimes Image Location value doesn't follow
63 // the supposed processor endianity.
64 // see gdcmData/cr172241.dcm
65 if ( GrPixel == 0xe07f )
70 if ( GrPixel != 0x7fe0 )
72 // This is a kludge for old dirty Philips imager.
80 // Now, we know GrPixel and NumPixel.
81 // Let's create a VirtualDictEntry to allow a further VR modification
82 // and force VR to match with BitsAllocated.
84 DocEntry *entry = GetDocEntryByNumber(GrPixel, NumPixel);
89 // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
90 // more than 8 (i.e 12, 16) is a 'O Words'
91 if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
96 DictEntry* newEntry = NewVirtualDictEntry(
98 PixelVR, "PXL", "Pixel Data");
100 entry->SetDictEntry( newEntry );
105 * \brief Constructor used when we want to generate dicom files from scratch
110 InitializeDefaultHeader();
114 * \brief Canonical destructor.
121 * \brief Performs some consistency checking on various 'File related'
122 * (as opposed to 'DicomDir related') entries
123 * then writes in a file all the (Dicom Elements) included the Pixels
124 * @param fileName file name to write to
125 * @param filetype Type of the File to be written
126 * (ACR-NEMA, ExplicitVR, ImplicitVR)
128 bool Header::Write(std::string fileName, FileType filetype)
130 std::ofstream *fp = new std::ofstream(fileName.c_str(),
131 std::ios::out | std::ios::binary);
134 gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str());
139 if ( GetEntryByNumber(0x0028,0x0100) == "12")
141 SetEntryByNumber("16", 0x0028,0x0100);
144 /// \todo correct 'Pixel group' Length if necessary
146 int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel);
149 // no (GrPixel, NumPixel) element
150 std::string s_lgPix = Util::Format("%d", i_lgPix+12);
151 s_lgPix = Util::DicomString( s_lgPix.c_str() );
152 ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000);
155 // FIXME : should be nice if we could move it to File
156 // (or in future gdcmPixelData class)
158 // Drop Palette Color, if necessary
160 if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' )
162 // if SamplesPerPixel = 3, sure we don't need any LUT !
163 // Drop 0028|1101, 0028|1102, 0028|1103
164 // Drop 0028|1201, 0028|1202, 0028|1203
166 DocEntry *e = GetDocEntryByNumber(0x0028,0x01101);
169 RemoveEntryNoDestroy(e);
171 e = GetDocEntryByNumber(0x0028,0x1102);
174 RemoveEntryNoDestroy(e);
176 e = GetDocEntryByNumber(0x0028,0x1103);
179 RemoveEntryNoDestroy(e);
181 e = GetDocEntryByNumber(0x0028,0x01201);
184 RemoveEntryNoDestroy(e);
186 e = GetDocEntryByNumber(0x0028,0x1202);
189 RemoveEntryNoDestroy(e);
191 e = GetDocEntryByNumber(0x0028,0x1203);
194 RemoveEntryNoDestroy(e);
197 Document::WriteContent(fp,filetype);
205 //-----------------------------------------------------------------------------
209 //-----------------------------------------------------------------------------
213 * \brief This predicate, based on hopefully reasonable heuristics,
214 * decides whether or not the current Header was properly parsed
215 * and contains the mandatory information for being considered as
216 * a well formed and usable Dicom/Acr File.
217 * @return true when Header is the one of a reasonable Dicom/Acr file,
220 bool Header::IsReadable()
222 if( !Document::IsReadable() )
227 const std::string &res = GetEntryByNumber(0x0028, 0x0005);
228 if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
230 return false; // Image Dimensions
232 if ( !GetDocEntryByNumber(0x0028, 0x0100) )
234 return false; // "Bits Allocated"
236 if ( !GetDocEntryByNumber(0x0028, 0x0101) )
238 return false; // "Bits Stored"
240 if ( !GetDocEntryByNumber(0x0028, 0x0102) )
242 return false; // "High Bit"
244 if ( !GetDocEntryByNumber(0x0028, 0x0103) )
246 return false; // "Pixel Representation" i.e. 'Sign'
253 * \brief Retrieve the number of columns of image.
254 * @return The encountered size when found, 0 by default.
255 * 0 means the file is NOT USABLE. The caller will have to check
257 int Header::GetXSize()
259 const std::string &strSize = GetEntryByNumber(0x0028,0x0011);
260 if ( strSize == GDCM_UNFOUND )
265 return atoi( strSize.c_str() );
269 * \brief Retrieve the number of lines of image.
270 * \warning The defaulted value is 1 as opposed to Header::GetXSize()
271 * @return The encountered size when found, 1 by default
272 * (The ACR-NEMA file contains a Signal, not an Image).
274 int Header::GetYSize()
276 const std::string &strSize = GetEntryByNumber(0x0028,0x0010);
277 if ( strSize != GDCM_UNFOUND )
279 return atoi( strSize.c_str() );
286 // The Rows (0028,0010) entry was optional for ACR/NEMA. It might
287 // hence be a signal (1D image). So we default to 1:
292 * \brief Retrieve the number of planes of volume or the number
293 * of frames of a multiframe.
294 * \warning When present we consider the "Number of Frames" as the third
295 * dimension. When absent we consider the third dimension as
296 * being the ACR-NEMA "Planes" tag content.
297 * @return The encountered size when found, 1 by default (single image).
299 int Header::GetZSize()
301 // Both DicomV3 and ACR/Nema consider the "Number of Frames"
302 // as the third dimension.
303 const std::string &strSize = GetEntryByNumber(0x0028,0x0008);
304 if ( strSize != GDCM_UNFOUND )
306 return atoi( strSize.c_str() );
309 // We then consider the "Planes" entry as the third dimension
310 const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012);
311 if ( strSize2 != GDCM_UNFOUND )
313 return atoi( strSize2.c_str() );
320 * \brief gets the info from 0028,0030 : Pixel Spacing
322 * @return X dimension of a pixel
324 float Header::GetXSpacing()
326 float xspacing, yspacing;
327 const std::string &strSpacing = GetEntryByNumber(0x0028,0x0030);
329 if ( strSpacing == GDCM_UNFOUND )
331 gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" );
336 if( ( nbValues = sscanf( strSpacing.c_str(),
337 "%f\\%f", &yspacing, &xspacing)) != 2 )
339 // if single value is found, xspacing is defaulted to yspacing
345 if ( xspacing == 0.0 )
352 // to avoid troubles with David Clunie's-like images
353 if ( xspacing == 0. && yspacing == 0.)
358 gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem");
359 // seems to be a bug in the header ...
360 nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
361 gdcmAssertMacro( nbValues == 2 );
368 * \brief gets the info from 0028,0030 : Pixel Spacing
370 * @return Y dimension of a pixel
372 float Header::GetYSpacing()
375 std::string strSpacing = GetEntryByNumber(0x0028,0x0030);
377 if ( strSpacing == GDCM_UNFOUND )
379 gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)");
383 // if sscanf cannot read any float value, it won't affect yspacing
384 sscanf( strSpacing.c_str(), "%f", &yspacing);
386 if ( yspacing == 0.0 )
393 * \brief gets the info from 0018,0088 : Space Between Slices
394 * else from 0018,0050 : Slice Thickness
396 * @return Z dimension of a voxel-to be
398 float Header::GetZSpacing()
400 // Spacing Between Slices : distance entre le milieu de chaque coupe
401 // Les coupes peuvent etre :
402 // jointives (Spacing between Slices = Slice Thickness)
403 // chevauchantes (Spacing between Slices < Slice Thickness)
404 // disjointes (Spacing between Slices > Slice Thickness)
405 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
406 // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
407 // Si le Spacing Between Slices est absent,
408 // on suppose que les coupes sont jointives
410 const std::string &strSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
412 if ( strSpacingBSlices == GDCM_UNFOUND )
414 gdcmVerboseMacro("Unfound StrSpacingBSlices");
415 const std::string &strSliceThickness = GetEntryByNumber(0x0018,0x0050);
416 if ( strSliceThickness == GDCM_UNFOUND )
422 // if no 'Spacing Between Slices' is found,
423 // we assume slices join together
424 // (no overlapping, no interslice gap)
425 // if they don't, we're fucked up
426 return (float)atof( strSliceThickness.c_str() );
430 return (float)atof( strSpacingBSlices.c_str() );
434 *\brief gets the info from 0028,1052 : Rescale Intercept
435 * @return Rescale Intercept
437 float Header::GetRescaleIntercept()
440 /// 0028 1052 DS IMG Rescale Intercept
441 const std::string &strRescInter = GetEntryByNumber(0x0028,0x1052);
442 if ( strRescInter != GDCM_UNFOUND )
444 if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
446 // bug in the element 0x0028,0x1052
447 gdcmVerboseMacro( "Rescale Intercept is empty." );
455 *\brief gets the info from 0028,1053 : Rescale Slope
456 * @return Rescale Slope
458 float Header::GetRescaleSlope()
461 //0028 1053 DS IMG Rescale Slope
462 std::string strRescSlope = GetEntryByNumber(0x0028,0x1053);
463 if ( strRescSlope != GDCM_UNFOUND )
465 if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
467 // bug in the element 0x0028,0x1053
468 gdcmVerboseMacro( "Rescale Slope is empty.");
476 * \brief This function is intended to user who doesn't want
477 * to have to manage a LUT and expects to get an RBG Pixel image
478 * (or a monochrome one ...)
479 * \warning to be used with GetImagePixels()
480 * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
482 int Header::GetNumberOfScalarComponents()
484 if ( GetSamplesPerPixel() == 3 )
489 // 0028 0100 US IMG Bits Allocated
490 // (in order no to be messed up by old RGB images)
491 if ( GetEntryByNumber(0x0028,0x0100) == "24" )
496 std::string strPhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
498 if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
500 if ( HasLUT() )// PALETTE COLOR is NOT enough
510 // beware of trailing space at end of string
511 // DICOM tags are never of odd length
512 if ( strPhotometricInterpretation == GDCM_UNFOUND ||
513 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
514 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
520 // we assume that *all* kinds of YBR are dealt with
526 * \brief This function is intended to user that DOESN'T want
527 * to get RGB pixels image when it's stored as a PALETTE COLOR image
528 * - the (vtk) user is supposed to know how deal with LUTs -
529 * \warning to be used with GetImagePixelsRaw()
530 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
532 int Header::GetNumberOfScalarComponentsRaw()
534 // 0028 0100 US IMG Bits Allocated
535 // (in order no to be messed up by old RGB images)
536 if ( Header::GetEntryByNumber(0x0028,0x0100) == "24" )
541 // we assume that *all* kinds of YBR are dealt with
542 return GetSamplesPerPixel();
546 // -------------- Remember ! ----------------------------------
548 // Image Position Patient (0020,0032):
549 // If not found (ACR_NEMA) we try Image Position (0020,0030)
550 // If not found (ACR-NEMA), we consider Slice Location (0020,1041)
551 // or Location (0020,0050)
552 // as the Z coordinate,
553 // 0. for all the coordinates if nothing is found
555 // \todo find a way to inform the caller nothing was found
556 // \todo How to tell the caller a wrong number of values was found?
558 // ---------------------------------------------------------------
562 * \brief gets the info from 0020,0032 : Image Position Patient
563 * else from 0020,0030 : Image Position (RET)
565 * @return up-left image corner X position
567 float Header::GetXOrigin()
569 float xImPos, yImPos, zImPos;
570 std::string strImPos = GetEntryByNumber(0x0020,0x0032);
572 if ( strImPos == GDCM_UNFOUND )
574 gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
575 strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
576 if ( strImPos == GDCM_UNFOUND )
578 gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
579 /// \todo How to tell the caller nothing was found ?
584 if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
593 * \brief gets the info from 0020,0032 : Image Position Patient
594 * else from 0020,0030 : Image Position (RET)
596 * @return up-left image corner Y position
598 float Header::GetYOrigin()
600 float xImPos, yImPos, zImPos;
601 std::string strImPos = GetEntryByNumber(0x0020,0x0032);
603 if ( strImPos == GDCM_UNFOUND)
605 gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
606 strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
607 if ( strImPos == GDCM_UNFOUND )
609 gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
610 /// \todo How to tell the caller nothing was found ?
615 if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
624 * \brief gets the info from 0020,0032 : Image Position Patient
625 * else from 0020,0030 : Image Position (RET)
626 * else from 0020,1041 : Slice Location
627 * else from 0020,0050 : Location
629 * @return up-left image corner Z position
631 float Header::GetZOrigin()
633 float xImPos, yImPos, zImPos;
634 std::string strImPos = GetEntryByNumber(0x0020,0x0032);
636 if ( strImPos != GDCM_UNFOUND )
638 if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
640 gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)");
641 return 0.; // bug in the element 0x0020,0x0032
649 strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
650 if ( strImPos != GDCM_UNFOUND )
652 if( sscanf( strImPos.c_str(),
653 "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
655 gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)");
656 return 0.; // bug in the element 0x0020,0x0032
664 std::string strSliceLocation = GetEntryByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images
665 if ( strSliceLocation != GDCM_UNFOUND )
667 if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
669 gdcmVerboseMacro( "Wrong Slice Location (0020,1041)");
670 return 0.; // bug in the element 0x0020,0x1041
677 gdcmVerboseMacro( "Unfound Slice Location (0020,1041)");
679 std::string strLocation = GetEntryByNumber(0x0020,0x0050);
680 if ( strLocation != GDCM_UNFOUND )
682 if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
684 gdcmVerboseMacro( "Wrong Location (0020,0050)");
685 return 0.; // bug in the element 0x0020,0x0050
692 gdcmVerboseMacro( "Unfound Location (0020,0050)");
694 return 0.; // Hopeless
698 * \brief gets the info from 0020,0013 : Image Number else 0.
699 * @return image number
701 int Header::GetImageNumber()
703 // The function i atoi() takes the address of an area of memory as
704 // parameter and converts the string stored at that location to an integer
705 // using the external decimal to internal binary conversion rules. This may
706 // be preferable to sscanf() since atoi() is a much smaller, simpler and
707 // faster function. sscanf() can do all possible conversions whereas
708 // atoi() can only do single decimal integer conversions.
709 //0020 0013 IS REL Image Number
710 std::string strImNumber = GetEntryByNumber(0x0020,0x0013);
711 if ( strImNumber != GDCM_UNFOUND )
713 return atoi( strImNumber.c_str() );
719 * \brief gets the info from 0008,0060 : Modality
720 * @return Modality Type
722 ModalityType Header::GetModality()
724 // 0008 0060 CS ID Modality
725 std::string strModality = GetEntryByNumber(0x0008,0x0060);
726 if ( strModality != GDCM_UNFOUND )
728 if ( strModality.find("AU") < strModality.length()) return AU;
729 else if ( strModality.find("AS") < strModality.length()) return AS;
730 else if ( strModality.find("BI") < strModality.length()) return BI;
731 else if ( strModality.find("CF") < strModality.length()) return CF;
732 else if ( strModality.find("CP") < strModality.length()) return CP;
733 else if ( strModality.find("CR") < strModality.length()) return CR;
734 else if ( strModality.find("CT") < strModality.length()) return CT;
735 else if ( strModality.find("CS") < strModality.length()) return CS;
736 else if ( strModality.find("DD") < strModality.length()) return DD;
737 else if ( strModality.find("DF") < strModality.length()) return DF;
738 else if ( strModality.find("DG") < strModality.length()) return DG;
739 else if ( strModality.find("DM") < strModality.length()) return DM;
740 else if ( strModality.find("DS") < strModality.length()) return DS;
741 else if ( strModality.find("DX") < strModality.length()) return DX;
742 else if ( strModality.find("ECG") < strModality.length()) return ECG;
743 else if ( strModality.find("EPS") < strModality.length()) return EPS;
744 else if ( strModality.find("FA") < strModality.length()) return FA;
745 else if ( strModality.find("FS") < strModality.length()) return FS;
746 else if ( strModality.find("HC") < strModality.length()) return HC;
747 else if ( strModality.find("HD") < strModality.length()) return HD;
748 else if ( strModality.find("LP") < strModality.length()) return LP;
749 else if ( strModality.find("LS") < strModality.length()) return LS;
750 else if ( strModality.find("MA") < strModality.length()) return MA;
751 else if ( strModality.find("MR") < strModality.length()) return MR;
752 else if ( strModality.find("NM") < strModality.length()) return NM;
753 else if ( strModality.find("OT") < strModality.length()) return OT;
754 else if ( strModality.find("PT") < strModality.length()) return PT;
755 else if ( strModality.find("RF") < strModality.length()) return RF;
756 else if ( strModality.find("RG") < strModality.length()) return RG;
757 else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE;
758 else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE;
759 else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN;
760 else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT;
761 else if ( strModality.find("SM") < strModality.length()) return SM;
762 else if ( strModality.find("ST") < strModality.length()) return ST;
763 else if ( strModality.find("TG") < strModality.length()) return TG;
764 else if ( strModality.find("US") < strModality.length()) return US;
765 else if ( strModality.find("VF") < strModality.length()) return VF;
766 else if ( strModality.find("XA") < strModality.length()) return XA;
767 else if ( strModality.find("XC") < strModality.length()) return XC;
771 /// \todo throw error return value ???
772 /// specified <> unknow in our database
781 * \brief Retrieve the number of Bits Stored (actually used)
782 * (as opposite to number of Bits Allocated)
783 * @return The encountered number of Bits Stored, 0 by default.
784 * 0 means the file is NOT USABLE. The caller has to check it !
786 int Header::GetBitsStored()
788 std::string strSize = GetEntryByNumber( 0x0028, 0x0101 );
789 if ( strSize == GDCM_UNFOUND )
791 gdcmVerboseMacro("This is supposed to be mandatory");
792 return 0; // It's supposed to be mandatory
793 // the caller will have to check
795 return atoi( strSize.c_str() );
799 * \brief Retrieve the high bit position.
800 * \warning The method defaults to 0 when information is absent.
801 * The responsability of checking this value is left to the caller.
802 * @return The high bit positin when present. 0 when absent.
804 int Header::GetHighBitPosition()
806 std::string strSize = GetEntryByNumber( 0x0028, 0x0102 );
807 if ( strSize == GDCM_UNFOUND )
809 gdcmVerboseMacro( "This is supposed to be mandatory");
812 return atoi( strSize.c_str() );
816 * \brief Check wether the pixels are signed or UNsigned data.
817 * \warning The method defaults to false (UNsigned) when information is absent.
818 * The responsability of checking this value is left to the caller.
819 * @return True when signed, false when UNsigned
821 bool Header::IsSignedPixelData()
823 std::string strSize = GetEntryByNumber( 0x0028, 0x0103 );
824 if ( strSize == GDCM_UNFOUND )
826 gdcmVerboseMacro( "This is supposed to be mandatory");
829 int sign = atoi( strSize.c_str() );
838 * \brief Retrieve the number of Bits Allocated
839 * (8, 12 -compacted ACR-NEMA files, 16, ...)
840 * @return The encountered number of Bits Allocated, 0 by default.
841 * 0 means the file is NOT USABLE. The caller has to check it !
843 int Header::GetBitsAllocated()
845 std::string strSize = GetEntryByNumber(0x0028,0x0100);
846 if ( strSize == GDCM_UNFOUND )
848 gdcmVerboseMacro( "This is supposed to be mandatory");
849 return 0; // It's supposed to be mandatory
850 // the caller will have to check
852 return atoi( strSize.c_str() );
856 * \brief Retrieve the number of Samples Per Pixel
857 * (1 : gray level, 3 : RGB -1 or 3 Planes-)
858 * @return The encountered number of Samples Per Pixel, 1 by default.
859 * (Gray level Pixels)
861 int Header::GetSamplesPerPixel()
863 const std::string& strSize = GetEntryByNumber(0x0028,0x0002);
864 if ( strSize == GDCM_UNFOUND )
866 gdcmVerboseMacro( "This is supposed to be mandatory");
867 return 1; // Well, it's supposed to be mandatory ...
868 // but sometimes it's missing : *we* assume Gray pixels
870 return atoi( strSize.c_str() );
874 * \brief Check wether this a monochrome picture or not by accessing
875 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
876 * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
878 bool Header::IsMonochrome()
880 const std::string& PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
881 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
882 || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
886 if ( PhotometricInterp == GDCM_UNFOUND )
888 gdcmVerboseMacro( "Absent Photometric Interpretation");
894 * \brief Check wether this a "PALETTE COLOR" picture or not by accessing
895 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
896 * @return true when "PALETTE COLOR". False otherwise.
898 bool Header::IsPaletteColor()
900 std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
901 if ( PhotometricInterp == "PALETTE COLOR " )
905 if ( PhotometricInterp == GDCM_UNFOUND )
907 gdcmVerboseMacro( "Absent Palette color");
913 * \brief Check wether this a "YBR_FULL" color picture or not by accessing
914 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
915 * @return true when "YBR_FULL". False otherwise.
917 bool Header::IsYBRFull()
919 std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
920 if ( PhotometricInterp == "YBR_FULL" )
924 if ( PhotometricInterp == GDCM_UNFOUND )
926 gdcmVerboseMacro( "Absent YBR Full");
932 * \brief Retrieve the Planar Configuration for RGB images
933 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
934 * @return The encountered Planar Configuration, 0 by default.
936 int Header::GetPlanarConfiguration()
938 std::string strSize = GetEntryByNumber(0x0028,0x0006);
939 if ( strSize == GDCM_UNFOUND )
941 gdcmVerboseMacro( "Absent Planar Configuration");
944 return atoi( strSize.c_str() );
948 * \brief Return the size (in bytes) of a single pixel of data.
949 * @return The size in bytes of a single pixel of data; 0 by default
950 * 0 means the file is NOT USABLE; the caller will have to check
952 int Header::GetPixelSize()
954 // 0028 0100 US IMG Bits Allocated
955 // (in order no to be messed up by old RGB images)
956 // if (Header::GetEntryByNumber(0x0028,0x0100) == "24")
959 std::string pixelType = GetPixelType();
960 if ( pixelType == "8U" || pixelType == "8S" )
964 if ( pixelType == "16U" || pixelType == "16S")
968 if ( pixelType == "32U" || pixelType == "32S")
972 if ( pixelType == "FD" )
976 gdcmVerboseMacro( "Unknown pixel type");
981 * \brief Build the Pixel Type of the image.
982 * Possible values are:
983 * - 8U unsigned 8 bit,
985 * - 16U unsigned 16 bit,
986 * - 16S signed 16 bit,
987 * - 32U unsigned 32 bit,
988 * - 32S signed 32 bit,
989 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
990 * \warning 12 bit images appear as 16 bit.
991 * 24 bit images appear as 8 bit
992 * @return 0S if nothing found. NOT USABLE file. The caller has to check
994 std::string Header::GetPixelType()
996 std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
997 if ( bitsAlloc == GDCM_UNFOUND )
999 gdcmVerboseMacro( "Unfound Bits Allocated");
1003 if ( bitsAlloc == "64" )
1007 else if ( bitsAlloc == "12" )
1009 // It will be unpacked
1012 else if ( bitsAlloc == "24" )
1014 // (in order no to be messed up
1015 bitsAlloc = "8"; // by old RGB images)
1018 std::string sign = GetEntryByNumber(0x0028, 0x0103);//"Pixel Representation"
1020 if (sign == GDCM_UNFOUND )
1022 gdcmVerboseMacro( "Unfound Pixel Representation");
1025 else if ( sign == "0" )
1033 return bitsAlloc + sign;
1038 * \brief Recover the offset (from the beginning of the file)
1039 * of *image* pixels (not *icone image* pixels, if any !)
1040 * @return Pixel Offset
1042 size_t Header::GetPixelOffset()
1044 DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
1047 return pxlElement->GetOffset();
1052 std::cout << "Big trouble : Pixel Element ("
1053 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
1060 /// \todo TODO : unify those two (previous one and next one)
1062 * \brief Recover the pixel area length (in Bytes)
1063 * @return Pixel Element Length, as stored in the header
1064 * (NOT the memory space necessary to hold the Pixels
1065 * -in case of embeded compressed image-)
1066 * 0 : NOT USABLE file. The caller has to check.
1068 size_t Header::GetPixelAreaLength()
1070 DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel);
1073 return pxlElement->GetLength();
1078 std::cout << "Big trouble : Pixel Element ("
1079 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
1087 * \brief tells us if LUT are used
1088 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
1089 * are NOT considered as LUT, since nobody knows
1090 * how to deal with them
1091 * Please warn me if you know sbdy that *does* know ... jprx
1092 * @return true if LUT Descriptors and LUT Tables were found
1094 bool Header::HasLUT()
1096 // Check the presence of the LUT Descriptors, and LUT Tables
1098 if ( !GetDocEntryByNumber(0x0028,0x1101) )
1102 // LutDescriptorGreen
1103 if ( !GetDocEntryByNumber(0x0028,0x1102) )
1107 // LutDescriptorBlue
1108 if ( !GetDocEntryByNumber(0x0028,0x1103) )
1112 // Red Palette Color Lookup Table Data
1113 if ( !GetDocEntryByNumber(0x0028,0x1201) )
1117 // Green Palette Color Lookup Table Data
1118 if ( !GetDocEntryByNumber(0x0028,0x1202) )
1122 // Blue Palette Color Lookup Table Data
1123 if ( !GetDocEntryByNumber(0x0028,0x1203) )
1128 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
1129 // NOT taken into account, but we don't know how to use it ...
1134 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
1136 * @return Lookup Table number of Bits , 0 by default
1137 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
1138 * @ return bit number of each LUT item
1140 int Header::GetLUTNbits()
1142 std::vector<std::string> tokens;
1145 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
1146 // = Lookup Table Desc-Blue
1147 // Consistency already checked in GetLUTLength
1148 std::string lutDescription = GetEntryByNumber(0x0028,0x1101);
1149 if ( lutDescription == GDCM_UNFOUND )
1154 tokens.clear(); // clean any previous value
1155 Util::Tokenize ( lutDescription, tokens, "\\" );
1156 //LutLength=atoi(tokens[0].c_str());
1157 //LutDepth=atoi(tokens[1].c_str());
1159 lutNbits = atoi( tokens[2].c_str() );
1166 * \brief Accesses the info from 0002,0010 : Transfert Syntax and TS
1168 * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID)
1170 std::string Header::GetTransfertSyntaxName()
1172 // use the TS (TS : Transfert Syntax)
1173 std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010);
1175 if ( transfertSyntax == GDCM_NOTLOADED )
1177 gdcmVerboseMacro( "Transfert Syntax not loaded. " << std::endl
1178 << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" );
1179 return "Uncompressed ACR-NEMA";
1181 if ( transfertSyntax == GDCM_UNFOUND )
1183 gdcmVerboseMacro( "Unfound Transfert Syntax (0002,0010)");
1184 return "Uncompressed ACR-NEMA";
1187 while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) )
1189 transfertSyntax.erase(transfertSyntax.length()-1, 1);
1191 // we do it only when we need it
1192 TS* ts = Global::GetTS();
1193 std::string tsName = ts->GetValue( transfertSyntax );
1195 //delete ts; /// \todo Seg Fault when deleted ?!
1199 //-----------------------------------------------------------------------------
1203 * \brief anonymize a Header (removes Patient's personal info)
1204 * (read the code to see which ones ...)
1206 bool Header::AnonymizeHeader()
1208 // If exist, replace by spaces
1209 SetEntryByNumber (" ",0x0010, 0x2154); // Telephone
1210 SetEntryByNumber (" ",0x0010, 0x1040); // Adress
1211 SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID
1213 DocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
1215 if ( patientNameHE ) // we replace it by Study Instance UID (why not)
1217 std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
1218 if ( studyInstanceUID != GDCM_UNFOUND )
1220 ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010);
1224 ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010);
1229 // (if any) remove or replace all the stuff that contains a Date
1231 //0008 0012 DA ID Instance Creation Date
1232 //0008 0020 DA ID Study Date
1233 //0008 0021 DA ID Series Date
1234 //0008 0022 DA ID Acquisition Date
1235 //0008 0023 DA ID Content Date
1236 //0008 0024 DA ID Overlay Date
1237 //0008 0025 DA ID Curve Date
1238 //0008 002a DT ID Acquisition Datetime
1239 //0018 9074 DT ACQ Frame Acquisition Datetime
1240 //0018 9151 DT ACQ Frame Reference Datetime
1241 //0018 a002 DT ACQ Contribution Date Time
1242 //0020 3403 SH REL Modified Image Date (RET)
1243 //0032 0032 DA SDY Study Verified Date
1244 //0032 0034 DA SDY Study Read Date
1245 //0032 1000 DA SDY Scheduled Study Start Date
1246 //0032 1010 DA SDY Scheduled Study Stop Date
1247 //0032 1040 DA SDY Study Arrival Date
1248 //0032 1050 DA SDY Study Completion Date
1249 //0038 001a DA VIS Scheduled Admission Date
1250 //0038 001c DA VIS Scheduled Discharge Date
1251 //0038 0020 DA VIS Admitting Date
1252 //0038 0030 DA VIS Discharge Date
1253 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1254 //0040 0004 DA PRC Scheduled Procedure Step End Date
1255 //0040 0244 DA PRC Performed Procedure Step Start Date
1256 //0040 0250 DA PRC Performed Procedure Step End Date
1257 //0040 2004 DA PRC Issue Date of Imaging Service Request
1258 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1259 //0040 4011 DT PRC Expected Completion Date and Time
1260 //0040 a030 DT PRC Verification Date Time
1261 //0040 a032 DT PRC Observation Date Time
1262 //0040 a120 DT PRC DateTime
1263 //0040 a121 DA PRC Date
1264 //0040 a13a DT PRC Referenced Datetime
1265 //0070 0082 DA ??? Presentation Creation Date
1266 //0100 0420 DT ??? SOP Autorization Date and Time
1267 //0400 0105 DT ??? Digital Signature DateTime
1268 //2100 0040 DA PJ Creation Date
1269 //3006 0008 DA SSET Structure Set Date
1270 //3008 0024 DA ??? Treatment Control Point Date
1271 //3008 0054 DA ??? First Treatment Date
1272 //3008 0056 DA ??? Most Recent Treatment Date
1273 //3008 0162 DA ??? Safe Position Exit Date
1274 //3008 0166 DA ??? Safe Position Return Date
1275 //3008 0250 DA ??? Treatment Date
1276 //300a 0006 DA RT RT Plan Date
1277 //300a 022c DA RT Air Kerma Rate Reference Date
1278 //300e 0004 DA RT Review Date
1284 * \brief gets the info from 0020,0037 : Image Orientation Patient
1285 * @param iop adress of the (6)float aray to receive values
1286 * @return cosines of image orientation patient
1288 void Header::GetImageOrientationPatient( float iop[6] )
1290 std::string strImOriPat;
1291 //iop is supposed to be float[6]
1292 iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
1294 // 0020 0037 DS REL Image Orientation (Patient)
1295 if ( (strImOriPat = GetEntryByNumber(0x0020,0x0037)) != GDCM_UNFOUND )
1297 if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
1298 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
1300 gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
1304 // 0020 0035 DS REL Image Orientation (RET)
1305 else if ( (strImOriPat = GetEntryByNumber(0x0020,0x0035)) != GDCM_UNFOUND )
1307 if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
1308 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
1310 gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
1316 * \brief Initialize a default DICOM header that should contain all the
1317 * field require by other reader. DICOM standard does not
1318 * explicitely defines those fields, heuristic has been choosen.
1319 * This is not perfect as we are writting a CT image...
1321 void Header::InitializeDefaultHeader()
1328 } DICOM_DEFAULT_VALUE;
1330 std::string date = Util::GetCurrentDate();
1331 std::string time = Util::GetCurrentTime();
1332 std::string uid = Util::CreateUniqueUID();
1333 std::string uidMedia = uid;
1334 std::string uidClass = uid + ".1";
1335 std::string uidInst = uid + ".10";
1336 std::string uidStudy = uid + ".100";
1337 std::string uidSerie = uid + ".1000";
1339 static DICOM_DEFAULT_VALUE defaultvalue[] = {
1340 { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ?
1341 { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage)
1342 { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID
1343 { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID
1344 { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title
1346 { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date
1347 { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time
1348 { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID
1349 { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID
1350 { "CT", 0x0008, 0x0060}, // Modality
1351 { "GDCM", 0x0008, 0x0070}, // Manufacturer
1352 { "GDCM", 0x0008, 0x0080}, // Institution Name
1353 { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address
1355 { "GDCM", 0x0010, 0x0010}, // Patient's Name
1356 { "GDCMID", 0x0010, 0x0020}, // Patient ID
1358 { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID
1359 { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID
1360 { "1", 0x0020, 0x0010}, // StudyID
1361 { "1", 0x0020, 0x0011}, // SeriesNumber
1363 { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3
1364 { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation
1365 { "0", 0x0028, 0x0010}, // nbRows
1366 { "0", 0x0028, 0x0011}, // nbCols
1367 { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16
1368 { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated
1369 { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1
1370 { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed)
1375 // Special case this is the image (not a string)
1378 ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel);
1380 // All remaining strings:
1382 DICOM_DEFAULT_VALUE current = defaultvalue[i];
1383 while( current.value )
1385 ReplaceOrCreateByNumber(current.value, current.group, current.elem);
1386 current = defaultvalue[++i];
1391 //-----------------------------------------------------------------------------
1394 //-----------------------------------------------------------------------------
1396 } // end namespace gdcm