1 /*=========================================================================
4 Module: $RCSfile: gdcmFile.cxx,v $
6 Date: $Date: 2005/11/05 13:24:39 $
7 Version: $Revision: 1.302 $
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 =========================================================================*/
20 // -------------- Remember ! ----------------------------------
22 // Image Position (Patient) (0020,0032):
23 // If not found (ACR_NEMA) we try Image Position (0020,0030)
24 // If not found (ACR-NEMA), we consider Slice Location (0020,1041)
25 // or Location (0020,0050)
26 // as the Z coordinate,
27 // 0. for all the coordinates if nothing is found
29 // Image Position (Patient) (0020,0032) VM=3
31 // The attribute Patient Orientation (0020,0020) from the General Image Module
32 // is of type 2C and has the condition Required if image does not require
33 // Image Orientation (0020,0037) and Image Position (0020,0032).
34 // However, if the image does require the attributes
35 // - Image Orientation (Patient) (0020,0037), VM=6
36 // - Image Position (Patient) (0020,0032), VM=3
37 // then attribute Patient Orientation (0020,0020) should not be present
41 // Patient Position (0018,5100) values :
43 // HFS = Head First-Supine, where increasing (positive axis direction) :
44 // X -> to the direction pointed to by the patient's oustretched left arm
45 // Y -> to the anterior-to-posterior direction in the patient's body
46 // Z -> to the feet-to-head direction in the patient's body
48 // HFP = Head First-Prone, where increasing (positive axis direction) :
49 // X -> to the direction pointed to by the patient's oustretched left arm
50 // Y -> to the anterior-to-posterior direction in the patient's body
51 // Z -> to the feet-to-head direction in the patient's body
53 // FFS = Feet First-Supine, where increasing (positive axis direction) :
54 // X -> to the direction pointed to by the patient's oustretched left arm
55 // Y -> to the anterior-to-posterion direction in the patient's body
56 // Z -> to the feet-to-head direction in the patient's body
58 // FFP = Feet First-Prone, where increasing (positive axis direction) :
59 // X -> to the direction pointed to by the patient's oustretched left arm
60 // Y -> to the posterior-to-anterior direction in the patient's body
61 // Z -> to the feet-to-head direction in the patient's body
63 // HFDR = Head First-Decubitus Right
64 // HFDL = Head First-Decubitus Left
65 // FFDR = Feet First-Decubitus Right
66 // FFDL = Feet First-Decubitus Left
68 // we can also find (non standard!)
73 // CS 2 Patient Orientation (0020 0020)
74 // When the coordinates of the image
75 // are always present, this field is almost never used.
76 // Better we don't trust it too much ...
85 // (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ]
88 // ---------------------------------------------------------------
91 #include "gdcmGlobal.h"
93 #include "gdcmDebug.h"
95 #include "gdcmSeqEntry.h"
96 #include "gdcmRLEFramesInfo.h"
97 #include "gdcmJPEGFragmentsInfo.h"
98 #include "gdcmDataEntry.h"
101 #include <stdio.h> //sscanf
102 #include <stdlib.h> // for atoi
107 //-----------------------------------------------------------------------------
108 // Constructor / Destructor
111 * \brief Constructor used when we want to generate dicom files from scratch
116 RLEInfo = new RLEFramesInfo;
117 JPEGInfo = new JPEGFragmentsInfo;
118 GrPixel = 0x7fe0; // to avoid further troubles
120 BasicOffsetTableItemValue = 0;
125 * \brief Canonical destructor.
133 delete[] BasicOffsetTableItemValue;
136 //-----------------------------------------------------------------------------
140 * @return false if file cannot be open or no swap info was found,
141 * or no tag was found.
145 if ( ! this->Document::Load( ) )
148 return DoTheLoadingJob( );
152 * \brief Does the Loading Job (internal use only)
153 * @return false if file cannot be open or no swap info was found,
154 * or no tag was found.
156 bool File::DoTheLoadingJob( )
159 // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
160 // We may encounter the 'RETired' (0x0028, 0x0200) tag
161 // (Image Location") . This entry contains the number of
162 // the group that contains the pixel data (hence the "Pixel Data"
163 // is found by indirection through the "Image Location").
164 // Inside the group pointed by "Image Location" the searched element
165 // is conventionally the element 0x0010 (when the norm is respected).
166 // When the "Image Location" is missing we default to group 0x7fe0.
167 // Note: this IS the right place for the code
170 const std::string &imgLocation = GetEntryString(0x0028, 0x0200);
171 if ( imgLocation == GDCM_UNFOUND )
178 GrPixel = (uint16_t) atoi( imgLocation.c_str() );
181 // sometimes Image Location value doesn't follow
182 // the supposed processor endianness.
183 // see gdcmData/cr172241.dcm
184 if ( GrPixel == 0xe07f )
189 if ( GrPixel != 0x7fe0 )
191 // This is a kludge for old dirty Philips imager.
199 // Now, we know GrPixel and NumPixel.
200 // Let's create a VirtualDictEntry to allow a further VR modification
201 // and force VR to match with BitsAllocated.
202 DocEntry *entry = GetDocEntry(GrPixel, NumPixel);
205 // Compute the RLE or JPEG info
207 const std::string &ts = GetTransferSyntax();
208 Fp->seekg( entry->GetOffset(), std::ios::beg );
209 if ( Global::GetTS()->IsRLELossless(ts) )
211 else if ( Global::GetTS()->IsJPEG(ts) )
212 ComputeJPEGFragmentInfo();
215 // Create a new DataEntry to change the DictEntry
216 // The changed DictEntry will have
217 // - a correct PixelVR OB or OW)
218 // - the name to "Pixel Data"
219 DataEntry *oldEntry = dynamic_cast<DataEntry *>(entry);
223 // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
224 // more than 8 (i.e 12, 16) is a 'O Words'
225 if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
230 // Change only made if usefull
231 if ( PixelVR != oldEntry->GetVR() )
233 DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
234 PixelVR,"1","Pixel Data");
236 DataEntry *newEntry = DataEntry::New(newDict);
238 newEntry->Copy(entry);
239 newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
240 oldEntry->SetSelfArea(false);
242 RemoveEntry(oldEntry);
251 * \brief This predicate, based on hopefully reasonable heuristics,
252 * decides whether or not the current File was properly parsed
253 * and contains the mandatory information for being considered as
254 * a well formed and usable Dicom/Acr File.
255 * @return true when File is the one of a reasonable Dicom/Acr file,
258 bool File::IsReadable()
260 if ( !Document::IsReadable() )
265 const std::string &res = GetEntryString(0x0028, 0x0005);
266 if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
268 gdcmWarningMacro("Wrong Image Dimensions" << res);
269 return false; // Image Dimensions
271 bool b0028_0100 = true;
272 if ( !GetDocEntry(0x0028, 0x0100) )
274 gdcmWarningMacro("Bits Allocated (0028|0100) not found");
275 //return false; // "Bits Allocated"
278 bool b0028_0101 = true;
279 if ( !GetDocEntry(0x0028, 0x0101) )
281 gdcmWarningMacro("Bits Stored (0028|0101) not found");
282 //return false; // "Bits Stored"
285 bool b0028_0102 = true;
286 if ( !GetDocEntry(0x0028, 0x0102) )
288 gdcmWarningMacro("Hight Bit (0028|0102) not found");
289 //return false; // "High Bit"
292 bool b0028_0103 = true;
293 if ( !GetDocEntry(0x0028, 0x0103) )
295 gdcmWarningMacro("Pixel Representation (0028|0103) not found");
296 //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed)
300 if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103)
302 gdcmWarningMacro("Too much mandatory Tags missing !");
306 if ( !GetDocEntry(GrPixel, NumPixel) )
308 gdcmWarningMacro("Pixel Dicom Element " << std::hex <<
309 GrPixel << "|" << NumPixel << "not found");
310 return false; // Pixel Dicom Element not found :-(
316 * \brief gets the info from 0020,0013 : Image Number else 0.
317 * @return image number
319 int File::GetImageNumber()
321 //0020 0013 : Image Number
322 std::string strImNumber = GetEntryString(0x0020,0x0013);
323 if ( strImNumber != GDCM_UNFOUND )
325 return atoi( strImNumber.c_str() );
331 * \brief gets the info from 0008,0060 : Modality
332 * @return Modality Type
334 ModalityType File::GetModality()
336 // 0008 0060 : Modality
337 std::string strModality = GetEntryString(0x0008,0x0060);
338 if ( strModality != GDCM_UNFOUND )
340 if ( strModality.find("AU") < strModality.length()) return AU;
341 else if ( strModality.find("AS") < strModality.length()) return AS;
342 else if ( strModality.find("BI") < strModality.length()) return BI;
343 else if ( strModality.find("CF") < strModality.length()) return CF;
344 else if ( strModality.find("CP") < strModality.length()) return CP;
345 else if ( strModality.find("CR") < strModality.length()) return CR;
346 else if ( strModality.find("CT") < strModality.length()) return CT;
347 else if ( strModality.find("CS") < strModality.length()) return CS;
348 else if ( strModality.find("DD") < strModality.length()) return DD;
349 else if ( strModality.find("DF") < strModality.length()) return DF;
350 else if ( strModality.find("DG") < strModality.length()) return DG;
351 else if ( strModality.find("DM") < strModality.length()) return DM;
352 else if ( strModality.find("DS") < strModality.length()) return DS;
353 else if ( strModality.find("DX") < strModality.length()) return DX;
354 else if ( strModality.find("ECG") < strModality.length()) return ECG;
355 else if ( strModality.find("EPS") < strModality.length()) return EPS;
356 else if ( strModality.find("FA") < strModality.length()) return FA;
357 else if ( strModality.find("FS") < strModality.length()) return FS;
358 else if ( strModality.find("HC") < strModality.length()) return HC;
359 else if ( strModality.find("HD") < strModality.length()) return HD;
360 else if ( strModality.find("LP") < strModality.length()) return LP;
361 else if ( strModality.find("LS") < strModality.length()) return LS;
362 else if ( strModality.find("MA") < strModality.length()) return MA;
363 else if ( strModality.find("MR") < strModality.length()) return MR;
364 else if ( strModality.find("NM") < strModality.length()) return NM;
365 else if ( strModality.find("OT") < strModality.length()) return OT;
366 else if ( strModality.find("PT") < strModality.length()) return PT;
367 else if ( strModality.find("RF") < strModality.length()) return RF;
368 else if ( strModality.find("RG") < strModality.length()) return RG;
369 else if ( strModality.find("RTDOSE")
370 < strModality.length()) return RTDOSE;
371 else if ( strModality.find("RTIMAGE")
372 < strModality.length()) return RTIMAGE;
373 else if ( strModality.find("RTPLAN")
374 < strModality.length()) return RTPLAN;
375 else if ( strModality.find("RTSTRUCT")
376 < strModality.length()) return RTSTRUCT;
377 else if ( strModality.find("SM") < strModality.length()) return SM;
378 else if ( strModality.find("ST") < strModality.length()) return ST;
379 else if ( strModality.find("TG") < strModality.length()) return TG;
380 else if ( strModality.find("US") < strModality.length()) return US;
381 else if ( strModality.find("VF") < strModality.length()) return VF;
382 else if ( strModality.find("XA") < strModality.length()) return XA;
383 else if ( strModality.find("XC") < strModality.length()) return XC;
387 /// \todo throw error return value ???
388 /// specified <> unknown in our database
396 * \brief Retrieve the number of columns of image.
397 * @return The encountered size when found, 0 by default.
398 * 0 means the file is NOT USABLE. The caller will have to check
402 DataEntry *entry = GetDataEntry(0x0028,0x0011);
404 return (int)entry->GetValue(0);
409 * \brief Retrieve the number of lines of image.
410 * \warning The defaulted value is 1 as opposed to File::GetXSize()
411 * @return The encountered size when found, 1 by default
412 * (The ACR-NEMA file contains a Signal, not an Image).
416 DataEntry *entry = GetDataEntry(0x0028,0x0010);
418 return (int)entry->GetValue(0);
425 // The Rows (0028,0010) entry was optional for ACR/NEMA.
426 // (at least some images didn't have it.)
427 // It might hence be a signal (1D image). So we default to 1:
432 * \brief Retrieve the number of planes of volume or the number
433 * of frames of a multiframe.
434 * \warning When present we consider the "Number of Frames" as the third
435 * dimension. When missing we consider the third dimension as
436 * being the ACR-NEMA "Planes" tag content.
437 * @return The encountered size when found, 1 by default (single image).
441 // Both DicomV3 and ACR/Nema consider the "Number of Frames"
442 // as the third dimension.
443 DataEntry *entry = GetDataEntry(0x0028,0x0008);
445 return (int)entry->GetValue(0);
447 // We then consider the "Planes" entry as the third dimension
448 entry = GetDataEntry(0x0028,0x0012);
450 return (int)entry->GetValue(0);
455 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
456 * then 0028,0030 : Pixel Spacing
458 * @return X dimension of a pixel
460 float File::GetXSpacing()
462 float xspacing = 1.0;
465 // To follow David Clunie's advice, we first check ImagerPixelSpacing
467 DataEntry *entry = GetDataEntry(0x0018,0x1164);
470 nbValue = entry->GetValueCount();
471 // Can't use IsValueCountValid because of the complex heuristic.
473 gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) "
474 << "has a wrong number of values :" << nbValue);
477 xspacing = (float)entry->GetValue(2);
478 else if( nbValue >= 2 )
479 xspacing = (float)entry->GetValue(1);
481 xspacing = (float)entry->GetValue(0);
483 if ( xspacing == 0.0 )
489 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
492 entry = GetDataEntry(0x0028,0x0030);
495 nbValue = entry->GetValueCount();
497 gdcmWarningMacro("PixelSpacing (0x0018,0x0030) "
498 << "has a wrong number of values :" << nbValue);
501 xspacing = (float)entry->GetValue(2);
502 else if( nbValue >= 2 )
503 xspacing = (float)entry->GetValue(1);
505 xspacing = (float)entry->GetValue(0);
507 if ( xspacing == 0.0 )
513 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
520 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
521 * then from 0028,0030 : Pixel Spacing
523 * @return Y dimension of a pixel
525 float File::GetYSpacing()
527 float yspacing = 1.0;
528 // To follow David Clunie's advice, we first check ImagerPixelSpacing
530 DataEntry *entry = GetDataEntry(0x0018,0x1164);
533 yspacing = (float)entry->GetValue(0);
535 if ( yspacing == 0.0 )
541 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
544 entry = GetDataEntry(0x0028,0x0030);
547 yspacing = (float)entry->GetValue(0);
549 if ( yspacing == 0.0 )
555 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
562 * \brief gets the info from 0018,0088 : Space Between Slices
563 * else from 0018,0050 : Slice Thickness
565 * @return Z dimension of a voxel-to be
567 float File::GetZSpacing()
572 // For *Dicom* images, ZSpacing should be calculated using
573 // XOrigin, YOrigin, ZOrigin (of the top left image corner)
574 // of 2 consecutive images, and the Orientation
576 // Computing ZSpacing on a single image is not really meaningfull !
578 float zspacing = 1.0f;
580 // Spacing Between Slices : distance between the middle of 2 slices
582 // jointives (Spacing between Slices = Slice Thickness)
583 // overlapping (Spacing between Slices < Slice Thickness)
584 // disjointes (Spacing between Slices > Slice Thickness)
585 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
586 // It only concerns the MRI guys, not people wanting to visualize volumes
587 // If Spacing Between Slices is missing,
588 // we suppose slices joint together
589 DataEntry *entry = GetDataEntry(0x0018,0x0088);
592 zspacing = (float)entry->GetValue(0);
594 if ( zspacing == 0.0 )
599 gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
601 // if no 'Spacing Between Slices' is found,
602 // we assume slices join together
603 // (no overlapping, no interslice gap)
604 // if they don't, we're fucked up
605 entry = GetDataEntry(0x0018,0x0050);
608 zspacing = (float)entry->GetValue(0);
610 if ( zspacing == 0.0 )
615 gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
621 * \brief gets the info from 0020,0032 : Image Position Patient
622 * else from 0020,0030 : Image Position (RET)
624 * @return up-left image corner X position
626 float File::GetXOrigin()
628 DataEntry *entry = GetDataEntry(0x0020,0x0032);
631 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
632 entry = GetDataEntry(0x0020,0x0030);
635 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
640 if( entry->GetValueCount() == 3 )
642 if (!entry->IsValueCountValid() )
644 gdcmErrorMacro( "Invalid Value Count" );
646 return (float)entry->GetValue(0);
652 * \brief gets the info from 0020,0032 : Image Position Patient
653 * else from 0020,0030 : Image Position (RET)
655 * @return up-left image corner Y position
657 float File::GetYOrigin()
659 DataEntry *entry = GetDataEntry(0x0020,0x0032);
662 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
663 entry = GetDataEntry(0x0020,0x0030);
666 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
671 if( entry->GetValueCount() == 3 )
673 if (!entry->IsValueCountValid() )
675 gdcmErrorMacro( "Invalid Value Count" );
677 return (float)entry->GetValue(1);
683 * \brief gets the info from 0020,0032 : Image Position Patient
684 * else from 0020,0030 : Image Position (RET)
685 * else from 0020,1041 : Slice Location
686 * else from 0020,0050 : Location
688 * @return up-left image corner Z position
690 float File::GetZOrigin()
692 DataEntry *entry = GetDataEntry(0x0020,0x0032);
695 if( entry->GetValueCount() == 3 )
697 if (!entry->IsValueCountValid() )
699 gdcmErrorMacro( "Invalid Value Count" );
701 return (float)entry->GetValue(2);
703 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
707 entry = GetDataEntry(0x0020,0x0030);
710 if( entry->GetValueCount() == 3 )
712 if (!entry->IsValueCountValid() )
714 gdcmErrorMacro( "Invalid Value Count" );
716 return (float)entry->GetValue(2);
718 gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
722 // for *very* old ACR-NEMA images
723 entry = GetDataEntry(0x0020,0x1041);
726 if( entry->GetValueCount() == 1 )
728 if (!entry->IsValueCountValid() )
730 gdcmErrorMacro( "Invalid Value Count" );
732 return (float)entry->GetValue(0); // VM=1 !
734 gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
738 entry = GetDataEntry(0x0020,0x0050);
741 if( entry->GetValueCount() == 1 )
743 if (!entry->IsValueCountValid() )
745 gdcmErrorMacro( "Invalid Value Count" );
747 return (float)entry->GetValue(0);
749 gdcmWarningMacro( "Wrong Location (0020,0050)");
752 return 0.; // Hopeless
756 * \brief gets the info from 0020,0037 : Image Orientation Patient
757 * or from 0020 0035 : Image Orientation (RET)
758 * (needed to organize DICOM files based on their x,y,z position)
759 * @param iop adress of the (6)float array to receive values
760 * @return true when one of the tag is found
761 * false when nothing is found
763 bool File::GetImageOrientationPatient( float iop[6] )
765 std::string strImOriPat;
766 //iop is supposed to be float[6]
767 iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
769 // 0020 0037 DS REL Image Orientation (Patient)
770 if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
772 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
773 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
775 gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
776 << " Less than 6 values were found." );
781 // 0020 0035 DS REL Image Orientation (RET)
782 else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND )
784 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
785 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
787 gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
788 << "Less than 6 values were found." );
796 * \brief Retrieve the number of Bits Stored (actually used)
797 * (as opposed to number of Bits Allocated)
798 * @return The encountered number of Bits Stored, 0 by default.
799 * 0 means the file is NOT USABLE. The caller has to check it !
801 int File::GetBitsStored()
803 DataEntry *entry = GetDataEntry(0x0028,0x0101);
806 gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
809 return (int)entry->GetValue(0);
813 * \brief Retrieve the number of Bits Allocated
814 * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,)
815 * @return The encountered Number of Bits Allocated, 0 by default.
816 * 0 means the file is NOT USABLE. The caller has to check it !
818 int File::GetBitsAllocated()
820 DataEntry *entry = GetDataEntry(0x0028,0x0100);
823 gdcmWarningMacro("(0028,0100) is supposed to be mandatory");
826 return (int)entry->GetValue(0);
830 * \brief Retrieve the high bit position.
831 * \warning The method defaults to 0 when information is missing.
832 * The responsability of checking this value is left to the caller.
833 * @return The high bit position when present. 0 when missing.
835 int File::GetHighBitPosition()
837 DataEntry *entry = GetDataEntry(0x0028,0x0102);
840 gdcmWarningMacro("(0028,0102) is supposed to be mandatory");
843 return (int)entry->GetValue(0);
847 * \brief Retrieve the number of Samples Per Pixel
848 * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
849 * @return The encountered number of Samples Per Pixel, 1 by default.
850 * (we assume Gray level Pixels)
852 int File::GetSamplesPerPixel()
854 DataEntry *entry = GetDataEntry(0x0028,0x0002);
857 gdcmWarningMacro("(0028,0002) is supposed to be mandatory");
858 return 1; // Well, it's supposed to be mandatory ...
859 // but sometimes it's missing : *we* assume Gray pixels
861 return (int)entry->GetValue(0);
865 * \brief Retrieve the Planar Configuration for RGB images
866 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
867 * @return The encountered Planar Configuration, 0 by default.
869 int File::GetPlanarConfiguration()
871 DataEntry *entry = GetDataEntry(0x0028,0x0006);
876 return (int)entry->GetValue(0);
880 * \brief Return the size (in bytes) of a single pixel of data.
881 * @return The size in bytes of a single pixel of data; 0 by default
882 * 0 means the file is NOT USABLE; the caller will have to check
884 int File::GetPixelSize()
886 // 0028 0100 US IMG Bits Allocated
887 // (in order no to be messed up by old ACR-NEMA RGB images)
888 assert( !(GetEntryString(0x0028,0x0100) == "24") );
890 std::string pixelType = GetPixelType();
891 if ( pixelType == "8U" || pixelType == "8S" )
895 if ( pixelType == "16U" || pixelType == "16S")
899 if ( pixelType == "32U" || pixelType == "32S")
903 if ( pixelType == "FD" )
907 gdcmWarningMacro( "Unknown pixel type: " << pixelType);
912 * \brief Build the Pixel Type of the image.
913 * Possible values are:
914 * - 8U unsigned 8 bit,
916 * - 16U unsigned 16 bit,
917 * - 16S signed 16 bit,
918 * - 32U unsigned 32 bit,
919 * - 32S signed 32 bit,
920 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
921 * \warning 12 bit images appear as 16 bit.
922 * 24 bit images appear as 8 bit + photochromatic interp ="RGB "
923 * + Planar Configuration = 0
924 * @return 0S if nothing found. NOT USABLE file. The caller has to check
926 std::string File::GetPixelType()
928 std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
929 if ( bitsAlloc == GDCM_UNFOUND )
931 gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
932 bitsAlloc = "16"; // default and arbitrary value, not to polute the output
935 if ( bitsAlloc == "64" )
939 else if ( bitsAlloc == "12" )
941 // It will be unpacked
944 else if ( bitsAlloc == "24" )
946 // (in order no to be messed up by old RGB images)
951 if( IsSignedPixelData() )
959 return bitsAlloc + sign;
963 * \brief Check whether the pixels are signed (1) or UNsigned (0) data.
964 * \warning The method defaults to false (UNsigned) when tag 0028|0103
966 * The responsability of checking this value is left to the caller
967 * (NO transformation is performed on the pixels to make then >0)
968 * @return True when signed, false when UNsigned
970 bool File::IsSignedPixelData()
972 DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
975 gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
978 return entry->GetValue(0) != 0;
982 * \brief Check whether this a monochrome picture (gray levels) or not,
983 * using "Photometric Interpretation" tag (0x0028,0x0004).
984 * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
986 bool File::IsMonochrome()
988 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
989 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
990 || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
994 if ( PhotometricInterp == GDCM_UNFOUND )
996 gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
1002 * \brief Check whether this a MONOCHROME1 picture (high values = dark)
1003 * or not using "Photometric Interpretation" tag (0x0028,0x0004).
1004 * @return true when "MONOCHROME1" . False otherwise.
1006 bool File::IsMonochrome1()
1008 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1009 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
1013 if ( PhotometricInterp == GDCM_UNFOUND )
1015 gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
1021 * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
1022 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1023 * @return true when "PALETTE COLOR". False otherwise.
1025 bool File::IsPaletteColor()
1027 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1028 if ( PhotometricInterp == "PALETTE COLOR " )
1032 if ( PhotometricInterp == GDCM_UNFOUND )
1034 gdcmWarningMacro( "Not found : Palette color (0028,0004)");
1040 * \brief Check whether this a "YBR_FULL" color picture or not by accessing
1041 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1042 * @return true when "YBR_FULL". False otherwise.
1044 bool File::IsYBRFull()
1046 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1047 if ( PhotometricInterp == "YBR_FULL" )
1051 if ( PhotometricInterp == GDCM_UNFOUND )
1053 gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
1059 * \brief tells us if LUT are used
1060 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
1061 * are NOT considered as LUT, since nobody knows
1062 * how to deal with them
1063 * Please warn me if you know sbdy that *does* know ... jprx
1064 * @return true if LUT Descriptors and LUT Tables were found
1068 // Check the presence of the LUT Descriptors, and LUT Tables
1070 if ( !GetDocEntry(0x0028,0x1101) )
1074 // LutDescriptorGreen
1075 if ( !GetDocEntry(0x0028,0x1102) )
1079 // LutDescriptorBlue
1080 if ( !GetDocEntry(0x0028,0x1103) )
1084 // Red Palette Color Lookup Table Data
1085 if ( !GetDocEntry(0x0028,0x1201) )
1089 // Green Palette Color Lookup Table Data
1090 if ( !GetDocEntry(0x0028,0x1202) )
1094 // Blue Palette Color Lookup Table Data
1095 if ( !GetDocEntry(0x0028,0x1203) )
1100 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
1101 // NOT taken into account, but we don't know how to use it ...
1106 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
1108 * @return Lookup Table number of Bits , 0 by default
1109 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
1110 * @ return bit number of each LUT item
1112 int File::GetLUTNbits()
1114 std::vector<std::string> tokens;
1117 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
1118 // = Lookup Table Desc-Blue
1119 // Consistency already checked in GetLUTLength
1120 std::string lutDescription = GetEntryString(0x0028,0x1101);
1121 if ( lutDescription == GDCM_UNFOUND )
1126 tokens.clear(); // clean any previous value
1127 Util::Tokenize ( lutDescription, tokens, "\\" );
1128 //LutLength=atoi(tokens[0].c_str());
1129 //LutDepth=atoi(tokens[1].c_str());
1131 lutNbits = atoi( tokens[2].c_str() );
1138 *\brief gets the info from 0028,1052 : Rescale Intercept
1139 * @return Rescale Intercept
1141 float File::GetRescaleIntercept()
1143 // 0028 1052 DS IMG Rescale Intercept
1144 DataEntry *entry = GetDataEntry(0x0028, 0x1052);
1147 gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
1150 return (float)entry->GetValue(0);
1155 *\brief gets the info from 0028,1053 : Rescale Slope
1156 * @return Rescale Slope
1158 float File::GetRescaleSlope()
1160 // 0028 1053 DS IMG Rescale Slope
1161 DataEntry *entry = GetDataEntry(0x0028, 0x1053);
1164 gdcmWarningMacro( "Missing Rescale Slope (0028,1053)");
1167 return (float)entry->GetValue(0);
1171 * \brief This function is intended to user who doesn't want
1172 * to have to manage a LUT and expects to get an RBG Pixel image
1173 * (or a monochrome one ...)
1174 * \warning to be used with GetImagePixels()
1175 * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
1177 int File::GetNumberOfScalarComponents()
1179 if ( GetSamplesPerPixel() == 3 )
1184 // 0028 0100 US IMG Bits Allocated
1185 // (in order no to be messed up by old RGB images)
1186 if ( GetEntryString(0x0028,0x0100) == "24" )
1191 std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
1193 if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
1195 if ( HasLUT() )// PALETTE COLOR is NOT enough
1205 // beware of trailing space at end of string
1206 // DICOM tags are never of odd length
1207 if ( strPhotometricInterpretation == GDCM_UNFOUND ||
1208 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
1209 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
1215 // we assume that *all* kinds of YBR are dealt with
1221 * \brief This function is intended to user that DOESN'T want
1222 * to get RGB pixels image when it's stored as a PALETTE COLOR image
1223 * - the (vtk) user is supposed to know how deal with LUTs -
1224 * \warning to be used with GetImagePixelsRaw()
1225 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
1227 int File::GetNumberOfScalarComponentsRaw()
1229 // 0028 0100 US IMG Bits Allocated
1230 // (in order no to be messed up by old RGB images)
1231 if ( File::GetEntryString(0x0028,0x0100) == "24" )
1236 // we assume that *all* kinds of YBR are dealt with
1237 return GetSamplesPerPixel();
1241 * \brief Recover the offset (from the beginning of the file)
1242 * of *image* pixels (not *icone image* pixels, if any !)
1243 * @return Pixel Offset
1245 size_t File::GetPixelOffset()
1247 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1250 return pxlElement->GetOffset();
1254 gdcmDebugMacro( "Big trouble : Pixel Element ("
1255 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1261 * \brief Recover the pixel area length (in Bytes)
1262 * @return Pixel Element Length, as stored in the header
1263 * (NOT the memory space necessary to hold the Pixels
1264 * -in case of embeded compressed image-)
1265 * 0 : NOT USABLE file. The caller has to check.
1267 size_t File::GetPixelAreaLength()
1269 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1272 return pxlElement->GetLength();
1276 gdcmDebugMacro( "Big trouble : Pixel Element ("
1277 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1283 * \brief Adds the characteristics of a new element we want to anonymize
1284 * @param group Group number of the target tag.
1285 * @param elem Element number of the target tag.
1286 * @param value new value (string) to substitute with
1288 void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
1289 std::string const &value)
1295 UserAnonymizeList.push_back(el);
1299 * \brief Overwrites in the file the values of the DicomElements
1302 void File::AnonymizeNoLoad()
1304 std::fstream *fp = new std::fstream(Filename.c_str(),
1305 std::ios::in | std::ios::out | std::ios::binary);
1309 uint32_t valLgth = 0;
1310 std::string *spaces;
1311 for (ListElements::iterator it = UserAnonymizeList.begin();
1312 it != UserAnonymizeList.end();
1315 d = GetDocEntry( (*it).Group, (*it).Elem);
1320 if ( dynamic_cast<SeqEntry *>(d) )
1322 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1326 offset = d->GetOffset();
1327 lgth = d->GetLength();
1330 spaces = new std::string( lgth-valLgth, ' ');
1331 (*it).Value = (*it).Value + *spaces;
1334 fp->seekp( offset, std::ios::beg );
1335 fp->write( (*it).Value.c_str(), lgth );
1343 * \brief anonymize a File (remove Patient's personal info passed with
1344 * AddAnonymizeElement()
1345 * \note You cannot Anonymize a DataEntry (to be fixed)
1347 bool File::AnonymizeFile()
1349 // If Anonymisation list is empty, let's perform some basic anonymization
1350 if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
1352 // If exist, replace by spaces
1353 SetEntryString(" ",0x0010, 0x2154); // Telephone
1354 SetEntryString(" ",0x0010, 0x1040); // Adress
1355 SetEntryString(" ",0x0010, 0x0020); // Patient ID
1357 DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
1359 if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
1361 std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
1362 if ( studyInstanceUID != GDCM_UNFOUND )
1364 SetEntryString(studyInstanceUID, 0x0010, 0x0010);
1368 SetEntryString("anonymized", 0x0010, 0x0010);
1375 for (ListElements::iterator it = UserAnonymizeList.begin();
1376 it != UserAnonymizeList.end();
1379 d = GetDocEntry( (*it).Group, (*it).Elem);
1384 if ( dynamic_cast<SeqEntry *>(d) )
1386 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1390 if ( dynamic_cast<DataEntry *>(d) )
1392 gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
1396 SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
1400 // In order to make definitively impossible any further identification
1401 // remove or replace all the stuff that contains a Date
1403 //0008 0012 DA ID Instance Creation Date
1404 //0008 0020 DA ID Study Date
1405 //0008 0021 DA ID Series Date
1406 //0008 0022 DA ID Acquisition Date
1407 //0008 0023 DA ID Content Date
1408 //0008 0024 DA ID Overlay Date
1409 //0008 0025 DA ID Curve Date
1410 //0008 002a DT ID Acquisition Datetime
1411 //0018 9074 DT ACQ Frame Acquisition Datetime
1412 //0018 9151 DT ACQ Frame Reference Datetime
1413 //0018 a002 DT ACQ Contribution Date Time
1414 //0020 3403 SH REL Modified Image Date (RET)
1415 //0032 0032 DA SDY Study Verified Date
1416 //0032 0034 DA SDY Study Read Date
1417 //0032 1000 DA SDY Scheduled Study Start Date
1418 //0032 1010 DA SDY Scheduled Study Stop Date
1419 //0032 1040 DA SDY Study Arrival Date
1420 //0032 1050 DA SDY Study Completion Date
1421 //0038 001a DA VIS Scheduled Admission Date
1422 //0038 001c DA VIS Scheduled Discharge Date
1423 //0038 0020 DA VIS Admitting Date
1424 //0038 0030 DA VIS Discharge Date
1425 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1426 //0040 0004 DA PRC Scheduled Procedure Step End Date
1427 //0040 0244 DA PRC Performed Procedure Step Start Date
1428 //0040 0250 DA PRC Performed Procedure Step End Date
1429 //0040 2004 DA PRC Issue Date of Imaging Service Request
1430 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1431 //0040 4011 DT PRC Expected Completion Date and Time
1432 //0040 a030 DT PRC Verification Date Time
1433 //0040 a032 DT PRC Observation Date Time
1434 //0040 a120 DT PRC DateTime
1435 //0040 a121 DA PRC Date
1436 //0040 a13a DT PRC Referenced Datetime
1437 //0070 0082 DA ??? Presentation Creation Date
1438 //0100 0420 DT ??? SOP Autorization Date and Time
1439 //0400 0105 DT ??? Digital Signature DateTime
1440 //2100 0040 DA PJ Creation Date
1441 //3006 0008 DA SSET Structure Set Date
1442 //3008 0024 DA ??? Treatment Control Point Date
1443 //3008 0054 DA ??? First Treatment Date
1444 //3008 0056 DA ??? Most Recent Treatment Date
1445 //3008 0162 DA ??? Safe Position Exit Date
1446 //3008 0166 DA ??? Safe Position Return Date
1447 //3008 0250 DA ??? Treatment Date
1448 //300a 0006 DA RT RT Plan Date
1449 //300a 022c DA RT Air Kerma Rate Reference Date
1450 //300e 0004 DA RT Review Date
1456 * \brief Performs some consistency checking on various 'File related'
1457 * (as opposed to 'DicomDir related') entries
1458 * then writes in a file all the (Dicom Elements) included the Pixels
1459 * @param fileName file name to write to
1460 * @param writetype type of the file to be written
1461 * (ACR, ExplicitVR, ImplicitVR)
1463 bool File::Write(std::string fileName, FileType writetype)
1465 std::ofstream *fp = new std::ofstream(fileName.c_str(),
1466 std::ios::out | std::ios::binary);
1469 gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
1473 // Entry : 0002|0000 = group length -> recalculated
1474 DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
1477 std::ostringstream sLen;
1478 sLen << ComputeGroup0002Length( );
1479 e0000->SetString(sLen.str());
1482 // FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
1483 if( writetype != JPEG )
1485 int i_lgPix = GetEntryLength(GrPixel, NumPixel);
1488 // no (GrPixel, NumPixel) element
1489 std::string s_lgPix = Util::Format("%d", i_lgPix+12);
1490 s_lgPix = Util::DicomString( s_lgPix.c_str() );
1491 InsertEntryString(s_lgPix,GrPixel, 0x0000);
1494 Document::WriteContent(fp, writetype);
1502 //-----------------------------------------------------------------------------
1506 //-----------------------------------------------------------------------------
1509 * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
1510 * Compute the RLE extra information and store it in \ref RLEInfo
1511 * for later pixel retrieval usage.
1513 void File::ComputeRLEInfo()
1515 std::string ts = GetTransferSyntax();
1516 if ( !Global::GetTS()->IsRLELossless(ts) )
1521 // Encoded pixel data: for the time being we are only concerned with
1522 // Jpeg or RLE Pixel data encodings.
1523 // As stated in PS 3.5-2003, section 8.2 p44:
1524 // "If sent in Encapsulated Format (i.e. other than the Native Format) the
1525 // value representation OB is used".
1526 // Hence we expect an OB value representation. Concerning OB VR,
1527 // the section PS 3.5-2003, section A.4.c p 58-59, states:
1528 // "For the Value Representations OB and OW, the encoding shall meet the
1529 // following specifications depending on the Data element tag:"
1531 // - the first item in the sequence of items before the encoded pixel
1532 // data stream shall be basic offset table item. The basic offset table
1533 // item value, however, is not required to be present"
1534 ReadEncapsulatedBasicOffsetTable();
1536 // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
1537 // Loop on the individual frame[s] and store the information
1538 // on the RLE fragments in a RLEFramesInfo.
1539 // Note: - when only a single frame is present, this is a
1541 // - when more than one frame are present, then we are in
1542 // the case of a multi-frame image.
1546 while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1548 // Since we have read the basic offset table, let's check the value were correct
1549 // or else produce a warning:
1550 if ( BasicOffsetTableItemValue )
1552 // If a BasicOffsetTableItemValue was read
1553 uint32_t individualLength = BasicOffsetTableItemValue[i];
1554 assert( individualLength == sum ); // REMOVE that if this is a problem
1555 if( individualLength != sum )
1557 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" );
1559 sum += frameLength + 8;
1562 // Parse the RLE Header and store the corresponding RLE Segment
1563 // Offset Table information on fragments of this current Frame.
1564 // Note that the fragment pixels themselves are not loaded
1565 // (but just skipped).
1566 long frameOffset = Fp->tellg();
1568 uint32_t nbRleSegments = ReadInt32();
1569 if ( nbRleSegments > 16 )
1571 // There should be at most 15 segments (refer to RLEFrame class)
1572 gdcmWarningMacro( "Too many segments.");
1575 uint32_t rleSegmentOffsetTable[16];
1576 for( int k = 1; k <= 15; k++ )
1578 rleSegmentOffsetTable[k] = ReadInt32();
1581 // Deduce from both RLE Header and frameLength
1582 // the fragment length, and again store this info
1583 // in a RLEFramesInfo.
1584 long rleSegmentLength[15];
1585 // skipping (not reading) RLE Segments
1586 if ( nbRleSegments > 1)
1588 for(unsigned int k = 1; k <= nbRleSegments-1; k++)
1590 rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
1591 - rleSegmentOffsetTable[k];
1592 SkipBytes(rleSegmentLength[k]);
1596 rleSegmentLength[nbRleSegments] = frameLength
1597 - rleSegmentOffsetTable[nbRleSegments];
1598 SkipBytes(rleSegmentLength[nbRleSegments]);
1600 // Store the collected info
1601 RLEFrame *newFrame = new RLEFrame;
1602 newFrame->SetNumberOfFragments(nbRleSegments);
1603 for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
1605 newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
1606 newFrame->SetLength(uk,rleSegmentLength[uk]);
1608 RLEInfo->AddFrame(newFrame);
1611 // Make sure that we encounter a 'Sequence Delimiter Item'
1612 // at the end of the item :
1613 if ( !ReadTag(0xfffe, 0xe0dd) )
1615 gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
1620 * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
1621 * Compute the jpeg extra information (fragment[s] offset[s] and
1622 * length) and store it[them] in \ref JPEGInfo for later pixel
1625 void File::ComputeJPEGFragmentInfo()
1627 // If you need to, look for comments of ComputeRLEInfo().
1628 std::string ts = GetTransferSyntax();
1629 if ( ! Global::GetTS()->IsJPEG(ts) )
1634 ReadEncapsulatedBasicOffsetTable();
1636 // Loop on the fragments[s] and store the parsed information in a
1638 long fragmentLength;
1641 while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1643 // Since we have read the basic offset table, let's check the value were correct
1644 // or else produce a warning:
1645 // A.4 Transfer syntaxes for encapsulation of encoded pixel data:
1646 // When the Item Value is present, the Basic Offset Table Item Value shall contain
1647 // concatenated 32-bit unsigned integer values that are byte offsets to the first
1648 // byte of the Item Tag of the first fragment for each frame in the Sequence of
1649 // Items. These offsets are measured from the first byte of the first Item Tag
1650 // following the Basic Offset Table item (See Table A.4-2).
1652 if ( BasicOffsetTableItemValue )
1654 // If a BasicOffsetTableItemValue was read
1655 uint32_t individualLength = BasicOffsetTableItemValue[i];
1656 //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ??
1657 if( individualLength != sum )
1659 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" <<
1660 individualLength << " != " << sum );
1662 sum += fragmentLength + 8;
1666 long fragmentOffset = Fp->tellg();
1667 // Store the collected info
1668 JPEGFragment *newFragment = new JPEGFragment;
1669 newFragment->SetOffset(fragmentOffset);
1670 newFragment->SetLength(fragmentLength);
1671 JPEGInfo->AddFragment(newFragment);
1673 SkipBytes(fragmentLength);
1676 // Make sure that we encounter a 'Sequence Delimiter Item'
1677 // at the end of the item :
1678 if ( !ReadTag(0xfffe, 0xe0dd) )
1680 gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
1685 * \brief Assuming the internal file pointer \ref Document::Fp
1686 * is placed at the beginning of a tag, check whether this
1687 * tag is (TestGroup, TestElem).
1688 * \warning On success the internal file pointer \ref Document::Fp
1689 * is modified to point after the tag.
1690 * On failure (i.e. when the tag wasn't the expected tag
1691 * (TestGroup, TestElem) the internal file pointer
1692 * \ref Document::Fp is restored to it's original position.
1693 * @param testGroup The expected group of the tag.
1694 * @param testElem The expected Element of the tag.
1695 * @return True on success, false otherwise.
1697 bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
1699 long positionOnEntry = Fp->tellg();
1700 long currentPosition = Fp->tellg(); // On debugging purposes
1702 // Read the Item Tag group and element, and make
1703 // sure they are what we expected:
1704 uint16_t itemTagGroup;
1705 uint16_t itemTagElem;
1708 itemTagGroup = ReadInt16();
1709 itemTagElem = ReadInt16();
1711 catch ( FormatError )
1713 gdcmErrorMacro( "Can not read tag for "
1714 << " We should have found tag ("
1715 << DictEntry::TranslateToKey(testGroup,testElem) << ")"
1720 if ( itemTagGroup != testGroup || itemTagElem != testElem )
1722 // in order not to pollute output we don't warn on 'delimitors'
1723 if (itemTagGroup != 0xfffe || testGroup != 0xfffe )
1724 gdcmErrorMacro( "Wrong Item Tag found:"
1725 << " We should have found tag ("
1726 << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
1727 << " but instead we encountered tag ("
1728 << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
1729 << " at address: " << " 0x(" << std::hex
1730 << (unsigned int)currentPosition << std::dec << ")"
1732 Fp->seekg(positionOnEntry, std::ios::beg);
1740 * \brief Assuming the internal file pointer \ref Document::Fp
1741 * is placed at the beginning of a tag (TestGroup, TestElement),
1742 * read the length associated to the Tag.
1743 * \warning On success the internal file pointer \ref Document::Fp
1744 * is modified to point after the tag and it's length.
1745 * On failure (i.e. when the tag wasn't the expected tag
1746 * (TestGroup, TestElement) the internal file pointer
1747 * \ref Document::Fp is restored to it's original position.
1748 * @param testGroup The expected Group of the tag.
1749 * @param testElem The expected Element of the tag.
1750 * @return On success returns the length associated to the tag. On failure
1753 uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
1756 if ( !ReadTag(testGroup, testElem) )
1758 // Avoid polutting output
1759 if ( testGroup != 0xfffe )
1760 gdcmErrorMacro( "ReadTag did not succeed for ("
1761 << DictEntry::TranslateToKey(testGroup,testElem)
1766 //// Then read the associated Item Length
1767 long currentPosition = Fp->tellg();
1768 uint32_t itemLength = ReadInt32();
1769 gdcmDebugMacro( "Basic Item Length is: " << itemLength
1770 << " at address: " << std::hex << (unsigned int)currentPosition);
1775 * \brief When parsing the Pixel Data of an encapsulated file, read
1776 * the basic offset table (when present, and BTW dump it).
1778 void File::ReadEncapsulatedBasicOffsetTable()
1780 //// Read the Basic Offset Table Item Tag length...
1781 uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
1783 // When present, read the basic offset table itself.
1784 // Notes: - since the presence of this basic offset table is optional
1785 // we can't rely on it for the implementation, and we will simply
1786 // trash it's content (when present).
1787 // - still, when present, we could add some further checks on the
1788 // lengths, but we won't bother with such fuses for the time being.
1789 if ( itemLength != 0 )
1791 char *charBasicOffsetTableItemValue = new char[itemLength];
1792 Fp->read(charBasicOffsetTableItemValue, itemLength);
1793 unsigned int nbEntries = itemLength/4;
1794 assert( nbEntries*4 == itemLength); // Make sure this is a multiple
1795 BasicOffsetTableItemValue = new uint32_t[nbEntries];
1797 for (unsigned int i=0; i < nbEntries; i++ )
1799 BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i]));
1800 #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION)
1801 uint32_t val = BasicOffsetTableItemValue[i];
1802 BasicOffsetTableItemValue[i]
1803 = ( (val<<24) | ((val<<8) & 0x00ff0000) |
1804 ( (val>>8) & 0x0000ff00) | (val>>24) );
1806 gdcmDebugMacro( "Read one length for: " <<
1807 std::hex << BasicOffsetTableItemValue[i] );
1810 delete[] charBasicOffsetTableItemValue;
1814 // These are the deprecated method that one day should be removed (after the next release)
1816 #ifndef GDCM_LEGACY_REMOVE
1818 * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API)
1819 * @ param fileName file to be open for parsing
1820 * @ return false if file cannot be open or no swap info was found,
1821 * or no tag was found.
1822 * @ deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
1824 bool File::Load( std::string const &fileName )
1826 GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
1828 SetFileName( fileName );
1829 if ( ! this->Document::Load( ) )
1832 return DoTheLoadingJob( );
1836 //-----------------------------------------------------------------------------
1839 //-----------------------------------------------------------------------------
1840 } // end namespace gdcm