1 /*=========================================================================
4 Module: $RCSfile: gdcmFile.cxx,v $
6 Date: $Date: 2006/03/29 16:13:00 $
7 Version: $Revision: 1.317 $
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;
121 FourthDimensionLocation = TagKey(0,0);
126 * \brief Canonical destructor.
134 delete[] BasicOffsetTableItemValue;
137 //-----------------------------------------------------------------------------
141 * @return false if file cannot be open or no swap info was found,
142 * or no tag was found.
146 if ( ! this->Document::Load( ) )
149 return DoTheLoadingJob( );
153 * \brief Does the Loading Job (internal use only)
154 * @return false if file cannot be open or no swap info was found,
155 * or no tag was found.
157 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);
252 * \brief This predicate, based on hopefully reasonable heuristics,
253 * decides whether or not the current File was properly parsed
254 * and contains the mandatory information for being considered as
255 * a well formed and usable Dicom/Acr File.
256 * @return true when File is the one of a reasonable Dicom/Acr file,
259 bool File::IsReadable()
261 if ( !Document::IsReadable() )
266 const std::string &res = GetEntryString(0x0028, 0x0005);
267 if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
269 gdcmWarningMacro("Wrong Image Dimensions" << res);
270 return false; // Image Dimensions
272 bool b0028_0100 = true;
273 if ( !GetDocEntry(0x0028, 0x0100) )
275 gdcmWarningMacro("Bits Allocated (0028|0100) not found");
276 //return false; // "Bits Allocated"
279 bool b0028_0101 = true;
280 if ( !GetDocEntry(0x0028, 0x0101) )
282 gdcmWarningMacro("Bits Stored (0028|0101) not found");
283 //return false; // "Bits Stored"
286 bool b0028_0102 = true;
287 if ( !GetDocEntry(0x0028, 0x0102) )
289 gdcmWarningMacro("Hight Bit (0028|0102) not found");
290 //return false; // "High Bit"
293 bool b0028_0103 = true;
294 if ( !GetDocEntry(0x0028, 0x0103) )
296 gdcmWarningMacro("Pixel Representation (0028|0103) not found");
297 //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed)
301 if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103)
303 gdcmWarningMacro("Too much mandatory Tags missing !");
307 if ( !GetDocEntry(GrPixel, NumPixel) )
309 gdcmWarningMacro("Pixel Dicom Element " << std::hex <<
310 GrPixel << "|" << NumPixel << "not found");
311 return false; // Pixel Dicom Element not found :-(
317 * \brief gets the info from 0020,0013 : Image Number else 0.
318 * @return image number
320 int File::GetImageNumber()
322 //0020 0013 : Image Number
323 std::string strImNumber = GetEntryString(0x0020,0x0013);
324 if ( strImNumber != GDCM_UNFOUND )
326 return atoi( strImNumber.c_str() );
332 * \brief gets the info from 0008,0060 : Modality
333 * @return Modality Type
335 ModalityType File::GetModality()
337 // 0008 0060 : Modality
338 std::string strModality = GetEntryString(0x0008,0x0060);
339 if ( strModality != GDCM_UNFOUND )
341 if ( strModality.find("AU") < strModality.length()) return AU;
342 else if ( strModality.find("AS") < strModality.length()) return AS;
343 else if ( strModality.find("BI") < strModality.length()) return BI;
344 else if ( strModality.find("CF") < strModality.length()) return CF;
345 else if ( strModality.find("CP") < strModality.length()) return CP;
346 else if ( strModality.find("CR") < strModality.length()) return CR;
347 else if ( strModality.find("CT") < strModality.length()) return CT;
348 else if ( strModality.find("CS") < strModality.length()) return CS;
349 else if ( strModality.find("DD") < strModality.length()) return DD;
350 else if ( strModality.find("DF") < strModality.length()) return DF;
351 else if ( strModality.find("DG") < strModality.length()) return DG;
352 else if ( strModality.find("DM") < strModality.length()) return DM;
353 else if ( strModality.find("DS") < strModality.length()) return DS;
354 else if ( strModality.find("DX") < strModality.length()) return DX;
355 else if ( strModality.find("ECG") < strModality.length()) return ECG;
356 else if ( strModality.find("EPS") < strModality.length()) return EPS;
357 else if ( strModality.find("FA") < strModality.length()) return FA;
358 else if ( strModality.find("FS") < strModality.length()) return FS;
359 else if ( strModality.find("HC") < strModality.length()) return HC;
360 else if ( strModality.find("HD") < strModality.length()) return HD;
361 else if ( strModality.find("LP") < strModality.length()) return LP;
362 else if ( strModality.find("LS") < strModality.length()) return LS;
363 else if ( strModality.find("MA") < strModality.length()) return MA;
364 else if ( strModality.find("MR") < strModality.length()) return MR;
365 else if ( strModality.find("NM") < strModality.length()) return NM;
366 else if ( strModality.find("OT") < strModality.length()) return OT;
367 else if ( strModality.find("PT") < strModality.length()) return PT;
368 else if ( strModality.find("RF") < strModality.length()) return RF;
369 else if ( strModality.find("RG") < strModality.length()) return RG;
370 else if ( strModality.find("RTDOSE")
371 < strModality.length()) return RTDOSE;
372 else if ( strModality.find("RTIMAGE")
373 < strModality.length()) return RTIMAGE;
374 else if ( strModality.find("RTPLAN")
375 < strModality.length()) return RTPLAN;
376 else if ( strModality.find("RTSTRUCT")
377 < strModality.length()) return RTSTRUCT;
378 else if ( strModality.find("SM") < strModality.length()) return SM;
379 else if ( strModality.find("ST") < strModality.length()) return ST;
380 else if ( strModality.find("TG") < strModality.length()) return TG;
381 else if ( strModality.find("US") < strModality.length()) return US;
382 else if ( strModality.find("VF") < strModality.length()) return VF;
383 else if ( strModality.find("XA") < strModality.length()) return XA;
384 else if ( strModality.find("XC") < strModality.length()) return XC;
388 /// \todo throw error return value ???
389 /// specified <> unknown in our database
397 * \brief Retrieve the number of columns of image.
398 * @return The encountered size when found, 0 by default.
399 * 0 means the file is NOT USABLE. The caller will have to check
403 DataEntry *entry = GetDataEntry(0x0028,0x0011);
405 return (int)entry->GetValue(0);
410 * \brief Retrieve the number of lines of image.
411 * \warning The defaulted value is 1 as opposed to File::GetXSize()
412 * @return The encountered size when found, 1 by default
413 * (The ACR-NEMA file contains a Signal, not an Image).
417 DataEntry *entry = GetDataEntry(0x0028,0x0010);
419 return (int)entry->GetValue(0);
426 // The Rows (0028,0010) entry was optional for ACR/NEMA.
427 // (at least some images didn't have it.)
428 // It might hence be a signal (1D image). So we default to 1:
433 * \brief Retrieve the number of planes of volume or the number
434 * of frames of a multiframe.
435 * \warning When present we consider the "Number of Frames" as the third
436 * dimension. When missing we consider the third dimension as
437 * being the ACR-NEMA "Planes" tag content.
438 * @return The encountered size when found, 1 by default (single image).
442 // Both DicomV3 and ACR/Nema consider the "Number of Frames"
443 // as the third dimension.
444 DataEntry *entry = GetDataEntry(0x0028,0x0008);
446 return (int)entry->GetValue(0);
448 // We then consider the "Planes" entry as the third dimension
449 entry = GetDataEntry(0x0028,0x0012);
451 return (int)entry->GetValue(0);
456 * \brief Retrieve the -unnormalized- number of 'times' of '4D image'.
457 * User has to tell gdcm the location of this '4th Dimension component'
458 * using SetFourthDimensionLocation() method before.
459 * \warning The defaulted value is 1.
460 * @return The encountered size when found, 1 by default
461 * (The file doesn't contain a '4D image'.).
465 if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object
468 DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(),
469 FourthDimensionLocation.GetElement() );
472 gdcmWarningMacro( " FourthDimensionLocation not found at : " <<
473 std::hex << FourthDimensionLocation.GetGroup()
474 << "|" << FourthDimensionLocation.GetElement());
479 return (int)entry->GetValue(0);
484 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
485 * then 0028,0030 : Pixel Spacing
487 * @return X dimension of a pixel
489 float File::GetXSpacing()
491 float xspacing = 1.0;
494 // To follow David Clunie's advice, we first check ImagerPixelSpacing
496 DataEntry *entry = GetDataEntry(0x0018,0x1164);
499 nbValue = entry->GetValueCount();
500 // Can't use IsValueCountValid because of the complex heuristic.
502 gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) "
503 << "has a wrong number of values :" << nbValue);
506 xspacing = (float)entry->GetValue(2);
507 else if( nbValue >= 2 )
508 xspacing = (float)entry->GetValue(1);
510 xspacing = (float)entry->GetValue(0);
512 if ( xspacing == 0.0 )
518 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
521 entry = GetDataEntry(0x0028,0x0030);
524 nbValue = entry->GetValueCount();
526 gdcmWarningMacro("PixelSpacing (0x0018,0x0030) "
527 << "has a wrong number of values :" << nbValue);
530 xspacing = (float)entry->GetValue(2);
531 else if( nbValue >= 2 )
532 xspacing = (float)entry->GetValue(1);
534 xspacing = (float)entry->GetValue(0);
536 if ( xspacing == 0.0 )
542 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
548 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
549 * then from 0028,0030 : Pixel Spacing
551 * @return Y dimension of a pixel
553 float File::GetYSpacing()
555 float yspacing = 1.0;
556 // To follow David Clunie's advice, we first check ImagerPixelSpacing
558 DataEntry *entry = GetDataEntry(0x0018,0x1164);
561 yspacing = (float)entry->GetValue(0);
563 if ( yspacing == 0.0 )
569 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
572 entry = GetDataEntry(0x0028,0x0030);
575 yspacing = (float)entry->GetValue(0);
577 if ( yspacing == 0.0 )
583 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
590 * \brief gets the info from 0018,0088 : Space Between Slices
591 * else from 0018,0050 : Slice Thickness
594 * When an element is missing, we suppose slices join together
595 * (no overlapping, no interslice gap) but we have no way to check it !
596 * For *Dicom* images, ZSpacing *should be* calculated using
597 * XOrigin, YOrigin, ZOrigin (of the top left image corner)
598 * of 2 consecutive images, and the Orientation
599 * Computing ZSpacing on a single image is not really meaningfull !
600 * @return Z dimension of a voxel-to be
602 float File::GetZSpacing()
605 float zspacing = 1.0f;
607 // Spacing Between Slices : distance between the middle of 2 slices
609 // jointives (Spacing between Slices = Slice Thickness)
610 // overlapping (Spacing between Slices < Slice Thickness)
611 // disjointes (Spacing between Slices > Slice Thickness)
612 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
613 // It only concerns the MRI guys, not people wanting to visualize volumes
614 // If Spacing Between Slices is missing,
615 // we suppose slices joint together
616 DataEntry *entry = GetDataEntry(0x0018,0x0088);
619 zspacing = (float)entry->GetValue(0);
621 if ( zspacing == 0.0 )
626 gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
628 // if no 'Spacing Between Slices' is found,
629 // we assume slices join together
630 // (no overlapping, no interslice gap)
631 entry = GetDataEntry(0x0018,0x0050);
634 zspacing = (float)entry->GetValue(0);
636 if ( zspacing == 0.0 )
641 gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
643 // if no 'Spacing Between Slices' is found,
644 // we assume slices join together
645 // (no overlapping, no interslice gap)
646 entry = GetDataEntry(0x3004,0x000c);
649 float z1 = (float)entry->GetValue(0);
650 float z2 = (float)entry->GetValue(1);
651 zspacing = z2 - z1; // can be negative...
653 if ( zspacing == 0.0 )
662 * \brief gets the info from 0020,0032 : Image Position Patient
663 * else from 0020,0030 : Image Position (RET)
665 * @return up-left image corner X position
667 float File::GetXOrigin()
669 DataEntry *entry = GetDataEntry(0x0020,0x0032);
672 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
673 entry = GetDataEntry(0x0020,0x0030);
676 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
681 if( entry->GetValueCount() == 3 )
683 if (!entry->IsValueCountValid() )
685 gdcmErrorMacro( "Invalid Value Count" );
687 return (float)entry->GetValue(0);
693 * \brief gets the info from 0020,0032 : Image Position Patient
694 * else from 0020,0030 : Image Position (RET)
696 * @return up-left image corner Y position
698 float File::GetYOrigin()
700 DataEntry *entry = GetDataEntry(0x0020,0x0032);
703 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
704 entry = GetDataEntry(0x0020,0x0030);
707 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
712 if( entry->GetValueCount() == 3 )
714 if (!entry->IsValueCountValid() )
716 gdcmErrorMacro( "Invalid Value Count" );
718 return (float)entry->GetValue(1);
724 * \brief gets the info from 0020,0032 : Image Position Patient
725 * else from 0020,0030 : Image Position (RET)
726 * else from 0020,1041 : Slice Location
727 * else from 0020,0050 : Location
729 * @return up-left image corner Z position
731 float File::GetZOrigin()
733 DataEntry *entry = GetDataEntry(0x0020,0x0032);
736 if( entry->GetValueCount() == 3 )
738 if (!entry->IsValueCountValid() )
740 gdcmErrorMacro( "Invalid Value Count" );
742 return (float)entry->GetValue(2);
744 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
748 entry = GetDataEntry(0x0020,0x0030);
751 if( entry->GetValueCount() == 3 )
753 if (!entry->IsValueCountValid() )
755 gdcmErrorMacro( "Invalid Value Count" );
757 return (float)entry->GetValue(2);
759 gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
763 // for *very* old ACR-NEMA images
764 entry = GetDataEntry(0x0020,0x1041);
767 if( entry->GetValueCount() == 1 )
769 if (!entry->IsValueCountValid() )
771 gdcmErrorMacro( "Invalid Value Count" );
773 return (float)entry->GetValue(0); // VM=1 !
775 gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
779 entry = GetDataEntry(0x0020,0x0050);
782 if( entry->GetValueCount() == 1 )
784 if (!entry->IsValueCountValid() )
786 gdcmErrorMacro( "Invalid Value Count" );
788 return (float)entry->GetValue(0);
790 gdcmWarningMacro( "Wrong Location (0020,0050)");
793 return 0.; // Hopeless
797 * \brief gets the info from 0020,0037 : Image Orientation Patient
798 * or from 0020 0035 : Image Orientation (RET)
800 * (needed to organize DICOM files based on their x,y,z position)
802 * @param iop adress of the (6)float array to receive values.
803 * (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff-
805 * @return true when one of the tag -with consistent values- is found
806 * false when nothing or inconsistent stuff - is found
808 bool File::GetImageOrientationPatient( float iop[6] )
810 std::string strImOriPat;
811 //iop is supposed to be float[6]
812 iop[0] = iop[4] = 1.;
813 iop[1] = iop[2] = iop[3] = iop[5] = 0.;
815 // 0020 0037 DS REL Image Orientation (Patient)
816 if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
818 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
819 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
821 gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
822 << " Less than 6 values were found." );
828 // 0020 0035 DS REL Image Orientation (RET)
829 else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND )
831 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
832 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
834 gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
835 << "Less than 6 values were found." );
844 * \brief Retrieve the number of Bits Stored (actually used)
845 * (as opposed to number of Bits Allocated)
846 * @return The encountered number of Bits Stored, 0 by default.
847 * 0 means the file is NOT USABLE. The caller has to check it !
849 int File::GetBitsStored()
851 DataEntry *entry = GetDataEntry(0x0028,0x0101);
854 gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory");
857 return (int)entry->GetValue(0);
861 * \brief Retrieve the number of Bits Allocated
862 * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,)
863 * @return The encountered Number of Bits Allocated, 0 by default.
864 * 0 means the file is NOT USABLE. The caller has to check it !
866 int File::GetBitsAllocated()
868 DataEntry *entry = GetDataEntry(0x0028,0x0100);
871 gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory");
874 return (int)entry->GetValue(0);
878 * \brief Retrieve the high bit position.
879 * \warning The method defaults to 0 when information is missing.
880 * The responsability of checking this value is left to the caller.
881 * @return The high bit position when present. 0 when missing.
883 int File::GetHighBitPosition()
885 DataEntry *entry = GetDataEntry(0x0028,0x0102);
888 gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory");
891 return (int)entry->GetValue(0);
895 * \brief Retrieve the number of Samples Per Pixel
896 * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
897 * @return The encountered number of Samples Per Pixel, 1 by default.
898 * (we assume Gray level Pixels)
900 int File::GetSamplesPerPixel()
902 DataEntry *entry = GetDataEntry(0x0028,0x0002);
905 gdcmWarningMacro("SamplesPerPixel (0028,0002) is supposed to be mandatory");
906 return 1; // Well, it's supposed to be mandatory ...
907 // but sometimes it's missing : *we* assume Gray pixels
909 return (int)entry->GetValue(0);
913 * \brief Retrieve the Planar Configuration for RGB images
914 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
915 * @return The encountered Planar Configuration, 0 by default.
917 int File::GetPlanarConfiguration()
919 DataEntry *entry = GetDataEntry(0x0028,0x0006);
924 return (int)entry->GetValue(0);
928 * \brief Return the size (in bytes) of a single pixel of data.
929 * @return The size in bytes of a single pixel of data; 0 by default
930 * 0 means the file is NOT USABLE; the caller will have to check
932 int File::GetPixelSize()
934 // 0028 0100 US IMG Bits Allocated
935 // (in order no to be messed up by old ACR-NEMA RGB images)
936 assert( !(GetEntryString(0x0028,0x0100) == "24") );
938 std::string pixelType = GetPixelType();
939 if ( pixelType == "8U" || pixelType == "8S" )
943 if ( pixelType == "16U" || pixelType == "16S")
947 if ( pixelType == "32U" || pixelType == "32S")
951 if ( pixelType == "FD" )
955 gdcmWarningMacro( "Unknown pixel type: " << pixelType);
960 * \brief Build the Pixel Type of the image.
961 * Possible values are:
962 * - 8U unsigned 8 bit,
964 * - 16U unsigned 16 bit,
965 * - 16S signed 16 bit,
966 * - 32U unsigned 32 bit,
967 * - 32S signed 32 bit,
968 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
969 * \warning 12 bit images appear as 16 bit.
970 * 24 bit images appear as 8 bit + photochromatic interp ="RGB "
971 * + Planar Configuration = 0
972 * @return 0S if nothing found. NOT USABLE file. The caller has to check
974 std::string File::GetPixelType()
976 std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
977 if ( bitsAlloc == GDCM_UNFOUND )
979 gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory");
980 bitsAlloc = "16"; // default and arbitrary value, not to polute the output
983 if ( bitsAlloc == "64" )
987 else if ( bitsAlloc == "12" )
989 // It will be unpacked
992 else if ( bitsAlloc == "24" )
994 // (in order no to be messed up by old RGB images)
999 if( IsSignedPixelData() )
1007 return bitsAlloc + sign;
1011 * \brief Check whether the pixels are signed (1) or UNsigned (0) data.
1012 * \warning The method defaults to false (UNsigned) when tag 0028|0103
1014 * The responsability of checking this value is left to the caller
1015 * (NO transformation is performed on the pixels to make then >0)
1016 * @return True when signed, false when UNsigned
1018 bool File::IsSignedPixelData()
1020 DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
1023 gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be "
1027 return entry->GetValue(0) != 0;
1031 * \brief Check whether this a monochrome picture (gray levels) or not,
1032 * using "Photometric Interpretation" tag (0x0028,0x0004).
1033 * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
1035 bool File::IsMonochrome()
1037 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1038 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
1039 || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
1043 if ( PhotometricInterp == GDCM_UNFOUND )
1045 gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be "
1052 * \brief Check whether this a MONOCHROME1 picture (high values = dark)
1053 * or not using "Photometric Interpretation" tag (0x0028,0x0004).
1054 * @return true when "MONOCHROME1" . False otherwise.
1056 bool File::IsMonochrome1()
1058 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1059 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
1063 if ( PhotometricInterp == GDCM_UNFOUND )
1065 gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to"
1066 << " be mandatory! ");
1072 * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
1073 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1074 * @return true when "PALETTE COLOR". False otherwise.
1076 bool File::IsPaletteColor()
1078 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1079 if ( PhotometricInterp == "PALETTE COLOR " )
1083 if ( PhotometricInterp == GDCM_UNFOUND )
1085 gdcmDebugMacro( "Not found : Palette color (0028,0004)");
1091 * \brief Check whether this a "YBR_FULL" color picture or not by accessing
1092 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1093 * @return true when "YBR_FULL". False otherwise.
1095 bool File::IsYBRFull()
1097 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1098 if ( PhotometricInterp == "YBR_FULL" )
1102 if ( PhotometricInterp == GDCM_UNFOUND )
1104 gdcmDebugMacro( "Not found : YBR Full (0028,0004)");
1110 * \brief tells us if LUT are used
1111 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
1112 * are NOT considered as LUT, since nobody knows
1113 * how to deal with them
1114 * Please warn me if you know sbdy that *does* know ... jprx
1115 * @return true if LUT Descriptors and LUT Tables were found
1119 // Check the presence of the LUT Descriptors, and LUT Tables
1121 if ( !GetDocEntry(0x0028,0x1101) )
1125 // LutDescriptorGreen
1126 if ( !GetDocEntry(0x0028,0x1102) )
1130 // LutDescriptorBlue
1131 if ( !GetDocEntry(0x0028,0x1103) )
1135 // Red Palette Color Lookup Table Data
1136 if ( !GetDocEntry(0x0028,0x1201) )
1140 // Green Palette Color Lookup Table Data
1141 if ( !GetDocEntry(0x0028,0x1202) )
1145 // Blue Palette Color Lookup Table Data
1146 if ( !GetDocEntry(0x0028,0x1203) )
1151 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
1152 // NOT taken into account, but we don't know how to use it ...
1157 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
1159 * @return Lookup Table number of Bits , 0 by default
1160 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
1161 * @ return bit number of each LUT item
1163 int File::GetLUTNbits()
1165 std::vector<std::string> tokens;
1168 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
1169 // = Lookup Table Desc-Blue
1170 // Consistency already checked in GetLUTLength
1171 std::string lutDescription = GetEntryString(0x0028,0x1101);
1172 if ( lutDescription == GDCM_UNFOUND )
1177 tokens.clear(); // clean any previous value
1178 Util::Tokenize ( lutDescription, tokens, "\\" );
1179 //LutLength=atoi(tokens[0].c_str());
1180 //LutDepth=atoi(tokens[1].c_str());
1182 lutNbits = atoi( tokens[2].c_str() );
1189 *\brief gets the info from 0028,1052 : Rescale Intercept
1190 * @return Rescale Intercept. defaulted to 0.0 is not found or empty
1192 float File::GetRescaleIntercept()
1194 // 0028 1052 DS IMG Rescale Intercept
1195 DataEntry *entry = GetDataEntry(0x0028, 0x1052);
1198 gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
1201 return (float)entry->GetValue(0);
1206 *\brief gets the info from 0028,1053 : Rescale Slope
1207 * @return Rescale Slope. defaulted to 1.0 is not found or empty
1209 float File::GetRescaleSlope()
1211 // 0028 1053 DS IMG Rescale Slope
1212 DataEntry *entry = GetDataEntry(0x0028, 0x1053);
1215 gdcmDebugMacro( "Missing Rescale Slope (0028,1053)");
1218 return (float)entry->GetValue(0);
1222 * \brief This function is intended to user who doesn't want
1223 * to have to manage a LUT and expects to get an RBG Pixel image
1224 * (or a monochrome one, if no LUT found ...)
1225 * \warning to be used with GetImagePixels()
1226 * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
1228 int File::GetNumberOfScalarComponents()
1230 if ( GetSamplesPerPixel() == 3 )
1235 // 0028 0100 US IMG Bits Allocated
1236 // (in order no to be messed up by old RGB images)
1237 if ( GetEntryString(0x0028,0x0100) == "24" )
1242 std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
1244 if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
1246 if ( HasLUT() )// PALETTE COLOR is NOT enough
1256 // beware of trailing space at end of string
1257 // DICOM tags are never of odd length
1258 if ( strPhotometricInterpretation == GDCM_UNFOUND ||
1259 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
1260 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
1266 // we assume that *all* kinds of YBR are dealt with
1272 * \brief This function is intended to user that DOESN'T want
1273 * to get RGB pixels image when it's stored as a PALETTE COLOR image
1274 * - the (vtk) user is supposed to know how deal with LUTs -
1275 * \warning to be used with GetImagePixelsRaw()
1276 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
1278 int File::GetNumberOfScalarComponentsRaw()
1280 // 0028 0100 US IMG Bits Allocated
1281 // (in order no to be messed up by old RGB images)
1282 if ( File::GetEntryString(0x0028,0x0100) == "24" )
1287 // we assume that *all* kinds of YBR are dealt with
1288 return GetSamplesPerPixel();
1292 * \brief Recover the offset (from the beginning of the file)
1293 * of *image* pixels (not *icone image* pixels, if any !)
1294 * @return Pixel Offset
1296 size_t File::GetPixelOffset()
1298 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1301 return pxlElement->GetOffset();
1305 gdcmWarningMacro( "Big trouble : Pixel Element ("
1306 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1312 * \brief Recover the pixel area length (in Bytes)
1313 * @return Pixel Element Length, as stored in the header
1314 * (NOT the memory space necessary to hold the Pixels
1315 * -in case of embeded compressed image-)
1316 * 0 : NOT USABLE file. The caller has to check.
1318 size_t File::GetPixelAreaLength()
1320 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1323 return pxlElement->GetLength();
1327 gdcmWarningMacro( "Big trouble : Pixel Element ("
1328 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1334 * \brief Adds the characteristics of a new element we want to anonymize
1335 * @param group Group number of the target tag.
1336 * @param elem Element number of the target tag.
1337 * @param value new value (string) to substitute with
1339 void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
1340 std::string const &value)
1346 UserAnonymizeList.push_back(el);
1350 * \brief Overwrites in the file the values of the DicomElements
1353 void File::AnonymizeNoLoad()
1355 std::fstream *fp = new std::fstream(Filename.c_str(),
1356 std::ios::in | std::ios::out | std::ios::binary);
1360 uint32_t valLgth = 0;
1361 std::string *spaces;
1362 for (ListElements::iterator it = UserAnonymizeList.begin();
1363 it != UserAnonymizeList.end();
1366 d = GetDocEntry( (*it).Group, (*it).Elem);
1371 if ( dynamic_cast<SeqEntry *>(d) )
1373 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1377 offset = d->GetOffset();
1378 lgth = d->GetLength();
1381 spaces = new std::string( lgth-valLgth, ' ');
1382 (*it).Value = (*it).Value + *spaces;
1385 fp->seekp( offset, std::ios::beg );
1386 fp->write( (*it).Value.c_str(), lgth );
1394 * \brief anonymize a File (remove Patient's personal info passed with
1395 * AddAnonymizeElement()
1396 * \note You cannot Anonymize a DataEntry (to be fixed)
1398 bool File::AnonymizeFile()
1400 // If Anonymisation list is empty, let's perform some basic anonymization
1401 if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
1403 // If exist, replace by spaces
1404 SetEntryString(" ",0x0010, 0x2154); // Telephone
1405 SetEntryString(" ",0x0010, 0x1040); // Adress
1406 SetEntryString(" ",0x0010, 0x0020); // Patient ID
1408 DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
1410 if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
1412 std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
1413 if ( studyInstanceUID != GDCM_UNFOUND )
1415 SetEntryString(studyInstanceUID, 0x0010, 0x0010);
1419 SetEntryString("anonymized", 0x0010, 0x0010);
1426 for (ListElements::iterator it = UserAnonymizeList.begin();
1427 it != UserAnonymizeList.end();
1430 d = GetDocEntry( (*it).Group, (*it).Elem);
1435 if ( dynamic_cast<SeqEntry *>(d) )
1437 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1441 if ( dynamic_cast<DataEntry *>(d) )
1443 gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
1447 SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
1451 // In order to make definitively impossible any further identification
1452 // remove or replace all the stuff that contains a Date
1454 //0008 0012 DA ID Instance Creation Date
1455 //0008 0020 DA ID Study Date
1456 //0008 0021 DA ID Series Date
1457 //0008 0022 DA ID Acquisition Date
1458 //0008 0023 DA ID Content Date
1459 //0008 0024 DA ID Overlay Date
1460 //0008 0025 DA ID Curve Date
1461 //0008 002a DT ID Acquisition Datetime
1462 //0018 9074 DT ACQ Frame Acquisition Datetime
1463 //0018 9151 DT ACQ Frame Reference Datetime
1464 //0018 a002 DT ACQ Contribution Date Time
1465 //0020 3403 SH REL Modified Image Date (RET)
1466 //0032 0032 DA SDY Study Verified Date
1467 //0032 0034 DA SDY Study Read Date
1468 //0032 1000 DA SDY Scheduled Study Start Date
1469 //0032 1010 DA SDY Scheduled Study Stop Date
1470 //0032 1040 DA SDY Study Arrival Date
1471 //0032 1050 DA SDY Study Completion Date
1472 //0038 001a DA VIS Scheduled Admission Date
1473 //0038 001c DA VIS Scheduled Discharge Date
1474 //0038 0020 DA VIS Admitting Date
1475 //0038 0030 DA VIS Discharge Date
1476 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1477 //0040 0004 DA PRC Scheduled Procedure Step End Date
1478 //0040 0244 DA PRC Performed Procedure Step Start Date
1479 //0040 0250 DA PRC Performed Procedure Step End Date
1480 //0040 2004 DA PRC Issue Date of Imaging Service Request
1481 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1482 //0040 4011 DT PRC Expected Completion Date and Time
1483 //0040 a030 DT PRC Verification Date Time
1484 //0040 a032 DT PRC Observation Date Time
1485 //0040 a120 DT PRC DateTime
1486 //0040 a121 DA PRC Date
1487 //0040 a13a DT PRC Referenced Datetime
1488 //0070 0082 DA ??? Presentation Creation Date
1489 //0100 0420 DT ??? SOP Autorization Date and Time
1490 //0400 0105 DT ??? Digital Signature DateTime
1491 //2100 0040 DA PJ Creation Date
1492 //3006 0008 DA SSET Structure Set Date
1493 //3008 0024 DA ??? Treatment Control Point Date
1494 //3008 0054 DA ??? First Treatment Date
1495 //3008 0056 DA ??? Most Recent Treatment Date
1496 //3008 0162 DA ??? Safe Position Exit Date
1497 //3008 0166 DA ??? Safe Position Return Date
1498 //3008 0250 DA ??? Treatment Date
1499 //300a 0006 DA RT RT Plan Date
1500 //300a 022c DA RT Air Kerma Rate Reference Date
1501 //300e 0004 DA RT Review Date
1507 * \brief Performs some consistency checking on various 'File related'
1508 * (as opposed to 'DicomDir related') entries
1509 * then writes in a file all the (Dicom Elements) included the Pixels
1510 * @param fileName file name to write to
1511 * @param writetype type of the file to be written
1512 * (ACR, ExplicitVR, ImplicitVR)
1514 bool File::Write(std::string fileName, FileType writetype)
1516 std::ofstream *fp = new std::ofstream(fileName.c_str(),
1517 std::ios::out | std::ios::binary);
1520 gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
1524 // Entry : 0002|0000 = group length -> recalculated
1525 DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
1528 std::ostringstream sLen;
1529 sLen << ComputeGroup0002Length( );
1530 e0000->SetString(sLen.str());
1533 /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
1534 if( writetype != JPEG )
1536 int i_lgPix = GetEntryLength(GrPixel, NumPixel);
1539 // no (GrPixel, NumPixel) element
1540 std::string s_lgPix = Util::Format("%d", i_lgPix+12);
1541 s_lgPix = Util::DicomString( s_lgPix.c_str() );
1542 InsertEntryString(s_lgPix,GrPixel, 0x0000);
1545 Document::WriteContent(fp, writetype);
1553 //-----------------------------------------------------------------------------
1557 //-----------------------------------------------------------------------------
1560 * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
1561 * Compute the RLE extra information and store it in \ref RLEInfo
1562 * for later pixel retrieval usage.
1564 void File::ComputeRLEInfo()
1566 std::string ts = GetTransferSyntax();
1567 if ( !Global::GetTS()->IsRLELossless(ts) )
1572 // Encoded pixel data: for the time being we are only concerned with
1573 // Jpeg or RLE Pixel data encodings.
1574 // As stated in PS 3.5-2003, section 8.2 p44:
1575 // "If sent in Encapsulated Format (i.e. other than the Native Format) the
1576 // value representation OB is used".
1577 // Hence we expect an OB value representation. Concerning OB VR,
1578 // the section PS 3.5-2003, section A.4.c p 58-59, states:
1579 // "For the Value Representations OB and OW, the encoding shall meet the
1580 // following specifications depending on the Data element tag:"
1582 // - the first item in the sequence of items before the encoded pixel
1583 // data stream shall be basic offset table item. The basic offset table
1584 // item value, however, is not required to be present"
1585 ReadEncapsulatedBasicOffsetTable();
1587 // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
1588 // Loop on the individual frame[s] and store the information
1589 // on the RLE fragments in a RLEFramesInfo.
1590 // Note: - when only a single frame is present, this is a
1592 // - when more than one frame are present, then we are in
1593 // the case of a multi-frame image.
1597 while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1599 // Since we have read the basic offset table, let's check the value were correct
1600 // or else produce a warning:
1601 if ( BasicOffsetTableItemValue )
1603 // If a BasicOffsetTableItemValue was read
1604 uint32_t individualLength = BasicOffsetTableItemValue[i];
1605 assert( individualLength == sum ); // REMOVE that if this is a problem
1606 if( individualLength != sum )
1608 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" );
1610 sum += frameLength + 8;
1613 // Parse the RLE Header and store the corresponding RLE Segment
1614 // Offset Table information on fragments of this current Frame.
1615 // Note that the fragment pixels themselves are not loaded
1616 // (but just skipped).
1617 long frameOffset = Fp->tellg(); // once per fragment
1619 uint32_t nbRleSegments = ReadInt32();
1620 if ( nbRleSegments > 16 )
1622 // There should be at most 15 segments (refer to RLEFrame class)
1623 gdcmWarningMacro( "Too many segments.");
1626 uint32_t rleSegmentOffsetTable[16];
1627 for( int k = 1; k <= 15; k++ )
1629 rleSegmentOffsetTable[k] = ReadInt32();
1632 // Deduce from both RLE Header and frameLength
1633 // the fragment length, and again store this info
1634 // in a RLEFramesInfo.
1635 long rleSegmentLength[15];
1636 // skipping (not reading) RLE Segments
1637 if ( nbRleSegments > 1)
1639 for(unsigned int k = 1; k <= nbRleSegments-1; k++)
1641 rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
1642 - rleSegmentOffsetTable[k];
1643 SkipBytes(rleSegmentLength[k]);
1647 rleSegmentLength[nbRleSegments] = frameLength
1648 - rleSegmentOffsetTable[nbRleSegments];
1649 SkipBytes(rleSegmentLength[nbRleSegments]);
1651 // Store the collected info
1652 RLEFrame *newFrame = new RLEFrame;
1653 newFrame->SetNumberOfFragments(nbRleSegments);
1654 for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
1656 newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
1657 newFrame->SetLength(uk,rleSegmentLength[uk]);
1659 RLEInfo->AddFrame(newFrame);
1662 // Make sure that we encounter a 'Sequence Delimiter Item'
1663 // at the end of the item :
1664 if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File
1666 gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
1671 * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
1672 * Compute the jpeg extra information (fragment[s] offset[s] and
1673 * length) and store it[them] in \ref JPEGInfo for later pixel
1676 void File::ComputeJPEGFragmentInfo()
1678 // If you need to, look for comments of ComputeRLEInfo().
1679 std::string ts = GetTransferSyntax();
1680 if ( ! Global::GetTS()->IsJPEG(ts) )
1685 ReadEncapsulatedBasicOffsetTable();
1687 // Loop on the fragments[s] and store the parsed information in a
1689 long fragmentLength;
1692 while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1694 // Since we have read the basic offset table, let's check the value were correct
1695 // or else produce a warning:
1696 // A.4 Transfer syntaxes for encapsulation of encoded pixel data:
1697 // When the Item Value is present, the Basic Offset Table Item Value shall contain
1698 // concatenated 32-bit unsigned integer values that are byte offsets to the first
1699 // byte of the Item Tag of the first fragment for each frame in the Sequence of
1700 // Items. These offsets are measured from the first byte of the first Item Tag
1701 // following the Basic Offset Table item (See Table A.4-2).
1703 if ( BasicOffsetTableItemValue )
1705 // If a BasicOffsetTableItemValue was read
1706 uint32_t individualLength = BasicOffsetTableItemValue[i];
1707 //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ??
1708 if( individualLength != sum )
1710 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" <<
1711 individualLength << " != " << sum );
1713 sum += fragmentLength + 8;
1717 long fragmentOffset = Fp->tellg(); // Once per fragment
1718 // Store the collected info
1719 JPEGFragment *newFragment = new JPEGFragment;
1720 newFragment->SetOffset(fragmentOffset);
1721 newFragment->SetLength(fragmentLength);
1722 JPEGInfo->AddFragment(newFragment);
1724 SkipBytes(fragmentLength);
1727 // Make sure that we encounter a 'Sequence Delimiter Item'
1728 // at the end of the item :
1729 if ( !ReadTag(0xfffe, 0xe0dd) )
1731 gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
1736 * \brief Assuming the internal file pointer \ref Document::Fp
1737 * is placed at the beginning of a tag, check whether this
1738 * tag is (TestGroup, TestElem).
1739 * \warning On success the internal file pointer \ref Document::Fp
1740 * is modified to point after the tag.
1741 * On failure (i.e. when the tag wasn't the expected tag
1742 * (TestGroup, TestElem) the internal file pointer
1743 * \ref Document::Fp is restored to it's original position.
1744 * @param testGroup The expected group of the tag.
1745 * @param testElem The expected Element of the tag.
1746 * @return True on success, false otherwise.
1748 bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
1750 long positionOnEntry = Fp->tellg(); // Only when reading fragments
1751 //long currentPosition = positionOnEntry; // On debugging purposes
1753 // Read the Item Tag group and element, and make
1754 // sure they are what we expected:
1755 uint16_t itemTagGroup;
1756 uint16_t itemTagElem;
1759 itemTagGroup = ReadInt16();
1760 itemTagElem = ReadInt16();
1762 catch ( FormatError )
1764 gdcmErrorMacro( "Can not read tag for "
1765 << " We should have found tag ("
1766 << DictEntry::TranslateToKey(testGroup,testElem) << ")"
1771 if ( itemTagGroup != testGroup || itemTagElem != testElem )
1773 // in order not to pollute output we don't warn on 'delimitors'
1774 if (itemTagGroup != 0xfffe || testGroup != 0xfffe )
1775 gdcmWarningMacro( "Wrong Item Tag found:"
1776 << " We should have found tag ("
1777 << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
1778 << " but instead we encountered tag ("
1779 << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
1780 << " at address: " << " 0x(" << std::hex
1781 << (unsigned int)positionOnEntry << std::dec << ")"
1783 Fp->seekg(positionOnEntry, std::ios::beg);
1791 * \brief Assuming the internal file pointer \ref Document::Fp
1792 * is placed at the beginning of a tag (TestGroup, TestElement),
1793 * read the length associated to the Tag.
1794 * \warning On success the internal file pointer \ref Document::Fp
1795 * is modified to point after the tag and it's length.
1796 * On failure (i.e. when the tag wasn't the expected tag
1797 * (TestGroup, TestElement) the internal file pointer
1798 * \ref Document::Fp is restored to it's original position.
1799 * @param testGroup The expected Group of the tag.
1800 * @param testElem The expected Element of the tag.
1801 * @return On success returns the length associated to the tag. On failure
1804 uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
1807 if ( !ReadTag(testGroup, testElem) )
1809 // Avoid polutting output
1810 if ( testGroup != 0xfffe )
1811 gdcmErrorMacro( "ReadTag did not succeed for ("
1812 << DictEntry::TranslateToKey(testGroup,testElem)
1817 //// Then read the associated Item Length
1819 // long currentPosition = Fp->tellg(); // save time // JPRx
1820 uint32_t itemLength = ReadInt32();
1821 gdcmDebugMacro( "Basic Item Length is: " << itemLength
1822 // << " at address: " << std::hex << (unsigned int)currentPosition
1828 * \brief When parsing the Pixel Data of an encapsulated file, read
1829 * the basic offset table (when present, and BTW dump it).
1831 void File::ReadEncapsulatedBasicOffsetTable()
1833 //// Read the Basic Offset Table Item Tag length...
1834 uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
1836 // When present, read the basic offset table itself.
1837 // Notes: - since the presence of this basic offset table is optional
1838 // we can't rely on it for the implementation, and we will simply
1839 // trash it's content (when present).
1840 // - still, when present, we could add some further checks on the
1841 // lengths, but we won't bother with such fuses for the time being.
1842 if ( itemLength != 0 )
1844 char *charBasicOffsetTableItemValue = new char[itemLength];
1845 Fp->read(charBasicOffsetTableItemValue, itemLength);
1846 unsigned int nbEntries = itemLength/4;
1847 assert( nbEntries*4 == itemLength); // Make sure this is a multiple
1848 BasicOffsetTableItemValue = new uint32_t[nbEntries];
1850 for (unsigned int i=0; i < nbEntries; i++ )
1852 BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i]));
1853 #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION)
1854 uint32_t val = BasicOffsetTableItemValue[i];
1855 BasicOffsetTableItemValue[i]
1856 = ( (val<<24) | ((val<<8) & 0x00ff0000) |
1857 ( (val>>8) & 0x0000ff00) | (val>>24) );
1859 gdcmDebugMacro( "Read one length for: " <<
1860 std::hex << BasicOffsetTableItemValue[i] );
1863 delete[] charBasicOffsetTableItemValue;
1867 // These are the deprecated method that one day should be removed (after the next release)
1869 #ifndef GDCM_LEGACY_REMOVE
1871 * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API)
1872 * @ param fileName file to be open for parsing
1873 * @ return false if file cannot be open or no swap info was found,
1874 * or no tag was found.
1875 * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
1877 bool File::Load( std::string const &fileName )
1879 GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
1881 SetFileName( fileName );
1882 if ( ! this->Document::Load( ) )
1885 return DoTheLoadingJob( );
1889 //-----------------------------------------------------------------------------
1892 //-----------------------------------------------------------------------------
1893 } // end namespace gdcm