1 /*=========================================================================
4 Module: $RCSfile: gdcmFile.cxx,v $
6 Date: $Date: 2006/02/16 20:06:14 $
7 Version: $Revision: 1.315 $
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( )
158 // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
159 // We may encounter the 'RETired' (0x0028, 0x0200) tag
160 // (Image Location") . This entry contains the number of
161 // the group that contains the pixel data (hence the "Pixel Data"
162 // is found by indirection through the "Image Location").
163 // Inside the group pointed by "Image Location" the searched element
164 // is conventionally the element 0x0010 (when the norm is respected).
165 // When the "Image Location" is missing we default to group 0x7fe0.
166 // Note: this IS the right place for the code
169 const std::string &imgLocation = GetEntryString(0x0028, 0x0200);
170 if ( imgLocation == GDCM_UNFOUND )
177 GrPixel = (uint16_t) atoi( imgLocation.c_str() );
180 // sometimes Image Location value doesn't follow
181 // the supposed processor endianness.
182 // see gdcmData/cr172241.dcm
183 if ( GrPixel == 0xe07f )
188 if ( GrPixel != 0x7fe0 )
190 // This is a kludge for old dirty Philips imager.
198 // Now, we know GrPixel and NumPixel.
199 // Let's create a VirtualDictEntry to allow a further VR modification
200 // and force VR to match with BitsAllocated.
201 DocEntry *entry = GetDocEntry(GrPixel, NumPixel);
204 // Compute the RLE or JPEG info
206 const std::string &ts = GetTransferSyntax();
207 Fp->seekg( entry->GetOffset(), std::ios::beg );
208 if ( Global::GetTS()->IsRLELossless(ts) )
210 else if ( Global::GetTS()->IsJPEG(ts) )
211 ComputeJPEGFragmentInfo();
214 // Create a new DataEntry to change the DictEntry
215 // The changed DictEntry will have
216 // - a correct PixelVR OB or OW)
217 // - the name to "Pixel Data"
218 DataEntry *oldEntry = dynamic_cast<DataEntry *>(entry);
222 // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
223 // more than 8 (i.e 12, 16) is a 'O Words'
224 if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
229 // Change only made if usefull
230 if ( PixelVR != oldEntry->GetVR() )
232 DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
233 PixelVR,"1","Pixel Data");
235 DataEntry *newEntry = DataEntry::New(newDict);
237 newEntry->Copy(entry);
238 newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
239 oldEntry->SetSelfArea(false);
241 RemoveEntry(oldEntry);
250 * \brief This predicate, based on hopefully reasonable heuristics,
251 * decides whether or not the current File was properly parsed
252 * and contains the mandatory information for being considered as
253 * a well formed and usable Dicom/Acr File.
254 * @return true when File is the one of a reasonable Dicom/Acr file,
257 bool File::IsReadable()
259 if ( !Document::IsReadable() )
264 const std::string &res = GetEntryString(0x0028, 0x0005);
265 if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
267 gdcmWarningMacro("Wrong Image Dimensions" << res);
268 return false; // Image Dimensions
270 bool b0028_0100 = true;
271 if ( !GetDocEntry(0x0028, 0x0100) )
273 gdcmWarningMacro("Bits Allocated (0028|0100) not found");
274 //return false; // "Bits Allocated"
277 bool b0028_0101 = true;
278 if ( !GetDocEntry(0x0028, 0x0101) )
280 gdcmWarningMacro("Bits Stored (0028|0101) not found");
281 //return false; // "Bits Stored"
284 bool b0028_0102 = true;
285 if ( !GetDocEntry(0x0028, 0x0102) )
287 gdcmWarningMacro("Hight Bit (0028|0102) not found");
288 //return false; // "High Bit"
291 bool b0028_0103 = true;
292 if ( !GetDocEntry(0x0028, 0x0103) )
294 gdcmWarningMacro("Pixel Representation (0028|0103) not found");
295 //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed)
299 if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103)
301 gdcmWarningMacro("Too much mandatory Tags missing !");
305 if ( !GetDocEntry(GrPixel, NumPixel) )
307 gdcmWarningMacro("Pixel Dicom Element " << std::hex <<
308 GrPixel << "|" << NumPixel << "not found");
309 return false; // Pixel Dicom Element not found :-(
315 * \brief gets the info from 0020,0013 : Image Number else 0.
316 * @return image number
318 int File::GetImageNumber()
320 //0020 0013 : Image Number
321 std::string strImNumber = GetEntryString(0x0020,0x0013);
322 if ( strImNumber != GDCM_UNFOUND )
324 return atoi( strImNumber.c_str() );
330 * \brief gets the info from 0008,0060 : Modality
331 * @return Modality Type
333 ModalityType File::GetModality()
335 // 0008 0060 : Modality
336 std::string strModality = GetEntryString(0x0008,0x0060);
337 if ( strModality != GDCM_UNFOUND )
339 if ( strModality.find("AU") < strModality.length()) return AU;
340 else if ( strModality.find("AS") < strModality.length()) return AS;
341 else if ( strModality.find("BI") < strModality.length()) return BI;
342 else if ( strModality.find("CF") < strModality.length()) return CF;
343 else if ( strModality.find("CP") < strModality.length()) return CP;
344 else if ( strModality.find("CR") < strModality.length()) return CR;
345 else if ( strModality.find("CT") < strModality.length()) return CT;
346 else if ( strModality.find("CS") < strModality.length()) return CS;
347 else if ( strModality.find("DD") < strModality.length()) return DD;
348 else if ( strModality.find("DF") < strModality.length()) return DF;
349 else if ( strModality.find("DG") < strModality.length()) return DG;
350 else if ( strModality.find("DM") < strModality.length()) return DM;
351 else if ( strModality.find("DS") < strModality.length()) return DS;
352 else if ( strModality.find("DX") < strModality.length()) return DX;
353 else if ( strModality.find("ECG") < strModality.length()) return ECG;
354 else if ( strModality.find("EPS") < strModality.length()) return EPS;
355 else if ( strModality.find("FA") < strModality.length()) return FA;
356 else if ( strModality.find("FS") < strModality.length()) return FS;
357 else if ( strModality.find("HC") < strModality.length()) return HC;
358 else if ( strModality.find("HD") < strModality.length()) return HD;
359 else if ( strModality.find("LP") < strModality.length()) return LP;
360 else if ( strModality.find("LS") < strModality.length()) return LS;
361 else if ( strModality.find("MA") < strModality.length()) return MA;
362 else if ( strModality.find("MR") < strModality.length()) return MR;
363 else if ( strModality.find("NM") < strModality.length()) return NM;
364 else if ( strModality.find("OT") < strModality.length()) return OT;
365 else if ( strModality.find("PT") < strModality.length()) return PT;
366 else if ( strModality.find("RF") < strModality.length()) return RF;
367 else if ( strModality.find("RG") < strModality.length()) return RG;
368 else if ( strModality.find("RTDOSE")
369 < strModality.length()) return RTDOSE;
370 else if ( strModality.find("RTIMAGE")
371 < strModality.length()) return RTIMAGE;
372 else if ( strModality.find("RTPLAN")
373 < strModality.length()) return RTPLAN;
374 else if ( strModality.find("RTSTRUCT")
375 < strModality.length()) return RTSTRUCT;
376 else if ( strModality.find("SM") < strModality.length()) return SM;
377 else if ( strModality.find("ST") < strModality.length()) return ST;
378 else if ( strModality.find("TG") < strModality.length()) return TG;
379 else if ( strModality.find("US") < strModality.length()) return US;
380 else if ( strModality.find("VF") < strModality.length()) return VF;
381 else if ( strModality.find("XA") < strModality.length()) return XA;
382 else if ( strModality.find("XC") < strModality.length()) return XC;
386 /// \todo throw error return value ???
387 /// specified <> unknown in our database
395 * \brief Retrieve the number of columns of image.
396 * @return The encountered size when found, 0 by default.
397 * 0 means the file is NOT USABLE. The caller will have to check
401 DataEntry *entry = GetDataEntry(0x0028,0x0011);
403 return (int)entry->GetValue(0);
408 * \brief Retrieve the number of lines of image.
409 * \warning The defaulted value is 1 as opposed to File::GetXSize()
410 * @return The encountered size when found, 1 by default
411 * (The ACR-NEMA file contains a Signal, not an Image).
415 DataEntry *entry = GetDataEntry(0x0028,0x0010);
417 return (int)entry->GetValue(0);
424 // The Rows (0028,0010) entry was optional for ACR/NEMA.
425 // (at least some images didn't have it.)
426 // It might hence be a signal (1D image). So we default to 1:
431 * \brief Retrieve the number of planes of volume or the number
432 * of frames of a multiframe.
433 * \warning When present we consider the "Number of Frames" as the third
434 * dimension. When missing we consider the third dimension as
435 * being the ACR-NEMA "Planes" tag content.
436 * @return The encountered size when found, 1 by default (single image).
440 // Both DicomV3 and ACR/Nema consider the "Number of Frames"
441 // as the third dimension.
442 DataEntry *entry = GetDataEntry(0x0028,0x0008);
444 return (int)entry->GetValue(0);
446 // We then consider the "Planes" entry as the third dimension
447 entry = GetDataEntry(0x0028,0x0012);
449 return (int)entry->GetValue(0);
454 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
455 * then 0028,0030 : Pixel Spacing
457 * @return X dimension of a pixel
459 float File::GetXSpacing()
461 float xspacing = 1.0;
464 // To follow David Clunie's advice, we first check ImagerPixelSpacing
466 DataEntry *entry = GetDataEntry(0x0018,0x1164);
469 nbValue = entry->GetValueCount();
470 // Can't use IsValueCountValid because of the complex heuristic.
472 gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) "
473 << "has a wrong number of values :" << nbValue);
476 xspacing = (float)entry->GetValue(2);
477 else if( nbValue >= 2 )
478 xspacing = (float)entry->GetValue(1);
480 xspacing = (float)entry->GetValue(0);
482 if ( xspacing == 0.0 )
488 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
491 entry = GetDataEntry(0x0028,0x0030);
494 nbValue = entry->GetValueCount();
496 gdcmWarningMacro("PixelSpacing (0x0018,0x0030) "
497 << "has a wrong number of values :" << nbValue);
500 xspacing = (float)entry->GetValue(2);
501 else if( nbValue >= 2 )
502 xspacing = (float)entry->GetValue(1);
504 xspacing = (float)entry->GetValue(0);
506 if ( xspacing == 0.0 )
512 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
519 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
520 * then from 0028,0030 : Pixel Spacing
522 * @return Y dimension of a pixel
524 float File::GetYSpacing()
526 float yspacing = 1.0;
527 // To follow David Clunie's advice, we first check ImagerPixelSpacing
529 DataEntry *entry = GetDataEntry(0x0018,0x1164);
532 yspacing = (float)entry->GetValue(0);
534 if ( yspacing == 0.0 )
540 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
543 entry = GetDataEntry(0x0028,0x0030);
546 yspacing = (float)entry->GetValue(0);
548 if ( yspacing == 0.0 )
554 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
561 * \brief gets the info from 0018,0088 : Space Between Slices
562 * else from 0018,0050 : Slice Thickness
565 * When an element is missing, we suppose slices join together
566 * (no overlapping, no interslice gap) but we have no way to check it !
567 * For *Dicom* images, ZSpacing *should be* calculated using
568 * XOrigin, YOrigin, ZOrigin (of the top left image corner)
569 * of 2 consecutive images, and the Orientation
570 * Computing ZSpacing on a single image is not really meaningfull !
571 * @return Z dimension of a voxel-to be
573 float File::GetZSpacing()
576 float zspacing = 1.0f;
578 // Spacing Between Slices : distance between the middle of 2 slices
580 // jointives (Spacing between Slices = Slice Thickness)
581 // overlapping (Spacing between Slices < Slice Thickness)
582 // disjointes (Spacing between Slices > Slice Thickness)
583 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
584 // It only concerns the MRI guys, not people wanting to visualize volumes
585 // If Spacing Between Slices is missing,
586 // we suppose slices joint together
587 DataEntry *entry = GetDataEntry(0x0018,0x0088);
590 zspacing = (float)entry->GetValue(0);
592 if ( zspacing == 0.0 )
597 gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
599 // if no 'Spacing Between Slices' is found,
600 // we assume slices join together
601 // (no overlapping, no interslice gap)
602 entry = GetDataEntry(0x0018,0x0050);
605 zspacing = (float)entry->GetValue(0);
607 if ( zspacing == 0.0 )
612 gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
614 // if no 'Spacing Between Slices' is found,
615 // we assume slices join together
616 // (no overlapping, no interslice gap)
617 entry = GetDataEntry(0x3004,0x000c);
620 float z1 = (float)entry->GetValue(0);
621 float z2 = (float)entry->GetValue(1);
622 zspacing = z2 - z1; // can be negative...
624 if ( zspacing == 0.0 )
633 * \brief gets the info from 0020,0032 : Image Position Patient
634 * else from 0020,0030 : Image Position (RET)
636 * @return up-left image corner X position
638 float File::GetXOrigin()
640 DataEntry *entry = GetDataEntry(0x0020,0x0032);
643 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
644 entry = GetDataEntry(0x0020,0x0030);
647 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
652 if( entry->GetValueCount() == 3 )
654 if (!entry->IsValueCountValid() )
656 gdcmErrorMacro( "Invalid Value Count" );
658 return (float)entry->GetValue(0);
664 * \brief gets the info from 0020,0032 : Image Position Patient
665 * else from 0020,0030 : Image Position (RET)
667 * @return up-left image corner Y position
669 float File::GetYOrigin()
671 DataEntry *entry = GetDataEntry(0x0020,0x0032);
674 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
675 entry = GetDataEntry(0x0020,0x0030);
678 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
683 if( entry->GetValueCount() == 3 )
685 if (!entry->IsValueCountValid() )
687 gdcmErrorMacro( "Invalid Value Count" );
689 return (float)entry->GetValue(1);
695 * \brief gets the info from 0020,0032 : Image Position Patient
696 * else from 0020,0030 : Image Position (RET)
697 * else from 0020,1041 : Slice Location
698 * else from 0020,0050 : Location
700 * @return up-left image corner Z position
702 float File::GetZOrigin()
704 DataEntry *entry = GetDataEntry(0x0020,0x0032);
707 if( entry->GetValueCount() == 3 )
709 if (!entry->IsValueCountValid() )
711 gdcmErrorMacro( "Invalid Value Count" );
713 return (float)entry->GetValue(2);
715 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
719 entry = GetDataEntry(0x0020,0x0030);
722 if( entry->GetValueCount() == 3 )
724 if (!entry->IsValueCountValid() )
726 gdcmErrorMacro( "Invalid Value Count" );
728 return (float)entry->GetValue(2);
730 gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
734 // for *very* old ACR-NEMA images
735 entry = GetDataEntry(0x0020,0x1041);
738 if( entry->GetValueCount() == 1 )
740 if (!entry->IsValueCountValid() )
742 gdcmErrorMacro( "Invalid Value Count" );
744 return (float)entry->GetValue(0); // VM=1 !
746 gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
750 entry = GetDataEntry(0x0020,0x0050);
753 if( entry->GetValueCount() == 1 )
755 if (!entry->IsValueCountValid() )
757 gdcmErrorMacro( "Invalid Value Count" );
759 return (float)entry->GetValue(0);
761 gdcmWarningMacro( "Wrong Location (0020,0050)");
764 return 0.; // Hopeless
768 * \brief gets the info from 0020,0037 : Image Orientation Patient
769 * or from 0020 0035 : Image Orientation (RET)
771 * (needed to organize DICOM files based on their x,y,z position)
773 * @param iop adress of the (6)float array to receive values.
774 * (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff-
776 * @return true when one of the tag -with consistent values- is found
777 * false when nothing or inconsistent stuff - is found
779 bool File::GetImageOrientationPatient( float iop[6] )
781 std::string strImOriPat;
782 //iop is supposed to be float[6]
783 iop[0] = iop[4] = 1.;
784 iop[1] = iop[2] = iop[3] = iop[5] = 0.;
786 // 0020 0037 DS REL Image Orientation (Patient)
787 if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
789 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
790 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
792 gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
793 << " Less than 6 values were found." );
799 // 0020 0035 DS REL Image Orientation (RET)
800 else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND )
802 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
803 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
805 gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
806 << "Less than 6 values were found." );
815 * \brief Retrieve the number of Bits Stored (actually used)
816 * (as opposed to number of Bits Allocated)
817 * @return The encountered number of Bits Stored, 0 by default.
818 * 0 means the file is NOT USABLE. The caller has to check it !
820 int File::GetBitsStored()
822 DataEntry *entry = GetDataEntry(0x0028,0x0101);
825 gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory");
828 return (int)entry->GetValue(0);
832 * \brief Retrieve the number of Bits Allocated
833 * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,)
834 * @return The encountered Number of Bits Allocated, 0 by default.
835 * 0 means the file is NOT USABLE. The caller has to check it !
837 int File::GetBitsAllocated()
839 DataEntry *entry = GetDataEntry(0x0028,0x0100);
842 gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory");
845 return (int)entry->GetValue(0);
849 * \brief Retrieve the high bit position.
850 * \warning The method defaults to 0 when information is missing.
851 * The responsability of checking this value is left to the caller.
852 * @return The high bit position when present. 0 when missing.
854 int File::GetHighBitPosition()
856 DataEntry *entry = GetDataEntry(0x0028,0x0102);
859 gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory");
862 return (int)entry->GetValue(0);
866 * \brief Retrieve the number of Samples Per Pixel
867 * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
868 * @return The encountered number of Samples Per Pixel, 1 by default.
869 * (we assume Gray level Pixels)
871 int File::GetSamplesPerPixel()
873 DataEntry *entry = GetDataEntry(0x0028,0x0002);
876 gdcmWarningMacro("SamplesPerPixel (0028,0002) is supposed to be mandatory");
877 return 1; // Well, it's supposed to be mandatory ...
878 // but sometimes it's missing : *we* assume Gray pixels
880 return (int)entry->GetValue(0);
884 * \brief Retrieve the Planar Configuration for RGB images
885 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
886 * @return The encountered Planar Configuration, 0 by default.
888 int File::GetPlanarConfiguration()
890 DataEntry *entry = GetDataEntry(0x0028,0x0006);
895 return (int)entry->GetValue(0);
899 * \brief Return the size (in bytes) of a single pixel of data.
900 * @return The size in bytes of a single pixel of data; 0 by default
901 * 0 means the file is NOT USABLE; the caller will have to check
903 int File::GetPixelSize()
905 // 0028 0100 US IMG Bits Allocated
906 // (in order no to be messed up by old ACR-NEMA RGB images)
907 assert( !(GetEntryString(0x0028,0x0100) == "24") );
909 std::string pixelType = GetPixelType();
910 if ( pixelType == "8U" || pixelType == "8S" )
914 if ( pixelType == "16U" || pixelType == "16S")
918 if ( pixelType == "32U" || pixelType == "32S")
922 if ( pixelType == "FD" )
926 gdcmWarningMacro( "Unknown pixel type: " << pixelType);
931 * \brief Build the Pixel Type of the image.
932 * Possible values are:
933 * - 8U unsigned 8 bit,
935 * - 16U unsigned 16 bit,
936 * - 16S signed 16 bit,
937 * - 32U unsigned 32 bit,
938 * - 32S signed 32 bit,
939 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
940 * \warning 12 bit images appear as 16 bit.
941 * 24 bit images appear as 8 bit + photochromatic interp ="RGB "
942 * + Planar Configuration = 0
943 * @return 0S if nothing found. NOT USABLE file. The caller has to check
945 std::string File::GetPixelType()
947 std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
948 if ( bitsAlloc == GDCM_UNFOUND )
950 gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory");
951 bitsAlloc = "16"; // default and arbitrary value, not to polute the output
954 if ( bitsAlloc == "64" )
958 else if ( bitsAlloc == "12" )
960 // It will be unpacked
963 else if ( bitsAlloc == "24" )
965 // (in order no to be messed up by old RGB images)
970 if( IsSignedPixelData() )
978 return bitsAlloc + sign;
982 * \brief Check whether the pixels are signed (1) or UNsigned (0) data.
983 * \warning The method defaults to false (UNsigned) when tag 0028|0103
985 * The responsability of checking this value is left to the caller
986 * (NO transformation is performed on the pixels to make then >0)
987 * @return True when signed, false when UNsigned
989 bool File::IsSignedPixelData()
991 DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
994 gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be "
998 return entry->GetValue(0) != 0;
1002 * \brief Check whether this a monochrome picture (gray levels) or not,
1003 * using "Photometric Interpretation" tag (0x0028,0x0004).
1004 * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
1006 bool File::IsMonochrome()
1008 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1009 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
1010 || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
1014 if ( PhotometricInterp == GDCM_UNFOUND )
1016 gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be "
1023 * \brief Check whether this a MONOCHROME1 picture (high values = dark)
1024 * or not using "Photometric Interpretation" tag (0x0028,0x0004).
1025 * @return true when "MONOCHROME1" . False otherwise.
1027 bool File::IsMonochrome1()
1029 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1030 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
1034 if ( PhotometricInterp == GDCM_UNFOUND )
1036 gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to"
1037 << " be mandatory! ");
1043 * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
1044 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1045 * @return true when "PALETTE COLOR". False otherwise.
1047 bool File::IsPaletteColor()
1049 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1050 if ( PhotometricInterp == "PALETTE COLOR " )
1054 if ( PhotometricInterp == GDCM_UNFOUND )
1056 gdcmDebugMacro( "Not found : Palette color (0028,0004)");
1062 * \brief Check whether this a "YBR_FULL" color picture or not by accessing
1063 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1064 * @return true when "YBR_FULL". False otherwise.
1066 bool File::IsYBRFull()
1068 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1069 if ( PhotometricInterp == "YBR_FULL" )
1073 if ( PhotometricInterp == GDCM_UNFOUND )
1075 gdcmDebugMacro( "Not found : YBR Full (0028,0004)");
1081 * \brief tells us if LUT are used
1082 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
1083 * are NOT considered as LUT, since nobody knows
1084 * how to deal with them
1085 * Please warn me if you know sbdy that *does* know ... jprx
1086 * @return true if LUT Descriptors and LUT Tables were found
1090 // Check the presence of the LUT Descriptors, and LUT Tables
1092 if ( !GetDocEntry(0x0028,0x1101) )
1096 // LutDescriptorGreen
1097 if ( !GetDocEntry(0x0028,0x1102) )
1101 // LutDescriptorBlue
1102 if ( !GetDocEntry(0x0028,0x1103) )
1106 // Red Palette Color Lookup Table Data
1107 if ( !GetDocEntry(0x0028,0x1201) )
1111 // Green Palette Color Lookup Table Data
1112 if ( !GetDocEntry(0x0028,0x1202) )
1116 // Blue Palette Color Lookup Table Data
1117 if ( !GetDocEntry(0x0028,0x1203) )
1122 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
1123 // NOT taken into account, but we don't know how to use it ...
1128 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
1130 * @return Lookup Table number of Bits , 0 by default
1131 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
1132 * @ return bit number of each LUT item
1134 int File::GetLUTNbits()
1136 std::vector<std::string> tokens;
1139 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
1140 // = Lookup Table Desc-Blue
1141 // Consistency already checked in GetLUTLength
1142 std::string lutDescription = GetEntryString(0x0028,0x1101);
1143 if ( lutDescription == GDCM_UNFOUND )
1148 tokens.clear(); // clean any previous value
1149 Util::Tokenize ( lutDescription, tokens, "\\" );
1150 //LutLength=atoi(tokens[0].c_str());
1151 //LutDepth=atoi(tokens[1].c_str());
1153 lutNbits = atoi( tokens[2].c_str() );
1160 *\brief gets the info from 0028,1052 : Rescale Intercept
1161 * @return Rescale Intercept. defaulted to 0.0 is not found or empty
1163 float File::GetRescaleIntercept()
1165 // 0028 1052 DS IMG Rescale Intercept
1166 DataEntry *entry = GetDataEntry(0x0028, 0x1052);
1169 gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
1172 return (float)entry->GetValue(0);
1177 *\brief gets the info from 0028,1053 : Rescale Slope
1178 * @return Rescale Slope. defaulted to 1.0 is not found or empty
1180 float File::GetRescaleSlope()
1182 // 0028 1053 DS IMG Rescale Slope
1183 DataEntry *entry = GetDataEntry(0x0028, 0x1053);
1186 gdcmDebugMacro( "Missing Rescale Slope (0028,1053)");
1189 return (float)entry->GetValue(0);
1193 * \brief This function is intended to user who doesn't want
1194 * to have to manage a LUT and expects to get an RBG Pixel image
1195 * (or a monochrome one ...)
1196 * \warning to be used with GetImagePixels()
1197 * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
1199 int File::GetNumberOfScalarComponents()
1201 if ( GetSamplesPerPixel() == 3 )
1206 // 0028 0100 US IMG Bits Allocated
1207 // (in order no to be messed up by old RGB images)
1208 if ( GetEntryString(0x0028,0x0100) == "24" )
1213 std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
1215 if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
1217 if ( HasLUT() )// PALETTE COLOR is NOT enough
1227 // beware of trailing space at end of string
1228 // DICOM tags are never of odd length
1229 if ( strPhotometricInterpretation == GDCM_UNFOUND ||
1230 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
1231 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
1237 // we assume that *all* kinds of YBR are dealt with
1243 * \brief This function is intended to user that DOESN'T want
1244 * to get RGB pixels image when it's stored as a PALETTE COLOR image
1245 * - the (vtk) user is supposed to know how deal with LUTs -
1246 * \warning to be used with GetImagePixelsRaw()
1247 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
1249 int File::GetNumberOfScalarComponentsRaw()
1251 // 0028 0100 US IMG Bits Allocated
1252 // (in order no to be messed up by old RGB images)
1253 if ( File::GetEntryString(0x0028,0x0100) == "24" )
1258 // we assume that *all* kinds of YBR are dealt with
1259 return GetSamplesPerPixel();
1263 * \brief Recover the offset (from the beginning of the file)
1264 * of *image* pixels (not *icone image* pixels, if any !)
1265 * @return Pixel Offset
1267 size_t File::GetPixelOffset()
1269 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1272 return pxlElement->GetOffset();
1276 gdcmWarningMacro( "Big trouble : Pixel Element ("
1277 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1283 * \brief Recover the pixel area length (in Bytes)
1284 * @return Pixel Element Length, as stored in the header
1285 * (NOT the memory space necessary to hold the Pixels
1286 * -in case of embeded compressed image-)
1287 * 0 : NOT USABLE file. The caller has to check.
1289 size_t File::GetPixelAreaLength()
1291 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1294 return pxlElement->GetLength();
1298 gdcmWarningMacro( "Big trouble : Pixel Element ("
1299 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1305 * \brief Adds the characteristics of a new element we want to anonymize
1306 * @param group Group number of the target tag.
1307 * @param elem Element number of the target tag.
1308 * @param value new value (string) to substitute with
1310 void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
1311 std::string const &value)
1317 UserAnonymizeList.push_back(el);
1321 * \brief Overwrites in the file the values of the DicomElements
1324 void File::AnonymizeNoLoad()
1326 std::fstream *fp = new std::fstream(Filename.c_str(),
1327 std::ios::in | std::ios::out | std::ios::binary);
1331 uint32_t valLgth = 0;
1332 std::string *spaces;
1333 for (ListElements::iterator it = UserAnonymizeList.begin();
1334 it != UserAnonymizeList.end();
1337 d = GetDocEntry( (*it).Group, (*it).Elem);
1342 if ( dynamic_cast<SeqEntry *>(d) )
1344 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1348 offset = d->GetOffset();
1349 lgth = d->GetLength();
1352 spaces = new std::string( lgth-valLgth, ' ');
1353 (*it).Value = (*it).Value + *spaces;
1356 fp->seekp( offset, std::ios::beg );
1357 fp->write( (*it).Value.c_str(), lgth );
1365 * \brief anonymize a File (remove Patient's personal info passed with
1366 * AddAnonymizeElement()
1367 * \note You cannot Anonymize a DataEntry (to be fixed)
1369 bool File::AnonymizeFile()
1371 // If Anonymisation list is empty, let's perform some basic anonymization
1372 if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
1374 // If exist, replace by spaces
1375 SetEntryString(" ",0x0010, 0x2154); // Telephone
1376 SetEntryString(" ",0x0010, 0x1040); // Adress
1377 SetEntryString(" ",0x0010, 0x0020); // Patient ID
1379 DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
1381 if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
1383 std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
1384 if ( studyInstanceUID != GDCM_UNFOUND )
1386 SetEntryString(studyInstanceUID, 0x0010, 0x0010);
1390 SetEntryString("anonymized", 0x0010, 0x0010);
1397 for (ListElements::iterator it = UserAnonymizeList.begin();
1398 it != UserAnonymizeList.end();
1401 d = GetDocEntry( (*it).Group, (*it).Elem);
1406 if ( dynamic_cast<SeqEntry *>(d) )
1408 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1412 if ( dynamic_cast<DataEntry *>(d) )
1414 gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
1418 SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
1422 // In order to make definitively impossible any further identification
1423 // remove or replace all the stuff that contains a Date
1425 //0008 0012 DA ID Instance Creation Date
1426 //0008 0020 DA ID Study Date
1427 //0008 0021 DA ID Series Date
1428 //0008 0022 DA ID Acquisition Date
1429 //0008 0023 DA ID Content Date
1430 //0008 0024 DA ID Overlay Date
1431 //0008 0025 DA ID Curve Date
1432 //0008 002a DT ID Acquisition Datetime
1433 //0018 9074 DT ACQ Frame Acquisition Datetime
1434 //0018 9151 DT ACQ Frame Reference Datetime
1435 //0018 a002 DT ACQ Contribution Date Time
1436 //0020 3403 SH REL Modified Image Date (RET)
1437 //0032 0032 DA SDY Study Verified Date
1438 //0032 0034 DA SDY Study Read Date
1439 //0032 1000 DA SDY Scheduled Study Start Date
1440 //0032 1010 DA SDY Scheduled Study Stop Date
1441 //0032 1040 DA SDY Study Arrival Date
1442 //0032 1050 DA SDY Study Completion Date
1443 //0038 001a DA VIS Scheduled Admission Date
1444 //0038 001c DA VIS Scheduled Discharge Date
1445 //0038 0020 DA VIS Admitting Date
1446 //0038 0030 DA VIS Discharge Date
1447 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1448 //0040 0004 DA PRC Scheduled Procedure Step End Date
1449 //0040 0244 DA PRC Performed Procedure Step Start Date
1450 //0040 0250 DA PRC Performed Procedure Step End Date
1451 //0040 2004 DA PRC Issue Date of Imaging Service Request
1452 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1453 //0040 4011 DT PRC Expected Completion Date and Time
1454 //0040 a030 DT PRC Verification Date Time
1455 //0040 a032 DT PRC Observation Date Time
1456 //0040 a120 DT PRC DateTime
1457 //0040 a121 DA PRC Date
1458 //0040 a13a DT PRC Referenced Datetime
1459 //0070 0082 DA ??? Presentation Creation Date
1460 //0100 0420 DT ??? SOP Autorization Date and Time
1461 //0400 0105 DT ??? Digital Signature DateTime
1462 //2100 0040 DA PJ Creation Date
1463 //3006 0008 DA SSET Structure Set Date
1464 //3008 0024 DA ??? Treatment Control Point Date
1465 //3008 0054 DA ??? First Treatment Date
1466 //3008 0056 DA ??? Most Recent Treatment Date
1467 //3008 0162 DA ??? Safe Position Exit Date
1468 //3008 0166 DA ??? Safe Position Return Date
1469 //3008 0250 DA ??? Treatment Date
1470 //300a 0006 DA RT RT Plan Date
1471 //300a 022c DA RT Air Kerma Rate Reference Date
1472 //300e 0004 DA RT Review Date
1478 * \brief Performs some consistency checking on various 'File related'
1479 * (as opposed to 'DicomDir related') entries
1480 * then writes in a file all the (Dicom Elements) included the Pixels
1481 * @param fileName file name to write to
1482 * @param writetype type of the file to be written
1483 * (ACR, ExplicitVR, ImplicitVR)
1485 bool File::Write(std::string fileName, FileType writetype)
1487 std::ofstream *fp = new std::ofstream(fileName.c_str(),
1488 std::ios::out | std::ios::binary);
1491 gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
1495 // Entry : 0002|0000 = group length -> recalculated
1496 DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
1499 std::ostringstream sLen;
1500 sLen << ComputeGroup0002Length( );
1501 e0000->SetString(sLen.str());
1504 /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
1505 if( writetype != JPEG )
1507 int i_lgPix = GetEntryLength(GrPixel, NumPixel);
1510 // no (GrPixel, NumPixel) element
1511 std::string s_lgPix = Util::Format("%d", i_lgPix+12);
1512 s_lgPix = Util::DicomString( s_lgPix.c_str() );
1513 InsertEntryString(s_lgPix,GrPixel, 0x0000);
1516 Document::WriteContent(fp, writetype);
1524 //-----------------------------------------------------------------------------
1528 //-----------------------------------------------------------------------------
1531 * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
1532 * Compute the RLE extra information and store it in \ref RLEInfo
1533 * for later pixel retrieval usage.
1535 void File::ComputeRLEInfo()
1537 std::string ts = GetTransferSyntax();
1538 if ( !Global::GetTS()->IsRLELossless(ts) )
1543 // Encoded pixel data: for the time being we are only concerned with
1544 // Jpeg or RLE Pixel data encodings.
1545 // As stated in PS 3.5-2003, section 8.2 p44:
1546 // "If sent in Encapsulated Format (i.e. other than the Native Format) the
1547 // value representation OB is used".
1548 // Hence we expect an OB value representation. Concerning OB VR,
1549 // the section PS 3.5-2003, section A.4.c p 58-59, states:
1550 // "For the Value Representations OB and OW, the encoding shall meet the
1551 // following specifications depending on the Data element tag:"
1553 // - the first item in the sequence of items before the encoded pixel
1554 // data stream shall be basic offset table item. The basic offset table
1555 // item value, however, is not required to be present"
1556 ReadEncapsulatedBasicOffsetTable();
1558 // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
1559 // Loop on the individual frame[s] and store the information
1560 // on the RLE fragments in a RLEFramesInfo.
1561 // Note: - when only a single frame is present, this is a
1563 // - when more than one frame are present, then we are in
1564 // the case of a multi-frame image.
1568 while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1570 // Since we have read the basic offset table, let's check the value were correct
1571 // or else produce a warning:
1572 if ( BasicOffsetTableItemValue )
1574 // If a BasicOffsetTableItemValue was read
1575 uint32_t individualLength = BasicOffsetTableItemValue[i];
1576 assert( individualLength == sum ); // REMOVE that if this is a problem
1577 if( individualLength != sum )
1579 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" );
1581 sum += frameLength + 8;
1584 // Parse the RLE Header and store the corresponding RLE Segment
1585 // Offset Table information on fragments of this current Frame.
1586 // Note that the fragment pixels themselves are not loaded
1587 // (but just skipped).
1588 long frameOffset = Fp->tellg(); // once per fragment
1590 uint32_t nbRleSegments = ReadInt32();
1591 if ( nbRleSegments > 16 )
1593 // There should be at most 15 segments (refer to RLEFrame class)
1594 gdcmWarningMacro( "Too many segments.");
1597 uint32_t rleSegmentOffsetTable[16];
1598 for( int k = 1; k <= 15; k++ )
1600 rleSegmentOffsetTable[k] = ReadInt32();
1603 // Deduce from both RLE Header and frameLength
1604 // the fragment length, and again store this info
1605 // in a RLEFramesInfo.
1606 long rleSegmentLength[15];
1607 // skipping (not reading) RLE Segments
1608 if ( nbRleSegments > 1)
1610 for(unsigned int k = 1; k <= nbRleSegments-1; k++)
1612 rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
1613 - rleSegmentOffsetTable[k];
1614 SkipBytes(rleSegmentLength[k]);
1618 rleSegmentLength[nbRleSegments] = frameLength
1619 - rleSegmentOffsetTable[nbRleSegments];
1620 SkipBytes(rleSegmentLength[nbRleSegments]);
1622 // Store the collected info
1623 RLEFrame *newFrame = new RLEFrame;
1624 newFrame->SetNumberOfFragments(nbRleSegments);
1625 for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
1627 newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
1628 newFrame->SetLength(uk,rleSegmentLength[uk]);
1630 RLEInfo->AddFrame(newFrame);
1633 // Make sure that we encounter a 'Sequence Delimiter Item'
1634 // at the end of the item :
1635 if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File
1637 gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
1642 * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
1643 * Compute the jpeg extra information (fragment[s] offset[s] and
1644 * length) and store it[them] in \ref JPEGInfo for later pixel
1647 void File::ComputeJPEGFragmentInfo()
1649 // If you need to, look for comments of ComputeRLEInfo().
1650 std::string ts = GetTransferSyntax();
1651 if ( ! Global::GetTS()->IsJPEG(ts) )
1656 ReadEncapsulatedBasicOffsetTable();
1658 // Loop on the fragments[s] and store the parsed information in a
1660 long fragmentLength;
1663 while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1665 // Since we have read the basic offset table, let's check the value were correct
1666 // or else produce a warning:
1667 // A.4 Transfer syntaxes for encapsulation of encoded pixel data:
1668 // When the Item Value is present, the Basic Offset Table Item Value shall contain
1669 // concatenated 32-bit unsigned integer values that are byte offsets to the first
1670 // byte of the Item Tag of the first fragment for each frame in the Sequence of
1671 // Items. These offsets are measured from the first byte of the first Item Tag
1672 // following the Basic Offset Table item (See Table A.4-2).
1674 if ( BasicOffsetTableItemValue )
1676 // If a BasicOffsetTableItemValue was read
1677 uint32_t individualLength = BasicOffsetTableItemValue[i];
1678 //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ??
1679 if( individualLength != sum )
1681 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" <<
1682 individualLength << " != " << sum );
1684 sum += fragmentLength + 8;
1688 long fragmentOffset = Fp->tellg(); // Once per fragment
1689 // Store the collected info
1690 JPEGFragment *newFragment = new JPEGFragment;
1691 newFragment->SetOffset(fragmentOffset);
1692 newFragment->SetLength(fragmentLength);
1693 JPEGInfo->AddFragment(newFragment);
1695 SkipBytes(fragmentLength);
1698 // Make sure that we encounter a 'Sequence Delimiter Item'
1699 // at the end of the item :
1700 if ( !ReadTag(0xfffe, 0xe0dd) )
1702 gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
1707 * \brief Assuming the internal file pointer \ref Document::Fp
1708 * is placed at the beginning of a tag, check whether this
1709 * tag is (TestGroup, TestElem).
1710 * \warning On success the internal file pointer \ref Document::Fp
1711 * is modified to point after the tag.
1712 * On failure (i.e. when the tag wasn't the expected tag
1713 * (TestGroup, TestElem) the internal file pointer
1714 * \ref Document::Fp is restored to it's original position.
1715 * @param testGroup The expected group of the tag.
1716 * @param testElem The expected Element of the tag.
1717 * @return True on success, false otherwise.
1719 bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
1721 long positionOnEntry = Fp->tellg(); // Only when reading fragments
1722 //long currentPosition = positionOnEntry; // On debugging purposes
1724 // Read the Item Tag group and element, and make
1725 // sure they are what we expected:
1726 uint16_t itemTagGroup;
1727 uint16_t itemTagElem;
1730 itemTagGroup = ReadInt16();
1731 itemTagElem = ReadInt16();
1733 catch ( FormatError )
1735 gdcmErrorMacro( "Can not read tag for "
1736 << " We should have found tag ("
1737 << DictEntry::TranslateToKey(testGroup,testElem) << ")"
1742 if ( itemTagGroup != testGroup || itemTagElem != testElem )
1744 // in order not to pollute output we don't warn on 'delimitors'
1745 if (itemTagGroup != 0xfffe || testGroup != 0xfffe )
1746 gdcmWarningMacro( "Wrong Item Tag found:"
1747 << " We should have found tag ("
1748 << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
1749 << " but instead we encountered tag ("
1750 << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
1751 << " at address: " << " 0x(" << std::hex
1752 << (unsigned int)positionOnEntry << std::dec << ")"
1754 Fp->seekg(positionOnEntry, std::ios::beg);
1762 * \brief Assuming the internal file pointer \ref Document::Fp
1763 * is placed at the beginning of a tag (TestGroup, TestElement),
1764 * read the length associated to the Tag.
1765 * \warning On success the internal file pointer \ref Document::Fp
1766 * is modified to point after the tag and it's length.
1767 * On failure (i.e. when the tag wasn't the expected tag
1768 * (TestGroup, TestElement) the internal file pointer
1769 * \ref Document::Fp is restored to it's original position.
1770 * @param testGroup The expected Group of the tag.
1771 * @param testElem The expected Element of the tag.
1772 * @return On success returns the length associated to the tag. On failure
1775 uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
1778 if ( !ReadTag(testGroup, testElem) )
1780 // Avoid polutting output
1781 if ( testGroup != 0xfffe )
1782 gdcmErrorMacro( "ReadTag did not succeed for ("
1783 << DictEntry::TranslateToKey(testGroup,testElem)
1788 //// Then read the associated Item Length
1790 // long currentPosition = Fp->tellg(); // save time // JPRx
1791 uint32_t itemLength = ReadInt32();
1792 gdcmDebugMacro( "Basic Item Length is: " << itemLength
1793 // << " at address: " << std::hex << (unsigned int)currentPosition
1799 * \brief When parsing the Pixel Data of an encapsulated file, read
1800 * the basic offset table (when present, and BTW dump it).
1802 void File::ReadEncapsulatedBasicOffsetTable()
1804 //// Read the Basic Offset Table Item Tag length...
1805 uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
1807 // When present, read the basic offset table itself.
1808 // Notes: - since the presence of this basic offset table is optional
1809 // we can't rely on it for the implementation, and we will simply
1810 // trash it's content (when present).
1811 // - still, when present, we could add some further checks on the
1812 // lengths, but we won't bother with such fuses for the time being.
1813 if ( itemLength != 0 )
1815 char *charBasicOffsetTableItemValue = new char[itemLength];
1816 Fp->read(charBasicOffsetTableItemValue, itemLength);
1817 unsigned int nbEntries = itemLength/4;
1818 assert( nbEntries*4 == itemLength); // Make sure this is a multiple
1819 BasicOffsetTableItemValue = new uint32_t[nbEntries];
1821 for (unsigned int i=0; i < nbEntries; i++ )
1823 BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i]));
1824 #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION)
1825 uint32_t val = BasicOffsetTableItemValue[i];
1826 BasicOffsetTableItemValue[i]
1827 = ( (val<<24) | ((val<<8) & 0x00ff0000) |
1828 ( (val>>8) & 0x0000ff00) | (val>>24) );
1830 gdcmDebugMacro( "Read one length for: " <<
1831 std::hex << BasicOffsetTableItemValue[i] );
1834 delete[] charBasicOffsetTableItemValue;
1838 // These are the deprecated method that one day should be removed (after the next release)
1840 #ifndef GDCM_LEGACY_REMOVE
1842 * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API)
1843 * @ param fileName file to be open for parsing
1844 * @ return false if file cannot be open or no swap info was found,
1845 * or no tag was found.
1846 * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
1848 bool File::Load( std::string const &fileName )
1850 GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
1852 SetFileName( fileName );
1853 if ( ! this->Document::Load( ) )
1856 return DoTheLoadingJob( );
1860 //-----------------------------------------------------------------------------
1863 //-----------------------------------------------------------------------------
1864 } // end namespace gdcm