1 /*=========================================================================
4 Module: $RCSfile: gdcmFile.cxx,v $
6 Date: $Date: 2006/04/11 16:03:26 $
7 Version: $Revision: 1.318 $
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"
221 //==> Just change the VR !
224 DataEntry *oldEntry = dynamic_cast<DataEntry *>(entry);
228 // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
229 // more than 8 (i.e 12, 16) is a 'O Words'
230 if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
235 // Change only made if usefull
236 if ( PixelVR != oldEntry->GetVR() )
238 //DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
239 // PixelVR,"1","Pixel Data");
240 //DataEntry *newEntry = DataEntry::New(newDict);
242 //newEntry->Copy(entry);
243 //newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
244 //oldEntry->SetSelfArea(false);
246 //RemoveEntry(oldEntry);
247 //AddEntry(newEntry);
248 //newEntry->Delete();
254 // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
255 // more than 8 (i.e 12, 16) is a 'O Words'
256 if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
260 // Change only made if usefull
261 if ( PixelVR != entry->GetVR() )
263 entry->SetVR(PixelVR);
270 * \brief This predicate, based on hopefully reasonable heuristics,
271 * decides whether or not the current File was properly parsed
272 * and contains the mandatory information for being considered as
273 * a well formed and usable Dicom/Acr File.
274 * @return true when File is the one of a reasonable Dicom/Acr file,
277 bool File::IsReadable()
279 if ( !Document::IsReadable() )
284 const std::string &res = GetEntryString(0x0028, 0x0005);
285 if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
287 gdcmWarningMacro("Wrong Image Dimensions" << res);
288 return false; // Image Dimensions
290 bool b0028_0100 = true;
291 if ( !GetDocEntry(0x0028, 0x0100) )
293 gdcmWarningMacro("Bits Allocated (0028|0100) not found");
294 //return false; // "Bits Allocated"
297 bool b0028_0101 = true;
298 if ( !GetDocEntry(0x0028, 0x0101) )
300 gdcmWarningMacro("Bits Stored (0028|0101) not found");
301 //return false; // "Bits Stored"
304 bool b0028_0102 = true;
305 if ( !GetDocEntry(0x0028, 0x0102) )
307 gdcmWarningMacro("Hight Bit (0028|0102) not found");
308 //return false; // "High Bit"
311 bool b0028_0103 = true;
312 if ( !GetDocEntry(0x0028, 0x0103) )
314 gdcmWarningMacro("Pixel Representation (0028|0103) not found");
315 //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed)
319 if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103)
321 gdcmWarningMacro("Too much mandatory Tags missing !");
325 if ( !GetDocEntry(GrPixel, NumPixel) )
327 gdcmWarningMacro("Pixel Dicom Element " << std::hex <<
328 GrPixel << "|" << NumPixel << "not found");
329 return false; // Pixel Dicom Element not found :-(
335 * \brief gets the info from 0020,0013 : Image Number else 0.
336 * @return image number
338 int File::GetImageNumber()
340 //0020 0013 : Image Number
341 std::string strImNumber = GetEntryString(0x0020,0x0013);
342 if ( strImNumber != GDCM_UNFOUND )
344 return atoi( strImNumber.c_str() );
350 * \brief gets the info from 0008,0060 : Modality
351 * @return Modality Type
353 ModalityType File::GetModality()
355 // 0008 0060 : Modality
356 std::string strModality = GetEntryString(0x0008,0x0060);
357 if ( strModality != GDCM_UNFOUND )
359 if ( strModality.find("AU") < strModality.length()) return AU;
360 else if ( strModality.find("AS") < strModality.length()) return AS;
361 else if ( strModality.find("BI") < strModality.length()) return BI;
362 else if ( strModality.find("CF") < strModality.length()) return CF;
363 else if ( strModality.find("CP") < strModality.length()) return CP;
364 else if ( strModality.find("CR") < strModality.length()) return CR;
365 else if ( strModality.find("CT") < strModality.length()) return CT;
366 else if ( strModality.find("CS") < strModality.length()) return CS;
367 else if ( strModality.find("DD") < strModality.length()) return DD;
368 else if ( strModality.find("DF") < strModality.length()) return DF;
369 else if ( strModality.find("DG") < strModality.length()) return DG;
370 else if ( strModality.find("DM") < strModality.length()) return DM;
371 else if ( strModality.find("DS") < strModality.length()) return DS;
372 else if ( strModality.find("DX") < strModality.length()) return DX;
373 else if ( strModality.find("ECG") < strModality.length()) return ECG;
374 else if ( strModality.find("EPS") < strModality.length()) return EPS;
375 else if ( strModality.find("FA") < strModality.length()) return FA;
376 else if ( strModality.find("FS") < strModality.length()) return FS;
377 else if ( strModality.find("HC") < strModality.length()) return HC;
378 else if ( strModality.find("HD") < strModality.length()) return HD;
379 else if ( strModality.find("LP") < strModality.length()) return LP;
380 else if ( strModality.find("LS") < strModality.length()) return LS;
381 else if ( strModality.find("MA") < strModality.length()) return MA;
382 else if ( strModality.find("MR") < strModality.length()) return MR;
383 else if ( strModality.find("NM") < strModality.length()) return NM;
384 else if ( strModality.find("OT") < strModality.length()) return OT;
385 else if ( strModality.find("PT") < strModality.length()) return PT;
386 else if ( strModality.find("RF") < strModality.length()) return RF;
387 else if ( strModality.find("RG") < strModality.length()) return RG;
388 else if ( strModality.find("RTDOSE")
389 < strModality.length()) return RTDOSE;
390 else if ( strModality.find("RTIMAGE")
391 < strModality.length()) return RTIMAGE;
392 else if ( strModality.find("RTPLAN")
393 < strModality.length()) return RTPLAN;
394 else if ( strModality.find("RTSTRUCT")
395 < strModality.length()) return RTSTRUCT;
396 else if ( strModality.find("SM") < strModality.length()) return SM;
397 else if ( strModality.find("ST") < strModality.length()) return ST;
398 else if ( strModality.find("TG") < strModality.length()) return TG;
399 else if ( strModality.find("US") < strModality.length()) return US;
400 else if ( strModality.find("VF") < strModality.length()) return VF;
401 else if ( strModality.find("XA") < strModality.length()) return XA;
402 else if ( strModality.find("XC") < strModality.length()) return XC;
406 /// \todo throw error return value ???
407 /// specified <> unknown in our database
415 * \brief Retrieve the number of columns of image.
416 * @return The encountered size when found, 0 by default.
417 * 0 means the file is NOT USABLE. The caller will have to check
421 DataEntry *entry = GetDataEntry(0x0028,0x0011);
423 return (int)entry->GetValue(0);
428 * \brief Retrieve the number of lines of image.
429 * \warning The defaulted value is 1 as opposed to File::GetXSize()
430 * @return The encountered size when found, 1 by default
431 * (The ACR-NEMA file contains a Signal, not an Image).
435 DataEntry *entry = GetDataEntry(0x0028,0x0010);
437 return (int)entry->GetValue(0);
444 // The Rows (0028,0010) entry was optional for ACR/NEMA.
445 // (at least some images didn't have it.)
446 // It might hence be a signal (1D image). So we default to 1:
451 * \brief Retrieve the number of planes of volume or the number
452 * of frames of a multiframe.
453 * \warning When present we consider the "Number of Frames" as the third
454 * dimension. When missing we consider the third dimension as
455 * being the ACR-NEMA "Planes" tag content.
456 * @return The encountered size when found, 1 by default (single image).
460 // Both DicomV3 and ACR/Nema consider the "Number of Frames"
461 // as the third dimension.
462 DataEntry *entry = GetDataEntry(0x0028,0x0008);
464 return (int)entry->GetValue(0);
466 // We then consider the "Planes" entry as the third dimension
467 entry = GetDataEntry(0x0028,0x0012);
469 return (int)entry->GetValue(0);
474 * \brief Retrieve the -unnormalized- number of 'times' of '4D image'.
475 * User has to tell gdcm the location of this '4th Dimension component'
476 * using SetFourthDimensionLocation() method before.
477 * \warning The defaulted value is 1.
478 * @return The encountered size when found, 1 by default
479 * (The file doesn't contain a '4D image'.).
483 if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object
486 DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(),
487 FourthDimensionLocation.GetElement() );
490 gdcmWarningMacro( " FourthDimensionLocation not found at : " <<
491 std::hex << FourthDimensionLocation.GetGroup()
492 << "|" << FourthDimensionLocation.GetElement());
497 return (int)entry->GetValue(0);
502 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
503 * then 0028,0030 : Pixel Spacing
505 * @return X dimension of a pixel
507 float File::GetXSpacing()
509 float xspacing = 1.0;
512 // To follow David Clunie's advice, we first check ImagerPixelSpacing
514 DataEntry *entry = GetDataEntry(0x0018,0x1164);
517 nbValue = entry->GetValueCount();
518 // Can't use IsValueCountValid because of the complex heuristic.
520 gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) "
521 << "has a wrong number of values :" << nbValue);
524 xspacing = (float)entry->GetValue(2);
525 else if( nbValue >= 2 )
526 xspacing = (float)entry->GetValue(1);
528 xspacing = (float)entry->GetValue(0);
530 if ( xspacing == 0.0 )
536 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
539 entry = GetDataEntry(0x0028,0x0030);
542 nbValue = entry->GetValueCount();
544 gdcmWarningMacro("PixelSpacing (0x0018,0x0030) "
545 << "has a wrong number of values :" << nbValue);
548 xspacing = (float)entry->GetValue(2);
549 else if( nbValue >= 2 )
550 xspacing = (float)entry->GetValue(1);
552 xspacing = (float)entry->GetValue(0);
554 if ( xspacing == 0.0 )
560 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
566 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
567 * then from 0028,0030 : Pixel Spacing
569 * @return Y dimension of a pixel
571 float File::GetYSpacing()
573 float yspacing = 1.0;
574 // To follow David Clunie's advice, we first check ImagerPixelSpacing
576 DataEntry *entry = GetDataEntry(0x0018,0x1164);
579 yspacing = (float)entry->GetValue(0);
581 if ( yspacing == 0.0 )
587 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
590 entry = GetDataEntry(0x0028,0x0030);
593 yspacing = (float)entry->GetValue(0);
595 if ( yspacing == 0.0 )
601 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
608 * \brief gets the info from 0018,0088 : Space Between Slices
609 * else from 0018,0050 : Slice Thickness
612 * When an element is missing, we suppose slices join together
613 * (no overlapping, no interslice gap) but we have no way to check it !
614 * For *Dicom* images, ZSpacing *should be* calculated using
615 * XOrigin, YOrigin, ZOrigin (of the top left image corner)
616 * of 2 consecutive images, and the Orientation
617 * Computing ZSpacing on a single image is not really meaningfull !
618 * @return Z dimension of a voxel-to be
620 float File::GetZSpacing()
623 float zspacing = 1.0f;
625 // Spacing Between Slices : distance between the middle of 2 slices
627 // jointives (Spacing between Slices = Slice Thickness)
628 // overlapping (Spacing between Slices < Slice Thickness)
629 // disjointes (Spacing between Slices > Slice Thickness)
630 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
631 // It only concerns the MRI guys, not people wanting to visualize volumes
632 // If Spacing Between Slices is missing,
633 // we suppose slices joint together
634 DataEntry *entry = GetDataEntry(0x0018,0x0088);
637 zspacing = (float)entry->GetValue(0);
639 if ( zspacing == 0.0 )
644 gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
646 // if no 'Spacing Between Slices' is found,
647 // we assume slices join together
648 // (no overlapping, no interslice gap)
649 entry = GetDataEntry(0x0018,0x0050);
652 zspacing = (float)entry->GetValue(0);
654 if ( zspacing == 0.0 )
659 gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
661 // if no 'Spacing Between Slices' is found,
662 // we assume slices join together
663 // (no overlapping, no interslice gap)
664 entry = GetDataEntry(0x3004,0x000c);
667 float z1 = (float)entry->GetValue(0);
668 float z2 = (float)entry->GetValue(1);
669 zspacing = z2 - z1; // can be negative...
671 if ( zspacing == 0.0 )
680 * \brief gets the info from 0020,0032 : Image Position Patient
681 * else from 0020,0030 : Image Position (RET)
683 * @return up-left image corner X position
685 float File::GetXOrigin()
687 DataEntry *entry = GetDataEntry(0x0020,0x0032);
690 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
691 entry = GetDataEntry(0x0020,0x0030);
694 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
699 if( entry->GetValueCount() == 3 )
701 if (!entry->IsValueCountValid() )
703 gdcmErrorMacro( "Invalid Value Count" );
705 return (float)entry->GetValue(0);
711 * \brief gets the info from 0020,0032 : Image Position Patient
712 * else from 0020,0030 : Image Position (RET)
714 * @return up-left image corner Y position
716 float File::GetYOrigin()
718 DataEntry *entry = GetDataEntry(0x0020,0x0032);
721 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
722 entry = GetDataEntry(0x0020,0x0030);
725 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
730 if( entry->GetValueCount() == 3 )
732 if (!entry->IsValueCountValid() )
734 gdcmErrorMacro( "Invalid Value Count" );
736 return (float)entry->GetValue(1);
742 * \brief gets the info from 0020,0032 : Image Position Patient
743 * else from 0020,0030 : Image Position (RET)
744 * else from 0020,1041 : Slice Location
745 * else from 0020,0050 : Location
747 * @return up-left image corner Z position
749 float File::GetZOrigin()
751 DataEntry *entry = GetDataEntry(0x0020,0x0032);
754 if( entry->GetValueCount() == 3 )
756 if (!entry->IsValueCountValid() )
758 gdcmErrorMacro( "Invalid Value Count" );
760 return (float)entry->GetValue(2);
762 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
766 entry = GetDataEntry(0x0020,0x0030);
769 if( entry->GetValueCount() == 3 )
771 if (!entry->IsValueCountValid() )
773 gdcmErrorMacro( "Invalid Value Count" );
775 return (float)entry->GetValue(2);
777 gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
781 // for *very* old ACR-NEMA images
782 entry = GetDataEntry(0x0020,0x1041);
785 if( entry->GetValueCount() == 1 )
787 if (!entry->IsValueCountValid() )
789 gdcmErrorMacro( "Invalid Value Count" );
791 return (float)entry->GetValue(0); // VM=1 !
793 gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
797 entry = GetDataEntry(0x0020,0x0050);
800 if( entry->GetValueCount() == 1 )
802 if (!entry->IsValueCountValid() )
804 gdcmErrorMacro( "Invalid Value Count" );
806 return (float)entry->GetValue(0);
808 gdcmWarningMacro( "Wrong Location (0020,0050)");
811 return 0.; // Hopeless
815 * \brief gets the info from 0020,0037 : Image Orientation Patient
816 * or from 0020 0035 : Image Orientation (RET)
818 * (needed to organize DICOM files based on their x,y,z position)
820 * @param iop adress of the (6)float array to receive values.
821 * (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff-
823 * @return true when one of the tag -with consistent values- is found
824 * false when nothing or inconsistent stuff - is found
826 bool File::GetImageOrientationPatient( float iop[6] )
828 std::string strImOriPat;
829 //iop is supposed to be float[6]
830 iop[0] = iop[4] = 1.;
831 iop[1] = iop[2] = iop[3] = iop[5] = 0.;
833 // 0020 0037 DS REL Image Orientation (Patient)
834 if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
836 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
837 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
839 gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
840 << " Less than 6 values were found." );
846 // 0020 0035 DS REL Image Orientation (RET)
847 else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND )
849 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
850 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
852 gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
853 << "Less than 6 values were found." );
862 * \brief Retrieve the number of Bits Stored (actually used)
863 * (as opposed to number of Bits Allocated)
864 * @return The encountered number of Bits Stored, 0 by default.
865 * 0 means the file is NOT USABLE. The caller has to check it !
867 int File::GetBitsStored()
869 DataEntry *entry = GetDataEntry(0x0028,0x0101);
872 gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory");
875 return (int)entry->GetValue(0);
879 * \brief Retrieve the number of Bits Allocated
880 * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,)
881 * @return The encountered Number of Bits Allocated, 0 by default.
882 * 0 means the file is NOT USABLE. The caller has to check it !
884 int File::GetBitsAllocated()
886 DataEntry *entry = GetDataEntry(0x0028,0x0100);
889 gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory");
892 return (int)entry->GetValue(0);
896 * \brief Retrieve the high bit position.
897 * \warning The method defaults to 0 when information is missing.
898 * The responsability of checking this value is left to the caller.
899 * @return The high bit position when present. 0 when missing.
901 int File::GetHighBitPosition()
903 DataEntry *entry = GetDataEntry(0x0028,0x0102);
906 gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory");
909 return (int)entry->GetValue(0);
913 * \brief Retrieve the number of Samples Per Pixel
914 * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
915 * @return The encountered number of Samples Per Pixel, 1 by default.
916 * (we assume Gray level Pixels)
918 int File::GetSamplesPerPixel()
920 DataEntry *entry = GetDataEntry(0x0028,0x0002);
923 gdcmWarningMacro("SamplesPerPixel (0028,0002) is supposed to be mandatory");
924 return 1; // Well, it's supposed to be mandatory ...
925 // but sometimes it's missing : *we* assume Gray pixels
927 return (int)entry->GetValue(0);
931 * \brief Retrieve the Planar Configuration for RGB images
932 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
933 * @return The encountered Planar Configuration, 0 by default.
935 int File::GetPlanarConfiguration()
937 DataEntry *entry = GetDataEntry(0x0028,0x0006);
942 return (int)entry->GetValue(0);
946 * \brief Return the size (in bytes) of a single pixel of data.
947 * @return The size in bytes of a single pixel of data; 0 by default
948 * 0 means the file is NOT USABLE; the caller will have to check
950 int File::GetPixelSize()
952 // 0028 0100 US IMG Bits Allocated
953 // (in order no to be messed up by old ACR-NEMA RGB images)
954 assert( !(GetEntryString(0x0028,0x0100) == "24") );
956 std::string pixelType = GetPixelType();
957 if ( pixelType == "8U" || pixelType == "8S" )
961 if ( pixelType == "16U" || pixelType == "16S")
965 if ( pixelType == "32U" || pixelType == "32S")
969 if ( pixelType == "FD" )
973 gdcmWarningMacro( "Unknown pixel type: " << pixelType);
978 * \brief Build the Pixel Type of the image.
979 * Possible values are:
980 * - 8U unsigned 8 bit,
982 * - 16U unsigned 16 bit,
983 * - 16S signed 16 bit,
984 * - 32U unsigned 32 bit,
985 * - 32S signed 32 bit,
986 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
987 * \warning 12 bit images appear as 16 bit.
988 * 24 bit images appear as 8 bit + photochromatic interp ="RGB "
989 * + Planar Configuration = 0
990 * @return 0S if nothing found. NOT USABLE file. The caller has to check
992 std::string File::GetPixelType()
994 std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
995 if ( bitsAlloc == GDCM_UNFOUND )
997 gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory");
998 bitsAlloc = "16"; // default and arbitrary value, not to polute the output
1001 if ( bitsAlloc == "64" )
1005 else if ( bitsAlloc == "12" )
1007 // It will be unpacked
1010 else if ( bitsAlloc == "24" )
1012 // (in order no to be messed up by old RGB images)
1017 if( IsSignedPixelData() )
1025 return bitsAlloc + sign;
1029 * \brief Check whether the pixels are signed (1) or UNsigned (0) data.
1030 * \warning The method defaults to false (UNsigned) when tag 0028|0103
1032 * The responsability of checking this value is left to the caller
1033 * (NO transformation is performed on the pixels to make then >0)
1034 * @return True when signed, false when UNsigned
1036 bool File::IsSignedPixelData()
1038 DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
1041 gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be "
1045 return entry->GetValue(0) != 0;
1049 * \brief Check whether this a monochrome picture (gray levels) or not,
1050 * using "Photometric Interpretation" tag (0x0028,0x0004).
1051 * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
1053 bool File::IsMonochrome()
1055 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1056 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
1057 || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
1061 if ( PhotometricInterp == GDCM_UNFOUND )
1063 gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be "
1070 * \brief Check whether this a MONOCHROME1 picture (high values = dark)
1071 * or not using "Photometric Interpretation" tag (0x0028,0x0004).
1072 * @return true when "MONOCHROME1" . False otherwise.
1074 bool File::IsMonochrome1()
1076 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1077 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
1081 if ( PhotometricInterp == GDCM_UNFOUND )
1083 gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to"
1084 << " be mandatory! ");
1090 * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
1091 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1092 * @return true when "PALETTE COLOR". False otherwise.
1094 bool File::IsPaletteColor()
1096 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1097 if ( PhotometricInterp == "PALETTE COLOR " )
1101 if ( PhotometricInterp == GDCM_UNFOUND )
1103 gdcmDebugMacro( "Not found : Palette color (0028,0004)");
1109 * \brief Check whether this a "YBR_FULL" color picture or not by accessing
1110 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1111 * @return true when "YBR_FULL". False otherwise.
1113 bool File::IsYBRFull()
1115 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1116 if ( PhotometricInterp == "YBR_FULL" )
1120 if ( PhotometricInterp == GDCM_UNFOUND )
1122 gdcmDebugMacro( "Not found : YBR Full (0028,0004)");
1128 * \brief tells us if LUT are used
1129 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
1130 * are NOT considered as LUT, since nobody knows
1131 * how to deal with them
1132 * Please warn me if you know sbdy that *does* know ... jprx
1133 * @return true if LUT Descriptors and LUT Tables were found
1137 // Check the presence of the LUT Descriptors, and LUT Tables
1139 if ( !GetDocEntry(0x0028,0x1101) )
1143 // LutDescriptorGreen
1144 if ( !GetDocEntry(0x0028,0x1102) )
1148 // LutDescriptorBlue
1149 if ( !GetDocEntry(0x0028,0x1103) )
1153 // Red Palette Color Lookup Table Data
1154 if ( !GetDocEntry(0x0028,0x1201) )
1158 // Green Palette Color Lookup Table Data
1159 if ( !GetDocEntry(0x0028,0x1202) )
1163 // Blue Palette Color Lookup Table Data
1164 if ( !GetDocEntry(0x0028,0x1203) )
1169 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
1170 // NOT taken into account, but we don't know how to use it ...
1175 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
1177 * @return Lookup Table number of Bits , 0 by default
1178 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
1179 * @ return bit number of each LUT item
1181 int File::GetLUTNbits()
1183 std::vector<std::string> tokens;
1186 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
1187 // = Lookup Table Desc-Blue
1188 // Consistency already checked in GetLUTLength
1189 std::string lutDescription = GetEntryString(0x0028,0x1101);
1190 if ( lutDescription == GDCM_UNFOUND )
1195 tokens.clear(); // clean any previous value
1196 Util::Tokenize ( lutDescription, tokens, "\\" );
1197 //LutLength=atoi(tokens[0].c_str());
1198 //LutDepth=atoi(tokens[1].c_str());
1200 lutNbits = atoi( tokens[2].c_str() );
1207 *\brief gets the info from 0028,1052 : Rescale Intercept
1208 * @return Rescale Intercept. defaulted to 0.0 is not found or empty
1210 float File::GetRescaleIntercept()
1212 // 0028 1052 DS IMG Rescale Intercept
1213 DataEntry *entry = GetDataEntry(0x0028, 0x1052);
1216 gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
1219 return (float)entry->GetValue(0);
1224 *\brief gets the info from 0028,1053 : Rescale Slope
1225 * @return Rescale Slope. defaulted to 1.0 is not found or empty
1227 float File::GetRescaleSlope()
1229 // 0028 1053 DS IMG Rescale Slope
1230 DataEntry *entry = GetDataEntry(0x0028, 0x1053);
1233 gdcmDebugMacro( "Missing Rescale Slope (0028,1053)");
1236 return (float)entry->GetValue(0);
1240 * \brief This function is intended to user who doesn't want
1241 * to have to manage a LUT and expects to get an RBG Pixel image
1242 * (or a monochrome one, if no LUT found ...)
1243 * \warning to be used with GetImagePixels()
1244 * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
1246 int File::GetNumberOfScalarComponents()
1248 if ( GetSamplesPerPixel() == 3 )
1253 // 0028 0100 US IMG Bits Allocated
1254 // (in order no to be messed up by old RGB images)
1255 if ( GetEntryString(0x0028,0x0100) == "24" )
1260 std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
1262 if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
1264 if ( HasLUT() )// PALETTE COLOR is NOT enough
1274 // beware of trailing space at end of string
1275 // DICOM tags are never of odd length
1276 if ( strPhotometricInterpretation == GDCM_UNFOUND ||
1277 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
1278 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
1284 // we assume that *all* kinds of YBR are dealt with
1290 * \brief This function is intended to user that DOESN'T want
1291 * to get RGB pixels image when it's stored as a PALETTE COLOR image
1292 * - the (vtk) user is supposed to know how deal with LUTs -
1293 * \warning to be used with GetImagePixelsRaw()
1294 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
1296 int File::GetNumberOfScalarComponentsRaw()
1298 // 0028 0100 US IMG Bits Allocated
1299 // (in order no to be messed up by old RGB images)
1300 if ( File::GetEntryString(0x0028,0x0100) == "24" )
1305 // we assume that *all* kinds of YBR are dealt with
1306 return GetSamplesPerPixel();
1310 * \brief Recover the offset (from the beginning of the file)
1311 * of *image* pixels (not *icone image* pixels, if any !)
1312 * @return Pixel Offset
1314 size_t File::GetPixelOffset()
1316 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1319 return pxlElement->GetOffset();
1323 gdcmWarningMacro( "Big trouble : Pixel Element ("
1324 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1330 * \brief Recover the pixel area length (in Bytes)
1331 * @return Pixel Element Length, as stored in the header
1332 * (NOT the memory space necessary to hold the Pixels
1333 * -in case of embeded compressed image-)
1334 * 0 : NOT USABLE file. The caller has to check.
1336 size_t File::GetPixelAreaLength()
1338 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1341 return pxlElement->GetLength();
1345 gdcmWarningMacro( "Big trouble : Pixel Element ("
1346 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1352 * \brief Adds the characteristics of a new element we want to anonymize
1353 * @param group Group number of the target tag.
1354 * @param elem Element number of the target tag.
1355 * @param value new value (string) to substitute with
1357 void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
1358 std::string const &value)
1364 UserAnonymizeList.push_back(el);
1368 * \brief Overwrites in the file the values of the DicomElements
1371 void File::AnonymizeNoLoad()
1373 std::fstream *fp = new std::fstream(Filename.c_str(),
1374 std::ios::in | std::ios::out | std::ios::binary);
1378 uint32_t valLgth = 0;
1379 std::string *spaces;
1380 for (ListElements::iterator it = UserAnonymizeList.begin();
1381 it != UserAnonymizeList.end();
1384 d = GetDocEntry( (*it).Group, (*it).Elem);
1389 if ( dynamic_cast<SeqEntry *>(d) )
1391 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1395 offset = d->GetOffset();
1396 lgth = d->GetLength();
1399 spaces = new std::string( lgth-valLgth, ' ');
1400 (*it).Value = (*it).Value + *spaces;
1403 fp->seekp( offset, std::ios::beg );
1404 fp->write( (*it).Value.c_str(), lgth );
1412 * \brief anonymize a File (remove Patient's personal info passed with
1413 * AddAnonymizeElement()
1414 * \note You cannot Anonymize a DataEntry (to be fixed)
1416 bool File::AnonymizeFile()
1418 // If Anonymisation list is empty, let's perform some basic anonymization
1419 if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
1421 // If exist, replace by spaces
1422 SetEntryString(" ",0x0010, 0x2154); // Telephone
1423 SetEntryString(" ",0x0010, 0x1040); // Adress
1424 SetEntryString(" ",0x0010, 0x0020); // Patient ID
1426 DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
1428 if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
1430 std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
1431 if ( studyInstanceUID != GDCM_UNFOUND )
1433 SetEntryString(studyInstanceUID, 0x0010, 0x0010);
1437 SetEntryString("anonymized", 0x0010, 0x0010);
1444 for (ListElements::iterator it = UserAnonymizeList.begin();
1445 it != UserAnonymizeList.end();
1448 d = GetDocEntry( (*it).Group, (*it).Elem);
1453 if ( dynamic_cast<SeqEntry *>(d) )
1455 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1459 if ( dynamic_cast<DataEntry *>(d) )
1461 gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
1465 SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
1469 // In order to make definitively impossible any further identification
1470 // remove or replace all the stuff that contains a Date
1472 //0008 0012 DA ID Instance Creation Date
1473 //0008 0020 DA ID Study Date
1474 //0008 0021 DA ID Series Date
1475 //0008 0022 DA ID Acquisition Date
1476 //0008 0023 DA ID Content Date
1477 //0008 0024 DA ID Overlay Date
1478 //0008 0025 DA ID Curve Date
1479 //0008 002a DT ID Acquisition Datetime
1480 //0018 9074 DT ACQ Frame Acquisition Datetime
1481 //0018 9151 DT ACQ Frame Reference Datetime
1482 //0018 a002 DT ACQ Contribution Date Time
1483 //0020 3403 SH REL Modified Image Date (RET)
1484 //0032 0032 DA SDY Study Verified Date
1485 //0032 0034 DA SDY Study Read Date
1486 //0032 1000 DA SDY Scheduled Study Start Date
1487 //0032 1010 DA SDY Scheduled Study Stop Date
1488 //0032 1040 DA SDY Study Arrival Date
1489 //0032 1050 DA SDY Study Completion Date
1490 //0038 001a DA VIS Scheduled Admission Date
1491 //0038 001c DA VIS Scheduled Discharge Date
1492 //0038 0020 DA VIS Admitting Date
1493 //0038 0030 DA VIS Discharge Date
1494 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1495 //0040 0004 DA PRC Scheduled Procedure Step End Date
1496 //0040 0244 DA PRC Performed Procedure Step Start Date
1497 //0040 0250 DA PRC Performed Procedure Step End Date
1498 //0040 2004 DA PRC Issue Date of Imaging Service Request
1499 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1500 //0040 4011 DT PRC Expected Completion Date and Time
1501 //0040 a030 DT PRC Verification Date Time
1502 //0040 a032 DT PRC Observation Date Time
1503 //0040 a120 DT PRC DateTime
1504 //0040 a121 DA PRC Date
1505 //0040 a13a DT PRC Referenced Datetime
1506 //0070 0082 DA ??? Presentation Creation Date
1507 //0100 0420 DT ??? SOP Autorization Date and Time
1508 //0400 0105 DT ??? Digital Signature DateTime
1509 //2100 0040 DA PJ Creation Date
1510 //3006 0008 DA SSET Structure Set Date
1511 //3008 0024 DA ??? Treatment Control Point Date
1512 //3008 0054 DA ??? First Treatment Date
1513 //3008 0056 DA ??? Most Recent Treatment Date
1514 //3008 0162 DA ??? Safe Position Exit Date
1515 //3008 0166 DA ??? Safe Position Return Date
1516 //3008 0250 DA ??? Treatment Date
1517 //300a 0006 DA RT RT Plan Date
1518 //300a 022c DA RT Air Kerma Rate Reference Date
1519 //300e 0004 DA RT Review Date
1525 * \brief Performs some consistency checking on various 'File related'
1526 * (as opposed to 'DicomDir related') entries
1527 * then writes in a file all the (Dicom Elements) included the Pixels
1528 * @param fileName file name to write to
1529 * @param writetype type of the file to be written
1530 * (ACR, ExplicitVR, ImplicitVR)
1532 bool File::Write(std::string fileName, FileType writetype)
1534 std::ofstream *fp = new std::ofstream(fileName.c_str(),
1535 std::ios::out | std::ios::binary);
1538 gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
1542 // Entry : 0002|0000 = group length -> recalculated
1543 DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
1546 std::ostringstream sLen;
1547 sLen << ComputeGroup0002Length( );
1548 e0000->SetString(sLen.str());
1551 /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
1552 if( writetype != JPEG )
1554 int i_lgPix = GetEntryLength(GrPixel, NumPixel);
1557 // no (GrPixel, NumPixel) element
1558 std::string s_lgPix = Util::Format("%d", i_lgPix+12);
1559 s_lgPix = Util::DicomString( s_lgPix.c_str() );
1560 InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL");
1563 Document::WriteContent(fp, writetype);
1571 //-----------------------------------------------------------------------------
1575 //-----------------------------------------------------------------------------
1578 * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
1579 * Compute the RLE extra information and store it in \ref RLEInfo
1580 * for later pixel retrieval usage.
1582 void File::ComputeRLEInfo()
1584 std::string ts = GetTransferSyntax();
1585 if ( !Global::GetTS()->IsRLELossless(ts) )
1590 // Encoded pixel data: for the time being we are only concerned with
1591 // Jpeg or RLE Pixel data encodings.
1592 // As stated in PS 3.5-2003, section 8.2 p44:
1593 // "If sent in Encapsulated Format (i.e. other than the Native Format) the
1594 // value representation OB is used".
1595 // Hence we expect an OB value representation. Concerning OB VR,
1596 // the section PS 3.5-2003, section A.4.c p 58-59, states:
1597 // "For the Value Representations OB and OW, the encoding shall meet the
1598 // following specifications depending on the Data element tag:"
1600 // - the first item in the sequence of items before the encoded pixel
1601 // data stream shall be basic offset table item. The basic offset table
1602 // item value, however, is not required to be present"
1603 ReadEncapsulatedBasicOffsetTable();
1605 // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
1606 // Loop on the individual frame[s] and store the information
1607 // on the RLE fragments in a RLEFramesInfo.
1608 // Note: - when only a single frame is present, this is a
1610 // - when more than one frame are present, then we are in
1611 // the case of a multi-frame image.
1615 while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1617 // Since we have read the basic offset table, let's check the value were correct
1618 // or else produce a warning:
1619 if ( BasicOffsetTableItemValue )
1621 // If a BasicOffsetTableItemValue was read
1622 uint32_t individualLength = BasicOffsetTableItemValue[i];
1623 assert( individualLength == sum ); // REMOVE that if this is a problem
1624 if( individualLength != sum )
1626 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" );
1628 sum += frameLength + 8;
1631 // Parse the RLE Header and store the corresponding RLE Segment
1632 // Offset Table information on fragments of this current Frame.
1633 // Note that the fragment pixels themselves are not loaded
1634 // (but just skipped).
1635 long frameOffset = Fp->tellg(); // once per fragment
1637 uint32_t nbRleSegments = ReadInt32();
1638 if ( nbRleSegments > 16 )
1640 // There should be at most 15 segments (refer to RLEFrame class)
1641 gdcmWarningMacro( "Too many segments.");
1644 uint32_t rleSegmentOffsetTable[16];
1645 for( int k = 1; k <= 15; k++ )
1647 rleSegmentOffsetTable[k] = ReadInt32();
1650 // Deduce from both RLE Header and frameLength
1651 // the fragment length, and again store this info
1652 // in a RLEFramesInfo.
1653 long rleSegmentLength[15];
1654 // skipping (not reading) RLE Segments
1655 if ( nbRleSegments > 1)
1657 for(unsigned int k = 1; k <= nbRleSegments-1; k++)
1659 rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
1660 - rleSegmentOffsetTable[k];
1661 SkipBytes(rleSegmentLength[k]);
1665 rleSegmentLength[nbRleSegments] = frameLength
1666 - rleSegmentOffsetTable[nbRleSegments];
1667 SkipBytes(rleSegmentLength[nbRleSegments]);
1669 // Store the collected info
1670 RLEFrame *newFrame = new RLEFrame;
1671 newFrame->SetNumberOfFragments(nbRleSegments);
1672 for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
1674 newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
1675 newFrame->SetLength(uk,rleSegmentLength[uk]);
1677 RLEInfo->AddFrame(newFrame);
1680 // Make sure that we encounter a 'Sequence Delimiter Item'
1681 // at the end of the item :
1682 if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File
1684 gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
1689 * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
1690 * Compute the jpeg extra information (fragment[s] offset[s] and
1691 * length) and store it[them] in \ref JPEGInfo for later pixel
1694 void File::ComputeJPEGFragmentInfo()
1696 // If you need to, look for comments of ComputeRLEInfo().
1697 std::string ts = GetTransferSyntax();
1698 if ( ! Global::GetTS()->IsJPEG(ts) )
1703 ReadEncapsulatedBasicOffsetTable();
1705 // Loop on the fragments[s] and store the parsed information in a
1707 long fragmentLength;
1710 while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1712 // Since we have read the basic offset table, let's check the value were correct
1713 // or else produce a warning:
1714 // A.4 Transfer syntaxes for encapsulation of encoded pixel data:
1715 // When the Item Value is present, the Basic Offset Table Item Value shall contain
1716 // concatenated 32-bit unsigned integer values that are byte offsets to the first
1717 // byte of the Item Tag of the first fragment for each frame in the Sequence of
1718 // Items. These offsets are measured from the first byte of the first Item Tag
1719 // following the Basic Offset Table item (See Table A.4-2).
1721 if ( BasicOffsetTableItemValue )
1723 // If a BasicOffsetTableItemValue was read
1724 uint32_t individualLength = BasicOffsetTableItemValue[i];
1725 //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ??
1726 if( individualLength != sum )
1728 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" <<
1729 individualLength << " != " << sum );
1731 sum += fragmentLength + 8;
1735 long fragmentOffset = Fp->tellg(); // Once per fragment
1736 // Store the collected info
1737 JPEGFragment *newFragment = new JPEGFragment;
1738 newFragment->SetOffset(fragmentOffset);
1739 newFragment->SetLength(fragmentLength);
1740 JPEGInfo->AddFragment(newFragment);
1742 SkipBytes(fragmentLength);
1745 // Make sure that we encounter a 'Sequence Delimiter Item'
1746 // at the end of the item :
1747 if ( !ReadTag(0xfffe, 0xe0dd) )
1749 gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
1754 * \brief Assuming the internal file pointer \ref Document::Fp
1755 * is placed at the beginning of a tag, check whether this
1756 * tag is (TestGroup, TestElem).
1757 * \warning On success the internal file pointer \ref Document::Fp
1758 * is modified to point after the tag.
1759 * On failure (i.e. when the tag wasn't the expected tag
1760 * (TestGroup, TestElem) the internal file pointer
1761 * \ref Document::Fp is restored to it's original position.
1762 * @param testGroup The expected group of the tag.
1763 * @param testElem The expected Element of the tag.
1764 * @return True on success, false otherwise.
1766 bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
1768 long positionOnEntry = Fp->tellg(); // Only when reading fragments
1769 //long currentPosition = positionOnEntry; // On debugging purposes
1771 // Read the Item Tag group and element, and make
1772 // sure they are what we expected:
1773 uint16_t itemTagGroup;
1774 uint16_t itemTagElem;
1777 itemTagGroup = ReadInt16();
1778 itemTagElem = ReadInt16();
1780 catch ( FormatError )
1782 gdcmErrorMacro( "Can not read tag for "
1783 << " We should have found tag ("
1784 << DictEntry::TranslateToKey(testGroup,testElem) << ")"
1789 if ( itemTagGroup != testGroup || itemTagElem != testElem )
1791 // in order not to pollute output we don't warn on 'delimitors'
1792 if (itemTagGroup != 0xfffe || testGroup != 0xfffe )
1793 gdcmWarningMacro( "Wrong Item Tag found:"
1794 << " We should have found tag ("
1795 << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
1796 << " but instead we encountered tag ("
1797 << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
1798 << " at address: " << " 0x(" << std::hex
1799 << (unsigned int)positionOnEntry << std::dec << ")"
1801 Fp->seekg(positionOnEntry, std::ios::beg);
1809 * \brief Assuming the internal file pointer \ref Document::Fp
1810 * is placed at the beginning of a tag (TestGroup, TestElement),
1811 * read the length associated to the Tag.
1812 * \warning On success the internal file pointer \ref Document::Fp
1813 * is modified to point after the tag and it's length.
1814 * On failure (i.e. when the tag wasn't the expected tag
1815 * (TestGroup, TestElement) the internal file pointer
1816 * \ref Document::Fp is restored to it's original position.
1817 * @param testGroup The expected Group of the tag.
1818 * @param testElem The expected Element of the tag.
1819 * @return On success returns the length associated to the tag. On failure
1822 uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
1825 if ( !ReadTag(testGroup, testElem) )
1827 // Avoid polutting output
1828 if ( testGroup != 0xfffe )
1829 gdcmErrorMacro( "ReadTag did not succeed for ("
1830 << DictEntry::TranslateToKey(testGroup,testElem)
1835 //// Then read the associated Item Length
1837 // long currentPosition = Fp->tellg(); // save time // JPRx
1838 uint32_t itemLength = ReadInt32();
1839 gdcmDebugMacro( "Basic Item Length is: " << itemLength
1840 // << " at address: " << std::hex << (unsigned int)currentPosition
1846 * \brief When parsing the Pixel Data of an encapsulated file, read
1847 * the basic offset table (when present, and BTW dump it).
1849 void File::ReadEncapsulatedBasicOffsetTable()
1851 //// Read the Basic Offset Table Item Tag length...
1852 uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
1854 // When present, read the basic offset table itself.
1855 // Notes: - since the presence of this basic offset table is optional
1856 // we can't rely on it for the implementation, and we will simply
1857 // trash it's content (when present).
1858 // - still, when present, we could add some further checks on the
1859 // lengths, but we won't bother with such fuses for the time being.
1860 if ( itemLength != 0 )
1862 char *charBasicOffsetTableItemValue = new char[itemLength];
1863 Fp->read(charBasicOffsetTableItemValue, itemLength);
1864 unsigned int nbEntries = itemLength/4;
1865 assert( nbEntries*4 == itemLength); // Make sure this is a multiple
1866 BasicOffsetTableItemValue = new uint32_t[nbEntries];
1868 for (unsigned int i=0; i < nbEntries; i++ )
1870 BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i]));
1871 #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION)
1872 uint32_t val = BasicOffsetTableItemValue[i];
1873 BasicOffsetTableItemValue[i]
1874 = ( (val<<24) | ((val<<8) & 0x00ff0000) |
1875 ( (val>>8) & 0x0000ff00) | (val>>24) );
1877 gdcmDebugMacro( "Read one length for: " <<
1878 std::hex << BasicOffsetTableItemValue[i] );
1881 delete[] charBasicOffsetTableItemValue;
1885 // These are the deprecated method that one day should be removed (after the next release)
1887 #ifndef GDCM_LEGACY_REMOVE
1889 * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API)
1890 * @ param fileName file to be open for parsing
1891 * @ return false if file cannot be open or no swap info was found,
1892 * or no tag was found.
1893 * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
1895 bool File::Load( std::string const &fileName )
1897 GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
1899 SetFileName( fileName );
1900 if ( ! this->Document::Load( ) )
1903 return DoTheLoadingJob( );
1907 //-----------------------------------------------------------------------------
1910 //-----------------------------------------------------------------------------
1911 } // end namespace gdcm