1 /*=========================================================================
4 Module: $RCSfile: gdcmFile.cxx,v $
6 Date: $Date: 2005/10/23 15:26:43 $
7 Version: $Revision: 1.289 $
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 What is it used for?
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
73 // CS 2 Patient Orientation (0020 0020)
74 // When the coordinates of the image
75 // are always present, this field is almost never used.
76 // Better we don't trust it too much ...
85 // (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ]
88 // ---------------------------------------------------------------
91 #include "gdcmGlobal.h"
93 #include "gdcmDebug.h"
95 #include "gdcmSeqEntry.h"
96 #include "gdcmRLEFramesInfo.h"
97 #include "gdcmJPEGFragmentsInfo.h"
98 #include "gdcmDataEntry.h"
101 #include <stdio.h> //sscanf
102 #include <stdlib.h> // for atoi
107 //-----------------------------------------------------------------------------
108 // Constructor / Destructor
111 * \brief Constructor used when we want to generate dicom files from scratch
116 RLEInfo = new RLEFramesInfo;
117 JPEGInfo = new JPEGFragmentsInfo;
118 GrPixel = 0x7fe0; // to avoid further troubles
120 BasicOffsetTableItemValue = 0;
125 * \brief Canonical destructor.
133 delete[] BasicOffsetTableItemValue;
136 //-----------------------------------------------------------------------------
140 * @return false if file cannot be open or no swap info was found,
141 * or no tag was found.
145 if ( ! this->Document::Load( ) )
148 return DoTheLoadingJob( );
152 * \brief Does the Loading Job (internal use only)
153 * @return false if file cannot be open or no swap info was found,
154 * or no tag was found.
156 bool File::DoTheLoadingJob( )
159 // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
160 // We may encounter the 'RETired' (0x0028, 0x0200) tag
161 // (Image Location") . This entry contains the number of
162 // the group that contains the pixel data (hence the "Pixel Data"
163 // is found by indirection through the "Image Location").
164 // Inside the group pointed by "Image Location" the searched element
165 // is conventionally the element 0x0010 (when the norm is respected).
166 // When the "Image Location" is missing we default to group 0x7fe0.
167 // Note: this IS the right place for the code
170 const std::string &imgLocation = GetEntryString(0x0028, 0x0200);
171 if ( imgLocation == GDCM_UNFOUND )
178 GrPixel = (uint16_t) atoi( imgLocation.c_str() );
181 // sometimes Image Location value doesn't follow
182 // the supposed processor endianness.
183 // see gdcmData/cr172241.dcm
184 if ( GrPixel == 0xe07f )
189 if ( GrPixel != 0x7fe0 )
191 // This is a kludge for old dirty Philips imager.
199 // Now, we know GrPixel and NumPixel.
200 // Let's create a VirtualDictEntry to allow a further VR modification
201 // and force VR to match with BitsAllocated.
202 DocEntry *entry = GetDocEntry(GrPixel, NumPixel);
205 // Compute the RLE or JPEG info
207 const std::string &ts = GetTransferSyntax();
208 Fp->seekg( entry->GetOffset(), std::ios::beg );
209 if ( Global::GetTS()->IsRLELossless(ts) )
211 else if ( Global::GetTS()->IsJPEG(ts) )
212 ComputeJPEGFragmentInfo();
215 // Create a new DataEntry to change the DictEntry
216 // The changed DictEntry will have
217 // - a correct PixelVR OB or OW)
218 // - the name to "Pixel Data"
219 DataEntry *oldEntry = dynamic_cast<DataEntry *>(entry);
223 // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
224 // more than 8 (i.e 12, 16) is a 'O Words'
225 if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
230 // Change only made if usefull
231 if ( PixelVR != oldEntry->GetVR() )
233 DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
234 PixelVR,"1","Pixel Data");
236 DataEntry *newEntry = new DataEntry(newDict);
238 newEntry->Copy(entry);
239 newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
240 oldEntry->SetSelfArea(false);
242 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 xspacing = (float)entry->GetValue(2);
474 xspacing = (float)entry->GetValue(1);
476 xspacing = (float)entry->GetValue(0);
478 if ( xspacing == 0.0 )
484 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
487 entry = GetDataEntry(0x0028,0x0030);
490 nbValue = entry->GetValueCount();
492 xspacing = (float)entry->GetValue(2);
494 xspacing = (float)entry->GetValue(1);
496 xspacing = (float)entry->GetValue(0);
498 if ( xspacing == 0.0 )
504 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
511 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
512 * then from 0028,0030 : Pixel Spacing
514 * @return Y dimension of a pixel
516 float File::GetYSpacing()
518 float yspacing = 1.0;
519 // To follow David Clunie's advice, we first check ImagerPixelSpacing
521 DataEntry *entry = GetDataEntry(0x0018,0x1164);
524 yspacing = (float)entry->GetValue(0);
526 if ( yspacing == 0.0 )
532 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
535 entry = GetDataEntry(0x0028,0x0030);
538 yspacing = (float)entry->GetValue(0);
540 if ( yspacing == 0.0 )
546 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
553 * \brief gets the info from 0018,0088 : Space Between Slices
554 * else from 0018,0050 : Slice Thickness
556 * @return Z dimension of a voxel-to be
558 float File::GetZSpacing()
563 // For *Dicom* images, ZSpacing should be calculated using
564 // XOrigin, YOrigin, ZOrigin (of the top left image corner)
565 // of 2 consecutive images, and the Orientation
567 // Computing ZSpacing on a single image is not really meaningfull !
569 float zspacing = 1.0f;
571 // Spacing Between Slices : distance between the middle of 2 slices
573 // jointives (Spacing between Slices = Slice Thickness)
574 // overlapping (Spacing between Slices < Slice Thickness)
575 // disjointes (Spacing between Slices > Slice Thickness)
576 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
577 // It only concerns the MRI guys, not people wanting to visualize volumes
578 // If Spacing Between Slices is missing,
579 // we suppose slices joint together
580 DataEntry *entry = GetDataEntry(0x0018,0x0088);
583 zspacing = (float)entry->GetValue(0);
585 if ( zspacing == 0.0 )
590 gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
592 // if no 'Spacing Between Slices' is found,
593 // we assume slices join together
594 // (no overlapping, no interslice gap)
595 // if they don't, we're fucked up
596 entry = GetDataEntry(0x0018,0x0050);
599 zspacing = (float)entry->GetValue(0);
601 if ( zspacing == 0.0 )
606 gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
612 * \brief gets the info from 0020,0032 : Image Position Patient
613 * else from 0020,0030 : Image Position (RET)
615 * @return up-left image corner X position
617 float File::GetXOrigin()
619 DataEntry *entry = GetDataEntry(0x0020,0x0032);
622 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
623 entry = GetDataEntry(0x0020,0x0030);
626 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
631 if( entry->GetValueCount() == 3 )
633 gdcmAssertMacro( entry->IsValueCountValid() );
634 return (float)entry->GetValue(0);
640 * \brief gets the info from 0020,0032 : Image Position Patient
641 * else from 0020,0030 : Image Position (RET)
643 * @return up-left image corner Y position
645 float File::GetYOrigin()
647 DataEntry *entry = GetDataEntry(0x0020,0x0032);
650 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
651 entry = GetDataEntry(0x0020,0x0030);
654 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
659 if( entry->GetValueCount() == 3 )
661 gdcmAssertMacro( entry->IsValueCountValid() );
662 return (float)entry->GetValue(1);
668 * \brief gets the info from 0020,0032 : Image Position Patient
669 * else from 0020,0030 : Image Position (RET)
670 * else from 0020,1041 : Slice Location
671 * else from 0020,0050 : Location
673 * @return up-left image corner Z position
675 float File::GetZOrigin()
677 DataEntry *entry = GetDataEntry(0x0020,0x0032);
680 if( entry->GetValueCount() == 3 )
682 gdcmAssertMacro( entry->IsValueCountValid() );
683 return (float)entry->GetValue(2);
685 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
689 entry = GetDataEntry(0x0020,0x0030);
692 if( entry->GetValueCount() == 3 )
694 gdcmAssertMacro( entry->IsValueCountValid() );
695 return (float)entry->GetValue(2);
697 gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
701 // for *very* old ACR-NEMA images
702 entry = GetDataEntry(0x0020,0x1041);
705 if( entry->GetValueCount() == 1 )
707 gdcmAssertMacro( entry->IsValueCountValid() );
708 return (float)entry->GetValue(0); // VM=1 !
710 gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
714 entry = GetDataEntry(0x0020,0x0050);
717 if( entry->GetValueCount() == 1 )
719 gdcmAssertMacro( entry->IsValueCountValid() );
720 return (float)entry->GetValue(0);
722 gdcmWarningMacro( "Wrong Location (0020,0050)");
725 return 0.; // Hopeless
729 * \brief gets the info from 0020,0037 : Image Orientation Patient
730 * or from 0020 0035 : Image Orientation (RET)
731 * (needed to organize DICOM files based on their x,y,z position)
732 * @param iop adress of the (6)float array to receive values
733 * @return true when one of the tag is found
734 * false when nothing is found
736 bool File::GetImageOrientationPatient( float iop[6] )
738 std::string strImOriPat;
739 //iop is supposed to be float[6]
740 iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
742 // 0020 0037 DS REL Image Orientation (Patient)
743 if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
745 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
746 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
748 gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
749 << " Less than 6 values were found." );
754 // 0020 0035 DS REL Image Orientation (RET)
755 else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND )
757 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
758 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
760 gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
761 << "Less than 6 values were found." );
769 * \brief Retrieve the number of Bits Stored (actually used)
770 * (as opposed to number of Bits Allocated)
771 * @return The encountered number of Bits Stored, 0 by default.
772 * 0 means the file is NOT USABLE. The caller has to check it !
774 int File::GetBitsStored()
776 DataEntry *entry = GetDataEntry(0x0028,0x0101);
779 gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
782 return (int)entry->GetValue(0);
786 * \brief Retrieve the number of Bits Allocated
787 * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,)
788 * @return The encountered Number of Bits Allocated, 0 by default.
789 * 0 means the file is NOT USABLE. The caller has to check it !
791 int File::GetBitsAllocated()
793 DataEntry *entry = GetDataEntry(0x0028,0x0100);
796 gdcmWarningMacro("(0028,0100) is supposed to be mandatory");
799 return (int)entry->GetValue(0);
803 * \brief Retrieve the high bit position.
804 * \warning The method defaults to 0 when information is missing.
805 * The responsability of checking this value is left to the caller.
806 * @return The high bit position when present. 0 when missing.
808 int File::GetHighBitPosition()
810 DataEntry *entry = GetDataEntry(0x0028,0x0102);
813 gdcmWarningMacro("(0028,0102) is supposed to be mandatory");
816 return (int)entry->GetValue(0);
820 * \brief Retrieve the number of Samples Per Pixel
821 * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
822 * @return The encountered number of Samples Per Pixel, 1 by default.
823 * (we assume Gray level Pixels)
825 int File::GetSamplesPerPixel()
827 DataEntry *entry = GetDataEntry(0x0028,0x0002);
830 gdcmWarningMacro("(0028,0002) is supposed to be mandatory");
831 return 1; // Well, it's supposed to be mandatory ...
832 // but sometimes it's missing : *we* assume Gray pixels
834 return (int)entry->GetValue(0);
838 * \brief Retrieve the Planar Configuration for RGB images
839 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
840 * @return The encountered Planar Configuration, 0 by default.
842 int File::GetPlanarConfiguration()
844 DataEntry *entry = GetDataEntry(0x0028,0x0006);
847 gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
850 return (int)entry->GetValue(0);
854 * \brief Return the size (in bytes) of a single pixel of data.
855 * @return The size in bytes of a single pixel of data; 0 by default
856 * 0 means the file is NOT USABLE; the caller will have to check
858 int File::GetPixelSize()
860 // 0028 0100 US IMG Bits Allocated
861 // (in order no to be messed up by old ACR-NEMA RGB images)
862 assert( !(GetEntryString(0x0028,0x0100) == "24") );
864 std::string pixelType = GetPixelType();
865 if ( pixelType == "8U" || pixelType == "8S" )
869 if ( pixelType == "16U" || pixelType == "16S")
873 if ( pixelType == "32U" || pixelType == "32S")
877 if ( pixelType == "FD" )
881 gdcmWarningMacro( "Unknown pixel type: " << pixelType);
886 * \brief Build the Pixel Type of the image.
887 * Possible values are:
888 * - 8U unsigned 8 bit,
890 * - 16U unsigned 16 bit,
891 * - 16S signed 16 bit,
892 * - 32U unsigned 32 bit,
893 * - 32S signed 32 bit,
894 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
895 * \warning 12 bit images appear as 16 bit.
896 * 24 bit images appear as 8 bit + photochromatic interp ="RGB "
897 * + Planar Configuration = 0
898 * @return 0S if nothing found. NOT USABLE file. The caller has to check
900 std::string File::GetPixelType()
902 std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
903 if ( bitsAlloc == GDCM_UNFOUND )
905 gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
906 bitsAlloc = "16"; // default and arbitrary value, not to polute the output
909 if ( bitsAlloc == "64" )
913 else if ( bitsAlloc == "12" )
915 // It will be unpacked
918 else if ( bitsAlloc == "24" )
920 // (in order no to be messed up by old RGB images)
925 if( IsSignedPixelData() )
933 return bitsAlloc + sign;
937 * \brief Check whether the pixels are signed (1) or UNsigned (0) data.
938 * \warning The method defaults to false (UNsigned) when tag 0028|0103
940 * The responsability of checking this value is left to the caller
941 * (NO transformation is performed on the pixels to make then >0)
942 * @return True when signed, false when UNsigned
944 bool File::IsSignedPixelData()
946 DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
949 gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
952 return entry->GetValue(0) != 0;
956 * \brief Check whether this a monochrome picture (gray levels) or not,
957 * using "Photometric Interpretation" tag (0x0028,0x0004).
958 * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
960 bool File::IsMonochrome()
962 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
963 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
964 || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
968 if ( PhotometricInterp == GDCM_UNFOUND )
970 gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
976 * \brief Check whether this a MONOCHROME1 picture (high values = dark)
977 * or not using "Photometric Interpretation" tag (0x0028,0x0004).
978 * @return true when "MONOCHROME1" . False otherwise.
980 bool File::IsMonochrome1()
982 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
983 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
987 if ( PhotometricInterp == GDCM_UNFOUND )
989 gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
995 * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
996 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
997 * @return true when "PALETTE COLOR". False otherwise.
999 bool File::IsPaletteColor()
1001 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1002 if ( PhotometricInterp == "PALETTE COLOR " )
1006 if ( PhotometricInterp == GDCM_UNFOUND )
1008 gdcmWarningMacro( "Not found : Palette color (0028,0004)");
1014 * \brief Check whether this a "YBR_FULL" color picture or not by accessing
1015 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1016 * @return true when "YBR_FULL". False otherwise.
1018 bool File::IsYBRFull()
1020 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1021 if ( PhotometricInterp == "YBR_FULL" )
1025 if ( PhotometricInterp == GDCM_UNFOUND )
1027 gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
1033 * \brief tells us if LUT are used
1034 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
1035 * are NOT considered as LUT, since nobody knows
1036 * how to deal with them
1037 * Please warn me if you know sbdy that *does* know ... jprx
1038 * @return true if LUT Descriptors and LUT Tables were found
1042 // Check the presence of the LUT Descriptors, and LUT Tables
1044 if ( !GetDocEntry(0x0028,0x1101) )
1048 // LutDescriptorGreen
1049 if ( !GetDocEntry(0x0028,0x1102) )
1053 // LutDescriptorBlue
1054 if ( !GetDocEntry(0x0028,0x1103) )
1058 // Red Palette Color Lookup Table Data
1059 if ( !GetDocEntry(0x0028,0x1201) )
1063 // Green Palette Color Lookup Table Data
1064 if ( !GetDocEntry(0x0028,0x1202) )
1068 // Blue Palette Color Lookup Table Data
1069 if ( !GetDocEntry(0x0028,0x1203) )
1074 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
1075 // NOT taken into account, but we don't know how to use it ...
1080 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
1082 * @return Lookup Table number of Bits , 0 by default
1083 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
1084 * @ return bit number of each LUT item
1086 int File::GetLUTNbits()
1088 std::vector<std::string> tokens;
1091 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
1092 // = Lookup Table Desc-Blue
1093 // Consistency already checked in GetLUTLength
1094 std::string lutDescription = GetEntryString(0x0028,0x1101);
1095 if ( lutDescription == GDCM_UNFOUND )
1100 tokens.clear(); // clean any previous value
1101 Util::Tokenize ( lutDescription, tokens, "\\" );
1102 //LutLength=atoi(tokens[0].c_str());
1103 //LutDepth=atoi(tokens[1].c_str());
1105 lutNbits = atoi( tokens[2].c_str() );
1112 *\brief gets the info from 0028,1052 : Rescale Intercept
1113 * @return Rescale Intercept
1115 float File::GetRescaleIntercept()
1117 // 0028 1052 DS IMG Rescale Intercept
1118 DataEntry *entry = GetDataEntry(0x0028, 0x1052);
1121 gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
1124 return (float)entry->GetValue(0);
1129 *\brief gets the info from 0028,1053 : Rescale Slope
1130 * @return Rescale Slope
1132 float File::GetRescaleSlope()
1134 // 0028 1053 DS IMG Rescale Slope
1135 DataEntry *entry = GetDataEntry(0x0028, 0x1053);
1138 gdcmWarningMacro( "Missing Rescale Slope (0028,1053)");
1141 return (float)entry->GetValue(0);
1145 * \brief This function is intended to user who doesn't want
1146 * to have to manage a LUT and expects to get an RBG Pixel image
1147 * (or a monochrome one ...)
1148 * \warning to be used with GetImagePixels()
1149 * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
1151 int File::GetNumberOfScalarComponents()
1153 if ( GetSamplesPerPixel() == 3 )
1158 // 0028 0100 US IMG Bits Allocated
1159 // (in order no to be messed up by old RGB images)
1160 if ( GetEntryString(0x0028,0x0100) == "24" )
1165 std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
1167 if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
1169 if ( HasLUT() )// PALETTE COLOR is NOT enough
1179 // beware of trailing space at end of string
1180 // DICOM tags are never of odd length
1181 if ( strPhotometricInterpretation == GDCM_UNFOUND ||
1182 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
1183 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
1189 // we assume that *all* kinds of YBR are dealt with
1195 * \brief This function is intended to user that DOESN'T want
1196 * to get RGB pixels image when it's stored as a PALETTE COLOR image
1197 * - the (vtk) user is supposed to know how deal with LUTs -
1198 * \warning to be used with GetImagePixelsRaw()
1199 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
1201 int File::GetNumberOfScalarComponentsRaw()
1203 // 0028 0100 US IMG Bits Allocated
1204 // (in order no to be messed up by old RGB images)
1205 if ( File::GetEntryString(0x0028,0x0100) == "24" )
1210 // we assume that *all* kinds of YBR are dealt with
1211 return GetSamplesPerPixel();
1215 * \brief Recover the offset (from the beginning of the file)
1216 * of *image* pixels (not *icone image* pixels, if any !)
1217 * @return Pixel Offset
1219 size_t File::GetPixelOffset()
1221 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1224 return pxlElement->GetOffset();
1228 gdcmDebugMacro( "Big trouble : Pixel Element ("
1229 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1235 * \brief Recover the pixel area length (in Bytes)
1236 * @return Pixel Element Length, as stored in the header
1237 * (NOT the memory space necessary to hold the Pixels
1238 * -in case of embeded compressed image-)
1239 * 0 : NOT USABLE file. The caller has to check.
1241 size_t File::GetPixelAreaLength()
1243 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1246 return pxlElement->GetLength();
1250 gdcmDebugMacro( "Big trouble : Pixel Element ("
1251 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1257 * \brief Adds the characteristics of a new element we want to anonymize
1258 * @param group Group number of the target tag.
1259 * @param elem Element number of the target tag.
1260 * @param value new value (string) to substitute with
1262 void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
1263 std::string const &value)
1269 UserAnonymizeList.push_back(el);
1273 * \brief Overwrites in the file the values of the DicomElements
1276 void File::AnonymizeNoLoad()
1278 std::fstream *fp = new std::fstream(Filename.c_str(),
1279 std::ios::in | std::ios::out | std::ios::binary);
1283 uint32_t valLgth = 0;
1284 std::string *spaces;
1285 for (ListElements::iterator it = UserAnonymizeList.begin();
1286 it != UserAnonymizeList.end();
1289 d = GetDocEntry( (*it).Group, (*it).Elem);
1294 if ( dynamic_cast<SeqEntry *>(d) )
1296 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1300 offset = d->GetOffset();
1301 lgth = d->GetLength();
1304 spaces = new std::string( lgth-valLgth, ' ');
1305 (*it).Value = (*it).Value + *spaces;
1308 fp->seekp( offset, std::ios::beg );
1309 fp->write( (*it).Value.c_str(), lgth );
1317 * \brief anonymize a File (remove Patient's personal info passed with
1318 * AddAnonymizeElement()
1319 * \note You cannot Anonymize a DataEntry (to be fixed)
1321 bool File::AnonymizeFile()
1323 // If Anonymisation list is empty, let's perform some basic anonymization
1324 if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
1326 // If exist, replace by spaces
1327 SetEntryString(" ",0x0010, 0x2154); // Telephone
1328 SetEntryString(" ",0x0010, 0x1040); // Adress
1329 SetEntryString(" ",0x0010, 0x0020); // Patient ID
1331 DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
1333 if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
1335 std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
1336 if ( studyInstanceUID != GDCM_UNFOUND )
1338 SetEntryString(studyInstanceUID, 0x0010, 0x0010);
1342 SetEntryString("anonymized", 0x0010, 0x0010);
1349 for (ListElements::iterator it = UserAnonymizeList.begin();
1350 it != UserAnonymizeList.end();
1353 d = GetDocEntry( (*it).Group, (*it).Elem);
1358 if ( dynamic_cast<SeqEntry *>(d) )
1360 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1364 if ( dynamic_cast<DataEntry *>(d) )
1366 gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
1370 SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
1374 // In order to make definitively impossible any further identification
1375 // remove or replace all the stuff that contains a Date
1377 //0008 0012 DA ID Instance Creation Date
1378 //0008 0020 DA ID Study Date
1379 //0008 0021 DA ID Series Date
1380 //0008 0022 DA ID Acquisition Date
1381 //0008 0023 DA ID Content Date
1382 //0008 0024 DA ID Overlay Date
1383 //0008 0025 DA ID Curve Date
1384 //0008 002a DT ID Acquisition Datetime
1385 //0018 9074 DT ACQ Frame Acquisition Datetime
1386 //0018 9151 DT ACQ Frame Reference Datetime
1387 //0018 a002 DT ACQ Contribution Date Time
1388 //0020 3403 SH REL Modified Image Date (RET)
1389 //0032 0032 DA SDY Study Verified Date
1390 //0032 0034 DA SDY Study Read Date
1391 //0032 1000 DA SDY Scheduled Study Start Date
1392 //0032 1010 DA SDY Scheduled Study Stop Date
1393 //0032 1040 DA SDY Study Arrival Date
1394 //0032 1050 DA SDY Study Completion Date
1395 //0038 001a DA VIS Scheduled Admission Date
1396 //0038 001c DA VIS Scheduled Discharge Date
1397 //0038 0020 DA VIS Admitting Date
1398 //0038 0030 DA VIS Discharge Date
1399 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1400 //0040 0004 DA PRC Scheduled Procedure Step End Date
1401 //0040 0244 DA PRC Performed Procedure Step Start Date
1402 //0040 0250 DA PRC Performed Procedure Step End Date
1403 //0040 2004 DA PRC Issue Date of Imaging Service Request
1404 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1405 //0040 4011 DT PRC Expected Completion Date and Time
1406 //0040 a030 DT PRC Verification Date Time
1407 //0040 a032 DT PRC Observation Date Time
1408 //0040 a120 DT PRC DateTime
1409 //0040 a121 DA PRC Date
1410 //0040 a13a DT PRC Referenced Datetime
1411 //0070 0082 DA ??? Presentation Creation Date
1412 //0100 0420 DT ??? SOP Autorization Date and Time
1413 //0400 0105 DT ??? Digital Signature DateTime
1414 //2100 0040 DA PJ Creation Date
1415 //3006 0008 DA SSET Structure Set Date
1416 //3008 0024 DA ??? Treatment Control Point Date
1417 //3008 0054 DA ??? First Treatment Date
1418 //3008 0056 DA ??? Most Recent Treatment Date
1419 //3008 0162 DA ??? Safe Position Exit Date
1420 //3008 0166 DA ??? Safe Position Return Date
1421 //3008 0250 DA ??? Treatment Date
1422 //300a 0006 DA RT RT Plan Date
1423 //300a 022c DA RT Air Kerma Rate Reference Date
1424 //300e 0004 DA RT Review Date
1430 * \brief Performs some consistency checking on various 'File related'
1431 * (as opposed to 'DicomDir related') entries
1432 * then writes in a file all the (Dicom Elements) included the Pixels
1433 * @param fileName file name to write to
1434 * @param writetype type of the file to be written
1435 * (ACR, ExplicitVR, ImplicitVR)
1437 bool File::Write(std::string fileName, FileType writetype)
1439 std::ofstream *fp = new std::ofstream(fileName.c_str(),
1440 std::ios::out | std::ios::binary);
1443 gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
1447 // Entry : 0002|0000 = group length -> recalculated
1448 DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
1451 std::ostringstream sLen;
1452 sLen << ComputeGroup0002Length( );
1453 e0000->SetString(sLen.str());
1456 // Derma?.dcm does not have it...let's remove it FIXME FIXME
1457 if( writetype != JPEG )
1459 int i_lgPix = GetEntryLength(GrPixel, NumPixel);
1462 // no (GrPixel, NumPixel) element
1463 std::string s_lgPix = Util::Format("%d", i_lgPix+12);
1464 s_lgPix = Util::DicomString( s_lgPix.c_str() );
1465 InsertEntryString(s_lgPix,GrPixel, 0x0000);
1469 Document::WriteContent(fp, writetype);
1477 //-----------------------------------------------------------------------------
1481 //-----------------------------------------------------------------------------
1484 * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
1485 * Compute the RLE extra information and store it in \ref RLEInfo
1486 * for later pixel retrieval usage.
1488 void File::ComputeRLEInfo()
1490 std::string ts = GetTransferSyntax();
1491 if ( !Global::GetTS()->IsRLELossless(ts) )
1496 // Encoded pixel data: for the time being we are only concerned with
1497 // Jpeg or RLE Pixel data encodings.
1498 // As stated in PS 3.5-2003, section 8.2 p44:
1499 // "If sent in Encapsulated Format (i.e. other than the Native Format) the
1500 // value representation OB is used".
1501 // Hence we expect an OB value representation. Concerning OB VR,
1502 // the section PS 3.5-2003, section A.4.c p 58-59, states:
1503 // "For the Value Representations OB and OW, the encoding shall meet the
1504 // following specifications depending on the Data element tag:"
1506 // - the first item in the sequence of items before the encoded pixel
1507 // data stream shall be basic offset table item. The basic offset table
1508 // item value, however, is not required to be present"
1509 ReadEncapsulatedBasicOffsetTable();
1511 // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
1512 // Loop on the individual frame[s] and store the information
1513 // on the RLE fragments in a RLEFramesInfo.
1514 // Note: - when only a single frame is present, this is a
1516 // - when more than one frame are present, then we are in
1517 // the case of a multi-frame image.
1521 while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1523 // Since we have read the basic offset table, let's check the value were correct
1524 // or else produce a warning:
1525 if ( BasicOffsetTableItemValue )
1527 // If a BasicOffsetTableItemValue was read
1528 uint32_t individualLength = BasicOffsetTableItemValue[i];
1529 assert( individualLength == sum ); // REMOVE that if this is a problem
1530 if( individualLength != sum )
1532 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" );
1534 sum += frameLength + 8;
1537 // Parse the RLE Header and store the corresponding RLE Segment
1538 // Offset Table information on fragments of this current Frame.
1539 // Note that the fragment pixels themselves are not loaded
1540 // (but just skipped).
1541 long frameOffset = Fp->tellg();
1543 uint32_t nbRleSegments = ReadInt32();
1544 if ( nbRleSegments > 16 )
1546 // There should be at most 15 segments (refer to RLEFrame class)
1547 gdcmWarningMacro( "Too many segments.");
1550 uint32_t rleSegmentOffsetTable[16];
1551 for( int k = 1; k <= 15; k++ )
1553 rleSegmentOffsetTable[k] = ReadInt32();
1556 // Deduce from both RLE Header and frameLength
1557 // the fragment length, and again store this info
1558 // in a RLEFramesInfo.
1559 long rleSegmentLength[15];
1560 // skipping (not reading) RLE Segments
1561 if ( nbRleSegments > 1)
1563 for(unsigned int k = 1; k <= nbRleSegments-1; k++)
1565 rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
1566 - rleSegmentOffsetTable[k];
1567 SkipBytes(rleSegmentLength[k]);
1571 rleSegmentLength[nbRleSegments] = frameLength
1572 - rleSegmentOffsetTable[nbRleSegments];
1573 SkipBytes(rleSegmentLength[nbRleSegments]);
1575 // Store the collected info
1576 RLEFrame *newFrame = new RLEFrame;
1577 newFrame->SetNumberOfFragments(nbRleSegments);
1578 for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
1580 newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
1581 newFrame->SetLength(uk,rleSegmentLength[uk]);
1583 RLEInfo->AddFrame(newFrame);
1586 // Make sure that we encounter a 'Sequence Delimiter Item'
1587 // at the end of the item :
1588 if ( !ReadTag(0xfffe, 0xe0dd) )
1590 gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
1595 * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
1596 * Compute the jpeg extra information (fragment[s] offset[s] and
1597 * length) and store it[them] in \ref JPEGInfo for later pixel
1600 void File::ComputeJPEGFragmentInfo()
1602 // If you need to, look for comments of ComputeRLEInfo().
1603 std::string ts = GetTransferSyntax();
1604 if ( ! Global::GetTS()->IsJPEG(ts) )
1609 ReadEncapsulatedBasicOffsetTable();
1611 // Loop on the fragments[s] and store the parsed information in a
1613 long fragmentLength;
1616 while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1618 // Since we have read the basic offset table, let's check the value were correct
1619 // or else produce a warning:
1620 // A.4 Transfer syntaxes for encapsulation of encoded pixel data:
1621 // When the Item Value is present, the Basic Offset Table Item Value shall contain
1622 // concatenated 32-bit unsigned integer values that are byte offsets to the first
1623 // byte of the Item Tag of the first fragment for each frame in the Sequence of
1624 // Items. These offsets are measured from the first byte of the first Item Tag
1625 // following the Basic Offset Table item (See Table A.4-2).
1627 if ( BasicOffsetTableItemValue )
1629 // If a BasicOffsetTableItemValue was read
1630 uint32_t individualLength = BasicOffsetTableItemValue[i];
1631 //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ??
1632 if( individualLength != sum )
1634 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" <<
1635 individualLength << " != " << sum );
1637 sum += fragmentLength + 8;
1641 long fragmentOffset = Fp->tellg();
1642 // Store the collected info
1643 JPEGFragment *newFragment = new JPEGFragment;
1644 newFragment->SetOffset(fragmentOffset);
1645 newFragment->SetLength(fragmentLength);
1646 JPEGInfo->AddFragment(newFragment);
1648 SkipBytes(fragmentLength);
1651 // Make sure that we encounter a 'Sequence Delimiter Item'
1652 // at the end of the item :
1653 if ( !ReadTag(0xfffe, 0xe0dd) )
1655 gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
1660 * \brief Assuming the internal file pointer \ref Document::Fp
1661 * is placed at the beginning of a tag check whether this
1662 * tag is (TestGroup, TestElem).
1663 * \warning On success the internal file pointer \ref Document::Fp
1664 * is modified to point after the tag.
1665 * On failure (i.e. when the tag wasn't the expected tag
1666 * (TestGroup, TestElem) the internal file pointer
1667 * \ref Document::Fp is restored to it's original position.
1668 * @param testGroup The expected group of the tag.
1669 * @param testElem The expected Element of the tag.
1670 * @return True on success, false otherwise.
1672 bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
1674 long positionOnEntry = Fp->tellg();
1675 long currentPosition = Fp->tellg(); // On debugging purposes
1677 // Read the Item Tag group and element, and make
1678 // sure they are what we expected:
1679 uint16_t itemTagGroup;
1680 uint16_t itemTagElem;
1683 itemTagGroup = ReadInt16();
1684 itemTagElem = ReadInt16();
1686 catch ( FormatError )
1688 gdcmErrorMacro( "Can not read tag for "
1689 << " We should have found tag ("
1690 << DictEntry::TranslateToKey(testGroup,testElem) << ")"
1695 if ( itemTagGroup != testGroup || itemTagElem != testElem )
1697 gdcmErrorMacro( "Wrong Item Tag found:"
1698 << " We should have found tag ("
1699 << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
1700 << " but instead we encountered tag ("
1701 << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
1702 << " at address: " << " 0x(" << std::hex
1703 << (unsigned int)currentPosition << std::dec << ")"
1705 Fp->seekg(positionOnEntry, std::ios::beg);
1713 * \brief Assuming the internal file pointer \ref Document::Fp
1714 * is placed at the beginning of a tag (TestGroup, TestElement),
1715 * read the length associated to the Tag.
1716 * \warning On success the internal file pointer \ref Document::Fp
1717 * is modified to point after the tag and it's length.
1718 * On failure (i.e. when the tag wasn't the expected tag
1719 * (TestGroup, TestElement) the internal file pointer
1720 * \ref Document::Fp is restored to it's original position.
1721 * @param testGroup The expected Group of the tag.
1722 * @param testElem The expected Element of the tag.
1723 * @return On success returns the length associated to the tag. On failure
1726 uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
1729 if ( !ReadTag(testGroup, testElem) )
1731 gdcmErrorMacro( "ReadTag did not succeed for ("
1732 << DictEntry::TranslateToKey(testGroup,testElem)
1737 //// Then read the associated Item Length
1738 long currentPosition = Fp->tellg();
1739 uint32_t itemLength = ReadInt32();
1740 gdcmDebugMacro( "Basic Item Length is: " << itemLength
1741 << " at address: " << std::hex << (unsigned int)currentPosition);
1746 * \brief When parsing the Pixel Data of an encapsulated file, read
1747 * the basic offset table (when present, and BTW dump it).
1749 void File::ReadEncapsulatedBasicOffsetTable()
1751 //// Read the Basic Offset Table Item Tag length...
1752 uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
1754 // When present, read the basic offset table itself.
1755 // Notes: - since the presence of this basic offset table is optional
1756 // we can't rely on it for the implementation, and we will simply
1757 // trash it's content (when present).
1758 // - still, when present, we could add some further checks on the
1759 // lengths, but we won't bother with such fuses for the time being.
1760 if ( itemLength != 0 )
1762 char *charBasicOffsetTableItemValue = new char[itemLength];
1763 Fp->read(charBasicOffsetTableItemValue, itemLength);
1764 unsigned int nbEntries = itemLength/4;
1765 assert( nbEntries*4 == itemLength); // Make sure this is a multiple
1766 BasicOffsetTableItemValue = new uint32_t[nbEntries];
1768 for (unsigned int i=0; i < nbEntries; i++ )
1770 BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i]));
1771 #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION)
1772 uint32_t val = BasicOffsetTableItemValue[i];
1773 BasicOffsetTableItemValue[i]
1774 = ( (val<<24) | ((val<<8) & 0x00ff0000) |
1775 ((val>>8) & 0x0000ff00) | (val>>24) );
1777 gdcmWarningMacro( "Read one length for: " <<
1778 std::hex << BasicOffsetTableItemValue[i] );
1781 delete[] charBasicOffsetTableItemValue;
1785 // These are the deprecated method that one day should be removed (after the next release)
1787 #ifndef GDCM_LEGACY_REMOVE
1789 * brief Constructor (DEPRECATED : temporaryly kept not to break the API)
1790 * param filename name of the file whose header we want to analyze
1791 * deprecated do not use any longer
1793 File::File( std::string const &filename )
1796 RLEInfo = new RLEFramesInfo;
1797 JPEGInfo = new JPEGFragmentsInfo;
1799 SetFileName( filename );
1800 Load( ); // gdcm::Document is first Loaded, then the 'File part'
1804 * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API)
1805 * @ param fileName file to be open for parsing
1806 * @ return false if file cannot be open or no swap info was found,
1807 * or no tag was found.
1808 * @ deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
1810 bool File::Load( std::string const &fileName )
1812 GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
1814 SetFileName( fileName );
1815 if ( ! this->Document::Load( ) )
1818 return DoTheLoadingJob( );
1822 //-----------------------------------------------------------------------------
1825 //-----------------------------------------------------------------------------
1826 } // end namespace gdcm