1 /*=========================================================================
4 Module: $RCSfile: gdcmFile.cxx,v $
6 Date: $Date: 2005/10/21 12:12:18 $
7 Version: $Revision: 1.285 $
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();
471 xspacing = (float)entry->GetValue(2);
473 xspacing = (float)entry->GetValue(1);
475 xspacing = (float)entry->GetValue(0);
477 if ( xspacing == 0.0 )
483 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
486 /* const std::string &strImagerPixelSpacing = GetEntryString(0x0018,0x1164);
487 if ( strImagerPixelSpacing != GDCM_UNFOUND )
489 if ( ( nbValues = sscanf( strImagerPixelSpacing.c_str(),
490 "%f\\%f", &yspacing, &xspacing)) != 2 )
492 // if no values, xspacing is set to 1.0
495 // if single value is found, xspacing is defaulted to yspacing
499 if ( xspacing == 0.0 )
505 entry = GetDataEntry(0x0028,0x0030);
508 nbValue = entry->GetValueCount();
510 xspacing = (float)entry->GetValue(2);
512 xspacing = (float)entry->GetValue(1);
514 xspacing = (float)entry->GetValue(0);
516 if ( xspacing == 0.0 )
522 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
525 /* const std::string &strSpacing = GetEntryString(0x0028,0x0030);
526 if ( strSpacing == GDCM_UNFOUND )
528 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
532 if ( ( nbValues = sscanf( strSpacing.c_str(),
533 "%f \\%f ", &yspacing, &xspacing)) != 2 )
535 // if no values, xspacing is set to 1.0
538 // if single value is found, xspacing is defaulted to yspacing
542 if ( xspacing == 0.0 )
548 // to avoid troubles with David Clunie's-like images (at least one)
549 /* if ( xspacing == 0.0 && yspacing == 0.0)
552 if ( xspacing == 0.0)
554 gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm-like problem");
555 // seems to be a bug in the header ...
556 nbValues = sscanf( strSpacing.c_str(), "%f \\0\\%f ", &yspacing, &xspacing);
557 gdcmAssertMacro( nbValues == 2 );
564 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
565 * then from 0028,0030 : Pixel Spacing
567 * @return Y dimension of a pixel
569 float File::GetYSpacing()
571 float yspacing = 1.0;
572 // To follow David Clunie's advice, we first check ImagerPixelSpacing
574 DataEntry *entry = GetDataEntry(0x0018,0x1164);
577 yspacing = (float)entry->GetValue(0);
579 if ( yspacing == 0.0 )
585 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
587 /* const std::string &strImagerPixelSpacing = GetEntryString(0x0018,0x1164);
588 if ( strImagerPixelSpacing != GDCM_UNFOUND )
590 nbValues = sscanf( strImagerPixelSpacing.c_str(), "%f", &yspacing);
592 // if sscanf cannot read any float value, it won't affect yspacing
596 if ( yspacing == 0.0 )
602 entry = GetDataEntry(0x0028,0x0030);
605 yspacing = (float)entry->GetValue(0);
607 if ( yspacing == 0.0 )
613 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
615 /* std::string strSpacing = GetEntryString(0x0028,0x0030);
616 if ( strSpacing == GDCM_UNFOUND )
618 gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
622 // if sscanf cannot read any float value, it won't affect yspacing
623 nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing);
625 // if no values, yspacing is set to 1.0
629 if ( yspacing == 0.0 )
636 * \brief gets the info from 0018,0088 : Space Between Slices
637 * else from 0018,0050 : Slice Thickness
639 * @return Z dimension of a voxel-to be
641 float File::GetZSpacing()
646 // For *Dicom* images, ZSpacing should be calculated using
647 // XOrigin, YOrigin, ZOrigin (of the top left image corner)
648 // of 2 consecutive images, and the Orientation
650 // Computing ZSpacing on a single image is not really meaningfull !
652 float zspacing = 1.0f;
654 // Spacing Between Slices : distance between the middle of 2 slices
656 // jointives (Spacing between Slices = Slice Thickness)
657 // overlapping (Spacing between Slices < Slice Thickness)
658 // disjointes (Spacing between Slices > Slice Thickness)
659 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
660 // It only concerns the MRI guys, not people wanting to visualize volumes
661 // If Spacing Between Slices is missing,
662 // we suppose slices joint together
663 DataEntry *entry = GetDataEntry(0x0018,0x0088);
666 zspacing = (float)entry->GetValue(0);
668 if ( zspacing == 0.0 )
673 gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
675 // if no 'Spacing Between Slices' is found,
676 // we assume slices join together
677 // (no overlapping, no interslice gap)
678 // if they don't, we're fucked up
679 entry = GetDataEntry(0x0018,0x0050);
682 zspacing = (float)entry->GetValue(0);
684 if ( zspacing == 0.0 )
689 gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
693 /* const std::string &strSpacingBSlices = GetEntryString(0x0018,0x0088);
694 if ( strSpacingBSlices == GDCM_UNFOUND )
696 gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
697 const std::string &strSliceThickness = GetEntryString(0x0018,0x0050);
698 if ( strSliceThickness == GDCM_UNFOUND )
700 gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
705 // if no 'Spacing Between Slices' is found,
706 // we assume slices join together
707 // (no overlapping, no interslice gap)
708 // if they don't, we're fucked up
709 return (float)atof( strSliceThickness.c_str() );
713 float zsp = (float)atof( strSpacingBSlices.c_str());
714 if (zsp == 0.0) // last change not to break further computations ...
720 * \brief gets the info from 0020,0032 : Image Position Patient
721 * else from 0020,0030 : Image Position (RET)
723 * @return up-left image corner X position
725 float File::GetXOrigin()
727 DataEntry *entry = GetDataEntry(0x0020,0x0032);
730 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
731 entry = GetDataEntry(0x0020,0x0030);
734 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
739 if( entry->GetValueCount() == 3 )
740 return (float)entry->GetValue(0);
743 /* std::string strImPos = GetEntryString(0x0020,0x0032);
744 if ( strImPos == GDCM_UNFOUND )
746 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
747 strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
748 if ( strImPos == GDCM_UNFOUND )
750 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
755 if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
764 * \brief gets the info from 0020,0032 : Image Position Patient
765 * else from 0020,0030 : Image Position (RET)
767 * @return up-left image corner Y position
769 float File::GetYOrigin()
771 DataEntry *entry = GetDataEntry(0x0020,0x0032);
774 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
775 entry = GetDataEntry(0x0020,0x0030);
778 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
783 if( entry->GetValueCount() == 3 )
784 return (float)entry->GetValue(1);
786 /* float xImPos, yImPos, zImPos;
787 std::string strImPos = GetEntryString(0x0020,0x0032);
789 if ( strImPos == GDCM_UNFOUND)
791 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
792 strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
793 if ( strImPos == GDCM_UNFOUND )
795 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
800 if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 )
809 * \brief gets the info from 0020,0032 : Image Position Patient
810 * else from 0020,0030 : Image Position (RET)
811 * else from 0020,1041 : Slice Location
812 * else from 0020,0050 : Location
814 * @return up-left image corner Z position
816 float File::GetZOrigin()
818 DataEntry *entry = GetDataEntry(0x0020,0x0032);
821 if( entry->GetValueCount() == 3 )
822 return (float)entry->GetValue(0);
823 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
826 /* float xImPos, yImPos, zImPos;
827 std::string strImPos = GetEntryString(0x0020,0x0032);
829 if ( strImPos != GDCM_UNFOUND )
831 if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3)
833 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
834 return 0.; // bug in the element 0x0020,0x0032
842 entry = GetDataEntry(0x0020,0x0030);
845 if( entry->GetValueCount() == 3 )
846 return (float)entry->GetValue(0);
847 gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
850 /* strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images
851 if ( strImPos != GDCM_UNFOUND )
853 if ( sscanf( strImPos.c_str(),
854 "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos ) != 3 )
856 gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
857 return 0.; // bug in the element 0x0020,0x0032
865 // for *very* old ACR-NEMA images
866 entry = GetDataEntry(0x0020,0x1041);
869 if( entry->GetValueCount() == 1 )
870 return (float)entry->GetValue(0);
871 gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
874 /* std::string strSliceLocation = GetEntryString(0x0020,0x1041);
875 if ( strSliceLocation != GDCM_UNFOUND )
877 if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1)
879 gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
880 return 0.; // bug in the element 0x0020,0x1041
887 gdcmWarningMacro( "Unfound Slice Location (0020,1041)");*/
889 entry = GetDataEntry(0x0020,0x0050);
892 gdcmWarningMacro( "Unfound Location (0020,0050)");
893 if( entry->GetValueCount() == 1 )
894 return (float)entry->GetValue(0);
895 gdcmWarningMacro( "Wrong Location (0020,0050)");
898 /* std::string strLocation = GetEntryString(0x0020,0x0050);
899 if ( strLocation != GDCM_UNFOUND )
901 if ( sscanf( strLocation.c_str(), "%f ", &zImPos) != 1 )
903 gdcmWarningMacro( "Wrong Location (0020,0050)");
904 return 0.; // bug in the element 0x0020,0x0050
911 gdcmWarningMacro( "Unfound Location (0020,0050)");*/
913 return 0.; // Hopeless
917 * \brief gets the info from 0020,0037 : Image Orientation Patient
918 * or from 0020 0035 : Image Orientation (RET)
919 * (needed to organize DICOM files based on their x,y,z position)
920 * @param iop adress of the (6)float array to receive values
921 * @return true when one of the tag is found
922 * false when nothing is found
924 bool File::GetImageOrientationPatient( float iop[6] )
926 std::string strImOriPat;
927 //iop is supposed to be float[6]
928 iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
930 // 0020 0037 DS REL Image Orientation (Patient)
931 if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
933 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
934 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
936 gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
937 << " Less than 6 values were found." );
942 // 0020 0035 DS REL Image Orientation (RET)
943 else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND )
945 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
946 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
948 gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
949 << "Less than 6 values were found." );
959 * \brief Retrieve the number of Bits Stored (actually used)
960 * (as opposed to number of Bits Allocated)
961 * @return The encountered number of Bits Stored, 0 by default.
962 * 0 means the file is NOT USABLE. The caller has to check it !
964 int File::GetBitsStored()
966 DataEntry *entry = GetDataEntry(0x0028,0x0101);
969 gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
972 return (int)entry->GetValue(0);
974 /* std::string strSize = GetEntryString( 0x0028, 0x0101 );
975 if ( strSize == GDCM_UNFOUND )
977 gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
978 return 0; // It's supposed to be mandatory
979 // the caller will have to check
981 return atoi( strSize.c_str() );*/
985 * \brief Retrieve the number of Bits Allocated
986 * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,)
987 * @return The encountered Number of Bits Allocated, 0 by default.
988 * 0 means the file is NOT USABLE. The caller has to check it !
990 int File::GetBitsAllocated()
992 DataEntry *entry = GetDataEntry(0x0028,0x0100);
995 gdcmWarningMacro("(0028,0100) is supposed to be mandatory");
998 return (int)entry->GetValue(0);
1000 /* std::string strSize = GetEntryString(0x0028,0x0100);
1001 if ( strSize == GDCM_UNFOUND )
1003 gdcmWarningMacro( "(0028,0100) is supposed to be mandatory");
1004 return 0; // It's supposed to be mandatory
1005 // the caller will have to check
1007 return atoi( strSize.c_str() );*/
1011 * \brief Retrieve the high bit position.
1012 * \warning The method defaults to 0 when information is missing.
1013 * The responsability of checking this value is left to the caller.
1014 * @return The high bit position when present. 0 when missing.
1016 int File::GetHighBitPosition()
1018 DataEntry *entry = GetDataEntry(0x0028,0x0102);
1021 gdcmWarningMacro("(0028,0102) is supposed to be mandatory");
1024 return (int)entry->GetValue(0);
1026 /* std::string strSize = GetEntryString( 0x0028, 0x0102 );
1027 if ( strSize == GDCM_UNFOUND )
1029 gdcmWarningMacro( "(0028,0102) is supposed to be mandatory");
1032 return atoi( strSize.c_str() );*/
1036 * \brief Retrieve the number of Samples Per Pixel
1037 * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
1038 * @return The encountered number of Samples Per Pixel, 1 by default.
1039 * (we assume Gray level Pixels)
1041 int File::GetSamplesPerPixel()
1043 DataEntry *entry = GetDataEntry(0x0028,0x0002);
1046 gdcmWarningMacro("(0028,0002) is supposed to be mandatory");
1047 return 1; // Well, it's supposed to be mandatory ...
1048 // but sometimes it's missing : *we* assume Gray pixels
1050 return (int)entry->GetValue(0);
1052 /* const std::string &strSize = GetEntryString(0x0028,0x0002);
1053 if ( strSize == GDCM_UNFOUND )
1055 gdcmWarningMacro( "(0028,0002) is supposed to be mandatory");
1056 return 1; // Well, it's supposed to be mandatory ...
1057 // but sometimes it's missing : *we* assume Gray pixels
1059 return atoi( strSize.c_str() );*/
1063 * \brief Retrieve the Planar Configuration for RGB images
1064 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
1065 * @return The encountered Planar Configuration, 0 by default.
1067 int File::GetPlanarConfiguration()
1069 DataEntry *entry = GetDataEntry(0x0028,0x0006);
1072 gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
1075 return (int)entry->GetValue(0);
1077 /* std::string strSize = GetEntryString(0x0028,0x0006);
1078 if ( strSize == GDCM_UNFOUND )
1080 gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
1083 return atoi( strSize.c_str() );*/
1087 * \brief Return the size (in bytes) of a single pixel of data.
1088 * @return The size in bytes of a single pixel of data; 0 by default
1089 * 0 means the file is NOT USABLE; the caller will have to check
1091 int File::GetPixelSize()
1093 // 0028 0100 US IMG Bits Allocated
1094 // (in order no to be messed up by old ACR-NEMA RGB images)
1095 assert( !(GetEntryString(0x0028,0x0100) == "24") );
1097 std::string pixelType = GetPixelType();
1098 if ( pixelType == "8U" || pixelType == "8S" )
1102 if ( pixelType == "16U" || pixelType == "16S")
1106 if ( pixelType == "32U" || pixelType == "32S")
1110 if ( pixelType == "FD" )
1114 gdcmWarningMacro( "Unknown pixel type: " << pixelType);
1119 * \brief Build the Pixel Type of the image.
1120 * Possible values are:
1121 * - 8U unsigned 8 bit,
1122 * - 8S signed 8 bit,
1123 * - 16U unsigned 16 bit,
1124 * - 16S signed 16 bit,
1125 * - 32U unsigned 32 bit,
1126 * - 32S signed 32 bit,
1127 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
1128 * \warning 12 bit images appear as 16 bit.
1129 * 24 bit images appear as 8 bit + photochromatic interp ="RGB "
1130 * + Planar Configuration = 0
1131 * @return 0S if nothing found. NOT USABLE file. The caller has to check
1133 std::string File::GetPixelType()
1135 std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
1136 if ( bitsAlloc == GDCM_UNFOUND )
1138 gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
1139 bitsAlloc = "16"; // default and arbitrary value, not to polute the output
1142 if ( bitsAlloc == "64" )
1146 else if ( bitsAlloc == "12" )
1148 // It will be unpacked
1151 else if ( bitsAlloc == "24" )
1153 // (in order no to be messed up by old RGB images)
1158 if( IsSignedPixelData() )
1167 /* std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
1168 if ( bitsAlloc == GDCM_UNFOUND )
1170 gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
1171 bitsAlloc = "16"; // default and arbitrary value, not to polute the output
1174 if ( bitsAlloc == "64" )
1178 else if ( bitsAlloc == "12" )
1180 // It will be unpacked
1183 else if ( bitsAlloc == "24" )
1185 // (in order no to be messed up by old RGB images)
1189 std::string sign = GetEntryString(0x0028, 0x0103);//"Pixel Representation"
1191 if (sign == GDCM_UNFOUND )
1193 gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
1194 sign = "U"; // default and arbitrary value, not to polute the output
1196 else if ( sign == "0" )
1204 return bitsAlloc + sign;
1208 * \brief Check whether the pixels are signed (1) or UNsigned (0) data.
1209 * \warning The method defaults to false (UNsigned) when tag 0028|0103
1211 * The responsability of checking this value is left to the caller
1212 * (NO transformation is performed on the pixels to make then >0)
1213 * @return True when signed, false when UNsigned
1215 bool File::IsSignedPixelData()
1217 DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
1220 gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
1223 return entry->GetValue(0) != 0;
1224 /* std::string strSign = GetEntryString( 0x0028, 0x0103 );
1225 if ( strSign == GDCM_UNFOUND )
1227 gdcmWarningMacro( "(0028,0103) is supposed to be mandatory");
1230 int sign = atoi( strSign.c_str() );
1239 * \brief Check whether this a monochrome picture (gray levels) or not,
1240 * using "Photometric Interpretation" tag (0x0028,0x0004).
1241 * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
1243 bool File::IsMonochrome()
1245 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1246 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
1247 || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
1251 if ( PhotometricInterp == GDCM_UNFOUND )
1253 gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
1259 * \brief Check whether this a MONOCHROME1 picture (high values = dark)
1260 * or not using "Photometric Interpretation" tag (0x0028,0x0004).
1261 * @return true when "MONOCHROME1" . False otherwise.
1263 bool File::IsMonochrome1()
1265 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1266 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
1270 if ( PhotometricInterp == GDCM_UNFOUND )
1272 gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
1278 * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
1279 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1280 * @return true when "PALETTE COLOR". False otherwise.
1282 bool File::IsPaletteColor()
1284 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1285 if ( PhotometricInterp == "PALETTE COLOR " )
1289 if ( PhotometricInterp == GDCM_UNFOUND )
1291 gdcmWarningMacro( "Not found : Palette color (0028,0004)");
1297 * \brief Check whether this a "YBR_FULL" color picture or not by accessing
1298 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1299 * @return true when "YBR_FULL". False otherwise.
1301 bool File::IsYBRFull()
1303 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1304 if ( PhotometricInterp == "YBR_FULL" )
1308 if ( PhotometricInterp == GDCM_UNFOUND )
1310 gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
1316 * \brief tells us if LUT are used
1317 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
1318 * are NOT considered as LUT, since nobody knows
1319 * how to deal with them
1320 * Please warn me if you know sbdy that *does* know ... jprx
1321 * @return true if LUT Descriptors and LUT Tables were found
1325 // Check the presence of the LUT Descriptors, and LUT Tables
1327 if ( !GetDocEntry(0x0028,0x1101) )
1331 // LutDescriptorGreen
1332 if ( !GetDocEntry(0x0028,0x1102) )
1336 // LutDescriptorBlue
1337 if ( !GetDocEntry(0x0028,0x1103) )
1341 // Red Palette Color Lookup Table Data
1342 if ( !GetDocEntry(0x0028,0x1201) )
1346 // Green Palette Color Lookup Table Data
1347 if ( !GetDocEntry(0x0028,0x1202) )
1351 // Blue Palette Color Lookup Table Data
1352 if ( !GetDocEntry(0x0028,0x1203) )
1357 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
1358 // NOT taken into account, but we don't know how to use it ...
1363 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
1365 * @return Lookup Table number of Bits , 0 by default
1366 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
1367 * @ return bit number of each LUT item
1369 int File::GetLUTNbits()
1371 std::vector<std::string> tokens;
1374 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
1375 // = Lookup Table Desc-Blue
1376 // Consistency already checked in GetLUTLength
1377 std::string lutDescription = GetEntryString(0x0028,0x1101);
1378 if ( lutDescription == GDCM_UNFOUND )
1383 tokens.clear(); // clean any previous value
1384 Util::Tokenize ( lutDescription, tokens, "\\" );
1385 //LutLength=atoi(tokens[0].c_str());
1386 //LutDepth=atoi(tokens[1].c_str());
1388 lutNbits = atoi( tokens[2].c_str() );
1395 *\brief gets the info from 0028,1052 : Rescale Intercept
1396 * @return Rescale Intercept
1398 float File::GetRescaleIntercept()
1400 // 0028 1052 DS IMG Rescale Intercept
1401 DataEntry *entry = GetDataEntry(0x0028, 0x1052);
1404 gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
1407 return (float)entry->GetValue(0);
1409 /* float resInter = 0.;
1410 /// 0028 1052 DS IMG Rescale Intercept
1411 const std::string &strRescInter = GetEntryString(0x0028,0x1052);
1412 if ( strRescInter != GDCM_UNFOUND )
1414 if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 )
1416 // bug in the element 0x0028,0x1052
1417 gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
1425 *\brief gets the info from 0028,1053 : Rescale Slope
1426 * @return Rescale Slope
1428 float File::GetRescaleSlope()
1430 // 0028 1053 DS IMG Rescale Slope
1431 DataEntry *entry = GetDataEntry(0x0028, 0x1053);
1434 gdcmWarningMacro( "Missing Rescale Slope (0028,1053)");
1437 return (float)entry->GetValue(0);
1438 /* float resSlope = 1.;
1439 //0028 1053 DS IMG Rescale Slope
1440 std::string strRescSlope = GetEntryString(0x0028,0x1053);
1441 if ( strRescSlope != GDCM_UNFOUND )
1443 if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 )
1445 // bug in the element 0x0028,0x1053
1446 gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
1454 * \brief This function is intended to user who doesn't want
1455 * to have to manage a LUT and expects to get an RBG Pixel image
1456 * (or a monochrome one ...)
1457 * \warning to be used with GetImagePixels()
1458 * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
1460 int File::GetNumberOfScalarComponents()
1462 if ( GetSamplesPerPixel() == 3 )
1467 // 0028 0100 US IMG Bits Allocated
1468 // (in order no to be messed up by old RGB images)
1469 if ( GetEntryString(0x0028,0x0100) == "24" )
1474 std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
1476 if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
1478 if ( HasLUT() )// PALETTE COLOR is NOT enough
1488 // beware of trailing space at end of string
1489 // DICOM tags are never of odd length
1490 if ( strPhotometricInterpretation == GDCM_UNFOUND ||
1491 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
1492 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
1498 // we assume that *all* kinds of YBR are dealt with
1504 * \brief This function is intended to user that DOESN'T want
1505 * to get RGB pixels image when it's stored as a PALETTE COLOR image
1506 * - the (vtk) user is supposed to know how deal with LUTs -
1507 * \warning to be used with GetImagePixelsRaw()
1508 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
1510 int File::GetNumberOfScalarComponentsRaw()
1512 // 0028 0100 US IMG Bits Allocated
1513 // (in order no to be messed up by old RGB images)
1514 if ( File::GetEntryString(0x0028,0x0100) == "24" )
1519 // we assume that *all* kinds of YBR are dealt with
1520 return GetSamplesPerPixel();
1524 * \brief Recover the offset (from the beginning of the file)
1525 * of *image* pixels (not *icone image* pixels, if any !)
1526 * @return Pixel Offset
1528 size_t File::GetPixelOffset()
1530 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1533 return pxlElement->GetOffset();
1537 gdcmDebugMacro( "Big trouble : Pixel Element ("
1538 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1544 * \brief Recover the pixel area length (in Bytes)
1545 * @return Pixel Element Length, as stored in the header
1546 * (NOT the memory space necessary to hold the Pixels
1547 * -in case of embeded compressed image-)
1548 * 0 : NOT USABLE file. The caller has to check.
1550 size_t File::GetPixelAreaLength()
1552 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1555 return pxlElement->GetLength();
1559 gdcmDebugMacro( "Big trouble : Pixel Element ("
1560 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1566 * \brief Adds the characteristics of a new element we want to anonymize
1567 * @param group Group number of the target tag.
1568 * @param elem Element number of the target tag.
1569 * @param value new value (string) to substitute with
1571 void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
1572 std::string const &value)
1578 UserAnonymizeList.push_back(el);
1582 * \brief Overwrites in the file the values of the DicomElements
1585 void File::AnonymizeNoLoad()
1587 std::fstream *fp = new std::fstream(Filename.c_str(),
1588 std::ios::in | std::ios::out | std::ios::binary);
1592 uint32_t valLgth = 0;
1593 std::string *spaces;
1594 for (ListElements::iterator it = UserAnonymizeList.begin();
1595 it != UserAnonymizeList.end();
1598 d = GetDocEntry( (*it).Group, (*it).Elem);
1603 if ( dynamic_cast<SeqEntry *>(d) )
1605 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1609 offset = d->GetOffset();
1610 lgth = d->GetLength();
1613 spaces = new std::string( lgth-valLgth, ' ');
1614 (*it).Value = (*it).Value + *spaces;
1617 fp->seekp( offset, std::ios::beg );
1618 fp->write( (*it).Value.c_str(), lgth );
1626 * \brief anonymize a File (remove Patient's personal info passed with
1627 * AddAnonymizeElement()
1628 * \note You cannot Anonymize a DataEntry (to be fixed)
1630 bool File::AnonymizeFile()
1632 // If Anonymisation list is empty, let's perform some basic anonymization
1633 if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
1635 // If exist, replace by spaces
1636 SetEntryString(" ",0x0010, 0x2154); // Telephone
1637 SetEntryString(" ",0x0010, 0x1040); // Adress
1638 SetEntryString(" ",0x0010, 0x0020); // Patient ID
1640 DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
1642 if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
1644 std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
1645 if ( studyInstanceUID != GDCM_UNFOUND )
1647 SetEntryString(studyInstanceUID, 0x0010, 0x0010);
1651 SetEntryString("anonymized", 0x0010, 0x0010);
1658 for (ListElements::iterator it = UserAnonymizeList.begin();
1659 it != UserAnonymizeList.end();
1662 d = GetDocEntry( (*it).Group, (*it).Elem);
1667 if ( dynamic_cast<SeqEntry *>(d) )
1669 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1673 if ( dynamic_cast<DataEntry *>(d) )
1675 gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
1679 SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
1683 // In order to make definitively impossible any further identification
1684 // remove or replace all the stuff that contains a Date
1686 //0008 0012 DA ID Instance Creation Date
1687 //0008 0020 DA ID Study Date
1688 //0008 0021 DA ID Series Date
1689 //0008 0022 DA ID Acquisition Date
1690 //0008 0023 DA ID Content Date
1691 //0008 0024 DA ID Overlay Date
1692 //0008 0025 DA ID Curve Date
1693 //0008 002a DT ID Acquisition Datetime
1694 //0018 9074 DT ACQ Frame Acquisition Datetime
1695 //0018 9151 DT ACQ Frame Reference Datetime
1696 //0018 a002 DT ACQ Contribution Date Time
1697 //0020 3403 SH REL Modified Image Date (RET)
1698 //0032 0032 DA SDY Study Verified Date
1699 //0032 0034 DA SDY Study Read Date
1700 //0032 1000 DA SDY Scheduled Study Start Date
1701 //0032 1010 DA SDY Scheduled Study Stop Date
1702 //0032 1040 DA SDY Study Arrival Date
1703 //0032 1050 DA SDY Study Completion Date
1704 //0038 001a DA VIS Scheduled Admission Date
1705 //0038 001c DA VIS Scheduled Discharge Date
1706 //0038 0020 DA VIS Admitting Date
1707 //0038 0030 DA VIS Discharge Date
1708 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1709 //0040 0004 DA PRC Scheduled Procedure Step End Date
1710 //0040 0244 DA PRC Performed Procedure Step Start Date
1711 //0040 0250 DA PRC Performed Procedure Step End Date
1712 //0040 2004 DA PRC Issue Date of Imaging Service Request
1713 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1714 //0040 4011 DT PRC Expected Completion Date and Time
1715 //0040 a030 DT PRC Verification Date Time
1716 //0040 a032 DT PRC Observation Date Time
1717 //0040 a120 DT PRC DateTime
1718 //0040 a121 DA PRC Date
1719 //0040 a13a DT PRC Referenced Datetime
1720 //0070 0082 DA ??? Presentation Creation Date
1721 //0100 0420 DT ??? SOP Autorization Date and Time
1722 //0400 0105 DT ??? Digital Signature DateTime
1723 //2100 0040 DA PJ Creation Date
1724 //3006 0008 DA SSET Structure Set Date
1725 //3008 0024 DA ??? Treatment Control Point Date
1726 //3008 0054 DA ??? First Treatment Date
1727 //3008 0056 DA ??? Most Recent Treatment Date
1728 //3008 0162 DA ??? Safe Position Exit Date
1729 //3008 0166 DA ??? Safe Position Return Date
1730 //3008 0250 DA ??? Treatment Date
1731 //300a 0006 DA RT RT Plan Date
1732 //300a 022c DA RT Air Kerma Rate Reference Date
1733 //300e 0004 DA RT Review Date
1739 * \brief Performs some consistency checking on various 'File related'
1740 * (as opposed to 'DicomDir related') entries
1741 * then writes in a file all the (Dicom Elements) included the Pixels
1742 * @param fileName file name to write to
1743 * @param writetype type of the file to be written
1744 * (ACR, ExplicitVR, ImplicitVR)
1746 bool File::Write(std::string fileName, FileType writetype)
1748 std::ofstream *fp = new std::ofstream(fileName.c_str(),
1749 std::ios::out | std::ios::binary);
1752 gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
1756 // Entry : 0002|0000 = group length -> recalculated
1757 DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
1760 std::ostringstream sLen;
1761 sLen << ComputeGroup0002Length( );
1762 e0000->SetString(sLen.str());
1765 // Derma?.dcm does not have it...let's remove it FIXME FIXME
1766 if( writetype != JPEG )
1768 int i_lgPix = GetEntryLength(GrPixel, NumPixel);
1771 // no (GrPixel, NumPixel) element
1772 std::string s_lgPix = Util::Format("%d", i_lgPix+12);
1773 s_lgPix = Util::DicomString( s_lgPix.c_str() );
1774 InsertEntryString(s_lgPix,GrPixel, 0x0000);
1778 Document::WriteContent(fp, writetype);
1786 //-----------------------------------------------------------------------------
1790 //-----------------------------------------------------------------------------
1793 * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
1794 * Compute the RLE extra information and store it in \ref RLEInfo
1795 * for later pixel retrieval usage.
1797 void File::ComputeRLEInfo()
1799 std::string ts = GetTransferSyntax();
1800 if ( !Global::GetTS()->IsRLELossless(ts) )
1805 // Encoded pixel data: for the time being we are only concerned with
1806 // Jpeg or RLE Pixel data encodings.
1807 // As stated in PS 3.5-2003, section 8.2 p44:
1808 // "If sent in Encapsulated Format (i.e. other than the Native Format) the
1809 // value representation OB is used".
1810 // Hence we expect an OB value representation. Concerning OB VR,
1811 // the section PS 3.5-2003, section A.4.c p 58-59, states:
1812 // "For the Value Representations OB and OW, the encoding shall meet the
1813 // following specifications depending on the Data element tag:"
1815 // - the first item in the sequence of items before the encoded pixel
1816 // data stream shall be basic offset table item. The basic offset table
1817 // item value, however, is not required to be present"
1818 ReadEncapsulatedBasicOffsetTable();
1820 // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
1821 // Loop on the individual frame[s] and store the information
1822 // on the RLE fragments in a RLEFramesInfo.
1823 // Note: - when only a single frame is present, this is a
1825 // - when more than one frame are present, then we are in
1826 // the case of a multi-frame image.
1830 while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1832 // Since we have read the basic offset table, let's check the value were correct
1833 // or else produce a warning:
1834 if ( BasicOffsetTableItemValue )
1836 // If a BasicOffsetTableItemValue was read
1837 uint32_t individualLength = BasicOffsetTableItemValue[i];
1838 assert( individualLength == sum ); // REMOVE that if this is a problem
1839 if( individualLength != sum )
1841 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" );
1843 sum += frameLength + 8;
1846 // Parse the RLE Header and store the corresponding RLE Segment
1847 // Offset Table information on fragments of this current Frame.
1848 // Note that the fragment pixels themselves are not loaded
1849 // (but just skipped).
1850 long frameOffset = Fp->tellg();
1852 uint32_t nbRleSegments = ReadInt32();
1853 if ( nbRleSegments > 16 )
1855 // There should be at most 15 segments (refer to RLEFrame class)
1856 gdcmWarningMacro( "Too many segments.");
1859 uint32_t rleSegmentOffsetTable[16];
1860 for( int k = 1; k <= 15; k++ )
1862 rleSegmentOffsetTable[k] = ReadInt32();
1865 // Deduce from both RLE Header and frameLength
1866 // the fragment length, and again store this info
1867 // in a RLEFramesInfo.
1868 long rleSegmentLength[15];
1869 // skipping (not reading) RLE Segments
1870 if ( nbRleSegments > 1)
1872 for(unsigned int k = 1; k <= nbRleSegments-1; k++)
1874 rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
1875 - rleSegmentOffsetTable[k];
1876 SkipBytes(rleSegmentLength[k]);
1880 rleSegmentLength[nbRleSegments] = frameLength
1881 - rleSegmentOffsetTable[nbRleSegments];
1882 SkipBytes(rleSegmentLength[nbRleSegments]);
1884 // Store the collected info
1885 RLEFrame *newFrame = new RLEFrame;
1886 newFrame->SetNumberOfFragments(nbRleSegments);
1887 for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
1889 newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
1890 newFrame->SetLength(uk,rleSegmentLength[uk]);
1892 RLEInfo->AddFrame(newFrame);
1895 // Make sure that we encounter a 'Sequence Delimiter Item'
1896 // at the end of the item :
1897 if ( !ReadTag(0xfffe, 0xe0dd) )
1899 gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
1904 * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
1905 * Compute the jpeg extra information (fragment[s] offset[s] and
1906 * length) and store it[them] in \ref JPEGInfo for later pixel
1909 void File::ComputeJPEGFragmentInfo()
1911 // If you need to, look for comments of ComputeRLEInfo().
1912 std::string ts = GetTransferSyntax();
1913 if ( ! Global::GetTS()->IsJPEG(ts) )
1918 ReadEncapsulatedBasicOffsetTable();
1920 // Loop on the fragments[s] and store the parsed information in a
1922 long fragmentLength;
1925 while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
1927 // Since we have read the basic offset table, let's check the value were correct
1928 // or else produce a warning:
1929 // A.4 Transfer syntaxes for encapsulation of encoded pixel data:
1930 // When the Item Value is present, the Basic Offset Table Item Value shall contain
1931 // concatenated 32-bit unsigned integer values that are byte offsets to the first
1932 // byte of the Item Tag of the first fragment for each frame in the Sequence of
1933 // Items. These offsets are measured from the first byte of the first Item Tag
1934 // following the Basic Offset Table item (See Table A.4-2).
1936 if ( BasicOffsetTableItemValue )
1938 // If a BasicOffsetTableItemValue was read
1939 uint32_t individualLength = BasicOffsetTableItemValue[i];
1940 //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ??
1941 if( individualLength != sum )
1943 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" <<
1944 individualLength << " != " << sum );
1946 sum += fragmentLength + 8;
1950 long fragmentOffset = Fp->tellg();
1951 // Store the collected info
1952 JPEGFragment *newFragment = new JPEGFragment;
1953 newFragment->SetOffset(fragmentOffset);
1954 newFragment->SetLength(fragmentLength);
1955 JPEGInfo->AddFragment(newFragment);
1957 SkipBytes(fragmentLength);
1960 // Make sure that we encounter a 'Sequence Delimiter Item'
1961 // at the end of the item :
1962 if ( !ReadTag(0xfffe, 0xe0dd) )
1964 gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
1969 * \brief Assuming the internal file pointer \ref Document::Fp
1970 * is placed at the beginning of a tag check whether this
1971 * tag is (TestGroup, TestElem).
1972 * \warning On success the internal file pointer \ref Document::Fp
1973 * is modified to point after the tag.
1974 * On failure (i.e. when the tag wasn't the expected tag
1975 * (TestGroup, TestElem) the internal file pointer
1976 * \ref Document::Fp is restored to it's original position.
1977 * @param testGroup The expected group of the tag.
1978 * @param testElem The expected Element of the tag.
1979 * @return True on success, false otherwise.
1981 bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
1983 long positionOnEntry = Fp->tellg();
1984 long currentPosition = Fp->tellg(); // On debugging purposes
1986 // Read the Item Tag group and element, and make
1987 // sure they are what we expected:
1988 uint16_t itemTagGroup;
1989 uint16_t itemTagElem;
1992 itemTagGroup = ReadInt16();
1993 itemTagElem = ReadInt16();
1995 catch ( FormatError )
1997 gdcmErrorMacro( "Can not read tag for "
1998 << " We should have found tag ("
1999 << DictEntry::TranslateToKey(testGroup,testElem) << ")"
2004 if ( itemTagGroup != testGroup || itemTagElem != testElem )
2006 gdcmErrorMacro( "Wrong Item Tag found:"
2007 << " We should have found tag ("
2008 << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
2009 << " but instead we encountered tag ("
2010 << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
2011 << " at address: " << " 0x(" << std::hex
2012 << (unsigned int)currentPosition << std::dec << ")"
2014 Fp->seekg(positionOnEntry, std::ios::beg);
2022 * \brief Assuming the internal file pointer \ref Document::Fp
2023 * is placed at the beginning of a tag (TestGroup, TestElement),
2024 * read the length associated to the Tag.
2025 * \warning On success the internal file pointer \ref Document::Fp
2026 * is modified to point after the tag and it's length.
2027 * On failure (i.e. when the tag wasn't the expected tag
2028 * (TestGroup, TestElement) the internal file pointer
2029 * \ref Document::Fp is restored to it's original position.
2030 * @param testGroup The expected Group of the tag.
2031 * @param testElem The expected Element of the tag.
2032 * @return On success returns the length associated to the tag. On failure
2035 uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
2038 if ( !ReadTag(testGroup, testElem) )
2040 gdcmErrorMacro( "ReadTag did not succeed for ("
2041 << DictEntry::TranslateToKey(testGroup,testElem)
2046 //// Then read the associated Item Length
2047 long currentPosition = Fp->tellg();
2048 uint32_t itemLength = ReadInt32();
2049 gdcmDebugMacro( "Basic Item Length is: " << itemLength
2050 << " at address: " << std::hex << (unsigned int)currentPosition);
2055 * \brief When parsing the Pixel Data of an encapsulated file, read
2056 * the basic offset table (when present, and BTW dump it).
2058 void File::ReadEncapsulatedBasicOffsetTable()
2060 //// Read the Basic Offset Table Item Tag length...
2061 uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
2063 // When present, read the basic offset table itself.
2064 // Notes: - since the presence of this basic offset table is optional
2065 // we can't rely on it for the implementation, and we will simply
2066 // trash it's content (when present).
2067 // - still, when present, we could add some further checks on the
2068 // lengths, but we won't bother with such fuses for the time being.
2069 if ( itemLength != 0 )
2071 char *charBasicOffsetTableItemValue = new char[itemLength];
2072 Fp->read(charBasicOffsetTableItemValue, itemLength);
2073 unsigned int nbEntries = itemLength/4;
2074 assert( nbEntries*4 == itemLength); // Make sure this is a multiple
2075 BasicOffsetTableItemValue = new uint32_t[nbEntries];
2077 for (unsigned int i=0; i < nbEntries; i++ )
2079 BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i]));
2080 #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION)
2081 uint32_t val = BasicOffsetTableItemValue[i];
2082 BasicOffsetTableItemValue[i]
2083 = ( (val<<24) | ((val<<8) & 0x00ff0000) |
2084 ((val>>8) & 0x0000ff00) | (val>>24) );
2086 gdcmWarningMacro( "Read one length for: " <<
2087 std::hex << BasicOffsetTableItemValue[i] );
2090 delete[] charBasicOffsetTableItemValue;
2094 // These are the deprecated method that one day should be removed (after the next release)
2096 #ifndef GDCM_LEGACY_REMOVE
2098 * \brief Constructor (DEPRECATED : temporaryly kept not to break the API)
2099 * @param filename name of the file whose header we want to analyze
2100 * @deprecated do not use any longer
2102 File::File( std::string const &filename )
2105 RLEInfo = new RLEFramesInfo;
2106 JPEGInfo = new JPEGFragmentsInfo;
2108 SetFileName( filename );
2109 Load( ); // gdcm::Document is first Loaded, then the 'File part'
2113 * \brief Loader. (DEPRECATED : temporaryly kept not to break the API)
2114 * @param fileName file to be open for parsing
2115 * @return false if file cannot be open or no swap info was found,
2116 * or no tag was found.
2117 * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
2119 bool File::Load( std::string const &fileName )
2121 GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
2123 SetFileName( fileName );
2124 if ( ! this->Document::Load( ) )
2127 return DoTheLoadingJob( );
2131 //-----------------------------------------------------------------------------
2134 //-----------------------------------------------------------------------------
2135 } // end namespace gdcm