1 /*=========================================================================
4 Module: $RCSfile: gdcmFile.cxx,v $
6 Date: $Date: 2007/08/27 16:14:47 $
7 Version: $Revision: 1.336 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
20 // -------------- Remember ! ----------------------------------
22 // Image Position (Patient) (0020,0032):
23 // If not found (ACR_NEMA) we try Image Position (0020,0030)
24 // If not found (ACR-NEMA), we consider Slice Location (0020,1041)
25 // or Location (0020,0050)
26 // as the Z coordinate,
27 // 0. for all the coordinates if nothing is found
29 // Image Position (Patient) (0020,0032) VM=3
31 // The attribute Patient Orientation (0020,0020) from the General Image Module
32 // is of type 2C and has the condition Required if image does not require
33 // Image Orientation (0020,0037) and Image Position (0020,0032).
34 // However, if the image does require the attributes
35 // - Image Orientation (Patient) (0020,0037), VM=6
36 // - Image Position (Patient) (0020,0032), VM=3
37 // then attribute Patient Orientation (0020,0020) should not be present
41 // Patient Position (0018,5100) values :
43 // HFS = Head First-Supine, where increasing (positive axis direction) :
44 // X -> to the direction pointed to by the patient's oustretched left arm
45 // Y -> to the anterior-to-posterior direction in the patient's body
46 // Z -> to the feet-to-head direction in the patient's body
48 // HFP = Head First-Prone, where increasing (positive axis direction) :
49 // X -> to the direction pointed to by the patient's oustretched left arm
50 // Y -> to the anterior-to-posterior direction in the patient's body
51 // Z -> to the feet-to-head direction in the patient's body
53 // FFS = Feet First-Supine, where increasing (positive axis direction) :
54 // X -> to the direction pointed to by the patient's oustretched left arm
55 // Y -> to the anterior-to-posterion direction in the patient's body
56 // Z -> to the feet-to-head direction in the patient's body
58 // FFP = Feet First-Prone, where increasing (positive axis direction) :
59 // X -> to the direction pointed to by the patient's oustretched left arm
60 // Y -> to the posterior-to-anterior direction in the patient's body
61 // Z -> to the feet-to-head direction in the patient's body
63 // HFDR = Head First-Decubitus Right
64 // HFDL = Head First-Decubitus Left
65 // FFDR = Feet First-Decubitus Right
66 // FFDL = Feet First-Decubitus Left
68 // we can also find (non standard!)
73 // CS 2 Patient Orientation (0020 0020)
74 // When the coordinates of the image
75 // are always present, this field is almost never used.
76 // Better we don't trust it too much ...
85 // (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ]
88 // ---------------------------------------------------------------
91 #include "gdcmGlobal.h"
93 #include "gdcmDebug.h"
95 #include "gdcmSeqEntry.h"
96 #include "gdcmRLEFramesInfo.h"
97 #include "gdcmJPEGFragmentsInfo.h"
98 #include "gdcmDataEntry.h"
99 #include "gdcmSQItem.h"
102 #include <stdio.h> //sscanf
103 #include <stdlib.h> // for atoi
105 namespace GDCM_NAME_SPACE
108 //-----------------------------------------------------------------------------
109 // Constructor / Destructor
112 * \brief Constructor used when we want to generate dicom files from scratch
117 RLEInfo = new RLEFramesInfo;
118 JPEGInfo = new JPEGFragmentsInfo;
119 GrPixel = 0x7fe0; // to avoid further troubles
121 BasicOffsetTableItemValue = 0;
122 FourthDimensionLocation = TagKey(0,0);
127 * \brief Canonical destructor.
135 delete[] BasicOffsetTableItemValue;
138 //-----------------------------------------------------------------------------
142 * @return false if file cannot be open or no swap info was found,
143 * or no tag was found.
147 if ( ! this->Document::Load( ) )
150 return DoTheLoadingJob( );
154 * \brief Does the Loading Job (internal use only)
155 * @return false if file cannot be open or no swap info was found,
156 * or no tag was found.
158 bool File::DoTheLoadingJob( )
160 // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
161 // We may encounter the 'RETired' (0x0028, 0x0200) tag
162 // (Image Location") . This entry contains the number of
163 // the group that contains the pixel data (hence the "Pixel Data"
164 // is found by indirection through the "Image Location").
165 // Inside the group pointed by "Image Location" the searched element
166 // is conventionally the element 0x0010 (when the norm is respected).
167 // When the "Image Location" is missing we default to group 0x7fe0.
168 // Note: this IS the right place for the code
171 const std::string &imgLocation = GetEntryString(0x0028, 0x0200);
172 if ( imgLocation == GDCM_UNFOUND )
179 GrPixel = (uint16_t) atoi( imgLocation.c_str() );
182 // sometimes Image Location value doesn't follow
183 // the supposed processor endianness.
184 // see gdcmData/cr172241.dcm
185 if ( GrPixel == 0xe07f )
190 if ( GrPixel != 0x7fe0 )
192 // This is a kludge for old dirty Philips imager.
200 // Now, we know GrPixel and NumPixel.
201 // Let's create a VirtualDictEntry to allow a further VR modification
202 // and force VR to match with BitsAllocated.
203 DocEntry *entry = GetDocEntry(GrPixel, NumPixel);
206 // Compute the RLE or JPEG info
208 const std::string &ts = GetTransferSyntax();
209 Fp->seekg( entry->GetOffset(), std::ios::beg );
210 if ( Global::GetTS()->IsRLELossless(ts) )
212 else if ( Global::GetTS()->IsJPEG(ts) )
213 ComputeJPEGFragmentInfo();
216 // Create a new DataEntry to change the DictEntry
217 // The changed DictEntry will have
218 // - a correct PixelVR OB or OW)
219 // - the name to "Pixel Data"
222 //==> Just change the VR !
225 DataEntry *oldEntry = dynamic_cast<DataEntry *>(entry);
229 // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
230 // more than 8 (i.e 12, 16) is a 'O Words'
231 if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
236 // Change only made if usefull
237 if ( PixelVR != oldEntry->GetVR() )
239 //DictEntry* newDict = DictEntry::New(GrPixel,NumPixel,
240 // PixelVR,"1","Pixel Data");
241 //DataEntry *newEntry = DataEntry::New(newDict);
243 //newEntry->Copy(entry);
244 //newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea());
245 //oldEntry->SetSelfArea(false);
247 //RemoveEntry(oldEntry);
248 //AddEntry(newEntry);
249 //newEntry->Delete();
254 // 8 bits allocated is a 'OB(ytes)' , as well as 24 (old ACR-NEMA RGB)
255 // more than 8 (i.e 12, 16) is a 'OW(ords)'
256 if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
260 // Change only made if usefull
261 if ( PixelVR != entry->GetVR() )
263 entry->SetVR(PixelVR);
270 * \brief This predicate, based on hopefully reasonable heuristics,
271 * decides whether or not the current File was properly parsed
272 * and contains the mandatory information for being considered as
273 * a well formed and usable Dicom/Acr File.
274 * @return true when File is the one of a reasonable Dicom/Acr file,
277 bool File::IsReadable()
279 if ( !Document::IsReadable() )
284 const std::string &res = GetEntryString(0x0028, 0x0005);
285 if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
287 gdcmWarningMacro("Wrong Image Dimensions" << res);
288 return false; // Image Dimensions
290 bool b0028_0100 = true;
291 if ( !GetDocEntry(0x0028, 0x0100) )
293 gdcmWarningMacro("Bits Allocated (0028|0100) not found");
294 //return false; // "Bits Allocated"
297 bool b0028_0101 = true;
298 if ( !GetDocEntry(0x0028, 0x0101) )
300 gdcmWarningMacro("Bits Stored (0028|0101) not found");
301 //return false; // "Bits Stored"
304 bool b0028_0102 = true;
305 if ( !GetDocEntry(0x0028, 0x0102) )
307 gdcmWarningMacro("Hight Bit (0028|0102) not found");
308 //return false; // "High Bit"
311 bool b0028_0103 = true;
312 if ( !GetDocEntry(0x0028, 0x0103) )
314 gdcmWarningMacro("Pixel Representation (0028|0103) not found");
315 //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed)
319 if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103)
321 gdcmWarningMacro("Too much mandatory Tags missing !");
325 if ( !GetDocEntry(GrPixel, NumPixel) )
327 gdcmWarningMacro("Pixel Dicom Element " << std::hex <<
328 GrPixel << "|" << NumPixel << "not found");
329 return false; // Pixel Dicom Element not found :-(
335 * \brief gets the info from 0020,0013 : Image Number else 0.
336 * @return image number
338 int File::GetImageNumber()
340 //0020 0013 : Image Number
341 std::string strImNumber = GetEntryString(0x0020,0x0013);
342 if ( strImNumber != GDCM_UNFOUND )
344 return atoi( strImNumber.c_str() );
350 * \brief gets the info from 0008,0060 : Modality
351 * @return Modality Type
353 ModalityType File::GetModality()
355 // 0008 0060 : Modality
356 std::string strModality = GetEntryString(0x0008,0x0060);
357 if ( strModality != GDCM_UNFOUND )
359 if ( strModality.find("AU") < strModality.length()) return AU;
360 else if ( strModality.find("AS") < strModality.length()) return AS;
361 else if ( strModality.find("BI") < strModality.length()) return BI;
362 else if ( strModality.find("CF") < strModality.length()) return CF;
363 else if ( strModality.find("CP") < strModality.length()) return CP;
364 else if ( strModality.find("CR") < strModality.length()) return CR;
365 else if ( strModality.find("CT") < strModality.length()) return CT;
366 else if ( strModality.find("CS") < strModality.length()) return CS;
367 else if ( strModality.find("DD") < strModality.length()) return DD;
368 else if ( strModality.find("DF") < strModality.length()) return DF;
369 else if ( strModality.find("DG") < strModality.length()) return DG;
370 else if ( strModality.find("DM") < strModality.length()) return DM;
371 else if ( strModality.find("DS") < strModality.length()) return DS;
372 else if ( strModality.find("DX") < strModality.length()) return DX;
373 else if ( strModality.find("ECG") < strModality.length()) return ECG;
374 else if ( strModality.find("EPS") < strModality.length()) return EPS;
375 else if ( strModality.find("FA") < strModality.length()) return FA;
376 else if ( strModality.find("FS") < strModality.length()) return FS;
377 else if ( strModality.find("HC") < strModality.length()) return HC;
378 else if ( strModality.find("HD") < strModality.length()) return HD;
379 else if ( strModality.find("LP") < strModality.length()) return LP;
380 else if ( strModality.find("LS") < strModality.length()) return LS;
381 else if ( strModality.find("MA") < strModality.length()) return MA;
382 else if ( strModality.find("MR") < strModality.length()) return MR;
383 else if ( strModality.find("NM") < strModality.length()) return NM;
384 else if ( strModality.find("OT") < strModality.length()) return OT;
385 else if ( strModality.find("PT") < strModality.length()) return PT;
386 else if ( strModality.find("RF") < strModality.length()) return RF;
387 else if ( strModality.find("RG") < strModality.length()) return RG;
388 else if ( strModality.find("RTDOSE")
389 < strModality.length()) return RTDOSE;
390 else if ( strModality.find("RTIMAGE")
391 < strModality.length()) return RTIMAGE;
392 else if ( strModality.find("RTPLAN")
393 < strModality.length()) return RTPLAN;
394 else if ( strModality.find("RTSTRUCT")
395 < strModality.length()) return RTSTRUCT;
396 else if ( strModality.find("SM") < strModality.length()) return SM;
397 else if ( strModality.find("ST") < strModality.length()) return ST;
398 else if ( strModality.find("TG") < strModality.length()) return TG;
399 else if ( strModality.find("US") < strModality.length()) return US;
400 else if ( strModality.find("VF") < strModality.length()) return VF;
401 else if ( strModality.find("XA") < strModality.length()) return XA;
402 else if ( strModality.find("XC") < strModality.length()) return XC;
406 /// \todo throw error return value ???
407 /// specified <> unknown in our database
415 * \brief Retrieve the number of columns of image.
416 * @return The encountered size when found, 0 by default.
417 * 0 means the file is NOT USABLE. The caller will have to check
421 DataEntry *entry = GetDataEntry(0x0028,0x0011);
423 return (int)entry->GetValue(0);
428 * \brief Retrieve the number of lines of image.
429 * \warning The defaulted value is 1 as opposed to File::GetXSize()
430 * @return The encountered size when found, 1 by default
431 * (The ACR-NEMA file contains a Signal, not an Image).
435 DataEntry *entry = GetDataEntry(0x0028,0x0010);
437 return (int)entry->GetValue(0);
444 // The Rows (0028,0010) entry was optional for ACR/NEMA.
445 // (at least some images didn't have it.)
446 // It might hence be a signal (1D image). So we default to 1:
451 * \brief Retrieve the number of planes of volume or the number
452 * of frames of a multiframe.
453 * \warning When present we consider the "Number of Frames" as the third
454 * dimension. When missing we consider the third dimension as
455 * being the ACR-NEMA "Planes" tag content.
456 * @return The encountered size when found, 1 by default (single image).
460 // Both DicomV3 and ACR/Nema consider the "Number of Frames"
461 // as the third dimension.
462 DataEntry *entry = GetDataEntry(0x0028,0x0008);
464 return (int)entry->GetValue(0);
466 // We then consider the "Planes" entry as the third dimension
467 entry = GetDataEntry(0x0028,0x0012);
469 return (int)entry->GetValue(0);
474 // ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage";
475 bool File::GetSpacing(float &xspacing, float &yspacing, float &zspacing)
477 xspacing = yspacing = zspacing = 1.0;
478 TS *ts = Global::GetTS();
479 std::string sopclassuid_used;
480 // D 0002|0002 [UI] [Media Storage SOP Class UID]
482 //const std::string &mediastoragesopclassuid_str = GetEntryValue(0x0002,0x0002);
483 const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002);
484 const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str);
485 //D 0008|0016 [UI] [SOP Class UID]
486 const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016);
487 const std::string &sopclassuid = ts->GetValue(sopclassuid_str);
488 if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND )
494 if( mediastoragesopclassuid == sopclassuid )
496 sopclassuid_used = mediastoragesopclassuid;
500 gdcmWarningMacro( "Inconsistant SOP Class UID: "
501 << mediastoragesopclassuid << " and " << sopclassuid );
505 // ok we have now the correc SOP Class UID
506 if( sopclassuid_used == "Enhanced MR Image Storage" )
508 SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230);
509 unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems();
510 if( !n ) return false;
511 SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem();
512 DocEntry *p = item1->GetDocEntry(0x0028,0x9110);
513 if( !p ) return false;
514 SeqEntry *seq = dynamic_cast<SeqEntry*>(p);
515 unsigned int n1 = seq->GetNumberOfSQItems();
516 if( !n1 ) return false;
517 SQItem *item2 = seq->GetFirstSQItem();
518 // D 0028|0030 [DS] [Pixel Spacing] [0.83333331346511\0.83333331346511 ]
519 DocEntry *p2 = item2->GetDocEntry(0x0028,0x0030);
520 if( !p2 ) return false;
521 DataEntry *entry = dynamic_cast<DataEntry *>(p2);
522 std::string spacing = entry->GetString();
523 if ( sscanf( spacing.c_str(), "%f\\%f", &yspacing, &xspacing) != 2 )
525 xspacing = yspacing = 1.;
528 // D 0018|0050 [DS] [Slice Thickness] [1 ]
529 DocEntry *p3 = item2->GetDocEntry(0x0018,0x0050);
530 if( !p3 ) return false;
531 DataEntry *entry2 = dynamic_cast<DataEntry *>(p3);
532 std::string thickness = entry2->GetString();
533 if ( sscanf( thickness.c_str(), "%f", &zspacing) != 1 )
544 * \brief Retrieve the -unnormalized- number of 'times' of '4D image'.
545 * User has to tell gdcm the location of this '4th Dimension component'
546 * using SetFourthDimensionLocation() method before.
547 * \warning The defaulted value is 1.
548 * @return The encountered size when found, 1 by default
549 * (The file doesn't contain a '4D image'.).
553 if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object
556 DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(),
557 FourthDimensionLocation.GetElement() );
560 gdcmWarningMacro( " FourthDimensionLocation not found at : " <<
561 std::hex << FourthDimensionLocation.GetGroup()
562 << "|" << FourthDimensionLocation.GetElement());
567 return (int)entry->GetValue(0);
574 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
575 * then 0028,0030 : Pixel Spacing
577 * @return X dimension of a pixel
579 float File::GetXSpacing()
581 float xspacing = 1.0;
582 float yspacing = 1.0;
583 float zspacing = 1.0;
588 if ( GetSpacing(xspacing,yspacing,zspacing) )
595 From:David Clunie - view profile
596 Date:Wed, May 24 2006 1:12 pm
597 Email:David Clunie <dclu...@dclunie.com>
598 Groups:comp.protocols.dicom
600 The short answer is that:
602 - (0018,1164) describes a spacing equivalent to that which
603 would be measured off a film in projection radiography
605 - (0018,7022) does not describe the image pixels themselves,
606 since detector elements may have been binned to produce
609 - (0018,7020) may be different from (0018,7022) since there
610 may be non-sensitive material separating individual
611 detectors (i.e. the size is smaller than the spacing
614 Only (0018,1164) is relevant when measuring things; the
615 detector-specific attributes are there to describe the
620 PS. For ultrasound you need to use Region Calibration.
624 It *SHOULD* first find the IOD and then deduce which tags to read
625 Eg: Cross section this is in Pixel Spacing (0028,0030)
626 CR is in Imager Pixel Spacing (0018,1164)
627 US is in Pixel Aspect Ratio (0028,0034)
629 (3002,0011) Image Plane Pixel Spacing
630 (3002,0012) RT Image Position
632 (3004,000c) for deducing Z spacing
635 std::string SOPClassUID = GetEntryString(0x0008,0x0016);
637 /// \todo check the various SOP Class
638 /// to get the Pixel Spacing at the proper location
640 ///\todo find images to check if it *actually* works
642 if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6")
643 // Ultrasound Image Storage (Retired)
644 || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1")
645 // Ultrasound Image Storage
646 || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3")
647 // Ultrasound Multi-Frame Storage (Retired)
648 || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") )
649 // Ultrasound Multi-FrameImage Storage
651 // - check if SOPClassUID contains 2 parts (e.g. "4\3")
652 // - guess how to deduce the spacing (FOV ?, ??)
654 entry = GetDataEntry(0x0028,0x0034);
657 nbValue = entry->GetValueCount();
659 gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) "
660 << "has a wrong number of values :" << nbValue);
662 xspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ...
670 if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.1") )
671 // Computed Radiography Image Storage
673 // CR is in Imager Pixel Spacing (0018,1164)//
676 // go on with old method ...
677 // ---------------------
678 // To follow David Clunie's advice, we first check ImagerPixelSpacing
680 entry = GetDataEntry(0x0018,0x1164);
683 nbValue = entry->GetValueCount();
684 // Can't use IsValueCountValid because of the complex heuristic.
686 gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) "
687 << "has a wrong number of values :" << nbValue);
690 xspacing = (float)entry->GetValue(2);
691 else if( nbValue >= 2 )
692 xspacing = (float)entry->GetValue(1);
694 xspacing = (float)entry->GetValue(0);
696 if ( xspacing == 0.0 )
702 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
705 entry = GetDataEntry(0x0028,0x0030);
708 nbValue = entry->GetValueCount();
710 gdcmWarningMacro("PixelSpacing (0x0018,0x0030) "
711 << "has a wrong number of values :" << nbValue);
714 xspacing = (float)entry->GetValue(2);
715 else if( nbValue >= 2 )
716 xspacing = (float)entry->GetValue(1);
718 xspacing = (float)entry->GetValue(0);
720 if ( xspacing == 0.0 )
726 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
732 * \brief gets the info from 0018,1164 : ImagerPixelSpacing
733 * then from 0028,0030 : Pixel Spacing
735 * @return Y dimension of a pixel
737 float File::GetYSpacing()
739 float xspacing = 1., yspacing = 1.0, zspacing = 1.;
743 if ( GetSpacing(xspacing,yspacing,zspacing) )
749 std::string SOPClassUID = GetEntryString(0x0008,0x0016);
751 /// \todo check the various SOP Class
752 /// to get the Pixel Spacing at the proper location
754 ///\todo find images to check if it *actually* works
756 if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6")
757 // Ultrasound Image Storage (Retired)
758 || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1")
759 // Ultrasound Image Storage
760 || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3")
761 // Ultrasound Multi-Frame Storage (Retired)
762 || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") )
763 // Ultrasound Multi-FrameImage Storage
765 // - check if SOPClassUID contains 2 parts (e.g. "4\3")
766 // - no way to deduce the spacing/
768 entry = GetDataEntry(0x0028,0x0034);
771 nbValue = entry->GetValueCount();
773 yspacing = (float)entry->GetValue(0)/(float)entry->GetValue(1);
774 //std::cout << "ys " << yspacing << std::endl;
779 gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) "
780 << "has a wrong number of values :" << nbValue);
784 else if (nbValue == 1 ) {
785 yspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ...
795 // go on with old method ...
796 // ---------------------
797 // To follow David Clunie's advice, we first check ImagerPixelSpacing
799 // To follow David Clunie's advice, we first check ImagerPixelSpacing
801 entry = GetDataEntry(0x0018,0x1164);
804 yspacing = (float)entry->GetValue(0);
806 if ( yspacing == 0.0 )
812 gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" );
815 entry = GetDataEntry(0x0028,0x0030);
818 yspacing = (float)entry->GetValue(0);
820 if ( yspacing == 0.0 )
826 gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
833 * \brief gets the info from 0018,0088 : Space Between Slices
834 * else from 0018,0050 : Slice Thickness
837 * When an element is missing, we suppose slices join together
838 * (no overlapping, no interslice gap) but we have no way to check it !
839 * For *Dicom* images, ZSpacing *should be* calculated using
840 * XOrigin, YOrigin, ZOrigin (of the top left image corner)
841 * of 2 consecutive images, and the Orientation
842 * Computing ZSpacing on a single image is not really meaningfull !
843 * @return Z dimension of a voxel-to be
845 float File::GetZSpacing()
848 float xspacing = 1.0;
849 float yspacing = 1.0;
850 float zspacing = 1.0;
851 if ( GetSpacing(xspacing,yspacing,zspacing) )
856 // Spacing Between Slices : distance between the middle of 2 slices
858 // jointives (Spacing between Slices = Slice Thickness)
859 // overlapping (Spacing between Slices < Slice Thickness)
860 // disjointes (Spacing between Slices > Slice Thickness)
861 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
862 // It only concerns the MRI guys, not people wanting to visualize volumes
863 // If Spacing Between Slices is missing,
864 // we suppose slices joint together
865 DataEntry *entry = GetDataEntry(0x0018,0x0088);
867 { zspacing = (float)entry->GetValue(0);
869 if ( zspacing == 0.0 )
874 gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
876 // if no 'Spacing Between Slices' is found,
877 // we assume slices join together
878 // (no overlapping, no interslice gap)
879 entry = GetDataEntry(0x0018,0x0050);
882 zspacing = (float)entry->GetValue(0);
884 if ( zspacing == 0.0 )
889 gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
891 // if no 'Spacing Between Slices' is found,
892 // we assume slices join together
893 // (no overlapping, no interslice gap)
894 entry = GetDataEntry(0x3004,0x000c);
897 float z1 = (float)entry->GetValue(0);
898 float z2 = (float)entry->GetValue(1);
899 zspacing = z2 - z1; // can be negative...
901 if ( zspacing == 0.0 )
910 * \brief gets the info from 0020,0032 : Image Position Patient
911 * else from 0020,0030 : Image Position (RET)
913 * @return up-left image corner X position
915 float File::GetXOrigin()
917 DataEntry *entry = GetDataEntry(0x0020,0x0032);
920 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
921 entry = GetDataEntry(0x0020,0x0030);
924 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
929 if( entry->GetValueCount() == 3 )
931 if (!entry->IsValueCountValid() )
933 gdcmErrorMacro( "Invalid Value Count" );
935 return (float)entry->GetValue(0);
941 * \brief gets the info from 0020,0032 : Image Position Patient
942 * else from 0020,0030 : Image Position (RET)
944 * @return up-left image corner Y position
946 float File::GetYOrigin()
948 DataEntry *entry = GetDataEntry(0x0020,0x0032);
951 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
952 entry = GetDataEntry(0x0020,0x0030);
955 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
960 if( entry->GetValueCount() == 3 )
962 if (!entry->IsValueCountValid() )
964 gdcmErrorMacro( "Invalid Value Count" );
966 return (float)entry->GetValue(1);
972 * \brief gets the info from 0020,0032 : Image Position Patient
973 * else from 0020,0030 : Image Position (RET)
974 * else from 0020,1041 : Slice Location
975 * else from 0020,0050 : Location
977 * @return up-left image corner Z position
979 float File::GetZOrigin()
981 DataEntry *entry = GetDataEntry(0x0020,0x0032);
984 if( entry->GetValueCount() == 3 )
986 if (!entry->IsValueCountValid() )
988 gdcmErrorMacro( "Invalid Value Count" );
990 return (float)entry->GetValue(2);
992 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
996 entry = GetDataEntry(0x0020,0x0030);
999 if( entry->GetValueCount() == 3 )
1001 if (!entry->IsValueCountValid() )
1003 gdcmErrorMacro( "Invalid Value Count" );
1005 return (float)entry->GetValue(2);
1007 gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
1011 // for *very* old ACR-NEMA images
1012 entry = GetDataEntry(0x0020,0x1041);
1015 if( entry->GetValueCount() == 1 )
1017 if (!entry->IsValueCountValid() )
1019 gdcmErrorMacro( "Invalid Value Count" );
1021 return (float)entry->GetValue(0); // VM=1 !
1023 gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
1027 entry = GetDataEntry(0x0020,0x0050);
1030 if( entry->GetValueCount() == 1 )
1032 if (!entry->IsValueCountValid() )
1034 gdcmErrorMacro( "Invalid Value Count" );
1036 return (float)entry->GetValue(0);
1038 gdcmWarningMacro( "Wrong Location (0020,0050)");
1041 return 0.; // Hopeless
1045 * \brief gets the info from 0020,0037 : Image Orientation Patient
1046 * or from 0020 0035 : Image Orientation (RET)
1048 * (needed to organize DICOM files based on their x,y,z position)
1050 * @param iop adress of the (6)float array to receive values.
1051 * (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff-
1053 * @return true when one of the tag -with consistent values- is found
1054 * false when nothing or inconsistent stuff - is found
1056 bool File::GetImageOrientationPatient( float iop[6] )
1058 std::string strImOriPat;
1059 //iop is supposed to be float[6]
1060 iop[0] = iop[4] = 1.;
1061 iop[1] = iop[2] = iop[3] = iop[5] = 0.;
1063 // 0020 0037 DS REL Image Orientation (Patient)
1064 if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
1066 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
1067 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
1069 gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
1070 << " Less than 6 values were found." );
1076 // 0020 0035 DS REL Image Orientation (RET)
1077 else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND )
1079 if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
1080 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
1082 gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
1083 << "Less than 6 values were found." );
1092 * \brief gets the cosine of image X axis, against patient X axis
1093 * (Sorry, but Python needs it :-( )
1094 * @return cosine of image X axis, against patient X axis
1096 float File::GetXCosineOnX()
1099 GetImageOrientationPatient( iop );
1104 * \brief gets the cosine of image X axis, against patient Y axis
1105 * (Sorry, but Python needs it :-( )
1106 * @return cosine of image X axis, against patient Y axis
1108 float File::GetXCosineOnY()
1111 GetImageOrientationPatient( iop );
1116 * \brief gets the cosine of image X axis, against patient Z axis
1117 * (Sorry, but Python needs it :-( )
1118 * @return cosine of image X axis, against patient Z axis
1120 float File::GetXCosineOnZ()
1123 GetImageOrientationPatient( iop );
1128 * \brief gets the cosine of image Y axis, against patient X axis
1129 * (Sorry, but Python needs it :-( )
1130 * @return cosine of image Y axis, against patient X axis
1132 float File::GetYCosineOnX()
1135 GetImageOrientationPatient( iop );
1140 * \brief gets the cosine of image Y axis, against patient Y axis
1141 * (Sorry, but Python needs it :-( )
1142 * @return cosine of image Y axis, against patient Y axis
1144 float File::GetYCosineOnY()
1147 GetImageOrientationPatient( iop );
1152 * \brief gets the cosine of image Y axis, against patient Z axis
1153 * (Sorry, but Python needs it :-( )
1154 * @return cosine of image Y axis, against patient Z axis
1156 float File::GetYCosineOnZ()
1159 GetImageOrientationPatient( iop );
1163 * \brief gets the info from 0020,0032 : Image Position Patient
1164 * or from 0020 0030 : Image Position (RET)
1166 * @param ipp adress of the (3)float array to receive values.
1167 * (defaulted as 0.,0.,0. if nothing -or inconsistent stuff-
1169 * @return true when one of the tag -with consistent values- is found
1170 * false when nothing or inconsistent stuff - is found
1172 bool File::GetImagePositionPatient( float ipp[3] )
1174 std::string strImPosiPat;
1175 //ipp is supposed to be float[3]
1176 ipp[0] = ipp[1] = ipp[2] = 0.;
1178 // 0020 0032 DS REL Image Position (Patient)
1179 strImPosiPat = GetEntryString(0x0020,0x0032);
1180 if ( strImPosiPat != GDCM_UNFOUND )
1182 if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ",
1183 &ipp[0], &ipp[1], &ipp[2]) != 3 )
1185 gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)."
1186 << " Less than 3 values were found." );
1192 // 0020 0030 DS REL Image Position (RET)
1193 else if ( (strImPosiPat = GetEntryString(0x0020,0x0030)) != GDCM_UNFOUND )
1195 if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ",
1196 &ipp[0], &ipp[1], &ipp[2]) != 3 )
1198 gdcmWarningMacro( "wrong Image Position Patient (0020,0030). "
1199 << "Less than 3 values were found." );
1208 * \brief Retrieve the number of Bits Stored (actually used)
1209 * (as opposed to number of Bits Allocated)
1210 * @return The encountered number of Bits Stored, 0 by default.
1211 * 0 means the file is NOT USABLE. The caller has to check it !
1213 int File::GetBitsStored()
1215 DataEntry *entry = GetDataEntry(0x0028,0x0101);
1218 gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory");
1221 return (int)entry->GetValue(0);
1225 * \brief Retrieve the number of Bits Allocated
1226 * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,)
1227 * @return The encountered Number of Bits Allocated, 0 by default.
1228 * 0 means the file is NOT USABLE. The caller has to check it !
1230 int File::GetBitsAllocated()
1232 DataEntry *entry = GetDataEntry(0x0028,0x0100);
1235 gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory");
1238 return (int)entry->GetValue(0);
1242 * \brief Retrieve the high bit position.
1243 * \warning The method defaults to 0 when information is missing.
1244 * The responsability of checking this value is left to the caller.
1245 * @return The high bit position when present. 0 when missing.
1247 int File::GetHighBitPosition()
1249 DataEntry *entry = GetDataEntry(0x0028,0x0102);
1252 gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory");
1255 return (int)entry->GetValue(0);
1259 * \brief Retrieve the number of Samples Per Pixel
1260 * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
1261 * @return The encountered number of Samples Per Pixel, 1 by default.
1262 * (we assume Gray level Pixels)
1264 int File::GetSamplesPerPixel()
1266 DataEntry *entry = GetDataEntry(0x0028,0x0002);
1269 gdcmWarningMacro("SamplesPerPixel (0028,0002) is supposed to be mandatory");
1270 return 1; // Well, it's supposed to be mandatory ...
1271 // but sometimes it's missing : *we* assume Gray pixels
1273 return (int)entry->GetValue(0);
1277 * \brief Retrieve the Planar Configuration for RGB images
1278 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
1279 * @return The encountered Planar Configuration, 0 by default.
1281 int File::GetPlanarConfiguration()
1283 DataEntry *entry = GetDataEntry(0x0028,0x0006);
1288 return (int)entry->GetValue(0);
1292 * \brief Return the size (in bytes) of a single pixel of data.
1293 * @return The size in bytes of a single pixel of data; 0 by default
1294 * 0 means the file is NOT USABLE; the caller will have to check
1296 int File::GetPixelSize()
1298 // 0028 0100 US IMG Bits Allocated
1299 // (in order no to be messed up by old ACR-NEMA RGB images)
1300 assert( !(GetEntryString(0x0028,0x0100) == "24") );
1302 std::string pixelType = GetPixelType();
1303 if ( pixelType == "8U" || pixelType == "8S" )
1307 if ( pixelType == "16U" || pixelType == "16S")
1311 if ( pixelType == "32U" || pixelType == "32S")
1315 if ( pixelType == "FD" )
1319 gdcmWarningMacro( "Unknown pixel type: " << pixelType);
1324 * \brief Build the Pixel Type of the image.
1325 * Possible values are:
1326 * - 8U unsigned 8 bit,
1327 * - 8S signed 8 bit,
1328 * - 16U unsigned 16 bit,
1329 * - 16S signed 16 bit,
1330 * - 32U unsigned 32 bit,
1331 * - 32S signed 32 bit,
1332 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
1333 * \warning 12 bit images appear as 16 bit.
1334 * 24 bit images appear as 8 bit + photochromatic interp ="RGB "
1335 * + Planar Configuration = 0
1336 * @return 0S if nothing found. NOT USABLE file. The caller has to check
1338 std::string File::GetPixelType()
1340 std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated
1341 if ( bitsAlloc == GDCM_UNFOUND )
1343 gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory");
1344 bitsAlloc = "16"; // default and arbitrary value, not to polute the output
1347 else if ( bitsAlloc == "64" )
1351 // useless since we have to bypass a bug ( >8 && < 16)
1352 else if ( bitsAlloc == "12" )
1354 // It will be unpacked
1358 else if ( bitsAlloc == "24" )
1360 // (in order no to be messed up by old RGB images)
1364 int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers
1365 if ( i > 8 && i < 16 )
1371 if( IsSignedPixelData() )
1379 return bitsAlloc + sign;
1383 * \brief Check whether the pixels are signed (1) or UNsigned (0) data.
1384 * \warning The method defaults to false (UNsigned) when tag 0028|0103
1386 * The responsability of checking this value is left to the caller
1387 * (NO transformation is performed on the pixels to make then >0)
1388 * @return True when signed, false when UNsigned
1390 bool File::IsSignedPixelData()
1392 DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation"
1395 gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be "
1399 return entry->GetValue(0) != 0;
1403 * \brief Check whether this a monochrome picture (gray levels) or not,
1404 * using "Photometric Interpretation" tag (0x0028,0x0004).
1405 * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
1407 bool File::IsMonochrome()
1409 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1410 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
1411 || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
1415 if ( PhotometricInterp == GDCM_UNFOUND )
1417 gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be "
1419 // to deal with old ACR-NEMA images
1420 if (GetNumberOfScalarComponents() == 1)
1427 * \brief Check whether this a MONOCHROME1 picture (high values = dark)
1428 * or not using "Photometric Interpretation" tag (0x0028,0x0004).
1429 * @return true when "MONOCHROME1" . False otherwise.
1431 bool File::IsMonochrome1()
1433 const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1434 if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") )
1438 if ( PhotometricInterp == GDCM_UNFOUND )
1440 gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to"
1441 << " be mandatory! ");
1447 * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
1448 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1449 * @return true when "PALETTE COLOR". False otherwise.
1451 bool File::IsPaletteColor()
1453 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1454 if ( PhotometricInterp == "PALETTE COLOR " )
1458 if ( PhotometricInterp == GDCM_UNFOUND )
1460 gdcmDebugMacro( "Not found : Palette color (0028,0004)");
1466 * \brief Check whether this a "YBR_FULL" color picture or not by accessing
1467 * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
1468 * @return true when "YBR_FULL". False otherwise.
1470 bool File::IsYBRFull()
1472 std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 );
1473 if ( PhotometricInterp == "YBR_FULL" )
1477 if ( PhotometricInterp == GDCM_UNFOUND )
1479 gdcmDebugMacro( "Not found : YBR Full (0028,0004)");
1485 * \brief tells us if LUT are used
1486 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
1487 * are NOT considered as LUT, since nobody knows
1488 * how to deal with them
1489 * Please warn me if you know sbdy that *does* know ... jprx
1490 * @return true if LUT Descriptors and LUT Tables were found
1494 // Check the presence of the LUT Descriptors, and LUT Tables
1496 if ( !GetDocEntry(0x0028,0x1101) )
1500 // LutDescriptorGreen
1501 if ( !GetDocEntry(0x0028,0x1102) )
1505 // LutDescriptorBlue
1506 if ( !GetDocEntry(0x0028,0x1103) )
1510 // Red Palette Color Lookup Table Data
1511 if ( !GetDocEntry(0x0028,0x1201) )
1515 // Green Palette Color Lookup Table Data
1516 if ( !GetDocEntry(0x0028,0x1202) )
1520 // Blue Palette Color Lookup Table Data
1521 if ( !GetDocEntry(0x0028,0x1203) )
1526 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
1527 // NOT taken into account, but we don't know how to use it ...
1532 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
1534 * @return Lookup Table number of Bits , 0 by default
1535 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
1536 * @ return bit number of each LUT item
1538 int File::GetLUTNbits()
1540 std::vector<std::string> tokens;
1543 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
1544 // = Lookup Table Desc-Blue
1545 // Consistency already checked in GetLUTLength
1546 std::string lutDescription = GetEntryString(0x0028,0x1101);
1547 if ( lutDescription == GDCM_UNFOUND )
1552 tokens.clear(); // clean any previous value
1553 Util::Tokenize ( lutDescription, tokens, "\\" );
1554 //LutLength=atoi(tokens[0].c_str());
1555 //LutDepth=atoi(tokens[1].c_str());
1557 lutNbits = atoi( tokens[2].c_str() );
1564 // ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage";
1565 bool File::GetRescaleSlopeIntercept(double &slope, double &intercept)
1569 TS *ts = Global::GetTS();
1570 std::string sopclassuid_used;
1571 // D 0002|0002 [UI] [Media Storage SOP Class UID]
1572 const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002);
1573 const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str);
1574 //D 0008|0016 [UI] [SOP Class UID]
1575 const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016);
1576 const std::string &sopclassuid = ts->GetValue(sopclassuid_str);
1577 if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND )
1583 if( mediastoragesopclassuid == sopclassuid )
1585 sopclassuid_used = mediastoragesopclassuid;
1589 gdcmWarningMacro( "Inconsistant SOP Class UID: "
1590 << mediastoragesopclassuid << " and " << sopclassuid );
1594 // ok we have now the correc SOP Class UID
1595 if( sopclassuid_used == "Enhanced MR Image Storage" )
1597 SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230);
1598 unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems();
1599 if( !n ) return false;
1600 SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem();
1601 DocEntry *p = item1->GetDocEntry(0x0028,0x9145);
1602 if( !p ) return false;
1603 SeqEntry *seq = dynamic_cast<SeqEntry*>(p);
1604 unsigned int n1 = seq->GetNumberOfSQItems();
1605 if( !n1 ) return false;
1606 SQItem *item2 = seq->GetFirstSQItem();
1607 // D 0028|1052 [DS] [Rescale Intercept] [0 ]
1608 DocEntry *p2 = item2->GetDocEntry(0x0028,0x1052);
1609 if( !p2 ) return false;
1610 DataEntry *entry = dynamic_cast<DataEntry *>(p2);
1611 std::string intercept_str = entry->GetString();
1612 if ( sscanf( intercept_str.c_str(), "%lf", &intercept) != 1 )
1617 // D 0028|1053 [DS] [Rescale Slope] [5.65470085470085]
1618 DocEntry *p3 = item2->GetDocEntry(0x0028,0x1053);
1619 if( !p3 ) return false;
1620 DataEntry *entry2 = dynamic_cast<DataEntry *>(p3);
1621 std::string slope_str = entry2->GetString();
1622 if ( sscanf( slope_str.c_str(), "%lf", &slope) != 1 )
1633 *\brief gets the info from 0028,1052 : Rescale Intercept
1634 * @return Rescale Intercept. defaulted to 0.0 if not found or empty
1636 double File::GetRescaleIntercept()
1638 // 0028 1052 DS IMG Rescale Intercept
1639 DataEntry *entry = GetDataEntry(0x0028, 0x1052);
1642 gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)");
1645 return (float)entry->GetValue(0);
1650 *\brief gets the info from 0028,1053 : Rescale Slope
1651 * @return Rescale Slope. defaulted to 1.0 if not found or empty
1653 double File::GetRescaleSlope()
1655 double resInter = 0.;
1656 double resSlope = 1.;
1657 if ( GetRescaleSlopeIntercept(resSlope, resInter) )
1661 //0028 1053 DS IMG Rescale Slope
1662 std::string strRescSlope = GetEntryString(0x0028,0x1053);
1663 if ( strRescSlope != GDCM_UNFOUND )
1665 if ( sscanf( strRescSlope.c_str(), "%lf ", &resSlope) != 1 )
1667 // bug in the element 0x0028,0x1053
1668 gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
1676 * \brief This function is intended to user who doesn't want
1677 * to have to manage a LUT and expects to get an RBG Pixel image
1678 * (or a monochrome one, if no LUT found ...)
1679 * \warning to be used with GetImagePixels()
1680 * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
1682 int File::GetNumberOfScalarComponents()
1684 if ( GetSamplesPerPixel() == 3 )
1689 // 0028 0100 US IMG Bits Allocated
1690 // (in order no to be messed up by old RGB images)
1691 if ( GetEntryString(0x0028,0x0100) == "24" )
1696 std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004);
1698 if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
1700 if ( HasLUT() )// PALETTE COLOR is NOT enough
1710 // beware of trailing space at end of string
1711 // DICOM tags are never of odd length
1712 if ( strPhotometricInterpretation == GDCM_UNFOUND ||
1713 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
1714 Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
1720 // we assume that *all* kinds of YBR are dealt with
1726 * \brief This function is intended to user that DOESN'T want
1727 * to get RGB pixels image when it's stored as a PALETTE COLOR image
1728 * - the (vtk) user is supposed to know how deal with LUTs -
1729 * \warning to be used with GetImagePixelsRaw()
1730 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
1732 int File::GetNumberOfScalarComponentsRaw()
1734 // 0028 0100 US IMG Bits Allocated
1735 // (in order no to be messed up by old RGB images)
1736 if ( File::GetEntryString(0x0028,0x0100) == "24" )
1741 // we assume that *all* kinds of YBR are dealt with
1742 return GetSamplesPerPixel();
1746 * \brief Recover the offset (from the beginning of the file)
1747 * of *image* pixels (not *icone image* pixels, if any !)
1748 * @return Pixel Offset
1750 size_t File::GetPixelOffset()
1752 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1755 return pxlElement->GetOffset();
1759 gdcmWarningMacro( "Big trouble : Pixel Element ("
1760 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1766 * \brief Recover the pixel area length (in Bytes)
1767 * @return Pixel Element Length, as stored in the header
1768 * (NOT the memory space necessary to hold the Pixels
1769 * -in case of embeded compressed image-)
1770 * 0 : NOT USABLE file. The caller has to check.
1772 size_t File::GetPixelAreaLength()
1774 DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel);
1777 return pxlElement->GetLength();
1781 gdcmWarningMacro( "Big trouble : Pixel Element ("
1782 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
1788 * \brief Adds the characteristics of a new element we want to anonymize
1789 * @param group Group number of the target tag.
1790 * @param elem Element number of the target tag.
1791 * @param value new value (string) to substitute with
1793 void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
1794 std::string const &value)
1800 UserAnonymizeList.push_back(el);
1804 * \brief Overwrites in the file the values of the DicomElements
1807 void File::AnonymizeNoLoad()
1809 std::fstream *fp = new std::fstream(Filename.c_str(),
1810 std::ios::in | std::ios::out | std::ios::binary);
1811 GDCM_NAME_SPACE::DocEntry *d;
1814 uint32_t valLgth = 0;
1815 std::string *spaces;
1816 for (ListElements::iterator it = UserAnonymizeList.begin();
1817 it != UserAnonymizeList.end();
1821 //std::cout << "File::AnonymizeNoLoad -------" << std::hex <<(*it).Group <<"|"<<
1823 // << "[" << (*it).Value << "] "<< std::dec << std::endl;
1824 d = GetDocEntry( (*it).Group, (*it).Elem);
1829 if ( dynamic_cast<SeqEntry *>(d) )
1831 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1835 valLgth = (*it).Value.size();
1839 offset = d->GetOffset();
1840 lgth = d->GetLength();
1842 //std::cout << "lgth " << lgth << " valLgth " << valLgth << std::endl;
1845 spaces = new std::string( lgth-valLgth, ' ');
1846 (*it).Value = (*it).Value + *spaces;
1847 //std::cout << "[" << (*it).Value << "] " << lgth << std::endl;
1850 fp->seekp( offset, std::ios::beg );
1851 fp->write( (*it).Value.c_str(), lgth );
1859 * \brief anonymize a File (remove Patient's personal info passed with
1860 * AddAnonymizeElement()
1861 * \note You cannot Anonymize a DataEntry (to be fixed)
1863 bool File::AnonymizeFile()
1865 // If Anonymisation list is empty, let's perform some basic anonymization
1866 if ( UserAnonymizeList.begin() == UserAnonymizeList.end() )
1868 // If exist, replace by spaces
1869 SetEntryString(" ",0x0010, 0x2154); // Telephone
1870 SetEntryString(" ",0x0010, 0x1040); // Adress
1871 SetEntryString(" ",0x0010, 0x0020); // Patient ID
1873 DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010);
1875 if ( patientNameHE ) // we replace it by Study Instance UID (why not ?)
1877 std::string studyInstanceUID = GetEntryString (0x0020, 0x000d);
1878 if ( studyInstanceUID != GDCM_UNFOUND )
1880 SetEntryString(studyInstanceUID, 0x0010, 0x0010);
1884 SetEntryString("anonymized", 0x0010, 0x0010);
1890 GDCM_NAME_SPACE::DocEntry *d;
1891 for (ListElements::iterator it = UserAnonymizeList.begin();
1892 it != UserAnonymizeList.end();
1895 d = GetDocEntry( (*it).Group, (*it).Elem);
1900 if ( dynamic_cast<SeqEntry *>(d) )
1902 gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
1906 if ( dynamic_cast<DataEntry *>(d) )
1908 gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) ");
1912 SetEntryString ((*it).Value, (*it).Group, (*it).Elem);
1916 // In order to make definitively impossible any further identification
1917 // remove or replace all the stuff that contains a Date
1919 //0008 0012 DA ID Instance Creation Date
1920 //0008 0020 DA ID Study Date
1921 //0008 0021 DA ID Series Date
1922 //0008 0022 DA ID Acquisition Date
1923 //0008 0023 DA ID Content Date
1924 //0008 0024 DA ID Overlay Date
1925 //0008 0025 DA ID Curve Date
1926 //0008 002a DT ID Acquisition Datetime
1927 //0018 9074 DT ACQ Frame Acquisition Datetime
1928 //0018 9151 DT ACQ Frame Reference Datetime
1929 //0018 a002 DT ACQ Contribution Date Time
1930 //0020 3403 SH REL Modified Image Date (RET)
1931 //0032 0032 DA SDY Study Verified Date
1932 //0032 0034 DA SDY Study Read Date
1933 //0032 1000 DA SDY Scheduled Study Start Date
1934 //0032 1010 DA SDY Scheduled Study Stop Date
1935 //0032 1040 DA SDY Study Arrival Date
1936 //0032 1050 DA SDY Study Completion Date
1937 //0038 001a DA VIS Scheduled Admission Date
1938 //0038 001c DA VIS Scheduled Discharge Date
1939 //0038 0020 DA VIS Admitting Date
1940 //0038 0030 DA VIS Discharge Date
1941 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1942 //0040 0004 DA PRC Scheduled Procedure Step End Date
1943 //0040 0244 DA PRC Performed Procedure Step Start Date
1944 //0040 0250 DA PRC Performed Procedure Step End Date
1945 //0040 2004 DA PRC Issue Date of Imaging Service Request
1946 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1947 //0040 4011 DT PRC Expected Completion Date and Time
1948 //0040 a030 DT PRC Verification Date Time
1949 //0040 a032 DT PRC Observation Date Time
1950 //0040 a120 DT PRC DateTime
1951 //0040 a121 DA PRC Date
1952 //0040 a13a DT PRC Referenced Datetime
1953 //0070 0082 DA ??? Presentation Creation Date
1954 //0100 0420 DT ??? SOP Autorization Date and Time
1955 //0400 0105 DT ??? Digital Signature DateTime
1956 //2100 0040 DA PJ Creation Date
1957 //3006 0008 DA SSET Structure Set Date
1958 //3008 0024 DA ??? Treatment Control Point Date
1959 //3008 0054 DA ??? First Treatment Date
1960 //3008 0056 DA ??? Most Recent Treatment Date
1961 //3008 0162 DA ??? Safe Position Exit Date
1962 //3008 0166 DA ??? Safe Position Return Date
1963 //3008 0250 DA ??? Treatment Date
1964 //300a 0006 DA RT RT Plan Date
1965 //300a 022c DA RT Air Kerma Rate Reference Date
1966 //300e 0004 DA RT Review Date
1972 * \brief Performs some consistency checking on various 'File related'
1973 * (as opposed to 'DicomDir related') entries
1974 * then writes in a file all the (Dicom Elements) included the Pixels
1975 * @param fileName file name to write to
1976 * @param writetype type of the file to be written
1977 * (ACR, ExplicitVR, ImplicitVR)
1979 bool File::Write(std::string fileName, FileType writetype)
1981 gdcmDebugMacro(" File::Write ");
1982 std::ofstream *fp = new std::ofstream(fileName.c_str(),
1983 std::ios::out | std::ios::binary);
1986 gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
1990 // Entry : 0002|0000 = group length -> recalculated
1991 DataEntry *e0000 = GetDataEntry(0x0002,0x0000);
1994 std::ostringstream sLen;
1995 sLen << ComputeGroup0002Length( );
1996 e0000->SetString(sLen.str());
1999 /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx
2000 if( writetype != JPEG && writetype != JPEG2000)
2002 int i_lgPix = GetEntryLength(GrPixel, NumPixel);
2003 if (i_lgPix != -2) /// \todo wtf "-2" ?!?
2005 // no (GrPixel, NumPixel) element
2006 std::string s_lgPix = Util::Format("%d", i_lgPix+12);
2007 s_lgPix = Util::DicomString( s_lgPix.c_str() );
2008 InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL");
2011 Document::WriteContent(fp, writetype);
2019 //-----------------------------------------------------------------------------
2023 //-----------------------------------------------------------------------------
2026 * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
2027 * Compute the RLE extra information and store it in \ref RLEInfo
2028 * for later pixel retrieval usage.
2030 void File::ComputeRLEInfo()
2032 std::string ts = GetTransferSyntax();
2033 if ( !Global::GetTS()->IsRLELossless(ts) )
2038 // Encoded pixel data: for the time being we are only concerned with
2039 // Jpeg or RLE Pixel data encodings.
2040 // As stated in PS 3.5-2003, section 8.2 p44:
2041 // "If sent in Encapsulated Format (i.e. other than the Native Format) the
2042 // value representation OB is used".
2043 // Hence we expect an OB value representation. Concerning OB VR,
2044 // the section PS 3.5-2003, section A.4.c p 58-59, states:
2045 // "For the Value Representations OB and OW, the encoding shall meet the
2046 // following specifications depending on the Data element tag:"
2048 // - the first item in the sequence of items before the encoded pixel
2049 // data stream shall be basic offset table item. The basic offset table
2050 // item value, however, is not required to be present"
2051 ReadEncapsulatedBasicOffsetTable();
2053 // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
2054 // Loop on the individual frame[s] and store the information
2055 // on the RLE fragments in a RLEFramesInfo.
2056 // Note: - when only a single frame is present, this is a
2058 // - when more than one frame are present, then we are in
2059 // the case of a multi-frame image.
2063 while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
2065 // Since we have read the basic offset table, let's check the value were correct
2066 // or else produce a warning:
2067 if ( BasicOffsetTableItemValue )
2069 // If a BasicOffsetTableItemValue was read
2070 uint32_t individualLength = BasicOffsetTableItemValue[i];
2071 assert( individualLength == sum ); // REMOVE that if this is a problem
2072 if( individualLength != sum )
2074 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" );
2076 sum += frameLength + 8;
2079 // Parse the RLE Header and store the corresponding RLE Segment
2080 // Offset Table information on fragments of this current Frame.
2081 // Note that the fragment pixels themselves are not loaded
2082 // (but just skipped).
2083 long frameOffset = Fp->tellg(); // once per fragment
2085 uint32_t nbRleSegments = ReadInt32();
2086 if ( nbRleSegments > 16 )
2088 // There should be at most 15 segments (refer to RLEFrame class)
2089 gdcmWarningMacro( "Too many segments.");
2092 uint32_t rleSegmentOffsetTable[16];
2093 for( int k = 1; k <= 15; k++ )
2095 rleSegmentOffsetTable[k] = ReadInt32();
2098 // Deduce from both RLE Header and frameLength
2099 // the fragment length, and again store this info
2100 // in a RLEFramesInfo.
2101 long rleSegmentLength[15];
2102 // skipping (not reading) RLE Segments
2103 if ( nbRleSegments > 1)
2105 for(unsigned int k = 1; k <= nbRleSegments-1; k++)
2107 rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
2108 - rleSegmentOffsetTable[k];
2109 SkipBytes(rleSegmentLength[k]);
2113 rleSegmentLength[nbRleSegments] = frameLength
2114 - rleSegmentOffsetTable[nbRleSegments];
2115 SkipBytes(rleSegmentLength[nbRleSegments]);
2117 // Store the collected info
2118 RLEFrame *newFrame = new RLEFrame;
2119 newFrame->SetNumberOfFragments(nbRleSegments);
2120 for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
2122 newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
2123 newFrame->SetLength(uk,rleSegmentLength[uk]);
2125 RLEInfo->AddFrame(newFrame);
2128 // Make sure that we encounter a 'Sequence Delimiter Item'
2129 // at the end of the item :
2130 if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File
2132 gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
2137 * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
2138 * Compute the jpeg extra information (fragment[s] offset[s] and
2139 * length) and store it[them] in \ref JPEGInfo for later pixel
2142 void File::ComputeJPEGFragmentInfo()
2144 // If you need to, look for comments of ComputeRLEInfo().
2145 std::string ts = GetTransferSyntax();
2146 if ( ! Global::GetTS()->IsJPEG(ts) )
2151 ReadEncapsulatedBasicOffsetTable();
2153 // Loop on the fragments[s] and store the parsed information in a
2155 long fragmentLength;
2158 while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
2160 // Since we have read the basic offset table, let's check the value were correct
2161 // or else produce a warning:
2162 // A.4 Transfer syntaxes for encapsulation of encoded pixel data:
2163 // When the Item Value is present, the Basic Offset Table Item Value shall contain
2164 // concatenated 32-bit unsigned integer values that are byte offsets to the first
2165 // byte of the Item Tag of the first fragment for each frame in the Sequence of
2166 // Items. These offsets are measured from the first byte of the first Item Tag
2167 // following the Basic Offset Table item (See Table A.4-2).
2169 if ( BasicOffsetTableItemValue )
2171 // If a BasicOffsetTableItemValue was read
2172 uint32_t individualLength = BasicOffsetTableItemValue[i];
2173 //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ??
2174 if( individualLength != sum )
2176 gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" <<
2177 individualLength << " != " << sum );
2179 sum += fragmentLength + 8;
2183 long fragmentOffset = Fp->tellg(); // Once per fragment
2184 // Store the collected info
2185 JPEGFragment *newFragment = new JPEGFragment;
2186 newFragment->SetOffset(fragmentOffset);
2187 newFragment->SetLength(fragmentLength);
2188 JPEGInfo->AddFragment(newFragment);
2190 SkipBytes(fragmentLength);
2193 // Make sure that we encounter a 'Sequence Delimiter Item'
2194 // at the end of the item :
2195 if ( !ReadTag(0xfffe, 0xe0dd) )
2197 gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
2202 * \brief Assuming the internal file pointer \ref Document::Fp
2203 * is placed at the beginning of a tag, check whether this
2204 * tag is (TestGroup, TestElem).
2205 * \warning On success the internal file pointer \ref Document::Fp
2206 * is modified to point after the tag.
2207 * On failure (i.e. when the tag wasn't the expected tag
2208 * (TestGroup, TestElem) the internal file pointer
2209 * \ref Document::Fp is restored to its original position.
2210 * @param testGroup The expected group of the tag.
2211 * @param testElem The expected Element of the tag.
2212 * @return True on success, false otherwise.
2214 bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
2216 long positionOnEntry = Fp->tellg(); // Only when reading fragments
2217 //long currentPosition = positionOnEntry; // On debugging purposes
2219 // Read the Item Tag group and element, and make
2220 // sure they are what we expected:
2221 uint16_t itemTagGroup;
2222 uint16_t itemTagElem;
2225 itemTagGroup = ReadInt16();
2226 itemTagElem = ReadInt16();
2228 catch ( FormatError )
2230 gdcmErrorMacro( "Can not read tag for "
2231 << " We should have found tag ("
2232 << DictEntry::TranslateToKey(testGroup,testElem) << ")"
2237 if ( itemTagGroup != testGroup || itemTagElem != testElem )
2239 // in order not to pollute output we don't warn on 'delimitors'
2240 if (itemTagGroup != 0xfffe || testGroup != 0xfffe )
2241 gdcmWarningMacro( "Wrong Item Tag found:"
2242 << " We should have found tag ("
2243 << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl
2244 << " but instead we encountered tag ("
2245 << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")"
2246 << " at address: " << " 0x(" << std::hex
2247 << (unsigned int)positionOnEntry << std::dec << ")"
2249 Fp->seekg(positionOnEntry, std::ios::beg);
2257 * \brief Assuming the internal file pointer \ref Document::Fp
2258 * is placed at the beginning of a tag (TestGroup, TestElement),
2259 * read the length associated to the Tag.
2260 * \warning On success the internal file pointer \ref Document::Fp
2261 * is modified to point after the tag and its length.
2262 * On failure (i.e. when the tag wasn't the expected tag
2263 * (TestGroup, TestElement) the internal file pointer
2264 * \ref Document::Fp is restored to its original position.
2265 * @param testGroup The expected Group of the tag.
2266 * @param testElem The expected Element of the tag.
2267 * @return On success returns the length associated to the tag. On failure
2270 uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
2273 if ( !ReadTag(testGroup, testElem) )
2275 // Avoid polutting output
2276 if ( testGroup != 0xfffe )
2277 gdcmErrorMacro( "ReadTag did not succeed for ("
2278 << DictEntry::TranslateToKey(testGroup,testElem)
2283 //// Then read the associated Item Length
2285 // long currentPosition = Fp->tellg(); // save time // JPRx
2286 uint32_t itemLength = ReadInt32();
2287 gdcmDebugMacro( "Basic Item Length is: " << itemLength
2288 // << " at address: " << std::hex << (unsigned int)currentPosition
2294 * \brief When parsing the Pixel Data of an encapsulated file, read
2295 * the basic offset table (when present, and BTW dump it).
2297 void File::ReadEncapsulatedBasicOffsetTable()
2299 //// Read the Basic Offset Table Item Tag length...
2300 uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
2302 // When present, read the basic offset table itself.
2303 // Notes: - since the presence of this basic offset table is optional
2304 // we can't rely on it for the implementation, and we will simply
2305 // trash its content (when present).
2306 // - still, when present, we could add some further checks on the
2307 // lengths, but we won't bother with such fuses for the time being.
2308 if ( itemLength != 0 )
2310 char *charBasicOffsetTableItemValue = new char[itemLength];
2311 Fp->read(charBasicOffsetTableItemValue, itemLength);
2312 unsigned int nbEntries = itemLength/4;
2313 assert( nbEntries*4 == itemLength); // Make sure this is a multiple
2314 BasicOffsetTableItemValue = new uint32_t[nbEntries];
2316 for (unsigned int i=0; i < nbEntries; i++ )
2318 BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i]));
2319 #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION)
2320 uint32_t val = BasicOffsetTableItemValue[i];
2321 BasicOffsetTableItemValue[i]
2322 = ( (val<<24) | ((val<<8) & 0x00ff0000) |
2323 ( (val>>8) & 0x0000ff00) | (val>>24) );
2325 gdcmDebugMacro( "Read one length for: " <<
2326 std::hex << BasicOffsetTableItemValue[i] );
2329 delete[] charBasicOffsetTableItemValue;
2333 // These are the deprecated method that one day should be removed (after the next release)
2335 //#ifndef GDCM_LEGACY_REMOVE
2337 * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API)
2338 * @ param fileName file to be open for parsing
2339 * @ return false if file cannot be open or no swap info was found,
2340 * or no tag was found.
2341 * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
2344 bool File::Load( std::string const &fileName )
2346 GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
2348 SetFileName( fileName );
2349 if ( ! this->Document::Load( ) )
2352 return DoTheLoadingJob( );
2356 //-----------------------------------------------------------------------------
2359 //-----------------------------------------------------------------------------
2360 } // end namespace gdcm