1 /*=========================================================================
4 Module: $RCSfile: gdcmSerieHelper.cxx,v $
6 Date: $Date: 2006/04/11 16:03:26 $
7 Version: $Revision: 1.51 $
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 =========================================================================*/
19 #include "gdcmSerieHelper.h"
20 #include "gdcmDirList.h"
22 //#include "gdcmDictEntry.h" // for TranslateToKey : no more !
23 #include "gdcmDebug.h"
30 #include <stdio.h> //for sscanf
35 //-----------------------------------------------------------------------------
36 // Constructor / Destructor
38 * \brief Constructor from a given SerieHelper
40 SerieHelper::SerieHelper()
42 m_UseSeriesDetails = false;
44 UserLessThanFunction = 0;
49 * \brief Canonical destructor.
51 SerieHelper::~SerieHelper()
57 * \brief Preventively, clear everything at constructor time.
58 * ( use it at destructor time.)
60 void SerieHelper::ClearAll()
62 // For all the 'Single SerieUID' Filesets that may already exist
63 FileList *l = GetFirstSingleSerieUIDFileSet();
66 // For all the gdcm::File of a File set
67 for (gdcm::FileList::iterator it = l->begin();
71 (*it)->Delete(); // remove each entry
74 delete l; // remove the container
75 l = GetNextSingleSerieUIDFileSet();
77 // Need to clear that too:
78 SingleSerieUIDFileSetHT.clear();
81 //-----------------------------------------------------------------------------
83 //-----------------------------------------------------------------------------
87 * \brief add a gdcm::File to the Fileset corresponding to its Serie UID
88 * @param filename Name of the file to deal with
90 void SerieHelper::AddFileName(std::string const &filename)
92 // Create a DICOM file
93 File *header = File::New();
94 header->SetLoadMode(LoadMode);
95 header->SetFileName( filename );
98 if ( header->IsReadable() )
100 if ( !AddFile( header ) )
102 // at least one rule was unmatched we need to deallocate the file:
108 gdcmWarningMacro("Could not read file: " << filename );
114 * \brief add a gdcm::File to the first (and supposed to be unique) file set
115 * of the gdcm::SerieHelper.
116 * \warning : this method should be used by aware users only!
117 * Passing a gdcm::File* has the same effect than passing a file name!
118 * \todo : decide which one is wrong (the method, or the commentary)!
119 * the following comment doesn't match the method :-(
120 * User is supposed to know the files he want to deal with
121 * and consider them they belong to the same Serie
122 * (even if their Serie UID is different)
123 * user will probabely OrderFileList() this list (actually, ordering
124 * user choosen gdm::File is the sole interest of this method)
125 * Moreover, using vtkGdcmReader::SetCoherentFileList() will avoid
126 * vtkGdcmReader parsing twice the same files.
127 * *no* coherence check is performed, but those specified
128 * by SerieHelper::AddRestriction()
129 * @param header gdcm::File* of the file to deal with
130 * @return true if file was added, false if file was rejected
132 bool SerieHelper::AddFile(File *header)
135 // First step the user has defined a set of rules for the DICOM
136 // he is looking for.
137 // make sure the file correspond to his set of rules:
140 for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
141 it2 != ExRestrictions.end();
144 const ExRule &r = *it2;
145 s = header->GetEntryString( r.group, r.elem );
146 if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
148 // Argh ! This rule is unmatched; let's just quit
154 if ( allrules ) // all rules are respected:
156 // Allright! we have a found a DICOM that matches the user expectation.
157 // Let's add it to the specific 'id' which by default is uid (Serie UID)
158 // but can be `refined` by user with more paramater (see AddRestriction(g,e))
160 std::string id = CreateUniqueSeriesIdentifier( header );
161 // if id == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
162 // no need here to do anything special
164 if ( SingleSerieUIDFileSetHT.count(id) == 0 )
166 gdcmDebugMacro(" New Serie UID :[" << id << "]");
167 // create a std::list in 'id' position
168 SingleSerieUIDFileSetHT[id] = new FileList;
170 // Current Serie UID and DICOM header seems to match add the file:
171 SingleSerieUIDFileSetHT[id]->push_back( header );
175 // one rule not matched, tell user:
182 * \brief add a rule for restricting a DICOM file to be in the serie we are
183 * trying to find. For example you can select only the DICOM files from a
184 * directory which would have a particular EchoTime==4.0.
185 * This method is a user level, value is not required to be formatted as a DICOM
187 * \todo find a trick to allow user to say if he wants the Rectrictions
188 * to be *ored* (and not only *anded*)
189 * @param key Target tag we want restrict on a given value
190 * @param value value to be checked to exclude File
191 * @param op operator we want to use to check
193 void SerieHelper::AddRestriction(TagKey const &key,
194 std::string const &value, int op)
201 ExRestrictions.push_back( r );
204 void SerieHelper::AddRestriction(TagKey const &key)
209 ExRefine.push_back( r );
212 #ifndef GDCM_LEGACY_REMOVE
214 * \brief add a rule for restricting a DICOM file to be in the serie we are
215 * trying to find. For example you can select only the DICOM files from a
216 * directory which would have a particular EchoTime==4.0.
217 * This method is a user level, value is not required to be formatted as a DICOM
219 * @param group tag group number we want restrict on a given value
220 * @param elem tag element number we want restrict on a given value
221 * @param value value to be checked to exclude File
222 * @param op operator we want to use to check
223 * @deprecated use : AddRestriction(TagKey const &key,
224 * std::string const &value, int op);
226 void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
227 std::string const &value, int op)
229 TagKey t(group, elem);
230 AddRestriction(t, value, op);
235 * \brief add an extra 'SerieDetail' for building a 'Serie Identifier'
236 * that ensures (hope so) File constistency (Series Instance UID doesn't.
237 * @param group tag group number we want restrict on a given value
238 * @param elem tag element number we want restrict on a given value
239 * @param convert wether we want 'convertion', to allow further ordering
240 * e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK
242 void SerieHelper::AddSeriesDetail(uint16_t group, uint16_t elem, bool convert)
249 ExDetails.push_back( d );
252 * \brief Sets the root Directory
253 * @param dir Name of the directory to deal with
254 * @param recursive whether we want explore recursively the root Directory
256 void SerieHelper::SetDirectory(std::string const &dir, bool recursive)
258 DirList dirList(dir, recursive); // OS specific
260 DirListType filenames_list = dirList.GetFilenames();
261 for( DirListType::const_iterator it = filenames_list.begin();
262 it != filenames_list.end(); ++it)
269 * \brief Sorts the given Fileset
270 * \warning This could be implemented in a 'Strategy Pattern' approach
271 * But as I don't know how to do it, I leave it this way
272 * BTW, this is also a Strategy, I don't know this is
273 * the best approach :)
275 void SerieHelper::OrderFileList(FileList *fileSet)
277 // Only computed during ImagePositionPatientOrdering
278 // (need to sort the FileList using IPP and IOP !)
281 if ( SerieHelper::UserLessThanFunction )
283 UserOrdering( fileSet );
286 else if ( ImagePositionPatientOrdering( fileSet ) )
290 else if ( ImageNumberOrdering(fileSet ) )
296 FileNameOrdering(fileSet );
301 * \brief Elementary coherence checking of the files with the same Serie UID
302 * Only sizes and pixel type are checked right now ...
304 bool SerieHelper::IsCoherent(FileList *fileSet)
306 if(fileSet->size() == 1)
309 FileList::const_iterator it = fileSet->begin();
311 int nX = (*it)->GetXSize();
312 int nY = (*it)->GetYSize();
313 int pixelSize = (*it)->GetPixelSize();
314 bool signedPixelData = (*it)->IsSignedPixelData();
317 it != fileSet->end();
320 if ( (*it)->GetXSize() != nX )
322 if ( (*it)->GetYSize() != nY )
324 if ( (*it)->GetPixelSize() != pixelSize )
326 if ( (*it)->IsSignedPixelData() != signedPixelData )
328 // probabely more is to be checked (?)
333 #ifndef GDCM_LEGACY_REMOVE
335 * \brief accessor (DEPRECATED : use GetFirstSingleSerieUIDFileSet )
336 * Warning : 'coherent' means here they have the same Serie UID
337 * @return The first FileList if found, otherwhise NULL
339 FileList *SerieHelper::GetFirstCoherentFileList()
341 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
342 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
343 return ItFileSetHt->second;
348 * \brief accessor (DEPRECATED : use GetNextSingleSerieUIDFileSet )
349 * Warning : 'coherent' means here they have the same Serie UID
350 * \note : meaningfull only if GetFirstCoherentFileList() already called
351 * @return The next FileList if found, otherwhise NULL
353 FileList *SerieHelper::GetNextCoherentFileList()
355 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
358 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
359 return ItFileSetHt->second;
364 * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet )
365 * Warning : 'coherent' means here they have the same Serie UID
366 * @param SerieUID SerieUID
367 * \return pointer to the FileList if found, otherwhise NULL
369 FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
371 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
373 return SingleSerieUIDFileSetHT[SerieUID];
379 * \brief Get the first Fileset while visiting the SingleSerieUIDFileSetmap
380 * @return The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0
382 FileList *SerieHelper::GetFirstSingleSerieUIDFileSet()
384 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
385 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
386 return ItFileSetHt->second;
391 * \brief Get the next Fileset while visiting the SingleSerieUIDFileSetmap
392 * \note : meaningfull only if GetNextSingleSerieUIDFileSet() already called
393 * @return The next FileList (SingleSerieUIDFileSet) if found, otherwhise 0
395 FileList *SerieHelper::GetNextSingleSerieUIDFileSet()
397 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
400 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
401 return ItFileSetHt->second;
406 * \brief Get the SingleSerieUIDFileSet according to its Serie UID
407 * @param SerieUID SerieUID to retrieve
408 * \return pointer to the FileList (SingleSerieUIDFileSet) if found, otherwhise 0
410 FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID)
412 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
414 return SingleSerieUIDFileSetHT[SerieUID];
418 * \brief Splits a Single SerieUID Fileset according to the Orientations
419 * @param fileSet File Set to be splitted
420 * \return std::map of 'Xcoherent' File sets
423 XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet)
425 XCoherentFileSetmap CoherentFileSet;
427 int nb = fileSet->size();
429 return CoherentFileSet;
431 std::string strOrient;
432 std::ostringstream ossOrient;
434 FileList::const_iterator it = fileSet->begin();
437 it != fileSet->end();
440 // Information is in :
441 // 0020 0037 : Image Orientation (Patient) or
442 // 0020 0035 : Image Orientation (RET)
444 // Let's build again the 'cosines' string, to be sure of it's format
445 (*it)->GetImageOrientationPatient(iop);
448 for (int i = 1; i < 6; i++)
453 strOrient = ossOrient.str();
455 if ( CoherentFileSet.count(strOrient) == 0 )
457 gdcmDebugMacro(" New Orientation :[" << strOrient << "]");
458 // create a File set in 'orientation' position
459 CoherentFileSet[strOrient] = new FileList;
461 // Current Orientation and DICOM header match; add the file:
462 CoherentFileSet[strOrient]->push_back( (*it) );
464 return CoherentFileSet;
468 * \brief Splits a 'Single SerieUID' Fileset according to the Positions
469 * @param fileSet File Set to be splitted
470 * \return std::map of 'Xcoherent' File sets
473 XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet)
475 XCoherentFileSetmap CoherentFileSet;
477 int nb = fileSet->size();
479 return CoherentFileSet;
481 std::string strImPos; // read on disc
482 std::ostringstream ossPosition;
483 std::string strPosition; // re computed
484 FileList::const_iterator it = fileSet->begin();
487 it != fileSet->end();
490 // Information is in :
491 // 0020,0032 : Image Position Patient
492 // 0020,0030 : Image Position (RET)
494 strImPos = (*it)->GetEntryString(0x0020,0x0032);
495 if ( strImPos == GDCM_UNFOUND)
497 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
498 strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images
499 if ( strImPos == GDCM_UNFOUND )
501 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
502 // User wants to split on the 'Position'
503 // No 'Position' info found.
504 // We return an empty Htable !
505 return CoherentFileSet;
509 if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ",
510 &pos[0], &pos[1], &pos[2]) != 3 )
512 gdcmWarningMacro( "Wrong number for Position : ["
513 << strImPos << "]" );
514 return CoherentFileSet;
517 // Let's build again the 'position' string, to be sure of it's format
519 ossPosition << pos[0];
520 for (int i = 1; i < 3; i++)
523 ossPosition << pos[i];
525 strPosition = ossPosition.str();
528 if ( CoherentFileSet.count(strPosition) == 0 )
530 gdcmDebugMacro(" New Position :[" << strPosition << "]");
531 // create a File set in 'position' position
532 CoherentFileSet[strPosition] = new FileList;
534 // Current Position and DICOM header match; add the file:
535 CoherentFileSet[strPosition]->push_back( (*it) );
537 return CoherentFileSet;
541 * \brief Splits a 'Single SerieUID' File set Coherent according to the
542 * value of a given Tag
543 * @param fileSet File Set to be splitted
544 * @param group group number of the target Element
545 * @param elem element number of the target Element
546 * \return std::map of 'Xcoherent' File sets
549 XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
550 uint16_t group, uint16_t element)
552 XCoherentFileSetmap CoherentFileSet;
554 int nb = fileSet->size();
556 return CoherentFileSet;
558 std::string strTagValue; // read on disc
560 FileList::const_iterator it = fileSet->begin();
563 it != fileSet->end();
566 // Information is in :
567 // 0020,0032 : Image Position Patient
568 // 0020,0030 : Image Position (RET)
570 strTagValue = (*it)->GetEntryString(group,element);
572 if ( CoherentFileSet.count(strTagValue) == 0 )
574 gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]");
575 // create a File set in 'position' position
576 CoherentFileSet[strTagValue] = new FileList;
578 // Current Tag value and DICOM header match; add the file:
579 CoherentFileSet[strTagValue]->push_back( (*it) );
581 return CoherentFileSet;
584 //-----------------------------------------------------------------------------
587 //-----------------------------------------------------------------------------
590 * \brief sorts the images, according to their Patient Position.
591 * As a side effect, it computes the ZSpacing, according to Jolinda Smith'
592 * algorithm. (get it with double GetZSpacing() !)
593 * We may order, considering :
594 * -# Image Position Patient
597 * -# More to come :-)
598 * \note : FileList = std::vector<File* >
599 * @param fileList Coherent File list (same Serie UID) to sort
600 * @return false only if the header is bugged !
602 bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList )
603 //based on Jolinda Smith's algorithm
605 //Tags always use the same coordinate system, where "x" is left
606 //to right, "y" is posterior to anterior, and "z" is foot to head (RAH).
608 //iop is calculated based on the file file
613 double min = 0, max = 0;
615 ZSpacing = -1.0; // will be updated if process doesn't fail
617 std::multimap<double,File *> distmultimap;
618 // Use a multimap to sort the distances from 0,0,0
619 for ( FileList::const_iterator
620 it = fileList->begin();
621 it != fileList->end(); ++it )
625 (*it)->GetImageOrientationPatient( cosines );
627 // The "Image Orientation Patient" tag gives the direction cosines
628 // for the rows and columns for the three axes defined above.
629 // Typical axial slices will have a value 1/0/0/0/1/0:
630 // rows increase from left to right,
631 // columns increase from posterior to anterior. This is your everyday
632 // "looking up from the bottom of the head with the eyeballs up" image.
634 // The "Image Position Patient" tag gives the coordinates of the first
635 // voxel in the image in the "RAH" coordinate system, relative to some
638 // First, calculate the slice normal from IOP :
640 // You only have to do this once for all slices in the volume. Next,
641 // for each slice, calculate the distance along the slice normal
642 // using the IPP ("Image Position Patient") tag.
643 // ("dist" is initialized to zero before reading the first slice) :
644 normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
645 normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
646 normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
648 // For each slice (here : the first), calculate the distance along
649 // the slice normal using the IPP tag
651 ipp[0] = (*it)->GetXOrigin();
652 ipp[1] = (*it)->GetYOrigin();
653 ipp[2] = (*it)->GetZOrigin();
656 for ( int i = 0; i < 3; ++i )
658 dist += normal[i]*ipp[i];
661 distmultimap.insert(std::pair<const double,File *>(dist, *it));
668 // Next, for each slice, calculate the distance along the slice normal
670 ipp[0] = (*it)->GetXOrigin();
671 ipp[1] = (*it)->GetYOrigin();
672 ipp[2] = (*it)->GetZOrigin();
675 for ( int i = 0; i < 3; ++i )
677 dist += normal[i]*ipp[i];
680 distmultimap.insert(std::pair<const double,File *>(dist, *it));
682 min = (min < dist) ? min : dist;
683 max = (max > dist) ? max : dist;
687 // Find out if min/max are coherent
690 gdcmWarningMacro("Looks like all images have the exact same image position"
691 << ". No PositionPatientOrdering sort performed" );
695 // Check to see if image shares a common position
697 for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
698 it2 != distmultimap.end();
701 if (distmultimap.count((*it2).first) != 1)
703 gdcmErrorMacro("File: "
704 << ((*it2).second->GetFileName())
707 << " position is not unique");
717 // Now, we could calculate Z Spacing as the difference
718 // between the "dist" values for the first two slices.
720 // The following (un)-commented out code is let here
721 // to be re-used by whomsoever is interested...
723 std::multimap<double, File *>::iterator it5 = distmultimap.begin();
724 double d1 = (*it5).first;
726 double d2 = (*it5).first;
729 ZSpacing = - ZSpacing;
731 fileList->clear(); // doesn't delete list elements, only nodes
733 // Acording to user requierement, we sort direct order or reverse order.
736 for (std::multimap<double, File *>::iterator it3 = distmultimap.begin();
737 it3 != distmultimap.end();
740 fileList->push_back( (*it3).second );
743 else // user asked for reverse order
745 std::multimap<double, File *>::const_iterator it4;
746 it4 = distmultimap.end();
750 fileList->push_back( (*it4).second );
751 } while (it4 != distmultimap.begin() );
754 distmultimap.clear();
759 bool SerieHelper::ImageNumberLessThan(File *file1, File *file2)
761 return file1->GetImageNumber() < file2->GetImageNumber();
764 bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2)
766 return file1->GetImageNumber() > file2->GetImageNumber();
770 * \brief sorts the images, according to their Image Number
771 * \note Works only on bona fide files (i.e image number is a character string
772 * corresponding to an integer)
773 * within a bona fide serie (i.e image numbers are consecutive)
774 * @param fileList File set (same Serie UID) to sort
775 * @return false if non bona fide stuff encountered
777 bool SerieHelper::ImageNumberOrdering(FileList *fileList)
780 int n = fileList->size();
782 FileList::const_iterator it = fileList->begin();
783 min = max = (*it)->GetImageNumber();
785 for (; it != fileList->end(); ++it, ++n)
787 pos = (*it)->GetImageNumber();
788 min = (min < pos) ? min : pos;
789 max = (max > pos) ? max : pos;
792 // Find out if image numbers are coherent (consecutive)
793 if ( min == max || max == 0 || max >= (n+min) )
795 gdcmWarningMacro( " 'Image numbers' not coherent. "
796 << " No ImageNumberOrdering sort performed.");
800 Sort(fileList,SerieHelper::ImageNumberLessThan);
802 Sort(fileList,SerieHelper::ImageNumberGreaterThan);
807 bool SerieHelper::FileNameLessThan(File *file1, File *file2)
809 return file1->GetFileName() < file2->GetFileName();
812 bool SerieHelper::FileNameGreaterThan(File *file1, File *file2)
814 return file1->GetFileName() > file2->GetFileName();
817 * \brief sorts the images, according to their File Name
818 * @param fileList Coherent File list (same Serie UID) to sort
819 * @return false only if the header is bugged !
821 bool SerieHelper::FileNameOrdering(FileList *fileList)
824 Sort(fileList,SerieHelper::FileNameLessThan);
826 Sort(fileList,SerieHelper::FileNameGreaterThan);
832 * \brief sorts the images, according to user supplied function
833 * @param fileList Coherent File list (same Serie UID) to sort
834 * @return false only if the header is bugged !
836 bool SerieHelper::UserOrdering(FileList *fileList)
838 Sort(fileList,SerieHelper::UserLessThanFunction);
841 std::reverse(fileList->begin(), fileList->end());
846 //-----------------------------------------------------------------------------
849 * \brief Canonical printer.
851 void SerieHelper::Print(std::ostream &os, std::string const &indent)
853 // For all the Coherent File lists of the gdcm::Serie
854 SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
855 if ( itl == SingleSerieUIDFileSetHT.end() )
857 gdcmWarningMacro( "No SingleSerieUID File set found" );
860 while (itl != SingleSerieUIDFileSetHT.end())
862 os << "Serie UID :[" << itl->first << "]" << std::endl;
864 // For all the files of a SingleSerieUID File set
865 for (FileList::iterator it = (itl->second)->begin();
866 it != (itl->second)->end();
869 os << indent << " --- " << (*it)->GetFileName() << std::endl;
875 void SerieHelper::CreateDefaultUniqueSeriesIdentifier()
877 // If the user requests, additional information can be appended
878 // to the SeriesUID to further differentiate volumes in the DICOM
879 // objects being processed.
881 // 0020 0011 Series Number
882 // A scout scan prior to a CT volume scan can share the same
883 // SeriesUID, but they will sometimes have a different Series Number
884 AddRestriction( TagKey(0x0020, 0x0011) );
885 // 0018 0024 Sequence Name
886 // For T1-map and phase-contrast MRA, the different flip angles and
887 // directions are only distinguished by the Sequence Name
888 AddRestriction( TagKey(0x0018, 0x0024) );
889 // 0018 0050 Slice Thickness
890 // On some CT systems, scout scans and subsequence volume scans will
891 // have the same SeriesUID and Series Number - YET the slice
892 // thickness will differ from the scout slice and the volume slices.
893 AddRestriction( TagKey(0x0018, 0x0050));
895 // If the 2D images in a sequence don't have the same number of rows,
896 // then it is difficult to reconstruct them into a 3D volume.
897 AddRestriction( TagKey(0x0028, 0x0010));
899 // If the 2D images in a sequence don't have the same number of columns,
900 // then it is difficult to reconstruct them into a 3D volume.
901 AddRestriction( TagKey(0x0028, 0x0011));
905 * \brief Heuristics to *try* to build a Serie Identifier that would ensure
906 * all the images are coherent.
908 * By default, uses the SeriesUID. If UseSeriesDetails(true) has been called,
909 * then additional identifying information is used.
910 * We allow user to add his own critierions, using AddSeriesDetail
911 * (he knows more than we do about his images!)
912 * ex : in tagging series, the only pertnent tag is
913 * 0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN
914 * @param inFile gdcm::File we want to build a Serie Identifier for.
915 * @return the SeriesIdentifier
917 std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile )
919 if( inFile->IsReadable() )
921 // 0020 000e UI REL Series Instance UID
922 std::string uid = inFile->GetEntryString (0x0020, 0x000e);
923 std::string id = uid.c_str();
924 if(m_UseSeriesDetails)
926 for(SerieExRestrictions::iterator it2 = ExRefine.begin();
927 it2 != ExRefine.end();
930 const ExRule &r = *it2;
931 std::string s = inFile->GetEntryString( r.group, r.elem );
932 if( s == gdcm::GDCM_UNFOUND )
936 if( id == uid && !s.empty() )
938 id += "."; // add separator
943 // Eliminate non-alnum characters, including whitespace...
944 // that may have been introduced by concats.
945 for(unsigned int i=0; i<id.size(); i++)
949 || (id[i] >= 'a' && id[i] <= 'z')
950 || (id[i] >= '0' && id[i] <= '9')
951 || (id[i] >= 'A' && id[i] <= 'Z')))
958 else // Could not open inFile
960 gdcmWarningMacro("Could not parse series info.");
961 std::string id = gdcm::GDCM_UNFOUND;
967 * \brief Allow user to build is own File Identifier (to be able to sort
968 * temporal series just as he wants)
969 * Criterions will be set with AddSeriesDetail.
970 * (Maybe the method should be moved elsewhere
971 * -File class? FileHelper class?-
972 * @return FileIdentifier (Tokenizable on '%%%'. Hope it's enough !)
974 std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile )
976 // Deal with all user supplied tags.
977 // (user knows more than we do about his images!)
982 char charConverted[17];
984 for(SeriesExDetails::iterator it2 = ExDetails.begin();
985 it2 != ExDetails.end();
988 const ExDetail &r = *it2;
989 s = inFile->GetEntryString( r.group, r.elem );
991 // User is allowed to ask 'convertion', to allow further ordering
992 // e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK
995 if ( s != GDCM_UNFOUND) // Don't convert unfound fields !
997 converted = atof(s.c_str());
998 // probabely something much more complicated is possible,
999 // using C++ features
1000 /// \todo check the behaviour when there are >0 and <0 numbers
1001 sprintf(charConverted, "%016.6f",converted);
1005 // Eliminate non-alphanum characters, including whitespace.
1006 for(unsigned int i=0; i<s.size(); i++)
1009 && !( s[i] == '.' || s[i] == '%'
1010 || (s[i] >= 'a' && s[i] <= 'z')
1011 || (s[i] >= '0' && s[i] <= '9')
1012 || (s[i] >= 'A' && s[i] <= 'Z')))
1019 id += "%%%"; // make the FileIdentifier Tokenizable
1025 //-----------------------------------------------------------------------------
1028 * \brief Sort FileList.
1030 void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) )
1032 std::sort(fileList->begin(), fileList->end(), pt2Func );
1035 //-----------------------------------------------------------------------------
1036 } // end namespace gdcm