1 /*=========================================================================
4 Module: $RCSfile: gdcmSerieHelper.cxx,v $
6 Date: $Date: 2006/03/30 16:41:22 $
7 Version: $Revision: 1.48 $
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
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)
278 if ( SerieHelper::UserLessThanFunction )
280 UserOrdering( fileSet );
283 else if ( ImagePositionPatientOrdering( fileSet ) )
287 else if ( ImageNumberOrdering(fileSet ) )
293 FileNameOrdering(fileSet );
298 * \brief Elementary coherence checking of the files with the same Serie UID
299 * Only sizes and pixel type are checked right now ...
301 bool SerieHelper::IsCoherent(FileList *fileSet)
303 if(fileSet->size() == 1)
306 FileList::const_iterator it = fileSet->begin();
308 int nX = (*it)->GetXSize();
309 int nY = (*it)->GetYSize();
310 int pixelSize = (*it)->GetPixelSize();
311 bool signedPixelData = (*it)->IsSignedPixelData();
314 it != fileSet->end();
317 if ( (*it)->GetXSize() != nX )
319 if ( (*it)->GetYSize() != nY )
321 if ( (*it)->GetPixelSize() != pixelSize )
323 if ( (*it)->IsSignedPixelData() != signedPixelData )
325 // probabely more is to be checked (?)
330 #ifndef GDCM_LEGACY_REMOVE
332 * \brief accessor (DEPRECATED : use GetFirstSingleSerieUIDFileSet )
333 * Warning : 'coherent' means here they have the same Serie UID
334 * @return The first FileList if found, otherwhise NULL
336 FileList *SerieHelper::GetFirstCoherentFileList()
338 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
339 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
340 return ItFileSetHt->second;
345 * \brief accessor (DEPRECATED : use GetNextSingleSerieUIDFileSet )
346 * Warning : 'coherent' means here they have the same Serie UID
347 * \note : meaningfull only if GetFirstCoherentFileList() already called
348 * @return The next FileList if found, otherwhise NULL
350 FileList *SerieHelper::GetNextCoherentFileList()
352 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
355 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
356 return ItFileSetHt->second;
361 * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet )
362 * Warning : 'coherent' means here they have the same Serie UID
363 * @param SerieUID SerieUID
364 * \return pointer to the FileList if found, otherwhise NULL
366 FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
368 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
370 return SingleSerieUIDFileSetHT[SerieUID];
376 * \brief Get the first Fileset while visiting the SingleSerieUIDFileSetmap
377 * @return The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0
379 FileList *SerieHelper::GetFirstSingleSerieUIDFileSet()
381 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
382 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
383 return ItFileSetHt->second;
388 * \brief Get the next Fileset while visiting the SingleSerieUIDFileSetmap
389 * \note : meaningfull only if GetNextSingleSerieUIDFileSet() already called
390 * @return The next FileList (SingleSerieUIDFileSet) if found, otherwhise 0
392 FileList *SerieHelper::GetNextSingleSerieUIDFileSet()
394 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
397 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
398 return ItFileSetHt->second;
403 * \brief Get the SingleSerieUIDFileSet according to its Serie UID
404 * @param SerieUID SerieUID to retrieve
405 * \return pointer to the FileList (SingleSerieUIDFileSet) if found, otherwhise 0
407 FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID)
409 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
411 return SingleSerieUIDFileSetHT[SerieUID];
415 * \brief Splits a Single SerieUID Fileset according to the Orientations
416 * @param fileSet File Set to be splitted
417 * \return std::map of 'Xcoherent' File sets
420 XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet)
422 XCoherentFileSetmap CoherentFileSet;
424 int nb = fileSet->size();
426 return CoherentFileSet;
428 std::string strOrient;
429 std::ostringstream ossOrient;
431 FileList::const_iterator it = fileSet->begin();
434 it != fileSet->end();
437 // Information is in :
438 // 0020 0037 : Image Orientation (Patient) or
439 // 0020 0035 : Image Orientation (RET)
441 // Let's build again the 'cosines' string, to be sure of it's format
442 (*it)->GetImageOrientationPatient(iop);
445 for (int i = 1; i < 6; i++)
450 strOrient = ossOrient.str();
452 if ( CoherentFileSet.count(strOrient) == 0 )
454 gdcmDebugMacro(" New Orientation :[" << strOrient << "]");
455 // create a File set in 'orientation' position
456 CoherentFileSet[strOrient] = new FileList;
458 // Current Orientation and DICOM header match; add the file:
459 CoherentFileSet[strOrient]->push_back( (*it) );
461 return CoherentFileSet;
465 * \brief Splits a 'Single SerieUID' Fileset according to the Positions
466 * @param fileSet File Set to be splitted
467 * \return std::map of 'Xcoherent' File sets
470 XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet)
472 XCoherentFileSetmap CoherentFileSet;
474 int nb = fileSet->size();
476 return CoherentFileSet;
478 std::string strImPos; // read on disc
479 std::ostringstream ossPosition;
480 std::string strPosition; // re computed
481 FileList::const_iterator it = fileSet->begin();
484 it != fileSet->end();
487 // Information is in :
488 // 0020,0032 : Image Position Patient
489 // 0020,0030 : Image Position (RET)
491 strImPos = (*it)->GetEntryString(0x0020,0x0032);
492 if ( strImPos == GDCM_UNFOUND)
494 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
495 strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images
496 if ( strImPos == GDCM_UNFOUND )
498 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
499 // User wants to split on the 'Position'
500 // No 'Position' info found.
501 // We return an empty Htable !
502 return CoherentFileSet;
506 if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ",
507 &pos[0], &pos[1], &pos[2]) != 3 )
509 gdcmWarningMacro( "Wrong number for Position : ["
510 << strImPos << "]" );
511 return CoherentFileSet;
514 // Let's build again the 'position' string, to be sure of it's format
516 ossPosition << pos[0];
517 for (int i = 1; i < 3; i++)
520 ossPosition << pos[i];
522 strPosition = ossPosition.str();
525 if ( CoherentFileSet.count(strPosition) == 0 )
527 gdcmDebugMacro(" New Position :[" << strPosition << "]");
528 // create a File set in 'position' position
529 CoherentFileSet[strPosition] = new FileList;
531 // Current Position and DICOM header match; add the file:
532 CoherentFileSet[strPosition]->push_back( (*it) );
534 return CoherentFileSet;
538 * \brief Splits a 'Single SerieUID' File set Coherent according to the
539 * value of a given Tag
540 * @param fileSet File Set to be splitted
541 * @param group group number of the target Element
542 * @param elem element number of the target Element
543 * \return std::map of 'Xcoherent' File sets
546 XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
547 uint16_t group, uint16_t element)
549 XCoherentFileSetmap CoherentFileSet;
551 int nb = fileSet->size();
553 return CoherentFileSet;
555 std::string strTagValue; // read on disc
557 FileList::const_iterator it = fileSet->begin();
560 it != fileSet->end();
563 // Information is in :
564 // 0020,0032 : Image Position Patient
565 // 0020,0030 : Image Position (RET)
567 strTagValue = (*it)->GetEntryString(group,element);
569 if ( CoherentFileSet.count(strTagValue) == 0 )
571 gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]");
572 // create a File set in 'position' position
573 CoherentFileSet[strTagValue] = new FileList;
575 // Current Tag value and DICOM header match; add the file:
576 CoherentFileSet[strTagValue]->push_back( (*it) );
578 return CoherentFileSet;
581 //-----------------------------------------------------------------------------
584 //-----------------------------------------------------------------------------
587 * \brief sorts the images, according to their Patient Position.
588 * As a side effect, it computes the ZSpacing, according to Jolinda Smith'
589 * algorithm. (get it with double GetZSpacing() !)
590 * We may order, considering :
591 * -# Image Position Patient
594 * -# More to come :-)
595 * \note : FileList = std::vector<File* >
596 * @param fileList Coherent File list (same Serie UID) to sort
597 * @return false only if the header is bugged !
599 bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList )
600 //based on Jolinda Smith's algorithm
602 gdcmDebugMacro( "In ImagePositionPatientOrdering()" << std::endl );
603 std::cout << "In ImagePositionPatientOrdering()" << std::endl;
604 //Tags always use the same coordinate system, where "x" is left
605 //to right, "y" is posterior to anterior, and "z" is foot to head (RAH).
607 //iop is calculated based on the file file
612 double min = 0, max = 0;
614 ZSpacing = -1.0; // will be updated if process doesn't fail
616 std::multimap<double,File *> distmultimap;
617 // Use a multimap to sort the distances from 0,0,0
618 for ( FileList::const_iterator
619 it = fileList->begin();
620 it != fileList->end(); ++it )
624 (*it)->GetImageOrientationPatient( cosines );
626 // The "Image Orientation Patient" tag gives the direction cosines
627 // for the rows and columns for the three axes defined above.
628 // Typical axial slices will have a value 1/0/0/0/1/0:
629 // rows increase from left to right,
630 // columns increase from posterior to anterior. This is your everyday
631 // "looking up from the bottom of the head with the eyeballs up" image.
633 // The "Image Position Patient" tag gives the coordinates of the first
634 // voxel in the image in the "RAH" coordinate system, relative to some
637 // First, calculate the slice normal from IOP :
639 // You only have to do this once for all slices in the volume. Next,
640 // for each slice, calculate the distance along the slice normal
641 // using the IPP ("Image Position Patient") tag.
642 // ("dist" is initialized to zero before reading the first slice) :
643 normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
644 normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
645 normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
647 // For each slice (here : the first), calculate the distance along
648 // the slice normal using the IPP tag
650 ipp[0] = (*it)->GetXOrigin();
651 ipp[1] = (*it)->GetYOrigin();
652 ipp[2] = (*it)->GetZOrigin();
655 for ( int i = 0; i < 3; ++i )
657 dist += normal[i]*ipp[i];
660 distmultimap.insert(std::pair<const double,File *>(dist, *it));
667 // Next, for each slice, calculate the distance along the slice normal
669 ipp[0] = (*it)->GetXOrigin();
670 ipp[1] = (*it)->GetYOrigin();
671 ipp[2] = (*it)->GetZOrigin();
674 for ( int i = 0; i < 3; ++i )
676 dist += normal[i]*ipp[i];
679 distmultimap.insert(std::pair<const double,File *>(dist, *it));
681 min = (min < dist) ? min : dist;
682 max = (max > dist) ? max : dist;
686 // Find out if min/max are coherent
689 gdcmWarningMacro("Looks like all images have the exact same image position"
690 << ". No PositionPatientOrdering sort performed" );
694 // Check to see if image shares a common position
696 for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
697 it2 != distmultimap.end();
700 if (distmultimap.count((*it2).first) != 1)
702 gdcmErrorMacro("File: "
703 << ((*it2).second->GetFileName())
706 << " position is not unique");
716 // Now, we could calculate Z Spacing as the difference
717 // between the "dist" values for the first two slices.
719 // The following (un)-commented out code is let here
720 // to be re-used by whomsoever is interested...
722 std::multimap<double, File *>::iterator it5 = distmultimap.begin();
723 double d1 = (*it5).first;
725 double d2 = (*it5).first;
728 ZSpacing = - ZSpacing;
730 fileList->clear(); // doesn't delete list elements, only nodes
732 // Acording to user requierement, we sort direct order or reverse order.
735 for (std::multimap<double, File *>::iterator it3 = distmultimap.begin();
736 it3 != distmultimap.end();
739 fileList->push_back( (*it3).second );
742 else // user asked for reverse order
744 std::multimap<double, File *>::const_iterator it4;
745 it4 = distmultimap.end();
749 fileList->push_back( (*it4).second );
750 } while (it4 != distmultimap.begin() );
753 distmultimap.clear();
758 bool SerieHelper::ImageNumberLessThan(File *file1, File *file2)
760 return file1->GetImageNumber() < file2->GetImageNumber();
763 bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2)
765 return file1->GetImageNumber() > file2->GetImageNumber();
769 * \brief sorts the images, according to their Image Number
770 * \note Works only on bona fide files (i.e image number is a character string
771 * corresponding to an integer)
772 * within a bona fide serie (i.e image numbers are consecutive)
773 * @param fileList File set (same Serie UID) to sort
774 * @return false if non bona fide stuff encountered
776 bool SerieHelper::ImageNumberOrdering(FileList *fileList)
779 int n = fileList->size();
781 FileList::const_iterator it = fileList->begin();
782 min = max = (*it)->GetImageNumber();
784 for (; it != fileList->end(); ++it, ++n)
786 pos = (*it)->GetImageNumber();
787 min = (min < pos) ? min : pos;
788 max = (max > pos) ? max : pos;
791 // Find out if image numbers are coherent (consecutive)
792 if ( min == max || max == 0 || max >= (n+min) )
794 gdcmWarningMacro( " 'Image numbers' not coherent. "
795 << " No ImageNumberOrdering sort performed.");
799 Sort(fileList,SerieHelper::ImageNumberLessThan);
801 Sort(fileList,SerieHelper::ImageNumberGreaterThan);
806 bool SerieHelper::FileNameLessThan(File *file1, File *file2)
808 return file1->GetFileName() < file2->GetFileName();
811 bool SerieHelper::FileNameGreaterThan(File *file1, File *file2)
813 return file1->GetFileName() > file2->GetFileName();
816 * \brief sorts the images, according to their File Name
817 * @param fileList Coherent File list (same Serie UID) to sort
818 * @return false only if the header is bugged !
820 bool SerieHelper::FileNameOrdering(FileList *fileList)
823 Sort(fileList,SerieHelper::FileNameLessThan);
825 Sort(fileList,SerieHelper::FileNameGreaterThan);
831 * \brief sorts the images, according to user supplied function
832 * @param fileList Coherent File list (same Serie UID) to sort
833 * @return false only if the header is bugged !
835 bool SerieHelper::UserOrdering(FileList *fileList)
837 Sort(fileList,SerieHelper::UserLessThanFunction);
840 std::reverse(fileList->begin(), fileList->end());
845 //-----------------------------------------------------------------------------
848 * \brief Canonical printer.
850 void SerieHelper::Print(std::ostream &os, std::string const &indent)
852 // For all the Coherent File lists of the gdcm::Serie
853 SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
854 if ( itl == SingleSerieUIDFileSetHT.end() )
856 gdcmWarningMacro( "No SingleSerieUID File set found" );
859 while (itl != SingleSerieUIDFileSetHT.end())
861 os << "Serie UID :[" << itl->first << "]" << std::endl;
863 // For all the files of a SingleSerieUID File set
864 for (FileList::iterator it = (itl->second)->begin();
865 it != (itl->second)->end();
868 os << indent << " --- " << (*it)->GetFileName() << std::endl;
874 void SerieHelper::CreateDefaultUniqueSeriesIdentifier()
876 // If the user requests, additional information can be appended
877 // to the SeriesUID to further differentiate volumes in the DICOM
878 // objects being processed.
880 // 0020 0011 Series Number
881 // A scout scan prior to a CT volume scan can share the same
882 // SeriesUID, but they will sometimes have a different Series Number
883 AddRestriction( TagKey(0x0020, 0x0011) );
884 // 0018 0024 Sequence Name
885 // For T1-map and phase-contrast MRA, the different flip angles and
886 // directions are only distinguished by the Sequence Name
887 AddRestriction( TagKey(0x0018, 0x0024) );
888 // 0018 0050 Slice Thickness
889 // On some CT systems, scout scans and subsequence volume scans will
890 // have the same SeriesUID and Series Number - YET the slice
891 // thickness will differ from the scout slice and the volume slices.
892 AddRestriction( TagKey(0x0018, 0x0050));
894 // If the 2D images in a sequence don't have the same number of rows,
895 // then it is difficult to reconstruct them into a 3D volume.
896 AddRestriction( TagKey(0x0028, 0x0010));
898 // If the 2D images in a sequence don't have the same number of columns,
899 // then it is difficult to reconstruct them into a 3D volume.
900 AddRestriction( TagKey(0x0028, 0x0011));
904 * \brief Heuristics to *try* to build a Serie Identifier that would ensure
905 * all the images are coherent.
907 * By default, uses the SeriesUID. If UseSeriesDetails(true) has been called,
908 * then additional identifying information is used.
909 * We allow user to add his own critierions, using AddSeriesDetail
910 * (he knows more than we do about his images!)
911 * ex : in tagging series, the only pertnent tag is
912 * 0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN
913 * @param inFile gdcm::File we want to build a Serie Identifier for.
914 * @return the SeriesIdentifier
916 std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile )
918 if( inFile->IsReadable() )
920 // 0020 000e UI REL Series Instance UID
921 std::string uid = inFile->GetEntryString (0x0020, 0x000e);
922 std::string id = uid.c_str();
923 if(m_UseSeriesDetails)
925 for(SerieExRestrictions::iterator it2 = ExRefine.begin();
926 it2 != ExRefine.end();
929 const ExRule &r = *it2;
930 std::string s = inFile->GetEntryString( r.group, r.elem );
931 if( s == gdcm::GDCM_UNFOUND )
935 if( id == uid && !s.empty() )
937 id += "."; // add separator
942 // Eliminate non-alnum characters, including whitespace...
943 // that may have been introduced by concats.
944 for(unsigned int i=0; i<id.size(); i++)
948 || (id[i] >= 'a' && id[i] <= 'z')
949 || (id[i] >= '0' && id[i] <= '9')
950 || (id[i] >= 'A' && id[i] <= 'Z')))
957 else // Could not open inFile
959 gdcmWarningMacro("Could not parse series info.");
960 std::string id = gdcm::GDCM_UNFOUND;
966 * \brief Allow user to build is own File Identifier (to be able to sort
967 * temporal series just as he wants)
968 * Criterions will be set with AddSeriesDetail.
969 * (Maybe the method should be moved elsewhere
970 * -File class? FileHelper class?-
971 * @return FileIdentifier (Tokenizable on '%%%'. Hope it's enough !)
973 std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile )
975 // Deal with all user supplied tags.
976 // (user knows more than we do about his images!)
981 char charConverted[17];
983 for(SeriesExDetails::iterator it2 = ExDetails.begin();
984 it2 != ExDetails.end();
987 const ExDetail &r = *it2;
988 s = inFile->GetEntryString( r.group, r.elem );
990 // User is allowed to ask 'convertion', to allow further ordering
991 // e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK
994 if ( s != GDCM_UNFOUND) // Don't convert unfound fields !
996 converted = atof(s.c_str());
997 // probabely something much more complicated is possible,
998 // using C++ features
999 /// \todo check the behaviour when there are >0 and <0 numbers
1000 sprintf(charConverted, "%016.6f",converted);
1004 // Eliminate non-alphanum characters, including whitespace.
1005 for(unsigned int i=0; i<s.size(); i++)
1008 && !( s[i] == '.' || s[i] == '%'
1009 || (s[i] >= 'a' && s[i] <= 'z')
1010 || (s[i] >= '0' && s[i] <= '9')
1011 || (s[i] >= 'A' && s[i] <= 'Z')))
1018 id += "%%%"; // make the FileIdentifier Tokenizable
1024 //-----------------------------------------------------------------------------
1027 * \brief Sort FileList.
1029 void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) )
1031 std::sort(fileList->begin(), fileList->end(), pt2Func );
1034 //-----------------------------------------------------------------------------
1035 } // end namespace gdcm