1 /*=========================================================================
4 Module: $RCSfile: gdcmSerieHelper.cxx,v $
6 Date: $Date: 2007/06/08 12:49:37 $
7 Version: $Revision: 1.57 $
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
32 namespace GDCM_NAME_SPACE
35 //-----------------------------------------------------------------------------
36 // Constructor / Destructor
38 * \brief Constructor from a given SerieHelper
40 SerieHelper::SerieHelper()
42 m_UseSeriesDetails = false;
44 UserLessThanFunction = 0;
50 * \brief Canonical destructor.
52 SerieHelper::~SerieHelper()
58 * \brief Preventively, clear everything at constructor time.
59 * ( use it at destructor time.)
61 void SerieHelper::ClearAll()
63 // For all the 'Single SerieUID' Filesets that may already exist
64 FileList *l = GetFirstSingleSerieUIDFileSet();
67 // For all the GDCM_NAME_SPACE::File of a File set
68 for (GDCM_NAME_SPACE::FileList::iterator it = l->begin();
72 (*it)->Delete(); // remove each entry
75 delete l; // remove the container
76 l = GetNextSingleSerieUIDFileSet();
78 // Need to clear that too:
79 SingleSerieUIDFileSetHT.clear();
82 //-----------------------------------------------------------------------------
84 //-----------------------------------------------------------------------------
88 * \brief add a GDCM_NAME_SPACE::File to the Fileset corresponding to its Serie UID
89 * @param filename Name of the file to deal with
91 void SerieHelper::AddFileName(std::string const &filename)
93 // Create a DICOM file
94 File *header = File::New();
95 header->SetLoadMode(LoadMode);
96 header->SetFileName( filename );
99 if ( header->IsReadable() )
101 if ( !AddFile( header ) )
103 // at least one rule was unmatched we need to deallocate the file:
109 gdcmWarningMacro("Could not read file: " << filename );
115 * \brief add a GDCM_NAME_SPACE::File to the first (and supposed to be unique) file set
116 * of the GDCM_NAME_SPACE::SerieHelper.
117 * \warning : this method should be used by aware users only!
118 * Passing a GDCM_NAME_SPACE::File* has the same effect than passing a file name!
119 * \todo : decide which one is wrong (the method, or the commentary)!
120 * the following comment doesn't match the method :-(
121 * User is supposed to know the files he want to deal with
122 * and consider them they belong to the same Serie
123 * (even if their Serie UID is different)
124 * user will probabely OrderFileList() this list (actually, ordering
125 * user choosen gdm::File is the sole interest of this method)
126 * Moreover, using vtkGdcmReader::SetCoherentFileList() will avoid
127 * vtkGdcmReader parsing twice the same files.
128 * *no* coherence check is performed, but those specified
129 * by SerieHelper::AddRestriction()
130 * @param header GDCM_NAME_SPACE::File* of the file to deal with
131 * @return true if file was added, false if file was rejected
133 bool SerieHelper::AddFile(File *header)
136 // First step the user has defined a set of rules for the DICOM
137 // he is looking for.
138 // make sure the file correspond to his set of rules:
141 for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
142 it2 != ExRestrictions.end();
145 const ExRule &r = *it2;
146 s = header->GetEntryString( r.group, r.elem );
147 if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
149 // Argh ! This rule is unmatched; let's just quit
155 if ( allrules ) // all rules are respected:
157 // Allright! we have a found a DICOM that matches the user expectation.
158 // Let's add it to the specific 'id' which by default is uid (Serie UID)
159 // but can be `refined` by user with more paramater (see AddRestriction(g,e))
161 std::string id = CreateUniqueSeriesIdentifier( header );
162 // if id == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
163 // no need here to do anything special
165 if ( SingleSerieUIDFileSetHT.count(id) == 0 )
167 gdcmDebugMacro(" New/gdcmSerieHelper.cxx Serie UID :[" << id << "]");
168 // create a std::list in 'id' position
169 SingleSerieUIDFileSetHT[id] = new FileList;
171 // Current Serie UID and DICOM header seems to match add the file:
172 SingleSerieUIDFileSetHT[id]->push_back( header );
176 // one rule not matched, tell user:
183 * \brief add a rule for restricting a DICOM file to be in the serie we are
184 * trying to find. For example you can select only the DICOM files from a
185 * directory which would have a particular EchoTime==4.0.
186 * This method is a user level, value is not required to be formatted as a DICOM
188 * \todo find a trick to allow user to say if he wants the Rectrictions
189 * to be *ored* (and not only *anded*)
190 * @param key Target tag we want restrict on a given value
191 * @param value value to be checked to exclude File
192 * @param op operator we want to use to check
194 void SerieHelper::AddRestriction(TagKey const &key,
195 std::string const &value, int op)
202 ExRestrictions.push_back( r );
205 void SerieHelper::AddRestriction(TagKey const &key)
210 ExRefine.push_back( r );
213 //#ifndef GDCM_LEGACY_REMOVE
215 * \brief add a rule for restricting a DICOM file to be in the serie we are
216 * trying to find. For example you can select only the DICOM files from a
217 * directory which would have a particular EchoTime==4.0.
218 * This method is a user level, value is not required to be formatted as a DICOM
220 * @param group tag group number we want restrict on a given value
221 * @param elem tag element number we want restrict on a given value
222 * @param value value to be checked to exclude File
223 * @param op operator we want to use to check
224 * @deprecated use : AddRestriction(TagKey const &key,
225 * std::string const &value, int op);
228 void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
229 std::string const &value, int op)
231 TagKey t(group, elem);
232 AddRestriction(t, value, op);
238 * \brief add an extra 'SerieDetail' for building a 'Serie Identifier'
239 * that ensures (hope so) File constistency (Series Instance UID doesn't.
240 * @param group tag group number we want restrict on a given value
241 * @param elem tag element number we want restrict on a given value
242 * @param convert wether we want 'convertion', to allow further ordering
243 * e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK
245 void SerieHelper::AddSeriesDetail(uint16_t group, uint16_t elem, bool convert)
251 ExDetails.push_back( d );
254 * \brief Sets the root Directory
255 * @param dir Name of the directory to deal with
256 * @param recursive whether we want explore recursively the root Directory
258 void SerieHelper::SetDirectory(std::string const &dir, bool recursive)
260 DirList dirList(dir, recursive); // OS specific
262 DirListType filenames_list = dirList.GetFilenames();
263 for( DirListType::const_iterator it = filenames_list.begin();
264 it != filenames_list.end(); ++it)
271 * \brief Sets the DicomDirSerie
272 * @param se DicomDirSerie to deal with
274 void SerieHelper::SetDicomDirSerie(DicomDirSerie *se)
278 DirListType filenames_list = dirList.GetFilenames();
279 for( DirListType::const_iterator it = filenames_list.begin();
280 it != filenames_list.end(); ++it)
287 * \brief Sorts the given Fileset
288 * \warning This could be implemented in a 'Strategy Pattern' approach
289 * But as I don't know how to do it, I leave it this way
290 * BTW, this is also a Strategy, I don't know this is
291 * the best approach :)
293 void SerieHelper::OrderFileList(FileList *fileSet)
295 // Only computed during ImagePositionPatientOrdering
296 // (need to sort the FileList using IPP and IOP !)
299 if ( SerieHelper::UserLessThanFunction )
301 UserOrdering( fileSet );
304 else if ( ImagePositionPatientOrdering( fileSet ) )
308 else if ( ImageNumberOrdering(fileSet ) )
314 FileNameOrdering(fileSet );
319 * \brief Elementary coherence checking of the files with the same Serie UID
320 * Only sizes and pixel type are checked right now ...
322 bool SerieHelper::IsCoherent(FileList *fileSet)
324 if(fileSet->size() == 1)
327 FileList::const_iterator it = fileSet->begin();
329 int nX = (*it)->GetXSize();
330 int nY = (*it)->GetYSize();
331 int pixelSize = (*it)->GetPixelSize();
332 bool signedPixelData = (*it)->IsSignedPixelData();
335 it != fileSet->end();
338 if ( (*it)->GetXSize() != nX )
340 if ( (*it)->GetYSize() != nY )
342 if ( (*it)->GetPixelSize() != pixelSize )
344 if ( (*it)->IsSignedPixelData() != signedPixelData )
346 // probabely more is to be checked (?)
351 //#ifndef GDCM_LEGACY_REMOVE
353 * \brief accessor (DEPRECATED : use GetFirstSingleSerieUIDFileSet )
354 * Warning : 'coherent' means here they have the same Serie UID
355 * @return The first FileList if found, otherwhise NULL
358 FileList *SerieHelper::GetFirstCoherentFileList()
360 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
361 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
362 return ItFileSetHt->second;
367 * \brief accessor (DEPRECATED : use GetNextSingleSerieUIDFileSet )
368 * Warning : 'coherent' means here they have the same Serie UID
369 * \note : meaningfull only if GetFirstCoherentFileList() already called
370 * @return The next FileList if found, otherwhise NULL
373 FileList *SerieHelper::GetNextCoherentFileList()
375 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
378 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
379 return ItFileSetHt->second;
385 * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet )
386 * Warning : 'coherent' means here they have the same Serie UID
387 * @param SerieUID SerieUID
388 * \return pointer to the FileList if found, otherwhise NULL
391 FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
393 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
395 return SingleSerieUIDFileSetHT[SerieUID];
402 * \brief Get the first Fileset while visiting the SingleSerieUIDFileSetmap
403 * @return The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0
405 FileList *SerieHelper::GetFirstSingleSerieUIDFileSet()
407 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
408 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
409 return ItFileSetHt->second;
414 * \brief Get the next Fileset while visiting the SingleSerieUIDFileSetmap
415 * \note : meaningfull only if GetNextSingleSerieUIDFileSet() already called
416 * @return The next FileList (SingleSerieUIDFileSet) if found, otherwhise 0
418 FileList *SerieHelper::GetNextSingleSerieUIDFileSet()
420 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
423 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
424 return ItFileSetHt->second;
429 * \brief Get the SingleSerieUIDFileSet according to its Serie UID
430 * @param SerieUID SerieUID to retrieve
431 * \return pointer to the FileList (SingleSerieUIDFileSet) if found, otherwhise 0
433 FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID)
435 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
437 return SingleSerieUIDFileSetHT[SerieUID];
441 * \brief Splits a Single SerieUID Fileset according to the Orientations
442 * @param fileSet File Set to be splitted
443 * \return std::map of 'Xcoherent' File sets
446 XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet)
448 XCoherentFileSetmap CoherentFileSet;
450 int nb = fileSet->size();
452 return CoherentFileSet;
454 std::string strOrient;
455 std::ostringstream ossOrient;
457 FileList::const_iterator it = fileSet->begin();
460 it != fileSet->end();
463 // Information is in :
464 // 0020 0037 : Image Orientation (Patient) or
465 // 0020 0035 : Image Orientation (RET)
467 // Let's build again the 'cosines' string, to be sure of it's format
468 (*it)->GetImageOrientationPatient(iop);
471 for (int i = 1; i < 6; i++)
476 strOrient = ossOrient.str();
478 if ( CoherentFileSet.count(strOrient) == 0 )
480 gdcmDebugMacro(" New Orientation :[" << strOrient << "]");
481 // create a File set in 'orientation' position
482 CoherentFileSet[strOrient] = new FileList;
484 // Current Orientation and DICOM header match; add the file:
485 CoherentFileSet[strOrient]->push_back( (*it) );
487 return CoherentFileSet;
491 * \brief Splits a 'Single SerieUID' Fileset according to the Positions
492 * @param fileSet File Set to be splitted
493 * \return std::map of 'Xcoherent' File sets
496 XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet)
498 XCoherentFileSetmap CoherentFileSet;
500 int nb = fileSet->size();
502 return CoherentFileSet;
504 std::string strImPos; // read on disc
505 std::ostringstream ossPosition;
506 std::string strPosition; // re computed
507 FileList::const_iterator it = fileSet->begin();
510 it != fileSet->end();
513 // Information is in :
514 // 0020,0032 : Image Position Patient
515 // 0020,0030 : Image Position (RET)
517 strImPos = (*it)->GetEntryString(0x0020,0x0032);
518 if ( strImPos == GDCM_UNFOUND)
520 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
521 strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images
522 if ( strImPos == GDCM_UNFOUND )
524 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
525 // User wants to split on the 'Position'
526 // No 'Position' info found.
527 // We return an empty Htable !
528 return CoherentFileSet;
532 if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ",
533 &pos[0], &pos[1], &pos[2]) != 3 )
535 gdcmWarningMacro( "Wrong number for Position : ["
536 << strImPos << "]" );
537 return CoherentFileSet;
540 // Let's build again the 'position' string, to be sure of it's format
542 ossPosition << pos[0];
543 for (int i = 1; i < 3; i++)
546 ossPosition << pos[i];
548 strPosition = ossPosition.str();
551 if ( CoherentFileSet.count(strPosition) == 0 )
553 gdcmDebugMacro(" New Position :[" << strPosition << "]");
554 // create a File set in 'position' position
555 CoherentFileSet[strPosition] = new FileList;
557 // Current Position and DICOM header match; add the file:
558 CoherentFileSet[strPosition]->push_back( (*it) );
560 return CoherentFileSet;
564 * \brief Splits a 'Single SerieUID' File set Coherent according to the
565 * value of a given Tag
566 * @param fileSet File Set to be splitted
567 * @param group group number of the target Element
568 * @param element element number of the target Element
569 * \return std::map of 'Xcoherent' File sets
572 XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
573 uint16_t group, uint16_t element)
575 XCoherentFileSetmap CoherentFileSet;
577 int nb = fileSet->size();
579 return CoherentFileSet;
581 std::string strTagValue; // read on disc
583 FileList::const_iterator it = fileSet->begin();
586 it != fileSet->end();
589 // Information is in :
590 // 0020,0032 : Image Position Patient
591 // 0020,0030 : Image Position (RET)
593 strTagValue = (*it)->GetEntryString(group,element);
595 if ( CoherentFileSet.count(strTagValue) == 0 )
597 gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]");
598 // create a File set in 'position' position
599 CoherentFileSet[strTagValue] = new FileList;
601 // Current Tag value and DICOM header match; add the file:
602 CoherentFileSet[strTagValue]->push_back( (*it) );
604 return CoherentFileSet;
607 //-----------------------------------------------------------------------------
610 //-----------------------------------------------------------------------------
613 * \brief sorts the images, according to their Patient Position.
614 * As a side effect, it computes the ZSpacing, according to Jolinda Smith'
615 * algorithm. (get it with double GetZSpacing() !)
616 * We may order, considering :
617 * -# Image Position Patient
620 * -# More to come :-)
621 * \note : FileList = std::vector<File* >
622 * @param fileList Coherent File list (same Serie UID) to sort
623 * @return false only if the header is bugged !
625 bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList )
626 //based on Jolinda Smith's algorithm
628 //Tags always use the same coordinate system, where "x" is left
629 //to right, "y" is posterior to anterior, and "z" is foot to head (RAH).
631 //iop is calculated based on the file file
636 double min = 0, max = 0;
638 ZSpacing = -1.0; // will be updated if process doesn't fail
640 std::multimap<double,File *> distmultimap;
641 // Use a multimap to sort the distances from 0,0,0
642 for ( FileList::const_iterator
643 it = fileList->begin();
644 it != fileList->end(); ++it )
648 (*it)->GetImageOrientationPatient( cosines );
650 // The "Image Orientation Patient" tag gives the direction cosines
651 // for the rows and columns for the three axes defined above.
652 // Typical axial slices will have a value 1/0/0/0/1/0:
653 // rows increase from left to right,
654 // columns increase from posterior to anterior. This is your everyday
655 // "looking up from the bottom of the head with the eyeballs up" image.
657 // The "Image Position Patient" tag gives the coordinates of the first
658 // voxel in the image in the "RAH" coordinate system, relative to some
661 // First, calculate the slice normal from IOP :
663 // You only have to do this once for all slices in the volume. Next,
664 // for each slice, calculate the distance along the slice normal
665 // using the IPP ("Image Position Patient") tag.
666 // ("dist" is initialized to zero before reading the first slice) :
667 normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
668 normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
669 normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
671 // For each slice (here : the first), calculate the distance along
672 // the slice normal using the IPP tag
674 ipp[0] = (*it)->GetXOrigin();
675 ipp[1] = (*it)->GetYOrigin();
676 ipp[2] = (*it)->GetZOrigin();
679 for ( int i = 0; i < 3; ++i )
681 dist += normal[i]*ipp[i];
684 distmultimap.insert(std::pair<const double,File *>(dist, *it));
691 // Next, for each slice, calculate the distance along the slice normal
693 ipp[0] = (*it)->GetXOrigin();
694 ipp[1] = (*it)->GetYOrigin();
695 ipp[2] = (*it)->GetZOrigin();
698 for ( int i = 0; i < 3; ++i )
700 dist += normal[i]*ipp[i];
703 distmultimap.insert(std::pair<const double,File *>(dist, *it));
705 min = (min < dist) ? min : dist;
706 max = (max > dist) ? max : dist;
710 // Find out if min/max are coherent
713 gdcmWarningMacro("Looks like all images have the exact same image position. "
714 << "No PositionPatientOrdering sort performed. "
715 << "No 'ZSpacing' calculated! ");
719 // Check to see if image shares a common position
721 for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
722 it2 != distmultimap.end();
725 if (distmultimap.count((*it2).first) != 1)
727 gdcmErrorMacro("File: ["
728 << ((*it2).second->GetFileName())
729 << "] : more than ONE file at distance: '"
731 << " (position is not unique!) "
732 << "No PositionPatientOrdering sort performed. "
733 << "No 'ZSpacing' calculated! ");
740 if (! DropDuplicatePositions)
744 // Now, we could calculate Z Spacing as the difference
745 // between the "dist" values for the first two slices.
747 // The following (un)-commented out code is let here
748 // to be re-used by whomsoever is interested...
750 std::multimap<double, File *>::iterator it5 = distmultimap.begin();
751 double d1 = (*it5).first;
753 double d2 = (*it5).first;
756 ZSpacing = - ZSpacing;
758 fileList->clear(); // doesn't delete list elements, only nodes
760 // Acording to user requierement, we sort direct order or reverse order.
763 for (std::multimap<double, File *>::iterator it3 = distmultimap.begin();
764 it3 != distmultimap.end();
767 fileList->push_back( (*it3).second );
768 if (DropDuplicatePositions)
770 it3 = distmultimap.upper_bound((*it3).first); // skip all duplicates
771 if (it3 == distmultimap.end() ) // if last image, stop iterate
776 else // user asked for reverse order
778 std::multimap<double, File *>::const_iterator it4;
779 it4 = distmultimap.end();
783 fileList->push_back( (*it4).second );
784 if (DropDuplicatePositions) // skip all duplicates
786 it4 = distmultimap.upper_bound((*it4).first);
787 if (it4 == distmultimap.begin() ) // if first image, stop iterate
790 } while (it4 != distmultimap.begin() );
793 distmultimap.clear();
798 bool SerieHelper::ImageNumberLessThan(File *file1, File *file2)
800 return file1->GetImageNumber() < file2->GetImageNumber();
803 bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2)
805 return file1->GetImageNumber() > file2->GetImageNumber();
809 * \brief sorts the images, according to their Image Number
810 * \note Works only on bona fide files (i.e image number is a character string
811 * corresponding to an integer)
812 * within a bona fide serie (i.e image numbers are consecutive)
813 * @param fileList File set (same Serie UID) to sort
814 * @return false if non bona fide stuff encountered
816 bool SerieHelper::ImageNumberOrdering(FileList *fileList)
819 int n = fileList->size();
821 FileList::const_iterator it = fileList->begin();
822 min = max = (*it)->GetImageNumber();
824 for (; it != fileList->end(); ++it, ++n)
826 pos = (*it)->GetImageNumber();
827 min = (min < pos) ? min : pos;
828 max = (max > pos) ? max : pos;
831 // Find out if image numbers are coherent (consecutive)
832 if ( min == max || max == 0 || max >= (n+min) )
834 gdcmWarningMacro( " 'Image numbers' not coherent. "
835 << " No ImageNumberOrdering sort performed.");
839 Sort(fileList,SerieHelper::ImageNumberLessThan);
841 Sort(fileList,SerieHelper::ImageNumberGreaterThan);
846 bool SerieHelper::FileNameLessThan(File *file1, File *file2)
848 return file1->GetFileName() < file2->GetFileName();
851 bool SerieHelper::FileNameGreaterThan(File *file1, File *file2)
853 return file1->GetFileName() > file2->GetFileName();
856 * \brief sorts the images, according to their File Name
857 * @param fileList Coherent File list (same Serie UID) to sort
858 * @return false only if the header is bugged !
860 bool SerieHelper::FileNameOrdering(FileList *fileList)
863 Sort(fileList,SerieHelper::FileNameLessThan);
865 Sort(fileList,SerieHelper::FileNameGreaterThan);
871 * \brief sorts the images, according to user supplied function
872 * @param fileList Coherent File list (same Serie UID) to sort
873 * @return false only if the header is bugged !
875 bool SerieHelper::UserOrdering(FileList *fileList)
877 Sort(fileList,SerieHelper::UserLessThanFunction);
880 std::reverse(fileList->begin(), fileList->end());
885 //-----------------------------------------------------------------------------
888 * \brief Canonical printer.
890 void SerieHelper::Print(std::ostream &os, std::string const &indent)
892 // For all the Coherent File lists of the GDCM_NAME_SPACE::Serie
893 SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
894 if ( itl == SingleSerieUIDFileSetHT.end() )
896 gdcmWarningMacro( "No SingleSerieUID File set found" );
899 while (itl != SingleSerieUIDFileSetHT.end())
901 os << "Serie UID :[" << itl->first << "]" << std::endl;
903 // For all the files of a SingleSerieUID File set
904 for (FileList::iterator it = (itl->second)->begin();
905 it != (itl->second)->end();
908 os << indent << " --- " << (*it)->GetFileName() << std::endl;
914 void SerieHelper::CreateDefaultUniqueSeriesIdentifier()
916 // If the user requests, additional information can be appended
917 // to the SeriesUID to further differentiate volumes in the DICOM
918 // objects being processed.
920 // 0020 0011 Series Number
921 // A scout scan prior to a CT volume scan can share the same
922 // SeriesUID, but they will sometimes have a different Series Number
923 AddRestriction( TagKey(0x0020, 0x0011) );
925 // 0018 0024 Sequence Name
926 // For T1-map and phase-contrast MRA, the different flip angles and
927 // directions are only distinguished by the Sequence Name
928 AddRestriction( TagKey(0x0018, 0x0024) );
930 // 0018 0050 Slice Thickness
931 // On some CT systems, scout scans and subsequence volume scans will
932 // have the same SeriesUID and Series Number - YET the slice
933 // thickness will differ from the scout slice and the volume slices.
934 AddRestriction( TagKey(0x0018, 0x0050));
937 // If the 2D images in a sequence don't have the same number of rows,
938 // then it is difficult to reconstruct them into a 3D volume.
939 AddRestriction( TagKey(0x0028, 0x0010));
942 // If the 2D images in a sequence don't have the same number of columns,
943 // then it is difficult to reconstruct them into a 3D volume.
944 AddRestriction( TagKey(0x0028, 0x0011));
948 * \brief Heuristics to *try* to build a Serie Identifier that would ensure
949 * all the images are coherent.
951 * By default, uses the SeriesUID. If UseSeriesDetails(true) has been called,
952 * then additional identifying information is used.
953 * We allow user to add his own critierions, using AddSeriesDetail
954 * (he knows more than we do about his images!)
955 * ex : in tagging series, the only pertnent tag is
956 * 0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN
957 * @param inFile GDCM_NAME_SPACE::File we want to build a Serie Identifier for.
958 * @return the SeriesIdentifier
960 std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile )
962 if( inFile->IsReadable() )
964 // 0020 000e UI REL Series Instance UID
965 std::string uid = inFile->GetEntryString (0x0020, 0x000e);
966 std::string id = uid.c_str();
967 if(m_UseSeriesDetails)
969 for(SerieExRestrictions::iterator it2 = ExRefine.begin();
970 it2 != ExRefine.end();
973 const ExRule &r = *it2;
974 std::string s = inFile->GetEntryString( r.group, r.elem );
975 if( s == GDCM_UNFOUND )
979 if( id == uid && !s.empty() )
981 id += "."; // add separator
986 // Eliminate non-alnum characters, including whitespace...
987 // that may have been introduced by concats.
988 for(unsigned int i=0; i<id.size(); i++)
992 || (id[i] >= 'a' && id[i] <= 'z')
993 || (id[i] >= '0' && id[i] <= '9')
994 || (id[i] >= 'A' && id[i] <= 'Z')))
1001 else // Could not open inFile
1003 gdcmWarningMacro("Could not parse series info.");
1004 std::string id = GDCM_UNFOUND;
1010 * \brief Allow user to build is own File Identifier (to be able to sort
1011 * temporal series just as he wants)
1012 * Criterions will be set with AddSeriesDetail.
1013 * (Maybe the method should be moved elsewhere
1014 * -File class? FileHelper class?-
1015 * @return FileIdentifier (Tokenizable on '%%%'. Hope it's enough !)
1017 std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile )
1019 // Deal with all user supplied tags.
1020 // (user knows more than we do about his images!)
1025 char charConverted[17];
1027 for(SeriesExDetails::iterator it2 = ExDetails.begin();
1028 it2 != ExDetails.end();
1031 const ExDetail &r = *it2;
1032 s = inFile->GetEntryString( r.group, r.elem );
1034 // User is allowed to ask for 'convertion', to allow further ordering
1035 // e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK
1038 if ( s != GDCM_UNFOUND) // Don't convert unfound fields !
1040 converted = atof(s.c_str());
1041 // probabely something much more complicated is possible,
1042 // using C++ features
1043 /// \todo check the behaviour when there are >0 and <0 numbers
1044 sprintf(charConverted, "%016.6f",converted);
1048 // Eliminate non-alphanum characters, including whitespace.
1049 for(unsigned int i=0; i<s.size(); i++)
1052 && !( s[i] == '.' || s[i] == '%'
1053 || (s[i] >= 'a' && s[i] <= 'z')
1054 || (s[i] >= '0' && s[i] <= '9')
1055 || (s[i] >= 'A' && s[i] <= 'Z')))
1062 id += "%%%"; // make the FileIdentifier Tokenizable
1068 //-----------------------------------------------------------------------------
1071 * \brief Sort FileList.
1073 void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) )
1075 std::sort(fileList->begin(), fileList->end(), pt2Func );
1079 #ifndef GDCM_LEGACY_REMOVE
1080 bool SerieHelper::AddGdcmFile(File* header)
1082 return AddFile(header);
1087 //-----------------------------------------------------------------------------
1088 } // end namespace gdcm