1 /*=========================================================================
4 Module: $RCSfile: gdcmSerieHelper.cxx,v $
6 Date: $Date: 2005/10/18 08:35:50 $
7 Version: $Revision: 1.24 $
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
34 //-----------------------------------------------------------------------------
36 //-----------------------------------------------------------------------------
37 // Constructor / Destructor
39 * \brief Constructor from a given SerieHelper
41 SerieHelper::SerieHelper()
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 delete *it; // remove each entry
74 delete l; // remove the container
75 l = GetNextSingleSerieUIDFileSet();
79 //-----------------------------------------------------------------------------
81 //-----------------------------------------------------------------------------
85 * \brief add a gdcm::File to the Fileset corresponding to its Serie UID
86 * @param filename Name of the file to deal with
88 void SerieHelper::AddFileName(std::string const &filename)
90 // Create a DICOM file
91 File *header = new File ();
92 header->SetLoadMode(LoadMode);
93 header->SetFileName( filename );
96 if ( header->IsReadable() )
99 // First step : the user defined a set of rules for the DICOM file
100 // he is looking for.
101 // Make sure the file corresponds to his set of rules:
104 for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
105 it2 != ExRestrictions.end();
108 const ExRule &r = *it2;
109 s = header->GetEntryString( r.group, r.elem );
110 if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
112 // Argh ! This rule is unmatched; let's just quit
118 if ( allrules ) // all rules are respected:
120 // Allright! we have a found a DICOM that matches the user expectation.
123 // 0020 000e UI REL Series Instance UID
124 const std::string &uid = header->GetEntryString(0x0020, 0x000e);
125 // if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
126 // no need here to do anything special
128 if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
130 gdcmDebugMacro(" New Serie UID :[" << uid << "]");
131 // create a std::list in 'uid' position
132 SingleSerieUIDFileSetHT[uid] = new FileList;
134 // Current Serie UID and DICOM header seems to match; add the file:
135 SingleSerieUIDFileSetHT[uid]->push_back( header );
139 // at least one rule was unmatched we need to deallocate the file:
145 gdcmWarningMacro("Could not read file: " << filename );
151 * \brief add a gdcm::File to the first (and supposed to be unique) file set
152 * of the gdcm::SerieHelper.
153 * \warning : this method should be used by aware users only!
154 * Passing a gdcm::File* has the same effect than passing a file name!
155 * \TODO : decide which one is wrong (the method, or the commentary)!
156 * the following comment doesn't match the method :-(
157 * User is supposed to know the files he want to deal with
158 * and consider them they belong to the same Serie
159 * (even if their Serie UID is different)
160 * user will probabely OrderFileList() this list (actually, ordering
161 * user choosen gdm::File is the sole interest of this method)
162 * Moreover, using vtkGdcmReader::SetCoherentFileList() will avoid
163 * vtkGdcmReader parsing twice the same files.
164 * *no* coherence check is performed, but those specified
165 * by SerieHelper::AddRestriction()
166 * @param header gdcm::File* of the file to deal with
168 void SerieHelper::AddGdcmFile(File *header)
171 // First step the user has defined a set of rules for the DICOM
172 // he is looking for.
173 // make sure the file correspond to his set of rules:
174 for(SerieRestrictions::iterator it = Restrictions.begin();
175 it != Restrictions.end();
179 const std::string s;// = header->GetEntryValue( r.first );
180 if ( !Util::DicomStringEqual(s, r.second.c_str()) )
182 // Argh ! This rule is unmatch let's just quit
187 if ( allrules ) // all rules are respected:
189 // Allright ! we have a found a DICOM that match the user expectation.
192 const std::string &uid = "0";
193 // Serie UID of the gdcm::File* may be different.
194 // User is supposed to know what he wants
196 if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
198 gdcmDebugMacro(" New Serie UID :[" << uid << "]");
199 // create a std::list in 'uid' position
200 SingleSerieUIDFileSetHT[uid] = new FileList;
202 // Current Serie UID and DICOM header seems to match; add the file:
203 SingleSerieUIDFileSetHT[uid]->push_back( header );
205 // Even if a rule was unmatch we don't deallocate the gdcm::File:
209 * \brief add a rules for restricting a DICOM file to be in the serie we are
210 * trying to find. For example you can select only the DICOM file from a
211 * directory which would have a particular EchoTime==4.0.
212 * This method is a user level, value is not required to be formatted as a DICOM
214 * @param group Group number of the target tag.
215 * @param elem Element number of the target tag.
216 * @param value value to be checked to exclude File
217 * @param op operator we want to use to check
219 void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
220 std::string const &value, int op)
227 ExRestrictions.push_back( r );
230 #ifndef GDCM_LEGACY_REMOVE
232 * \brief add a rules for restricting a DICOM file to be in the serie we are
233 * trying to find. For example you can select only the DICOM file from a
234 * directory which would have a particular EchoTime==4.0.
235 * This method is a user level, value is not required to be formatted as a DICOM
237 * @param group Group number of the target tag.
238 * @param elem Element number of the target tag.
239 * @param value value to be checked to exclude File
240 * @deprecated use : AddRestriction(uint16_t group, uint16_t elem,
241 * std::string const &value, int op);
243 void SerieHelper::AddRestriction(TagKey const &key, std::string const &value)
248 Restrictions.push_back( r );
253 * \brief Sets the root Directory
254 * @param dir Name of the directory to deal with
255 * @param recursive whether we want explore recursively the root Directory
257 void SerieHelper::SetDirectory(std::string const &dir, bool recursive)
259 DirList dirList(dir, recursive); // OS specific
261 DirListType filenames_list = dirList.GetFilenames();
262 for( DirListType::const_iterator it = filenames_list.begin();
263 it != filenames_list.end(); ++it)
270 * \brief Sorts the given Fileset
271 * \warning This could be implemented in a 'Strategy Pattern' approach
272 * But as I don't know how to do it, I leave it this way
273 * BTW, this is also a Strategy, I don't know this is
274 * the best approach :)
276 void SerieHelper::OrderFileList(FileList *fileSet)
279 if ( SerieHelper::UserLessThanFunction )
281 UserOrdering( fileSet );
284 else if ( ImagePositionPatientOrdering( fileSet ) )
288 else if ( ImageNumberOrdering(fileSet ) )
294 FileNameOrdering(fileSet );
299 * \brief Elementary coherence checking of the files with the same Serie UID
300 * Only sizes and pixel type are checked right now ...
302 bool SerieHelper::IsCoherent(FileList *fileSet)
304 if(fileSet->size() == 1)
307 FileList::const_iterator it = fileSet->begin();
309 int nX = (*it)->GetXSize();
310 int nY = (*it)->GetYSize();
311 int pixelSize = (*it)->GetPixelSize();
315 it != fileSet->end();
318 if ( (*it)->GetXSize() != nX )
320 if ( (*it)->GetYSize() != nY )
322 if ( (*it)->GetPixelSize() != pixelSize )
324 // probabely more is to be checked (?)
329 #ifndef GDCM_LEGACY_REMOVE
331 * \brief accessor (DEPRECATED : use GetFirstSingleSerieUIDFileSet )
332 * Warning : 'coherent' means here they have the same Serie UID
333 * @return The first FileList if found, otherwhise NULL
335 FileList *SerieHelper::GetFirstCoherentFileList()
337 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
338 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
339 return ItFileSetHt->second;
344 * \brief accessor (DEPRECATED : use GetNextSingleSerieUIDFileSet )
345 * Warning : 'coherent' means here they have the same Serie UID
346 * \note : meaningfull only if GetFirstCoherentFileList() already called
347 * @return The next FileList if found, otherwhise NULL
349 FileList *SerieHelper::GetNextCoherentFileList()
351 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
354 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
355 return ItFileSetHt->second;
360 * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet )
361 * Warning : 'coherent' means here they have the same Serie UID
362 * @param SerieUID SerieUID
363 * \return pointer to the FileList if found, otherwhise NULL
365 FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
367 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
369 return SingleSerieUIDFileSetHT[SerieUID];
375 * \brief Get the first Fileset while visiting the SingleSerieUIDFileSetmap
376 * @return The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0
378 FileList *SerieHelper::GetFirstSingleSerieUIDFileSet()
380 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
381 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
382 return ItFileSetHt->second;
387 * \brief Get the next Fileset while visiting the SingleSerieUIDFileSetmap
388 * \note : meaningfull only if GetNextSingleSerieUIDFileSet() already called
389 * @return The next FileList (SingleSerieUIDFileSet) if found, otherwhise 0
391 FileList *SerieHelper::GetNextSingleSerieUIDFileSet()
393 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
396 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
397 return ItFileSetHt->second;
402 * \brief Get the SingleSerieUIDFileSet according to its Serie UID
403 * @param SerieUID SerieUID to retrieve
404 * \return pointer to the FileList (SingleSerieUIDFileSet) if found, otherwhise 0
406 FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID)
408 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
410 return SingleSerieUIDFileSetHT[SerieUID];
414 * \brief Splits a Single SerieUID Fileset according to the Orientations
415 * @param fileSet File Set to be splitted
416 * \return std::map of 'Xcoherent' File sets
419 XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet)
421 XCoherentFileSetmap CoherentFileSet;
423 int nb = fileSet->size();
425 return CoherentFileSet;
427 std::ostringstream ossOrient;
428 std::string strOrient;
430 FileList::const_iterator it = fileSet->begin();
433 it != fileSet->end();
436 // Information is in :
437 // 0020 0037 : Image Orientation (Patient) or
438 // 0020 0035 : Image Orientation (RET)
440 // Let's build again the 'cosines' string, to be sure of it's format
441 (*it)->GetImageOrientationPatient(iop);
443 for (int i = 1; i < 6; i++)
448 strOrient = ossOrient.str();
450 if ( CoherentFileSet.count(strOrient) == 0 )
452 gdcmDebugMacro(" New Orientation :[" << strOrient << "]");
453 // create a File set in 'orientation' position
454 CoherentFileSet[strOrient] = new FileList;
456 // Current Orientation and DICOM header match; add the file:
457 CoherentFileSet[strOrient]->push_back( (*it) );
459 return CoherentFileSet;
463 * \brief Splits a Single SerieUID Fileset according to the Positions
464 * @param fileSet File Set to be splitted
465 * \return std::map of 'Xcoherent' File sets
468 XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet)
470 XCoherentFileSetmap CoherentFileSet;
472 int nb = fileSet->size();
474 return CoherentFileSet;
476 std::string strImPos; // read on disc
477 std::ostringstream ossPosition;
478 std::string strPosition; // re computed
479 FileList::const_iterator it = fileSet->begin();
482 it != fileSet->end();
485 // Information is in :
486 // 0020,0032 : Image Position Patient
487 // 0020,0030 : Image Position (RET)
489 strImPos = (*it)->GetEntryString(0x0020,0x0032);
490 if ( strImPos == GDCM_UNFOUND)
492 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
493 strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images
494 if ( strImPos == GDCM_UNFOUND )
496 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
497 // User wants to split on the 'Position'
498 // No 'Position' info found.
499 // We return an empty Htable !
500 return CoherentFileSet;
504 if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ",
505 &pos[0], &pos[1], &pos[2]) != 3 )
507 gdcmWarningMacro( "Wrong number for Position : ["
508 << strImPos << "]" );
509 return CoherentFileSet;
512 // Let's build again the 'position' string, to be sure of it's format
514 ossPosition << pos[0];
515 for (int i = 1; i < 3; i++)
518 ossPosition << pos[i];
520 strPosition = ossPosition.str();
522 if ( CoherentFileSet.count(strPosition) == 0 )
524 gdcmDebugMacro(" New Position :[" << strPosition << "]");
525 // create a File set in 'position' position
526 CoherentFileSet[strPosition] = new FileList;
528 // Current Position and DICOM header match; add the file:
529 CoherentFileSet[strPosition]->push_back( (*it) );
531 return CoherentFileSet;
535 * \brief Splits a SingleSerieUID File set Coherent according to the
536 * value of a given Tag
537 * @param fileSet File Set to be splitted
538 * \return std::map of 'Xcoherent' File sets
541 XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
542 uint16_t group, uint16_t element)
544 XCoherentFileSetmap CoherentFileSet;
546 int nb = fileSet->size();
548 return CoherentFileSet;
550 std::string strTagValue; // read on disc
552 FileList::const_iterator it = fileSet->begin();
555 it != fileSet->end();
558 // Information is in :
559 // 0020,0032 : Image Position Patient
560 // 0020,0030 : Image Position (RET)
562 strTagValue = (*it)->GetEntryString(group,element);
564 if ( CoherentFileSet.count(strTagValue) == 0 )
566 gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]");
567 // create a File set in 'position' position
568 CoherentFileSet[strTagValue] = new FileList;
570 // Current Tag value and DICOM header match; add the file:
571 CoherentFileSet[strTagValue]->push_back( (*it) );
573 return CoherentFileSet;
576 //-----------------------------------------------------------------------------
579 //-----------------------------------------------------------------------------
582 * \brief sorts the images, according to their Patient Position
583 * We may order, considering :
584 * -# Image Position Patient
586 * -# More to come :-)
587 * WARNING : FileList = std::vector<File* >
588 * @param fileList Coherent File list (same Serie UID) to sort
589 * @return false only if the header is bugged !
591 bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList )
592 //based on Jolinda Smith's algorithm
594 //iop is calculated based on the file file
599 float min = 0, max = 0;
602 std::vector<float> distlist;
604 //!\todo rewrite this for loop.
605 for ( FileList::const_iterator
606 it = fileList->begin();
607 it != fileList->end(); ++it )
611 (*it)->GetImageOrientationPatient( cosines );
613 // You only have to do this once for all slices in the volume. Next,
614 // for each slice, calculate the distance along the slice normal
615 // using the IPP ("Image Position Patient") tag.
616 // ("dist" is initialized to zero before reading the first slice) :
617 normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
618 normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
619 normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
621 ipp[0] = (*it)->GetXOrigin();
622 ipp[1] = (*it)->GetYOrigin();
623 ipp[2] = (*it)->GetZOrigin();
626 for ( int i = 0; i < 3; ++i )
628 dist += normal[i]*ipp[i];
631 distlist.push_back( dist );
638 ipp[0] = (*it)->GetXOrigin();
639 ipp[1] = (*it)->GetYOrigin();
640 ipp[2] = (*it)->GetZOrigin();
643 for ( int i = 0; i < 3; ++i )
645 dist += normal[i]*ipp[i];
648 distlist.push_back( dist );
650 min = (min < dist) ? min : dist;
651 max = (max > dist) ? max : dist;
656 // Then I order the slices according to the value "dist". Finally, once
657 // I've read in all the slices, I calculate the z-spacing as the difference
658 // between the "dist" values for the first two slices.
659 FileVector CoherentFileVector(n);
660 // CoherentFileVector.reserve( n );
661 CoherentFileVector.resize( n );
662 // gdcmAssertMacro( CoherentFileVector.capacity() >= n );
664 // Find out if min/max are coherent
667 gdcmWarningMacro("Looks like all images have the exact same image position"
668 << ". No PositionPatientOrdering sort performed" );
672 float step = (max - min)/(n - 1);
676 //VC++ don't understand what scope is !! it -> it2
677 for (FileList::const_iterator it2 = fileList->begin();
678 it2 != fileList->end(); ++it2, ++n)
681 //Assumption: all files are present (no one missing)
682 pos = (int)( fabs( (distlist[n]-min)/step) + .5 );
684 // a Dicom 'Serie' may contain scout views
685 // and images may have differents directions
686 // -> More than one may have the same 'pos'
687 // Sorting has then NO meaning !
688 if (CoherentFileVector[pos]==NULL)
689 CoherentFileVector[pos] = *it2;
692 gdcmWarningMacro( "At least 2 files with same position."
693 << " No PositionPatientOrdering sort performed");
698 fileList->clear(); // doesn't delete list elements, only nodes
702 //VC++ don't understand what scope is !! it -> it3
703 for (FileVector::const_iterator it3 = CoherentFileVector.begin();
704 it3 != CoherentFileVector.end(); ++it3)
706 fileList->push_back( *it3 );
709 else // user asked for reverse order
711 FileVector::const_iterator it4;
712 it4 = CoherentFileVector.end();
716 fileList->push_back( *it4 );
717 } while (it4 != CoherentFileVector.begin() );
721 CoherentFileVector.clear();
726 bool SerieHelper::ImageNumberLessThan(File *file1, File *file2)
728 return file1->GetImageNumber() < file2->GetImageNumber();
731 bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2)
733 return file1->GetImageNumber() > file2->GetImageNumber();
737 * \brief sorts the images, according to their Image Number
738 * \note Works only on bona fide files (i.e image number is a character string
739 * corresponding to an integer)
740 * within a bona fide serie (i.e image numbers are consecutive)
741 * @param fileList Coherent File list (same Serie UID) to sort
742 * @return false if non bona fide stuff encountered
744 bool SerieHelper::ImageNumberOrdering(FileList *fileList)
747 int n = fileList->size();
749 FileList::const_iterator it = fileList->begin();
750 min = max = (*it)->GetImageNumber();
752 for (; it != fileList->end(); ++it, ++n)
754 pos = (*it)->GetImageNumber();
755 min = (min < pos) ? min : pos;
756 max = (max > pos) ? max : pos;
759 // Find out if image numbers are coherent (consecutive)
760 if ( min == max || max == 0 || max >= (n+min) )
762 gdcmWarningMacro( " 'Image numbers' not coherent. "
763 << " No ImageNumberOrdering sort performed.");
767 std::sort(fileList->begin(), fileList->end(),
768 SerieHelper::ImageNumberLessThan );
770 std::sort(fileList->begin(), fileList->end(),
771 SerieHelper::ImageNumberGreaterThan );
776 bool SerieHelper::FileNameLessThan(File *file1, File *file2)
778 return file1->GetFileName() < file2->GetFileName();
781 bool SerieHelper::FileNameGreaterThan(File *file1, File *file2)
783 return file1->GetFileName() > file2->GetFileName();
786 * \brief sorts the images, according to their File Name
787 * @param fileList Coherent File list (same Serie UID) to sort
788 * @return false only if the header is bugged !
790 bool SerieHelper::FileNameOrdering(FileList *fileList)
793 std::sort(fileList->begin(), fileList->end(),
794 SerieHelper::FileNameLessThan);
796 std::sort(fileList->begin(), fileList->end(),
797 SerieHelper::FileNameGreaterThan);
803 * \brief sorts the images, according to user supplied function
804 * @param fileList Coherent File list (same Serie UID) to sort
805 * @return false only if the header is bugged !
807 bool SerieHelper::UserOrdering(FileList *fileList)
809 std::sort(fileList->begin(), fileList->end(),
810 SerieHelper::UserLessThanFunction);
813 std::reverse(fileList->begin(), fileList->end());
818 //-----------------------------------------------------------------------------
821 * \brief Canonical printer.
823 void SerieHelper::Print(std::ostream &os, std::string const &indent)
825 // For all the Coherent File lists of the gdcm::Serie
826 SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
827 if ( itl == SingleSerieUIDFileSetHT.end() )
829 gdcmWarningMacro( "No SingleSerieUID File set found" );
832 while (itl != SingleSerieUIDFileSetHT.end())
834 os << "Serie UID :[" << itl->first << "]" << std::endl;
836 // For all the files of a SingleSerieUID File set
837 for (FileList::iterator it = (itl->second)->begin();
838 it != (itl->second)->end();
841 os << indent << " --- " << (*it)->GetFileName() << std::endl;
847 //-----------------------------------------------------------------------------
848 } // end namespace gdcm