1 /*=========================================================================
4 Module: $RCSfile: gdcmSerieHelper.cxx,v $
6 Date: $Date: 2005/11/21 09:46:27 $
7 Version: $Revision: 1.35 $
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 (*it)->Delete(); // 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 = File::New();
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
119 if ( allrules ) // all rules are respected:
121 // Allright! we have a found a DICOM that matches the user expectation.
124 // 0020 000e UI REL Series Instance UID
125 const std::string &uid = header->GetEntryString(0x0020, 0x000e);
126 // if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
127 // no need here to do anything special
130 if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
132 gdcmDebugMacro(" New Serie UID :[" << uid << "]");
133 // create a std::list in 'uid' position
134 SingleSerieUIDFileSetHT[uid] = new FileList;
136 // Current Serie UID and DICOM header seems to match; add the file:
137 SingleSerieUIDFileSetHT[uid]->push_back( header );
141 // at least one rule was unmatched we need to deallocate the file:
147 gdcmWarningMacro("Could not read file: " << filename );
153 * \brief add a gdcm::File to the first (and supposed to be unique) file set
154 * of the gdcm::SerieHelper.
155 * \warning : this method should be used by aware users only!
156 * Passing a gdcm::File* has the same effect than passing a file name!
157 * \todo : decide which one is wrong (the method, or the commentary)!
158 * the following comment doesn't match the method :-(
159 * User is supposed to know the files he want to deal with
160 * and consider them they belong to the same Serie
161 * (even if their Serie UID is different)
162 * user will probabely OrderFileList() this list (actually, ordering
163 * user choosen gdm::File is the sole interest of this method)
164 * Moreover, using vtkGdcmReader::SetCoherentFileList() will avoid
165 * vtkGdcmReader parsing twice the same files.
166 * *no* coherence check is performed, but those specified
167 * by SerieHelper::AddRestriction()
168 * @param header gdcm::File* of the file to deal with
170 void SerieHelper::AddGdcmFile(File *header)
173 // First step the user has defined a set of rules for the DICOM
174 // he is looking for.
175 // make sure the file correspond to his set of rules:
176 for(SerieRestrictions::iterator it = Restrictions.begin();
177 it != Restrictions.end();
181 const std::string s;// = header->GetEntryValue( r.first );
182 if ( !Util::DicomStringEqual(s, r.second.c_str()) )
184 // Argh ! This rule is unmatch let's just quit
189 if ( allrules ) // all rules are respected:
191 // Allright ! we have a found a DICOM that match the user expectation.
194 const std::string &uid = "0";
195 // Serie UID of the gdcm::File* may be different.
196 // User is supposed to know what he wants
198 if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
200 gdcmDebugMacro(" New Serie UID :[" << uid << "]");
201 // create a std::list in 'uid' position
202 SingleSerieUIDFileSetHT[uid] = new FileList;
204 // Current Serie UID and DICOM header seems to match; add the file:
205 SingleSerieUIDFileSetHT[uid]->push_back( header );
207 // Even if a rule was unmatch we don't deallocate the gdcm::File:
211 * \brief add a rules for restricting a DICOM file to be in the serie we are
212 * trying to find. For example you can select only the DICOM file from a
213 * directory which would have a particular EchoTime==4.0.
214 * This method is a user level, value is not required to be formatted as a DICOM
216 * @param key Target tag we want restrict on a given value
217 * @param value value to be checked to exclude File
218 * @param op operator we want to use to check
220 void SerieHelper::AddRestriction(TagKey const &key,
221 std::string const &value, int op)
228 ExRestrictions.push_back( r );
232 * \brief Sets the root Directory
233 * @param dir Name of the directory to deal with
234 * @param recursive whether we want explore recursively the root Directory
236 void SerieHelper::SetDirectory(std::string const &dir, bool recursive)
238 DirList dirList(dir, recursive); // OS specific
240 DirListType filenames_list = dirList.GetFilenames();
241 for( DirListType::const_iterator it = filenames_list.begin();
242 it != filenames_list.end(); ++it)
249 * \brief Sorts the given Fileset
250 * \warning This could be implemented in a 'Strategy Pattern' approach
251 * But as I don't know how to do it, I leave it this way
252 * BTW, this is also a Strategy, I don't know this is
253 * the best approach :)
255 void SerieHelper::OrderFileList(FileList *fileSet)
258 if ( SerieHelper::UserLessThanFunction )
260 UserOrdering( fileSet );
263 else if ( ImagePositionPatientOrdering( fileSet ) )
267 else if ( ImageNumberOrdering(fileSet ) )
273 FileNameOrdering(fileSet );
278 * \brief Elementary coherence checking of the files with the same Serie UID
279 * Only sizes and pixel type are checked right now ...
281 bool SerieHelper::IsCoherent(FileList *fileSet)
283 if(fileSet->size() == 1)
286 FileList::const_iterator it = fileSet->begin();
288 int nX = (*it)->GetXSize();
289 int nY = (*it)->GetYSize();
290 int pixelSize = (*it)->GetPixelSize();
291 bool signedPixelData = (*it)->IsSignedPixelData();
294 it != fileSet->end();
297 if ( (*it)->GetXSize() != nX )
299 if ( (*it)->GetYSize() != nY )
301 if ( (*it)->GetPixelSize() != pixelSize )
303 if ( (*it)->IsSignedPixelData() != signedPixelData )
305 // probabely more is to be checked (?)
310 #ifndef GDCM_LEGACY_REMOVE
312 FileList *SerieHelper::GetFirstCoherentFileList()
314 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
315 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
316 return ItFileSetHt->second;
321 FileList *SerieHelper::GetNextCoherentFileList()
323 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
326 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
327 return ItFileSetHt->second;
332 FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
334 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
336 return SingleSerieUIDFileSetHT[SerieUID];
342 * \brief Get the first Fileset while visiting the SingleSerieUIDFileSetmap
343 * @return The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0
345 FileList *SerieHelper::GetFirstSingleSerieUIDFileSet()
347 ItFileSetHt = SingleSerieUIDFileSetHT.begin();
348 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
349 return ItFileSetHt->second;
354 * \brief Get the next Fileset while visiting the SingleSerieUIDFileSetmap
355 * \note : meaningfull only if GetNextSingleSerieUIDFileSet() already called
356 * @return The next FileList (SingleSerieUIDFileSet) if found, otherwhise 0
358 FileList *SerieHelper::GetNextSingleSerieUIDFileSet()
360 gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
363 if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
364 return ItFileSetHt->second;
369 * \brief Get the SingleSerieUIDFileSet according to its Serie UID
370 * @param SerieUID SerieUID to retrieve
371 * \return pointer to the FileList (SingleSerieUIDFileSet) if found, otherwhise 0
373 FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID)
375 if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
377 return SingleSerieUIDFileSetHT[SerieUID];
381 * \brief Splits a Single SerieUID Fileset according to the Orientations
382 * @param fileSet File Set to be splitted
383 * \return std::map of 'Xcoherent' File sets
386 XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet)
388 XCoherentFileSetmap CoherentFileSet;
390 int nb = fileSet->size();
392 return CoherentFileSet;
395 std::string strOrient;
396 std::ostringstream ossOrient;
397 FileList::const_iterator it = fileSet->begin();
400 it != fileSet->end();
403 // Information is in :
404 // 0020 0037 : Image Orientation (Patient) or
405 // 0020 0035 : Image Orientation (RET)
407 // Let's build again the 'cosines' string, to be sure of it's format
408 (*it)->GetImageOrientationPatient(iop);
411 for (int i = 1; i < 6; i++)
416 strOrient = ossOrient.str();
418 // FIXME : is it a 'cleaner' way to initialize an ostringstream?
420 if ( CoherentFileSet.count(strOrient) == 0 )
422 gdcmDebugMacro(" New Orientation :[" << strOrient << "]");
423 // create a File set in 'orientation' position
424 CoherentFileSet[strOrient] = new FileList;
426 // Current Orientation and DICOM header match; add the file:
427 CoherentFileSet[strOrient]->push_back( (*it) );
429 return CoherentFileSet;
433 * \brief Splits a 'Single SerieUID' Fileset according to the Positions
434 * @param fileSet File Set to be splitted
435 * \return std::map of 'Xcoherent' File sets
438 XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet)
440 XCoherentFileSetmap CoherentFileSet;
442 int nb = fileSet->size();
444 return CoherentFileSet;
446 std::string strImPos; // read on disc
447 std::ostringstream ossPosition;
448 std::string strPosition; // re computed
449 FileList::const_iterator it = fileSet->begin();
452 it != fileSet->end();
455 // Information is in :
456 // 0020,0032 : Image Position Patient
457 // 0020,0030 : Image Position (RET)
459 strImPos = (*it)->GetEntryString(0x0020,0x0032);
460 if ( strImPos == GDCM_UNFOUND)
462 gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
463 strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images
464 if ( strImPos == GDCM_UNFOUND )
466 gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
467 // User wants to split on the 'Position'
468 // No 'Position' info found.
469 // We return an empty Htable !
470 return CoherentFileSet;
474 if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ",
475 &pos[0], &pos[1], &pos[2]) != 3 )
477 gdcmWarningMacro( "Wrong number for Position : ["
478 << strImPos << "]" );
479 return CoherentFileSet;
482 // Let's build again the 'position' string, to be sure of it's format
484 ossPosition << pos[0];
485 for (int i = 1; i < 3; i++)
488 ossPosition << pos[i];
490 strPosition = ossPosition.str();
493 if ( CoherentFileSet.count(strPosition) == 0 )
495 gdcmDebugMacro(" New Position :[" << strPosition << "]");
496 // create a File set in 'position' position
497 CoherentFileSet[strPosition] = new FileList;
499 // Current Position and DICOM header match; add the file:
500 CoherentFileSet[strPosition]->push_back( (*it) );
502 return CoherentFileSet;
506 * \brief Splits a 'Single SerieUID' File set Coherent according to the
507 * value of a given Tag
508 * @param fileSet File Set to be splitted
509 * @param group group number of the target Element
510 * @param elem element number of the target Element
511 * \return std::map of 'Xcoherent' File sets
514 XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
515 uint16_t group, uint16_t elem)
517 XCoherentFileSetmap CoherentFileSet;
519 int nb = fileSet->size();
521 return CoherentFileSet;
523 std::string strTagValue; // read on disc
525 FileList::const_iterator it = fileSet->begin();
528 it != fileSet->end();
531 // Information is in :
532 // 0020,0032 : Image Position Patient
533 // 0020,0030 : Image Position (RET)
535 strTagValue = (*it)->GetEntryString(group,elem);
537 if ( CoherentFileSet.count(strTagValue) == 0 )
539 gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]");
540 // create a File set in 'position' position
541 CoherentFileSet[strTagValue] = new FileList;
543 // Current Tag value and DICOM header match; add the file:
544 CoherentFileSet[strTagValue]->push_back( (*it) );
546 return CoherentFileSet;
549 //-----------------------------------------------------------------------------
552 //-----------------------------------------------------------------------------
555 * \brief sorts the images, according to their Patient Position.
557 * We may order, considering :
558 * -# Image Position Patient
561 * -# More to come :-)
562 * \note : FileList = std::vector<File* >
563 * @param fileList Coherent File list (same Serie UID) to sort
564 * @return false only if the header is bugged !
566 bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList )
567 //based on Jolinda Smith's algorithm
569 //iop is calculated based on the file file
574 float min = 0, max = 0;
577 std::vector<float> distlist;
579 //!\todo rewrite this for loop.
580 for ( FileList::const_iterator
581 it = fileList->begin();
582 it != fileList->end(); ++it )
586 (*it)->GetImageOrientationPatient( cosines );
588 // You only have to do this once for all slices in the volume. Next,
589 // for each slice, calculate the distance along the slice normal
590 // using the IPP ("Image Position Patient") tag.
591 // ("dist" is initialized to zero before reading the first slice) :
592 normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
593 normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
594 normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
596 ipp[0] = (*it)->GetXOrigin();
597 ipp[1] = (*it)->GetYOrigin();
598 ipp[2] = (*it)->GetZOrigin();
601 for ( int i = 0; i < 3; ++i )
603 dist += normal[i]*ipp[i];
606 distlist.push_back( dist );
613 ipp[0] = (*it)->GetXOrigin();
614 ipp[1] = (*it)->GetYOrigin();
615 ipp[2] = (*it)->GetZOrigin();
618 for ( int i = 0; i < 3; ++i )
620 dist += normal[i]*ipp[i];
623 distlist.push_back( dist );
625 min = (min < dist) ? min : dist;
626 max = (max > dist) ? max : dist;
631 // Then I order the slices according to the value "dist". Finally, once
632 // I've read in all the slices, I calculate the z-spacing as the difference
633 // between the "dist" values for the first two slices.
634 FileVector CoherentFileVector(n);
635 // CoherentFileVector.reserve( n );
636 CoherentFileVector.resize( n );
637 // gdcmAssertMacro( CoherentFileVector.capacity() >= n );
639 // Find out if min/max are coherent
642 gdcmWarningMacro("Looks like all images have the exact same image position"
643 << ". No PositionPatientOrdering sort performed" );
647 float step = (max - min)/(n - 1);
651 //VC++ don't understand what scope is !! it -> it2
652 for (FileList::const_iterator it2 = fileList->begin();
653 it2 != fileList->end(); ++it2, ++n)
656 //Assumption: all files are present (no one missing)
657 pos = (int)( fabs( (distlist[n]-min)/step) + .5 );
659 // a Dicom 'Serie' may contain scout views
660 // and images may have differents directions
661 // -> More than one may have the same 'pos'
662 // Sorting has then NO meaning !
663 if (CoherentFileVector[pos]==NULL)
664 CoherentFileVector[pos] = *it2;
667 gdcmWarningMacro( "At least 2 files with same position."
668 << " No PositionPatientOrdering sort performed");
673 fileList->clear(); // doesn't delete list elements, only nodes
677 //VC++ don't understand what scope is !! it -> it3
678 for (FileVector::const_iterator it3 = CoherentFileVector.begin();
679 it3 != CoherentFileVector.end(); ++it3)
681 fileList->push_back( *it3 );
684 else // user asked for reverse order
686 FileVector::const_iterator it4;
687 it4 = CoherentFileVector.end();
691 fileList->push_back( *it4 );
692 } while (it4 != CoherentFileVector.begin() );
696 CoherentFileVector.clear();
701 bool SerieHelper::ImageNumberLessThan(File *file1, File *file2)
703 return file1->GetImageNumber() < file2->GetImageNumber();
706 bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2)
708 return file1->GetImageNumber() > file2->GetImageNumber();
712 * \brief sorts the images, according to their Image Number
713 * \note Works only on bona fide files (i.e image number is a character string
714 * corresponding to an integer)
715 * within a bona fide serie (i.e image numbers are consecutive)
716 * @param fileList File set (same Serie UID) to sort
717 * @return false if non bona fide stuff encountered
719 bool SerieHelper::ImageNumberOrdering(FileList *fileList)
722 int n = fileList->size();
724 FileList::const_iterator it = fileList->begin();
725 min = max = (*it)->GetImageNumber();
727 for (; it != fileList->end(); ++it, ++n)
729 pos = (*it)->GetImageNumber();
730 min = (min < pos) ? min : pos;
731 max = (max > pos) ? max : pos;
734 // Find out if image numbers are coherent (consecutive)
735 if ( min == max || max == 0 || max >= (n+min) )
737 gdcmWarningMacro( " 'Image numbers' not coherent. "
738 << " No ImageNumberOrdering sort performed.");
742 std::sort(fileList->begin(), fileList->end(),
743 SerieHelper::ImageNumberLessThan );
745 std::sort(fileList->begin(), fileList->end(),
746 SerieHelper::ImageNumberGreaterThan );
751 bool SerieHelper::FileNameLessThan(File *file1, File *file2)
753 return file1->GetFileName() < file2->GetFileName();
756 bool SerieHelper::FileNameGreaterThan(File *file1, File *file2)
758 return file1->GetFileName() > file2->GetFileName();
761 * \brief sorts the images, according to their File Name
762 * @param fileList Coherent File list (same Serie UID) to sort
763 * @return false only if the header is bugged !
765 bool SerieHelper::FileNameOrdering(FileList *fileList)
768 std::sort(fileList->begin(), fileList->end(),
769 SerieHelper::FileNameLessThan);
771 std::sort(fileList->begin(), fileList->end(),
772 SerieHelper::FileNameGreaterThan);
778 * \brief sorts the images, according to user supplied function
779 * @param fileList Coherent File list (same Serie UID) to sort
780 * @return false only if the header is bugged !
782 bool SerieHelper::UserOrdering(FileList *fileList)
784 std::sort(fileList->begin(), fileList->end(),
785 SerieHelper::UserLessThanFunction);
788 std::reverse(fileList->begin(), fileList->end());
793 //-----------------------------------------------------------------------------
796 * \brief Canonical printer.
798 void SerieHelper::Print(std::ostream &os, std::string const &indent)
800 // For all the Coherent File lists of the gdcm::Serie
801 SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
802 if ( itl == SingleSerieUIDFileSetHT.end() )
804 gdcmWarningMacro( "No SingleSerieUID File set found" );
807 while (itl != SingleSerieUIDFileSetHT.end())
809 os << "Serie UID :[" << itl->first << "]" << std::endl;
811 // For all the files of a SingleSerieUID File set
812 for (FileList::iterator it = (itl->second)->begin();
813 it != (itl->second)->end();
816 os << indent << " --- " << (*it)->GetFileName() << std::endl;
822 //-----------------------------------------------------------------------------
823 } // end namespace gdcm