1 /*=========================================================================
4 Module: $RCSfile: gdcmSerieHeader.cxx,v $
6 Date: $Date: 2005/01/21 11:40:55 $
7 Version: $Revision: 1.12 $
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 "gdcmSerieHeader.h"
20 #include "gdcmDirList.h"
22 #include "gdcmDebug.h"
31 typedef std::vector<File* > GdcmFileVector;
32 //-----------------------------------------------------------------------------
33 // Constructor / Destructor
34 SerieHeader::SerieHeader()
36 CoherentGdcmFileList.clear();
37 // Later will contain: 0020 000e UI REL Series Instance UID
41 SerieHeader::~SerieHeader()
44 for ( GdcmFileList::const_iterator it = CoherentGdcmFileList.begin();
45 it != CoherentGdcmFileList.end(); ++it)
49 CoherentGdcmFileList.clear();
52 //-----------------------------------------------------------------------------
55 //-----------------------------------------------------------------------------
58 * \brief add a File to the list based on file name
59 * @param filename Name of the file to deal with
61 void SerieHeader::AddFileName(std::string const &filename)
63 //directly use string and not const char*:
64 File *header = new File( filename );
65 if( header->IsReadable() )
67 // 0020 000e UI REL Series Instance UID
68 std::string uid = header->GetEntry (0x0020, 0x000e);
69 // if uid == GDCM_UNFOUND then consistenly we should find GDCM_UNFOUND
70 // no need here to do anything special
71 if( CurrentSerieUID == "" )
73 // Set the current one
74 CurrentSerieUID = uid;
76 if( CurrentSerieUID == uid )
78 // Current Serie UID and DICOM header seems to match add the file:
79 CoherentGdcmFileList.push_back( header );
83 gdcmVerboseMacro("Wrong Serie Instance UID should be:" << CurrentSerieUID );
88 gdcmVerboseMacro("Could not read file: " << filename );
94 * \brief Sets the Directory
95 * @param dir Name of the directory to deal with
97 void SerieHeader::SetDirectory(std::string const &dir)
99 CurrentSerieUID = ""; //Reset previous Serie Instance UID
100 DirList dirList(dir); //OS specific
102 DirListType filenames_list = dirList.GetFilenames();
103 for( DirListType::const_iterator it = filenames_list.begin();
104 it != filenames_list.end(); ++it)
111 * \brief Sorts the File List
112 * \warning This could be implemented in a 'Strategy Pattern' approach
113 * But as I don't know how to do it, I leave it this way
114 * BTW, this is also a Strategy, I don't know this is the best approach :)
116 void SerieHeader::OrderGdcmFileList()
118 if( ImagePositionPatientOrdering() )
122 else if( ImageNumberOrdering() )
132 //-----------------------------------------------------------------------------
135 //-----------------------------------------------------------------------------
138 * \brief sorts the images, according to their Patient Position
139 * We may order, considering :
141 * -# Image Position Patient
143 * @return false only if the header is bugged !
145 bool SerieHeader::ImagePositionPatientOrdering()
146 //based on Jolinda's algorithm
148 //iop is calculated based on the file file
153 float min = 0, max = 0;
156 std::vector<float> distlist;
158 //!\todo rewrite this for loop.
159 for ( GdcmFileList::const_iterator
160 it = CoherentGdcmFileList.begin();
161 it != CoherentGdcmFileList.end(); ++it )
165 (*it)->GetImageOrientationPatient( cosines );
167 //You only have to do this once for all slices in the volume. Next,
168 // for each slice, calculate the distance along the slice normal
169 // using the IPP tag ("dist" is initialized to zero before reading
170 // the first slice) :
171 normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
172 normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
173 normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
175 ipp[0] = (*it)->GetXOrigin();
176 ipp[1] = (*it)->GetYOrigin();
177 ipp[2] = (*it)->GetZOrigin();
180 for ( int i = 0; i < 3; ++i )
182 dist += normal[i]*ipp[i];
190 distlist.push_back( dist );
197 ipp[0] = (*it)->GetXOrigin();
198 ipp[1] = (*it)->GetYOrigin();
199 ipp[2] = (*it)->GetZOrigin();
202 for ( int i = 0; i < 3; ++i )
204 dist += normal[i]*ipp[i];
212 distlist.push_back( dist );
214 min = (min < dist) ? min : dist;
215 max = (max > dist) ? max : dist;
220 // Then I order the slices according to the value "dist". Finally, once
221 // I've read in all the slices, I calculate the z-spacing as the difference
222 // between the "dist" values for the first two slices.
223 GdcmFileVector CoherentGdcmFileVector(n);
224 // CoherentGdcmFileVector.reserve( n );
225 CoherentGdcmFileVector.resize( n );
226 // gdcmAssertMacro( CoherentGdcmFileVector.capacity() >= n );
228 float step = (max - min)/(n - 1);
232 //VC++ don't understand what scope is !! it -> it2
233 for (GdcmFileList::const_iterator it2 = CoherentGdcmFileList.begin();
234 it2 != CoherentGdcmFileList.end(); ++it2, ++n)
237 //Assumption: all files are present (no one missing)
238 pos = (int)( fabs( (distlist[n]-min)/step) + .5 );
240 // a Dicom 'Serie' may contain scout views
241 // and images may have differents directions
242 // -> More than one may have the same 'pos'
243 // Sorting has then NO meaning !
244 if (CoherentGdcmFileVector[pos]==NULL)
245 CoherentGdcmFileVector[pos] = *it2;
250 CoherentGdcmFileList.clear(); //this doesn't delete list's element, node only
252 //VC++ don't understand what scope is !! it -> it3
253 for (GdcmFileVector::const_iterator it3 = CoherentGdcmFileVector.begin();
254 it3 != CoherentGdcmFileVector.end(); ++it3)
256 CoherentGdcmFileList.push_back( *it3 );
260 CoherentGdcmFileVector.clear();
266 * \brief sorts the images, according to their Image Number
267 * @return false only if the header is bugged !
270 bool SerieHeader::ImageNumberOrdering()
273 int n = 0;//CoherentGdcmFileList.size() is a O(N) operation
274 unsigned char *partition;
276 GdcmFileList::const_iterator it = CoherentGdcmFileList.begin();
277 min = max = (*it)->GetImageNumber();
279 for (; it != CoherentGdcmFileList.end(); ++it, ++n)
281 pos = (*it)->GetImageNumber();
284 min = (min < pos) ? min : pos;
285 max = (max > pos) ? max : pos;
288 // Find out if sorting worked:
289 if( min == max || max == 0 || max > (n+min)) return false;
291 //bzeros(partition, n); //This function is deprecated, better use memset.
292 partition = new unsigned char[n];
293 memset(partition, 0, n);
295 GdcmFileVector CoherentGdcmFileVector(n);
297 //VC++ don't understand what scope is !! it -> it2
298 for (GdcmFileList::const_iterator it2 = CoherentGdcmFileList.begin();
299 it2 != CoherentGdcmFileList.end(); ++it2)
301 pos = (*it2)->GetImageNumber();
302 CoherentGdcmFileVector[pos - min] = *it2;
303 partition[pos - min]++;
306 unsigned char mult = 1;
307 for( int i=0; i<n ; i++ )
309 mult *= partition[i];
312 //VC++ don't understand what scope is !! it -> it3
313 CoherentGdcmFileList.clear(); //this doesn't delete list's element, node only
314 for ( GdcmFileVector::const_iterator it3 = CoherentGdcmFileVector.begin();
315 it3 != CoherentGdcmFileVector.end(); ++it3 )
317 CoherentGdcmFileList.push_back( *it3 );
319 CoherentGdcmFileVector.clear();
328 * \brief sorts the images, according to their File Name
329 * @return false only if the header is bugged !
331 bool SerieHeader::FileNameOrdering()
334 //sort(CoherentGdcmFileList.begin(), CoherentGdcmFileList.end());
338 } // end namespace gdcm
339 //-----------------------------------------------------------------------------