1 /*=========================================================================
4 Module: $RCSfile: gdcmSerieHelper.h,v $
6 Date: $Date: 2007/08/22 16:14:04 $
7 Version: $Revision: 1.44 $
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 #ifndef _GDCMSERIEHELPER_H_
20 #define _GDCMSERIEHELPER_H_
22 #include "gdcmRefCounter.h"
23 #include "gdcmTagKey.h"
24 #include "gdcmDebug.h" // for LEGACY
26 #include "gdcmDicomDirSerie.h"
32 namespace GDCM_NAME_SPACE
36 typedef std::vector<File* > FileList;
37 #ifndef GDCM_LEGACY_REMOVE
38 typedef std::vector<File* > GdcmFileList;
41 /// \brief XCoherent stands for 'Extra Coherent',
42 /// (The name 'Coherent' would be enough but it was used before;
43 /// I don't want to put a bomb in the code)
44 /// Any 'better name' is welcome !
45 typedef std::map<std::string, FileList *> XCoherentFileSetmap;
47 typedef bool (*BOOL_FUNCTION_PFILE_PFILE_POINTER)(File *, File *);
49 //-----------------------------------------------------------------------------
52 * This class should be used for a stack of 2D dicom images.
54 * - It allows to explore (recursively or not) a directory and
55 * makes a set of 'Single SerieUID Filesets'
57 * - - to sort any of the 'Single SerieUID Fileset' on the image position.
58 * - - to split any of the Single SerieUID Filesets (better use this name than
59 * 'CoherentFileList' : it's NOT a std::list, files are NOT coherent ...)
60 * into several XCoherent Filesets
61 * XCoherent stands for 'Extra Coherent' (same orientation, or same position)
63 class GDCM_EXPORT SerieHelper : public RefCounter
65 gdcmTypeMacro(SerieHelper);
68 /// SingleSerieUIDFileSetmap replaces the former CoherentFileListmap
69 /// ( List were actually std::vectors, and where no coherent at all :
70 /// They were only Single SeriesInstanceUID File sets)
71 typedef std::map<std::string, FileList *> SingleSerieUIDFileSetmap;
73 typedef std::vector<File* > FileVector;
75 /// \brief Constructs a SerieHelper with a RefCounter
76 static SerieHelper *New() {return new SerieHelper();}
78 virtual ~SerieHelper();
79 void Print(std::ostream &os = std::cout, std::string const &indent = "" );
81 /// \todo should return bool or throw error ?
82 void AddFileName(std::string const &filename);
83 bool AddFile(File *header);
84 // GDCM_LEGACY(bool AddGdcmFile(File* header))
86 void SetDirectory(std::string const &dir, bool recursive=false);
87 void SetDicomDirSerie(DicomDirSerie *se);
89 bool IsCoherent(FileList *fileSet);
90 void OrderFileList(FileList *fileSet);
91 void Clear() { ClearAll(); }
93 /// \brief Gets the FIRST Single SerieUID Fileset.
94 /// Deprecated; kept not to break the API
95 /// \note Caller must call OrderFileList first
96 /// @return the (first) Single SerieUID Fileset
97 const FileList &GetFileList()
98 { return *SingleSerieUIDFileSetHT.begin()->second; }
100 // GDCM_LEGACY( FileList *GetFirstCoherentFileList() )
101 // GDCM_LEGACY( FileList *GetNextCoherentFileList() )
102 // GDCM_LEGACY( FileList *GetCoherentFileList(std::string serieUID) )
104 FileList *GetFirstSingleSerieUIDFileSet();
105 FileList *GetNextSingleSerieUIDFileSet();
106 FileList *GetSingleSerieUIDFileSet(std::string serieUID);
107 /// brief returns the 'Series Instance UID' Single SerieUID FileSet
108 std::string GetCurrentSerieUIDFileSetUID()
109 { return (*ItFileSetHt).first; }
111 /// \brief returns the distance between the 2 first -adjacent- slices,
112 /// along the slice normal; -1.0 if process failed
113 /// Computed during ImagePositionPatientOrdering() process.
114 /// To be use *immediately after* ImagePositionPatientOrdering()
115 /// (it's a member of the FileHelper, *not* of the FileList !)
116 double GetZSpacing() { return ZSpacing; }
118 /// All the following allow user to restrict DICOM file to be part
119 /// of a particular serie
120 /// \todo : find a trick to allow user to say the restrictions are ored
122 /// ex : keep the images whose SerieNumber is 101 or 102 or 103.
123 void AddRestriction(TagKey const &key);
124 void AddRestriction(TagKey const &key, std::string const &value, int op);
125 void AddRestriction(uint16_t group, uint16_t elem, std::string const &value,
128 /// \brief Use additional series information such as ProtocolName
129 /// and SeriesName to identify when a single SeriesUID contains
130 /// multiple 3D volumes - as can occur with perfusion and DTI imaging
131 void SetUseSeriesDetails( bool useSeriesDetails )
133 m_UseSeriesDetails = useSeriesDetails;
135 bool GetUseSeriesDetails()
137 return m_UseSeriesDetails;
139 /// \brief This function will add the following DICOM tag as being part of a
140 /// 'fake' uid. This is usefull when the Serie UID is not enough to disseminate
141 /// into multiple sub serie when needed:
142 /// 0020 0011 Series Number
143 /// 0018 0024 Sequence Name
144 /// 0018 0050 Slice Thickness
146 /// 0028 0011 Columns
147 void CreateDefaultUniqueSeriesIdentifier();
149 void AddSeriesDetail(uint16_t group, uint16_t elem, bool convert);
151 std::string CreateUserDefinedFileIdentifier( File * inFile );
153 /// \brief Create a string that uniquely identifies a series. By default
154 // uses the SeriesUID. If UseSeriesDetails(true) has been called,
155 // then additional identifying information is used.
156 std::string CreateUniqueSeriesIdentifier( File * inFile );
159 * \brief Sets the LoadMode as a boolean string.
160 * LD_NOSEQ, LD_NOSHADOW, LD_NOSHADOWSEQ
161 * ... (nothing more, right now)
162 * WARNING : before using LD_NOSHADOW, be sure *all* your files
163 * contain accurate values in the 0x0000 element (if any)
164 * of *each* Shadow Group. The parser will fail if the size is wrong !
165 * @param mode Load mode to be used
167 void SetLoadMode (int mode) { LoadMode = mode; }
170 * \brief Sets the DropDuplicatePositions as a boolean.
171 * @param drop DropDuplicatePositions mode to be used
173 void SetDropDuplicatePositions (bool drop) { DropDuplicatePositions = drop; }
175 /// Brief User wants the files to be sorted Direct Order (default value)
176 void SetSortOrderToDirect() { DirectOrder = true; }
178 /// Brief User wants the files to be sorted Reverse Order
179 void SetSortOrderToReverse() { DirectOrder = false; }
181 /// to allow user to give is own comparison function
182 void SetUserLessThanFunction( BOOL_FUNCTION_PFILE_PFILE_POINTER userFunc )
183 { UserLessThanFunction = userFunc; }
185 XCoherentFileSetmap SplitOnOrientation(FileList *fileSet);
186 XCoherentFileSetmap SplitOnPosition(FileList *fileSet);
187 XCoherentFileSetmap SplitOnTagValue(FileList *fileSet,
188 uint16_t group, uint16_t element);
194 bool UserOrdering(FileList *fileSet);
195 bool ImagePositionPatientOrdering(FileList *fileSet);
196 bool ImageNumberOrdering(FileList *fileSet);
197 bool FileNameOrdering(FileList *fileSet);
199 static bool ImageNumberLessThan(File *file1, File *file2);
200 static bool ImageNumberGreaterThan(File *file1, File *file2);
201 static bool FileNameLessThan(File *file1, File *file2);
202 static bool FileNameGreaterThan(File *file1, File *file2);
206 SingleSerieUIDFileSetmap SingleSerieUIDFileSetHT;
207 SingleSerieUIDFileSetmap::iterator ItFileSetHt;
209 #ifndef GDCM_LEGACY_REMOVE
210 typedef std::pair<TagKey, std::string> Rule;
211 typedef std::vector<Rule> SerieRestrictions;
212 SerieRestrictions Restrictions;
215 // New style for (extented) Rules
222 typedef std::vector<ExRule> SerieExRestrictions;
223 SerieExRestrictions ExRestrictions;
224 SerieExRestrictions ExRefine;
231 typedef std::vector<ExDetail> SeriesExDetails;
232 SeriesExDetails ExDetails;
235 /// \brief Bit string integer (each one considered as a boolean)
236 /// Bit 0 : Skip Sequences, if possible
237 /// Bit 1 : Skip Shadow Groups if possible
238 /// Probabely, some more to add
241 /// \brief whether we want to sort in direct order or not (reverse order).
242 /// To be used by aware user only
245 /// \brief If user knows more about his images than gdcm does,
246 /// he may supply his own comparison function.
247 BOOL_FUNCTION_PFILE_PFILE_POINTER UserLessThanFunction;
249 bool DropDuplicatePositions;
251 void Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) );
253 bool m_UseSeriesDetails;
254 /// \brief distance between the 2 first -adjancent- slices, along the slice normal
255 /// Computed during ImagePositionPatientOrdering() process.
256 /// (we need to sort the whole image set to do that)
257 /// To be used *immediately after* ImagePositionPatientOrdering()
258 /// (it's a member of the FileHelper, *not* of the FileList !)
262 } // end namespace gdcm
264 //-----------------------------------------------------------------------------