Program: gdcm
Module: $RCSfile: gdcmSerieHelper.h,v $
Language: C++
- Date: $Date: 2005/02/02 16:58:04 $
- Version: $Revision: 1.3 $
+ Date: $Date: 2011/03/29 07:36:00 $
+ Version: $Revision: 1.47 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
-#ifndef GDCMSERIEHELPER_H
-#define GDCMSERIEHELPER_H
+#ifndef _GDCMSERIEHELPER_H_
+#define _GDCMSERIEHELPER_H_
-#include "gdcmCommon.h"
+#include "gdcmRefCounter.h"
+#include "gdcmTagKey.h"
+#include "gdcmDebug.h" // for LEGACY
-#include <list>
+#include "gdcmDicomDirSerie.h"
+
#include <vector>
+#include <iostream>
#include <map>
-namespace gdcm
+namespace GDCM_NAME_SPACE
{
class File;
-typedef std::list<File* > GdcmFileList;
+
+ typedef std::vector<File* > FileList;
+#ifndef GDCM_LEGACY_REMOVE
+ typedef std::vector<File* > GdcmFileList;
+#endif
+
+ /// \brief XCoherent stands for 'Extra Coherent',
+ /// (The name 'Coherent' would be enough but it was used before;
+ /// I don't want to put a bomb in the code)
+ /// Any 'better name' is welcome !
+ typedef std::map<std::string, FileList *> XCoherentFileSetmap;
+
+ typedef bool (*BOOL_FUNCTION_PFILE_PFILE_POINTER)(File *, File *);
//-----------------------------------------------------------------------------
/**
* \brief
- * - This class should be used for a stack of 2D dicom images.
- * It allows to explore (recursively or not) a directory and
- * makes a set of 'Coherent Files' list (coherent : same Serie UID)
- * It allows to sort any of the Coherent File list on the image postion
+ * This class should be used for a stack of 2D dicom images.
+ *
+ * - It allows to explore (recursively or not) a directory and
+ * makes a set of 'Single SerieUID Filesets'
+ * - It allows :
+ * - - to sort any of the 'Single SerieUID Fileset' on the image position.
+ * - - to split any of the Single SerieUID Filesets (better use this name than
+ * 'CoherentFileList' : it's NOT a std::list, files are NOT coherent ...)
+ * into several XCoherent Filesets
+ * XCoherent stands for 'Extra Coherent' (same orientation, or same position)
*/
-class GDCM_EXPORT SerieHelper
+
+class GDCM_EXPORT SerieHelper : public RefCounter
{
+ gdcmTypeMacro(SerieHelper);
+
public:
- typedef std::map<std::string, GdcmFileList *> CoherentFileListmap;
- typedef std::vector<File* > GdcmFileVector;
+ /// SingleSerieUIDFileSetmap replaces the former CoherentFileListmap
+ /// (List were actually std::vectors, and where no coherent at all :
+ /// They were only Single SeriesInstanceUID File sets)
+ typedef std::map<std::string, FileList *> SingleSerieUIDFileSetmap;
- SerieHelper();
- ~SerieHelper();
- void Print();
+ typedef std::vector<File* > FileVector;
+
+/// \brief Constructs a SerieHelper with a RefCounter
+ static SerieHelper *New() {return new SerieHelper();}
+
+ virtual ~SerieHelper();
+ void Print(std::ostream &os = std::cout, std::string const &indent = "" );
/// \todo should return bool or throw error ?
void AddFileName(std::string const &filename);
+ bool AddFile(File *header);
+ // GDCM_LEGACY(bool AddGdcmFile(File* header))
+
void SetDirectory(std::string const &dir, bool recursive=false);
- void OrderGdcmFileList(GdcmFileList *CoherentGdcmFileList);
-
- /// \brief Gets the FIRST *coherent* File List.
+ void SetDicomDirSerie(DicomDirSerie *se);
+
+ bool IsCoherent(FileList *fileSet);
+ void OrderFileList(FileList *fileSet);
+ void Clear() { ClearAll(); }
+
+ bool UserOrdering(FileList *fileSet);
+ bool ImagePositionPatientOrdering(FileList *fileSet);
+ bool ImageNumberOrdering(FileList *fileSet);
+ bool FileNameOrdering(FileList *fileSet);
+
+ /// \brief Gets the FIRST Single SerieUID Fileset.
/// Deprecated; kept not to break the API
- /// \note Caller must call OrderGdcmFileList first
- /// @return the (first) *coherent* File List
- const GdcmFileList &GetGdcmFileList() { return
- *CoherentGdcmFileListHT.begin()->second; }
+ /// \note Caller must call OrderFileList first
+ /// @return the (first) Single SerieUID Fileset
+ const FileList &GetFileList()
+ { return *SingleSerieUIDFileSetHT.begin()->second; }
- GdcmFileList *GetFirstCoherentFileList();
- GdcmFileList *GetNextCoherentFileList();
- GdcmFileList *GetCoherentFileList(std::string SerieUID);
+ // GDCM_LEGACY( FileList *GetFirstCoherentFileList() )
+ // GDCM_LEGACY( FileList *GetNextCoherentFileList() )
+ // GDCM_LEGACY( FileList *GetCoherentFileList(std::string serieUID) )
+
+ FileList *GetFirstSingleSerieUIDFileSet();
+ FileList *GetNextSingleSerieUIDFileSet();
+ FileList *GetSingleSerieUIDFileSet(std::string serieUID);
+ /// brief returns the 'Series Instance UID' Single SerieUID FileSet
+ std::string GetCurrentSerieUIDFileSetUID()
+ { return (*ItFileSetHt).first; }
+
+ /// \brief returns the distance between the 2 first -adjacent- slices,
+ /// along the slice normal; -1.0 if process failed
+ /// Computed during ImagePositionPatientOrdering() process.
+ /// To be use *immediately after* ImagePositionPatientOrdering()
+ /// (it's a member of the FileHelper, *not* of the FileList !)
+ double GetZSpacing() { return ZSpacing; }
+
+ /// All the following allow user to restrict DICOM file to be part
+ /// of a particular serie
+ /// \todo : find a trick to allow user to say the restrictions are ored
+ /// (not only anded)
+ /// ex : keep the images whose SerieNumber is 101 or 102 or 103.
+ void AddRestriction(TagKey const &key);
+ void AddRestriction(TagKey const &key, std::string const &value, int op);
+ void AddRestriction(uint16_t group, uint16_t elem, std::string const &value,
+ int op);
+
+ /// \brief Use additional series information such as ProtocolName
+ /// and SeriesName to identify when a single SeriesUID contains
+ /// multiple 3D volumes - as can occur with perfusion and DTI imaging
+ void SetUseSeriesDetails( bool useSeriesDetails )
+ {
+ m_UseSeriesDetails = useSeriesDetails;
+ }
+ bool GetUseSeriesDetails()
+ {
+ return m_UseSeriesDetails;
+ }
+ /// \brief This function will add the following DICOM tag as being part of a
+ /// 'fake' uid. This is usefull when the Serie UID is not enough to disseminate
+ /// into multiple sub serie when needed:
+ /// 0020 0011 Series Number
+ /// 0018 0024 Sequence Name
+ /// 0018 0050 Slice Thickness
+ /// 0028 0010 Rows
+ /// 0028 0011 Columns
+ void CreateDefaultUniqueSeriesIdentifier();
+ void AddSeriesDetail(uint16_t group, uint16_t elem, bool convert);
+
+ std::string CreateUserDefinedFileIdentifier( File * inFile );
+
+ /// \brief Create a string that uniquely identifies a series. By default
+ // uses the SeriesUID. If UseSeriesDetails(true) has been called,
+ // then additional identifying information is used.
+ std::string CreateUniqueSeriesIdentifier( File * inFile );
+
+/**
+ * \brief Sets the LoadMode as a boolean string.
+ * LD_NOSEQ, LD_NOSHADOW, LD_NOSHADOWSEQ
+ * ... (nothing more, right now)
+ * WARNING : before using LD_NOSHADOW, be sure *all* your files
+ * contain accurate values in the 0x0000 element (if any)
+ * of *each* Shadow Group. The parser will fail if the size is wrong !
+ * @param mode Load mode to be used
+ */
+ void SetLoadMode (int mode) { LoadMode = mode; }
+
+/**
+ * \brief Sets the DropDuplicatePositions as a boolean.
+ * @param drop DropDuplicatePositions mode to be used
+ */
+ void SetDropDuplicatePositions (bool drop) { DropDuplicatePositions = drop; }
+
+/// Brief User wants the files to be sorted Direct Order (default value)
+ void SetSortOrderToDirect() { DirectOrder = true; }
+
+/// Brief User wants the files to be sorted Reverse Order
+ void SetSortOrderToReverse() { DirectOrder = false; }
+
+ /// to allow user to give is own comparison function
+ void SetUserLessThanFunction( BOOL_FUNCTION_PFILE_PFILE_POINTER userFunc )
+ { UserLessThanFunction = userFunc; }
+
+ XCoherentFileSetmap SplitOnOrientation(FileList *fileSet);
+ XCoherentFileSetmap SplitOnPosition(FileList *fileSet);
+ XCoherentFileSetmap SplitOnTagValue(FileList *fileSet,
+ uint16_t group, uint16_t element);
+ XCoherentFileSetmap SplitOnTagValueConvertToFloat(FileList *fileSet,
+ uint16_t group, uint16_t element);
+protected :
+ SerieHelper();
+
private:
- bool ImagePositionPatientOrdering(GdcmFileList *CoherentGdcmFileList);
- bool ImageNumberOrdering(GdcmFileList *CoherentGdcmFileList);
- bool FileNameOrdering(GdcmFileList *CoherentGdcmFileList);
+ void ClearAll();
+
+ /*
+ //move them to public (usefull for aware user!)
+ bool UserOrdering(FileList *fileSet);
+ bool ImagePositionPatientOrdering(FileList *fileSet);
+ bool ImageNumberOrdering(FileList *fileSet);
+ bool FileNameOrdering(FileList *fileSet);
+ */
+ static bool ImageNumberLessThan(File *file1, File *file2);
+ static bool ImageNumberGreaterThan(File *file1, File *file2);
+ static bool FileNameLessThan(File *file1, File *file2);
+ static bool FileNameGreaterThan(File *file1, File *file2);
+
+//Attributes:
- CoherentFileListmap CoherentGdcmFileListHT;
- CoherentFileListmap::iterator ItListHt;
+ SingleSerieUIDFileSetmap SingleSerieUIDFileSetHT;
+ SingleSerieUIDFileSetmap::iterator ItFileSetHt;
+
+#ifndef GDCM_LEGACY_REMOVE
+ typedef std::pair<TagKey, std::string> Rule;
+ typedef std::vector<Rule> SerieRestrictions;
+ SerieRestrictions Restrictions;
+#endif
+
+ // New style for (extented) Rules
+ typedef struct {
+ uint16_t group;
+ uint16_t elem;
+ std::string value;
+ int op;
+ } ExRule;
+ typedef std::vector<ExRule> SerieExRestrictions;
+ SerieExRestrictions ExRestrictions;
+ SerieExRestrictions ExRefine;
+
+ typedef struct {
+ uint16_t group;
+ uint16_t elem;
+ bool convert;
+ } ExDetail;
+ typedef std::vector<ExDetail> SeriesExDetails;
+ SeriesExDetails ExDetails;
+
+
+ /// \brief Bit string integer (each one considered as a boolean)
+ /// Bit 0 : Skip Sequences, if possible
+ /// Bit 1 : Skip Shadow Groups if possible
+ /// Probabely, some more to add
+ int LoadMode;
+
+ /// \brief whether we want to sort in direct order or not (reverse order).
+ /// To be used by aware user only
+ bool DirectOrder;
+
+ /// \brief If user knows more about his images than gdcm does,
+ /// he may supply his own comparison function.
+ BOOL_FUNCTION_PFILE_PFILE_POINTER UserLessThanFunction;
+
+ bool DropDuplicatePositions;
+
+ void Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) );
+
+ bool m_UseSeriesDetails;
+ /// \brief distance between the 2 first -adjancent- slices, along the slice normal
+ /// Computed during ImagePositionPatientOrdering() process.
+ /// (we need to sort the whole image set to do that)
+ /// To be used *immediately after* ImagePositionPatientOrdering()
+ /// (it's a member of the FileHelper, *not* of the FileList !)
+ double ZSpacing;
};
} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff