X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.h;h=2f20fe4f2911a43fcedcbef98ae1daf1d4dc9636;hb=fd5c14391627c6e42283ced90561271af2a161a2;hp=13db02af8e9b6b6e82c55e967830af1a7d3a9762;hpb=6cf34d5df01e8ec0572bcef6c6b91be58212ef77;p=gdcm.git diff --git a/src/gdcmSerieHelper.h b/src/gdcmSerieHelper.h index 13db02af..2f20fe4f 100644 --- a/src/gdcmSerieHelper.h +++ b/src/gdcmSerieHelper.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmSerieHelper.h,v $ Language: C++ - Date: $Date: 2005/06/03 16:08:16 $ - Version: $Revision: 1.10 $ + 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 @@ -16,71 +16,258 @@ =========================================================================*/ -#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 "gdcmDicomDirSerie.h" + #include #include #include -namespace gdcm +namespace GDCM_NAME_SPACE { class File; -typedef std::vector FileList; + + typedef std::vector FileList; +#ifndef GDCM_LEGACY_REMOVE + typedef std::vector 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 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 position + * 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 CoherentFileListmap; + /// 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 SingleSerieUIDFileSetmap; + typedef std::vector FileVector; - SerieHelper(); - ~SerieHelper(); +/// \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 OrderFileList(FileList *coherentFileList); - - /// \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 OrderFileList first - /// @return the (first) *coherent* File List - const FileList &GetFileList() { return *CoherentFileListHT.begin()->second; } + /// @return the (first) Single SerieUID Fileset + const FileList &GetFileList() + { return *SingleSerieUIDFileSetHT.begin()->second; } - FileList *GetFirstCoherentFileList(); - FileList *GetNextCoherentFileList(); - FileList *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 - void AddRestriction(TagKey const &key, std::string const &value); - + /// \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); -private: - bool ImagePositionPatientOrdering(FileList *coherentFileList); - bool ImageNumberOrdering(FileList *coherentFileList); - bool FileNameOrdering(FileList *coherentFileList); + /// \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: + 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); - CoherentFileListmap CoherentFileListHT; - CoherentFileListmap::iterator ItListHt; + static bool FileNameGreaterThan(File *file1, File *file2); + +//Attributes: + + SingleSerieUIDFileSetmap SingleSerieUIDFileSetHT; + SingleSerieUIDFileSetmap::iterator ItFileSetHt; - typedef std::pair Rule; +#ifndef GDCM_LEGACY_REMOVE + typedef std::pair Rule; typedef std::vector 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 SerieExRestrictions; + SerieExRestrictions ExRestrictions; + SerieExRestrictions ExRefine; + + typedef struct { + uint16_t group; + uint16_t elem; + bool convert; + } ExDetail; + typedef std::vector 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