469 lines
19 KiB
C++
469 lines
19 KiB
C++
/*
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*
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* Copyright (C) 2016, Open Connections GmbH
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* All rights reserved. See COPYRIGHT file for details.
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*
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* This software and supporting documentation are maintained by
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*
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* OFFIS e.V.
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* R&D Division Health
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* Escherweg 2
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* D-26121 Oldenburg, Germany
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*
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*
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* Module: dcmtract
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*
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* Author: Michael Onken
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*
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* Purpose: Class representing a Track Set from a Tractography Results IOD
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*
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*/
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#ifndef TRCTRACKSET_H
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#define TRCTRACKSET_H
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#include "dcmtk/config/osconfig.h"
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#include "dcmtk/dcmiod/modbase.h"
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#include "dcmtk/dcmiod/iodutil.h"
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#include "dcmtk/dcmiod/iodmacro.h" // for CodeSequenceMacro and CodeWithModifiers
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#include "dcmtk/dcmtract/trctypes.h"
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// Forward declarations
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class TrcTracksStatistic;
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class TrcTrackSetStatistic;
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class TrcTrack;
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class TrcMeasurement;
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/** Class representing a Track Set within the Tractography Results IOD. A Track
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* Set is a set of tracks (really), and might define a measurements and
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* statistics which then must be populated for all tracks in the set.
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*
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*/
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class DCMTK_DCMTRACT_EXPORT TrcTrackSet
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: public IODComponent
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{
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public:
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// Allow read/write functions in DcmIODUtil to access class internals
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friend class DcmIODUtil;
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/** Create TrcTrackSet object by proving required data
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* @param trackSetLabel Label for the Track Set (256 chars max, VR=LO)
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* @param trackSetDescription Description for the Track Set (2^32-2 bytes
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* maximum, VR=UT)
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* @param trackSetAnatomy Code for the anatomy the Track Set covers. DICOM
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* proposes CID 7710 "Tractography Anatomic Sites" (Baseline)
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* @param trackSetDiffusionModelCode Code for diffusion model used for Track
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* Set. DICOM prescribes code from CID 7261 "Diffusion Model Value
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* Types"
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* @param trackSetAlgorithmIdentification Algorithm used in order to
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* create Track Set. DICOM prescribes code from CID 7262 "Diffusion
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* Tractography Algorithm Families".
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* @param trackSet Returns the created Track Set, if successfull (NULL
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* otherwise)
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* @return EC_Normal if creation was successful, error otherwise
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*/
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static OFCondition create(const OFString& trackSetLabel,
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const OFString& trackSetDescription,
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const CodeWithModifiers& trackSetAnatomy,
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const CodeSequenceMacro& trackSetDiffusionModelCode,
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const CodeSequenceMacro& trackSetAlgorithmIdentification,
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TrcTrackSet*& trackSet /* result */);
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/** Destructor, frees memory
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*/
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virtual ~TrcTrackSet();
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/** Resets rules to their original values
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*/
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virtual void resetRules();
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/** Set missing values by inventing "default values". Automatically
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* called during write() by IODComponent.
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*/
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virtual void inventMissing();
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/** Get name of component
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* @return Name of the module ("TrackSetSequenceItem")
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*/
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virtual OFString getName() const;
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/** Clear all data
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*/
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virtual void clearData();
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/** Read attributes from given item into this class
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* @param source The source to read from
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* @param clearOldData If OFTrue, old data is cleared before reading. Otherwise
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* old data is overwritten (or amended)
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* @result EC_Normal if reading was successful, error otherwise
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*/
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virtual OFCondition read(DcmItem& source,
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const OFBool clearOldData = OFTrue);
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/** Get Tracks of this Track Set
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* @return Reference to Tracks of this Track Set
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*/
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virtual const OFVector<TrcTrack*>& getTracks();
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/** Write attributes from this class into given item
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* @param destination The item to write to
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* @result EC_Normal if writing was successful, error otherwise
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*/
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virtual OFCondition write(DcmItem& destination);
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/** Get Track Set Number (should be 1-n)
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* @param value Reference to variable in which the value should be stored
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* @param pos Index of the value to get (0..vm-1)
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition getTrackSetNumber(Uint16 &value,
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const unsigned long pos = 0) const;
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/** Get Track Set Label
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* @param value Reference to variable in which the value should be stored
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* @param pos Index of the value to get (0..vm-1), -1 for all components
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition getTrackSetLabel(OFString &value,
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const signed long pos = 0) const;
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/** Get Track Set Description
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* @param value Reference to variable in which the value should be stored
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* @param pos Index of the value to get (0..vm-1), -1 for all components
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition getTrackSetDescription(OFString &value,
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const signed long pos = 0) const;
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/** Get reference to Track Set Anatomical Type Code
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* @return Reference to the code
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*/
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virtual CodeWithModifiers& getTrackSetAnatomy();
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/** Get copy of Recommended Display CIELab Value
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* @param L Returns CIELab L value
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* @param a Returns CIELab a value
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* @param b Returns CIELab b value
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition getRecommendedDisplayCIELabValue(Uint16& L,
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Uint16& a,
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Uint16& b);
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/** Get Recommended Line Thickness
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* @param value Reference to the variable in which the value should be stored
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* @param pos Index of the value to get (0..vm-1)
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition getRecommendedLineThickness(Float32& value,
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const unsigned long pos = 0);
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/** Get Laterality.
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* @param laterality Reference to the variable in which the value should be stored.
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* If value in dataset is not set at all, LAT_UNKNOWN is returned. If
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* a value is present that is not covered by the standard LAT_ERROR
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* is returned.
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* @return EC_Normal if successful (i.e. not LAT_ERROR), error code otherwise
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*/
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virtual OFCondition getLaterality(TrcTypes::E_TrackSetLaterality& laterality);
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/** Find measurements of a specific type. They can be retrieved afterwards by
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* using getMeasurement().
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* @param type The measurement type to look for
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* @param measurementNumbers Returns the measurement indexes that are
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* of specified type.
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* @return Always returns EC_Normal (for now).
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*/
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virtual OFCondition findMeasurementsByType(const CodeSequenceMacro& type,
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OFVector<size_t>& measurementNumbers);
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/** Get measurement by index. The index can be identified by using
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* findMeasurementsByType() or getMeasurementInfos()
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* @param measurementIndex The index of the measurement (starting from 0)
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* @param measurement Returns a reference to the measurement requested
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* @return Returns EC_Normal if measurement exists, TRC_EC_NoSuchMeasurement
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* otherwise
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*/
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virtual OFCondition getMeasurement(const size_t measurementIndex,
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const TrcMeasurement*& measurement);
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/** Get descriptive information of all measurements
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* @param typesAndUnits Returns vector of pairs, which each pair holding
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* a code for type of measurement and its physical units.
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*/
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virtual void getMeasurementInfos(OFVector<OFPair<CodeSequenceMacro, CodeSequenceMacro> >& typesAndUnits);
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/** Get access to all statistics defined for the Tracks in this Track Set
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* @return Returns reference to all Track statistics
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*/
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virtual const OFVector<TrcTracksStatistic*>& getTrackStatistics();
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/** Get access to all statistics defined for the Tracks in this Track Set
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* @return Returns reference to all Track statistics
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*/
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virtual const OFVector<TrcTrackSetStatistic*>& getTrackSetStatistics();
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/** Get access to diffusion acquisition code
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* @returns Returns reference to diffusion acquisition code
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*/
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virtual CodeSequenceMacro& getDiffusionAcquisitionCode();
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/** Get access to diffusion model code used
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* @return Returns reference to diffusion model code
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*/
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virtual CodeSequenceMacro& getDiffusionModelCode();
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/** Get access to tracking algorithm identification codes
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* @return Reference to tracking algorithm identification codes
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*/
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virtual OFVector<CodeSequenceMacro*>& getTrackingAlgorithmIdentification();
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/** Returns number of Tracks in Track Set
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* @return Number of Tracks in Track Set
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*/
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size_t getNumberOfTracks();
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/** Returns number of Track Set Statistics in Track Set
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* @return Number of Track Set Statistics in Track Set
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*/
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size_t getNumberOfTrackSetStatistics();
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/** Returns number of Track Statistics in Track Set
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* @return Number of Track Statistics in Track Set
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*/
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size_t getNumberOfTrackStatistics();
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/** Returns number of Measurements in Track Set
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* @return Number of Measurements in Track Set
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*/
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size_t getNumberOfMeasurements();
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/** Add track to Track Set
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* @param pointData Array of points (x,y,z coordinate for each point)
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* @param numPoints Number of points in pointData (i.e. number of point
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* coordinates divided by 3)
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* @param recommendedCIELabColors Recommended display color(s) as CIELab
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* values, i.e. L,a,b component(s). There are 3 modes:
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* 1) Single color: All points in track will be colored in that color
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* 2) No color (NULL): Color is not defined on a per-track basis but
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* must be defined on Track Set level
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* 3) One color per point: Colors for all points are provided
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* separately.
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* @param numColors Number of colors defined in recommendedCIELabColors
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* (must be either 0, 1 or numPoints)
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* @param result Returns the resulting Track if creation was successful,
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* error otherwise
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*/
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virtual OFCondition addTrack(const Float32* pointData,
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const size_t numPoints,
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const Uint16* recommendedCIELabColors,
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const size_t numColors,
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TrcTrack*& result);
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/** Add measurement for this Track Set
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* @param measurementCode The type of measurement. DICOM prescribes a code
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* from CID 7263 "Diffusion Tractography Measurement Types"
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* @param measurementUnitCodes The physical units of the measured value.
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* DICOM prescribes a code from CID 82 "Units of Measurement".
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* @param measurement The created measurement, if successful, NULL otherwise
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* @return EC_Normal if successful, error otherwise
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*/
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virtual OFCondition addMeasurement(const CodeSequenceMacro& measurementCode,
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const CodeSequenceMacro& measurementUnitCodes,
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TrcMeasurement*& measurement /* result */);
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/** Add Track Statistic, i.e. statistic that is defined once and where a single
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* value must be provided for all tracks.
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* @param typeCode The type of statistic, DICOM prescribes code from CID
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* 7263 "Diffusion Tractography Measurement Types".
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* @param typeModifierCode The region of interest of this statistic. DICOM
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* prescribes code from CID 7464 "General Region of Interest
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* Measurement Modifiers"
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* @param unitsCode The physical units of the measured value. DICOM
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* prescribes a code from CID 82 "Units of Measurement".
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* @param values The statistical values, one for each track
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* @param numValues The number of values in statisticValues (must be equal to
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* number of tracks in this Track Set)
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* @param statistic Returns the created statistic, if successful. NULL
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* otherwise
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* @return Returns EC_Normal if successful, error otherwise
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*/
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virtual OFCondition addTrackStatistics(const CodeSequenceMacro& typeCode,
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const CodeSequenceMacro& typeModifierCode,
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const CodeSequenceMacro& unitsCode,
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const Float32* values,
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const size_t numValues,
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TrcTracksStatistic*& statistic /* result */);
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/** Add Track Set Statistic, i.e. a statistical value computed for the whole
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* Track Set.
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* @param typeCode The type of statistic, DICOM prescribes code from CID
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* 7263 "Diffusion Tractography Measurement Types".
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* @param typeModifierCode The region of interest of this statistic. DICOM
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* prescribes code from CID 7464 "General Region of Interest
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* Measurement Modifiers"
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* @param unitsCode The physical units of the measured value. DICOM
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* prescribes a code from CID 82 "Units of Measurement".
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* @param value The statistical value
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* @param statistic Returns the created statistic, if successful. NULL
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* otherwise
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*/
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virtual OFCondition addTrackSetStatistic(const CodeSequenceMacro& typeCode,
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const CodeSequenceMacro& typeModifierCode,
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const CodeSequenceMacro& unitsCode,
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const Float64 value,
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TrcTrackSetStatistic*& statistic /* result */);
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/** Set Track Set Label
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* @param value Value to be set (single value only) or "" for no value
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* @param checkValue Check 'value' for conformance with VR (LO) and VM (1)
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* if enabled
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition setTrackSetLabel(const OFString &value,
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const OFBool checkValue = OFTrue);
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/** Set Track Set Description
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* @param value Value to be set (single value only) or "" for no value
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* @param checkValue Check 'value' for conformance with VR (UT) and VM (1)
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* if enabled
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition setTrackSetDescription(const OFString &value,
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const OFBool checkValue = OFTrue);
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/** Set Recommended Display CIELab Value
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* @param L CIELab L component value
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* @param a CIELab a component value
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* @param b CIELab b component value
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition setRecommendedDisplayCIELabValue(const Uint16 L,
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const Uint16 a,
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const Uint16 b);
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/** Set Recommended Line Thickness
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* @param value Value to be set. The units shall be the same as the units
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* of the coordinate system in which the point coordinates are specified.
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* @param checkValue Check 'value' for conformance with VR (FL)
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* if enabled
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition setRecommendedLineThickness(const Float32& value,
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const OFBool checkValue = OFTrue);
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/** Set Laterality
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* @param value Value to be set
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* @param checkValue Check 'value' for conformance if enabled. Parameter is
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* not used but present for consistency with other functions.
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* @return EC_Normal if successful, an error code otherwise
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*/
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virtual OFCondition setLaterality(const TrcTypes::E_TrackSetLaterality value,
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const OFBool checkValue = OFTrue);
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protected:
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/** Protected constructor, use create() method to create a new Track Set
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*/
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TrcTrackSet();
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/** Reads Track statistics from item into dedicated structures
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* @param source The item to read from, must contain Track Set Statistics
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* Sequence
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* @return EC_Normal if reading was successful, error otherwise
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*/
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OFCondition readTrackStatistics(DcmItem& source);
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/** Reads Track Set statistics from item into dedicated structures
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* @param source The item to read from, must contain Track Statistics
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* Sequence
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* @return EC_Normal if reading was successful, error otherwise
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*/
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OFCondition readTrackSetStatistics(DcmItem& source);
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OFCondition readMeasurements(DcmItem& source);
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/** Reads Tracks from item into dedicated structures
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* @param source The item to read from, must contain Track Sequence
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* @return EC_Normal if reading was successful, error otherwise
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*/
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OFCondition readTracks(DcmItem& source);
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/** Write Track Statistics to given item
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* @param result Returns EC_Normal if writing was successful, error otherwise
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* or if result has not been EC_Normal when calling
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* @param destination The destination item to write to. The Track Statistic
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* Sequence will be written by this method.
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*/
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void writeTrackStatistics(OFCondition& result,
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DcmItem& destination);
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/** Write Track Statistics to given item
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* @param result Returns EC_Normal if writing was successful, error otherwise
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* or if result has not been EC_Normal when calling
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* @param destination The destination item to write to. The Track Set
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* Statistic Sequence will be written by this method.
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*/
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void writeTrackSetStatistics(OFCondition& result,
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DcmItem& destination);
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/** Write Measurements to given item
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* @param result Returns EC_Normal if writing was successful, error otherwise
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* or if result has not been EC_Normal when calling
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* @param destination The destination item to write to. The Measurements
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* Sequence will be written by this method.
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* @return Same as parameter "result"
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*/
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OFCondition writeMeasurements(OFCondition& result,
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DcmItem& destination);
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/** Write Tracks to given item
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* @param result Returns EC_Normal if writing was successful, error otherwise
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* or if result has not been EC_Normal when calling
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* @param destination The destination item to write to. The Tracks Sequence
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* will be written by this method.
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* @return Same as parameter "result"
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*/
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OFCondition writeTracks(OFCondition& result,
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DcmItem& destination);
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/** Check whether measurements have data for all tracks
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* @return EC_Normal measurement data is complete, TRC_EC_MeasurementDataMissing
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* otherwise
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*/
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OFCondition checkMeasurements();
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private:
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/// Data for all tracks (i.e. content of Track Sequence)
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OFVector<TrcTrack*> m_Tracks;
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/// Anatomy code for this Track Set
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CodeWithModifiers m_Anatomy;
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/// Measurements for this Track Set
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OFVector<TrcMeasurement*> m_Measurements;
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/// Statistics for Tracks in this Track Set
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OFVector<TrcTracksStatistic*> m_TrackStatistics;
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/// Statistics for Track Set
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OFVector<TrcTrackSetStatistic*> m_TrackSetStatistics;
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/// Code for diffusion acquisition used for this Track Set
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CodeSequenceMacro m_DiffusionAcquisitionCode;
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/// Code for diffusion model used for this Track Set
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CodeSequenceMacro m_DiffusionModelCode;
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/// Codes for algorithms used to create this Track Set
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OFVector<CodeSequenceMacro*> m_TrackingAlgorithmIdentification;
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};
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#endif // TRCTRACKSET_H
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