diff --git a/Framework/API/inc/MantidAPI/MatrixWorkspace.h b/Framework/API/inc/MantidAPI/MatrixWorkspace.h
index c71fb9decfce9ac997ec200b53108c1ad3f56183..7512599bc9eeadcf976b5447561786d0a99541c9 100644
--- a/Framework/API/inc/MantidAPI/MatrixWorkspace.h
+++ b/Framework/API/inc/MantidAPI/MatrixWorkspace.h
@@ -130,499 +130,409 @@ public:
virtual std::vector<size_t>
getDetectorIDToWorkspaceIndexVector(detid_t &offset,
bool throwIfMultipleDets = false) const;
- std::vector<specnum_t> &spectraList) const;
- virtual std::vector<size_t>
- getSpectrumToWorkspaceIndexVector(
- specnum_t &offset) const;
- std::vector<size_t> getIndicesFromSpectra(
- const std::vector<specnum_t> &spectraList) const;
- size_t getIndexFromSpectrumNumber(
- const specnum_t specNo) const;
- std::vector<size_t> getIndicesFromDetectorIDs(
- const std::vector<detid_t> &detIdList) const;
- std::vector<specnum_t> getSpectraFromDetectorIDs(
- const std::vector<detid_t> &detIdList) const;
-
- bool hasGroupedDetectors() const;
-
- /// Get the footprint in memory in bytes.
- size_t getMemorySize() const override;
- virtual size_t getMemorySizeForXAxes() const;
-
- // Section required for iteration
- /// Returns the number of single indexable items in the
- /// workspace
- virtual std::size_t size() const = 0;
- /// Returns the size of each block of data returned by
- /// the dataY accessors
- virtual std::size_t blocksize() const = 0;
- /// Returns the number of histograms in the workspace
- virtual std::size_t getNumberHistograms() const = 0;
-
- /// Sets MatrixWorkspace title
- void setTitle(const std::string &) override;
- /// Gets MatrixWorkspace title (same as Run object
- /// run_title property)
- const std::string getTitle() const override;
-
- virtual Kernel::DateAndTime getFirstPulseTime() const;
- Kernel::DateAndTime getLastPulseTime() const;
-
- /// Returns the bin index for a given X value of a given
- /// workspace index
- size_t binIndexOf(const double xValue,
- const std::size_t = 0) const;
-
- //----------------------------------------------------------------------
- // DATA ACCESSORS
- //----------------------------------------------------------------------
-
- /// Return the underlying ISpectrum ptr at the given
- /// workspace index.
- virtual ISpectrum *getSpectrum(const size_t index) = 0;
-
- /// Return the underlying ISpectrum ptr (const version)
- /// at the given workspace
- /// index.
- virtual const ISpectrum *
- getSpectrum(const size_t index) const = 0;
-
- // Methods for getting read-only access to the data.
- // Just passes through to the virtual dataX/Y/E function
- // (const version)
- /// Returns a read-only (i.e. const) reference to the
- /// specified X array
- /// @param index :: workspace index to retrieve.
- const MantidVec &readX(std::size_t const index) const {
- return getSpectrum(index)->dataX();
- }
- /// Returns a read-only (i.e. const) reference to the
- /// specified Y array
- /// @param index :: workspace index to retrieve.
- const MantidVec &readY(std::size_t const index) const {
- return getSpectrum(index)->dataY();
- }
- /// Returns a read-only (i.e. const) reference to the
- /// specified E array
- /// @param index :: workspace index to retrieve.
- const MantidVec &readE(std::size_t const index) const {
- return getSpectrum(index)->dataE();
- }
- /// Returns a read-only (i.e. const) reference to the
- /// specified X error array
- /// @param index :: workspace index to retrieve.
- const MantidVec &readDx(size_t const index) const {
- return getSpectrum(index)->dataDx();
- }
-
- /// Returns the x data
- virtual MantidVec &dataX(const std::size_t index) {
- invalidateCommonBinsFlag();
- return getSpectrum(index)->dataX();
- }
- /// Returns the y data
- virtual MantidVec &dataY(const std::size_t index) {
- return getSpectrum(index)->dataY();
- }
- /// Returns the error data
- virtual MantidVec &dataE(const std::size_t index) {
- return getSpectrum(index)->dataE();
- }
- /// Returns the x error data
- virtual MantidVec &dataDx(const std::size_t index) {
- return getSpectrum(index)->dataDx();
- }
-
- /// Returns the x data const
- virtual const MantidVec &
- dataX(const std::size_t index) const {
- return getSpectrum(index)->dataX();
- }
- /// Returns the y data const
- virtual const MantidVec &
- dataY(const std::size_t index) const {
- return getSpectrum(index)->dataY();
- }
- /// Returns the error const
- virtual const MantidVec &
- dataE(const std::size_t index) const {
- return getSpectrum(index)->dataE();
- }
- /// Returns the error const
- virtual const MantidVec &
- dataDx(const std::size_t index) const {
- return getSpectrum(index)->dataDx();
- }
-
- virtual double getXMin() const;
- virtual double getXMax() const;
- virtual void getXMinMax(double &xmin,
- double &xmax) const;
-
- /// Returns a pointer to the x data
- virtual Kernel::cow_ptr<MantidVec>
- refX(const std::size_t index) const {
- return getSpectrum(index)->ptrX();
- }
-
- /// Returns a pointer to the dX (X Error) data
- virtual Kernel::cow_ptr<MantidVec>
- refDx(const std::size_t index) const {
- return getSpectrum(index)->ptrDx();
- }
-
- /// Set the specified X array to point to the given
- /// existing array
- virtual void setX(const std::size_t index,
- const MantidVec &X) {
- getSpectrum(index)->setX(X);
- invalidateCommonBinsFlag();
- }
-
- /// Set the specified X array to point to the given
- /// existing array
- virtual void setX(const std::size_t index,
- const MantidVecPtr &X) {
- getSpectrum(index)->setX(X);
- invalidateCommonBinsFlag();
- }
-
- /// Set the specified X array to point to the given
- /// existing array
- virtual void setX(const std::size_t index,
- const MantidVecPtr::ptr_type &X) {
- getSpectrum(index)->setX(X);
- invalidateCommonBinsFlag();
- }
-
- /// Set the specified Dx (X Error) array to point to the
- /// given existing array
- virtual void setDx(const std::size_t index,
- const MantidVec &Dx) {
- getSpectrum(index)->setDx(Dx);
- invalidateCommonBinsFlag();
- }
-
- /// Set the specified Dx (X Error) array to point to the
- /// given existing array
- virtual void setDx(const std::size_t index,
- const MantidVecPtr &Dx) {
- getSpectrum(index)->setDx(Dx);
- invalidateCommonBinsFlag();
- }
-
- /// Set the specified Dx (X Error) array to point to the
- /// given existing array
- virtual void setDx(const std::size_t index,
- const MantidVecPtr::ptr_type &Dx) {
- getSpectrum(index)->setX(Dx);
- invalidateCommonBinsFlag();
- }
-
- /** Sets the data in the workspace
- @param index :: the workspace index to set.
- @param Y :: Y vector */
- virtual void setData(const std::size_t index,
- const MantidVecPtr &Y) {
- getSpectrum(index)->setData(Y);
- }
-
- /** Sets the data in the workspace
- @param index :: the workspace index to set.
- @param Y :: Y vector
- @param E :: Error vector */
- virtual void setData(const std::size_t index,
- const MantidVecPtr &Y,
- const MantidVecPtr &E) {
- getSpectrum(index)->setData(Y, E);
- }
-
- /** Sets the data in the workspace
- @param index :: the workspace index to set.
- @param Y :: Y vector
- @param E :: Error vector */
- virtual void setData(const std::size_t index,
- const MantidVecPtr::ptr_type &Y,
- const MantidVecPtr::ptr_type &E) {
- getSpectrum(index)->setData(Y, E);
- }
-
- /**
- * Probes if DX (X Error) values were set on a
- * particular spectrum
- * @param index: the spectrum index
- */
- virtual bool hasDx(const std::size_t index) const {
- return getSpectrum(index)->hasDx();
- }
-
- /// Generate the histogram or rebin the existing
- /// histogram.
- virtual void
- generateHistogram(const std::size_t index,
- const MantidVec &X, MantidVec &Y,
- MantidVec &E,
- bool skipError = false) const = 0;
-
- /// Return a vector with the integrated counts for all
- /// spectra withing the
- /// given range
- virtual void getIntegratedSpectra(
- std::vector<double> &out, const double minX,
- const double maxX, const bool entireRange) const;
-
- /// Return an index in the X vector for an x-value close
- /// to a given value
- std::pair<size_t, double>
- getXIndex(size_t i, double x, bool isLeft = true,
- size_t start = 0) const;
-
- //----------------------------------------------------------------------
-
- int axes() const;
- virtual Axis *
- getAxis(const std::size_t &axisIndex) const;
- void replaceAxis(const std::size_t &axisIndex,
- Axis *const newAxis);
-
- /// Returns true if the workspace contains data in
- /// histogram form (as opposed
- /// to point-like)
- virtual bool isHistogramData() const;
-
- /// Returns true if the workspace contains has common X
- /// bins
- virtual bool isCommonBins() const;
-
- std::string YUnit() const;
- void setYUnit(const std::string &newUnit);
- std::string YUnitLabel() const;
- void setYUnitLabel(const std::string &newLabel);
-
- /// Are the Y-values dimensioned?
- const bool &isDistribution() const;
- bool &isDistribution(bool newValue);
-
- /// Mask a given workspace index, setting the data and
- /// error values to zero
- void maskWorkspaceIndex(const std::size_t index);
-
- // Methods to set and access masked bins
- void maskBin(const size_t &workspaceIndex,
- const size_t &binIndex,
- const double &weight = 1.0);
- void flagMasked(const size_t &spectrumIndex,
- const size_t &binIndex,
- const double &weight = 1.0);
- bool hasMaskedBins(const size_t &spectrumIndex) const;
- /// Masked bins for each spectrum are stored as a set of
- /// pairs containing <bin
- /// index, weight>
- typedef std::map<size_t, double> MaskList;
- const MaskList &
- maskedBins(const size_t &spectrumIndex) const;
-
- // Methods handling the internal monitor workspace
- virtual void setMonitorWorkspace(
- const boost::shared_ptr<MatrixWorkspace> &
- monitorWS);
- boost::shared_ptr<MatrixWorkspace>
- monitorWorkspace() const;
-
- void saveInstrumentNexus(::NeXus::File *file) const;
- void loadInstrumentNexus(::NeXus::File *file);
- void saveSpectraMapNexus(
- ::NeXus::File *file, const std::vector<int> &spec,
- const ::NeXus::NXcompression compression =
- ::NeXus::LZW) const;
-
- //=====================================================================================
- // MD Geometry methods
- //=====================================================================================
- size_t getNumDims() const override;
- boost::shared_ptr<const Mantid::Geometry::IMDDimension>
- getDimension(size_t index) const override;
- boost::shared_ptr<const Mantid::Geometry::IMDDimension>
- getDimensionWithId(std::string id) const override;
- //=====================================================================================
- // End MD Geometry methods
- //=====================================================================================
-
- //=====================================================================================
- // IMDWorkspace methods
- //=====================================================================================
-
- /// Gets the number of points available on the
- /// workspace.
- uint64_t getNPoints() const override;
- /// Get the number of points available on the workspace.
- uint64_t getNEvents() const override {
- return this->getNPoints();
- }
- /// Dimension id for x-dimension.
- static const std::string xDimensionId;
- /// Dimensin id for y-dimension.
- static const std::string yDimensionId;
- /// Generate a line plot through the matrix workspace.
- LinePlot getLinePlot(const Mantid::Kernel::VMD &start,
- const Mantid::Kernel::VMD &end,
- Mantid::API::MDNormalization
- normalize) const override;
- /// Get the signal at a coordinate in the workspace.
- signal_t
- getSignalAtCoord(const coord_t *coords,
- const Mantid::API::MDNormalization &
- normalization) const override;
- /// Get the signal at a coordinate in the workspace
- signal_t getSignalWithMaskAtCoord(
- const coord_t *coords,
- const Mantid::API::MDNormalization &normalization)
- const override;
- /// Create iterators. Partitions the iterators according
- /// to the number of
- /// cores.
- std::vector<IMDIterator *> createIterators(
- size_t suggestedNumCores = 1,
- Mantid::Geometry::MDImplicitFunction *function =
- nullptr) const override;
-
- /// Apply masking.
- void setMDMasking(Mantid::Geometry::MDImplicitFunction *
- maskingRegion) override;
- /// Clear exsting masking.
- void clearMDMasking() override;
-
- /// @return the special coordinate system used if any.
- Mantid::Kernel::SpecialCoordinateSystem
- getSpecialCoordinateSystem() const override;
-
- //=====================================================================================
- // End IMDWorkspace methods
- //=====================================================================================
-
- //=====================================================================================
- // Image methods
- //=====================================================================================
-
- /// Get start and end x indices for images
- std::pair<size_t, size_t>
- getImageStartEndXIndices(size_t i, double startX,
- double endX) const;
- /// Create an image of Ys.
- MantidImage_sptr
- getImageY(size_t start = 0, size_t stop = 0,
- size_t width = 0, double startX = EMPTY_DBL(),
- double endX = EMPTY_DBL()) const;
- /// Create an image of Es.
- MantidImage_sptr
- getImageE(size_t start = 0, size_t stop = 0,
- size_t width = 0, double startX = EMPTY_DBL(),
- double endX = EMPTY_DBL()) const;
- /// Copy the data (Y's) from an image to this workspace.
- virtual void setImageY(const MantidImage &image,
- size_t start = 0,
- bool parallelExecution = true);
- /// Copy the data from an image to this workspace's
- /// errors.
- virtual void setImageE(const MantidImage &image,
- size_t start = 0,
- bool parallelExecution = true);
-
- //=====================================================================================
- // End image methods
- //=====================================================================================
-
- protected:
- /// Protected copy constructor. May be used by childs
- /// for cloning.
- MatrixWorkspace(const MatrixWorkspace &other);
- /// Protected copy assignment operator. Assignment not
- /// implemented.
- MatrixWorkspace &
- operator=(const MatrixWorkspace &other);
-
- MatrixWorkspace(
- Mantid::Geometry::INearestNeighboursFactory *
- factory = nullptr);
-
- /// Initialises the workspace. Sets the size and lengths
- /// of the arrays. Must
- /// be overloaded.
- virtual void init(const std::size_t &NVectors,
- const std::size_t &XLength,
- const std::size_t &YLength) = 0;
-
- /// Invalidates the commons bins flag. This is
- /// generally called when a method
- /// could allow the X values to be changed.
- void invalidateCommonBinsFlag() {
- m_isCommonBinsFlagSet = false;
- }
-
- /// A vector of pointers to the axes for this workspace
- std::vector<Axis *> m_axes;
-
- private:
- MatrixWorkspace *doClone() const override = 0;
-
- /// Create an MantidImage instance.
- MantidImage_sptr
- getImage(const MantidVec &(MatrixWorkspace::*read)(
- std::size_t const) const,
- size_t start, size_t stop, size_t width,
- size_t indexStart, size_t indexEnd) const;
- /// Copy data from an image.
- void setImage(MantidVec &(MatrixWorkspace::*dataVec)(
- const std::size_t),
- const MantidImage &image, size_t start,
- bool parallelExecution);
-
- /// Has this workspace been initialised?
- bool m_isInitialized;
-
- /// The unit for the data values (e.g. Counts)
- std::string m_YUnit;
- /// A text label for use when plotting spectra
- std::string m_YUnitLabel;
- /// Flag indicating whether the Y-values are
- /// dimensioned. False by default
- bool m_isDistribution;
-
- /// Flag indicating whether the m_isCommonBinsFlag has
- /// been set. False by
- /// default
- mutable bool m_isCommonBinsFlagSet;
- /// Flag indicating whether the data has common bins.
- /// False by default
- mutable bool m_isCommonBinsFlag;
-
- /// The set of masked bins in a map keyed on spectrum
- /// index
- std::map<int64_t, MaskList> m_masks;
-
- /// A workspace holding monitor data relating to the
- /// main data in the
- /// containing workspace (null if none).
- boost::shared_ptr<MatrixWorkspace> m_monitorWorkspace;
-
- protected:
- /// Assists conversions to and from 2D histogram
- /// indexing to 1D indexing.
- MatrixWSIndexCalculator m_indexCalculator;
-
- /// Scoped pointer to NearestNeighbours factory
- boost::scoped_ptr<
- Mantid::Geometry::INearestNeighboursFactory>
- m_nearestNeighboursFactory;
-
- /// Shared pointer to NearestNeighbours object
- mutable boost::shared_ptr<
- Mantid::Geometry::INearestNeighbours>
- m_nearestNeighbours;
-
- /// Getter for the dimension id based on the axis.
- std::string
- getDimensionIdFromAxis(const int &axisIndex) const;
+
+ virtual std::vector<size_t>
+ getSpectrumToWorkspaceIndexVector(specnum_t &offset) const;
+ std::vector<size_t>
+ getIndicesFromSpectra(const std::vector<specnum_t> &spectraList) const;
+ size_t getIndexFromSpectrumNumber(const specnum_t specNo) const;
+ std::vector<size_t>
+ getIndicesFromDetectorIDs(const std::vector<detid_t> &detIdList) const;
+ std::vector<specnum_t>
+ getSpectraFromDetectorIDs(const std::vector<detid_t> &detIdList) const;
+
+ bool hasGroupedDetectors() const;
+
+ /// Get the footprint in memory in bytes.
+ size_t getMemorySize() const override;
+ virtual size_t getMemorySizeForXAxes() const;
+
+ // Section required for iteration
+ /// Returns the number of single indexable items in the workspace
+ virtual std::size_t size() const = 0;
+ /// Returns the size of each block of data returned by the dataY accessors
+ virtual std::size_t blocksize() const = 0;
+ /// Returns the number of histograms in the workspace
+ virtual std::size_t getNumberHistograms() const = 0;
+
+ /// Sets MatrixWorkspace title
+ void setTitle(const std::string &) override;
+ /// Gets MatrixWorkspace title (same as Run object run_title property)
+ const std::string getTitle() const override;
+
+ virtual Kernel::DateAndTime getFirstPulseTime() const;
+ Kernel::DateAndTime getLastPulseTime() const;
+
+ /// Returns the bin index for a given X value of a given workspace index
+ size_t binIndexOf(const double xValue, const std::size_t = 0) const;
+
+ //----------------------------------------------------------------------
+ // DATA ACCESSORS
+ //----------------------------------------------------------------------
+
+ /// Return the underlying ISpectrum ptr at the given workspace index.
+ virtual ISpectrum *getSpectrum(const size_t index) = 0;
+
+ /// Return the underlying ISpectrum ptr (const version) at the given workspace
+ /// index.
+ virtual const ISpectrum *getSpectrum(const size_t index) const = 0;
+
+ // Methods for getting read-only access to the data.
+ // Just passes through to the virtual dataX/Y/E function (const version)
+ /// Returns a read-only (i.e. const) reference to the specified X array
+ /// @param index :: workspace index to retrieve.
+ const MantidVec &readX(std::size_t const index) const {
+ return getSpectrum(index)->dataX();
+ }
+ /// Returns a read-only (i.e. const) reference to the specified Y array
+ /// @param index :: workspace index to retrieve.
+ const MantidVec &readY(std::size_t const index) const {
+ return getSpectrum(index)->dataY();
+ }
+ /// Returns a read-only (i.e. const) reference to the specified E array
+ /// @param index :: workspace index to retrieve.
+ const MantidVec &readE(std::size_t const index) const {
+ return getSpectrum(index)->dataE();
+ }
+ /// Returns a read-only (i.e. const) reference to the specified X error array
+ /// @param index :: workspace index to retrieve.
+ const MantidVec &readDx(size_t const index) const {
+ return getSpectrum(index)->dataDx();
+ }
+
+ /// Returns the x data
+ virtual MantidVec &dataX(const std::size_t index) {
+ invalidateCommonBinsFlag();
+ return getSpectrum(index)->dataX();
+ }
+ /// Returns the y data
+ virtual MantidVec &dataY(const std::size_t index) {
+ return getSpectrum(index)->dataY();
+ }
+ /// Returns the error data
+ virtual MantidVec &dataE(const std::size_t index) {
+ return getSpectrum(index)->dataE();
+ }
+ /// Returns the x error data
+ virtual MantidVec &dataDx(const std::size_t index) {
+ return getSpectrum(index)->dataDx();
+ }
+
+ /// Returns the x data const
+ virtual const MantidVec &dataX(const std::size_t index) const {
+ return getSpectrum(index)->dataX();
+ }
+ /// Returns the y data const
+ virtual const MantidVec &dataY(const std::size_t index) const {
+ return getSpectrum(index)->dataY();
+ }
+ /// Returns the error const
+ virtual const MantidVec &dataE(const std::size_t index) const {
+ return getSpectrum(index)->dataE();
+ }
+ /// Returns the error const
+ virtual const MantidVec &dataDx(const std::size_t index) const {
+ return getSpectrum(index)->dataDx();
+ }
+
+ virtual double getXMin() const;
+ virtual double getXMax() const;
+ virtual void getXMinMax(double &xmin, double &xmax) const;
+
+ /// Returns a pointer to the x data
+ virtual Kernel::cow_ptr<MantidVec> refX(const std::size_t index) const {
+ return getSpectrum(index)->ptrX();
+ }
+
+ /// Returns a pointer to the dX (X Error) data
+ virtual Kernel::cow_ptr<MantidVec> refDx(const std::size_t index) const {
+ return getSpectrum(index)->ptrDx();
+ }
+
+ /// Set the specified X array to point to the given existing array
+ virtual void setX(const std::size_t index, const MantidVec &X) {
+ getSpectrum(index)->setX(X);
+ invalidateCommonBinsFlag();
+ }
+
+ /// Set the specified X array to point to the given existing array
+ virtual void setX(const std::size_t index, const MantidVecPtr &X) {
+ getSpectrum(index)->setX(X);
+ invalidateCommonBinsFlag();
+ }
+
+ /// Set the specified X array to point to the given existing array
+ virtual void setX(const std::size_t index, const MantidVecPtr::ptr_type &X) {
+ getSpectrum(index)->setX(X);
+ invalidateCommonBinsFlag();
+ }
+
+ /// Set the specified Dx (X Error) array to point to the given existing array
+ virtual void setDx(const std::size_t index, const MantidVec &Dx) {
+ getSpectrum(index)->setDx(Dx);
+ invalidateCommonBinsFlag();
+ }
+
+ /// Set the specified Dx (X Error) array to point to the given existing array
+ virtual void setDx(const std::size_t index, const MantidVecPtr &Dx) {
+ getSpectrum(index)->setDx(Dx);
+ invalidateCommonBinsFlag();
+ }
+
+ /// Set the specified Dx (X Error) array to point to the given existing array
+ virtual void setDx(const std::size_t index,
+ const MantidVecPtr::ptr_type &Dx) {
+ getSpectrum(index)->setX(Dx);
+ invalidateCommonBinsFlag();
+ }
+
+ /** Sets the data in the workspace
+ @param index :: the workspace index to set.
+ @param Y :: Y vector */
+ virtual void setData(const std::size_t index, const MantidVecPtr &Y) {
+ getSpectrum(index)->setData(Y);
+ }
+
+ /** Sets the data in the workspace
+ @param index :: the workspace index to set.
+ @param Y :: Y vector
+ @param E :: Error vector */
+ virtual void setData(const std::size_t index, const MantidVecPtr &Y,
+ const MantidVecPtr &E) {
+ getSpectrum(index)->setData(Y, E);
+ }
+
+ /** Sets the data in the workspace
+ @param index :: the workspace index to set.
+ @param Y :: Y vector
+ @param E :: Error vector */
+ virtual void setData(const std::size_t index, const MantidVecPtr::ptr_type &Y,
+ const MantidVecPtr::ptr_type &E) {
+ getSpectrum(index)->setData(Y, E);
+ }
+
+ /**
+ * Probes if DX (X Error) values were set on a particular spectrum
+ * @param index: the spectrum index
+ */
+ virtual bool hasDx(const std::size_t index) const {
+ return getSpectrum(index)->hasDx();
+ }
+
+ /// Generate the histogram or rebin the existing histogram.
+ virtual void generateHistogram(const std::size_t index, const MantidVec &X,
+ MantidVec &Y, MantidVec &E,
+ bool skipError = false) const = 0;
+
+ /// Return a vector with the integrated counts for all spectra withing the
+ /// given range
+ virtual void getIntegratedSpectra(std::vector<double> &out, const double minX,
+ const double maxX,
+ const bool entireRange) const;
+
+ /// Return an index in the X vector for an x-value close to a given value
+ std::pair<size_t, double> getXIndex(size_t i, double x, bool isLeft = true,
+ size_t start = 0) const;
+
+ //----------------------------------------------------------------------
+
+ int axes() const;
+ virtual Axis *getAxis(const std::size_t &axisIndex) const;
+ void replaceAxis(const std::size_t &axisIndex, Axis *const newAxis);
+
+ /// Returns true if the workspace contains data in histogram form (as opposed
+ /// to point-like)
+ virtual bool isHistogramData() const;
+
+ /// Returns true if the workspace contains has common X bins
+ virtual bool isCommonBins() const;
+
+ std::string YUnit() const;
+ void setYUnit(const std::string &newUnit);
+ std::string YUnitLabel() const;
+ void setYUnitLabel(const std::string &newLabel);
+
+ /// Are the Y-values dimensioned?
+ const bool &isDistribution() const;
+ bool &isDistribution(bool newValue);
+
+ /// Mask a given workspace index, setting the data and error values to zero
+ void maskWorkspaceIndex(const std::size_t index);
+
+ // Methods to set and access masked bins
+ void maskBin(const size_t &workspaceIndex, const size_t &binIndex,
+ const double &weight = 1.0);
+ void flagMasked(const size_t &spectrumIndex, const size_t &binIndex,
+ const double &weight = 1.0);
+ bool hasMaskedBins(const size_t &spectrumIndex) const;
+ /// Masked bins for each spectrum are stored as a set of pairs containing <bin
+ /// index, weight>
+ typedef std::map<size_t, double> MaskList;
+ const MaskList &maskedBins(const size_t &spectrumIndex) const;
+
+ // Methods handling the internal monitor workspace
+ virtual void
+ setMonitorWorkspace(const boost::shared_ptr<MatrixWorkspace> &monitorWS);
+ boost::shared_ptr<MatrixWorkspace> monitorWorkspace() const;
+
+ void saveInstrumentNexus(::NeXus::File *file) const;
+ void loadInstrumentNexus(::NeXus::File *file);
+ void saveSpectraMapNexus(
+ ::NeXus::File *file, const std::vector<int> &spec,
+ const ::NeXus::NXcompression compression = ::NeXus::LZW) const;
+
+ //=====================================================================================
+ // MD Geometry methods
+ //=====================================================================================
+ size_t getNumDims() const override;
+ boost::shared_ptr<const Mantid::Geometry::IMDDimension>
+ getDimension(size_t index) const override;
+ boost::shared_ptr<const Mantid::Geometry::IMDDimension>
+ getDimensionWithId(std::string id) const override;
+ //=====================================================================================
+ // End MD Geometry methods
+ //=====================================================================================
+
+ //=====================================================================================
+ // IMDWorkspace methods
+ //=====================================================================================
+
+ /// Gets the number of points available on the workspace.
+ uint64_t getNPoints() const override;
+ /// Get the number of points available on the workspace.
+ uint64_t getNEvents() const override { return this->getNPoints(); }
+ /// Dimension id for x-dimension.
+ static const std::string xDimensionId;
+ /// Dimensin id for y-dimension.
+ static const std::string yDimensionId;
+ /// Generate a line plot through the matrix workspace.
+ LinePlot getLinePlot(const Mantid::Kernel::VMD &start,
+ const Mantid::Kernel::VMD &end,
+ Mantid::API::MDNormalization normalize) const override;
+ /// Get the signal at a coordinate in the workspace.
+ signal_t getSignalAtCoord(
+ const coord_t *coords,
+ const Mantid::API::MDNormalization &normalization) const override;
+ /// Get the signal at a coordinate in the workspace
+ signal_t getSignalWithMaskAtCoord(
+ const coord_t *coords,
+ const Mantid::API::MDNormalization &normalization) const override;
+ /// Create iterators. Partitions the iterators according to the number of
+ /// cores.
+ std::vector<IMDIterator *> createIterators(
+ size_t suggestedNumCores = 1,
+ Mantid::Geometry::MDImplicitFunction *function = nullptr) const override;
+
+ /// Apply masking.
+ void
+ setMDMasking(Mantid::Geometry::MDImplicitFunction *maskingRegion) override;
+ /// Clear exsting masking.
+ void clearMDMasking() override;
+
+ /// @return the special coordinate system used if any.
+ Mantid::Kernel::SpecialCoordinateSystem
+ getSpecialCoordinateSystem() const override;
+
+ //=====================================================================================
+ // End IMDWorkspace methods
+ //=====================================================================================
+
+ //=====================================================================================
+ // Image methods
+ //=====================================================================================
+
+ /// Get start and end x indices for images
+ std::pair<size_t, size_t> getImageStartEndXIndices(size_t i, double startX,
+ double endX) const;
+ /// Create an image of Ys.
+ MantidImage_sptr getImageY(size_t start = 0, size_t stop = 0,
+ size_t width = 0, double startX = EMPTY_DBL(),
+ double endX = EMPTY_DBL()) const;
+ /// Create an image of Es.
+ MantidImage_sptr getImageE(size_t start = 0, size_t stop = 0,
+ size_t width = 0, double startX = EMPTY_DBL(),
+ double endX = EMPTY_DBL()) const;
+ /// Copy the data (Y's) from an image to this workspace.
+ virtual void setImageY(const MantidImage &image, size_t start = 0,
+ bool parallelExecution = true);
+ /// Copy the data from an image to this workspace's errors.
+ virtual void setImageE(const MantidImage &image, size_t start = 0,
+ bool parallelExecution = true);
+
+ //=====================================================================================
+ // End image methods
+ //=====================================================================================
+
+protected:
+ /// Protected copy constructor. May be used by childs for cloning.
+ MatrixWorkspace(const MatrixWorkspace &other);
+ /// Protected copy assignment operator. Assignment not implemented.
+ MatrixWorkspace &operator=(const MatrixWorkspace &other);
+
+ MatrixWorkspace(
+ Mantid::Geometry::INearestNeighboursFactory *factory = nullptr);
+
+ /// Initialises the workspace. Sets the size and lengths of the arrays. Must
+ /// be overloaded.
+ virtual void init(const std::size_t &NVectors, const std::size_t &XLength,
+ const std::size_t &YLength) = 0;
+
+ /// Invalidates the commons bins flag. This is generally called when a method
+ /// could allow the X values to be changed.
+ void invalidateCommonBinsFlag() { m_isCommonBinsFlagSet = false; }
+
+ /// A vector of pointers to the axes for this workspace
+ std::vector<Axis *> m_axes;
+
+private:
+ MatrixWorkspace *doClone() const override = 0;
+
+ /// Create an MantidImage instance.
+ MantidImage_sptr
+ getImage(const MantidVec &(MatrixWorkspace::*read)(std::size_t const) const,
+ size_t start, size_t stop, size_t width, size_t indexStart,
+ size_t indexEnd) const;
+ /// Copy data from an image.
+ void setImage(MantidVec &(MatrixWorkspace::*dataVec)(const std::size_t),
+ const MantidImage &image, size_t start, bool parallelExecution);
+
+ /// Has this workspace been initialised?
+ bool m_isInitialized;
+
+ /// The unit for the data values (e.g. Counts)
+ std::string m_YUnit;
+ /// A text label for use when plotting spectra
+ std::string m_YUnitLabel;
+ /// Flag indicating whether the Y-values are dimensioned. False by default
+ bool m_isDistribution;
+
+ /// Flag indicating whether the m_isCommonBinsFlag has been set. False by
+ /// default
+ mutable bool m_isCommonBinsFlagSet;
+ /// Flag indicating whether the data has common bins. False by default
+ mutable bool m_isCommonBinsFlag;
+
+ /// The set of masked bins in a map keyed on spectrum index
+ std::map<int64_t, MaskList> m_masks;
+
+ /// A workspace holding monitor data relating to the main data in the
+ /// containing workspace (null if none).
+ boost::shared_ptr<MatrixWorkspace> m_monitorWorkspace;
+
+protected:
+ /// Assists conversions to and from 2D histogram indexing to 1D indexing.
+ MatrixWSIndexCalculator m_indexCalculator;
+
+ /// Scoped pointer to NearestNeighbours factory
+ boost::scoped_ptr<Mantid::Geometry::INearestNeighboursFactory>
+ m_nearestNeighboursFactory;
+
+ /// Shared pointer to NearestNeighbours object
+ mutable boost::shared_ptr<Mantid::Geometry::INearestNeighbours>
+ m_nearestNeighbours;
+
+ /// Getter for the dimension id based on the axis.
+ std::string getDimensionIdFromAxis(const int &axisIndex) const;
};
/// shared pointer to the matrix workspace base class