Newer
Older
Peterson, Peter
committed
#ifndef MANTID_API_MATRIXWORKSPACE_H_
#define MANTID_API_MATRIXWORKSPACE_H_
Peterson, Peter
committed
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidAPI/DllConfig.h"
#include "MantidAPI/ExperimentInfo.h"
#include "MantidAPI/IMDWorkspace.h"
#include "MantidAPI/MatrixWorkspace_fwd.h"
Owen Arnold
committed
#include "MantidAPI/MatrixWSIndexCalculator.h"
namespace Mantid {
//----------------------------------------------------------------------------
// Forward declarations
//----------------------------------------------------------------------------
namespace Geometry {
class ParameterMap;
class INearestNeighbours;
class INearestNeighboursFactory;
}
class Axis;
class SpectrumDetectorMapping;
/// typedef for the image type
typedef std::vector<std::vector<double>> MantidImage;
/// shared pointer to MantidImage
typedef boost::shared_ptr<MantidImage> MantidImage_sptr;
/// shared pointer to const MantidImage
typedef boost::shared_ptr<const MantidImage> MantidImage_const_sptr;
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
//----------------------------------------------------------------------
/** Base MatrixWorkspace Abstract Class.
@author Laurent C Chapon, ISIS, RAL
@date 26/09/2007
Copyright © 2007-2010 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
National Laboratory & European Spallation Source
This file is part of Mantid.
Mantid is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.
Mantid is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
File change history is stored at: <https://github.com/mantidproject/mantid>.
Code Documentation is available at: <http://doxygen.mantidproject.org>
*/
class MANTID_API_DLL MatrixWorkspace : public IMDWorkspace,
public ExperimentInfo {
private:
using ExperimentInfo::toString;
public:
// The Workspace Factory create-from-parent method needs direct access to the
// axes.
friend class WorkspaceFactoryImpl;
/// Initialize
void initialize(const std::size_t &NVectors, const std::size_t &XLength,
const std::size_t &YLength);
/// Delete
~MatrixWorkspace() override;
/// Returns a clone of the workspace
MatrixWorkspace_uptr clone() const { return MatrixWorkspace_uptr(doClone()); }
using IMDWorkspace::toString;
/// String description of state
const std::string toString() const override;
/**@name Instrument queries */
//@{
Geometry::IDetector_const_sptr getDetector(const size_t workspaceIndex) const;
double detectorTwoTheta(Geometry::IDetector_const_sptr det) const;
double detectorSignedTwoTheta(Geometry::IDetector_const_sptr det) const;
void populateInstrumentParameters() override;
/** @name Nearest neighbours */
/// Build and populate the NearestNeighbours object
void buildNearestNeighbours(const bool ignoreMaskedDetectors = false) const;
/// Causes the nearest neighbours map to be rebuilt
void rebuildNearestNeighbours();
/// Query the NearestNeighbours object for a detector
std::map<specnum_t, Mantid::Kernel::V3D>
getNeighbours(const Geometry::IDetector *comp, const double radius = 0.0,
const bool ignoreMaskedDetectors = false) const;
/// Query the NearestNeighbours object for a given spectrum index using a
/// search radius
std::map<specnum_t, Mantid::Kernel::V3D>
getNeighbours(specnum_t spec, const double radius,
const bool ignoreMaskedDetectors = false) const;
/// Query the NearestNeighbours object for a given spectrum index using the
/// direct number of nearest neighbours
std::map<specnum_t, Mantid::Kernel::V3D>
getNeighboursExact(specnum_t spec, const int nNeighbours,
const bool ignoreMaskedDetectors = false) const;
//@}
virtual void updateSpectraUsing(const SpectrumDetectorMapping &map);
/// Build the default spectra mapping, most likely wanted after an instrument
/// update
void rebuildSpectraMapping(const bool includeMonitors = true);
// More mapping
spec2index_map getSpectrumToWorkspaceIndexMap() const;
detid2index_map
getDetectorIDToWorkspaceIndexMap(bool throwIfMultipleDets = false) const;
virtual std::vector<size_t>
getDetectorIDToWorkspaceIndexVector(detid_t &offset,
bool throwIfMultipleDets = false) const;
std::vector<specnum_t> &spectraList) const;
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
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
typedef boost::shared_ptr<MatrixWorkspace> MatrixWorkspace_sptr;
/// shared pointer to the matrix workspace base class (const version)
typedef boost::shared_ptr<const MatrixWorkspace> MatrixWorkspace_const_sptr;
} // namespace API
} // namespace Mantid
Peterson, Peter
committed
#endif /*MANTID_API_MATRIXWORKSPACE_H_*/