PeaksWorkspace.cpp 34.7 KB
Newer Older
1
2
3
// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
4
5
//   NScD Oak Ridge National Laboratory, European Spallation Source,
//   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
6
// SPDX - License - Identifier: GPL - 3.0 +
7
#include "MantidDataObjects/PeaksWorkspace.h"
8
9
#include "MantidAPI/AlgorithmFactory.h"
#include "MantidAPI/Column.h"
Peterson, Peter's avatar
Peterson, Peter committed
10
#include "MantidAPI/ColumnFactory.h"
11
#include "MantidAPI/MatrixWorkspace.h"
12
13
#include "MantidAPI/Run.h"
#include "MantidAPI/Sample.h"
Peterson, Peter's avatar
Peterson, Peter committed
14
#include "MantidAPI/WorkspaceFactory.h"
15
#include "MantidDataObjects/Peak.h"
16
17
#include "MantidDataObjects/TableColumn.h"
#include "MantidDataObjects/TableWorkspace.h"
18
19
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Instrument/Goniometer.h"
20
21
22
#include "MantidKernel/DateAndTime.h"
#include "MantidKernel/Logger.h"
#include "MantidKernel/PhysicalConstants.h"
23
#include "MantidKernel/Quat.h"
24
#include "MantidKernel/Unit.h"
25
#include "MantidKernel/UnitConversion.h"
26
#include "MantidKernel/V3D.h"
27

Peterson, Peter's avatar
Peterson, Peter committed
28
#include <algorithm>
29
30
31
#include <cmath>
#include <cstdio>
#include <cstdlib>
Peterson, Peter's avatar
Peterson, Peter committed
32
33
#include <exception>
#include <fstream>
34
#include <memory>
35
// clang-format off
36
#include <nexus/NeXusFile.hpp>
37
38
#include <nexus/NeXusException.hpp>
// clang-format on
39
40
41
42
43
44
#include <ostream>
#include <string>

using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::Geometry;
Peterson, Peter's avatar
Peterson, Peter committed
45

46
47
48
namespace Mantid {
namespace DataObjects {
/// Register the workspace as a type
49
DECLARE_WORKSPACE(PeaksWorkspace)
50

51
52
Mantid::Kernel::Logger g_log("PeaksWorkspace");

Owen Arnold's avatar
Owen Arnold committed
53
//---------------------------------------------------------------------------------------------
54
55
56
57
/** Constructor. Create a table with all the required columns.
 *
 * @return PeaksWorkspace object
 */
58
59
60
61
PeaksWorkspace::PeaksWorkspace()
    : IPeaksWorkspace(), peaks(), columns(), columnNames(),
      m_coordSystem(None) {
  initColumns();
62
63
  // PeaksWorkspace does not use the grouping mechanism of ExperimentInfo.
  setNumberOfDetectorGroups(0);
64
}
65

66
67
68
69
70
71
72
//---------------------------------------------------------------------------------------------
/** Copy constructor
 *
 * @param other :: other PeaksWorkspace to copy from
 * @return
 */
PeaksWorkspace::PeaksWorkspace(const PeaksWorkspace &other)
73
74
    : IPeaksWorkspace(other), peaks(other.peaks), columns(), columnNames(),
      m_coordSystem(other.m_coordSystem) {
75
  initColumns();
76
77
  // PeaksWorkspace does not use the grouping mechanism of ExperimentInfo.
  setNumberOfDetectorGroups(0);
78
}
79

80
81
82
83
//=====================================================================================
//=====================================================================================
/** Comparator class for sorting peaks by one or more criteria
 */
84
class PeakComparator {
85
86
87
88
89
90
91
public:
  std::vector<std::pair<std::string, bool>> &criteria;

  /** Constructor for the comparator for sorting peaks
   * @param criteria : a vector with a list of pairs: column name, bool;
   *        where bool = true for ascending, false for descending sort.
   */
92
  explicit PeakComparator(std::vector<std::pair<std::string, bool>> &criteria)
93
94
95
96
      : criteria(criteria) {}

  /** Compare two peaks using the stored criteria */
  inline bool operator()(const Peak &a, const Peak &b) {
Hahn, Steven's avatar
Hahn, Steven committed
97
98
99
    for (auto &name : criteria) {
      std::string &col = name.first;
      bool ascending = name.second;
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
      bool lessThan = false;
      if (col == "BankName") {
        // If this criterion is equal, move on to the next one
        std::string valA = a.getBankName();
        std::string valB = b.getBankName();
        // Move on to lesser criterion if equal
        if (valA == valB)
          continue;
        lessThan = (valA < valB);
      } else {
        // General double comparison
        double valA = a.getValueByColName(col);
        double valB = b.getValueByColName(col);
        // Move on to lesser criterion if equal
        if (valA == valB)
          continue;
        lessThan = (valA < valB);
Owen Arnold's avatar
Owen Arnold committed
117
      }
118
119
120
      // Flip the sign of comparison if descending.
      if (ascending)
        return lessThan;
Owen Arnold's avatar
Owen Arnold committed
121
      else
122
        return !lessThan;
123
    }
124
125
126
127
    // If you reach here, all criteria were ==; so not <, so return false
    return false;
  }
};
128

129
130
131
132
133
134
135
136
137
138
139
140
//---------------------------------------------------------------------------------------------
/** Sort the peaks by one or more criteria
 *
 * @param criteria : a vector with a list of pairs: column name, bool;
 *        where bool = true for ascending, false for descending sort.
 *        The peaks are sorted by the first criterion first, then the 2nd if
 *equal, etc.
 */
void PeaksWorkspace::sort(std::vector<std::pair<std::string, bool>> &criteria) {
  PeakComparator comparator(criteria);
  std::stable_sort(peaks.begin(), peaks.end(), comparator);
}
141

142
143
144
145
//---------------------------------------------------------------------------------------------
/** @return the number of peaks
 */
int PeaksWorkspace::getNumberPeaks() const { return int(peaks.size()); }
146

147
148
149
150
151
//---------------------------------------------------------------------------------------------
/** @return the convention
 */
std::string PeaksWorkspace::getConvention() const { return convention; }

152
153
154
155
156
157
158
159
160
161
162
//---------------------------------------------------------------------------------------------
/** Removes the indicated peak
 * @param peakNum  the peak to remove. peakNum starts at 0
 */
void PeaksWorkspace::removePeak(const int peakNum) {
  if (peakNum >= static_cast<int>(peaks.size()) || peakNum < 0) {
    throw std::invalid_argument(
        "PeaksWorkspace::removePeak(): peakNum is out of range.");
  }
  peaks.erase(peaks.begin() + peakNum);
}
163

164
/** Removes multiple peaks
LamarMoore's avatar
LamarMoore committed
165
166
 * @param badPeaks peaks to be removed
 */
167
168
void PeaksWorkspace::removePeaks(std::vector<int> badPeaks) {
  if (badPeaks.empty())
Matthew Bowles's avatar
Matthew Bowles committed
169
    return;
Lynch, Vickie's avatar
Lynch, Vickie committed
170
171
172
173
174
175
  // if index of peak is in badPeaks remove
  int ip = -1;
  auto it =
      std::remove_if(peaks.begin(), peaks.end(), [&ip, badPeaks](Peak &pk) {
        (void)pk;
        ip++;
176
177
        return std::any_of(badPeaks.cbegin(), badPeaks.cend(),
                           [ip](int badPeak) { return badPeak == ip; });
Lynch, Vickie's avatar
Lynch, Vickie committed
178
179
      });
  peaks.erase(it, peaks.end());
180
181
}

182
183
//---------------------------------------------------------------------------------------------
/** Add a peak to the list
184
 * @param ipeak :: Peak object to add (copy) into this.
185
 */
Owen Arnold's avatar
Owen Arnold committed
186
void PeaksWorkspace::addPeak(const Geometry::IPeak &ipeak) {
187
  if (dynamic_cast<const Peak *>(&ipeak)) {
188
    peaks.emplace_back((const Peak &)ipeak);
189
  } else {
190
    peaks.emplace_back(Peak(ipeak));
191
192
  }
}
193

194
195
196
197
198
//---------------------------------------------------------------------------------------------
/** Add a peak to the list
 * @param position :: position on the peak in the specified coordinate frame
 * @param frame :: the coordinate frame that the position is specified in
 */
199
200
void PeaksWorkspace::addPeak(const V3D &position,
                             const SpecialCoordinateSystem &frame) {
201
202
203
204
  auto peak = createPeak(position, frame);
  addPeak(*peak);
}

205
206
//---------------------------------------------------------------------------------------------
/** Add a peak to the list
207
 * @param peak :: Peak object to add (move) into this.
208
 */
209
void PeaksWorkspace::addPeak(Peak &&peak) { peaks.emplace_back(peak); }
210

211
212
213
214
215
216
217
218
219
220
221
222
//---------------------------------------------------------------------------------------------
/** Return a reference to the Peak
 * @param peakNum :: index of the peak to get.
 * @return a reference to a Peak object.
 */
Peak &PeaksWorkspace::getPeak(const int peakNum) {
  if (peakNum >= static_cast<int>(peaks.size()) || peakNum < 0) {
    throw std::invalid_argument(
        "PeaksWorkspace::getPeak(): peakNum is out of range.");
  }
  return peaks[peakNum];
}
223

224
225
226
227
228
229
230
231
232
233
234
235
//---------------------------------------------------------------------------------------------
/** Return a const reference to the Peak
 * @param peakNum :: index of the peak to get.
 * @return a reference to a Peak object.
 */
const Peak &PeaksWorkspace::getPeak(const int peakNum) const {
  if (peakNum >= static_cast<int>(peaks.size()) || peakNum < 0) {
    throw std::invalid_argument(
        "PeaksWorkspace::getPeak(): peakNum is out of range.");
  }
  return peaks[peakNum];
}
236

237
238
239
//---------------------------------------------------------------------------------------------
/** Creates an instance of a Peak BUT DOES NOT ADD IT TO THE WORKSPACE
 * @param QLabFrame :: Q of the center of the peak, in reciprocal space
240
241
 * @param detectorDistance :: optional distance between the sample and the
 * detector. You do NOT need to explicitly provide this distance.
242
243
 * @return a pointer to a new Peak object.
 */
244
std::unique_ptr<Geometry::IPeak>
Hahn, Steven's avatar
Hahn, Steven committed
245
PeaksWorkspace::createPeak(const Kernel::V3D &QLabFrame,
246
                           boost::optional<double> detectorDistance) const {
247
  // create a peak using the qLab frame
248
249
  std::unique_ptr<IPeak> peak = std::make_unique<Peak>(
      this->getInstrument(), QLabFrame, detectorDistance);
250
  // Set the goniometer
251
  peak->setGoniometerMatrix(this->run().getGoniometer().getR());
252
253
254
255
  // Take the run number from this
  peak->setRunNumber(this->getRunNumber());

  return peak;
256
}
257

258
259
260
261
262
263
264
265
266
267
//---------------------------------------------------------------------------------------------
/** Creates an instance of a Peak BUT DOES NOT ADD IT TO THE WORKSPACE
 * @param position :: position of the center of the peak, in reciprocal space
 * @param frame :: the coordinate system that the position is specified in
 * detector. You do NOT need to explicitly provide this distance.
 * @return a pointer to a new Peak object.
 */
std::unique_ptr<Geometry::IPeak>
PeaksWorkspace::createPeak(const Kernel::V3D &position,
                           const Kernel::SpecialCoordinateSystem &frame) const {
268
  if (frame == Mantid::Kernel::HKL) {
269
    return createPeakHKL(position);
270
  } else if (frame == Mantid::Kernel::QLab) {
271
    return createPeak(position);
272
  } else {
273
    return createPeakQSample(position);
274
  }
275
276
277
278
}

//---------------------------------------------------------------------------------------------
/** Creates an instance of a Peak BUT DOES NOT ADD IT TO THE WORKSPACE
279
280
 * @param position :: QSample position of the center of the peak, in reciprocal
 * space
281
282
283
 * detector. You do NOT need to explicitly provide this distance.
 * @return a pointer to a new Peak object.
 */
284
285
std::unique_ptr<IPeak>
PeaksWorkspace::createPeakQSample(const V3D &position) const {
286
  // Create a peak from QSampleFrame
287
288
289
290

  Geometry::Goniometer goniometer;

  LogManager_const_sptr props = getLogs();
291
292
293
294
295
296
297
298
299
300
301
302
303
304
  // See if we can get a wavelength/energy
  // Then assume constant wavelenth
  double wavelength(0);
  if (props->hasProperty("wavelength")) {
    wavelength = props->getPropertyValueAsType<double>("wavelength");
  } else if (props->hasProperty("energy")) {
    wavelength = Kernel::UnitConversion::run(
        "Energy", "Wavelength", props->getPropertyValueAsType<double>("energy"),
        0, 0, 0, Kernel::DeltaEMode::Elastic, 0);
  } else if (getInstrument()->hasParameter("wavelength")) {
    wavelength = getInstrument()->getNumberParameter("wavelength").at(0);
  }

  if (wavelength > 0) {
305
    goniometer.calcFromQSampleAndWavelength(position, wavelength);
306
307
308
    g_log.information() << "Found goniometer rotation to be "
                        << goniometer.getEulerAngles()[0]
                        << " degrees for Q sample = " << position << "\n";
309
310
311
  } else {
    goniometer = run().getGoniometer();
  }
312
  // create a peak using the qLab frame
313
314
  std::unique_ptr<IPeak> peak =
      std::make_unique<Peak>(getInstrument(), position, goniometer.getR());
315
316
317
318
319
  // Take the run number from this
  peak->setRunNumber(getRunNumber());
  return peak;
}

320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
/**
 * Returns selected information for a "peak" at QLabFrame.
 *
 * @param qFrame      An arbitrary position in Q-space.  This does not have to
 *be the
 *                    position of a peak.
 * @param labCoords   Set true if the position is in the lab coordinate system,
 *false if
 *                    it is in the sample coordinate system.
 * @return a vector whose elements contain different information about the
 *"peak" at that position.
 *         each element is a pair of description of information and the string
 *form for the corresponding
 *         value.
 */
std::vector<std::pair<std::string, std::string>>
Hahn, Steven's avatar
Hahn, Steven committed
336
PeaksWorkspace::peakInfo(const Kernel::V3D &qFrame, bool labCoords) const {
337
338
339
340
  std::vector<std::pair<std::string, std::string>> Result;
  std::ostringstream oss;
  oss << std::setw(12) << std::fixed << std::setprecision(3) << (qFrame.norm());
  std::pair<std::string, std::string> QMag("|Q|", oss.str());
341
  Result.emplace_back(QMag);
342
343
344
345
346
347
348
349
350

  oss.str("");
  oss.clear();
  oss << std::setw(12) << std::fixed << std::setprecision(3)
      << (2.0 * M_PI / qFrame.norm());

  std::pair<std::string, std::string> dspc("d-spacing", oss.str());
  oss.str("");
  oss.clear();
351
  Result.emplace_back(dspc);
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367

  int seqNum = -1;
  bool hasOneRunNumber = true;
  int runNum = -1;
  int NPeaks = getNumberPeaks();
  try {
    double minDist = 10000000;
    for (int i = 0; i < NPeaks; i++) {
      Peak pk = getPeak(i);
      V3D Q = pk.getQLabFrame();
      if (!labCoords)
        Q = pk.getQSampleFrame();
      double D = qFrame.distance(Q);
      if (D < minDist) {
        minDist = D;
        seqNum = i;
368
      }
369

370
371
372
373
374
375
376
377
378
379
380
381
      int run = pk.getRunNumber();
      if (runNum < 0)
        runNum = run;
      else if (runNum != run)
        hasOneRunNumber = false;
    }
  } catch (...) {
    seqNum = -1; // peak could have been removed
  }
  V3D Qlab = qFrame;
  V3D Qsamp;
  Kernel::Matrix<double> Gon(3, 3, true);
382

383
384
385
  if (seqNum >= 0 && NPeaks == getNumberPeaks())
    Gon = getPeak(seqNum).getGoniometerMatrix();
  if (labCoords) {
386

387
388
389
    Kernel::Matrix<double> InvGon(Gon);
    InvGon.Invert();
    Qsamp = InvGon * Qlab;
390

391
392
393
394
  } else {
    Qsamp = qFrame;
    Qlab = Gon * Qsamp;
  }
395

396
  if (labCoords || seqNum >= 0)
397

398
399
400
  {
    std::pair<std::string, std::string> QlabStr(
        "Qlab", boost::lexical_cast<std::string>(Qlab));
401
    Result.emplace_back(QlabStr);
402
  }
403

404
  if (!labCoords || seqNum >= 0) {
405

406
407
    std::pair<std::string, std::string> QsampStr(
        "QSample", boost::lexical_cast<std::string>(Qsamp));
408
    Result.emplace_back(QsampStr);
409
  }
410

411
  try {
412
    auto peak = createPeak(Qlab);
413
    if (sample().hasOrientedLattice()) {
414

415
416
      peak->setGoniometerMatrix(Gon);
      const Geometry::OrientedLattice &lat = (sample().getOrientedLattice());
417

418
419
420
421
      const Kernel::Matrix<double> &UB0 = lat.getUB();
      Kernel::Matrix<double> UB(UB0);
      UB.Invert();
      V3D hkl = UB * Qsamp / 2 / M_PI;
Owen Arnold's avatar
Owen Arnold committed
422

423
424
      std::pair<std::string, std::string> HKL(
          "HKL", boost::lexical_cast<std::string>(hkl));
425
      Result.emplace_back(HKL);
426
427
    }

428
    if (hasOneRunNumber) {
429
430
      std::pair<std::string, std::string> runn("RunNumber",
                                               "   " + std::to_string(runNum));
431
      Result.emplace_back(runn);
432
    }
433

434
435
436
437
438
439
440
    //------- Now get phi, chi and omega ----------------
    Geometry::Goniometer GonG(Gon);
    std::vector<double> OmegaChiPhi = GonG.getEulerAngles("YZY");
    Kernel::V3D PhiChiOmega(OmegaChiPhi[2], OmegaChiPhi[1], OmegaChiPhi[0]);

    std::pair<std::string, std::string> GRead(
        "Goniometer Angles", boost::lexical_cast<std::string>(PhiChiOmega));
441
    Result.emplace_back(GRead);
442
443

    std::pair<std::string, std::string> SeqNum(
444
        "Seq Num,1st=1", "    " + std::to_string(seqNum + 1));
445
    Result.emplace_back(SeqNum);
446
447
448
449

    oss << std::setw(12) << std::fixed << std::setprecision(3)
        << (peak->getWavelength());
    std::pair<std::string, std::string> wl("Wavelength", oss.str());
450
    Result.emplace_back(wl);
451
452
453
454
455
456
457
    oss.str("");
    oss.clear();

    if (peak->findDetector()) {
      std::pair<std::string, std::string> detpos(
          "Position(x,y,z)",
          boost::lexical_cast<std::string>(peak->getDetPos()));
458
      Result.emplace_back(detpos);
459
460
461
462

      oss << std::setw(15) << std::fixed << std::setprecision(3)
          << (peak->getTOF());
      std::pair<std::string, std::string> tof("TOF", oss.str());
463
      Result.emplace_back(tof);
464
465
466
467
468
469
      oss.str("");
      oss.clear();

      oss << std::setw(12) << std::fixed << std::setprecision(3)
          << (peak->getFinalEnergy());
      std::pair<std::string, std::string> Energy("Energy", oss.str());
470
      Result.emplace_back(Energy);
471
472
473
474
      oss.str("");
      oss.clear();

      std::pair<std::string, std::string> row(
475
          "Row", "    " + std::to_string(peak->getRow()));
476
      Result.emplace_back(row);
477
478

      std::pair<std::string, std::string> col(
479
          "Col", "    " + std::to_string(peak->getCol()));
480
      Result.emplace_back(col);
481
482
483

      std::pair<std::string, std::string> bank("Bank",
                                               "    " + peak->getBankName());
484
      Result.emplace_back(bank);
485
486
487
488

      oss << std::setw(12) << std::fixed << std::setprecision(3)
          << (peak->getScattering());
      std::pair<std::string, std::string> scat("Scattering Angle", oss.str());
489
      Result.emplace_back(scat);
490
    }
491

492
493
494
495
496
  } catch (...) // Impossible position
  {
  }
  return Result;
}
497

498
499
500
501
502
503
504
/**
 * Create a Peak from a HKL value provided by the client.
 *
 *
 * @param HKL : reciprocal lattice vector coefficients
 * @return Fully formed peak.
 */
505
std::unique_ptr<IPeak> PeaksWorkspace::createPeakHKL(const V3D &HKL) const {
506
507
508
  /*
   The following allows us to add peaks where we have a single UB to work from.
   */
509
510
  const auto &lattice = this->sample().getOrientedLattice();
  const auto &goniometer = this->run().getGoniometer();
511

512
513
  // Calculate qLab from q HKL. As per Busing and Levy 1967, q_lab_frame = 2pi *
  // Goniometer * UB * HKL
514
  const V3D qLabFrame = goniometer.getR() * lattice.getUB() * HKL * 2 * M_PI;
515

516
  // create a peak using the qLab frame
517
518
519
  // This should calculate the detector positions too
  std::unique_ptr<IPeak> peak =
      std::make_unique<Peak>(this->getInstrument(), qLabFrame);
520
521
  // We need to set HKL separately to keep things consistent.
  peak->setHKL(HKL[0], HKL[1], HKL[2]);
522
  peak->setIntHKL(peak->getHKL());
523
524
525
526
  // Set the goniometer
  peak->setGoniometerMatrix(goniometer.getR());
  // Take the run number from this
  peak->setRunNumber(this->getRunNumber());
527

528
  return peak;
529
530
}

531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
/**
 * Returns selected information for a "peak" at QLabFrame.
 *
 * @param qFrame      An arbitrary position in Q-space.  This does not have to
 *be the
 *                    position of a peak.
 * @param labCoords  Set true if the position is in the lab coordinate system,
 *false if
 *                    it is in the sample coordinate system.
 * @return a vector whose elements contain different information about the
 *"peak" at that position.
 *         each element is a pair of description of information and the string
 *form for the corresponding
 *         value.
 */
Hahn, Steven's avatar
Hahn, Steven committed
546
547
int PeaksWorkspace::peakInfoNumber(const Kernel::V3D &qFrame,
                                   bool labCoords) const {
548
549
550
551
  std::vector<std::pair<std::string, std::string>> Result;
  std::ostringstream oss;
  oss << std::setw(12) << std::fixed << std::setprecision(3) << (qFrame.norm());
  std::pair<std::string, std::string> QMag("|Q|", oss.str());
552
  Result.emplace_back(QMag);
553
554
555
556
557
558
559
560
561

  oss.str("");
  oss.clear();
  oss << std::setw(12) << std::fixed << std::setprecision(3)
      << (2.0 * M_PI / qFrame.norm());

  std::pair<std::string, std::string> dspc("d-spacing", oss.str());
  oss.str("");
  oss.clear();
562
  Result.emplace_back(dspc);
563
564
565
566
567
568
569
570
571
572
573
574
575

  int seqNum = -1;
  double minDist = 10000000;

  for (int i = 0; i < getNumberPeaks(); i++) {
    Peak pk = getPeak(i);
    V3D Q = pk.getQLabFrame();
    if (!labCoords)
      Q = pk.getQSampleFrame();
    double D = qFrame.distance(Q);
    if (D < minDist) {
      minDist = D;
      seqNum = i + 1;
576
    }
577
578
579
  }
  return seqNum;
}
Peterson, Peter's avatar
Peterson, Peter committed
580

581
582
583
584
585
586
587
588
589
590
591
592
593
594
//---------------------------------------------------------------------------------------------
/** Return a reference to the Peaks vector */
std::vector<Peak> &PeaksWorkspace::getPeaks() { return peaks; }

/** Return a const reference to the Peaks vector */
const std::vector<Peak> &PeaksWorkspace::getPeaks() const { return peaks; }

/** Getter for the integration status.
 @return TRUE if it has been integrated using a peak integration algorithm.
 */
bool PeaksWorkspace::hasIntegratedPeaks() const {
  bool ret = false;
  const std::string peaksIntegrated = "PeaksIntegrated";
  if (this->run().hasProperty(peaksIntegrated)) {
595
    const auto value = boost::lexical_cast<int>(
596
597
598
599
600
        this->run().getProperty(peaksIntegrated)->value());
    ret = (value != 0);
  }
  return ret;
}
601

602
603
604
605
606
//---------------------------------------------------------------------------------------------
/// Return the memory used in bytes
size_t PeaksWorkspace::getMemorySize() const {
  return getNumberPeaks() * sizeof(Peak);
}
607

608
609
610
611
612
613
614
615
616
617
618
619
620
//---------------------------------------------------------------------------------------------
/**
 *  Creates a new TableWorkspace with detailing the contributing Detector IDs.
 * The table
 *  will have 2 columns: Index &  DetectorID, where Index maps into the current
 * index
 *  within the PeaksWorkspace of the peak
 */
API::ITableWorkspace_sptr PeaksWorkspace::createDetectorTable() const {
  auto table = API::WorkspaceFactory::Instance().createTable("TableWorkspace");
  table->addColumn("int", "Index");
  table->addColumn("int", "DetectorID");

621
  const auto npeaks(static_cast<int>(this->rowCount()));
622
623
624
625
626
627
628
629
630
631
  int nrows(0);
  for (int i = 0; i < npeaks; ++i) {
    const Peak &peak = this->peaks[i];
    auto detIDs = peak.getContributingDetIDs();
    auto itEnd = detIDs.end();
    for (auto it = detIDs.begin(); it != itEnd; ++it) {
      table->appendRow();
      table->cell<int>(nrows, 0) = i;
      table->cell<int>(nrows, 1) = *it;
      ++nrows;
Owen Arnold's avatar
Owen Arnold committed
632
    }
633
  }
634

635
636
  return table;
}
Peterson, Peter's avatar
Peterson, Peter committed
637

638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
//---------------------------------------------------------------------------------------------
/** Initialize all columns */
void PeaksWorkspace::initColumns() {
  // Note: The column types are controlled in PeakColumn.cpp
  addPeakColumn("RunNumber");
  addPeakColumn("DetID");
  addPeakColumn("h");
  addPeakColumn("k");
  addPeakColumn("l");
  addPeakColumn("Wavelength");
  addPeakColumn("Energy");
  addPeakColumn("TOF");
  addPeakColumn("DSpacing");
  addPeakColumn("Intens");
  addPeakColumn("SigInt");
  addPeakColumn("BinCount");
  addPeakColumn("BankName");
  addPeakColumn("Row");
  addPeakColumn("Col");
  addPeakColumn("QLab");
  addPeakColumn("QSample");
659
  addPeakColumn("PeakNumber");
660
  addPeakColumn("TBar");
661
}
Peterson, Peter's avatar
Peterson, Peter committed
662

663
664
665
666
667
668
669
//---------------------------------------------------------------------------------------------
/**
 * Add a PeakColumn
 * @param name :: The name of the column
 **/
void PeaksWorkspace::addPeakColumn(const std::string &name) {
  // Create the PeakColumn.
670
  columns.emplace_back(std::shared_ptr<DataObjects::PeakColumn>(
671
672
      new DataObjects::PeakColumn(this->peaks, name)));
  // Cache the names
673
  columnNames.emplace_back(name);
674
}
Peterson, Peter's avatar
Peterson, Peter committed
675

676
677
678
679
680
681
682
683
684
//---------------------------------------------------------------------------------------------
/// @return the index of the column with the given name.
size_t PeaksWorkspace::getColumnIndex(const std::string &name) const {
  for (size_t i = 0; i < columns.size(); i++)
    if (columns[i]->name() == name)
      return i;
  throw std::invalid_argument("Column named " + name +
                              " was not found in the PeaksWorkspace.");
}
Peterson, Peter's avatar
Peterson, Peter committed
685

686
687
//---------------------------------------------------------------------------------------------
/// Gets the shared pointer to a column by index.
688
std::shared_ptr<Mantid::API::Column> PeaksWorkspace::getColumn(size_t index) {
689
690
691
692
693
  if (index >= columns.size())
    throw std::invalid_argument(
        "PeaksWorkspace::getColumn() called with invalid index.");
  return columns[index];
}
694

695
696
//---------------------------------------------------------------------------------------------
/// Gets the shared pointer to a column by index.
697
std::shared_ptr<const Mantid::API::Column>
698
699
700
701
702
703
PeaksWorkspace::getColumn(size_t index) const {
  if (index >= columns.size())
    throw std::invalid_argument(
        "PeaksWorkspace::getColumn() called with invalid index.");
  return columns[index];
}
704

705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
void PeaksWorkspace::saveNexus(::NeXus::File *file) const {

  // Number of Peaks
  const size_t np(peaks.size());

  // Column vectors for peaks table
  std::vector<int> detectorID(np);
  std::vector<double> H(np);
  std::vector<double> K(np);
  std::vector<double> L(np);
  std::vector<double> intensity(np);
  std::vector<double> sigmaIntensity(np);
  std::vector<double> binCount(np);
  std::vector<double> initialEnergy(np);
  std::vector<double> finalEnergy(np);
  std::vector<double> waveLength(np);
  std::vector<double> scattering(np);
  std::vector<double> dSpacing(np);
  std::vector<double> TOF(np);
  std::vector<int> runNumber(np);
725
  std::vector<int> peakNumber(np);
726
  std::vector<double> tbar(np);
727
  std::vector<double> goniometerMatrix(9 * np);
728
  std::vector<std::string> shapes(np);
729
730

  // Populate column vectors from Peak Workspace
731
  size_t maxShapeJSONLength = 0;
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
  for (size_t i = 0; i < np; i++) {
    Peak p = peaks[i];
    detectorID[i] = p.getDetectorID();
    H[i] = p.getH();
    K[i] = p.getK();
    L[i] = p.getL();
    intensity[i] = p.getIntensity();
    sigmaIntensity[i] = p.getSigmaIntensity();
    binCount[i] = p.getBinCount();
    initialEnergy[i] = p.getInitialEnergy();
    finalEnergy[i] = p.getFinalEnergy();
    waveLength[i] = p.getWavelength();
    scattering[i] = p.getScattering();
    dSpacing[i] = p.getDSpacing();
    TOF[i] = p.getTOF();
    runNumber[i] = p.getRunNumber();
748
    peakNumber[i] = p.getPeakNumber();
749
    tbar[i] = p.getAbsorptionWeightedPathLength();
750
    {
751
752
753
754
755
756
757
758
759
760
      Matrix<double> gm = p.getGoniometerMatrix();
      goniometerMatrix[9 * i] = gm[0][0];
      goniometerMatrix[9 * i + 1] = gm[1][0];
      goniometerMatrix[9 * i + 2] = gm[2][0];
      goniometerMatrix[9 * i + 3] = gm[0][1];
      goniometerMatrix[9 * i + 4] = gm[1][1];
      goniometerMatrix[9 * i + 5] = gm[2][1];
      goniometerMatrix[9 * i + 6] = gm[0][2];
      goniometerMatrix[9 * i + 7] = gm[1][2];
      goniometerMatrix[9 * i + 8] = gm[2][2];
761
    }
762
763
    const std::string shapeJSON = p.getPeakShape().toJSON();
    shapes[i] = shapeJSON;
764
765
    if (shapeJSON.size() > maxShapeJSONLength) {
      maxShapeJSONLength = shapeJSON.size();
766
    }
767
  }
768

769
  // Start Peaks Workspace in Nexus File
770
771
772
  const std::string specifyInteger = "An integer";
  const std::string specifyDouble = "A double";
  const std::string specifyString = "A string";
773
774
775
  file->makeGroup("peaks_workspace", "NXentry",
                  true); // For when peaksWorkspace can be loaded

776
777
  // Coordinate system
  file->writeData("coordinate_system", static_cast<uint32_t>(m_coordSystem));
778

779
780
781
782
783
  // Write out the Qconvention
  // ki-kf for Inelastic convention; kf-ki for Crystallography convention
  std::string m_QConvention = this->getConvention();
  file->putAttr("QConvention", m_QConvention);

784
785
786
  // Detectors column
  file->writeData("column_1", detectorID);
  file->openData("column_1");
787
  file->putAttr("name", "Detector ID");
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
  file->putAttr("interpret_as", specifyInteger);
  file->putAttr("units", "Not known");
  file->closeData();

  // H column
  file->writeData("column_2", H);
  file->openData("column_2");
  file->putAttr("name", "H");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // K column
  file->writeData("column_3", K);
  file->openData("column_3");
  file->putAttr("name", "K");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // L column
  file->writeData("column_4", L);
  file->openData("column_4");
  file->putAttr("name", "L");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // Intensity column
  file->writeData("column_5", intensity);
  file->openData("column_5");
  file->putAttr("name", "Intensity");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // Sigma Intensity column
  file->writeData("column_6", sigmaIntensity);
  file->openData("column_6");
  file->putAttr("name", "Sigma Intensity");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // Bin Count column
  file->writeData("column_7", binCount);
  file->openData("column_7");
  file->putAttr("name", "Bin Count");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // Initial Energy column
  file->writeData("column_8", initialEnergy);
  file->openData("column_8");
  file->putAttr("name", "Initial Energy");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // Final Energy column
  file->writeData("column_9", finalEnergy);
  file->openData("column_9");
  file->putAttr("name", "Final Energy");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // Wave Length Column
  file->writeData("column_10", waveLength);
  file->openData("column_10");
  file->putAttr("name", "Wave Length");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // Scattering Column
  file->writeData("column_11", scattering);
  file->openData("column_11");
  file->putAttr("name", "Scattering");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // D Spacing Column
  file->writeData("column_12", dSpacing);
  file->openData("column_12");
  file->putAttr("name", "D Spacing");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // TOF Column
  file->writeData("column_13", TOF);
  file->openData("column_13");
  file->putAttr("name", "TOF");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

  // Run Number column
  file->writeData("column_14", runNumber);
  file->openData("column_14");
  file->putAttr("name", "Run Number");
  file->putAttr("interpret_as", specifyInteger);
  file->putAttr("units", "Not known"); // Units may need changing when known
894
895
896
  file->closeData();

  // Peak Number column
897
898
  file->writeData("column_17", peakNumber);
  file->openData("column_17");
899
900
901
  file->putAttr("name", "Peak Number");
  file->putAttr("interpret_as", specifyInteger);
  file->putAttr("units", "Not known"); // Units may need changing when known
902
903
  file->closeData();

904
905
906
907
908
909
910
911
  // TBar column
  file->writeData("column_18", tbar);
  file->openData("column_18");
  file->putAttr("name", "TBar");
  file->putAttr("interpret_as", specifyDouble);
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

912
913
  // Goniometer Matrix Column
  std::vector<int> array_dims;
914
915
  array_dims.emplace_back(static_cast<int>(peaks.size()));
  array_dims.emplace_back(9);
916
917
918
919
920
921
922
  file->writeData("column_15", goniometerMatrix, array_dims);
  file->openData("column_15");
  file->putAttr("name", "Goniometer Matrix");
  file->putAttr("interpret_as", "A matrix of 3x3 doubles");
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->closeData();

923
924
  // Shape
  std::vector<int64_t> dims;
925
926
  dims.emplace_back(np);
  dims.emplace_back(static_cast<int>(maxShapeJSONLength));
927
928
929
930
  const std::string name = "column_16";
  file->makeData(name, NeXus::CHAR, dims, false);
  file->openData(name);

931
  auto toNexus = new char[maxShapeJSONLength * np];
Owen Arnold's avatar
Owen Arnold committed
932
  for (size_t ii = 0; ii < np; ii++) {
933
934
935
    std::string rowStr = shapes[ii];
    for (size_t ic = 0; ic < rowStr.size(); ic++)
      toNexus[ii * maxShapeJSONLength + ic] = rowStr[ic];
936
937
    for (size_t ic = rowStr.size();
         ic < static_cast<size_t>(maxShapeJSONLength); ic++)
938
939
940
941
942
943
944
945
946
947
948
      toNexus[ii * maxShapeJSONLength + ic] = ' ';
  }

  file->putData((void *)(toNexus));

  delete[] toNexus;
  file->putAttr("units", "Not known"); // Units may need changing when known
  file->putAttr("name", "Shape");
  file->putAttr("interpret_as", specifyString);
  file->closeData();

949
950
951
952
  // QLab & QSample are calculated and do not need to be saved

  file->closeGroup(); // end of peaks workpace
}
953

954
955
956
957
958
/**
 * Set the special Q3D coordinate system.
 * @param coordinateSystem : Option to set.
 */
void PeaksWorkspace::setCoordinateSystem(
959
960
    const Kernel::SpecialCoordinateSystem coordinateSystem) {
  m_coordSystem = coordinateSystem;
961
}
962

963
964
965
/**
 * @return the special Q3D coordinate system.
 */
966
Kernel::SpecialCoordinateSystem
967
PeaksWorkspace::getSpecialCoordinateSystem() const {
968
  return m_coordSystem;
Peterson, Peter's avatar
Peterson, Peter committed
969
}
970

971
972
// prevent shared pointer from deleting this
struct NullDeleter {
973
  template <typename T> void operator()(T * /*unused*/) {}
974
};
975
/**Get access to shared pointer containing workspace porperties */
976
API::LogManager_sptr PeaksWorkspace::logs() {
977
  return API::LogManager_sptr(&(this->mutableRun()), NullDeleter());
978
}
979

980
981
982
983
984
985
986
/** Get constant access to shared pointer containing workspace porperties;
 * Copies logs into new LogManager variable Meaningfull only for some
 * multithereaded methods when a thread wants to have its own copy of logs */
API::LogManager_const_sptr PeaksWorkspace::getLogs() const {
  return API::LogManager_const_sptr(new API::LogManager(this->run()));
}

987
988
ITableWorkspace *PeaksWorkspace::doCloneColumns(
    const std::vector<std::string> & /*colNames*/) const {
989
990
  throw Kernel::Exception::NotImplementedError(
      "PeaksWorkspace cannot clone columns.");
991
}
LamarMoore's avatar
LamarMoore committed
992
993
} // namespace DataObjects
} // namespace Mantid
994

995
///\cond TEMPLATE
996

997
998
999
1000
1001
1002
1003
namespace Mantid {
namespace Kernel {

template <>
DLLExport Mantid::DataObjects::PeaksWorkspace_sptr
IPropertyManager::getValue<Mantid::DataObjects::PeaksWorkspace_sptr>(
    const std::string &name) const {
1004
1005
1006
  auto *prop = dynamic_cast<
      PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr> *>(
      getPointerToProperty(name));
1007
1008
1009
  if (prop) {
    return *prop;
  } else {
1010
1011
1012
    std::string message =
        "Attempt to assign property " + name +
        " to incorrect type. Expected shared_ptr<PeaksWorkspace>.";
1013
1014
1015
    throw std::runtime_error(message);
  }
}
1016

1017
1018
1019
1020
template <>
DLLExport Mantid::DataObjects::PeaksWorkspace_const_sptr
IPropertyManager::getValue<Mantid::DataObjects::PeaksWorkspace_const_sptr>(
    const std::string &name) const {
1021
1022
1023
  auto *prop = dynamic_cast<
      PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr> *>(
      getPointerToProperty(name));
1024
1025
1026
  if (prop) {
    return prop->operator()();
  } else {
1027
1028
1029
    std::string message =
        "Attempt to assign property " + name +
        " to incorrect type. Expected const shared_ptr<PeaksWorkspace>.";
1030
1031
1032
    throw std::runtime_error(message);
  }
}
1033

1034
} // namespace Kernel
1035
1036
} // namespace Mantid

1037
///\endcond TEMPLATE