PeaksWorkspace.cpp 33.9 KB
Newer Older
1
#include "MantidDataObjects/PeaksWorkspace.h"
2
3
#include "MantidAPI/AlgorithmFactory.h"
#include "MantidAPI/Column.h"
Peterson, Peter's avatar
Peterson, Peter committed
4
#include "MantidAPI/ColumnFactory.h"
5
#include "MantidAPI/MatrixWorkspace.h"
6
7
#include "MantidAPI/Run.h"
#include "MantidAPI/Sample.h"
Peterson, Peter's avatar
Peterson, Peter committed
8
#include "MantidAPI/WorkspaceFactory.h"
9
#include "MantidDataObjects/Peak.h"
10
11
#include "MantidDataObjects/TableColumn.h"
#include "MantidDataObjects/TableWorkspace.h"
12
13
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Instrument/Goniometer.h"
14
15
16
#include "MantidKernel/DateAndTime.h"
#include "MantidKernel/Logger.h"
#include "MantidKernel/PhysicalConstants.h"
17
#include "MantidKernel/Quat.h"
18
#include "MantidKernel/Unit.h"
19
#include "MantidKernel/UnitConversion.h"
20
#include "MantidKernel/V3D.h"
21

Peterson, Peter's avatar
Peterson, Peter committed
22
#include <algorithm>
23
#include <boost/shared_ptr.hpp>
24
25
26
#include <cmath>
#include <cstdio>
#include <cstdlib>
Peterson, Peter's avatar
Peterson, Peter committed
27
28
#include <exception>
#include <fstream>
29
30
#include <nexus/NeXusException.hpp>
#include <nexus/NeXusFile.hpp>
31
32
33
34
35
36
#include <ostream>
#include <string>

using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::Geometry;
Peterson, Peter's avatar
Peterson, Peter committed
37

38
39
40
namespace Mantid {
namespace DataObjects {
/// Register the workspace as a type
41
DECLARE_WORKSPACE(PeaksWorkspace)
42

43
44
Mantid::Kernel::Logger g_log("PeaksWorkspace");

Owen Arnold's avatar
Owen Arnold committed
45
//---------------------------------------------------------------------------------------------
46
47
48
49
/** Constructor. Create a table with all the required columns.
 *
 * @return PeaksWorkspace object
 */
50
51
52
53
PeaksWorkspace::PeaksWorkspace()
    : IPeaksWorkspace(), peaks(), columns(), columnNames(),
      m_coordSystem(None) {
  initColumns();
54
55
  // PeaksWorkspace does not use the grouping mechanism of ExperimentInfo.
  setNumberOfDetectorGroups(0);
56
}
57

58
59
60
61
62
63
64
//---------------------------------------------------------------------------------------------
/** Copy constructor
 *
 * @param other :: other PeaksWorkspace to copy from
 * @return
 */
PeaksWorkspace::PeaksWorkspace(const PeaksWorkspace &other)
65
66
    : IPeaksWorkspace(other), peaks(other.peaks), columns(), columnNames(),
      m_coordSystem(other.m_coordSystem) {
67
  initColumns();
68
69
  // PeaksWorkspace does not use the grouping mechanism of ExperimentInfo.
  setNumberOfDetectorGroups(0);
70
}
71

72
73
74
75
76
77
78
79
80
81
82
83
//=====================================================================================
//=====================================================================================
/** Comparator class for sorting peaks by one or more criteria
 */
class PeakComparator : public std::binary_function<Peak, Peak, bool> {
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.
   */
84
  explicit PeakComparator(std::vector<std::pair<std::string, bool>> &criteria)
85
86
87
88
      : 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
89
90
91
    for (auto &name : criteria) {
      std::string &col = name.first;
      bool ascending = name.second;
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
      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
109
      }
110
111
112
      // Flip the sign of comparison if descending.
      if (ascending)
        return lessThan;
Owen Arnold's avatar
Owen Arnold committed
113
      else
114
        return !lessThan;
115
    }
116
117
118
119
    // If you reach here, all criteria were ==; so not <, so return false
    return false;
  }
};
120

121
122
123
124
125
126
127
128
129
130
131
132
//---------------------------------------------------------------------------------------------
/** 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);
}
133

134
135
136
137
//---------------------------------------------------------------------------------------------
/** @return the number of peaks
 */
int PeaksWorkspace::getNumberPeaks() const { return int(peaks.size()); }
138

139
140
141
142
143
//---------------------------------------------------------------------------------------------
/** @return the convention
 */
std::string PeaksWorkspace::getConvention() const { return convention; }

144
145
146
147
148
149
150
151
152
153
154
//---------------------------------------------------------------------------------------------
/** 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);
}
155

156
/** Removes multiple peaks
Matthew Bowles's avatar
Matthew Bowles committed
157
* @param badPeaks peaks to be removed
158
*/
159
160
void PeaksWorkspace::removePeaks(std::vector<int> badPeaks) {
  if (badPeaks.empty())
Matthew Bowles's avatar
Matthew Bowles committed
161
    return;
Lynch, Vickie's avatar
Lynch, Vickie committed
162
163
164
165
166
167
  // 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++;
168
169
        for (int badPeak : badPeaks) {
          if (badPeak == ip)
Lynch, Vickie's avatar
Lynch, Vickie committed
170
171
            return true;
        }
172
        return false;
Lynch, Vickie's avatar
Lynch, Vickie committed
173
174
      });
  peaks.erase(it, peaks.end());
175
176
}

177
178
//---------------------------------------------------------------------------------------------
/** Add a peak to the list
179
 * @param ipeak :: Peak object to add (copy) into this.
180
 */
Owen Arnold's avatar
Owen Arnold committed
181
void PeaksWorkspace::addPeak(const Geometry::IPeak &ipeak) {
182
183
184
185
186
187
  if (dynamic_cast<const Peak *>(&ipeak)) {
    peaks.push_back((const Peak &)ipeak);
  } else {
    peaks.push_back(Peak(ipeak));
  }
}
188

189
190
191
192
193
//---------------------------------------------------------------------------------------------
/** 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
 */
194
195
void PeaksWorkspace::addPeak(const V3D &position,
                             const SpecialCoordinateSystem &frame) {
196
197
198
199
  auto peak = createPeak(position, frame);
  addPeak(*peak);
}

200
201
//---------------------------------------------------------------------------------------------
/** Add a peak to the list
202
 * @param peak :: Peak object to add (move) into this.
203
 */
204
void PeaksWorkspace::addPeak(Peak &&peak) { peaks.push_back(peak); }
205

206
207
208
209
210
211
212
213
214
215
216
217
//---------------------------------------------------------------------------------------------
/** 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];
}
218

219
220
221
222
223
224
225
226
227
228
229
230
//---------------------------------------------------------------------------------------------
/** 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];
}
231

232
233
234
//---------------------------------------------------------------------------------------------
/** 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
235
236
 * @param detectorDistance :: optional distance between the sample and the
 * detector. You do NOT need to explicitly provide this distance.
237
238
 * @return a pointer to a new Peak object.
 */
Owen Arnold's avatar
Owen Arnold committed
239
Geometry::IPeak *
Hahn, Steven's avatar
Hahn, Steven committed
240
PeaksWorkspace::createPeak(const Kernel::V3D &QLabFrame,
241
                           boost::optional<double> detectorDistance) const {
242
243
244
  Geometry::Goniometer goniometer = this->run().getGoniometer();

  // create a peak using the qLab frame
245
  auto peak = new Peak(this->getInstrument(), QLabFrame, detectorDistance);
246
247
248
249
250
251
252
253

  // Set the goniometer
  peak->setGoniometerMatrix(goniometer.getR());

  // Take the run number from this
  peak->setRunNumber(this->getRunNumber());

  return peak;
254
}
255

256
257
258
259
260
261
262
263
264
265
//---------------------------------------------------------------------------------------------
/** 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 {
266
267
268
269
270
271
272
  if (frame == Mantid::Kernel::HKL) {
    return std::unique_ptr<Geometry::IPeak>(createPeakHKL(position));
  } else if (frame == Mantid::Kernel::QLab) {
    return std::unique_ptr<Geometry::IPeak>(createPeak(position));
  } else {
    return std::unique_ptr<Geometry::IPeak>(createPeakQSample(position));
  }
273
274
275
276
}

//---------------------------------------------------------------------------------------------
/** Creates an instance of a Peak BUT DOES NOT ADD IT TO THE WORKSPACE
277
278
 * @param position :: QSample position of the center of the peak, in reciprocal
 * space
279
280
281
 * detector. You do NOT need to explicitly provide this distance.
 * @return a pointer to a new Peak object.
 */
282
Peak *PeaksWorkspace::createPeakQSample(const V3D &position) const {
283
  // Create a peak from QSampleFrame
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300

  Geometry::Goniometer goniometer;

  LogManager_const_sptr props = getLogs();
  if (props->hasProperty("wavelength") || props->hasProperty("energy")) {
    // Assume constant wavelenth
    // Calculate Q lab from Q sample and wavelength
    double wavelength;
    if (props->hasProperty("energy")) {
      wavelength = Kernel::UnitConversion::run(
          "Energy", "Wavelength",
          props->getPropertyValueAsType<double>("energy"), 0, 0, 0,
          Kernel::DeltaEMode::Elastic, 0);
    } else {
      wavelength = props->getPropertyValueAsType<double>("wavelength");
    }
    goniometer.calcFromQSampleAndWavelength(position, wavelength);
301
302
303
    g_log.information() << "Found goniometer rotation to be "
                        << goniometer.getEulerAngles()[0]
                        << " degrees for Q sample = " << position << "\n";
304
305
306
  } else {
    goniometer = run().getGoniometer();
  }
307
308
309
310
311
312
313
  // create a peak using the qLab frame
  auto peak = new Peak(getInstrument(), position, goniometer.getR());
  // Take the run number from this
  peak->setRunNumber(getRunNumber());
  return peak;
}

314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
/**
 * 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
330
PeaksWorkspace::peakInfo(const Kernel::V3D &qFrame, bool labCoords) const {
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
  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());
  Result.push_back(QMag);

  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();
  Result.push_back(dspc);

  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;
362
      }
363

364
365
366
367
368
369
370
371
372
373
374
375
      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);
376

377
378
379
  if (seqNum >= 0 && NPeaks == getNumberPeaks())
    Gon = getPeak(seqNum).getGoniometerMatrix();
  if (labCoords) {
380

381
382
383
    Kernel::Matrix<double> InvGon(Gon);
    InvGon.Invert();
    Qsamp = InvGon * Qlab;
384

385
386
387
388
  } else {
    Qsamp = qFrame;
    Qlab = Gon * Qsamp;
  }
389

390
  if (labCoords || seqNum >= 0)
391

392
393
394
395
396
  {
    std::pair<std::string, std::string> QlabStr(
        "Qlab", boost::lexical_cast<std::string>(Qlab));
    Result.push_back(QlabStr);
  }
397

398
  if (!labCoords || seqNum >= 0) {
399

400
401
402
403
    std::pair<std::string, std::string> QsampStr(
        "QSample", boost::lexical_cast<std::string>(Qsamp));
    Result.push_back(QsampStr);
  }
404

405
  try {
406

Owen Arnold's avatar
Owen Arnold committed
407
    Geometry::IPeak *peak = createPeak(Qlab);
408

409
    if (sample().hasOrientedLattice()) {
410

411
412
      peak->setGoniometerMatrix(Gon);
      const Geometry::OrientedLattice &lat = (sample().getOrientedLattice());
413

414
415
416
417
      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
418

419
420
421
      std::pair<std::string, std::string> HKL(
          "HKL", boost::lexical_cast<std::string>(hkl));
      Result.push_back(HKL);
422
423
    }

424
    if (hasOneRunNumber) {
425
426
      std::pair<std::string, std::string> runn("RunNumber",
                                               "   " + std::to_string(runNum));
427
      Result.push_back(runn);
428
    }
429

430
431
432
433
434
435
436
437
438
439
    //------- 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));
    Result.push_back(GRead);

    std::pair<std::string, std::string> SeqNum(
440
        "Seq Num,1st=1", "    " + std::to_string(seqNum + 1));
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
    Result.push_back(SeqNum);

    oss << std::setw(12) << std::fixed << std::setprecision(3)
        << (peak->getWavelength());
    std::pair<std::string, std::string> wl("Wavelength", oss.str());
    Result.push_back(wl);
    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()));
      Result.push_back(detpos);

      oss << std::setw(15) << std::fixed << std::setprecision(3)
          << (peak->getTOF());
      std::pair<std::string, std::string> tof("TOF", oss.str());
      Result.push_back(tof);
      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());
      Result.push_back(Energy);
      oss.str("");
      oss.clear();

      std::pair<std::string, std::string> row(
471
          "Row", "    " + std::to_string(peak->getRow()));
472
473
474
      Result.push_back(row);

      std::pair<std::string, std::string> col(
475
          "Col", "    " + std::to_string(peak->getCol()));
476
477
478
479
480
481
482
483
484
485
      Result.push_back(col);

      std::pair<std::string, std::string> bank("Bank",
                                               "    " + peak->getBankName());
      Result.push_back(bank);

      oss << std::setw(12) << std::fixed << std::setprecision(3)
          << (peak->getScattering());
      std::pair<std::string, std::string> scat("Scattering Angle", oss.str());
      Result.push_back(scat);
486
    }
487

488
489
490
491
492
  } catch (...) // Impossible position
  {
  }
  return Result;
}
493

494
495
496
497
498
499
500
/**
 * Create a Peak from a HKL value provided by the client.
 *
 *
 * @param HKL : reciprocal lattice vector coefficients
 * @return Fully formed peak.
 */
Hahn, Steven's avatar
Hahn, Steven committed
501
Peak *PeaksWorkspace::createPeakHKL(const V3D &HKL) const {
502
503
504
  /*
   The following allows us to add peaks where we have a single UB to work from.
   */
505

506
507
  Geometry::OrientedLattice lattice = this->sample().getOrientedLattice();
  Geometry::Goniometer goniometer = this->run().getGoniometer();
508

509
510
511
  // Calculate qLab from q HKL. As per Busing and Levy 1967, q_lab_frame = 2pi *
  // Goniometer * UB * HKL
  V3D qLabFrame = goniometer.getR() * lattice.getUB() * HKL * 2 * M_PI;
512

513
514
515
516
  // create a peak using the qLab frame
  auto peak =
      new Peak(this->getInstrument(),
               qLabFrame); // This should calculate the detector positions too.
517

518
519
  // We need to set HKL separately to keep things consistent.
  peak->setHKL(HKL[0], HKL[1], HKL[2]);
520

521
522
  // Set the goniometer
  peak->setGoniometerMatrix(goniometer.getR());
523

524
525
  // Take the run number from this
  peak->setRunNumber(this->getRunNumber());
526

527
  return peak;
528
529
}

530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
/**
 * 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
545
546
int PeaksWorkspace::peakInfoNumber(const Kernel::V3D &qFrame,
                                   bool labCoords) const {
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
  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());
  Result.push_back(QMag);

  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();
  Result.push_back(dspc);

  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;
575
    }
576
577
578
  }
  return seqNum;
}
Peterson, Peter's avatar
Peterson, Peter committed
579

580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
//---------------------------------------------------------------------------------------------
/** 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)) {
    const int value = boost::lexical_cast<int>(
        this->run().getProperty(peaksIntegrated)->value());
    ret = (value != 0);
  }
  return ret;
}
600

601
602
603
604
605
//---------------------------------------------------------------------------------------------
/// Return the memory used in bytes
size_t PeaksWorkspace::getMemorySize() const {
  return getNumberPeaks() * sizeof(Peak);
}
606

607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
//---------------------------------------------------------------------------------------------
/**
 *  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");

  const int npeaks(static_cast<int>(this->rowCount()));
  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
631
    }
632
  }
633

634
635
  return table;
}
Peterson, Peter's avatar
Peterson, Peter committed
636

637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
//---------------------------------------------------------------------------------------------
/** 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");
658
  addPeakColumn("PeakNumber");
659
}
Peterson, Peter's avatar
Peterson, Peter committed
660

661
662
663
664
665
666
667
668
669
670
671
672
//---------------------------------------------------------------------------------------------
/**
 * Add a PeakColumn
 * @param name :: The name of the column
 **/
void PeaksWorkspace::addPeakColumn(const std::string &name) {
  // Create the PeakColumn.
  columns.push_back(boost::shared_ptr<DataObjects::PeakColumn>(
      new DataObjects::PeakColumn(this->peaks, name)));
  // Cache the names
  columnNames.push_back(name);
}
Peterson, Peter's avatar
Peterson, Peter committed
673

674
675
676
677
678
679
680
681
682
//---------------------------------------------------------------------------------------------
/// @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
683

684
685
686
687
688
689
690
691
//---------------------------------------------------------------------------------------------
/// Gets the shared pointer to a column by index.
boost::shared_ptr<Mantid::API::Column> PeaksWorkspace::getColumn(size_t index) {
  if (index >= columns.size())
    throw std::invalid_argument(
        "PeaksWorkspace::getColumn() called with invalid index.");
  return columns[index];
}
692

693
694
695
696
697
698
699
700
701
//---------------------------------------------------------------------------------------------
/// Gets the shared pointer to a column by index.
boost::shared_ptr<const Mantid::API::Column>
PeaksWorkspace::getColumn(size_t index) const {
  if (index >= columns.size())
    throw std::invalid_argument(
        "PeaksWorkspace::getColumn() called with invalid index.");
  return columns[index];
}
702

703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
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);
723
  std::vector<int> peakNumber(np);
724
  std::vector<double> goniometerMatrix(9 * np);
725
  std::vector<std::string> shapes(np);
726
727

  // Populate column vectors from Peak Workspace
728
  size_t maxShapeJSONLength = 0;
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
  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();
745
    peakNumber[i] = p.getPeakNumber();
746
    {
747
748
749
750
751
752
753
754
755
756
      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];
757
    }
758
759
    const std::string shapeJSON = p.getPeakShape().toJSON();
    shapes[i] = shapeJSON;
760
761
    if (shapeJSON.size() > maxShapeJSONLength) {
      maxShapeJSONLength = shapeJSON.size();
762
    }
763
  }
764

765
  // Start Peaks Workspace in Nexus File
766
767
768
  const std::string specifyInteger = "An integer";
  const std::string specifyDouble = "A double";
  const std::string specifyString = "A string";
769
770
771
  file->makeGroup("peaks_workspace", "NXentry",
                  true); // For when peaksWorkspace can be loaded

772
773
  // Coordinate system
  file->writeData("coordinate_system", static_cast<uint32_t>(m_coordSystem));
774

775
776
777
778
779
  // 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);

780
781
782
  // Detectors column
  file->writeData("column_1", detectorID);
  file->openData("column_1");
783
  file->putAttr("name", "Detector ID");
784
785
786
787
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
  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
890
891
892
  file->closeData();

  // Peak Number column
893
894
  file->writeData("column_17", peakNumber);
  file->openData("column_17");
895
896
897
  file->putAttr("name", "Peak Number");
  file->putAttr("interpret_as", specifyInteger);
  file->putAttr("units", "Not known"); // Units may need changing when known
898
899
900
901
902
903
904
905
906
907
908
909
910
  file->closeData();

  // Goniometer Matrix Column
  std::vector<int> array_dims;
  array_dims.push_back(static_cast<int>(peaks.size()));
  array_dims.push_back(9);
  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();

911
912
913
914
915
916
917
918
  // Shape
  std::vector<int64_t> dims;
  dims.push_back(np);
  dims.push_back(static_cast<int>(maxShapeJSONLength));
  const std::string name = "column_16";
  file->makeData(name, NeXus::CHAR, dims, false);
  file->openData(name);

919
  auto toNexus = new char[maxShapeJSONLength * np];
Owen Arnold's avatar
Owen Arnold committed
920
  for (size_t ii = 0; ii < np; ii++) {
921
922
923
    std::string rowStr = shapes[ii];
    for (size_t ic = 0; ic < rowStr.size(); ic++)
      toNexus[ii * maxShapeJSONLength + ic] = rowStr[ic];
924
925
    for (size_t ic = rowStr.size();
         ic < static_cast<size_t>(maxShapeJSONLength); ic++)
926
927
928
929
930
931
932
933
934
935
936
      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();

937
938
939
940
  // QLab & QSample are calculated and do not need to be saved

  file->closeGroup(); // end of peaks workpace
}
941

942
943
944
945
946
/**
 * Set the special Q3D coordinate system.
 * @param coordinateSystem : Option to set.
 */
void PeaksWorkspace::setCoordinateSystem(
947
948
    const Kernel::SpecialCoordinateSystem coordinateSystem) {
  m_coordSystem = coordinateSystem;
949
}
950

951
952
953
/**
 * @return the special Q3D coordinate system.
 */
954
Kernel::SpecialCoordinateSystem
955
PeaksWorkspace::getSpecialCoordinateSystem() const {
956
  return m_coordSystem;
Peterson, Peter's avatar
Peterson, Peter committed
957
}
958

959
960
961
962
// prevent shared pointer from deleting this
struct NullDeleter {
  template <typename T> void operator()(T *) {}
};
963
/**Get access to shared pointer containing workspace porperties */
964
API::LogManager_sptr PeaksWorkspace::logs() {
965
  return API::LogManager_sptr(&(this->mutableRun()), NullDeleter());
966
}
967

968
969
970
971
972
973
974
/** 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()));
}

975
ITableWorkspace *
976
PeaksWorkspace::doCloneColumns(const std::vector<std::string> &) const {
977
978
  throw Kernel::Exception::NotImplementedError(
      "PeaksWorkspace cannot clone columns.");
979
}
980
981
}
}
982

983
///\cond TEMPLATE
984

985
986
987
988
989
990
991
992
993
994
995
996
997
998
namespace Mantid {
namespace Kernel {

template <>
DLLExport Mantid::DataObjects::PeaksWorkspace_sptr
IPropertyManager::getValue<Mantid::DataObjects::PeaksWorkspace_sptr>(
    const std::string &name) const {
  PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr> *prop =
      dynamic_cast<
          PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr> *>(
          getPointerToProperty(name));
  if (prop) {
    return *prop;
  } else {
999
1000
    std::string message =
        "Attempt to assign property " + name +