PeaksWorkspace.cpp 29.3 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"
Peterson, Peter's avatar
Peterson, Peter committed
6
#include "MantidAPI/WorkspaceFactory.h"
7
#include "MantidAPI/WorkspaceProperty.h"
8
#include "MantidDataObjects/Peak.h"
9
10
#include "MantidDataObjects/TableColumn.h"
#include "MantidDataObjects/TableWorkspace.h"
11
12
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Instrument/Goniometer.h"
13
14
15
#include "MantidKernel/DateAndTime.h"
#include "MantidKernel/Logger.h"
#include "MantidKernel/PhysicalConstants.h"
16
#include "MantidKernel/Quat.h"
17
#include "MantidKernel/Unit.h"
18
#include "MantidKernel/V3D.h"
Peterson, Peter's avatar
Peterson, Peter committed
19
#include <algorithm>
20
#include <boost/shared_ptr.hpp>
21
22
23
#include <cmath>
#include <cstdio>
#include <cstdlib>
Peterson, Peter's avatar
Peterson, Peter committed
24
25
#include <exception>
#include <fstream>
26
27
#include <nexus/NeXusException.hpp>
#include <nexus/NeXusFile.hpp>
28
29
30
31
32
33
#include <ostream>
#include <string>

using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::Geometry;
Peterson, Peter's avatar
Peterson, Peter committed
34

35
36
37
namespace Mantid {
namespace DataObjects {
/// Register the workspace as a type
38
DECLARE_WORKSPACE(PeaksWorkspace)
39

Owen Arnold's avatar
Owen Arnold committed
40
//---------------------------------------------------------------------------------------------
41
42
43
44
/** Constructor. Create a table with all the required columns.
 *
 * @return PeaksWorkspace object
 */
45
46
47
48
49
PeaksWorkspace::PeaksWorkspace()
    : IPeaksWorkspace(), peaks(), columns(), columnNames(),
      m_coordSystem(None) {
  initColumns();
}
50

51
52
53
54
55
56
57
//---------------------------------------------------------------------------------------------
/** Copy constructor
 *
 * @param other :: other PeaksWorkspace to copy from
 * @return
 */
PeaksWorkspace::PeaksWorkspace(const PeaksWorkspace &other)
58
59
    : IPeaksWorkspace(other), peaks(other.peaks), columns(), columnNames(),
      m_coordSystem(other.m_coordSystem) {
60
61
  initColumns();
}
62

63
64
65
66
67
68
69
70
71
72
73
74
//=====================================================================================
//=====================================================================================
/** 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.
   */
75
  explicit PeakComparator(std::vector<std::pair<std::string, bool>> &criteria)
76
77
78
79
      : 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
80
81
82
    for (auto &name : criteria) {
      std::string &col = name.first;
      bool ascending = name.second;
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
      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
100
      }
101
102
103
      // Flip the sign of comparison if descending.
      if (ascending)
        return lessThan;
Owen Arnold's avatar
Owen Arnold committed
104
      else
105
        return !lessThan;
106
    }
107
108
109
110
    // If you reach here, all criteria were ==; so not <, so return false
    return false;
  }
};
111

112
113
114
115
116
117
118
119
120
121
122
123
//---------------------------------------------------------------------------------------------
/** 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);
}
124

125
126
127
128
//---------------------------------------------------------------------------------------------
/** @return the number of peaks
 */
int PeaksWorkspace::getNumberPeaks() const { return int(peaks.size()); }
129

130
131
132
133
134
//---------------------------------------------------------------------------------------------
/** @return the convention
 */
std::string PeaksWorkspace::getConvention() const { return convention; }

135
136
137
138
139
140
141
142
143
144
145
//---------------------------------------------------------------------------------------------
/** 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);
}
146

147
148
149
150
//---------------------------------------------------------------------------------------------
/** Add a peak to the list
 * @param ipeak :: Peak object to add (copy) into this.
 */
Owen Arnold's avatar
Owen Arnold committed
151
void PeaksWorkspace::addPeak(const Geometry::IPeak &ipeak) {
152
153
154
155
156
157
  if (dynamic_cast<const Peak *>(&ipeak)) {
    peaks.push_back((const Peak &)ipeak);
  } else {
    peaks.push_back(Peak(ipeak));
  }
}
158

159
160
161
162
163
164
165
166
167
168
169
170
//---------------------------------------------------------------------------------------------
/** 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];
}
171

172
173
174
175
176
177
178
179
180
181
182
183
//---------------------------------------------------------------------------------------------
/** 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];
}
184

185
186
187
//---------------------------------------------------------------------------------------------
/** 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
188
189
 * @param detectorDistance :: optional distance between the sample and the
 * detector. You do NOT need to explicitly provide this distance.
190
191
 * @return a pointer to a new Peak object.
 */
Owen Arnold's avatar
Owen Arnold committed
192
Geometry::IPeak *
193
194
PeaksWorkspace::createPeak(Kernel::V3D QLabFrame,
                           boost::optional<double> detectorDistance) const {
195
196
197
  Geometry::Goniometer goniometer = this->run().getGoniometer();

  // create a peak using the qLab frame
198
  auto peak = new Peak(this->getInstrument(), QLabFrame, detectorDistance);
199
200
201
202
203
204
205
206

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

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

  return peak;
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
/**
 * 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>>
PeaksWorkspace::peakInfo(Kernel::V3D qFrame, bool labCoords) const {
  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;
257
      }
258

259
260
261
262
263
264
265
266
267
268
269
270
      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);
271

272
273
274
  if (seqNum >= 0 && NPeaks == getNumberPeaks())
    Gon = getPeak(seqNum).getGoniometerMatrix();
  if (labCoords) {
275

276
277
278
    Kernel::Matrix<double> InvGon(Gon);
    InvGon.Invert();
    Qsamp = InvGon * Qlab;
279

280
281
282
283
  } else {
    Qsamp = qFrame;
    Qlab = Gon * Qsamp;
  }
284

285
  if (labCoords || seqNum >= 0)
286

287
288
289
290
291
  {
    std::pair<std::string, std::string> QlabStr(
        "Qlab", boost::lexical_cast<std::string>(Qlab));
    Result.push_back(QlabStr);
  }
292

293
  if (!labCoords || seqNum >= 0) {
294

295
296
297
298
    std::pair<std::string, std::string> QsampStr(
        "QSample", boost::lexical_cast<std::string>(Qsamp));
    Result.push_back(QsampStr);
  }
299

300
  try {
301

Owen Arnold's avatar
Owen Arnold committed
302
    Geometry::IPeak *peak = createPeak(Qlab);
303

304
    if (sample().hasOrientedLattice()) {
305

306
307
      peak->setGoniometerMatrix(Gon);
      const Geometry::OrientedLattice &lat = (sample().getOrientedLattice());
308

309
310
311
312
      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
313

314
315
316
      std::pair<std::string, std::string> HKL(
          "HKL", boost::lexical_cast<std::string>(hkl));
      Result.push_back(HKL);
317
318
    }

319
    if (hasOneRunNumber) {
320
321
      std::pair<std::string, std::string> runn("RunNumber",
                                               "   " + std::to_string(runNum));
322
      Result.push_back(runn);
323
    }
324

325
326
327
328
329
330
331
332
333
334
    //------- 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(
335
        "Seq Num,1st=1", "    " + std::to_string(seqNum + 1));
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
    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(
366
          "Row", "    " + std::to_string(peak->getRow()));
367
368
369
      Result.push_back(row);

      std::pair<std::string, std::string> col(
370
          "Col", "    " + std::to_string(peak->getCol()));
371
372
373
374
375
376
377
378
379
380
      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);
381
    }
382

383
384
385
386
387
  } catch (...) // Impossible position
  {
  }
  return Result;
}
388

389
390
391
392
393
394
395
/**
 * Create a Peak from a HKL value provided by the client.
 *
 *
 * @param HKL : reciprocal lattice vector coefficients
 * @return Fully formed peak.
 */
396
397
398
399
Peak *PeaksWorkspace::createPeakHKL(V3D HKL) const {
  /*
   The following allows us to add peaks where we have a single UB to work from.
   */
400

401
402
  Geometry::OrientedLattice lattice = this->sample().getOrientedLattice();
  Geometry::Goniometer goniometer = this->run().getGoniometer();
403

404
405
406
  // 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;
407

408
409
410
411
  // create a peak using the qLab frame
  auto peak =
      new Peak(this->getInstrument(),
               qLabFrame); // This should calculate the detector positions too.
412

413
414
  // We need to set HKL separately to keep things consistent.
  peak->setHKL(HKL[0], HKL[1], HKL[2]);
415

416
417
  // Set the goniometer
  peak->setGoniometerMatrix(goniometer.getR());
418

419
420
  // Take the run number from this
  peak->setRunNumber(this->getRunNumber());
421

422
  return peak;
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
/**
 * 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.
 */
int PeaksWorkspace::peakInfoNumber(Kernel::V3D qFrame, bool labCoords) const {
  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;
469
    }
470
471
472
  }
  return seqNum;
}
Peterson, Peter's avatar
Peterson, Peter committed
473

474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
//---------------------------------------------------------------------------------------------
/** 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;
}
494

495
496
497
498
499
//---------------------------------------------------------------------------------------------
/// Return the memory used in bytes
size_t PeaksWorkspace::getMemorySize() const {
  return getNumberPeaks() * sizeof(Peak);
}
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
//---------------------------------------------------------------------------------------------
/**
 *  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
525
    }
526
  }
527

528
529
  return table;
}
Peterson, Peter's avatar
Peterson, Peter committed
530

531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
//---------------------------------------------------------------------------------------------
/** 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");
}
Peterson, Peter's avatar
Peterson, Peter committed
553

554
555
556
557
558
559
560
561
562
563
564
565
//---------------------------------------------------------------------------------------------
/**
 * 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
566

567
568
569
570
571
572
573
574
575
//---------------------------------------------------------------------------------------------
/// @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
576

577
578
579
580
581
582
583
584
//---------------------------------------------------------------------------------------------
/// 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];
}
585

586
587
588
589
590
591
592
593
594
//---------------------------------------------------------------------------------------------
/// 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];
}
595

596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
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);
  std::vector<double> goniometerMatrix(9 * np);
617
  std::vector<std::string> shapes(np);
618
619

  // Populate column vectors from Peak Workspace
620
  size_t maxShapeJSONLength = 0;
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
  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();
637
    {
638
639
640
641
642
643
644
645
646
647
      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];
648
    }
649
650
    const std::string shapeJSON = p.getPeakShape().toJSON();
    shapes[i] = shapeJSON;
651
652
    if (shapeJSON.size() > maxShapeJSONLength) {
      maxShapeJSONLength = shapeJSON.size();
653
    }
654
  }
655

656
  // Start Peaks Workspace in Nexus File
657
658
659
  const std::string specifyInteger = "An integer";
  const std::string specifyDouble = "A double";
  const std::string specifyString = "A string";
660
661
662
  file->makeGroup("peaks_workspace", "NXentry",
                  true); // For when peaksWorkspace can be loaded

663
664
  // Coordinate system
  file->writeData("coordinate_system", static_cast<uint32_t>(m_coordSystem));
665

666
667
668
669
670
  // 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);

671
672
673
  // Detectors column
  file->writeData("column_1", detectorID);
  file->openData("column_1");
674
  file->putAttr("name", "Detector ID");
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
  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
  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();

794
795
796
797
798
799
800
801
  // 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);

802
  auto toNexus = new char[maxShapeJSONLength * np];
Owen Arnold's avatar
Owen Arnold committed
803
  for (size_t ii = 0; ii < np; ii++) {
804
805
806
    std::string rowStr = shapes[ii];
    for (size_t ic = 0; ic < rowStr.size(); ic++)
      toNexus[ii * maxShapeJSONLength + ic] = rowStr[ic];
807
808
    for (size_t ic = rowStr.size();
         ic < static_cast<size_t>(maxShapeJSONLength); ic++)
809
810
811
812
813
814
815
816
817
818
819
      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();

820
821
822
823
  // QLab & QSample are calculated and do not need to be saved

  file->closeGroup(); // end of peaks workpace
}
824

825
826
827
828
829
/**
 * Set the special Q3D coordinate system.
 * @param coordinateSystem : Option to set.
 */
void PeaksWorkspace::setCoordinateSystem(
830
831
    const Kernel::SpecialCoordinateSystem coordinateSystem) {
  m_coordSystem = coordinateSystem;
832
}
833

834
835
836
/**
 * @return the special Q3D coordinate system.
 */
837
Kernel::SpecialCoordinateSystem
838
PeaksWorkspace::getSpecialCoordinateSystem() const {
839
  return m_coordSystem;
Peterson, Peter's avatar
Peterson, Peter committed
840
}
841

842
843
844
845
846
847
848
849
850
851
852
853
854
855
// prevent shared pointer from deleting this
struct NullDeleter {
  template <typename T> void operator()(T *) {}
};
/**Get access to shared pointer containing workspace porperties, cashes the
 shared pointer
 into internal class variable to not allow shared pointer being deleted */
API::LogManager_sptr PeaksWorkspace::logs() {
  if (m_logCash)
    return m_logCash;

  m_logCash = API::LogManager_sptr(&(this->mutableRun()), NullDeleter());
  return m_logCash;
}
856

857
ITableWorkspace *
858
PeaksWorkspace::doCloneColumns(const std::vector<std::string> &) const {
859
860
  throw Kernel::Exception::NotImplementedError(
      "PeaksWorkspace cannot clone columns.");
861
}
862
863
}
}
864

865
///\cond TEMPLATE
866

867
868
869
870
871
872
873
874
875
876
877
878
879
880
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 {
881
882
883
    std::string message =
        "Attempt to assign property " + name +
        " to incorrect type. Expected shared_ptr<PeaksWorkspace>.";
884
885
886
    throw std::runtime_error(message);
  }
}
887

888
889
890
891
892
893
894
895
896
897
898
template <>
DLLExport Mantid::DataObjects::PeaksWorkspace_const_sptr
IPropertyManager::getValue<Mantid::DataObjects::PeaksWorkspace_const_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->operator()();
  } else {
899
900
901
    std::string message =
        "Attempt to assign property " + name +
        " to incorrect type. Expected const shared_ptr<PeaksWorkspace>.";
902
903
904
    throw std::runtime_error(message);
  }
}
905

906
} // namespace Kernel
907
908
} // namespace Mantid

909
///\endcond TEMPLATE