PredictSatellitePeaks.cpp 18 KB
Newer Older
1
/*
Lynch, Vickie's avatar
Lynch, Vickie committed
2
3
4
5
6
 * PredictSatellitePeaks.cpp
 *
 *  Created on: July 15, 2018
 *      Author: Vickie Lynch
 */
7
#include "MantidCrystal/PredictSatellitePeaks.h"
Lynch, Vickie's avatar
Lynch, Vickie committed
8
#include "MantidAPI/OrientedLatticeValidator.h"
Lynch, Vickie's avatar
Lynch, Vickie committed
9
#include "MantidAPI/Run.h"
10
11
12
#include "MantidAPI/Sample.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidDataObjects/PeaksWorkspace.h"
Lynch, Vickie's avatar
Lynch, Vickie committed
13
14
#include "MantidGeometry/Crystal/BasicHKLFilters.h"
#include "MantidGeometry/Crystal/HKLGenerator.h"
15
16
17
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Objects/InstrumentRayTracer.h"
#include "MantidKernel/ArrayLengthValidator.h"
Lynch, Vickie's avatar
Lynch, Vickie committed
18
#include "MantidKernel/ArrayProperty.h"
19
20
21
22
#include "MantidKernel/EnabledWhenProperty.h"
#include <boost/math/special_functions/round.hpp>

namespace Mantid {
Lynch, Vickie's avatar
Lynch, Vickie committed
23
24
25
26
27
using namespace Mantid::DataObjects;
using namespace Mantid::API;
using namespace std;
using namespace Mantid::Geometry;
using namespace Mantid::Kernel;
28

Lynch, Vickie's avatar
Lynch, Vickie committed
29
30
31
32
namespace Crystal {

DECLARE_ALGORITHM(PredictSatellitePeaks)

33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
namespace {
/// Small helper function that return -1 if convention
/// is "Crystallography" and 1 otherwise.
double get_factor_for_q_convention(const std::string &convention) {
  if (convention == "Crystallography") {
    return -1.0;
  }
  return 1.0;
}
} // namespace

/** Constructor
 */

PredictSatellitePeaks::PredictSatellitePeaks()
    : m_qConventionFactor(get_factor_for_q_convention(
Lynch, Vickie's avatar
Lynch, Vickie committed
49
          ConfigService::Instance().getString("Q.convention"))) {}
50

Lynch, Vickie's avatar
Lynch, Vickie committed
51
52
/// Initialise the properties
void PredictSatellitePeaks::init() {
53
  auto latticeValidator = boost::make_shared<OrientedLatticeValidator>();
Lynch, Vickie's avatar
Lynch, Vickie committed
54
  declareProperty(
55
      std::make_unique<WorkspaceProperty<PeaksWorkspace>>(
56
          "Peaks", "", Direction::Input, latticeValidator),
Lynch, Vickie's avatar
Lynch, Vickie committed
57
58
59
60
      "Workspace of Peaks with orientation matrix that indexed the peaks and "
      "instrument loaded");

  declareProperty(
61
      std::make_unique<WorkspaceProperty<PeaksWorkspace>>("SatellitePeaks", "",
Sam Jenkins's avatar
Sam Jenkins committed
62
                                                          Direction::Output),
Lynch, Vickie's avatar
Lynch, Vickie committed
63
      "Workspace of Peaks with peaks with fractional h,k, and/or l values");
64
  declareProperty(std::make_unique<Kernel::ArrayProperty<double>>(
Lynch, Vickie's avatar
Lynch, Vickie committed
65
66
                      string("ModVector1"), "0.0,0.0,0.0"),
                  "Offsets for h, k, l directions ");
67
  declareProperty(std::make_unique<Kernel::ArrayProperty<double>>(
Lynch, Vickie's avatar
Lynch, Vickie committed
68
69
                      string("ModVector2"), "0.0,0.0,0.0"),
                  "Offsets for h, k, l directions ");
70
  declareProperty(std::make_unique<Kernel::ArrayProperty<double>>(
Lynch, Vickie's avatar
Lynch, Vickie committed
71
72
73
                      string("ModVector3"), "0.0,0.0,0.0"),
                  "Offsets for h, k, l directions ");
  declareProperty(
74
      std::make_unique<PropertyWithValue<int>>("MaxOrder", 0, Direction::Input),
Lynch, Vickie's avatar
Lynch, Vickie committed
75
76
      "Maximum order to apply ModVectors. Default = 0");

Lynch, Vickie's avatar
Lynch, Vickie committed
77
  declareProperty("GetModVectorsFromUB", false,
Lynch, Vickie's avatar
Lynch, Vickie committed
78
79
                  "If false Modulation Vectors will be read from input");

80
  declareProperty(std::make_unique<PropertyWithValue<bool>>("CrossTerms", false,
Sam Jenkins's avatar
Sam Jenkins committed
81
                                                            Direction::Input),
Lynch, Vickie's avatar
Lynch, Vickie committed
82
83
84
85
86
87
                  "Include cross terms (false)");

  declareProperty(
      "IncludeIntegerHKL", true,
      "If false order 0 peaks are not included in workspace (integer HKL)");

Lynch, Vickie's avatar
Lynch, Vickie committed
88
89
90
91
  declareProperty("IncludeAllPeaksInRange", false,
                  "If false only offsets from "
                  "peaks from Peaks workspace "
                  "in input are used");
Lynch, Vickie's avatar
Lynch, Vickie committed
92

Sam Jenkins's avatar
Sam Jenkins committed
93
94
  declareProperty(std::make_unique<PropertyWithValue<double>>(
                      "WavelengthMin", 0.1, Direction::Input),
Lynch, Vickie's avatar
Lynch, Vickie committed
95
96
                  "Minimum wavelength limit at which to start looking for "
                  "single-crystal peaks.");
Sam Jenkins's avatar
Sam Jenkins committed
97
98
  declareProperty(std::make_unique<PropertyWithValue<double>>(
                      "WavelengthMax", 100.0, Direction::Input),
Lynch, Vickie's avatar
Lynch, Vickie committed
99
100
                  "Maximum wavelength limit at which to start looking for "
                  "single-crystal peaks.");
Sam Jenkins's avatar
Sam Jenkins committed
101
102
  declareProperty(std::make_unique<PropertyWithValue<double>>(
                      "MinDSpacing", 0.1, Direction::Input),
Lynch, Vickie's avatar
Lynch, Vickie committed
103
                  "Minimum d-spacing of peaks to consider. Default = 1.0");
Sam Jenkins's avatar
Sam Jenkins committed
104
105
  declareProperty(std::make_unique<PropertyWithValue<double>>(
                      "MaxDSpacing", 100.0, Direction::Input),
Lynch, Vickie's avatar
Lynch, Vickie committed
106
107
108
109
                  "Maximum d-spacing of peaks to consider");

  setPropertySettings(
      "WavelengthMin",
110
      std::make_unique<Kernel::EnabledWhenProperty>(
Lynch, Vickie's avatar
Lynch, Vickie committed
111
112
113
114
          string("IncludeAllPeaksInRange"), Kernel::IS_EQUAL_TO, "1"));

  setPropertySettings(
      "WavelengthMax",
115
      std::make_unique<Kernel::EnabledWhenProperty>(
Lynch, Vickie's avatar
Lynch, Vickie committed
116
117
118
          string("IncludeAllPeaksInRange"), Kernel::IS_EQUAL_TO, "1"));
  setPropertySettings(
      "MinDSpacing",
119
      std::make_unique<Kernel::EnabledWhenProperty>(
Lynch, Vickie's avatar
Lynch, Vickie committed
120
121
122
123
          string("IncludeAllPeaksInRange"), Kernel::IS_EQUAL_TO, "1"));

  setPropertySettings(
      "MaxDSpacing",
124
      std::make_unique<Kernel::EnabledWhenProperty>(
Lynch, Vickie's avatar
Lynch, Vickie committed
125
126
127
128
129
130
          string("IncludeAllPeaksInRange"), Kernel::IS_EQUAL_TO, "1"));
}

/// Run the algorithm
void PredictSatellitePeaks::exec() {
  bool includePeaksInRange = getProperty("IncludeAllPeaksInRange");
131
132
133
134
  Peaks = getProperty("Peaks");
  if (!Peaks)
    throw std::invalid_argument(
        "Input workspace is not a PeaksWorkspace. Type=" + Peaks->id());
Lynch, Vickie's avatar
Lynch, Vickie committed
135
136
137
138
139
140
141
142
143
144
145
  if (!includePeaksInRange) {
    exec_peaks();
    return;
  }

  V3D offsets1 = getOffsetVector("ModVector1");
  V3D offsets2 = getOffsetVector("ModVector2");
  V3D offsets3 = getOffsetVector("ModVector3");
  int maxOrder = getProperty("MaxOrder");
  bool crossTerms = getProperty("CrossTerms");
  bool includeOrderZero = getProperty("IncludeIntegerHKL");
146
147
  // boolean for only including order zero once
  bool notOrderZero = false;
Lynch, Vickie's avatar
Lynch, Vickie committed
148
149
150
151
152
153
154
155
156
157

  if (Peaks->getNumberPeaks() <= 0) {
    g_log.error() << "There are No peaks in the input PeaksWorkspace\n";
    return;
  }

  API::Sample sample = Peaks->mutableSample();

  OrientedLattice lattice = sample.getOrientedLattice();

158
159
  bool fromUB = getProperty("GetModVectorsFromUB");
  if (fromUB) {
160
161
162
    offsets1 = lattice.getModVec(0);
    offsets2 = lattice.getModVec(1);
    offsets3 = lattice.getModVec(2);
Lynch, Vickie's avatar
Lynch, Vickie committed
163
164
    if (maxOrder == 0)
      maxOrder = lattice.getMaxOrder();
165
166
167
168
169
170
171
    crossTerms = lattice.getCrossTerm();
  } else {
    lattice.setModVec1(offsets1);
    lattice.setModVec2(offsets2);
    lattice.setModVec3(offsets3);
    lattice.setMaxOrder(maxOrder);
    lattice.setCrossTerm(crossTerms);
Lynch, Vickie's avatar
Lynch, Vickie committed
172
173
174
175
  }

  const auto instrument = Peaks->getInstrument();

176
  outPeaks = boost::dynamic_pointer_cast<IPeaksWorkspace>(
Lynch, Vickie's avatar
Lynch, Vickie committed
177
      WorkspaceFactory::Instance().createPeaks());
178
179
  outPeaks->setInstrument(instrument);
  outPeaks->mutableSample().setOrientedLattice(&lattice);
Lynch, Vickie's avatar
Lynch, Vickie committed
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212

  Kernel::Matrix<double> goniometer;
  goniometer.identityMatrix();

  const double lambdaMin = getProperty("WavelengthMin");
  const double lambdaMax = getProperty("WavelengthMax");
  IPeak &peak0 = Peaks->getPeak(0);

  std::vector<V3D> possibleHKLs;
  const double dMin = getProperty("MinDSpacing");
  const double dMax = getProperty("MaxDSpacing");
  Geometry::HKLGenerator gen(lattice, dMin);
  auto dSpacingFilter =
      boost::make_shared<HKLFilterDRange>(lattice, dMin, dMax);

  V3D hkl = *(gen.begin());
  g_log.information() << "HKL range for d_min of " << dMin << " to d_max of "
                      << dMax << " is from " << hkl << " to " << hkl * -1.0
                      << ", a total of " << gen.size() << " possible HKL's\n";
  if (gen.size() > MAX_NUMBER_HKLS)
    throw std::invalid_argument("More than 10 billion HKLs to search. Is "
                                "your d_min value too small?");

  possibleHKLs.clear();
  possibleHKLs.reserve(gen.size());
  std::remove_copy_if(gen.begin(), gen.end(), std::back_inserter(possibleHKLs),
                      (~dSpacingFilter)->fn());

  size_t N = possibleHKLs.size();
  N = max<size_t>(100, N);
  auto &UB = lattice.getUB();
  goniometer = peak0.getGoniometerMatrix();
  Progress prog(this, 0.0, 1.0, N);
Lynch, Vickie's avatar
Lynch, Vickie committed
213
  vector<vector<int>> AlreadyDonePeaks;
Lynch, Vickie's avatar
Lynch, Vickie committed
214
215
  auto orientedUB = goniometer * UB;
  HKLFilterWavelength lambdaFilter(orientedUB, lambdaMin, lambdaMax);
Lynch, Vickie's avatar
Lynch, Vickie committed
216
217
218
219
220
221
  outPeaks->mutableRun().addProperty<std::vector<double>>("Offset1", offsets1,
                                                          true);
  outPeaks->mutableRun().addProperty<std::vector<double>>("Offset2", offsets2,
                                                          true);
  outPeaks->mutableRun().addProperty<std::vector<double>>("Offset3", offsets3,
                                                          true);
Lynch, Vickie's avatar
Lynch, Vickie committed
222
223
224
  for (auto it = possibleHKLs.begin(); it != possibleHKLs.end(); ++it) {
    V3D hkl = *it;
    if (crossTerms) {
Lynch, Vickie's avatar
Lynch, Vickie committed
225
226
227
      predictOffsetsWithCrossTerms(offsets1, offsets2, offsets3, maxOrder, hkl,
                                   lambdaFilter, includePeaksInRange,
                                   includeOrderZero, AlreadyDonePeaks);
Lynch, Vickie's avatar
Lynch, Vickie committed
228
    } else {
229
      predictOffsets(0, offsets1, maxOrder, hkl, lambdaFilter,
Lynch, Vickie's avatar
Lynch, Vickie committed
230
                     includePeaksInRange, includeOrderZero, AlreadyDonePeaks);
231
      predictOffsets(1, offsets2, maxOrder, hkl, lambdaFilter,
232
                     includePeaksInRange, notOrderZero, AlreadyDonePeaks);
233
      predictOffsets(2, offsets3, maxOrder, hkl, lambdaFilter,
234
                     includePeaksInRange, notOrderZero, AlreadyDonePeaks);
Lynch, Vickie's avatar
Lynch, Vickie committed
235
236
    }
  }
237
238
239
  // Sort peaks by run number so that peaks with equal goniometer matrices are
  // adjacent
  std::vector<std::pair<std::string, bool>> criteria;
240
241
242
243
244
  criteria.emplace_back(std::pair<std::string, bool>("RunNumber", true));
  criteria.emplace_back(std::pair<std::string, bool>("BankName", true));
  criteria.emplace_back(std::pair<std::string, bool>("h", true));
  criteria.emplace_back(std::pair<std::string, bool>("k", true));
  criteria.emplace_back(std::pair<std::string, bool>("l", true));
245
246
247
248
249
250
  outPeaks->sort(criteria);

  for (int i = 0; i < static_cast<int>(outPeaks->getNumberPeaks()); ++i) {
    outPeaks->getPeak(i).setPeakNumber(i);
  }
  setProperty("SatellitePeaks", outPeaks);
Lynch, Vickie's avatar
Lynch, Vickie committed
251
252
253
254
255
256
257
258
259
260
}

void PredictSatellitePeaks::exec_peaks() {

  V3D offsets1 = getOffsetVector("ModVector1");
  V3D offsets2 = getOffsetVector("ModVector2");
  V3D offsets3 = getOffsetVector("ModVector3");
  int maxOrder = getProperty("MaxOrder");
  bool crossTerms = getProperty("CrossTerms");

Lynch, Vickie's avatar
Lynch, Vickie committed
261
262
263
264
  API::Sample sample = Peaks->mutableSample();

  OrientedLattice lattice = sample.getOrientedLattice();

265
266
  bool fromUB = getProperty("GetModVectorsFromUB");
  if (fromUB) {
267
268
269
    offsets1 = lattice.getModVec(0);
    offsets2 = lattice.getModVec(1);
    offsets3 = lattice.getModVec(2);
Lynch, Vickie's avatar
Lynch, Vickie committed
270
271
    if (maxOrder == 0)
      maxOrder = lattice.getMaxOrder();
272
273
274
275
276
277
278
    crossTerms = lattice.getCrossTerm();
  } else {
    lattice.setModVec1(offsets1);
    lattice.setModVec2(offsets2);
    lattice.setModVec3(offsets3);
    lattice.setMaxOrder(maxOrder);
    lattice.setCrossTerm(crossTerms);
Lynch, Vickie's avatar
Lynch, Vickie committed
279
280
  }

Lynch, Vickie's avatar
Lynch, Vickie committed
281
282
  bool includePeaksInRange = false;
  bool includeOrderZero = getProperty("IncludeIntegerHKL");
283
284
  // boolean for only including order zero once
  bool notOrderZero = false;
Lynch, Vickie's avatar
Lynch, Vickie committed
285
286
287
288
289
290
291
292

  if (Peaks->getNumberPeaks() <= 0) {
    g_log.error() << "There are No peaks in the input PeaksWorkspace\n";
    return;
  }

  const auto instrument = Peaks->getInstrument();

293
  outPeaks = boost::dynamic_pointer_cast<IPeaksWorkspace>(
Lynch, Vickie's avatar
Lynch, Vickie committed
294
      WorkspaceFactory::Instance().createPeaks());
295
296
  outPeaks->setInstrument(instrument);
  outPeaks->mutableSample().setOrientedLattice(&lattice);
Lynch, Vickie's avatar
Lynch, Vickie committed
297

Lynch, Vickie's avatar
Lynch, Vickie committed
298
  vector<vector<int>> AlreadyDonePeaks;
Lynch, Vickie's avatar
Lynch, Vickie committed
299
  HKLFilterWavelength lambdaFilter(DblMatrix(3, 3, true), 0.1, 100.);
Lynch, Vickie's avatar
Lynch, Vickie committed
300
301
302
303
304
305
  outPeaks->mutableRun().addProperty<std::vector<double>>("Offset1", offsets1,
                                                          true);
  outPeaks->mutableRun().addProperty<std::vector<double>>("Offset2", offsets2,
                                                          true);
  outPeaks->mutableRun().addProperty<std::vector<double>>("Offset3", offsets3,
                                                          true);
Lynch, Vickie's avatar
Lynch, Vickie committed
306
307
308
309
310
  std::vector<Peak> peaks = Peaks->getPeaks();
  for (auto it = peaks.begin(); it != peaks.end(); ++it) {
    auto peak = *it;
    V3D hkl = peak.getHKL();
    if (crossTerms) {
Lynch, Vickie's avatar
Lynch, Vickie committed
311
312
313
      predictOffsetsWithCrossTerms(offsets1, offsets2, offsets3, maxOrder, hkl,
                                   lambdaFilter, includePeaksInRange,
                                   includeOrderZero, AlreadyDonePeaks);
Lynch, Vickie's avatar
Lynch, Vickie committed
314
    } else {
315
      predictOffsets(0, offsets1, maxOrder, hkl, lambdaFilter,
Lynch, Vickie's avatar
Lynch, Vickie committed
316
                     includePeaksInRange, includeOrderZero, AlreadyDonePeaks);
317
318
319
320
      predictOffsets(1, offsets2, maxOrder, hkl, lambdaFilter,
                     includePeaksInRange, notOrderZero, AlreadyDonePeaks);
      predictOffsets(2, offsets3, maxOrder, hkl, lambdaFilter,
                     includePeaksInRange, notOrderZero, AlreadyDonePeaks);
Lynch, Vickie's avatar
Lynch, Vickie committed
321
322
    }
  }
323
324
325
  // Sort peaks by run number so that peaks with equal goniometer matrices are
  // adjacent
  std::vector<std::pair<std::string, bool>> criteria;
326
327
328
329
330
  criteria.emplace_back(std::pair<std::string, bool>("RunNumber", true));
  criteria.emplace_back(std::pair<std::string, bool>("BankName", true));
  criteria.emplace_back(std::pair<std::string, bool>("h", true));
  criteria.emplace_back(std::pair<std::string, bool>("k", true));
  criteria.emplace_back(std::pair<std::string, bool>("l", true));
331
332
333
334
335
336
337
  outPeaks->sort(criteria);

  for (int i = 0; i < static_cast<int>(outPeaks->getNumberPeaks()); ++i) {
    outPeaks->getPeak(i).setPeakNumber(i);
  }

  setProperty("SatellitePeaks", outPeaks);
Lynch, Vickie's avatar
Lynch, Vickie committed
338
339
340
}

void PredictSatellitePeaks::predictOffsets(
Lynch, Vickie's avatar
Lynch, Vickie committed
341
342
343
    int indexModulatedVector, V3D offsets, int &maxOrder, V3D &hkl,
    HKLFilterWavelength &lambdaFilter, bool &includePeaksInRange,
    bool &includeOrderZero, vector<vector<int>> &AlreadyDonePeaks) {
344
  if (offsets == V3D(0, 0, 0) && !includeOrderZero)
Lynch, Vickie's avatar
Lynch, Vickie committed
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
    return;
  const Kernel::DblMatrix &UB = Peaks->sample().getOrientedLattice().getUB();
  IPeak &peak1 = Peaks->getPeak(0);
  Kernel::Matrix<double> goniometer = peak1.getGoniometerMatrix();
  auto RunNumber = peak1.getRunNumber();
  Geometry::InstrumentRayTracer tracer(Peaks->getInstrument());
  for (int order = -maxOrder; order <= maxOrder; order++) {
    if (order == 0 && !includeOrderZero)
      continue; // exclude order 0
    V3D satelliteHKL(hkl);

    satelliteHKL += offsets * order;
    if (!lambdaFilter.isAllowed(satelliteHKL) && includePeaksInRange)
      continue;

Lynch, Vickie's avatar
Lynch, Vickie committed
360
361
    Kernel::V3D Qs =
        goniometer * UB * satelliteHKL * 2.0 * M_PI * m_qConventionFactor;
Lynch, Vickie's avatar
Lynch, Vickie committed
362
363

    // Check if Q is non-physical
364
    if (Qs.Z() * m_qConventionFactor <= 0)
Lynch, Vickie's avatar
Lynch, Vickie committed
365
      continue;
Lynch, Vickie's avatar
Lynch, Vickie committed
366
367
368
369
370
371
372

    auto peak(Peaks->createPeak(Qs, 1));

    peak->setGoniometerMatrix(goniometer);

    if (!peak->findDetector(tracer))
      continue;
Lynch, Vickie's avatar
Lynch, Vickie committed
373
374
375
    vector<int> SavPk{RunNumber, boost::math::iround(1000.0 * satelliteHKL[0]),
                      boost::math::iround(1000.0 * satelliteHKL[1]),
                      boost::math::iround(1000.0 * satelliteHKL[2])};
Lynch, Vickie's avatar
Lynch, Vickie committed
376
377
378
379
380

    bool foundPeak =
        binary_search(AlreadyDonePeaks.begin(), AlreadyDonePeaks.end(), SavPk);

    if (!foundPeak) {
381
      AlreadyDonePeaks.emplace_back(SavPk);
Lynch, Vickie's avatar
Lynch, Vickie committed
382
383
384
385
    } else {
      continue;
    }

386
387
    peak->setHKL(satelliteHKL * m_qConventionFactor);
    peak->setIntHKL(hkl * m_qConventionFactor);
Lynch, Vickie's avatar
Lynch, Vickie committed
388
389
    peak->setRunNumber(RunNumber);
    V3D mnp;
390
    mnp[indexModulatedVector] = order;
391
    peak->setIntMNP(mnp * m_qConventionFactor);
392
    outPeaks->addPeak(*peak);
Lynch, Vickie's avatar
Lynch, Vickie committed
393
394
395
396
  }
}

void PredictSatellitePeaks::predictOffsetsWithCrossTerms(
Lynch, Vickie's avatar
Lynch, Vickie committed
397
    V3D offsets1, V3D offsets2, V3D offsets3, int &maxOrder, V3D &hkl,
Lynch, Vickie's avatar
Lynch, Vickie committed
398
    HKLFilterWavelength &lambdaFilter, bool &includePeaksInRange,
Lynch, Vickie's avatar
Lynch, Vickie committed
399
    bool &includeOrderZero, vector<vector<int>> &AlreadyDonePeaks) {
Lynch, Vickie's avatar
Lynch, Vickie committed
400
  if (offsets1 == V3D(0, 0, 0) && offsets2 == V3D(0, 0, 0) &&
401
      offsets3 == V3D(0, 0, 0) && !includeOrderZero)
Lynch, Vickie's avatar
Lynch, Vickie committed
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
    return;
  const Kernel::DblMatrix &UB = Peaks->sample().getOrientedLattice().getUB();
  IPeak &peak1 = Peaks->getPeak(0);
  Kernel::Matrix<double> goniometer = peak1.getGoniometerMatrix();
  auto RunNumber = peak1.getRunNumber();
  Geometry::InstrumentRayTracer tracer(Peaks->getInstrument());
  DblMatrix offsetsMat(3, 3);
  offsetsMat.setColumn(0, offsets1);
  offsetsMat.setColumn(1, offsets2);
  offsetsMat.setColumn(2, offsets3);
  int maxOrder1 = maxOrder;
  if (offsets1 == V3D(0, 0, 0))
    maxOrder1 = 0;
  int maxOrder2 = maxOrder;
  if (offsets2 == V3D(0, 0, 0))
    maxOrder2 = 0;
  int maxOrder3 = maxOrder;
  if (offsets3 == V3D(0, 0, 0))
    maxOrder3 = 0;
  for (int m = -maxOrder1; m <= maxOrder1; m++)
    for (int n = -maxOrder2; n <= maxOrder2; n++)
      for (int p = -maxOrder3; p <= maxOrder3; p++) {
        if (m == 0 && n == 0 && p == 0 && !includeOrderZero)
          continue; // exclude 0,0,0
        V3D satelliteHKL(hkl);
        V3D mnp = V3D(m, n, p);
        satelliteHKL -= offsetsMat * mnp;
        if (!lambdaFilter.isAllowed(satelliteHKL) && includePeaksInRange)
          continue;

Lynch, Vickie's avatar
Lynch, Vickie committed
432
433
        Kernel::V3D Qs =
            goniometer * UB * satelliteHKL * 2.0 * M_PI * m_qConventionFactor;
Lynch, Vickie's avatar
Lynch, Vickie committed
434
435

        // Check if Q is non-physical
436
        if (Qs.Z() <= 0)
Lynch, Vickie's avatar
Lynch, Vickie committed
437
438
439
440
441
442
443
444
          continue;

        auto peak(Peaks->createPeak(Qs, 1));

        peak->setGoniometerMatrix(goniometer);

        if (!peak->findDetector(tracer))
          continue;
Lynch, Vickie's avatar
Lynch, Vickie committed
445
446
447
448
        vector<int> SavPk{RunNumber,
                          boost::math::iround(1000.0 * satelliteHKL[0]),
                          boost::math::iround(1000.0 * satelliteHKL[1]),
                          boost::math::iround(1000.0 * satelliteHKL[2])};
Lynch, Vickie's avatar
Lynch, Vickie committed
449
450
451
452
453

        bool foundPeak = binary_search(AlreadyDonePeaks.begin(),
                                       AlreadyDonePeaks.end(), SavPk);

        if (!foundPeak) {
454
          AlreadyDonePeaks.emplace_back(SavPk);
Lynch, Vickie's avatar
Lynch, Vickie committed
455
456
        } else {
          continue;
457
458
        }

459
460
        peak->setHKL(satelliteHKL * m_qConventionFactor);
        peak->setIntHKL(hkl * m_qConventionFactor);
Lynch, Vickie's avatar
Lynch, Vickie committed
461
        peak->setRunNumber(RunNumber);
462
        peak->setIntMNP(V3D(m, n, p) * m_qConventionFactor);
463
        outPeaks->addPeak(*peak);
Lynch, Vickie's avatar
Lynch, Vickie committed
464
465
466
467
468
469
      }
}

V3D PredictSatellitePeaks::getOffsetVector(const std::string &label) {
  vector<double> offsets = getProperty(label);
  if (offsets.empty()) {
470
471
472
    offsets.emplace_back(0.0);
    offsets.emplace_back(0.0);
    offsets.emplace_back(0.0);
Lynch, Vickie's avatar
Lynch, Vickie committed
473
474
475
476
477
478
479
  }
  V3D offsets1 = V3D(offsets[0], offsets[1], offsets[2]);
  return offsets1;
}

} // namespace Crystal
} // namespace Mantid