/
GetAllEi.cpp
1292 lines (1169 loc) · 49.1 KB
/
GetAllEi.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
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
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/GetAllEi.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidGeometry/IComponent.h"
#include "MantidGeometry/Instrument.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/FilteredTimeSeriesProperty.h"
#include "MantidKernel/EnabledWhenProperty.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/Unit.h"
#include "MantidKernel/VectorHelper.h"
#include <boost/format.hpp>
#include <boost/algorithm/string.hpp>
#include <string>
namespace Mantid {
namespace Algorithms {
DECLARE_ALGORITHM(GetAllEi)
/// Empty default constructor
GetAllEi::GetAllEi()
: Algorithm(), m_FilterWithDerivative(true),
// minimal resolution for all instruments
m_min_Eresolution(0.08),
// half maximal resolution for LET
m_max_Eresolution(0.5e-3), m_peakEnergyRatio2reject(0.1), m_phase(0),
m_chopper(), m_pFilterLog(nullptr) {}
/// Initialization method.
void GetAllEi::init() {
declareProperty(
Kernel::make_unique<API::WorkspaceProperty<API::MatrixWorkspace>>(
"Workspace", "", Kernel::Direction::Input),
"The input workspace containing the monitor's spectra "
"measured after the last chopper");
auto nonNegative = boost::make_shared<Kernel::BoundedValidator<int>>();
nonNegative->setLower(0);
declareProperty(
"Monitor1SpecID", EMPTY_INT(), nonNegative,
"The workspace index (ID) of the spectra, containing first monitor's"
" signal to analyze.");
declareProperty(
"Monitor2SpecID", EMPTY_INT(), nonNegative,
"The workspace index (ID) of the spectra, containing second monitor's"
" signal to analyze.");
declareProperty("ChopperSpeedLog", "Defined in IDF",
"Name of the instrument log, "
"containing chopper angular velocity. If 'Defined in IDF' "
"option is specified, "
"the log name is obtained from the IDF");
declareProperty(
"ChopperDelayLog", "Defined in IDF",
"Name of the instrument log, "
"containing chopper delay time or chopper phase v.r.t. the pulse time. "
"If 'Defined in IDF' option is specified, "
"the log name is obtained from IDF");
declareProperty(
"FilterBaseLog", "Defined in IDF",
"Name of the instrument log, "
"with positive values indicating that instrument is running\n "
"and 0 or negative that it is not.\n"
"The log is used to identify time interval to evaluate"
" chopper speed and chopper delay which matter.\n"
"If such log is not present, average log values are calculated "
"within experiment start&end time range.");
declareProperty(
"FilterWithDerivative", true,
"Use derivative of 'FilterBaseLog' "
"rather then log values itself to filter invalid time intervals.\n"
"Invalid values are then the "
"values where the derivative of the log turns zero.\n"
"E.g. the 'proton_chage' log grows for each frame "
"when instrument is counting and is constant otherwise.");
setPropertySettings("FilterWithDerivative",
Kernel::make_unique<Kernel::EnabledWhenProperty>(
"FilterBaseLog",
Kernel::ePropertyCriterion::IS_EQUAL_TO,
"Defined in IDF"));
auto maxInRange = boost::make_shared<Kernel::BoundedValidator<double>>();
maxInRange->setLower(1.e-6);
maxInRange->setUpper(0.1);
declareProperty("MaxInstrResolution", 0.0005, maxInRange,
"The maximal energy resolution possible for an "
"instrument at working energies (full width at half "
"maximum). \nPeaks, sharper then "
"this width are rejected. Accepted limits are: 1e^(-6)-0.1");
auto minInRange = boost::make_shared<Kernel::BoundedValidator<double>>();
minInRange->setLower(0.001);
minInRange->setUpper(0.5);
declareProperty(
"MinInstrResolution", 0.08, minInRange,
"The minimal energy resolution possible for an "
"instrument at working energies (full width at half maximum).\n"
"Peaks broader then this width are rejected. Accepted limits are: "
"0.001-0.5");
auto peakInRange = boost::make_shared<Kernel::BoundedValidator<double>>();
peakInRange->setLower(0.0);
minInRange->setUpper(1.);
declareProperty(
"PeaksRatioToReject", 0.1, peakInRange,
"Ratio of a peak energy to the maximal energy among all peaks. "
"If the ratio is lower then the value specified here, "
"peak is treated as insignificant and rejected.\n"
"Accepted limits are:0.0 (All accepted) to 1 -- only one peak \n"
"(or peaks with max and equal intensity) are accepted.");
declareProperty(
"IgnoreSecondMonitor", false,
"Usually peaks are analyzed and accepted "
"only if identified on both monitors. If this property is set to true, "
"only first monitor peaks are analyzed.\n"
"This is debugging option as getEi has to use both monitors.");
declareProperty(
Kernel::make_unique<API::WorkspaceProperty<API::Workspace>>(
"OutputWorkspace", "", Kernel::Direction::Output),
"Name of the output matrix workspace, containing single spectra with"
" monitor peaks energies\n"
"together with total intensity within each peak.");
}
// unnamed namespace for auxiliary file-based compilation units
namespace {
/**Simple template function to remove invalid data from vector
*@param guessValid -- boolean vector of indicating if each particular guess is
*valid
*@param guess -- vector guess values at input and values with removing
* invalid parameters at output
*/
template <class T>
void removeInvalidValues(const std::vector<bool> &guessValid,
std::vector<T> &guess) {
std::vector<T> new_guess;
new_guess.reserve(guess.size());
for (size_t i = 0; i < guessValid.size(); i++) {
if (guessValid[i]) {
new_guess.push_back(guess[i]);
}
}
new_guess.swap(guess);
}
/**Internal class to contain peak information */
struct peakKeeper {
double position;
double height;
double sigma;
double energy;
peakKeeper(double pos, double heigh, double sig)
: position(pos), height(heigh), sigma(sig) {
this->energy = std::sqrt(2 * M_PI) * height * sigma;
}
// to sort peaks
bool operator<(const peakKeeper &str) const { return (energy > str.energy); }
};
} // END unnamed namespace for auxiliary file-based compilation units
/** Executes the algorithm -- found all existing monitor peaks. */
void GetAllEi::exec() {
// Get pointers to the workspace, parameter map and table
API::MatrixWorkspace_sptr inputWS = getProperty("Workspace");
m_min_Eresolution = getProperty("MinInstrResolution");
m_max_Eresolution = getProperty("MaxInstrResolution");
m_peakEnergyRatio2reject = getProperty("PeaksRatioToReject");
////---> recalculate chopper delay to monitor position:
auto pInstrument = inputWS->getInstrument();
// auto lastChopPositionComponent =
// pInstrument->getComponentByName("chopper-position");
// auto chopPoint1 = pInstrument->getChopperPoint(0); ->TODO: BUG! this
// operation loses parameters map.
m_chopper = pInstrument->getComponentByName("chopper-position");
if (!m_chopper)
throw std::runtime_error("Instrument " + pInstrument->getName() +
" does not have 'chopper-position' component");
auto phase = m_chopper->getNumberParameter("initial_phase");
if (phase.empty()) {
throw std::runtime_error("Can not find initial_phase parameter"
" attached to the chopper-position component");
}
if (phase.size() > 1) {
throw std::runtime_error(
"Can not deal with multiple phases for initial_phase"
" parameter attached to the chopper-position component");
}
m_phase = phase[0];
this->setFilterLog(inputWS);
// auto chopPoint1 = pInstrument->getComponentByName("fermi-chopper");
// auto par = chopPoint1->getDoubleParameter("Delay (us)");
double chopSpeed, chopDelay;
findChopSpeedAndDelay(inputWS, chopSpeed, chopDelay);
g_log.debug() << boost::str(
boost::format("*Identified avrg ChopSpeed: %8.2f and Delay: %8.2f\n") %
chopSpeed % chopDelay);
auto moderator = pInstrument->getSource();
double chopDistance = m_chopper->getDistance(
*moderator); // location[0].distance(moderator->getPos());
double velocity = chopDistance / chopDelay;
// build workspace to find monitor's peaks
size_t det1WSIndex;
auto monitorWS = buildWorkspaceToFit(inputWS, det1WSIndex);
// recalculate delay time from chopper position to monitor position
auto detector1 = inputWS->getDetector(det1WSIndex);
double mon1Distance = detector1->getDistance(*moderator);
double TOF0 = mon1Distance / velocity;
//--->> below is reserved until full chopper's implementation is available;
// auto nChoppers = pInstrument->getNumberOfChopperPoints();
// get last chopper.
/*
if( nChoppers==0)throw std::runtime_error("Instrument does not have any
choppers defined");
auto lastChopper = pInstrument->getChopperPoint(nChoppers-1);
///<---------------------------------------------------
*/
auto baseSpectrum = inputWS->getSpectrum(det1WSIndex);
std::pair<double, double> TOF_range = baseSpectrum->getXDataRange();
double Period =
(0.5 * 1.e+6) / chopSpeed; // 0.5 because some choppers open twice.
// Would be nice to have it 1 or 0.5 depending on chopper type, but
// it looks like not enough information on what chopper is available on ws;
double unused(0.0);
auto destUnit = Kernel::UnitFactory::Instance().create("Energy");
std::vector<double> guess_opening;
this->findGuessOpeningTimes(TOF_range, TOF0, Period, guess_opening);
if (guess_opening.empty()) {
throw std::runtime_error(
"Can not find any chopper opening time within TOF range: " +
boost::lexical_cast<std::string>(TOF_range.first) + ':' +
boost::lexical_cast<std::string>(TOF_range.second));
} else {
destUnit->initialize(mon1Distance, 0., 0.,
static_cast<int>(Kernel::DeltaEMode::Elastic), 0.,
unused);
printDebugModeInfo(guess_opening, TOF_range, destUnit);
}
std::pair<double, double> Mon1_Erange =
monitorWS->getSpectrum(0)->getXDataRange();
std::pair<double, double> Mon2_Erange =
monitorWS->getSpectrum(1)->getXDataRange();
double eMin = std::max(Mon1_Erange.first, Mon2_Erange.first);
double eMax = std::min(Mon1_Erange.second, Mon2_Erange.second);
g_log.debug() << boost::str(
boost::format(
"Monitors record data in energy range Emin=%8.2f; Emax=%8.2f\n") %
eMin % eMax);
// convert to energy
std::vector<double> guess_ei;
guess_ei.reserve(guess_opening.size());
destUnit->initialize(mon1Distance, 0., 0.,
static_cast<int>(Kernel::DeltaEMode::Elastic), 0.,
unused);
for (double time : guess_opening) {
double eGuess = destUnit->singleFromTOF(time);
if (eGuess > eMin && eGuess < eMax) {
guess_ei.push_back(eGuess);
}
}
g_log.debug() << "*From all chopper opening only: " +
boost::lexical_cast<std::string>(guess_ei.size()) +
" fell within both monitor's recording energy range\n";
g_log.debug() << " Guess Energies are:\n";
for (double ei : guess_ei) {
g_log.debug() << boost::str(boost::format(" %8.2f; ") % ei);
}
g_log.debug() << std::endl;
std::sort(guess_ei.begin(), guess_ei.end());
std::vector<size_t> irange_min, irange_max;
std::vector<bool> guessValid;
// preprocess first monitors peaks;
g_log.debug() << "*Looking for real energy peaks on first monitor\n";
findBinRanges(monitorWS->readX(0), monitorWS->readY(0), guess_ei,
this->m_min_Eresolution / (2. * std::sqrt(2. * M_LN2)),
irange_min, irange_max, guessValid);
// remove invalid guess values
removeInvalidValues<double>(guessValid, guess_ei);
// preprocess second monitors peaks
std::vector<size_t> irange1_min, irange1_max;
if (!this->getProperty("IgnoreSecondMonitor")) {
g_log.debug() << "*Looking for real energy peaks on second monitor\n";
findBinRanges(monitorWS->readX(1), monitorWS->readY(1), guess_ei,
this->m_min_Eresolution / (2. * std::sqrt(2. * M_LN2)),
irange1_min, irange1_max, guessValid);
removeInvalidValues<double>(guessValid, guess_ei);
removeInvalidValues<size_t>(guessValid, irange_min);
removeInvalidValues<size_t>(guessValid, irange_max);
} else {
// this is wrong but will not be used anyway
// (except formally looping through vector)
irange1_min.assign(irange_min.begin(), irange_min.end());
irange1_max.assign(irange_max.begin(), irange_max.end());
}
g_log.debug()
<< "*Identified: " + boost::lexical_cast<std::string>(guess_ei.size()) +
" peaks with sufficient signal around guess chopper opening\n";
std::vector<peakKeeper> peaks;
double maxPeakEnergy(0);
std::vector<size_t> monsRangeMin(2), monsRangeMax(2);
for (size_t i = 0; i < guess_ei.size(); i++) {
monsRangeMin[0] = irange_min[i];
monsRangeMax[0] = irange_max[i];
monsRangeMin[1] = irange1_min[i];
monsRangeMax[1] = irange1_max[i];
double energy, height, twoSigma;
bool found = findMonitorPeak(monitorWS, guess_ei[i], monsRangeMin,
monsRangeMax, energy, height, twoSigma);
if (found) {
peaks.push_back(peakKeeper(energy, height, 0.5 * twoSigma));
if (peaks.back().energy > maxPeakEnergy)
maxPeakEnergy = peaks.back().energy;
}
}
monitorWS.reset();
size_t nPeaks = peaks.size();
if (nPeaks == 0) {
throw std::runtime_error("Can not identify any energy peaks");
}
// sort peaks and remove invalid one
guessValid.resize(nPeaks);
bool needsRemoval(false);
for (size_t i = 0; i < nPeaks; i++) {
peaks[i].energy /= maxPeakEnergy;
if (peaks[i].energy < m_peakEnergyRatio2reject) {
guessValid[i] = false;
g_log.debug() << "*Rejecting peak at Ei=" +
boost::lexical_cast<std::string>(peaks[i].position) +
" as its total energy lower then the threshold\n";
needsRemoval = true;
} else {
guessValid[i] = true;
}
}
if (needsRemoval)
removeInvalidValues<peakKeeper>(guessValid, peaks);
nPeaks = peaks.size();
// sort by energy decreasing -- see class definition
std::sort(peaks.begin(), peaks.end());
// finalize output
auto result_ws = API::WorkspaceFactory::Instance().create("Workspace2D", 1,
nPeaks, nPeaks);
MantidVec peaks_positions;
MantidVec &Signal = result_ws->dataY(0);
MantidVec &Error = result_ws->dataE(0);
for (size_t i = 0; i < nPeaks; i++) {
peaks_positions.push_back(peaks[i].position);
Signal[i] = peaks[i].height;
Error[i] = peaks[i].sigma;
}
result_ws->setX(0, peaks_positions);
setProperty("OutputWorkspace", result_ws);
}
/**Auxiliary method to print guess chopper energies in debug mode
*
* @param guess_opening -- vector witgh chopper opening times values
* @param TOF_range -- pair describing time interval the instrument
* is recording the results
* @param destUnit -- pointer to initialized class, converting TOF
* to energy in elastic mode using instrument
* parameters.
*/
void GetAllEi::printDebugModeInfo(const std::vector<double> &guess_opening,
const std::pair<double, double> &TOF_range,
boost::shared_ptr<Kernel::Unit> &destUnit) {
g_log.debug() << "*Found : " << guess_opening.size()
<< " chopper prospective opening within time frame: "
<< TOF_range.first << " to: " << TOF_range.second << std::endl;
g_log.debug() << " Timings are:\n";
for (double time : guess_opening) {
g_log.debug() << boost::str(boost::format(" %8.2f; ") % time);
}
g_log.debug() << std::endl;
g_log.debug() << " Corresponding to energies:\n";
for (double time : guess_opening) {
double ei = destUnit->singleFromTOF(time);
g_log.debug() << boost::str(boost::format(" %8.2f; ") % ei);
}
g_log.debug() << std::endl;
}
// unnamed namespace for auxiliary file-based functions, converted from lambda
// as not all Mantid compilers support lambda yet.
/**The internal procedure to set filter log from properties,
defining it.
* @param inputWS -- shared pointer to the input workspace with
logs to analyze
*/
void GetAllEi::setFilterLog(const API::MatrixWorkspace_sptr &inputWS) {
std::string filerLogName;
std::string filterBase = getProperty("FilterBaseLog");
if (boost::iequals(filterBase, "Defined in IDF")) {
filerLogName = m_chopper->getStringParameter("FilterBaseLog")[0];
m_FilterWithDerivative =
m_chopper->getBoolParameter("filter_with_derivative")[0];
} else {
filerLogName = filterBase;
m_FilterWithDerivative = getProperty("FilterWithDerivative");
}
try {
m_pFilterLog = dynamic_cast<Kernel::TimeSeriesProperty<double> *>(
inputWS->run().getProperty(filerLogName));
} catch (std::runtime_error &) {
g_log.warning() << " Can not retrieve (double) filtering log: " +
filerLogName +
" from current workspace\n"
" Using total experiment range to "
"find logs averages for chopper parameters\n";
m_FilterWithDerivative = false;
}
}
/**Former lambda to identify guess values for a peak at given index
* and set up these parameters as input for fitting algorithm
*
*@param inputWS -- the workspace to process
*@param index -- the number of the workspace spectra to process
*@param Ei -- incident energy
*@param monsRangeMin -- vector of left boundaries for the subintervals to look
*for peak
*@param monsRangeMax -- vector of right boundaries for the subintervals to look
*for peak
*
*@param peakPos -- output energy of the peak
*@param peakHeight -- output height of the peak assuming Gaussian shape
*@param peakTwoSigma -- output width of the peak assuming Gaussian shape
*/
bool GetAllEi::peakGuess(const API::MatrixWorkspace_sptr &inputWS, size_t index,
double Ei, const std::vector<size_t> &monsRangeMin,
const std::vector<size_t> &monsRangeMax,
double &peakPos, double &peakHeight,
double &peakTwoSigma) {
// calculate sigma from half-width parameters
double maxSigma = Ei * m_min_Eresolution / (2. * std::sqrt(2. * M_LN2));
double sMin(std::numeric_limits<double>::max());
double sMax(-sMin);
double xOfMax(0), dXmax(0);
double Intensity(0);
auto X = inputWS->readX(index);
auto S = inputWS->readY(index);
size_t ind_min = monsRangeMin[index];
size_t ind_max = monsRangeMax[index];
// interval too small -- not interested in a peak there
if (std::fabs(double(ind_max - ind_min)) < 5)
return false;
// double xMin = X[ind_min];
// double xMax = X[ind_max];
// size_t ind_Ofmax(ind_min);
for (size_t i = ind_min; i < ind_max; i++) {
double dX = X[i + 1] - X[i];
double signal = S[i] / dX;
if (signal < sMin)
sMin = signal;
if (signal > sMax) {
sMax = signal;
dXmax = dX;
xOfMax = X[i];
// ind_Ofmax=i;
}
Intensity += S[i];
}
// monitor peak should not have just two counts in it.
if (sMax * dXmax <= 2)
return false;
//
// size_t SearchAreaSize = ind_max - ind_min;
double SmoothRange = 2 * maxSigma;
std::vector<double> SAvrg, binsAvrg;
Kernel::VectorHelper::smoothInRange(S, SAvrg, SmoothRange, &X, ind_min,
ind_max, &binsAvrg);
double realPeakPos(xOfMax); // this position is less shifted
// due to the skew in averaging formula
bool foundRealPeakPos(false);
std::vector<double> der1Avrg, der2Avrg, peaks, hillsPos, SAvrg1, binsAvrg1;
size_t nPeaks =
this->calcDerivativeAndCountZeros(binsAvrg, SAvrg, der1Avrg, peaks);
size_t nHills =
this->calcDerivativeAndCountZeros(binsAvrg, der1Avrg, der2Avrg, hillsPos);
size_t nPrevHills = 2 * nHills;
if (nPeaks == 1) {
foundRealPeakPos = true;
realPeakPos = peaks[0];
}
size_t ic(0), stay_still_count(0);
bool iterations_fail(false);
while ((nPeaks > 1 || nHills > 2) && (!iterations_fail)) {
Kernel::VectorHelper::smoothInRange(SAvrg, SAvrg1, SmoothRange, &binsAvrg,
0, ind_max - ind_min, &binsAvrg1);
nPrevHills = nHills;
nPeaks =
this->calcDerivativeAndCountZeros(binsAvrg1, SAvrg1, der1Avrg, peaks);
nHills = this->calcDerivativeAndCountZeros(binsAvrg1, der1Avrg, der2Avrg,
hillsPos);
SAvrg.swap(SAvrg1);
binsAvrg.swap(binsAvrg1);
if (nPeaks == 1 && !foundRealPeakPos) { // fix first peak position found
foundRealPeakPos = true; // as averaging shift peaks on
realPeakPos = peaks[0]; // irregular grid.
}
ic++;
if (nPrevHills <= nHills) {
stay_still_count++;
} else {
stay_still_count = 0;
}
if (ic > 50 || stay_still_count > 3)
iterations_fail = true;
}
if (iterations_fail) {
g_log.information() << "*No peak search convergence after " +
boost::lexical_cast<std::string>(ic) +
" smoothing iterations at still_count: " +
boost::lexical_cast<std::string>(
stay_still_count) +
" Wrong energy or noisy peak at Ei=" +
boost::lexical_cast<std::string>(Ei)
<< std::endl;
}
g_log.debug() << "*Performed: " + boost::lexical_cast<std::string>(ic) +
" averages for spectra " +
boost::lexical_cast<std::string>(index) +
" at energy: " + boost::lexical_cast<std::string>(Ei) +
"\n and found: " +
boost::lexical_cast<std::string>(nPeaks) + "peaks and " +
boost::lexical_cast<std::string>(nHills) + " hills\n";
if (nPeaks != 1) {
g_log.debug() << "*Peak rejected as n-peaks !=1 after averaging\n";
return false;
}
peakPos = peaks[0];
if (nHills > 2) {
size_t peakIndex = Kernel::VectorHelper::getBinIndex(hillsPos, peaks[0]);
peakTwoSigma = hillsPos[peakIndex + 1] - hillsPos[peakIndex];
} else {
if (hillsPos.size() == 2) {
peakTwoSigma = hillsPos[1] - hillsPos[0];
} else {
g_log.debug() << "*Peak rejected as averaging gives: " +
boost::lexical_cast<std::string>(nPeaks) +
" peaks and " +
boost::lexical_cast<std::string>(nHills) +
" heals\n";
return false;
}
}
// assuming that averaging conserves intensity and removing linear
// background:
peakHeight = Intensity / (0.5 * std::sqrt(2. * M_PI) * peakTwoSigma) - sMin;
peakPos = realPeakPos;
return true;
}
/**Get energy of monitor peak if one is present
*@param inputWS -- the workspace to process
*@param Ei -- incident energy
*@param monsRangeMin -- vector of indexes of left boundaries
* for the subintervals to look for peak
*@param monsRangeMax -- vector of indexes of right boundaries
* for the subintervals to look for peak
*
*@param position -- output energy of the peak center.
*@param height -- output height of the peak assuming Gaussian shape
*@param twoSigma -- output width of the peak assuming Gaussian shape
*/
bool GetAllEi::findMonitorPeak(const API::MatrixWorkspace_sptr &inputWS,
double Ei,
const std::vector<size_t> &monsRangeMin,
const std::vector<size_t> &monsRangeMax,
double &position, double &height,
double &twoSigma) {
// calculate sigma from half-width parameters
double maxSigma = Ei * m_min_Eresolution / (2. * std::sqrt(2. * M_LN2));
double minSigma = Ei * m_max_Eresolution / (2. * std::sqrt(2. * M_LN2));
//--------------------------------------------------------------------
double peak1Pos, peak1TwoSigma, peak1Height;
if (!peakGuess(inputWS, 0, Ei, monsRangeMin, monsRangeMax, peak1Pos,
peak1Height, peak1TwoSigma))
return false;
if (0.25 * peak1TwoSigma > maxSigma || peak1TwoSigma < minSigma) {
g_log.debug() << "*Rejecting due to width: Peak at mon1 Ei=" +
boost::lexical_cast<std::string>(peak1Pos) +
" with Height:" +
boost::lexical_cast<std::string>(peak1Height) +
" and 2*Sigma: " +
boost::lexical_cast<std::string>(peak1TwoSigma)
<< std::endl;
return false;
}
if (!this->getProperty("IgnoreSecondMonitor")) {
double peak2Pos, peak2TwoSigma, peak2Height;
if (!peakGuess(inputWS, 1, Ei, monsRangeMin, monsRangeMax, peak2Pos,
peak2Height, peak2TwoSigma))
return false;
// Let's not check anything except peak position for monitor2, as
// its intensity may be very low for some instruments.
// if(0.25*peak2TwoSigma>maxSigma||peak2TwoSigma<minSigma)return false;
// peak in first and second monitors are too far from each other. May be the
// instrument
// is ill-calibrated but GetEi will probably not find this peak anyway.
if (std::fabs(peak1Pos - peak2Pos) >
0.25 * (peak1TwoSigma + peak2TwoSigma)) {
g_log.debug()
<< "*Rejecting due to displacement between Peak at mon1: Ei=" +
boost::lexical_cast<std::string>(peak1Pos) + " with Height:" +
boost::lexical_cast<std::string>(peak1Height) +
" and 2*Sigma: " +
boost::lexical_cast<std::string>(peak1TwoSigma) +
"\n and Peak at mon2: Ei= " +
boost::lexical_cast<std::string>(peak2Pos) + "and height: " +
boost::lexical_cast<std::string>(peak1Height) << std::endl;
return false;
}
}
position = peak1Pos;
twoSigma = peak1TwoSigma;
height = peak1Height;
return true;
}
namespace { // for lambda extracted from calcDerivativeAndCountZeros
/**former lambda from calcDerivativeAndCountZeros
*estimating if sign have changed from its previous value
*@param val -- current function value
*@param prevSign -- the sign of the function at previous value
*/
bool signChanged(double val, int &prevSign) {
int curSign = (val >= 0 ? 1 : -1);
bool changed = curSign != prevSign;
prevSign = curSign;
return changed;
}
}
/**Bare-bone function to calculate numerical derivative, and estimate number of
* zeros this derivative has. The function is assumed to be defined on the
* the left of a bin range so the derivative is calculated in the same point.
* No checks are performed for simplicity so data have to be correct
* form at input.
*@param bins -- vector of bin boundaries.
*@param signal -- vector of signal size of bins.size()-1
*@param deriv -- output vector of numerical derivative
*@param zeros -- coordinates of found zeros
*@return -- number of zeros, the derivative has in the interval provided.
*/
size_t GetAllEi::calcDerivativeAndCountZeros(const std::vector<double> &bins,
const std::vector<double> &signal,
std::vector<double> &deriv,
std::vector<double> &zeros) {
size_t nPoints = signal.size();
deriv.resize(nPoints);
zeros.resize(0);
std::list<double> funVal;
double bin0 = bins[1] - bins[0];
double f0 = signal[0] / bin0;
double bin1 = bins[2] - bins[1];
double f1 = signal[1] / bin1;
size_t nZeros(0);
funVal.push_front(f1);
deriv[0] = 2 * (f1 - f0) / (bin0 + bin1);
int prevSign = (deriv[0] >= 0 ? 1 : -1);
for (size_t i = 1; i < nPoints - 1; i++) {
bin1 = (bins[i + 2] - bins[i + 1]);
f1 = signal[i + 1] / bin1;
deriv[i] = (f1 - f0) / (bins[i + 2] - bins[i]);
f0 = funVal.back();
funVal.pop_back();
funVal.push_front(f1);
if (signChanged(deriv[i], prevSign)) {
nZeros++;
zeros.push_back(0.5 * (bins[i - 1] + bins[i]));
}
}
deriv[nPoints - 1] = 2 * (f1 - f0) / (bin1 + bin0);
if (signChanged(deriv[nPoints - 1], prevSign)) {
zeros.push_back(bins[nPoints - 1]);
nZeros++;
}
return nZeros;
}
namespace { // for lambda extracted from findBinRanges
// get bin range corresponding to the energy range
void getBinRange(const MantidVec &eBins, double eMin, double eMax,
size_t &index_min, size_t &index_max) {
size_t nBins = eBins.size();
if (eMin <= eBins[0]) {
index_min = 0;
} else {
index_min = Kernel::VectorHelper::getBinIndex(eBins, eMin);
}
if (eMax >= eBins[nBins - 1]) {
index_max = nBins - 1;
} else {
index_max = Kernel::VectorHelper::getBinIndex(eBins, eMax) + 1;
if (index_max >= nBins)
index_max = nBins - 1; // last bin range anyway. Should not happen
}
}
// refine bin range. May need better procedure for this.
bool refineEGuess(const MantidVec &eBins, const MantidVec &signal,
double &eGuess, size_t index_min, size_t index_max) {
size_t ind_Emax = index_min;
double SMax(0);
for (size_t i = index_min; i < index_max; i++) {
double dX = eBins[i + 1] - eBins[i];
double sig = signal[i] / dX;
if (sig > SMax) {
SMax = sig;
ind_Emax = i;
}
}
if (ind_Emax == index_min || ind_Emax == index_max) {
return false;
}
eGuess = 0.5 * (eBins[ind_Emax] + eBins[ind_Emax + 1]);
return true;
}
struct peakKeeper2 {
double left_rng;
double right_rng;
peakKeeper2() : left_rng(.0), right_rng(.0){};
peakKeeper2(double left, double right) : left_rng(left), right_rng(right) {}
};
}
/**Find indexes of each expected peak intervals from monotonous array of ranges.
*@param eBins -- bin ranges to look through
*@param signal -- vector of signal in the bins
*@param guess_energy -- vector of guess energies to look for
*@param eResolution -- instrument resolution in energy units
*@param irangeMin -- start indexes of energy intervals in the guess_energies
* vector.
*@param irangeMax -- final indexes of energy intervals in the guess_energies
* vector.
*@param guessValid -- output boolean vector, which specifies if guess energies
* in guess_energy vector are valid or not
*/
void GetAllEi::findBinRanges(const MantidVec &eBins, const MantidVec &signal,
const std::vector<double> &guess_energy,
double eResolution, std::vector<size_t> &irangeMin,
std::vector<size_t> &irangeMax,
std::vector<bool> &guessValid) {
// size_t nBins = eBins.size();
guessValid.resize(guess_energy.size());
// Do the job
size_t ind_min, ind_max;
irangeMin.resize(0);
irangeMax.resize(0);
// identify guess bin ranges
std::vector<peakKeeper2> guess_peak(guess_energy.size());
for (size_t nGuess = 0; nGuess < guess_energy.size(); nGuess++) {
double eGuess = guess_energy[nGuess];
getBinRange(eBins, eGuess * (1 - 4 * eResolution),
eGuess * (1 + 4 * eResolution), ind_min, ind_max);
guess_peak[nGuess] = peakKeeper2(eBins[ind_min], eBins[ind_max]);
}
// verify that the ranges not intercept and refine interceptions
for (size_t i = 1; i < guess_energy.size(); i++) {
if (guess_peak[i - 1].right_rng > guess_peak[i].left_rng) {
double mid_pnt =
0.5 * (guess_peak[i - 1].right_rng + guess_peak[i].left_rng);
guess_peak[i - 1].right_rng = mid_pnt;
guess_peak[i].left_rng = mid_pnt;
}
}
// identify final bin ranges
for (size_t nGuess = 0; nGuess < guess_energy.size(); nGuess++) {
double eGuess = guess_energy[nGuess];
getBinRange(eBins, guess_peak[nGuess].left_rng,
guess_peak[nGuess].right_rng, ind_min, ind_max);
if (refineEGuess(eBins, signal, eGuess, ind_min, ind_max)) {
getBinRange(eBins, std::max(guess_peak[nGuess].left_rng,
eGuess * (1 - 3 * eResolution)),
std::max(guess_peak[nGuess].right_rng,
eGuess * (1 + 3 * eResolution)),
ind_min, ind_max);
irangeMin.push_back(ind_min);
irangeMax.push_back(ind_max);
guessValid[nGuess] = true;
} else {
guessValid[nGuess] = false;
g_log.debug() << "*Incorrect guess energy: "
<< boost::lexical_cast<std::string>(eGuess)
<< " no energy peak found in 4*Sigma range\n";
}
}
// if array decreasing rather then increasing, indexes behave differently.
// Will it still work?
if (!irangeMax.empty()) {
if (irangeMax[0] < irangeMin[0]) {
irangeMax.swap(irangeMin);
}
}
}
/**Build 2-spectra workspace in units of energy, used as source
*to identify actual monitors spectra
*@param inputWS shared pointer to initial workspace
*@param wsIndex0 -- returns workspace index for first detector.
*@return shared pointer to intermediate workspace, in units of energy
* used to fit monitor's spectra.
*/
API::MatrixWorkspace_sptr
GetAllEi::buildWorkspaceToFit(const API::MatrixWorkspace_sptr &inputWS,
size_t &wsIndex0) {
// at this stage all properties are validated so its safe to access them
// without
// additional checks.
specnum_t specNum1 = getProperty("Monitor1SpecID");
wsIndex0 = inputWS->getIndexFromSpectrumNumber(specNum1);
specnum_t specNum2 = getProperty("Monitor2SpecID");
size_t wsIndex1 = inputWS->getIndexFromSpectrumNumber(specNum2);
auto pSpectr1 = inputWS->getSpectrum(wsIndex0);
auto pSpectr2 = inputWS->getSpectrum(wsIndex1);
// assuming equally binned ws.
// auto bins = inputWS->dataX(wsIndex0);
auto bins = pSpectr1->dataX();
size_t XLength = bins.size();
size_t YLength = inputWS->dataY(wsIndex0).size();
auto working_ws =
API::WorkspaceFactory::Instance().create(inputWS, 2, XLength, YLength);
// copy data --> very bad as implicitly assigns pointer
// to bins array and bins array have to exist out of this routine
// scope.
// This does not matter in this case as below we convert units
// which should decouple cow_pointer but very scary operation in
// general.
working_ws->setX(0, bins);
working_ws->setX(1, bins);
MantidVec &Signal1 = working_ws->dataY(0);
MantidVec &Error1 = working_ws->dataE(0);
MantidVec &Signal2 = working_ws->dataY(1);
MantidVec &Error2 = working_ws->dataE(1);
for (size_t i = 0; i < YLength; i++) {
Signal1[i] = inputWS->dataY(wsIndex0)[i];
Error1[i] = inputWS->dataE(wsIndex0)[i];
Signal2[i] = inputWS->dataY(wsIndex1)[i];
Error2[i] = inputWS->dataE(wsIndex1)[i];
}
// copy detector mapping
API::ISpectrum *spectrum = working_ws->getSpectrum(0);
spectrum->setSpectrumNo(specNum1);
spectrum->clearDetectorIDs();
spectrum->addDetectorIDs(pSpectr1->getDetectorIDs());
spectrum = working_ws->getSpectrum(1);
spectrum->setSpectrumNo(specNum2);
spectrum->clearDetectorIDs();
spectrum->addDetectorIDs(pSpectr2->getDetectorIDs());
if (inputWS->getAxis(0)->unit()->caption() != "Energy") {
API::IAlgorithm_sptr conv = createChildAlgorithm("ConvertUnits");
conv->initialize();
conv->setProperty("InputWorkspace", working_ws);
conv->setProperty("OutputWorkspace", working_ws);
conv->setPropertyValue("Target", "Energy");
conv->setPropertyValue("EMode", "Elastic");
// conv->setProperty("AlignBins",true); --> throws due to bug in
// ConvertUnits
conv->execute();
}
return working_ws;
}
/**function calculates list of provisional chopper opening times.
*@param TOF_range -- std::pair containing min and max time, of signal
* measured on monitors
*@param ChopDelay -- the time of flight neutrons travel from source
* to the chopper opening.
*@param Period -- period of chopper openings
*@param guess_opening_times -- output vector with time values
* at which neutrons may pass through the chopper.
*/
void GetAllEi::findGuessOpeningTimes(const std::pair<double, double> &TOF_range,
double ChopDelay, double Period,
std::vector<double> &guess_opening_times) {
if (ChopDelay >= TOF_range.second) {
std::string chop = boost::str(boost::format("%.2g") % ChopDelay);
std::string t_min = boost::str(boost::format("%.2g") % TOF_range.first);
std::string t_max = boost::str(boost::format("%.2g") % TOF_range.second);
throw std::runtime_error("Logical error: Chopper opening time: " + chop +
" is outside of time interval: " + t_min + ":" +
t_max + " of the signal, measured on monitors.");
}
// number of times chopper with specified rotation period opens.
size_t n_openings =
static_cast<size_t>((TOF_range.second - ChopDelay) / Period) + 1;
// number of periods falling outside of the time period, measuring on monitor.
size_t n_start(0);
if (ChopDelay < TOF_range.first) {
n_start = static_cast<size_t>((TOF_range.first - ChopDelay) / Period) + 1;
n_openings -= n_start;
}
guess_opening_times.resize(n_openings);
for (size_t i = n_start; i < n_openings + n_start; i++) {
guess_opening_times[i - n_start] =
ChopDelay + static_cast<double>(i) * Period;
}
}
/**Finds pointer to log value for the property with the name provided
*
*@param inputWS -- workspace with logs attached
*@param propertyName -- name of the property to find log for
*
*@return -- pointer to property which contain the log requested or nullptr if
* no log found or other errors identified. */
Kernel::Property *
GetAllEi::getPLogForProperty(const API::MatrixWorkspace_sptr &inputWS,
const std::string &propertyName) {
std::string LogName = this->getProperty(propertyName);
if (boost::iequals(LogName, "Defined in IDF")) {
auto AllNames = m_chopper->getStringParameter(propertyName);
if (AllNames.size() != 1)
return nullptr;
LogName = AllNames[0];
}
auto pIProperty = (inputWS->run().getProperty(LogName));
return pIProperty;
}
/**Return average time series log value for the appropriately filtered log
* @param inputWS -- shared pointer to the input workspace containing