-
Notifications
You must be signed in to change notification settings - Fork 122
/
IntegratePeakTimeSlices.cpp
2515 lines (2071 loc) · 83.9 KB
/
IntegratePeakTimeSlices.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
// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
// NScD Oak Ridge National Laboratory, European Spallation Source,
// Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
/*
* IntegratePeakTimeSlices.cpp
*
* Created on: May 5, 2011
* Author: ruth
*
*
*
*/
#include "MantidCrystal/IntegratePeakTimeSlices.h"
#include "MantidAPI/ConstraintFactory.h"
#include "MantidAPI/FuncMinimizerFactory.h"
#include "MantidAPI/FunctionDomain1D.h"
#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/IFuncMinimizer.h"
#include "MantidAPI/IFunction.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidHistogramData/BinEdges.h"
#include <boost/math/special_functions/round.hpp>
#include <utility>
using namespace Mantid::Kernel;
using namespace Mantid::API;
using namespace Mantid::DataObjects;
using namespace Mantid::Geometry;
using namespace Mantid::HistogramData;
using namespace std;
namespace Mantid::Crystal {
DECLARE_ALGORITHM(IntegratePeakTimeSlices)
// Attr, m_AttributeValues, and StatBase indicies
#define IStartRow 0
#define IStartCol 1
#define INRows 2
#define INCol 3
#define ISSIxx 4
#define ISSIyy 5
#define ISSIxy 6
#define ISSxx 7
#define ISSyy 8
#define ISSxy 9
#define ISSIx 10
#define ISSIy 11
#define ISSx 12
#define ISSy 13
#define IIntensities 14
#define ISS1 15
#define IVariance 16
#define ITotBoundary 17
#define INBoundary 18
#define IVarBoundary 19
#define NAttributes 20
// Parameter indicies
#define IBACK 0
#define ITINTENS 1
#define IXMEAN 2
#define IYMEAN 3
#define IVXX 4
#define IVYY 5
#define IVXY 6
// TODO: Edge Peaks-Return NoPeak(Intensity=0,variance=0) if any center on any
// slice is out of bounds
// TODO: Calc ratio for edge peaks, should use the slant of bivariate normal
// instead of assuming
// distribution axes are lined up with the row and col vectors
#define NParameters 7
namespace {
// # std sigs 0 .25 .5 .75 1 1.25 1.5 2 2.5
const double probs[9] = {.5f, .5987f, .6915f, .7734f, .8413f, .8944f, .9322f, .9599f, .9772f};
const int MinRowColSpan = 6;
const int MaxRowColSpan = 36;
const int MinTimeSpan = 3;
const double NeighborhoodRadiusDivPeakRadius = 1.5;
const double MaxNeighborhoodRadius = 10;
const double NStdDevPeakSpan = 2;
const double MaxGoodRatioFitvsExpIntenisites = 2.5;
const double MinGoodRatioFitvsExpIntenisites = .25;
const double MinGoodIoverSigI = 3.0;
const double MinVariationInXYvalues = .6; // Peak spans one pixel only
const double MaxCorrCoeffinXY = .9; // otherwise all data on one line
} // namespace
IntegratePeakTimeSlices::IntegratePeakTimeSlices()
: Algorithm(), m_R0(-1), m_ROW(0.), m_COL(0.), m_cellWidth(0.), m_cellHeight(0.), m_NROWS(0), m_NCOLS(0) {
m_debug = false;
if (m_debug)
g_log.setLevel(7);
m_EdgePeak = false;
m_NeighborIDs = new int[3];
m_NeighborIDs[0] = 3;
m_NeighborIDs[1] = 2;
m_AttributeNames[0] = "StartRow";
m_AttributeNames[1] = "StartCol";
m_AttributeNames[2] = "NRows";
m_AttributeNames[3] = "NCols";
m_AttributeNames[4] = "SSIxx";
m_AttributeNames[5] = "SSIyy";
m_AttributeNames[6] = "SSIxy";
m_AttributeNames[7] = "SSxx";
m_AttributeNames[8] = "SSyy";
m_AttributeNames[9] = "SSxy";
m_AttributeNames[10] = "SSIx";
m_AttributeNames[11] = "SSIy";
m_AttributeNames[12] = "SSx";
m_AttributeNames[13] = "SSy";
m_AttributeNames[14] = "Intensities";
m_AttributeNames[15] = " SS1";
m_AttributeNames[16] = "Variance";
m_AttributeNames[17] = "TotBoundary";
m_AttributeNames[18] = "NBoundary";
m_AttributeNames[19] = "VarianceBoundary";
m_ParameterNames[0] = "Background";
m_ParameterNames[1] = "Intensity";
m_ParameterNames[2] = "Mcol";
m_ParameterNames[3] = "Mrow";
m_ParameterNames[4] = "SScol";
m_ParameterNames[5] = "SSrow";
m_ParameterNames[6] = "SSrc";
std::fill(m_ParameterValues.begin(), m_ParameterValues.end(), 0.0);
}
double SQRT(double v) {
if (v < 0)
return -1;
return sqrt(v);
}
/// Destructor
IntegratePeakTimeSlices::~IntegratePeakTimeSlices() { delete[] m_NeighborIDs; }
void IntegratePeakTimeSlices::init() {
declareProperty(std::make_unique<WorkspaceProperty<MatrixWorkspace>>("InputWorkspace", "", Direction::Input),
"A 2D workspace with X values of time of flight");
declareProperty(std::make_unique<WorkspaceProperty<TableWorkspace>>("OutputWorkspace", "", Direction::Output),
"Name of the output table workspace with Log info");
declareProperty(std::make_unique<WorkspaceProperty<PeaksWorkspace>>("Peaks", "", Direction::Input),
"Workspace of Peaks");
declareProperty("PeakIndex", 0, "Index of peak in PeaksWorkspace to integrate");
declareProperty("PeakQspan", .06, "Max magnitude of Q of Peak to Q of Peak Center, where mod(Q)=1/d");
declareProperty("CalculateVariances", true, "Calc (co)variances given parameter values versus fit (co)Variances ");
declareProperty("Ties", "", "Tie parameters(Background,Intensity, Mrow,...) to values/formulas.");
declareProperty("NBadEdgePixels", 0, "Number of bad Edge Pixels");
declareProperty("Intensity", 0.0, "Peak Integrated Intensity", Direction::Output);
declareProperty("SigmaIntensity", 0.0, "Peak Integrated Intensity Error", Direction::Output);
}
/**
* Executes this algorithm
*
* Integrates one peak
* -First attempts to find row/col extents, time extents to fully get most of
*the peak
* -Integrate each time slice.
* -Report Results
*/
void IntegratePeakTimeSlices::exec() {
time_t seconds1;
seconds1 = time(nullptr);
double dQ = getProperty("PeakQspan");
g_log.debug("------------------Start Peak Integrate-------------------");
if (dQ <= 0) {
g_log.error("Negative PeakQspans are not allowed. Use .17/G where G is the "
"max unit cell length");
throw std::runtime_error("Negative PeakQspans are not allowed in IntegratePeakTimeSlices");
}
MatrixWorkspace_const_sptr inpWkSpace = getProperty("InputWorkspace");
if (!inpWkSpace) {
g_log.error("Improper Input Workspace");
throw std::runtime_error("Improper Input Workspace in IntegratePeakTimeSlices");
}
PeaksWorkspace_sptr peaksW;
peaksW = getProperty("Peaks");
if (!peaksW) {
g_log.error("Improper Peaks Input");
throw std::runtime_error("Improper Peaks Input");
}
int indx = getProperty("PeakIndex");
Peak &peak = peaksW->getPeak(indx);
//------------------------------- Get Panel
//--------------------------------------
std::shared_ptr<const Geometry::IComponent> panel_const =
peak.getInstrument()->getComponentByName(peak.getBankName());
std::shared_ptr<Geometry::IComponent> panel = std::const_pointer_cast<Geometry::IComponent>(panel_const);
if (!panel || !panel_const) {
g_log.error("Cannot get panel for a peak");
throw std::runtime_error("Cannot get panel for a peak");
}
BoundingBox box;
panel->getBoundingBox(box);
int detID = peak.getDetectorID();
if (!box.isPointInside(peak.getDetPos())) {
g_log.error("Detector pixel is NOT inside the Peaks Bank");
throw std::runtime_error("Detector pixel is NOT inside the Peaks Bank");
}
FindPlane(m_center, m_xvec, m_yvec, m_ROW, m_COL, m_NROWS, m_NCOLS, m_cellWidth, m_cellHeight, peak);
g_log.debug() << " Peak Index " << indx << '\n';
double TotVariance = 0;
double TotIntensity = 0;
double lastRow = m_ROW;
double Row0 = lastRow;
double lastCol = m_COL;
double Col0 = lastCol;
string spec_idList;
// For quickly looking up workspace index from det id
m_wi_to_detid_map = inpWkSpace->getDetectorIDToWorkspaceIndexMap();
TableWorkspace_sptr TabWS = std::make_shared<TableWorkspace>(0);
//----------------------------- get Peak extents
//------------------------------
try {
// Find the workspace index for this detector ID
detid2index_map::const_iterator it = m_wi_to_detid_map.find(detID);
size_t wsIndx = (it->second);
double R = CalculatePositionSpan(peak, dQ) / 2;
R = min<double>(MaxRowColSpan * max<double>(m_cellWidth, m_cellHeight), R);
R = max<double>(MinRowColSpan * max<double>(m_cellWidth, m_cellHeight), R);
R = 2 * R; // Gets a few more background cells.
int Chan;
const auto &X = inpWkSpace->x(wsIndx);
int dChan = CalculateTimeChannelSpan(peak, dQ, X, int(wsIndx), Chan);
dChan = max<int>(dChan, MinTimeSpan);
double Centy = Row0;
double Centx = Col0;
IDetector_const_sptr CenterDet = peak.getDetector();
double neighborRadius; // last radius for finding neighbors
neighborRadius = min<double>(MaxNeighborhoodRadius, NeighborhoodRadiusDivPeakRadius * R);
auto Nneighbors = static_cast<int>(neighborRadius * neighborRadius / m_cellWidth / m_cellHeight * 4);
Nneighbors = min<int>(Nneighbors, static_cast<int>(inpWkSpace->getNumberHistograms()) - 2);
delete[] m_NeighborIDs;
m_NeighborIDs = new int[Nneighbors + 2];
m_NeighborIDs[0] = Nneighbors + 2;
m_NeighborIDs[1] = 2;
Kernel::V3D Cent = (m_center + m_xvec * (Centx - m_COL) + m_yvec * (Centy - m_ROW));
getNeighborPixIDs(panel, Cent, neighborRadius, m_NeighborIDs);
if (m_NeighborIDs[1] < 10) {
g_log.error("Not enough neighboring pixels to fit ");
throw std::runtime_error("Not enough neighboring pixels to fit ");
}
int NBadEdgeCells = getProperty("NBadEdgePixels");
int MaxChan = -1;
double MaxCounts = -1;
// --------------- Find Time Chan with max counts----------------
for (int dir = 1; dir > -2; dir -= 2) {
bool done = false;
for (int t = 0; t < dChan && !done; t++)
if (dir < 0 && t == 0) {
Centy = Row0;
Centx = Col0;
} else if (Chan + dir * t < 0 || Chan + dir * t >= static_cast<int>(X.size()))
done = true;
else {
int NN = m_NeighborIDs[1];
MatrixWorkspace_sptr Data = WorkspaceFactory::Instance().create(std::string("Workspace2D"), 3, NN, NN);
auto XXX = std::make_shared<DataModeHandler>(R, R, Centy, Centx, m_cellWidth, m_cellHeight,
getProperty("CalculateVariances"), NBadEdgeCells,
m_NCOLS - NBadEdgeCells, NBadEdgeCells, m_NROWS - NBadEdgeCells);
m_AttributeValues = XXX;
XXX->setCurrentRadius(R);
SetUpData1(Data, inpWkSpace, Chan + dir * t, Chan + dir * t, R, CenterDet->getPos(), spec_idList);
if (m_AttributeValues->StatBaseVals(ISSIxx) > 0) {
if (m_AttributeValues->StatBaseVals(IIntensities) > MaxCounts) {
MaxCounts = m_AttributeValues->StatBaseVals(IIntensities);
MaxChan = Chan + dir * t;
}
if (m_AttributeValues->StatBaseVals(IIntensities) > 0) {
Centx = m_AttributeValues->StatBaseVals(ISSIx) / m_AttributeValues->StatBaseVals(IIntensities);
Centy = m_AttributeValues->StatBaseVals(ISSIy) / m_AttributeValues->StatBaseVals(IIntensities);
} else
done = true;
} else
done = true;
if (t >= 3 && (m_AttributeValues->StatBaseVals(IIntensities) < MaxCounts / 2.0) && MaxCounts >= 0)
done = true;
}
}
if (MaxChan > 0)
Chan = MaxChan;
g_log.debug() << " largest Channel,Radius,m_cellWidth,m_cellHeight = " << Chan << " " << R << " " << m_cellWidth
<< " " << m_cellHeight << '\n';
if (R < MinRowColSpan / 2 * max<double>(m_cellWidth, m_cellHeight) || dChan < MinTimeSpan) {
g_log.error("Not enough rows and cols or time channels ");
throw std::runtime_error("Not enough rows and cols or time channels ");
}
InitializeColumnNamesInTableWorkspace(TabWS);
//------------------------------------- Start the Integrating
//-------------------------------
double time;
int ncells;
Mantid::API::Progress prog(this, 0.0, 1.0, dChan);
// Set from attributes replace by m_R0
m_R0 = -1;
int LastTableRow = -1;
auto origAttributeList = std::make_shared<DataModeHandler>();
auto lastAttributeList = std::make_shared<DataModeHandler>();
for (int dir = 1; dir >= -1; dir -= 2) {
bool done = false;
for (int chan = 0; chan < dChan && !done; chan++)
if (dir < 0 && chan == 0) {
lastRow = Row0;
lastCol = Col0;
lastAttributeList = origAttributeList;
if (TabWS->rowCount() > 0)
LastTableRow = 0;
} else if (Chan + dir * chan < 0 || Chan + dir * chan >= static_cast<int>(X.size()))
done = true;
else {
int xchan = Chan + dir * chan;
size_t topIndex = xchan + 1;
if (topIndex >= X.size())
topIndex = X.size() - 1;
time = (X[xchan] + X[topIndex]) / 2.0;
double Radius = R;
if (m_R0 > 0)
Radius = m_R0;
MatrixWorkspace_sptr Data =
WorkspaceFactory::Instance().create(std::string("Workspace2D"), 3, m_NeighborIDs[1], m_NeighborIDs[1]);
g_log.debug() << " A:chan=" << xchan << " time=" << time << " Radius=" << Radius << "row= " << lastRow
<< " col=" << lastCol << '\n';
SetUpData(Data, inpWkSpace, panel, xchan, xchan, lastCol, lastRow, Cent, neighborRadius, Radius, spec_idList);
m_AttributeValues->setTime(time);
// if( dir==1 && chan ==0)
// origAttributeList= m_AttributeValues;
ncells = static_cast<int>(m_AttributeValues->StatBaseVals(ISS1));
std::vector<double> params;
std::vector<double> errs;
std::vector<std::string> names;
if (m_AttributeValues->StatBaseVals(ISSIxx) > 0 &&
m_AttributeValues->IsEnoughData(m_ParameterValues.data(), g_log) && m_ParameterValues[ITINTENS] > 0) {
double chisqOverDOF;
Fit(Data, chisqOverDOF, done, names, params, errs, lastRow, lastCol, neighborRadius);
if (!done) // Bivariate error happened
{
if (isGoodFit(params, errs, names, chisqOverDOF)) {
LastTableRow = UpdateOutputWS(TabWS, dir, xchan, params, errs, names, chisqOverDOF,
m_AttributeValues->time, spec_idList);
double TotSliceIntensity = m_AttributeValues->StatBaseVals(IIntensities);
double TotSliceVariance = m_AttributeValues->StatBaseVals(IVariance);
updatePeakInformation(params, errs, names, TotVariance, TotIntensity, TotSliceIntensity,
TotSliceVariance, chisqOverDOF, ncells);
lastAttributeList = m_AttributeValues;
if (dir == 1 && chan == 0)
origAttributeList = lastAttributeList;
} else
done = true;
}
} else //(!IsEnoughData() || ParameterValues[ITINTENS] <= 0
{
done = true;
}
if (done) // try to merge
{
done = false;
int chanMin, chanMax;
if ((dir == 1 && chan == 0) || lastAttributeList->CellHeight <= 0) {
chanMin = xchan;
chanMax = xchan + 1;
if (dir < 0)
chanMax++;
auto XXX = std::make_shared<DataModeHandler>(*m_AttributeValues);
m_AttributeValues = XXX;
if (!X.empty())
m_AttributeValues->setTime((X[chanMax] + X[chanMin]) / 2.0);
} else // lastAttributeList exists
{
chanMin = std::min<int>(xchan, xchan - dir);
chanMax = chanMin + 1;
if (lastAttributeList->case4)
chanMax++;
auto XXX = std::make_shared<DataModeHandler>(*lastAttributeList);
m_AttributeValues = XXX;
m_AttributeValues->setTime((time + m_AttributeValues->time) / 2.0);
}
if (updateNeighbors(panel, m_AttributeValues->getCurrentCenter(), Cent,
m_AttributeValues->getCurrentRadius(), neighborRadius))
Cent = m_AttributeValues->getCurrentCenter();
Data =
WorkspaceFactory::Instance().create(std::string("Workspace2D"), 3, m_NeighborIDs[1], m_NeighborIDs[1]);
SetUpData1(Data, inpWkSpace, chanMin, chanMax, m_AttributeValues->getCurrentRadius(),
m_AttributeValues->getCurrentCenter(), spec_idList);
double chisqOverDOF;
g_log.debug("Try Merge 2 time slices");
if (m_AttributeValues->StatBaseVals(ISSIxx) >= 0 &&
m_AttributeValues->IsEnoughData(m_ParameterValues.data(), g_log))
Fit(Data, chisqOverDOF, done, names, params, errs, lastRow, lastCol, neighborRadius);
else
chisqOverDOF = -1;
if (!done && isGoodFit(params, errs, names, chisqOverDOF)) {
if (LastTableRow >= 0 && LastTableRow < static_cast<int>(TabWS->rowCount()))
TabWS->removeRow(LastTableRow);
else
LastTableRow = -1;
LastTableRow = UpdateOutputWS(TabWS, dir, (chanMin + chanMax) / 2.0, params, errs, names, chisqOverDOF,
m_AttributeValues->time, spec_idList);
if (lastAttributeList->lastISAWVariance > 0 && lastAttributeList->CellHeight > 0) {
TotIntensity -= lastAttributeList->lastISAWIntensity;
TotVariance -= lastAttributeList->lastISAWVariance;
}
double TotSliceIntensity = m_AttributeValues->StatBaseVals(IIntensities);
double TotSliceVariance = m_AttributeValues->StatBaseVals(IVariance);
updatePeakInformation(params, errs, names, TotVariance, TotIntensity, TotSliceIntensity, TotSliceVariance,
chisqOverDOF, static_cast<int>(m_AttributeValues->StatBaseVals(ISS1)));
// lastAttributeList= m_AttributeValues;
if (dir == 1 && (chan == 0 || chan == 1)) {
m_AttributeValues->case4 = true;
origAttributeList = m_AttributeValues;
} else
LastTableRow = -1;
} else {
auto XXX = std::make_shared<DataModeHandler>();
lastAttributeList = XXX;
}
done = true;
}
// Get ready for the next round
Data.reset();
if (!done) {
// Now set up the center for this peak
int i = findNameInVector("Mrow", names);
if (i < 0) {
throw std::runtime_error("Inconsistency found in algorithm "
"execution. The index for the parameter "
"Mrow is negative.");
}
lastRow = boost::math::iround(params[i]);
i = findNameInVector("Mcol", names);
if (i >= 0)
lastCol = boost::math::iround(params[i]);
prog.report();
} else if (dir > 0)
prog.report(dChan / 2);
else
prog.report(dChan);
params.clear();
errs.clear();
names.clear();
}
}
} catch (std::exception &EE1) {
std::cout << "Error in main reason=" << EE1.what() << '\n';
throw std::runtime_error(" Error IntegratePeakTimeSlices:" + std::string(EE1.what()));
} catch (std::string &mess) {
throw std::runtime_error("Error IntegratePeakTimeSlices:" + mess);
} catch (...) {
throw std::runtime_error("Error IntegratePeakTimeSlices:");
}
try {
setProperty("OutputWorkspace", TabWS);
setProperty("Intensity", TotIntensity);
setProperty("SigmaIntensity", SQRT(TotVariance));
time_t seconds2;
seconds2 = time(nullptr);
double dif = difftime(seconds2, seconds1);
g_log.debug() << "Finished Integr peak number " << indx << " in " << dif << " seconds\n";
} catch (std::exception &ss) {
std::cout << "Error occurred XX " << ss.what() << '\n';
throw std::runtime_error(ss.what());
}
}
/**
* Finds all neighbors within a given Radius of the Center on the given
* component.
* @param comp -The component of interest
* @param Center- the center of the neighbors
* @param Radius - The radius from the center of neighbors to be included
* @param ArryofID -The detector ID's of the neighbors. The id of the pixel at
* the center may be included.
*/
bool IntegratePeakTimeSlices::getNeighborPixIDs(const std::shared_ptr<Geometry::IComponent> &comp,
const Kernel::V3D &Center, double &Radius, int *&ArryofID) {
int N = ArryofID[1];
int MaxN = ArryofID[0];
if (N >= MaxN)
return false;
Geometry::BoundingBox box;
comp->getBoundingBox(box);
double minx = Center.X() - Radius;
double miny = Center.Y() - Radius;
double minz = Center.Z() - Radius;
double maxx = Center.X() + Radius;
double maxy = Center.Y() + Radius;
double maxz = Center.Z() + Radius;
if (box.xMin() >= maxx)
return true;
if (box.xMax() <= minx)
return true;
;
if (box.yMin() >= maxy)
return true;
if (box.yMax() <= miny)
return true;
if (box.zMin() >= maxz)
return true;
if (box.zMax() <= minz)
return true;
;
auto det = std::dynamic_pointer_cast<Geometry::Detector>(comp);
if (det) {
V3D pos = det->getPos() - Center;
if (pos.X() * pos.X() + pos.Y() * pos.Y() + pos.Z() * pos.Z() < Radius * Radius) {
ArryofID[N] = det->getID();
N++;
ArryofID[1] = N;
}
return true;
}
auto Assembly = std::dynamic_pointer_cast<const Geometry::ICompAssembly>(comp);
if (!Assembly)
return true;
bool b = true;
for (int i = 0; i < Assembly->nelements() && b; i++)
b = getNeighborPixIDs(Assembly->getChild(i), Center, Radius, ArryofID);
return b;
}
/**
* Checks and updates if needed the list of m_NeighborIDs
* @param comp Component with the neighboring pixels
* @param CentPos new Center
* @param oldCenter old Center
* @param NewRadius new Radius
* @param neighborRadius old the new neighborhood radius
*/
bool IntegratePeakTimeSlices::updateNeighbors(const std::shared_ptr<Geometry::IComponent> &comp, const V3D &CentPos,
const V3D &oldCenter, double NewRadius, double &neighborRadius) {
double DD = (CentPos - oldCenter).norm();
bool changed = false;
if (DD + NewRadius > neighborRadius) {
auto NN = int(NStdDevPeakSpan * NeighborhoodRadiusDivPeakRadius * NewRadius / m_cellWidth * NStdDevPeakSpan *
NeighborhoodRadiusDivPeakRadius * NewRadius / m_cellHeight);
if (m_NeighborIDs[0] < NN) {
delete[] m_NeighborIDs;
m_NeighborIDs = new int[NN + 2];
m_NeighborIDs[0] = NN + 2;
}
m_NeighborIDs[1] = 2;
neighborRadius = NeighborhoodRadiusDivPeakRadius * NewRadius;
getNeighborPixIDs(comp, CentPos, neighborRadius, m_NeighborIDs);
changed = true;
} else // big enough neighborhood so
neighborRadius -= DD;
return changed;
}
/**
* Calculates the span in rows and columns needed to include all data within dQ
*of the
* specified peak
* @param peak The peak of interest
* @param dQ The offset from the peak's Q value for the data of interest
*
* NOTE: differentials of Q =mv*sin(scatAng/2)/2 were used to calculate this
* Also s=r*theta was used to transfer d ScatAng to distance on a bank.
*/
double IntegratePeakTimeSlices::CalculatePositionSpan(Peak const &peak, const double dQ) {
try {
double Q = 0, ScatAngle = 0, dScatAngle = 0, DetSpan = 0;
Q = peak.getQLabFrame().norm();
Geometry::Instrument_const_sptr instr = peak.getInstrument();
const Geometry::IComponent_const_sptr sample = instr->getSample();
V3D pos = peak.getDetPos() - sample->getPos();
ScatAngle = acos(pos.Z() / pos.norm());
dScatAngle = 2 * dQ / Q * tan(ScatAngle / 2);
DetSpan = pos.norm() * dScatAngle; // s=r*theta
DetSpan = fabs(DetSpan);
// IDetector_sptr det = peak.getDetector();
return DetSpan;
} catch (std::exception &s) {
std::cout << "err in getNRowsCols, reason=" << s.what() << '\n';
return 0;
}
}
/**
* Calculates the span of channels needed to encompass all data around the peak
*with Q values within dQ
* of this peak's Q value
*
* @param peak The peak of interest
* @param dQ The offset of peak's Q value whose data is considered part of
*the peak
* @param X The list of time channel values.
* @param specNum The spectral number for the pixel(Not Currently Used)
* @param Centerchan The center time channel number( from X)
*
* @return The number of time channels around Centerchan to use
*/
int IntegratePeakTimeSlices::CalculateTimeChannelSpan(Geometry::IPeak const &peak, const double dQ, const HistogramX &X,
const int specNum, int &Centerchan) {
UNUSED_ARG(specNum);
double Q = peak.getQLabFrame().norm(); // getQ( peak)/2/M_PI;
double time = peak.getTOF();
double dtime = dQ / Q * time;
int chanCenter = findTimeChannel(X, time);
Centerchan = chanCenter;
int chanLeft = findTimeChannel(X, time - dtime);
int chanRight = findTimeChannel(X, time + dtime);
int dchan = abs(chanCenter - chanLeft);
if (abs(chanRight - chanCenter) > dchan)
dchan = abs(chanRight - chanCenter);
dchan = max<int>(3, dchan);
return dchan + 5; // heuristic should be a lot more
}
/**
* For NonFlat banks, this determines the data of a small planar region
*approximating the instrument
* close to the peak
*
* @param center The position of the center of this plane
* @param xvec The direction the column values increase
* @param yvec The direction the row values increase
* @param ROW The row for this peak( 0 if undefined)
* @param COL The col for this peak( 0 if undefined)
* @param NROWS The number? of rows for this bANK
* @param NCOLS The number of columns for this bank
* @param pixWidthx The width of a pixel
* @param pixHeighty The height of a pixel
* @param peak
*/
void IntegratePeakTimeSlices::FindPlane(V3D ¢er, V3D &xvec, V3D &yvec, double &ROW, double &COL, int &NROWS,
int &NCOLS, double &pixWidthx, double &pixHeighty,
DataObjects::Peak const &peak) const {
NROWS = NCOLS = -1;
IDetector_const_sptr det = peak.getDetector();
V3D detPos = det->getPos();
center.setX(detPos.X());
center.setY(detPos.Y());
center.setZ(detPos.Z());
std::shared_ptr<const Detector> dett = std::dynamic_pointer_cast<const Detector>(det);
pixWidthx = dett->getWidth();
pixHeighty = dett->getHeight();
Kernel::Quat Qt = dett->getRotation();
V3D yaxis0(0.0, 1.0, 0.0);
Qt.rotate(yaxis0);
yaxis0.normalize();
V3D xaxis0(1, 0, 0);
Qt.rotate(xaxis0);
xaxis0.normalize();
xvec.setX(xaxis0.X());
xvec.setY(xaxis0.Y());
xvec.setZ(xaxis0.Z());
yvec.setX(yaxis0.X());
yvec.setY(yaxis0.Y());
yvec.setZ(yaxis0.Z());
ROW = peak.getRow();
COL = peak.getCol();
Geometry::Instrument_const_sptr inst = peak.getInstrument();
if (!inst)
throw std::invalid_argument("No instrument for peak");
std::shared_ptr<const IComponent> panel = inst->getComponentByName(peak.getBankName());
std::shared_ptr<const RectangularDetector> ddet = std::dynamic_pointer_cast<const RectangularDetector>(panel);
if (ddet) {
std::pair<int, int> CR = ddet->getXYForDetectorID(det->getID());
ROW = CR.second;
COL = CR.first;
pixWidthx = ddet->xstep();
pixHeighty = ddet->ystep();
NROWS = ddet->ypixels();
NCOLS = ddet->xpixels();
return;
}
// Get NROWS and NCOLS for other panels
NROWS = NCOLS = -1;
if (!inst)
return;
if (!panel)
return;
std::shared_ptr<const Component> compPanel = std::dynamic_pointer_cast<const Component>(panel);
std::shared_ptr<IComponent> panel1(compPanel->base()->clone());
BoundingBox B;
Quat rot = panel1->getRotation();
rot.inverse();
panel1->rotate(rot);
panel1->getBoundingBox(B);
NROWS = boost::math::iround((B.yMax() - B.yMin()) / pixHeighty);
NCOLS = boost::math::iround((B.xMax() - B.xMin()) / pixWidthx);
}
/**
* Updates the cumulative statistics for the data being considered
*
* @param intensity -The experimental intensity at the given pixel
* @param variance -The square of the errors in the above intensity
* @param row -The row of the given pixel
* @param col -The column of the given pixel
* @param StatBase -The data accumulator
*/
void IntegratePeakTimeSlices::updateStats(const double intensity, const double variance, const double row,
const double col, std::vector<double> &StatBase) {
StatBase[ISSIxx] += col * col * intensity;
StatBase[ISSIyy] += intensity * row * row;
StatBase[ISSIxy] += intensity * row * col;
StatBase[ISSxx] += col * col;
StatBase[ISSyy] += row * row;
StatBase[ISSxy] += row * col;
StatBase[ISSIx] += intensity * col;
StatBase[ISSIy] += intensity * row;
StatBase[ISSx] += col;
StatBase[ISSy] += row;
StatBase[IIntensities] += intensity;
StatBase[IVariance] += variance;
StatBase[ISS1] += 1;
}
/**
* Finds and saves the initial values and modes( like isEdge) for this data.
*
* @param Varx The Variance of the x(column) values
* @param Vary The Variance of the y(row) values
* @param b The background
*
* NOTE:Used only in GetParams which is used only in PreFit which is not
* currently used.
*/
std::vector<double> DataModeHandler::InitValues(double Varx, double Vary, double b) {
std::vector<double> Res(7);
Res[IVXX] = Varx;
Res[IVYY] = Vary;
Res[IVXY] = 0;
auto nCells = static_cast<int>(StatBase[ISS1]);
double Den = StatBase[IIntensities] - b * nCells;
Res[IXMEAN] = (StatBase[ISSIx] - b * StatBase[ISSx]) / Den;
Res[IYMEAN] = (StatBase[ISSIy] - b * StatBase[ISSy]) / Den;
Res[IBACK] = b;
Res[ITINTENS] = StatBase[IIntensities] - b * nCells;
//---- Is Edge Cell ???-------
double NstdX = 4 * (currentRadius / CellWidth - EdgeX) / sqrt(Varx);
double NstdY = 4 * (currentRadius / CellHeight - EdgeY) / sqrt(Vary);
double sigx = 1;
double sigy = 1;
if (NstdX < 0)
sigx = -1;
if (NstdY < 0)
sigy = -1;
double x = 1;
if (sigy * NstdY < 7 && sigy * NstdY >= 0) // is close to row edge
{
x = probs[std::lround(sigy * NstdY)];
if (sigy < 0)
x = 1 - x;
double My2 = StatBase[IStartRow];
if (Res[IYMEAN] - My2 > My2 + StatBase[INRows] - Res[IYMEAN])
My2 += StatBase[INRows];
Res[IYMEAN] = Res[IYMEAN] * x + (1 - x) * My2;
}
double x1 = 1;
if (sigx * NstdX < 7 && sigx * NstdX > 0) // is close to x edge
{
x1 = probs[std::lround(sigx * NstdX)];
if (sigx < 0)
x1 = 1 - x1;
double Mx2 = StatBase[IStartCol];
if (Res[IXMEAN] - Mx2 > Mx2 + StatBase[INCol] - Res[IXMEAN])
Mx2 += StatBase[INCol];
Res[IXMEAN] = Res[IXMEAN] * x1 + (1 - x1) * Mx2;
}
Res[ITINTENS] /= x * x1;
return Res;
}
/**
* Calculates the initial values of the parameters given background b.
* Used only in the PreFit method that is not used.
* @param b the background
*
* @return The vector of parameter values.
*/
std::vector<double> DataModeHandler::GetParams(double b) {
auto nCells = static_cast<int>(StatBase[ISS1]);
double Den = StatBase[IIntensities] - b * nCells;
double Varx, Vary;
Varx = VarxHW;
Vary = VaryHW;
double Rx = lastRCRadius / CellWidth - EdgeX;
double Ry = lastRCRadius / CellHeight - EdgeY;
if (Varx <= 0)
Varx = HalfWidthAtHalfHeightRadius * HalfWidthAtHalfHeightRadius;
if (Vary <= 0)
Vary = HalfWidthAtHalfHeightRadius * HalfWidthAtHalfHeightRadius;
// Use
if (Rx * Rx < 4 * Varx || Ry * Ry < 4 * Vary) {
return InitValues(Varx, Vary, b);
}
if (Den < 0)
return std::vector<double>();
double Mx = StatBase[ISSIx] - b * StatBase[ISSx];
double My = StatBase[ISSIy] - b * StatBase[ISSy];
double Sxx = (StatBase[ISSIxx] - b * StatBase[ISSxx] - Mx * Mx / Den) / Den;
double Syy = (StatBase[ISSIyy] - b * StatBase[ISSyy] - My * My / Den) / Den;
double Sxy = (StatBase[ISSIxy] - b * StatBase[ISSxy] - Mx * My / Den) / Den;
double Intensity = StatBase[IIntensities] - b * nCells;
double col = Mx / Den;
double row = My / Den;
std::vector<double> Result(7);
Result[IBACK] = b;
Result[ITINTENS] = Intensity;
Result[IXMEAN] = col;
Result[IYMEAN] = row;
Result[IVXX] = Sxx;
Result[IVYY] = Syy;
Result[IVXY] = Sxy;
return Result;
}