-
Notifications
You must be signed in to change notification settings - Fork 122
/
LoadISISNexus2.cpp
1297 lines (1157 loc) · 50 KB
/
LoadISISNexus2.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 "MantidDataHandling/LoadISISNexus2.h"
#include "MantidDataHandling/LoadEventNexus.h"
#include "MantidDataHandling/LoadRawHelper.h"
#include "MantidDataHandling/DataBlockGenerator.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/RegisterFileLoader.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/Detector.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/ListValidator.h"
//#include "MantidKernel/LogParser.h"
#include "MantidKernel/LogFilter.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/UnitFactory.h"
#include <boost/lexical_cast.hpp>
#include <nexus/NeXusFile.hpp>
#include <nexus/NeXusException.hpp>
#include <Poco/Path.h>
#include <Poco/DateTimeFormatter.h>
#include <Poco/DateTimeParser.h>
#include <Poco/DateTimeFormat.h>
#include <algorithm>
#include <cmath>
#include <cctype>
#include <climits>
#include <functional>
#include <sstream>
#include <vector>
namespace {
Mantid::DataHandling::DataBlockComposite
getMonitorsFromComposite(Mantid::DataHandling::DataBlockComposite &composite,
Mantid::DataHandling::DataBlockComposite &monitors) {
auto dataBlocks = composite.getDataBlocks();
auto monitorBlocks = monitors.getDataBlocks();
auto matchesMonitorBlock =
[&monitorBlocks](Mantid::DataHandling::DataBlock &dataBlock) {
return std::find(std::begin(monitorBlocks), std::end(monitorBlocks),
dataBlock) != std::end(monitorBlocks);
};
Mantid::DataHandling::DataBlockComposite newComposite;
for (auto &dataBlock : dataBlocks) {
if (matchesMonitorBlock(dataBlock)) {
newComposite.addDataBlock(dataBlock);
}
}
return newComposite;
}
}
namespace Mantid {
namespace DataHandling {
DECLARE_NEXUS_FILELOADER_ALGORITHM(LoadISISNexus2)
using namespace Kernel;
using namespace API;
using namespace NeXus;
using namespace HistogramData;
using std::size_t;
/// Empty default constructor
LoadISISNexus2::LoadISISNexus2()
: m_filename(), m_instrument_name(), m_samplename(), m_detBlockInfo(),
m_monBlockInfo(), m_loadBlockInfo(), m_have_detector(false),
m_load_selected_spectra(false), m_wsInd2specNum_map(), m_spec2det_map(),
m_entrynumber(0), m_tof_data(), m_proton_charge(0.), m_spec(),
m_spec_end(nullptr), m_monitors(), m_logCreator(), m_progress(),
m_cppFile() {}
/**
* Return the confidence criteria for this algorithm can load the file
* @param descriptor A descriptor for the file
* @returns An integer specifying the confidence level. 0 indicates it will not
* be used
*/
int LoadISISNexus2::confidence(Kernel::NexusDescriptor &descriptor) const {
if (descriptor.pathOfTypeExists("/raw_data_1", "NXentry")) {
// It also could be an Event Nexus file or a TOFRaw file,
// so confidence is set to less than 80.
return 75;
}
return 0;
}
/// Initialization method.
void LoadISISNexus2::init() {
const std::vector<std::string> exts{".nxs", ".n*"};
declareProperty(Kernel::make_unique<FileProperty>("Filename", "",
FileProperty::Load, exts),
"The name of the Nexus file to load");
declareProperty(make_unique<WorkspaceProperty<Workspace>>(
"OutputWorkspace", "", Direction::Output));
auto mustBePositive = boost::make_shared<BoundedValidator<int64_t>>();
mustBePositive->setLower(0);
declareProperty("SpectrumMin", static_cast<int64_t>(0), mustBePositive);
declareProperty("SpectrumMax", static_cast<int64_t>(EMPTY_INT()),
mustBePositive);
declareProperty(make_unique<ArrayProperty<int64_t>>("SpectrumList"));
declareProperty("EntryNumber", static_cast<int64_t>(0), mustBePositive,
"0 indicates that every entry is loaded, into a separate "
"workspace within a group. "
"A positive number identifies one entry to be loaded, into "
"one worskspace");
std::vector<std::string> monitorOptions{"Include", "Exclude", "Separate"};
std::map<std::string, std::string> monitorOptionsAliases;
monitorOptionsAliases["1"] = "Separate";
monitorOptionsAliases["0"] = "Exclude";
declareProperty(
"LoadMonitors", "Include",
boost::make_shared<Kernel::StringListValidator>(monitorOptions,
monitorOptionsAliases),
"Option to control the loading of monitors.\n"
"Allowed options are Include,Exclude, Separate.\n"
"Include:The default is Include option would load monitors with the "
"workspace if monitors spectra are within the range of loaded "
"detectors.\n"
"If the time binning for the monitors is different from the\n"
"binning of the detectors this option is equivalent to the Separate "
"option\n"
"Exclude:Exclude option excludes monitors from the output workspace.\n"
"Separate:Separate option loads monitors into a separate workspace "
"called: OutputWorkspace_monitors.\n"
"Defined aliases:\n"
"1: Equivalent to Separate.\n"
"0: Equivalent to Exclude.\n");
}
/** Executes the algorithm. Reading in the file and creating and populating
* the output workspace
*
* @throw Exception::FileError If the Nexus file cannot be found/opened
* @throw std::invalid_argument If the optional properties are set to invalid
*values
*/
void LoadISISNexus2::exec() {
//**********************************************************************
// process load monitor options request
bool bincludeMonitors, bseparateMonitors, bexcludeMonitors;
LoadRawHelper::ProcessLoadMonitorOptions(bincludeMonitors, bseparateMonitors,
bexcludeMonitors, this);
//**********************************************************************
m_filename = getPropertyValue("Filename");
// Create the root Nexus class
NXRoot root(m_filename);
// "Open" the same file but with the C++ interface
m_cppFile.reset(new ::NeXus::File(root.m_fileID));
// Open the raw data group 'raw_data_1'
NXEntry entry = root.openEntry("raw_data_1");
// Read in the instrument name from the Nexus file
m_instrument_name = entry.getString("name");
// Test if we have a detector block
size_t ndets(0);
try {
NXClass det_class = entry.openNXGroup("detector_1");
NXInt spectrum_index = det_class.openNXInt("spectrum_index");
spectrum_index.load();
ndets = spectrum_index.dim0();
// We assume that this spectrum list increases monotonically
m_spec = spectrum_index.sharedBuffer();
m_spec_end = m_spec.get() + ndets;
m_have_detector = true;
} catch (std::runtime_error &) {
ndets = 0;
}
NXInt nsp1 = entry.openNXInt("isis_vms_compat/NSP1");
nsp1.load();
NXInt udet = entry.openNXInt("isis_vms_compat/UDET");
udet.load();
NXInt spec = entry.openNXInt("isis_vms_compat/SPEC");
spec.load();
size_t nmons(0);
// Pull out the monitor blocks, if any exist
for (std::vector<NXClassInfo>::const_iterator it = entry.groups().begin();
it != entry.groups().end(); ++it) {
if (it->nxclass == "NXmonitor") // Count monitors
{
NXInt index =
entry.openNXInt(std::string(it->nxname) + "/spectrum_index");
index.load();
int64_t ind = *index();
// Spectrum index of 0 means no spectrum associated with that monitor,
// so only count those with index > 0
if (ind > 0) {
m_monitors[ind] = it->nxname;
++nmons;
}
}
}
if (ndets == 0 && nmons == 0) {
if (bexcludeMonitors) {
g_log.warning() << "Nothing to do. No detectors found and no monitor "
"loading requested";
return;
} else {
g_log.error()
<< "Invalid NeXus structure, cannot find detector or monitor blocks.";
throw std::runtime_error("Inconsistent NeXus file structure.");
}
}
// Determine the the data block for the detectors and monitors
bseparateMonitors =
findSpectraDetRangeInFile(entry, m_spec, ndets, nsp1[0], m_monitors,
bexcludeMonitors, bseparateMonitors);
size_t x_length = m_loadBlockInfo.getNumberOfChannels() + 1;
// Check input is consistent with the file, throwing if not
bseparateMonitors =
checkOptionalProperties(bseparateMonitors, bexcludeMonitors);
// Fill up m_spectraBlocks
size_t total_specs = prepareSpectraBlocks(m_monitors, m_loadBlockInfo);
m_progress = boost::make_shared<API::Progress>(
this, 0.0, 1.0, total_specs * m_detBlockInfo.getNumberOfPeriods());
DataObjects::Workspace2D_sptr local_workspace =
boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create(
"Workspace2D", total_specs, x_length,
m_loadBlockInfo.getNumberOfChannels()));
// Set the units on the workspace to TOF & Counts
local_workspace->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
local_workspace->setYUnit("Counts");
//
// Load instrument and other data once then copy it later
//
m_progress->report("Loading instrument and run details");
// load run details
loadRunDetails(local_workspace, entry);
// Test if IDF exists in Nexus otherwise load default instrument
bool foundInstrument = LoadEventNexus::runLoadIDFFromNexus(
m_filename, local_workspace, "raw_data_1", this);
if (m_load_selected_spectra)
m_spec2det_map = SpectrumDetectorMapping(spec(), udet(), udet.dim0());
else if (bseparateMonitors) {
m_spec2det_map = SpectrumDetectorMapping(spec(), udet(), udet.dim0());
local_workspace->updateSpectraUsing(m_spec2det_map);
} else {
local_workspace->updateSpectraUsing(
SpectrumDetectorMapping(spec(), udet(), udet.dim0()));
}
if (!foundInstrument) {
runLoadInstrument(local_workspace);
}
// Load logs and sample information
m_cppFile->openPath(entry.path());
local_workspace->loadSampleAndLogInfoNexus(m_cppFile.get());
// Load logs and sample information further information... See maintenance
// ticket #8697
loadSampleData(local_workspace, entry);
m_progress->report("Loading logs");
loadLogs(local_workspace, entry);
// Load first period outside loop
m_progress->report("Loading data");
if (ndets > 0) {
// Get the X data
NXFloat timeBins = entry.openNXFloat("detector_1/time_of_flight");
timeBins.load();
m_tof_data =
boost::make_shared<HistogramX>(timeBins(), timeBins() + x_length);
}
int64_t firstentry = (m_entrynumber > 0) ? m_entrynumber : 1;
loadPeriodData(firstentry, entry, local_workspace, m_load_selected_spectra);
// Clone the workspace at this point to provide a base object for future
// workspace generation.
DataObjects::Workspace2D_sptr period_free_workspace =
boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create(local_workspace));
createPeriodLogs(firstentry, local_workspace);
WorkspaceGroup_sptr wksp_group(new WorkspaceGroup);
if (m_loadBlockInfo.getNumberOfPeriods() > 1 && m_entrynumber == 0) {
wksp_group->setTitle(local_workspace->getTitle());
// This forms the name of the group
const std::string base_name = getPropertyValue("OutputWorkspace") + "_";
const std::string prop_name = "OutputWorkspace_";
for (int p = 1; p <= m_loadBlockInfo.getNumberOfPeriods(); ++p) {
std::ostringstream os;
os << p;
m_progress->report("Loading period " + os.str());
if (p > 1) {
local_workspace = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create(period_free_workspace));
loadPeriodData(p, entry, local_workspace, m_load_selected_spectra);
createPeriodLogs(p, local_workspace);
// Check consistency of logs data for multi-period workspaces and raise
// warnings where necessary.
validateMultiPeriodLogs(local_workspace);
}
declareProperty(Kernel::make_unique<WorkspaceProperty<Workspace>>(
prop_name + os.str(), base_name + os.str(), Direction::Output));
wksp_group->addWorkspace(local_workspace);
setProperty(prop_name + os.str(),
boost::static_pointer_cast<Workspace>(local_workspace));
}
// The group is the root property value
setProperty("OutputWorkspace",
boost::dynamic_pointer_cast<Workspace>(wksp_group));
} else {
setProperty("OutputWorkspace",
boost::dynamic_pointer_cast<Workspace>(local_workspace));
}
//***************************************************************************************************
// Workspace or group of workspaces without monitors is loaded. Now we are
// loading monitors separately.
if (bseparateMonitors) {
std::string wsName = getPropertyValue("OutputWorkspace");
if (m_monBlockInfo.getNumberOfSpectra() > 0) {
x_length = m_monBlockInfo.getNumberOfChannels() + 1;
// reset the size of the period free workspace to the monitor size
period_free_workspace =
boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create(
period_free_workspace, m_monBlockInfo.getNumberOfSpectra(),
x_length, m_monBlockInfo.getNumberOfChannels()));
auto monitor_workspace =
boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create(period_free_workspace));
m_spectraBlocks.clear();
m_wsInd2specNum_map.clear();
// at the moment here we clear this map to enable possibility to load
// monitors from the spectra block (wiring table bug).
// if monitor's spectra present in the detectors block due to this bug
// should be read from monitors, this map should be dealt with properly.
buildSpectraInd2SpectraNumMap(true /*hasRange*/, false /*hasSpectraList*/,
m_monBlockInfo);
// lo
prepareSpectraBlocks(m_monitors, m_monBlockInfo);
int64_t firstentry = (m_entrynumber > 0) ? m_entrynumber : 1;
loadPeriodData(firstentry, entry, monitor_workspace, true);
local_workspace->setMonitorWorkspace(monitor_workspace);
ISISRunLogs monLogCreator(monitor_workspace->run());
monLogCreator.addPeriodLogs(1, monitor_workspace->mutableRun());
const std::string monitorPropBase = "MonitorWorkspace";
const std::string monitorWsNameBase = wsName + "_monitors";
if (m_detBlockInfo.getNumberOfPeriods() > 1 && m_entrynumber == 0) {
WorkspaceGroup_sptr monitor_group(new WorkspaceGroup);
monitor_group->setTitle(monitor_workspace->getTitle());
for (int p = 1; p <= m_detBlockInfo.getNumberOfPeriods(); ++p) {
std::ostringstream os;
os << "_" << p;
m_progress->report("Loading period " + os.str());
if (p > 1) {
monitor_workspace =
boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
WorkspaceFactory::Instance().create(period_free_workspace));
loadPeriodData(p, entry, monitor_workspace,
m_load_selected_spectra);
monLogCreator.addPeriodLogs(p, monitor_workspace->mutableRun());
// Check consistency of logs data for multi-period workspaces and
// raise
// warnings where necessary.
validateMultiPeriodLogs(monitor_workspace);
auto data_ws = boost::static_pointer_cast<API::MatrixWorkspace>(
wksp_group->getItem(p - 1));
data_ws->setMonitorWorkspace(monitor_workspace);
}
declareProperty(Kernel::make_unique<WorkspaceProperty<Workspace>>(
monitorPropBase + os.str(), monitorWsNameBase + os.str(),
Direction::Output));
monitor_group->addWorkspace(monitor_workspace);
setProperty(monitorPropBase + os.str(),
boost::static_pointer_cast<Workspace>(monitor_workspace));
}
// The group is the root property value
declareProperty(Kernel::make_unique<WorkspaceProperty<Workspace>>(
monitorPropBase, monitorWsNameBase, Direction::Output));
setProperty(monitorPropBase,
boost::dynamic_pointer_cast<Workspace>(monitor_group));
} else {
declareProperty(Kernel::make_unique<WorkspaceProperty<Workspace>>(
monitorPropBase, monitorWsNameBase, Direction::Output));
setProperty(monitorPropBase,
boost::static_pointer_cast<Workspace>(monitor_workspace));
}
} else {
g_log.information() << " no monitors to load for workspace: " << wsName
<< '\n';
}
}
// Clear off the member variable containers
m_tof_data.reset();
m_spec.reset();
m_monitors.clear();
m_wsInd2specNum_map.clear();
}
// Function object for remove_if STL algorithm
namespace {
// Check the numbers supplied are not in the range and erase the ones that are
struct range_check {
range_check(int64_t min, int64_t max) : m_min(min), m_max(max) {}
bool operator()(int64_t x) { return (x >= m_min && x <= m_max); }
private:
int64_t m_min;
int64_t m_max;
};
}
/**
Check for a set of synthetic logs associated with multi-period log data. Raise
warnings where necessary.
*/
void LoadISISNexus2::validateMultiPeriodLogs(
Mantid::API::MatrixWorkspace_sptr ws) {
const Run &run = ws->run();
if (!run.hasProperty("current_period")) {
g_log.warning("Workspace has no current_period log.");
}
if (!run.hasProperty("nperiods")) {
g_log.warning("Workspace has no nperiods log");
}
if (!run.hasProperty("proton_charge_by_period")) {
g_log.warning("Workspace has not proton_charge_by_period log");
}
}
/**
* Check the validity of the optional properties of the algorithm and identify if
* partial data should be loaded.
* @param bseparateMonitors: flag indicating if the monitors are to be loaded
* separately
* @param bexcludeMonitor: flag indicating if the monitors are to be excluded
*/
bool LoadISISNexus2::checkOptionalProperties(bool bseparateMonitors,
bool bexcludeMonitor) {
// optional properties specify that only some spectra have to be loaded
bool range_supplied(false);
// Get the spectrum selection which were specfied by the user
int64_t spec_min = getProperty("SpectrumMin");
int64_t spec_max = getProperty("SpectrumMax");
// If spearate monitors or excluded monitors is selected then we
// need to build up a wsIndex to spectrum number map as well,
// since we cannot rely on contiguous blocks of detectors
if (bexcludeMonitor || bseparateMonitors) {
m_load_selected_spectra = true;
}
if (spec_min == 0)
spec_min = m_loadBlockInfo.getMinSpectrumID();
else {
range_supplied = true;
m_load_selected_spectra = true;
}
if (spec_max == EMPTY_INT())
spec_max = m_loadBlockInfo.getMaxSpectrumID();
else {
range_supplied = true;
m_load_selected_spectra = true;
}
// Sanity check for min/max
if (spec_min > spec_max) {
throw std::invalid_argument("Inconsistent range properties. SpectrumMin is "
"larger than SpectrumMax.");
}
if (spec_max > m_loadBlockInfo.getMaxSpectrumID()) {
std::string err =
"Inconsistent range property. SpectrumMax is larger than number of "
"spectra: " +
std::to_string(m_loadBlockInfo.getMaxSpectrumID());
throw std::invalid_argument(err);
}
// Check the entry number
m_entrynumber = getProperty("EntryNumber");
if (static_cast<int>(m_entrynumber) > m_loadBlockInfo.getNumberOfPeriods() ||
m_entrynumber < 0) {
std::string err = "Invalid entry number entered. File contains " +
std::to_string(m_loadBlockInfo.getNumberOfPeriods()) +
" period. ";
throw std::invalid_argument(err);
}
if (m_loadBlockInfo.getNumberOfPeriods() == 1) {
m_entrynumber = 1;
}
// Did the user provide a spectrum list
std::vector<int64_t> spec_list = getProperty("SpectrumList");
auto hasSpecList = false;
if (!spec_list.empty()) {
m_load_selected_spectra = true;
// Sort the list so that we can check it's range
std::sort(spec_list.begin(), spec_list.end());
// Check if the spectra list entries are outside of the bounds
// If we load the monitors separately, then we need to make sure that we
// take
// them
// into account
bool isSpectraListTooLarge;
bool isSpectraListTooSmall;
auto maxLoadBlock = m_loadBlockInfo.getMaxSpectrumID();
auto minLoadBlock = m_loadBlockInfo.getMinSpectrumID();
if (bseparateMonitors) {
auto maxMonBlock = m_monBlockInfo.getMaxSpectrumID();
auto minMonBlock = m_monBlockInfo.getMinSpectrumID();
isSpectraListTooLarge =
spec_list.back() > std::max(maxMonBlock, maxLoadBlock);
isSpectraListTooSmall =
spec_list.front() < std::min(minMonBlock, minLoadBlock);
} else {
isSpectraListTooLarge = spec_list.back() > maxLoadBlock;
isSpectraListTooSmall = spec_list.front() < minLoadBlock;
}
if (isSpectraListTooLarge) {
std::string err =
"The specified spectrum list contains a spectrum number which is "
"larger "
"than the largest loadable spectrum number for your selection of "
"excluded/included/separate monitors. The largest loadable "
"spectrum number is " +
std::to_string(m_loadBlockInfo.getMinSpectrumID());
throw std::invalid_argument(err);
}
if (isSpectraListTooSmall) {
std::string err =
"The specified spectrum list contains a spectrum number which is "
"smaller "
"than the smallest loadable spectrum number for your selection of "
"excluded/included/separate monitors. The smallest loadable "
"spectrum number is " +
std::to_string(m_loadBlockInfo.getMinSpectrumID());
throw std::invalid_argument(err);
}
// The users can provide a spectrum list and and a spectrum range. Handle
// this here.
if (range_supplied) {
// First remove all entries which are inside of the min and max spectrum,
// to avoid duplicates
auto isInRange = [&spec_min, &spec_max](int64_t x) {
return (spec_min <= x) && (x <= spec_max);
};
spec_list.erase(remove_if(spec_list.begin(), spec_list.end(), isInRange),
spec_list.end());
// The spec_min - spec_max range needs to be added to the spec list
for (int64_t i = spec_min; i < spec_max + 1; ++i) {
specnum_t spec_num = static_cast<specnum_t>(i);
spec_list.push_back(spec_num);
std::sort(spec_list.begin(), spec_list.end());
// supplied range converted into the list, so no more supplied range
}
}
auto monitorSpectra = m_monBlockInfo.getAllSpectrumNumbers();
// Create DataBlocks from the spectrum list
DataBlockComposite composite;
populateDataBlockCompositeWithContainer(
composite, spec_list, spec_list.size(),
m_loadBlockInfo.getNumberOfPeriods(),
m_loadBlockInfo.getNumberOfChannels(), monitorSpectra);
// If the monitors are to be loaded separately, then we have
// to remove them at this point, but we also have to check if the
if (bexcludeMonitor || bseparateMonitors) {
auto newMonitors = getMonitorsFromComposite(composite, m_monBlockInfo);
composite.removeSpectra(m_monBlockInfo);
// This is important. If there are no monitors which were specifically
// selected,
// then we load the full monitor range, else respect the selection.
if (!newMonitors.isEmpty()) {
m_monBlockInfo = newMonitors;
}
// Handle case where the composite is empty since it only contained
// monitors, but
// we want to load the monitors sepearately. In this case we should set
// the loadBlock
// to the selected monitors.
if (bseparateMonitors && composite.isEmpty()) {
composite = m_monBlockInfo;
bseparateMonitors = false;
}
}
m_loadBlockInfo = composite;
hasSpecList = true;
} else {
// At this point we don't have a spectrum list but there might have been a
// spectrum range which we need to take into account, by truncating
// the current range. If we load the monitors separately, we need to
// truncate
// them as well (provided they are affected)
if (range_supplied) {
m_loadBlockInfo.truncate(spec_min, spec_max);
auto new_monitors = m_monBlockInfo;
new_monitors.truncate(spec_min, spec_max);
m_monBlockInfo = new_monitors;
}
}
if (m_load_selected_spectra) {
buildSpectraInd2SpectraNumMap(range_supplied, hasSpecList, m_loadBlockInfo);
}
// Check that the load blocks contain anything at all.
if (m_loadBlockInfo.isEmpty()) {
throw std::invalid_argument(
"Your spectrum number selection was not valid. "
"Make sure that you select spectrum numbers "
"and ranges which are compatible with your "
"selection of excluded/included/separate monitors. ");
}
return bseparateMonitors;
}
/**
Build the list of spectra to load and include into spectra-detectors map.
The map should be built if the user either specified a range or if the user
provided a list of spectrum numbers.
@param range_supplied: if true specifies that the range of values provided
below have to be processed rather then spectra list
@param hasSpectraList: did the user specify a spectrum list
@param dataBlockComposite: a data block composite specfiying the spectra
intervals
**/
void LoadISISNexus2::buildSpectraInd2SpectraNumMap(
bool range_supplied, bool hasSpectraList,
DataBlockComposite &dataBlockComposite) {
if (range_supplied || hasSpectraList || true) {
auto generator = dataBlockComposite.getGenerator();
int64_t hist = 0;
for (; !generator->isDone(); generator->next()) {
specnum_t spec_num = static_cast<specnum_t>(generator->getValue());
m_wsInd2specNum_map.emplace(hist, spec_num);
++hist;
}
}
}
namespace {
/// Compare two spectra blocks for ordering
bool compareSpectraBlocks(const LoadISISNexus2::SpectraBlock &block1,
const LoadISISNexus2::SpectraBlock &block2) {
bool res = block1.last < block2.first;
if (!res) {
assert(block2.last < block1.first);
}
return res;
}
}
/**
* Analyze the spectra ranges and prepare a list contiguous blocks. Each monitor
* must be
* in a separate block.
* @return :: Number of spectra to load.
*/
size_t
LoadISISNexus2::prepareSpectraBlocks(std::map<int64_t, std::string> &monitors,
DataBlockComposite &LoadBlock) {
std::vector<int64_t> includedMonitors;
// Setup the SpectraBlocks based on the DataBlocks
auto dataBlocks = LoadBlock.getDataBlocks();
auto isMonitor = [&monitors](int64_t spectrumNumber) {
return monitors.find(spectrumNumber) != monitors.end();
};
for (const auto &dataBlock : dataBlocks) {
auto min = dataBlock.getMinSpectrumID();
if (isMonitor(min)) {
m_spectraBlocks.push_back(
SpectraBlock(min, min, true, monitors.find(min)->second));
includedMonitors.push_back(min);
} else {
auto max = dataBlock.getMaxSpectrumID();
m_spectraBlocks.push_back(SpectraBlock(min, max, false, ""));
}
}
// sort and check for overlapping
if (m_spectraBlocks.size() > 1) {
std::sort(m_spectraBlocks.begin(), m_spectraBlocks.end(),
compareSpectraBlocks);
}
// Remove monitors that have been used.
auto allMonitorsIncluded = monitors.size() == includedMonitors.size();
if (!includedMonitors.empty() && !allMonitorsIncluded) {
for (auto it = monitors.begin(); it != monitors.end();) {
if (std::find(includedMonitors.begin(), includedMonitors.end(),
it->first) != includedMonitors.end()) {
auto it1 = it;
++it;
monitors.erase(it1);
} else {
++it;
}
}
}
// Count the number of spectra.
size_t nSpec = 0;
for (auto &spectraBlock : m_spectraBlocks) {
nSpec += spectraBlock.last - spectraBlock.first + 1;
}
return nSpec;
}
/**
* Load a given period into the workspace
* @param period :: The period number to load (starting from 1)
* @param entry :: The opened root entry node for accessing the monitor and data
* nodes
* @param local_workspace :: The workspace to place the data in
* @param update_spectra2det_mapping :: reset spectra-detector map to the one
* calculated earlier. (Warning! -- this map has to be calculated correctly!)
*/
void LoadISISNexus2::loadPeriodData(
int64_t period, NXEntry &entry,
DataObjects::Workspace2D_sptr &local_workspace,
bool update_spectra2det_mapping) {
int64_t hist_index = 0;
int64_t period_index(period - 1);
// int64_t first_monitor_spectrum = 0;
for (auto &spectraBlock : m_spectraBlocks) {
if (spectraBlock.isMonitor) {
NXData monitor = entry.openNXData(spectraBlock.monName);
NXInt mondata = monitor.openIntData();
m_progress->report("Loading monitor");
mondata.load(1, static_cast<int>(period - 1)); // TODO this is just wrong
NXFloat timeBins = monitor.openNXFloat("time_of_flight");
timeBins.load();
local_workspace->setHistogram(
hist_index, BinEdges(timeBins(), timeBins() + timeBins.dim0()),
Counts(mondata(), mondata() + m_monBlockInfo.getNumberOfChannels()));
if (update_spectra2det_mapping) {
// local_workspace->getAxis(1)->setValue(hist_index,
// static_cast<specnum_t>(it->first));
auto &spec = local_workspace->getSpectrum(hist_index);
specnum_t specNum = m_wsInd2specNum_map.at(hist_index);
spec.setDetectorIDs(
m_spec2det_map.getDetectorIDsForSpectrumNo(specNum));
spec.setSpectrumNo(specNum);
}
hist_index++;
} else if (m_have_detector) {
NXData nxdata = entry.openNXData("detector_1");
NXDataSetTyped<int> data = nxdata.openIntData();
data.open();
// Start with the list members that are lower than the required spectrum
const int *const spec_begin = m_spec.get();
// When reading in blocks we need to be careful that the range is exactly
// divisible by the block-size
// and if not have an extra read of the left overs
const int64_t blocksize = 8;
const int64_t rangesize = spectraBlock.last - spectraBlock.first + 1;
const int64_t fullblocks = rangesize / blocksize;
int64_t spectra_no = spectraBlock.first;
// For this to work correctly, we assume that the spectrum list increases
// monotonically
int64_t filestart =
std::lower_bound(spec_begin, m_spec_end, spectra_no) - spec_begin;
if (fullblocks > 0) {
for (int64_t i = 0; i < fullblocks; ++i) {
loadBlock(data, blocksize, period_index, filestart, hist_index,
spectra_no, local_workspace);
filestart += blocksize;
}
}
int64_t finalblock = rangesize - (fullblocks * blocksize);
if (finalblock > 0) {
loadBlock(data, finalblock, period_index, filestart, hist_index,
spectra_no, local_workspace);
}
}
}
try {
const std::string title = entry.getString("title");
local_workspace->setTitle(title);
// write the title into the log file (run object)
local_workspace->mutableRun().addProperty("run_title", title, true);
} catch (std::runtime_error &) {
g_log.debug() << "No title was found in the input file, "
<< getPropertyValue("Filename") << '\n';
}
}
/**
* Creates period log data in the workspace
* @param period :: period number
* @param local_workspace :: workspace to add period log data to.
*/
void LoadISISNexus2::createPeriodLogs(
int64_t period, DataObjects::Workspace2D_sptr &local_workspace) {
m_logCreator->addPeriodLogs(static_cast<int>(period),
local_workspace->mutableRun());
}
/**
* Perform a call to nxgetslab, via the NexusClasses wrapped methods for a given
* block-size
* @param data :: The NXDataSet object
* @param blocksize :: The block-size to use
* @param period :: The period number
* @param start :: The index within the file to start reading from (zero based)
* @param hist :: The workspace index to start reading into
* @param spec_num :: The spectrum number that matches the hist variable
* @param local_workspace :: The workspace to fill the data with
*/
void LoadISISNexus2::loadBlock(NXDataSetTyped<int> &data, int64_t blocksize,
int64_t period, int64_t start, int64_t &hist,
int64_t &spec_num,
DataObjects::Workspace2D_sptr &local_workspace) {
data.load(static_cast<int>(blocksize), static_cast<int>(period),
static_cast<int>(start)); // TODO this is just wrong
int *data_start = data();
int *data_end = data_start + m_loadBlockInfo.getNumberOfChannels();
int64_t final(hist + blocksize);
while (hist < final) {
m_progress->report("Loading data");
local_workspace->setHistogram(hist, BinEdges(m_tof_data),
Counts(data_start, data_end));
data_start += m_detBlockInfo.getNumberOfChannels();
data_end += m_detBlockInfo.getNumberOfChannels();
if (m_load_selected_spectra) {
// local_workspace->getAxis(1)->setValue(hist,
// static_cast<specnum_t>(spec_num));
auto &spec = local_workspace->getSpectrum(hist);
specnum_t specNum = m_wsInd2specNum_map.at(hist);
// set detectors corresponding to spectra Number
spec.setDetectorIDs(m_spec2det_map.getDetectorIDsForSpectrumNo(specNum));
// set correct spectra Number
spec.setSpectrumNo(specNum);
}
++hist;
++spec_num;
}
}
/// Run the Child Algorithm LoadInstrument (or LoadInstrumentFromNexus)
void LoadISISNexus2::runLoadInstrument(
DataObjects::Workspace2D_sptr &localWorkspace) {
IAlgorithm_sptr loadInst = createChildAlgorithm("LoadInstrument");
// Now execute the Child Algorithm. Catch and log any error, but don't stop.
bool executionSuccessful(true);
try {
loadInst->setPropertyValue("InstrumentName", m_instrument_name);
loadInst->setProperty<MatrixWorkspace_sptr>("Workspace", localWorkspace);
loadInst->setProperty("RewriteSpectraMap",
Mantid::Kernel::OptionalBool(false));
loadInst->execute();
} catch (std::invalid_argument &) {
g_log.information("Invalid argument to LoadInstrument Child Algorithm");
executionSuccessful = false;
} catch (std::runtime_error &) {
g_log.information(
"Unable to successfully run LoadInstrument Child Algorithm");
executionSuccessful = false;
}
if (executionSuccessful) {
// If requested update the instrument to positions in the data file
const auto &pmap = localWorkspace->constInstrumentParameters();
if (pmap.contains(localWorkspace->getInstrument()->getComponentID(),
"det-pos-source")) {
boost::shared_ptr<Geometry::Parameter> updateDets = pmap.get(
localWorkspace->getInstrument()->getComponentID(), "det-pos-source");
std::string value = updateDets->value<std::string>();
if (value.substr(0, 8) == "datafile") {
IAlgorithm_sptr updateInst =
createChildAlgorithm("UpdateInstrumentFromFile");
updateInst->setProperty<MatrixWorkspace_sptr>("Workspace",
localWorkspace);
updateInst->setPropertyValue("Filename", m_filename);
if (value == "datafile-ignore-phi") {
updateInst->setProperty("IgnorePhi", true);
g_log.information("Detector positions in IDF updated with positions "
"in the data file except for the phi values");
} else {
g_log.information("Detector positions in IDF updated with positions "
"in the data file");
}
// We want this to throw if it fails to warn the user that the
// information is not correct.
updateInst->execute();
}
}
}
}
/**
* Load data about the run
* @param local_workspace :: The workspace to load the run information in to
* @param entry :: The Nexus entry
*/
void LoadISISNexus2::loadRunDetails(
DataObjects::Workspace2D_sptr &local_workspace, NXEntry &entry) {
API::Run &runDetails = local_workspace->mutableRun();
// Charge is stored as a float
m_proton_charge = static_cast<double>(entry.getFloat("proton_charge"));
runDetails.setProtonCharge(m_proton_charge);
std::string run_num = std::to_string(entry.getInt("run_number"));
runDetails.addProperty("run_number", run_num);
//
// Some details are only stored in the VMS comparability block so we'll pull
// everything from there
// for consistency
NXClass vms_compat = entry.openNXGroup("isis_vms_compat");
// Run header
NXChar char_data = vms_compat.openNXChar("HDR");
char_data.load();
// Space-separate the fields
char *nxsHdr = char_data();
char header[86] = {};
const size_t byte = sizeof(char);
const char fieldSep(' ');
size_t fieldWidths[7] = {3, 5, 20, 24, 12, 8, 8};
char *srcStart = nxsHdr;
char *destStart = header;
for (size_t i = 0; i < 7; ++i) {
size_t width = fieldWidths[i];
memcpy(destStart, srcStart, width * byte);
if (i < 6) // no space after last field
{
srcStart += width;
destStart += width;
memset(destStart, fieldSep, byte); // insert separator
destStart += 1;
}
}
runDetails.addProperty("run_header", std::string(header, header + 86));