-
Notifications
You must be signed in to change notification settings - Fork 122
/
CylinderPaalmanPingsCorrection2.py
574 lines (490 loc) · 23.9 KB
/
CylinderPaalmanPingsCorrection2.py
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
#pylint: disable=no-init,too-many-locals,too-many-instance-attributes,too-many-arguments,invalid-name
from mantid.simpleapi import *
from mantid.api import (PythonAlgorithm, AlgorithmFactory, PropertyMode, MatrixWorkspaceProperty,
WorkspaceGroupProperty, InstrumentValidator, WorkspaceUnitValidator)
from mantid.kernel import (StringListValidator, StringMandatoryValidator, IntBoundedValidator,
FloatBoundedValidator, Direction, logger, CompositeValidator)
import math
import numpy as np
class CylinderPaalmanPingsCorrection(PythonAlgorithm):
_sample_ws_name = None
_sample_chemical_formula = None
_sample_number_density = None
_sample_inner_radius = None
_sample_outer_radius = None
_use_can = False
_can_ws_name = None
_can_chemical_formula = None
_can_number_density = None
_can_outer_radius = None
_number_can = 1
_ms = 1
_number_wavelengths = 10
_emode = None
_efixed = 0.0
_step_size = None
_output_ws_name = None
_beam = list()
_angles = list()
_waves = list()
_elastic = 0.0
_sig_s = None
_sig_a = None
_density = None
_radii = None
#------------------------------------------------------------------------------
def version(self):
return 2
def category(self):
return "Workflow\\MIDAS;PythonAlgorithms;CorrectionFunctions\\AbsorptionCorrections"
def summary(self):
return "Calculates absorption corrections for a cylindrical or annular sample using Paalman & Pings format."
#------------------------------------------------------------------------------
def PyInit(self):
ws_validator = CompositeValidator([WorkspaceUnitValidator('Wavelength'), InstrumentValidator()])
self.declareProperty(MatrixWorkspaceProperty('SampleWorkspace', '',
validator=ws_validator,
direction=Direction.Input),
doc="Name for the input Sample workspace.")
self.declareProperty(name='SampleChemicalFormula', defaultValue='',
validator=StringMandatoryValidator(),
doc='Sample chemical formula')
self.declareProperty(name='SampleNumberDensity', defaultValue=0.1,
validator=FloatBoundedValidator(0.0),
doc='Sample number density')
self.declareProperty(name='SampleInnerRadius', defaultValue=0.05,
validator=FloatBoundedValidator(0.0),
doc='Sample inner radius')
self.declareProperty(name='SampleOuterRadius', defaultValue=0.1,
validator=FloatBoundedValidator(0.0),
doc='Sample outer radius')
self.declareProperty(MatrixWorkspaceProperty('CanWorkspace', '',
optional=PropertyMode.Optional,
validator=ws_validator,
direction=Direction.Input),
doc="Name for the input Can workspace.")
self.declareProperty(name='CanChemicalFormula', defaultValue='',
doc='Can chemical formula')
self.declareProperty(name='CanNumberDensity', defaultValue=0.1,
validator=FloatBoundedValidator(0.0),
doc='Can number density')
self.declareProperty(name='CanOuterRadius', defaultValue=0.15,
validator=FloatBoundedValidator(0.0),
doc='Can outer radius')
self.declareProperty(name='BeamHeight', defaultValue=3.0,
validator=FloatBoundedValidator(0.0),
doc='Beam height')
self.declareProperty(name='BeamWidth', defaultValue=2.0,
validator=FloatBoundedValidator(0.0),
doc='Beam width')
self.declareProperty(name='StepSize', defaultValue=0.002,
validator=FloatBoundedValidator(0.0),
doc='Step size')
self.declareProperty(name='Interpolate', defaultValue=True,
doc='Interpolate the correction workspaces to match the sample workspace')
self.declareProperty(name='NumberWavelengths', defaultValue=10,
validator=IntBoundedValidator(1),
doc='Number of wavelengths for calculation')
self.declareProperty(name='Emode', defaultValue='Elastic',
validator=StringListValidator(['Elastic', 'Indirect']),
doc='Emode: Elastic or Indirect')
self.declareProperty(name='Efixed', defaultValue=1.0,
doc='Analyser energy')
self.declareProperty(WorkspaceGroupProperty('OutputWorkspace', '',
direction=Direction.Output),
doc='The output corrections workspace group')
#------------------------------------------------------------------------------
def validateInputs(self):
self._setup()
issues = dict()
# Ensure that a can chemical formula is given when using a can workspace
if self._use_can:
can_chemical_formula = self.getPropertyValue('CanChemicalFormula')
if can_chemical_formula == '':
issues['CanChemicalFormula'] = 'Must provide a chemical foruma when providing a can workspace'
# Ensure there are enough steps
number_steps = int((self._sample_outer_radius - self._sample_inner_radius) / self._step_size)
if number_steps < 20:
issues['StepSize'] = 'Number of steps (%d) should be >= 20' % number_steps
return issues
#------------------------------------------------------------------------------
def PyExec(self):
self._setup()
self._sample()
self._wave_range()
self._get_angles()
self._transmission()
dataA1 = []
dataA2 = []
dataA3 = []
dataA4 = []
for angle in self._angles:
(A1, A2, A3, A4) = self._cyl_abs(angle)
logger.information('Angle : %f * successful' % (angle))
dataA1 = np.append(dataA1, A1)
dataA2 = np.append(dataA2, A2)
dataA3 = np.append(dataA3, A3)
dataA4 = np.append(dataA4, A4)
dataX = self._waves * len(self._angles)
# Create the output workspaces
ass_ws = self._output_ws_name + '_ass'
CreateWorkspace(OutputWorkspace=ass_ws, DataX=dataX, DataY=dataA1,
NSpec=len(self._angles), UnitX='Wavelength')
workspaces = [ass_ws]
if self._use_can:
assc_ws = self._output_ws_name + '_assc'
workspaces.append(assc_ws)
CreateWorkspace(OutputWorkspace=assc_ws, DataX=dataX, DataY=dataA2,
NSpec=len(self._angles), UnitX='Wavelength')
acsc_ws = self._output_ws_name + '_acsc'
workspaces.append(acsc_ws)
CreateWorkspace(OutputWorkspace=acsc_ws, DataX=dataX, DataY=dataA3,
NSpec=len(self._angles), UnitX='Wavelength')
acc_ws = self._output_ws_name + '_acc'
workspaces.append(acc_ws)
CreateWorkspace(OutputWorkspace=acc_ws, DataX=dataX, DataY=dataA4,
NSpec=len(self._angles), UnitX='Wavelength')
if self._interpolate:
self._interpolate_corrections(workspaces)
try:
self. _copy_detector_table(workspaces)
except RuntimeError:
logger.warning('Cannot copy spectra mapping. Check input workspace instrument.')
sample_log_workspaces = workspaces
sample_logs = [('sample_shape', 'cylinder'),
('sample_filename', self._sample_ws_name),
('sample_inner', self._sample_inner_radius),
('sample_outer', self._sample_outer_radius)]
if self._use_can:
sample_logs.append(('can_filename', self._can_ws_name))
sample_logs.append(('can_outer', self._can_outer_radius))
log_names = [item[0] for item in sample_logs]
log_values = [item[1] for item in sample_logs]
for ws_name in sample_log_workspaces:
AddSampleLogMultiple(Workspace=ws_name, LogNames=log_names, LogValues=log_values)
GroupWorkspaces(InputWorkspaces=','.join(workspaces), OutputWorkspace=self._output_ws_name)
self.setPropertyValue('OutputWorkspace', self._output_ws_name)
#------------------------------------------------------------------------------
def _setup(self):
self._sample_ws_name = self.getPropertyValue('SampleWorkspace')
self._sample_chemical_formula = self.getPropertyValue('SampleChemicalFormula')
self._sample_number_density = self.getProperty('SampleNumberDensity').value
self._sample_inner_radius = self.getProperty('SampleInnerRadius').value
self._sample_outer_radius = self.getProperty('SampleOuterRadius').value
self._number_can = 1
self._can_ws_name = self.getPropertyValue('CanWorkspace')
self._use_can = self._can_ws_name != ''
self._can_chemical_formula = self.getPropertyValue('CanChemicalFormula')
self._can_number_density = self.getProperty('CanNumberDensity').value
self._can_outer_radius = self.getProperty('CanOuterRadius').value
if self._use_can:
self._number_can = 2
self._step_size = self.getProperty('StepSize').value
self._radii = np.zeros(self._number_can +1)
self._radii[0] = self._sample_inner_radius
self._radii[1] = self._sample_outer_radius
if (self._radii[1] - self._radii[0]) < 1e-4:
raise ValueError('Sample outer radius not > inner radius')
else:
logger.information('Sample : inner radius = %f ; outer radius = %f' % (
self._radii[0], self._radii[1]))
self._ms = int((self._radii[1] - self._radii[0] + 0.0001)/self._step_size)
if self._ms < 20:
raise ValueError('Number of steps ( %i ) should be >= 20' % (self._ms))
else:
if self._ms < 1:
self._ms=1
logger.information('Sample : ms = %i ' % (self._ms))
if self._use_can:
self._radii[2] = self._can_outer_radius
if (self._radii[2] - self._radii[1]) < 1e-4:
raise ValueError('Can outer radius not > sample outer radius')
else:
logger.information('Can : inner radius = %f ; outer radius = %f' % (
self._radii[1], self._radii[2]))
beam_width = self.getProperty('BeamWidth').value
beam_height = self.getProperty('BeamHeight').value
self._beam = [beam_height,
0.5 * beam_width,
-0.5 * beam_width,
(beam_width / 2),
-(beam_width / 2),
0.0,
beam_height,
0.0,
beam_height]
self._interpolate = self.getProperty('Interpolate').value
self._number_wavelengths = self.getProperty('NumberWavelengths').value
self._emode = self.getPropertyValue('Emode')
self._efixed = self.getProperty('Efixed').value
self._output_ws_name = self.getPropertyValue('OutputWorkspace')
#------------------------------------------------------------------------------
def _sample(self):
SetSampleMaterial(self._sample_ws_name , ChemicalFormula=self._sample_chemical_formula,
SampleNumberDensity=self._sample_number_density)
sample = mtd[self._sample_ws_name].sample()
sam_material = sample.getMaterial()
# total scattering x-section
self._sig_s = np.zeros(self._number_can)
self._sig_s[0] = sam_material.totalScatterXSection()
# absorption x-section
self._sig_a = np.zeros(self._number_can)
self._sig_a[0] = sam_material.absorbXSection()
# density
self._density = np.zeros(self._number_can)
self._density[0] = self._sample_number_density
if self._use_can:
SetSampleMaterial(InputWorkspace=self._can_ws_name, ChemicalFormula=self._can_chemical_formula,
SampleNumberDensity=self._can_number_density)
can_sample = mtd[self._can_ws_name].sample()
can_material = can_sample.getMaterial()
self._sig_s[1] = can_material.totalScatterXSection()
self._sig_a[1] = can_material.absorbXSection()
self._density[1] = self._can_number_density
#------------------------------------------------------------------------------
def _get_angles(self):
num_hist = mtd[self._sample_ws_name].getNumberHistograms()
source_pos = mtd[self._sample_ws_name].getInstrument().getSource().getPos()
sample_pos = mtd[self._sample_ws_name].getInstrument().getSample().getPos()
beam_pos = sample_pos - source_pos
self._angles = list()
for index in range(0, num_hist):
detector = mtd[self._sample_ws_name].getDetector(index)
two_theta = detector.getTwoTheta(sample_pos, beam_pos) * 180.0 / math.pi
self._angles.append(two_theta)
logger.information('Detector angles : %i from %f to %f ' % (
len(self._angles), self._angles[0], self._angles[-1]))
#------------------------------------------------------------------------------
def _wave_range(self):
wave_range = '__wave_range'
ExtractSingleSpectrum(InputWorkspace=self._sample_ws_name, OutputWorkspace=wave_range, WorkspaceIndex=0)
Xin = mtd[wave_range].readX(0)
wave_min = mtd[wave_range].readX(0)[0]
wave_max = mtd[wave_range].readX(0)[len(Xin) - 1]
number_waves = self._number_wavelengths
wave_bin = (wave_max - wave_min) / (number_waves-1)
self._waves = list()
for idx in range(0, number_waves):
self._waves.append(wave_min + idx * wave_bin)
DeleteWorkspace(wave_range)
if self._emode == 'Elastic':
self._elastic = self._waves[int(len(self._waves) / 2)]
elif self._emode == 'Direct':
self._elastic = math.sqrt(81.787/self._efixed) # elastic wavelength
elif self._emode == 'Indirect':
self._elastic = math.sqrt(81.787/self._efixed) # elastic wavelength
logger.information('Elastic lambda : %f' % (self._elastic))
logger.information('Lambda : %i values from %f to %f' % (
len(self._waves), self._waves[0], self._waves[-1]))
#------------------------------------------------------------------------------
def _transmission(self):
distance = self._radii[1] - self._radii[0]
trans= math.exp(-distance*self._density[0]*(self._sig_s[0] + self._sig_a[0]))
logger.information('Sample transmission : %f' % (trans))
if self._use_can:
distance = self._radii[2] - self._radii[1]
trans= math.exp(-distance*self._density[1]*(self._sig_s[1] + self._sig_a[1]))
logger.information('Can transmission : %f' % (trans))
#------------------------------------------------------------------------------
def _interpolate_corrections(self, workspaces):
"""
Performs interpolation on the correction workspaces such that the number of bins
matches that of the input sample workspace.
@param workspaces List of correction workspaces to interpolate
"""
for ws in workspaces:
SplineInterpolation(WorkspaceToMatch=self._sample_ws_name,
WorkspaceToInterpolate=ws,
OutputWorkspace=ws,
OutputWorkspaceDeriv='')
#------------------------------------------------------------------------------
def _copy_detector_table(self, workspaces):
"""
Copy the detector table from the sample workspaces to the correction workspaces.
@param workspaces List of correction workspaces
"""
instrument = mtd[self._sample_ws_name].getInstrument().getName()
for ws in workspaces:
LoadInstrument(Workspace=ws,
InstrumentName=instrument)
CopyDetectorMapping(WorkspaceToMatch=self._sample_ws_name,
WorkspaceToRemap=ws,
IndexBySpectrumNumber=True)
#------------------------------------------------------------------------------
def _cyl_abs(self, angle):
# Parameters :
# self._step_size - step size
# self._beam - beam parameters
# nan - number of annuli
# radii - list of radii (for each annulus)
# density - list of densities (for each annulus)
# sigs - list of scattering cross-sections (for each annulus)
# siga - list of absorption cross-sections (for each annulus)
# angle - list of angles
# wavelas - elastic wavelength
# waves - list of wavelengths
# Output parameters : A1 - Ass ; A2 - Assc ; A3 - Acsc ; A4 - Acc
amu_scat = np.zeros(self._number_can)
amu_scat = self._density*self._sig_s
sig_abs = np.zeros(self._number_can)
sig_abs = self._density*self._sig_a
amu_tot_i = np.zeros(self._number_can)
amu_tot_s = np.zeros(self._number_can)
theta = angle*math.pi/180.
A1 = []
A2 = []
A3 = []
A4 = []
#loop over wavelengths
for wave in self._waves:
#loop over annuli
if self._emode == 'Elastic':
amu_tot_i = amu_scat + sig_abs*self._elastic/1.7979
amu_tot_s = amu_scat + sig_abs*self._elastic/1.7979
if self._emode == 'Direct':
amu_tot_i = amu_scat + sig_abs*self._elastic/1.7979
amu_tot_s = amu_scat + sig_abs*wave/1.7979
if self._emode == 'Indirect':
amu_tot_i = amu_scat + sig_abs*wave/1.7979
amu_tot_s = amu_scat + sig_abs*self._elastic/1.7979
(Ass, Assc, Acsc, Acc) = self._acyl(theta, amu_scat, amu_tot_i, amu_tot_s)
A1.append(Ass)
A2.append(Assc)
A3.append(Acsc)
A4.append(Acc)
return A1, A2, A3, A4
#------------------------------------------------------------------------------
def _acyl(self, theta, amu_scat, amu_tot_i, amu_tot_s):
A = self._beam[1]
Area_s = 0.0
Ass = 0.0
Acc = 0.0
Acsc = 0.0
Assc = 0.0
nan = self._number_can
if self._number_can < 2:
#
# No. STEPS ARE CHOSEN SO THAT STEP WIDTH IS THE SAME FOR ALL ANNULI
#
AAAA, BBBA, Area_A = self._sum_rom(0, 0, A, self._radii[0], self._radii[1], self._ms,
theta, amu_scat, amu_tot_i, amu_tot_s)
AAAB, BBBB, Area_B = self._sum_rom(0, 0, -A, self._radii[0], self._radii[1], self._ms,
theta, amu_scat, amu_tot_i, amu_tot_s)
Area_s += Area_A + Area_B
Ass += AAAA + AAAB
Ass = Ass/Area_s
else:
for i in range(0, self._number_can -1):
radius_1 = self._radii[i]
radius_2 = self._radii[i+1]
#
# No. STEPS ARE CHOSEN SO THAT STEP WIDTH IS THE SAME FOR ALL ANNULI
#
ms = int(self._ms*(radius_2 - radius_1)/(self._radii[1] - self._radii[0]))
if ms < 1:
ms = 1
AAAA, BBBA, Area_A = self._sum_rom(i, 0, A, radius_1, radius_2,
ms, theta, amu_scat, amu_tot_i, amu_tot_s)
AAAB, BBBB, Area_B = self._sum_rom(i, 0, -A, radius_1, radius_2,
ms, theta, amu_scat, amu_tot_i, amu_tot_s)
Area_s += Area_A + Area_B
Ass += AAAA + AAAB
Assc += BBBA + BBBB
Ass = Ass/Area_s
Assc = Assc/Area_s
radius_1 = self._radii[nan -1]
radius_2 = self._radii[nan]
ms = int(self._ms*(radius_2 - radius_1)/(self._radii[1] - self._radii[0]))
if ms < 1:
ms = 1
AAAA, BBBA, Area_A = self._sum_rom(nan-1, 1, A, radius_1, radius_2,
ms, theta, amu_scat, amu_tot_i, amu_tot_s)
AAAB, BBBB, Area_B = self._sum_rom(nan-1, 1, -A, radius_1, radius_2,
ms, theta, amu_scat, amu_tot_i, amu_tot_s)
Area_C = Area_A + Area_B
Acsc = (AAAA + AAAB)/Area_C
Acc = (BBBA + BBBB)/Area_C
return Ass, Assc, Acsc, Acc
#------------------------------------------------------------------------------
def _sum_rom(self, n_scat, n_abs, a, r1, r2, ms, theta, amu_scat, amu_tot_i, amu_tot_s):
#n_scat is region for scattering
#n_abs is region for absorption
nan = self._number_can
omega_add = 0.
if a < 0.:
omega_add = math.pi
AAA = 0.
BBB = 0.
Area = 0.
theta_deg = math.pi - theta
num = ms
r_step = (r2 - r1)/ms
r_add = -0.5*r_step + r1
# start loop over M
for M in range(1, num+1):
r = M*r_step + r_add
number_omega = int(math.pi*r/r_step)
omega_ster = math.pi/number_omega
omega_deg = -0.5*omega_ster + omega_add
Area_y = r*r_step*omega_ster*amu_scat[n_scat]
sum_1 = 0.
sum_2 = 0.
I = 1
Area_sum = 0.
for _ in range(1, number_omega +1):
omega = I*omega_ster + omega_deg
distance = r*math.sin(omega)
skip = True
if abs(distance) <= a:
#
# CALCULATE DISTANCE INCIDENT NEUTRON PASSES THROUGH EACH ANNULUS
LIS = []
for j in range(0, nan):
LIST = self._distance(r, self._radii[j], omega)
LISN = self._distance(r, self._radii[j+1], omega)
LIS.append(LISN - LIST)
#
# CALCULATE DISTANCE SCATTERED NEUTRON PASSES THROUGH EACH ANNULUS
O = omega + theta_deg
LSS = []
for j in range(0, nan):
LSST = self._distance(r, self._radii[j], O)
LSSN = self._distance(r, self._radii[j+1], O)
LSS.append(LSSN - LSST)
#
# CALCULATE ABSORBTION FOR PATH THROUGH ALL ANNULI,AND THROUGH INNER ANNULI
path = np.zeros(3)
# split into input (I) and scattered (S) paths
path[0] += amu_tot_i[0]*LIS[0] + amu_tot_s[0]*LSS[0]
if nan == 2:
path[2] += amu_tot_i[1]*LIS[1] + amu_tot_s[1]*LSS[1]
path[1] = path[0] + path[2]
sum_1 += math.exp(-path[n_abs])
sum_2 += math.exp(-path[n_abs +1])
Area_sum += 1.0
skip = False
if skip:
I = number_omega -I +2
else:
I += 1
AAA += sum_1*Area_y
BBB += sum_2*Area_y
Area += Area_sum*Area_y
return AAA, BBB, Area
#------------------------------------------------------------------------------
def _distance(self, r1, radius, omega):
r = r1
distance = 0.
b = r*math.sin(omega)
if abs(b) < radius:
t = r*math.cos(omega)
c = radius*radius -b*b
d = math.sqrt(c)
if r <= radius:
distance = t + d
else:
distance = d*(1.0 + math.copysign(1.0,t))
return distance
#------------------------------------------------------------------------------
# Register algorithm with Mantid
AlgorithmFactory.subscribe(CylinderPaalmanPingsCorrection)