sans_gen.py @ 318b5bbb

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2release_4.0.1ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 318b5bbb was 318b5bbb, checked in by Jae Cho <jhjcho@…>, 11 years ago
Added polarization and magnetic stuffs
Property mode set to `100644`
File size: 30.9 KB

Line
1	"""
2	SANS generic computation and sld file readers
3	"""
4	from sans.models.BaseComponent import BaseComponent
5	import sans.models.sans_extension.sld2i as mod
6	import numpy
7	import os
8
9	MFactor_AM = 2.853E-12
10	MFactor_mT = 2.3164E-9
11	METER2ANG = 1.0E+10
12
13	def mag2sld(mag, v_unit=None):
14	"""
15	Convert magnetization to magnatic SLD
16	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
17	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
18	"""
19	if v_unit == "A/m":
20	factor = MFactor_AM
21	elif v_unit == "mT":
22	factor = MFactor_mT
23	else:
24	raise ValueError, "Invalid valueunit"
25	sld_m = factor * mag
26	return sld_m
27
28	class GenSAS(BaseComponent):
29	"""
30	Generic SAS computation Model based on sld (n & m) arrays
31	"""
32	def __init__(self):
33	"""
34	Init
35
36	:Params sld_data: MagSLD object
37	"""
38	# Initialize BaseComponent
39	BaseComponent.__init__(self)
40	self.sld_data = None
41	self.data_pos_unit = None
42	self.data_x = None
43	self.data_y = None
44	self.data_z = None
45	self.data_sldn = None
46	self.data_mx = None
47	self.data_my = None
48	self.data_mz = None
49	self.volume = 1000 #[A^3]
50	## Name of the model
51	self.name = "GenSAS"
52	## Define parameters
53	self.params = {}
54	self.params['scale'] = 1.0
55	self.params['background'] = 0.0
56	self.params['Up_frac_i'] = 1.0
57	self.params['Up_frac_f'] = 1.0
58	self.params['Up_theta'] = 0.0
59	self.description='GenSAS'
60	## Parameter details [units, min, max]
61	self.details = {}
62	self.details['scale'] = ['', None, None]
63	self.details['background'] = ['[1/cm]', None, None]
64	self.details['Up_frac_i'] = ['[u/(u+d)]', None, None]
65	self.details['Up_frac_f'] = ['[u/(u+d)]', None, None]
66	self.details['Up_theta'] = ['[deg]', None, None]
67	# fixed parameters
68	self.fixed=[]
69
70	def set_pixel_volume(self, volume):
71	"""
72	Set the volume of a pixel in (A^3) unit
73	"""
74	self.volume = volume
75
76	def _gen(self, x, y, i):
77	"""
78	Evaluate the function
79	:Param x: x-value
80	:return: function value
81	"""
82	len_x = len(self.data_x)
83	len_q = len(x)
84	model = mod.new_GenI(len_x, self.data_x, self.data_y, self.data_z,
85	self.data_sldn, self.data_mx, self.data_my,
86	self.data_mz, self.params['Up_frac_i'],
87	self.params['Up_frac_f'], self.params['Up_theta'])
88	mod.genicom(model, len_q, x, y, i)
89	return self.params['scale'] * i * self.volume \
90	+ self.params['background']
91
92	def set_sld_data(self, sld_data=None):
93	"""
94	Sets sld_data
95	"""
96	self.sld_data = sld_data
97	self.data_pos_unit = sld_data.pos_unit
98	self.data_x = sld_data.pos_x
99	self.data_y = sld_data.pos_y
100	self.data_z = sld_data.pos_z
101	self.data_sldn = sld_data.sld_n
102	self.data_mx = sld_data.sld_mx
103	self.data_my = sld_data.sld_my
104	self.data_mz = sld_data.sld_mz
105
106	def getProfile(self):
107	"""
108	Get SLD profile
109
110	: return: sld_data
111	"""
112	return self.sld_data
113
114	def run(self, x = 0.0):
115	"""
116	Evaluate the model
117	:param x: simple value
118	:return: (I value)
119	"""
120	if x.__class__.__name__ == 'list':
121	i_out = numpy.zeros_like(x[0])
122	y_in = numpy.zero_like(x[0])
123	# 1D I is found at y =0 in the 2D pattern
124	return self._gen(x[0],y_in, i_out )
125	else:
126	msg = "Q must be given as list of qx's and qy's"
127	raise ValueError, msg
128
129	def runXY(self, x = 0.0):
130	"""
131	Evaluate the model
132	:param x: simple value
133	:return: I value
134	:Use this runXY() for the computation
135	"""
136	if x.__class__.__name__ == 'list':
137	i_out = numpy.zeros_like(x[0])
138	import time
139	s=time.time()
140	out = self._gen(x[0], x[1], i_out)
141	print "i_out_time",time.time()-s
142	return out
143	else:
144	msg = "Q must be given as list of qx's and qy's"
145	raise ValueError, msg
146
147	def evalDistribution(self, qdist):
148	"""
149	Evaluate a distribution of q-values.
150	* For 1D, a numpy array is expected as input:
151	evalDistribution(q)
152	where q is a numpy array.
153	* For 2D, a list of numpy arrays are expected: [qx_prime,qy_prime],
154	where 1D arrays,
155	:param qdist: ndarray of scalar q-values or list [qx,qy]
156	where qx,qy are 1D ndarrays
157	"""
158	if qdist.__class__.__name__ == 'list':
159	out = self.runXY(qdist)
160	return out
161	else:
162	mesg = "evalDistribution is expecting an ndarray of "
163	mesg += "a list [qx,qy] where qx,qy are arrays."
164	raise RuntimeError, mesg
165
166	class OMF2SLD:
167	"""
168	Convert OMFData to MAgData
169	"""
170	def __init__(self):
171	"""
172	Init
173	"""
174	self.pos_x = None
175	self.pos_y = None
176	self.pos_z = None
177	self.mx = None
178	self.my = None
179	self.mz = None
180	self.sld_n = None
181	self.output = None
182	self.omfdata = None
183
184	def set_data(self, omfdata, shape='rectangular'):
185	"""
186	Set all data
187	"""
188	self.omfdata = omfdata
189	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
190	pos_x = numpy.arange(omfdata.xmin,
191	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
192	omfdata.xstepsize)
193	pos_y = numpy.arange(omfdata.ymin,
194	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
195	omfdata.ystepsize)
196	pos_z = numpy.arange(omfdata.zmin,
197	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
198	omfdata.zstepsize)
199	self.pos_x = numpy.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
200	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
201	self.pos_y = numpy.tile(self.pos_y, int(omfdata.znodes))
202	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
203	self.mx = omfdata.mx
204	self.my = omfdata.my
205	self.mz = omfdata.mz
206	self.sld_n = numpy.zeros(length)
207
208	if omfdata.mx == None:
209	self.mx = numpy.zeros(length)
210	if omfdata.my == None:
211	self.my = numpy.zeros(length)
212	if omfdata.mz == None:
213	self.mz = numpy.zeros(length)
214
215	self._check_data_length(length)
216	self.remove_null_points()
217	mask = numpy.ones(len(self.sld_n), dtype=bool)
218	if shape == 'ellipsoid':
219	try:
220	# Pixel (step) size included
221	x_r = (max(self.pos_x) - min(self.pos_x) + \
222	omfdata.xstepsize) / 2.0
223	y_r = (max(self.pos_y) - min(self.pos_y) + \
224	omfdata.ystepsize) / 2.0
225	z_r = (max(self.pos_z) - min(self.pos_z) + \
226	omfdata.zstepsize) / 2.0
227	x_dir2 = (self.pos_x / x_r) * (self.pos_x / x_r)
228	y_dir2 = (self.pos_y / y_r) * (self.pos_y / y_r)
229	z_dir2 = (self.pos_z / z_r) * (self.pos_z / z_r)
230	mask = (x_dir2 + y_dir2 + z_dir2) <= 1
231	except:
232	pass
233	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
234	self.pos_z[mask], self.sld_n[mask],
235	self.mx[mask], self.my[mask], self.mz[mask])
236
237	def get_omfdata(self):
238	"""
239	Return all data
240	"""
241	return self.omfdata
242
243	def get_output(self):
244	"""
245	Return output
246	"""
247	return self.output
248
249	def _check_data_length(self, length):
250	"""
251	Check if the data lengths are consistent
252	:Params length: data length
253	"""
254	msg = "Error: Inconsistent data length."
255	if len(self.pos_x) != length:
256	raise ValueError, msg
257	if len(self.pos_y) != length:
258	raise ValueError, msg
259	if len(self.pos_z) != length:
260	raise ValueError, msg
261	if len(self.mx) != length:
262	raise ValueError, msg
263	if len(self.my) != length:
264	raise ValueError, msg
265	if len(self.mz) != length:
266	raise ValueError, msg
267
268	def remove_null_points(self, remove=False):
269	"""
270	Removes any mx, my, and mz = 0 points
271	"""
272	if remove:
273	is_nonzero = (numpy.fabs(self.mx) + numpy.fabs(self.my) +
274	numpy.fabs(self.mz)).nonzero()
275	if len(is_nonzero[0]) > 0:
276	self.pos_x = self.pos_x[is_nonzero]
277	self.pos_y = self.pos_y[is_nonzero]
278	self.pos_z = self.pos_z[is_nonzero]
279	self.sld_n = self.sld_n[is_nonzero]
280	self.mx = self.mx[is_nonzero]
281	self.my = self.my[is_nonzero]
282	self.mz = self.mz[is_nonzero]
283	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
284	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
285	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
286
287	def get_magsld(self):
288	"""
289	return MagSLD
290	"""
291	return self.output
292
293
294	class OMFReader:
295	"""
296	Class to load omf/ascii files (3 columns w/header).
297	"""
298	## File type
299	type_name = "OMF ASCII"
300
301	## Wildcards
302	type = ["OMF files (.OMF, .omf)\|*.omf"]
303	## List of allowed extensions
304	ext = ['.omf', '.OMF']
305
306	def read(self, path):
307	"""
308	Load data file
309	:param path: file path
310	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
311	"""
312	data_conv_m = None
313	desc = ""
314	mx = numpy.zeros(0)
315	my = numpy.zeros(0)
316	mz = numpy.zeros(0)
317	try:
318	data_conv_val = None
319	data_conv_mesh = None
320	input_f = open(path, 'rb')
321	buff = input_f.read()
322	lines = buff.split('\n')
323	input_f.close()
324	output = OMFData()
325	valueunit = None
326	for line in lines:
327	toks = line.split()
328	# Read data
329	try:
330	_mx = float(toks[0])
331	_my = float(toks[1])
332	_mz = float(toks[2])
333	_mx = mag2sld(_mx, valueunit)
334	_my = mag2sld(_my, valueunit)
335	_mz = mag2sld(_mz, valueunit)
336	mx = numpy.append(mx, _mx)
337	my = numpy.append(my, _my)
338	mz = numpy.append(mz, _mz)
339	except:
340	# Skip non-data lines
341	pass
342	#Reading Header; Segment count ignored
343	s_line = line.split(":", 1)
344	if s_line[0].lower().count("oommf") > 0:
345	oommf = s_line[1].lstrip()
346	if s_line[0].lower().count("title") > 0:
347	title = s_line[1].lstrip()
348	if s_line[0].lower().count("desc") > 0:
349	desc += s_line[1].lstrip()
350	desc += '\n'
351	if s_line[0].lower().count("meshtype") > 0:
352	meshtype = s_line[1].lstrip()
353	if s_line[0].lower().count("meshunit") > 0:
354	meshunit = s_line[1].lstrip()
355	if meshunit.count("m") < 1:
356	msg = "Error: \n"
357	msg += "We accept only m as meshunit"
358	raise ValueError, msg
359	if s_line[0].lower().count("xbase") > 0:
360	xbase = s_line[1].lstrip()
361	if s_line[0].lower().count("ybase") > 0:
362	ybase = s_line[1].lstrip()
363	if s_line[0].lower().count("zbase") > 0:
364	zbase = s_line[1].lstrip()
365	if s_line[0].lower().count("xstepsize") > 0:
366	xstepsize = s_line[1].lstrip()
367	if s_line[0].lower().count("ystepsize") > 0:
368	ystepsize = s_line[1].lstrip()
369	if s_line[0].lower().count("zstepsize") > 0:
370	zstepsize = s_line[1].lstrip()
371	if s_line[0].lower().count("xnodes") > 0:
372	xnodes = s_line[1].lstrip()
373	if s_line[0].lower().count("ynodes") > 0:
374	ynodes = s_line[1].lstrip()
375	if s_line[0].lower().count("znodes") > 0:
376	znodes = s_line[1].lstrip()
377	if s_line[0].lower().count("xmin") > 0:
378	xmin = s_line[1].lstrip()
379	if s_line[0].lower().count("ymin") > 0:
380	ymin = s_line[1].lstrip()
381	if s_line[0].lower().count("zmin") > 0:
382	zmin = s_line[1].lstrip()
383	if s_line[0].lower().count("xmax") > 0:
384	xmax = s_line[1].lstrip()
385	if s_line[0].lower().count("ymax") > 0:
386	ymax = s_line[1].lstrip()
387	if s_line[0].lower().count("zmax") > 0:
388	zmax = s_line[1].lstrip()
389	if s_line[0].lower().count("valueunit") > 0:
390	valueunit = s_line[1].lstrip().rstrip()
391	if s_line[0].lower().count("valuemultiplier") > 0:
392	valuemultiplier = s_line[1].lstrip()
393	if s_line[0].lower().count("valuerangeminmag") > 0:
394	valuerangeminmag = s_line[1].lstrip()
395	if s_line[0].lower().count("valuerangemaxmag") > 0:
396	valuerangemaxmag = s_line[1].lstrip()
397	if s_line[0].lower().count("end") > 0:
398	#output.set_sldms(mx, my, mz)
399	output.filename = os.path.basename(path)
400	output.oommf = oommf
401	output.title = title
402	output.desc = desc
403	output.meshtype = meshtype
404	output.xbase = float(xbase) * METER2ANG
405	output.ybase = float(ybase) * METER2ANG
406	output.zbase = float(zbase) * METER2ANG
407	output.xstepsize = float(xstepsize) * METER2ANG
408	output.ystepsize = float(ystepsize) * METER2ANG
409	output.zstepsize = float(zstepsize) * METER2ANG
410	output.xnodes = float(xnodes)
411	output.ynodes = float(ynodes)
412	output.znodes = float(znodes)
413	output.xmin = float(xmin) * METER2ANG
414	output.ymin = float(ymin) * METER2ANG
415	output.zmin = float(zmin) * METER2ANG
416	output.xmax = float(xmax) * METER2ANG
417	output.ymax = float(ymax) * METER2ANG
418	output.zmax = float(zmax) * METER2ANG
419	output.valuemultiplier = valuemultiplier
420	output.valuerangeminmag = mag2sld(float(valuerangeminmag),\
421	valueunit)
422	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag),\
423	valueunit)
424	output.set_m(mx, my, mz)
425	return output
426	except:
427	msg = "%s is not supported: \n" % path
428	msg += "We accept only Text format OMF file."
429	raise RuntimeError, msg
430
431	class SLDReader:
432	"""
433	Class to load ascii files (7 columns).
434	"""
435	## File type
436	type_name = "SLD ASCII"
437
438	## Wildcards
439	type = ["sld files (.SLD, .sld)\|*.sld",
440	"txt files (.TXT, .txt)\|*.txt"]
441	## List of allowed extensions
442	ext = ['.txt', '.TXT', '.sld', 'SLD', '.*']
443
444	def read(self, path):
445	"""
446	Load data file
447
448	:param path: file path
449
450	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
451
452	:raise RuntimeError: when the file can't be opened
453	:raise ValueError: when the length of the data vectors are inconsistent
454	"""
455	pos_x = numpy.zeros(0)
456	pos_y = numpy.zeros(0)
457	pos_z = numpy.zeros(0)
458	sld_n = numpy.zeros(0)
459	sld_mx = numpy.zeros(0)
460	sld_my = numpy.zeros(0)
461	sld_mz = numpy.zeros(0)
462	try:
463	input_f = open(path, 'rb')
464	buff = input_f.read()
465	lines = buff.split('\n')
466	input_f.close()
467	for line in lines:
468	toks = line.split()
469	try:
470	_pos_x = float(toks[0])
471	_pos_y = float(toks[1])
472	_pos_z = float(toks[2])
473	_sld_n = float(toks[3])
474	_sld_mx = float(toks[4])
475	_sld_my = float(toks[5])
476	_sld_mz = float(toks[6])
477
478	pos_x = numpy.append(pos_x, _pos_x)
479	pos_y = numpy.append(pos_y, _pos_y)
480	pos_z = numpy.append(pos_z, _pos_z)
481	sld_n = numpy.append(sld_n, _sld_n)
482	sld_mx = numpy.append(sld_mx, _sld_mx)
483	sld_my = numpy.append(sld_my, _sld_my)
484	sld_mz = numpy.append(sld_mz, _sld_mz)
485	except:
486	# Skip non-data lines
487	pass
488	pos_x -= (min(pos_x) + max(pos_x)) / 2.0
489	pos_y -= (min(pos_y) + max(pos_y)) / 2.0
490	pos_z -= (min(pos_z) + max(pos_z)) / 2.0
491
492	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
493	output.filename = os.path.basename(path)
494	return output
495	except:
496	RuntimeError, "%s is not a sld file" % path
497
498	def write(self, path, data):
499	"""
500	Write sld file
501
502	:Param path: file path
503	:Param data: MagSLD data object
504	"""
505	if path == None:
506	raise ValueError, "Missing the file path."
507	if data == None:
508	raise ValueError, "Missing the data to save."
509
510	x_val = data.pos_x
511	y_val = data.pos_y
512	z_val = data.pos_z
513
514	length = len(x_val)
515
516	sld_n = data.sld_n
517	if sld_n == None:
518	sld_n = numpy.zerros(length)
519
520	sld_mx = data.sld_mx
521	if sld_mx == None:
522	sld_mx = numpy.zerros(length)
523	sld_my = numpy.zerros(length)
524	sld_mz = numpy.zerros(length)
525	else:
526	sld_my = data.sld_my
527	sld_mz = data.sld_mz
528
529	out = open(path, 'w')
530	# First Line: Column names
531	out.write("X Y Z SLDN SLDMx SLDMy SLDMz")
532	for ind in range(length):
533	out.write("\n%g %g %g %g %g %g %g" % (x_val[ind], y_val[ind],
534	z_val[ind], sld_n[ind],
535	sld_mx[ind], sld_my[ind],
536	sld_mz[ind]))
537	out.close()
538
539
540	class OMFData:
541	"""
542	OMF Data.
543	"""
544	_meshunit = "A"
545	_valueunit = "A^(-2)"
546	def __init__(self):
547	"""
548	Init for mag SLD
549	"""
550	self.filename = 'default'
551	self.oommf = ''
552	self.title = ''
553	self.desc = ''
554	self.meshtype = ''
555	self.meshunit = self._meshunit
556	self.valueunit = self._valueunit
557	self.xbase = 0.0
558	self.ybase = 0.0
559	self.zbase = 0.0
560	self.xstepsize = 6.0
561	self.ystepsize = 6.0
562	self.zstepsize = 6.0
563	self.xnodes = 10.0
564	self.ynodes = 10.0
565	self.znodes = 10.0
566	self.xmin = 0.0
567	self.ymin = 0.0
568	self.zmin = 0.0
569	self.xmax = 60.0
570	self.ymax = 60.0
571	self.zmax = 60.0
572	self.mx = None
573	self.my = None
574	self.mz = None
575	self.valuemultiplier = 1.
576	self.valuerangeminmag = 0
577	self.valuerangemaxmag = 0
578
579	def __str__(self):
580	"""
581	doc strings
582	"""
583	_str = "Type: %s\n" % self.__class__.__name__
584	_str += "File: %s\n" % self.filename
585	_str += "OOMMF: %s\n" % self.oommf
586	_str += "Title: %s\n" % self.title
587	_str += "Desc: %s\n" % self.desc
588	_str += "meshtype: %s\n" % self.meshtype
589	_str += "meshunit: %s\n" % str(self.meshunit)
590	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
591	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
592	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
593	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
594	self.meshunit)
595	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
596	self.meshunit)
597	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
598	self.meshunit)
599	_str += "xnodes: %s\n" % str(self.xnodes)
600	_str += "ynodes: %s\n" % str(self.ynodes)
601	_str += "znodes: %s\n" % str(self.znodes)
602	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
603	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
604	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
605	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
606	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
607	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
608	_str += "valueunit: %s\n" % self.valueunit
609	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
610	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
611	self.valueunit)
612	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
613	self.valueunit)
614	return _str
615
616	def set_m(self, mx, my, mz):
617	"""
618	Set the Mx, My, Mz values
619	"""
620	self.mx = mx
621	self.my = my
622	self.mz = mz
623
624	class MagSLD:
625	"""
626	Magnetic SLD.
627	"""
628	pos_x = None
629	pos_y = None
630	pos_z = None
631	sld_n = None
632	sld_mx = None
633	sld_my = None
634	sld_mz = None
635	# Units
636	_pos_unit = 'A'
637	_sld_unit = '1/A^(2)'
638
639	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
640	sld_mx=None, sld_my=None, sld_mz=None):
641	"""
642	Init for mag SLD
643	:params : All should be numpy 1D array
644	"""
645	self.is_data = True
646	self.filename = ''
647	self.xstepsize = 6.0
648	self.ystepsize = 6.0
649	self.zstepsize = 6.0
650	self.xnodes = 10.0
651	self.ynodes = 10.0
652	self.znodes = 10.0
653	self.has_stepsize = False
654	self.pos_unit = self._pos_unit
655	self.sld_unit = self._sld_unit
656	self.pos_x = pos_x
657	self.pos_y = pos_y
658	self.pos_z = pos_z
659	self.sld_n = sld_n
660	self.sld_mx = sld_mx
661	self.sld_my = sld_my
662	self.sld_mz = sld_mz
663	self.sld_m = None
664	self.sld_phi = None
665	self.sld_theta = None
666	if sld_mx != None and sld_my != None and sld_mz != None:
667	self.set_sldms(sld_mx, sld_my, sld_mz)
668	self.set_nodes()
669
670	def __str__(self):
671	"""
672	doc strings
673	"""
674	_str = "Type: %s\n" % self.__class__.__name__
675	_str += "File: %s\n" % self.filename
676	_str += "Axis_unit: %s\n" % self.pos_unit
677	_str += "SLD_unit: %s\n" % self.sld_unit
678	return _str
679
680	def set_sldn(self, sld_n):
681	"""
682	Sets neutron SLD
683	"""
684	if sld_n.__class__.__name__ == 'float':
685	if self.is_data:
686	# For data, put the value to only the pixels w non-zero M
687	self.sld_n = numpy.zeros(len(self.pos_x))
688	is_nonzero = (numpy.fabs(self.sld_mx) +
689	numpy.fabs(self.sld_my) +
690	numpy.fabs(self.sld_mz)).nonzero()
691	self.sld_n[is_nonzero] = sld_n
692	else:
693	# For non-data, put the value to all the pixels
694	self.sld_n = numpy.ones(len(self.pos_x)) * sld_n
695	else:
696	self.sld_n = sld_n
697
698	def set_sldms(self, sld_mx, sld_my, sld_mz):
699	"""
700	Sets (\|m\|, m_theta, m_phi)
701	"""
702	if sld_mx.__class__.__name__ == 'float':
703	self.sld_mx = numpy.ones(len(self.pos_x)) * sld_mx
704	else:
705	self.sld_mx = sld_mx
706	if sld_my.__class__.__name__ == 'float':
707	self.sld_my = numpy.ones(len(self.pos_x)) * sld_my
708	else:
709	self.sld_my = sld_my
710	if sld_mz.__class__.__name__ == 'float':
711	self.sld_mz = numpy.ones(len(self.pos_x)) * sld_mz
712	else:
713	self.sld_mz = sld_mz
714
715	sld_m = numpy.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
716	sld_mz * sld_mz)
717	self.sld_m = sld_m
718
719	def get_sldn(self):
720	"""
721	Returns nuclear sld
722	"""
723	return self.sld_n
724
725	def get_sld_mxyz(self):
726	"""
727	Returns (sld_mx, sldmy, sld_mz)
728	"""
729	return (self.sld_mx, self.sldmy, self.sld_mz)
730
731	def get_sld_m(self):
732	"""
733	Returns (sldm, sld_theta, sld_phi)
734	"""
735	return (self.sldm, self.sld_theta, self.sld_phi)
736
737	def set_nodes(self):
738	"""
739	Set xnodes, ynodes, and znodes
740	"""
741	if not self.has_stepsize:
742	self.set_stepsize()
743	try:
744	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
745	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
746	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
747	self.xnodes = int(xdist) + 1
748	self.ynodes = int(ydist) + 1
749	self.znodes = int(zdist) + 1
750	except:
751	self.xnodes = None
752	self.ynodes = None
753	self.znodes = None
754
755	def set_stepsize(self):
756	"""
757	Set xtepsize, ystepsize, and zstepsize
758	"""
759	try:
760	xpos_pre = self.pos_x[0]
761	ypos_pre = self.pos_y[0]
762	zpos_pre = self.pos_z[0]
763	for x_pos in self.pos_x:
764	if xpos_pre != x_pos:
765	self.xstepsize = numpy.fabs(x_pos - xpos_pre)
766	break
767	for y_pos in self.pos_y:
768	if ypos_pre != y_pos:
769	self.ystepsize = numpy.fabs(y_pos - ypos_pre)
770	break
771	for z_pos in self.pos_z:
772	if zpos_pre != z_pos:
773	self.zstepsize = numpy.fabs(z_pos - zpos_pre)
774	break
775	self.has_stepsize = True
776	except:
777	self.xstepsize = None
778	self.ystepsize = None
779	self.zstepsize = None
780	self.has_stepsize = False
781	return self.xstepsize, self.ystepsize, self.zstepsize
782
783
784	def test_load():
785	from danse.common.plottools.arrow3d import Arrow3D
786	import os
787	dir = os.path.abspath(os.path.curdir)
788	print dir
789	for i in range(6):
790	dir, _ = os.path.split(dir)
791	tfile = os.path.join(dir, "test", "CoreXY_ShellZ.txt")
792	ofile = os.path.join(dir, "test", "A_Raw_Example-1.omf")
793	if os.path.isfile(tfile):
794	tfpath = tfile
795	ofpath = ofile
796	break
797	reader = SLDReader()
798	oreader = OMFReader()
799	output = reader.read(tfpath)
800	ooutput = oreader.read(ofpath)
801	foutput = OMF2SLD()
802	foutput.set_data(ooutput)
803
804	import matplotlib.pyplot as plt
805	from mpl_toolkits.mplot3d import Axes3D
806	fig = plt.figure()
807	ax = fig.gca(projection='3d')
808	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
809	alpha = 0.7, markeredgecolor='gray',rasterized=True)
810	gap = 7
811	max_mx = max(output.sld_mx)
812	max_my = max(output.sld_my)
813	max_mz = max(output.sld_mz)
814	max_m = max(max_mx,max_my,max_mz)
815	x2 = output.pos_x+output.sld_mx/max_m * gap
816	y2 = output.pos_y+output.sld_my/max_m * gap
817	z2 = output.pos_z+output.sld_mz/max_m * gap
818	x_arrow = numpy.column_stack((output.pos_x,x2))
819	y_arrow = numpy.column_stack((output.pos_y,y2))
820	z_arrow = numpy.column_stack((output.pos_z,z2))
821	unit_x2 = output.sld_mx / max_m
822	unit_y2 = output.sld_my / max_m
823	unit_z2 = output.sld_mz / max_m
824	color_x = numpy.fabs(unit_x2 * 0.8)
825	color_y = numpy.fabs(unit_y2 * 0.8)
826	color_z = numpy.fabs(unit_z2 * 0.8)
827	colors = numpy.column_stack((color_x, color_y, color_z))
828	a = Arrow3D(None, x_arrow,y_arrow,z_arrow, colors, mutation_scale=10, lw=1,
829	arrowstyle="->", color="y", alpha = 0.5)
830
831	ax.add_artist(a)
832	plt.show()
833
834	def test():
835	import os
836	dir = os.path.abspath(os.path.curdir)
837	for i in range(3):
838	dir, _ = os.path.split(dir)
839	#tfile = os.path.join(dir, "test", "C_Example_Converted.txt")
840	ofile = os.path.join(dir, "test", "A_Raw_Example-1.omf")
841	if os.path.isfile(ofile):
842	#tfpath = tfile
843	ofpath = ofile
844	break
845	#reader = SLDReader()
846	oreader = OMFReader()
847	#output = reader.read(tfpath)
848	ooutput = oreader.read(ofpath)
849	foutput = OMF2SLD()
850	foutput.set_data(ooutput)
851	writer = SLDReader()
852	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
853	foutput.output)
854	model = GenSAS()
855	model.set_sld_data(foutput.output)
856	x = numpy.arange(1000)/10000. + 1e-5
857	y = numpy.arange(1000)/10000. + 1e-5
858	z = numpy.arange(1000)/10000. + 1e-5
859	i = numpy.zeros(1000)
860	out = model.runXY([x,y,i])
861
862	if __name__ == "__main__":
863	#test()
864	test_load()

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SasView

source: sasview/sanscalculator/src/sans/calculator/sans_gen.py @ 318b5bbb

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