sas_gen.py @ 0cc77d8

Last change on this file since 0cc77d8 was 0cc77d8, checked in by GitHub <noreply@…>, 8 years ago
Merge branch 'master' into raise
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Line
1	# pylint: disable=invalid-name
2	"""
3	SAS generic computation and sld file readers
4	"""
5	from __future__ import print_function
6
7	import sas.sascalc.calculator.core.sld2i as mod
8	from sas.sascalc.calculator.BaseComponent import BaseComponent
9	from periodictable import formula
10	from periodictable import nsf
11	import numpy as np
12	import os
13	import copy
14	import sys
15	import logging
16
17	logger = logging.getLogger(__name__)
18
19	MFACTOR_AM = 2.853E-12
20	MFACTOR_MT = 2.3164E-9
21	METER2ANG = 1.0E+10
22	#Avogadro constant [1/mol]
23	NA = 6.02214129e+23
24
25	def mag2sld(mag, v_unit=None):
26	"""
27	Convert magnetization to magnatic SLD
28	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
29	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
30	"""
31	if v_unit == "A/m":
32	factor = MFACTOR_AM
33	elif v_unit == "mT":
34	factor = MFACTOR_MT
35	else:
36	raise ValueError("Invalid valueunit")
37	sld_m = factor * mag
38	return sld_m
39
40	def transform_center(pos_x, pos_y, pos_z):
41	"""
42	re-center
43	:return: posx, posy, posz [arrays]
44	"""
45	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
46	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
47	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
48	return posx, posy, posz
49
50	class GenSAS(BaseComponent):
51	"""
52	Generic SAS computation Model based on sld (n & m) arrays
53	"""
54	def __init__(self):
55	"""
56	Init
57	:Params sld_data: MagSLD object
58	"""
59	# Initialize BaseComponent
60	BaseComponent.__init__(self)
61	self.sld_data = None
62	self.data_pos_unit = None
63	self.data_x = None
64	self.data_y = None
65	self.data_z = None
66	self.data_sldn = None
67	self.data_mx = None
68	self.data_my = None
69	self.data_mz = None
70	self.data_vol = None #[A^3]
71	self.is_avg = False
72	## Name of the model
73	self.name = "GenSAS"
74	## Define parameters
75	self.params = {}
76	self.params['scale'] = 1.0
77	self.params['background'] = 0.0
78	self.params['solvent_SLD'] = 0.0
79	self.params['total_volume'] = 1.0
80	self.params['Up_frac_in'] = 1.0
81	self.params['Up_frac_out'] = 1.0
82	self.params['Up_theta'] = 0.0
83	self.description = 'GenSAS'
84	## Parameter details [units, min, max]
85	self.details = {}
86	self.details['scale'] = ['', 0.0, np.inf]
87	self.details['background'] = ['[1/cm]', 0.0, np.inf]
88	self.details['solvent_SLD'] = ['1/A^(2)', -np.inf, np.inf]
89	self.details['total_volume'] = ['A^(3)', 0.0, np.inf]
90	self.details['Up_frac_in'] = ['[u/(u+d)]', 0.0, 1.0]
91	self.details['Up_frac_out'] = ['[u/(u+d)]', 0.0, 1.0]
92	self.details['Up_theta'] = ['[deg]', -np.inf, np.inf]
93	# fixed parameters
94	self.fixed = []
95
96	def set_pixel_volumes(self, volume):
97	"""
98	Set the volume of a pixel in (A^3) unit
99	:Param volume: pixel volume [float]
100	"""
101	if self.data_vol is None:
102	raise
103	self.data_vol = volume
104
105	def set_is_avg(self, is_avg=False):
106	"""
107	Sets is_avg: [bool]
108	"""
109	self.is_avg = is_avg
110
111	def _gen(self, x, y, i):
112	"""
113	Evaluate the function
114	:Param x: array of x-values
115	:Param y: array of y-values
116	:Param i: array of initial i-value
117	:return: function value
118	"""
119	pos_x = self.data_x
120	pos_y = self.data_y
121	pos_z = self.data_z
122	len_x = len(pos_x)
123	if self.is_avg is None:
124	len_x *= -1
125	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
126	len_q = len(x)
127	sldn = copy.deepcopy(self.data_sldn)
128	sldn -= self.params['solvent_SLD']
129	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
130	sldn, self.data_mx, self.data_my,
131	self.data_mz, self.data_vol,
132	self.params['Up_frac_in'],
133	self.params['Up_frac_out'],
134	self.params['Up_theta'])
135	if y == []:
136	mod.genicom(model, len_q, x, i)
137	else:
138	mod.genicomXY(model, len_q, x, y, i)
139	vol_correction = self.data_total_volume / self.params['total_volume']
140	return self.params['scale'] * vol_correction * i + \
141	self.params['background']
142
143	def set_sld_data(self, sld_data=None):
144	"""
145	Sets sld_data
146	"""
147	self.sld_data = sld_data
148	self.data_pos_unit = sld_data.pos_unit
149	self.data_x = sld_data.pos_x
150	self.data_y = sld_data.pos_y
151	self.data_z = sld_data.pos_z
152	self.data_sldn = sld_data.sld_n
153	self.data_mx = sld_data.sld_mx
154	self.data_my = sld_data.sld_my
155	self.data_mz = sld_data.sld_mz
156	self.data_vol = sld_data.vol_pix
157	self.data_total_volume = sum(sld_data.vol_pix)
158	self.params['total_volume'] = sum(sld_data.vol_pix)
159
160	def getProfile(self):
161	"""
162	Get SLD profile
163	: return: sld_data
164	"""
165	return self.sld_data
166
167	def run(self, x=0.0):
168	"""
169	Evaluate the model
170	:param x: simple value
171	:return: (I value)
172	"""
173	if x.__class__.__name__ == 'list':
174	if len(x[1]) > 0:
175	msg = "Not a 1D."
176	raise ValueError(msg)
177	i_out = np.zeros_like(x[0])
178	# 1D I is found at y =0 in the 2D pattern
179	out = self._gen(x[0], [], i_out)
180	return out
181	else:
182	msg = "Q must be given as list of qx's and qy's"
183	raise ValueError(msg)
184
185	def runXY(self, x=0.0):
186	"""
187	Evaluate the model
188	:param x: simple value
189	:return: I value
190	:Use this runXY() for the computation
191	"""
192	if x.__class__.__name__ == 'list':
193	i_out = np.zeros_like(x[0])
194	out = self._gen(x[0], x[1], i_out)
195	return out
196	else:
197	msg = "Q must be given as list of qx's and qy's"
198	raise ValueError(msg)
199
200	def evalDistribution(self, qdist):
201	"""
202	Evaluate a distribution of q-values.
203
204	:param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy]
205	where qx,qy are 1D ndarrays (for 2D).
206	"""
207	if qdist.__class__.__name__ == 'list':
208	if len(qdist[1]) < 1:
209	out = self.run(qdist)
210	else:
211	out = self.runXY(qdist)
212	return out
213	else:
214	mesg = "evalDistribution is expecting an ndarray of "
215	mesg += "a list [qx,qy] where qx,qy are arrays."
216	raise RuntimeError(mesg)
217
218	class OMF2SLD(object):
219	"""
220	Convert OMFData to MAgData
221	"""
222	def __init__(self):
223	"""
224	Init
225	"""
226	self.pos_x = None
227	self.pos_y = None
228	self.pos_z = None
229	self.mx = None
230	self.my = None
231	self.mz = None
232	self.sld_n = None
233	self.vol_pix = None
234	self.output = None
235	self.omfdata = None
236
237	def set_data(self, omfdata, shape='rectangular'):
238	"""
239	Set all data
240	"""
241	self.omfdata = omfdata
242	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
243	pos_x = np.arange(omfdata.xmin,
244	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
245	omfdata.xstepsize)
246	pos_y = np.arange(omfdata.ymin,
247	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
248	omfdata.ystepsize)
249	pos_z = np.arange(omfdata.zmin,
250	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
251	omfdata.zstepsize)
252	self.pos_x = np.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
253	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
254	self.pos_y = np.tile(self.pos_y, int(omfdata.znodes))
255	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
256	self.mx = omfdata.mx
257	self.my = omfdata.my
258	self.mz = omfdata.mz
259	self.sld_n = np.zeros(length)
260
261	if omfdata.mx is None:
262	self.mx = np.zeros(length)
263	if omfdata.my is None:
264	self.my = np.zeros(length)
265	if omfdata.mz is None:
266	self.mz = np.zeros(length)
267
268	self._check_data_length(length)
269	self.remove_null_points(False, False)
270	mask = np.ones(len(self.sld_n), dtype=bool)
271	if shape.lower() == 'ellipsoid':
272	try:
273	# Pixel (step) size included
274	x_c = max(self.pos_x) + min(self.pos_x)
275	y_c = max(self.pos_y) + min(self.pos_y)
276	z_c = max(self.pos_z) + min(self.pos_z)
277	x_d = max(self.pos_x) - min(self.pos_x)
278	y_d = max(self.pos_y) - min(self.pos_y)
279	z_d = max(self.pos_z) - min(self.pos_z)
280	x_r = (x_d + omfdata.xstepsize) / 2.0
281	y_r = (y_d + omfdata.ystepsize) / 2.0
282	z_r = (z_d + omfdata.zstepsize) / 2.0
283	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
284	x_dir2 *= x_dir2
285	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
286	y_dir2 *= y_dir2
287	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
288	z_dir2 *= z_dir2
289	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
290	except:
291	logger.error(sys.exc_value)
292	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
293	self.pos_z[mask], self.sld_n[mask],
294	self.mx[mask], self.my[mask], self.mz[mask])
295	self.output.set_pix_type('pixel')
296	self.output.set_pixel_symbols('pixel')
297
298	def get_omfdata(self):
299	"""
300	Return all data
301	"""
302	return self.omfdata
303
304	def get_output(self):
305	"""
306	Return output
307	"""
308	return self.output
309
310	def _check_data_length(self, length):
311	"""
312	Check if the data lengths are consistent
313	:Params length: data length
314	"""
315	msg = "Error: Inconsistent data length."
316	if len(self.pos_x) != length:
317	raise ValueError(msg)
318	if len(self.pos_y) != length:
319	raise ValueError(msg)
320	if len(self.pos_z) != length:
321	raise ValueError(msg)
322	if len(self.mx) != length:
323	raise ValueError(msg)
324	if len(self.my) != length:
325	raise ValueError(msg)
326	if len(self.mz) != length:
327	raise ValueError(msg)
328
329	def remove_null_points(self, remove=False, recenter=False):
330	"""
331	Removes any mx, my, and mz = 0 points
332	"""
333	if remove:
334	is_nonzero = (np.fabs(self.mx) + np.fabs(self.my) +
335	np.fabs(self.mz)).nonzero()
336	if len(is_nonzero[0]) > 0:
337	self.pos_x = self.pos_x[is_nonzero]
338	self.pos_y = self.pos_y[is_nonzero]
339	self.pos_z = self.pos_z[is_nonzero]
340	self.sld_n = self.sld_n[is_nonzero]
341	self.mx = self.mx[is_nonzero]
342	self.my = self.my[is_nonzero]
343	self.mz = self.mz[is_nonzero]
344	if recenter:
345	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
346	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
347	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
348
349	def get_magsld(self):
350	"""
351	return MagSLD
352	"""
353	return self.output
354
355
356	class OMFReader(object):
357	"""
358	Class to load omf/ascii files (3 columns w/header).
359	"""
360	## File type
361	type_name = "OMF ASCII"
362
363	## Wildcards
364	type = ["OMF files (.OMF, .omf)\|*.omf"]
365	## List of allowed extensions
366	ext = ['.omf', '.OMF']
367
368	def read(self, path):
369	"""
370	Load data file
371	:param path: file path
372	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
373	"""
374	desc = ""
375	mx = np.zeros(0)
376	my = np.zeros(0)
377	mz = np.zeros(0)
378	try:
379	input_f = open(path, 'rb')
380	buff = input_f.read()
381	lines = buff.split('\n')
382	input_f.close()
383	output = OMFData()
384	valueunit = None
385	for line in lines:
386	toks = line.split()
387	# Read data
388	try:
389	_mx = float(toks[0])
390	_my = float(toks[1])
391	_mz = float(toks[2])
392	_mx = mag2sld(_mx, valueunit)
393	_my = mag2sld(_my, valueunit)
394	_mz = mag2sld(_mz, valueunit)
395	mx = np.append(mx, _mx)
396	my = np.append(my, _my)
397	mz = np.append(mz, _mz)
398	except:
399	# Skip non-data lines
400	logger.error(sys.exc_value)
401	#Reading Header; Segment count ignored
402	s_line = line.split(":", 1)
403	if s_line[0].lower().count("oommf") > 0:
404	oommf = s_line[1].lstrip()
405	if s_line[0].lower().count("title") > 0:
406	title = s_line[1].lstrip()
407	if s_line[0].lower().count("desc") > 0:
408	desc += s_line[1].lstrip()
409	desc += '\n'
410	if s_line[0].lower().count("meshtype") > 0:
411	meshtype = s_line[1].lstrip()
412	if s_line[0].lower().count("meshunit") > 0:
413	meshunit = s_line[1].lstrip()
414	if meshunit.count("m") < 1:
415	msg = "Error: \n"
416	msg += "We accept only m as meshunit"
417	raise ValueError(msg)
418	if s_line[0].lower().count("xbase") > 0:
419	xbase = s_line[1].lstrip()
420	if s_line[0].lower().count("ybase") > 0:
421	ybase = s_line[1].lstrip()
422	if s_line[0].lower().count("zbase") > 0:
423	zbase = s_line[1].lstrip()
424	if s_line[0].lower().count("xstepsize") > 0:
425	xstepsize = s_line[1].lstrip()
426	if s_line[0].lower().count("ystepsize") > 0:
427	ystepsize = s_line[1].lstrip()
428	if s_line[0].lower().count("zstepsize") > 0:
429	zstepsize = s_line[1].lstrip()
430	if s_line[0].lower().count("xnodes") > 0:
431	xnodes = s_line[1].lstrip()
432	if s_line[0].lower().count("ynodes") > 0:
433	ynodes = s_line[1].lstrip()
434	if s_line[0].lower().count("znodes") > 0:
435	znodes = s_line[1].lstrip()
436	if s_line[0].lower().count("xmin") > 0:
437	xmin = s_line[1].lstrip()
438	if s_line[0].lower().count("ymin") > 0:
439	ymin = s_line[1].lstrip()
440	if s_line[0].lower().count("zmin") > 0:
441	zmin = s_line[1].lstrip()
442	if s_line[0].lower().count("xmax") > 0:
443	xmax = s_line[1].lstrip()
444	if s_line[0].lower().count("ymax") > 0:
445	ymax = s_line[1].lstrip()
446	if s_line[0].lower().count("zmax") > 0:
447	zmax = s_line[1].lstrip()
448	if s_line[0].lower().count("valueunit") > 0:
449	valueunit = s_line[1].lstrip().rstrip()
450	if s_line[0].lower().count("valuemultiplier") > 0:
451	valuemultiplier = s_line[1].lstrip()
452	if s_line[0].lower().count("valuerangeminmag") > 0:
453	valuerangeminmag = s_line[1].lstrip()
454	if s_line[0].lower().count("valuerangemaxmag") > 0:
455	valuerangemaxmag = s_line[1].lstrip()
456	if s_line[0].lower().count("end") > 0:
457	output.filename = os.path.basename(path)
458	output.oommf = oommf
459	output.title = title
460	output.desc = desc
461	output.meshtype = meshtype
462	output.xbase = float(xbase) * METER2ANG
463	output.ybase = float(ybase) * METER2ANG
464	output.zbase = float(zbase) * METER2ANG
465	output.xstepsize = float(xstepsize) * METER2ANG
466	output.ystepsize = float(ystepsize) * METER2ANG
467	output.zstepsize = float(zstepsize) * METER2ANG
468	output.xnodes = float(xnodes)
469	output.ynodes = float(ynodes)
470	output.znodes = float(znodes)
471	output.xmin = float(xmin) * METER2ANG
472	output.ymin = float(ymin) * METER2ANG
473	output.zmin = float(zmin) * METER2ANG
474	output.xmax = float(xmax) * METER2ANG
475	output.ymax = float(ymax) * METER2ANG
476	output.zmax = float(zmax) * METER2ANG
477	output.valuemultiplier = valuemultiplier
478	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
479	valueunit)
480	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
481	valueunit)
482	output.set_m(mx, my, mz)
483	return output
484	except:
485	msg = "%s is not supported: \n" % path
486	msg += "We accept only Text format OMF file."
487	raise RuntimeError(msg)
488
489	class PDBReader(object):
490	"""
491	PDB reader class: limited for reading the lines starting with 'ATOM'
492	"""
493	type_name = "PDB"
494	## Wildcards
495	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
496	## List of allowed extensions
497	ext = ['.pdb', '.PDB']
498
499	def read(self, path):
500	"""
501	Load data file
502
503	:param path: file path
504	:return: MagSLD
505	:raise RuntimeError: when the file can't be opened
506	"""
507	pos_x = np.zeros(0)
508	pos_y = np.zeros(0)
509	pos_z = np.zeros(0)
510	sld_n = np.zeros(0)
511	sld_mx = np.zeros(0)
512	sld_my = np.zeros(0)
513	sld_mz = np.zeros(0)
514	vol_pix = np.zeros(0)
515	pix_symbol = np.zeros(0)
516	x_line = []
517	y_line = []
518	z_line = []
519	x_lines = []
520	y_lines = []
521	z_lines = []
522	try:
523	input_f = open(path, 'rb')
524	buff = input_f.read()
525	lines = buff.split('\n')
526	input_f.close()
527	num = 0
528	for line in lines:
529	try:
530	# check if line starts with "ATOM"
531	if line[0:6].strip().count('ATM') > 0 or \
532	line[0:6].strip() == 'ATOM':
533	# define fields of interest
534	atom_name = line[12:16].strip()
535	try:
536	float(line[12])
537	atom_name = atom_name[1].upper()
538	except:
539	if len(atom_name) == 4:
540	atom_name = atom_name[0].upper()
541	elif line[12] != ' ':
542	atom_name = atom_name[0].upper() + \
543	atom_name[1].lower()
544	else:
545	atom_name = atom_name[0].upper()
546	_pos_x = float(line[30:38].strip())
547	_pos_y = float(line[38:46].strip())
548	_pos_z = float(line[46:54].strip())
549	pos_x = np.append(pos_x, _pos_x)
550	pos_y = np.append(pos_y, _pos_y)
551	pos_z = np.append(pos_z, _pos_z)
552	try:
553	val = nsf.neutron_sld(atom_name)[0]
554	# sld in Ang^-2 unit
555	val *= 1.0e-6
556	sld_n = np.append(sld_n, val)
557	atom = formula(atom_name)
558	# cm to A units
559	vol = 1.0e+24 * atom.mass / atom.density / NA
560	vol_pix = np.append(vol_pix, vol)
561	except:
562	print("Error: set the sld of %s to zero"% atom_name)
563	sld_n = np.append(sld_n, 0.0)
564	sld_mx = np.append(sld_mx, 0)
565	sld_my = np.append(sld_my, 0)
566	sld_mz = np.append(sld_mz, 0)
567	pix_symbol = np.append(pix_symbol, atom_name)
568	elif line[0:6].strip().count('CONECT') > 0:
569	toks = line.split()
570	num = int(toks[1]) - 1
571	val_list = []
572	for val in toks[2:]:
573	try:
574	int_val = int(val)
575	except:
576	break
577	if int_val == 0:
578	break
579	val_list.append(int_val)
580	#need val_list ordered
581	for val in val_list:
582	index = val - 1
583	if (pos_x[index], pos_x[num]) in x_line and \
584	(pos_y[index], pos_y[num]) in y_line and \
585	(pos_z[index], pos_z[num]) in z_line:
586	continue
587	x_line.append((pos_x[num], pos_x[index]))
588	y_line.append((pos_y[num], pos_y[index]))
589	z_line.append((pos_z[num], pos_z[index]))
590	if len(x_line) > 0:
591	x_lines.append(x_line)
592	y_lines.append(y_line)
593	z_lines.append(z_line)
594	except:
595	logger.error(sys.exc_value)
596
597	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
598	output.set_conect_lines(x_line, y_line, z_line)
599	output.filename = os.path.basename(path)
600	output.set_pix_type('atom')
601	output.set_pixel_symbols(pix_symbol)
602	output.set_nodes()
603	output.set_pixel_volumes(vol_pix)
604	output.sld_unit = '1/A^(2)'
605	return output
606	except:
607	raise RuntimeError("%s is not a sld file" % path)
608
609	def write(self, path, data):
610	"""
611	Write
612	"""
613	print("Not implemented... ")
614
615	class SLDReader(object):
616	"""
617	Class to load ascii files (7 columns).
618	"""
619	## File type
620	type_name = "SLD ASCII"
621	## Wildcards
622	type = ["sld files (.SLD, .sld)\|*.sld",
623	"txt files (.TXT, .txt)\|*.txt",
624	"all files (.)\|."]
625	## List of allowed extensions
626	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
627	def read(self, path):
628	"""
629	Load data file
630	:param path: file path
631	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
632	:raise RuntimeError: when the file can't be opened
633	:raise ValueError: when the length of the data vectors are inconsistent
634	"""
635	try:
636	pos_x = np.zeros(0)
637	pos_y = np.zeros(0)
638	pos_z = np.zeros(0)
639	sld_n = np.zeros(0)
640	sld_mx = np.zeros(0)
641	sld_my = np.zeros(0)
642	sld_mz = np.zeros(0)
643	try:
644	# Use numpy to speed up loading
645	input_f = np.loadtxt(path, dtype='float', skiprows=1,
646	ndmin=1, unpack=True)
647	pos_x = np.array(input_f[0])
648	pos_y = np.array(input_f[1])
649	pos_z = np.array(input_f[2])
650	sld_n = np.array(input_f[3])
651	sld_mx = np.array(input_f[4])
652	sld_my = np.array(input_f[5])
653	sld_mz = np.array(input_f[6])
654	ncols = len(input_f)
655	if ncols == 8:
656	vol_pix = np.array(input_f[7])
657	elif ncols == 7:
658	vol_pix = None
659	except:
660	# For older version of numpy
661	input_f = open(path, 'rb')
662	buff = input_f.read()
663	lines = buff.split('\n')
664	input_f.close()
665	for line in lines:
666	toks = line.split()
667	try:
668	_pos_x = float(toks[0])
669	_pos_y = float(toks[1])
670	_pos_z = float(toks[2])
671	_sld_n = float(toks[3])
672	_sld_mx = float(toks[4])
673	_sld_my = float(toks[5])
674	_sld_mz = float(toks[6])
675	pos_x = np.append(pos_x, _pos_x)
676	pos_y = np.append(pos_y, _pos_y)
677	pos_z = np.append(pos_z, _pos_z)
678	sld_n = np.append(sld_n, _sld_n)
679	sld_mx = np.append(sld_mx, _sld_mx)
680	sld_my = np.append(sld_my, _sld_my)
681	sld_mz = np.append(sld_mz, _sld_mz)
682	try:
683	_vol_pix = float(toks[7])
684	vol_pix = np.append(vol_pix, _vol_pix)
685	except:
686	vol_pix = None
687	except:
688	# Skip non-data lines
689	logger.error(sys.exc_value)
690	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
691	sld_mx, sld_my, sld_mz)
692	output.filename = os.path.basename(path)
693	output.set_pix_type('pixel')
694	output.set_pixel_symbols('pixel')
695	if vol_pix is not None:
696	output.set_pixel_volumes(vol_pix)
697	return output
698	except:
699	raise RuntimeError("%s is not a sld file" % path)
700
701	def write(self, path, data):
702	"""
703	Write sld file
704	:Param path: file path
705	:Param data: MagSLD data object
706	"""
707	if path is None:
708	raise ValueError("Missing the file path.")
709	if data is None:
710	raise ValueError("Missing the data to save.")
711	x_val = data.pos_x
712	y_val = data.pos_y
713	z_val = data.pos_z
714	vol_pix = data.vol_pix
715	length = len(x_val)
716	sld_n = data.sld_n
717	if sld_n is None:
718	sld_n = np.zeros(length)
719	sld_mx = data.sld_mx
720	if sld_mx is None:
721	sld_mx = np.zeros(length)
722	sld_my = np.zeros(length)
723	sld_mz = np.zeros(length)
724	else:
725	sld_my = data.sld_my
726	sld_mz = data.sld_mz
727	out = open(path, 'w')
728	# First Line: Column names
729	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
730	for ind in range(length):
731	out.write("\n%g %g %g %g %g %g %g %g" % \
732	(x_val[ind], y_val[ind], z_val[ind], sld_n[ind],
733	sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind]))
734	out.close()
735
736
737	class OMFData(object):
738	"""
739	OMF Data.
740	"""
741	_meshunit = "A"
742	_valueunit = "A^(-2)"
743	def __init__(self):
744	"""
745	Init for mag SLD
746	"""
747	self.filename = 'default'
748	self.oommf = ''
749	self.title = ''
750	self.desc = ''
751	self.meshtype = ''
752	self.meshunit = self._meshunit
753	self.valueunit = self._valueunit
754	self.xbase = 0.0
755	self.ybase = 0.0
756	self.zbase = 0.0
757	self.xstepsize = 6.0
758	self.ystepsize = 6.0
759	self.zstepsize = 6.0
760	self.xnodes = 10.0
761	self.ynodes = 10.0
762	self.znodes = 10.0
763	self.xmin = 0.0
764	self.ymin = 0.0
765	self.zmin = 0.0
766	self.xmax = 60.0
767	self.ymax = 60.0
768	self.zmax = 60.0
769	self.mx = None
770	self.my = None
771	self.mz = None
772	self.valuemultiplier = 1.
773	self.valuerangeminmag = 0
774	self.valuerangemaxmag = 0
775
776	def __str__(self):
777	"""
778	doc strings
779	"""
780	_str = "Type: %s\n" % self.__class__.__name__
781	_str += "File: %s\n" % self.filename
782	_str += "OOMMF: %s\n" % self.oommf
783	_str += "Title: %s\n" % self.title
784	_str += "Desc: %s\n" % self.desc
785	_str += "meshtype: %s\n" % self.meshtype
786	_str += "meshunit: %s\n" % str(self.meshunit)
787	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
788	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
789	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
790	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
791	self.meshunit)
792	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
793	self.meshunit)
794	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
795	self.meshunit)
796	_str += "xnodes: %s\n" % str(self.xnodes)
797	_str += "ynodes: %s\n" % str(self.ynodes)
798	_str += "znodes: %s\n" % str(self.znodes)
799	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
800	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
801	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
802	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
803	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
804	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
805	_str += "valueunit: %s\n" % self.valueunit
806	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
807	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
808	self.valueunit)
809	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
810	self.valueunit)
811	return _str
812
813	def set_m(self, mx, my, mz):
814	"""
815	Set the Mx, My, Mz values
816	"""
817	self.mx = mx
818	self.my = my
819	self.mz = mz
820
821	class MagSLD(object):
822	"""
823	Magnetic SLD.
824	"""
825	pos_x = None
826	pos_y = None
827	pos_z = None
828	sld_n = None
829	sld_mx = None
830	sld_my = None
831	sld_mz = None
832	# Units
833	_pos_unit = 'A'
834	_sld_unit = '1/A^(2)'
835	_pix_type = 'pixel'
836
837	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
838	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
839	"""
840	Init for mag SLD
841	:params : All should be numpy 1D array
842	"""
843	self.is_data = True
844	self.filename = ''
845	self.xstepsize = 6.0
846	self.ystepsize = 6.0
847	self.zstepsize = 6.0
848	self.xnodes = 10.0
849	self.ynodes = 10.0
850	self.znodes = 10.0
851	self.has_stepsize = False
852	self.has_conect = False
853	self.pos_unit = self._pos_unit
854	self.sld_unit = self._sld_unit
855	self.pix_type = 'pixel'
856	self.pos_x = pos_x
857	self.pos_y = pos_y
858	self.pos_z = pos_z
859	self.sld_n = sld_n
860	self.line_x = None
861	self.line_y = None
862	self.line_z = None
863	self.sld_mx = sld_mx
864	self.sld_my = sld_my
865	self.sld_mz = sld_mz
866	self.vol_pix = vol_pix
867	self.sld_m = None
868	self.sld_phi = None
869	self.sld_theta = None
870	self.pix_symbol = None
871	if sld_mx is not None and sld_my is not None and sld_mz is not None:
872	self.set_sldms(sld_mx, sld_my, sld_mz)
873	self.set_nodes()
874
875	def __str__(self):
876	"""
877	doc strings
878	"""
879	_str = "Type: %s\n" % self.__class__.__name__
880	_str += "File: %s\n" % self.filename
881	_str += "Axis_unit: %s\n" % self.pos_unit
882	_str += "SLD_unit: %s\n" % self.sld_unit
883	return _str
884
885	def set_pix_type(self, pix_type):
886	"""
887	Set pixel type
888	:Param pix_type: string, 'pixel' or 'atom'
889	"""
890	self.pix_type = pix_type
891
892	def set_sldn(self, sld_n):
893	"""
894	Sets neutron SLD
895	"""
896	if sld_n.__class__.__name__ == 'float':
897	if self.is_data:
898	# For data, put the value to only the pixels w non-zero M
899	is_nonzero = (np.fabs(self.sld_mx) +
900	np.fabs(self.sld_my) +
901	np.fabs(self.sld_mz)).nonzero()
902	self.sld_n = np.zeros(len(self.pos_x))
903	if len(self.sld_n[is_nonzero]) > 0:
904	self.sld_n[is_nonzero] = sld_n
905	else:
906	self.sld_n.fill(sld_n)
907	else:
908	# For non-data, put the value to all the pixels
909	self.sld_n = np.ones(len(self.pos_x)) * sld_n
910	else:
911	self.sld_n = sld_n
912
913	def set_sldms(self, sld_mx, sld_my, sld_mz):
914	r"""
915	Sets (\\|m\\|, m_theta, m_phi)
916	"""
917	if sld_mx.__class__.__name__ == 'float':
918	self.sld_mx = np.ones(len(self.pos_x)) * sld_mx
919	else:
920	self.sld_mx = sld_mx
921	if sld_my.__class__.__name__ == 'float':
922	self.sld_my = np.ones(len(self.pos_x)) * sld_my
923	else:
924	self.sld_my = sld_my
925	if sld_mz.__class__.__name__ == 'float':
926	self.sld_mz = np.ones(len(self.pos_x)) * sld_mz
927	else:
928	self.sld_mz = sld_mz
929
930	sld_m = np.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
931	sld_mz * sld_mz)
932	self.sld_m = sld_m
933
934	def set_pixel_symbols(self, symbol='pixel'):
935	"""
936	Set pixel
937	:Params pixel: str; pixel or atomic symbol, or array of strings
938	"""
939	if self.sld_n is None:
940	return
941	if symbol.__class__.__name__ == 'str':
942	self.pix_symbol = np.repeat(symbol, len(self.sld_n))
943	else:
944	self.pix_symbol = symbol
945
946	def set_pixel_volumes(self, vol):
947	"""
948	Set pixel volumes
949	:Params pixel: str; pixel or atomic symbol, or array of strings
950	"""
951	if self.sld_n is None:
952	return
953	if vol.__class__.__name__ == 'ndarray':
954	self.vol_pix = vol
955	elif vol.__class__.__name__.count('float') > 0:
956	self.vol_pix = np.repeat(vol, len(self.sld_n))
957	else:
958	self.vol_pix = None
959
960	def get_sldn(self):
961	"""
962	Returns nuclear sld
963	"""
964	return self.sld_n
965
966	def set_nodes(self):
967	"""
968	Set xnodes, ynodes, and znodes
969	"""
970	self.set_stepsize()
971	if self.pix_type == 'pixel':
972	try:
973	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
974	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
975	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
976	self.xnodes = int(xdist) + 1
977	self.ynodes = int(ydist) + 1
978	self.znodes = int(zdist) + 1
979	except:
980	self.xnodes = None
981	self.ynodes = None
982	self.znodes = None
983	else:
984	self.xnodes = None
985	self.ynodes = None
986	self.znodes = None
987
988	def set_stepsize(self):
989	"""
990	Set xtepsize, ystepsize, and zstepsize
991	"""
992	if self.pix_type == 'pixel':
993	try:
994	xpos_pre = self.pos_x[0]
995	ypos_pre = self.pos_y[0]
996	zpos_pre = self.pos_z[0]
997	for x_pos in self.pos_x:
998	if xpos_pre != x_pos:
999	self.xstepsize = np.fabs(x_pos - xpos_pre)
1000	break
1001	for y_pos in self.pos_y:
1002	if ypos_pre != y_pos:
1003	self.ystepsize = np.fabs(y_pos - ypos_pre)
1004	break
1005	for z_pos in self.pos_z:
1006	if zpos_pre != z_pos:
1007	self.zstepsize = np.fabs(z_pos - zpos_pre)
1008	break
1009	#default pix volume
1010	self.vol_pix = np.ones(len(self.pos_x))
1011	vol = self.xstepsize * self.ystepsize * self.zstepsize
1012	self.set_pixel_volumes(vol)
1013	self.has_stepsize = True
1014	except:
1015	self.xstepsize = None
1016	self.ystepsize = None
1017	self.zstepsize = None
1018	self.vol_pix = None
1019	self.has_stepsize = False
1020	else:
1021	self.xstepsize = None
1022	self.ystepsize = None
1023	self.zstepsize = None
1024	self.has_stepsize = True
1025	return self.xstepsize, self.ystepsize, self.zstepsize
1026
1027	def set_conect_lines(self, line_x, line_y, line_z):
1028	"""
1029	Set bonding line data if taken from pdb
1030	"""
1031	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
1032	return
1033	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
1034	return
1035	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
1036	return
1037	self.has_conect = True
1038	self.line_x = line_x
1039	self.line_y = line_y
1040	self.line_z = line_z
1041
1042	def test_load():
1043	"""
1044	Test code
1045	"""
1046	from mpl_toolkits.mplot3d import Axes3D
1047	current_dir = os.path.abspath(os.path.curdir)
1048	print(current_dir)
1049	for i in range(6):
1050	current_dir, _ = os.path.split(current_dir)
1051	tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt")
1052	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
1053	if os.path.isfile(tfile):
1054	tfpath = tfile
1055	ofpath = ofile
1056	break
1057	reader = SLDReader()
1058	oreader = OMFReader()
1059	output = reader.read(tfpath)
1060	ooutput = oreader.read(ofpath)
1061	foutput = OMF2SLD()
1062	foutput.set_data(ooutput)
1063
1064	import matplotlib.pyplot as plt
1065	fig = plt.figure()
1066	ax = Axes3D(fig)
1067	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
1068	alpha=0.7, markeredgecolor='gray', rasterized=True)
1069	gap = 7
1070	max_mx = max(output.sld_mx)
1071	max_my = max(output.sld_my)
1072	max_mz = max(output.sld_mz)
1073	max_m = max(max_mx, max_my, max_mz)
1074	x2 = output.pos_x+output.sld_mx/max_m * gap
1075	y2 = output.pos_y+output.sld_my/max_m * gap
1076	z2 = output.pos_z+output.sld_mz/max_m * gap
1077	x_arrow = np.column_stack((output.pos_x, x2))
1078	y_arrow = np.column_stack((output.pos_y, y2))
1079	z_arrow = np.column_stack((output.pos_z, z2))
1080	unit_x2 = output.sld_mx / max_m
1081	unit_y2 = output.sld_my / max_m
1082	unit_z2 = output.sld_mz / max_m
1083	color_x = np.fabs(unit_x2 * 0.8)
1084	color_y = np.fabs(unit_y2 * 0.8)
1085	color_z = np.fabs(unit_z2 * 0.8)
1086	colors = np.column_stack((color_x, color_y, color_z))
1087	plt.show()
1088
1089	def test():
1090	"""
1091	Test code
1092	"""
1093	current_dir = os.path.abspath(os.path.curdir)
1094	for i in range(3):
1095	current_dir, _ = os.path.split(current_dir)
1096	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
1097	if os.path.isfile(ofile):
1098	ofpath = ofile
1099	break
1100	oreader = OMFReader()
1101	ooutput = oreader.read(ofpath)
1102	foutput = OMF2SLD()
1103	foutput.set_data(ooutput)
1104	writer = SLDReader()
1105	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
1106	foutput.output)
1107	model = GenSAS()
1108	model.set_sld_data(foutput.output)
1109	x = np.arange(1000)/10000. + 1e-5
1110	y = np.arange(1000)/10000. + 1e-5
1111	i = np.zeros(1000)
1112	model.runXY([x, y, i])
1113
1114	if __name__ == "__main__":
1115	test()
1116	test_load()

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SasView

source: sasview/src/sas/sascalc/calculator/sas_gen.py @ 0cc77d8

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