sas_gen.py @ ac7be54

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 ac7be54 was ac7be54, checked in by Paul Kienzle <pkienzle@…>, 9 years ago
fix sphinx errors in api manual
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Line
1	# pylint: disable=invalid-name
2	"""
3	SAS generic computation and sld file readers
4	"""
5	from sas.models.BaseComponent import BaseComponent
6	import sas.models.sas_extension.sld2i as mod
7	from periodictable import formula
8	from periodictable import nsf
9	import numpy
10	import os
11	import copy
12	import sys
13	import logging
14
15	MFACTOR_AM = 2.853E-12
16	MFACTOR_MT = 2.3164E-9
17	METER2ANG = 1.0E+10
18	#Avogadro constant [1/mol]
19	NA = 6.02214129e+23
20
21	def mag2sld(mag, v_unit=None):
22	"""
23	Convert magnetization to magnatic SLD
24	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
25	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
26	"""
27	if v_unit == "A/m":
28	factor = MFACTOR_AM
29	elif v_unit == "mT":
30	factor = MFACTOR_MT
31	else:
32	raise ValueError, "Invalid valueunit"
33	sld_m = factor * mag
34	return sld_m
35
36	def transform_center(pos_x, pos_y, pos_z):
37	"""
38	re-center
39	:return: posx, posy, posz [arrays]
40	"""
41	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
42	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
43	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
44	return posx, posy, posz
45
46	class GenSAS(BaseComponent):
47	"""
48	Generic SAS computation Model based on sld (n & m) arrays
49	"""
50	def __init__(self):
51	"""
52	Init
53	:Params sld_data: MagSLD object
54	"""
55	# Initialize BaseComponent
56	BaseComponent.__init__(self)
57	self.sld_data = None
58	self.data_pos_unit = None
59	self.data_x = None
60	self.data_y = None
61	self.data_z = None
62	self.data_sldn = None
63	self.data_mx = None
64	self.data_my = None
65	self.data_mz = None
66	self.data_vol = None #[A^3]
67	self.is_avg = False
68	## Name of the model
69	self.name = "GenSAS"
70	## Define parameters
71	self.params = {}
72	self.params['scale'] = 1.0
73	self.params['background'] = 0.0
74	self.params['solvent_SLD'] = 0.0
75	self.params['total_volume'] = 1.0
76	self.params['Up_frac_in'] = 1.0
77	self.params['Up_frac_out'] = 1.0
78	self.params['Up_theta'] = 0.0
79	self.description = 'GenSAS'
80	## Parameter details [units, min, max]
81	self.details = {}
82	self.details['scale'] = ['', None, None]
83	self.details['background'] = ['[1/cm]', None, None]
84	self.details['solvent_SLD'] = ['1/A^(2)', None, None]
85	self.details['total_volume'] = ['A^(3)', None, None]
86	self.details['Up_frac_in'] = ['[u/(u+d)]', None, None]
87	self.details['Up_frac_out'] = ['[u/(u+d)]', None, None]
88	self.details['Up_theta'] = ['[deg]', None, None]
89	# fixed parameters
90	self.fixed = []
91
92	def set_pixel_volumes(self, volume):
93	"""
94	Set the volume of a pixel in (A^3) unit
95	:Param volume: pixel volume [float]
96	"""
97	if self.data_vol == None:
98	raise
99	self.data_vol = volume
100
101	def set_is_avg(self, is_avg=False):
102	"""
103	Sets is_avg: [bool]
104	"""
105	self.is_avg = is_avg
106
107	def _gen(self, x, y, i):
108	"""
109	Evaluate the function
110	:Param x: array of x-values
111	:Param y: array of y-values
112	:Param i: array of initial i-value
113	:return: function value
114	"""
115	pos_x = self.data_x
116	pos_y = self.data_y
117	pos_z = self.data_z
118	len_x = len(pos_x)
119	if self.is_avg == None:
120	len_x *= -1
121	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
122	len_q = len(x)
123	sldn = copy.deepcopy(self.data_sldn)
124	sldn -= self.params['solvent_SLD']
125	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
126	sldn, self.data_mx, self.data_my,
127	self.data_mz, self.data_vol,
128	self.params['Up_frac_in'],
129	self.params['Up_frac_out'],
130	self.params['Up_theta'])
131	if y == []:
132	mod.genicom(model, len_q, x, i)
133	else:
134	mod.genicomXY(model, len_q, x, y, i)
135	vol_correction = self.data_total_volume / self.params['total_volume']
136	return self.params['scale'] * vol_correction * i + \
137	self.params['background']
138
139	def set_sld_data(self, sld_data=None):
140	"""
141	Sets sld_data
142	"""
143	self.sld_data = sld_data
144	self.data_pos_unit = sld_data.pos_unit
145	self.data_x = sld_data.pos_x
146	self.data_y = sld_data.pos_y
147	self.data_z = sld_data.pos_z
148	self.data_sldn = sld_data.sld_n
149	self.data_mx = sld_data.sld_mx
150	self.data_my = sld_data.sld_my
151	self.data_mz = sld_data.sld_mz
152	self.data_vol = sld_data.vol_pix
153	self.data_total_volume = sum(sld_data.vol_pix)
154	self.params['total_volume'] = sum(sld_data.vol_pix)
155
156	def getProfile(self):
157	"""
158	Get SLD profile
159	: return: sld_data
160	"""
161	return self.sld_data
162
163	def run(self, x=0.0):
164	"""
165	Evaluate the model
166	:param x: simple value
167	:return: (I value)
168	"""
169	if x.__class__.__name__ == 'list':
170	if len(x[1]) > 0:
171	msg = "Not a 1D."
172	raise ValueError, msg
173	i_out = numpy.zeros_like(x[0])
174	# 1D I is found at y =0 in the 2D pattern
175	out = self._gen(x[0], [], i_out)
176	return out
177	else:
178	msg = "Q must be given as list of qx's and qy's"
179	raise ValueError, msg
180
181	def runXY(self, x=0.0):
182	"""
183	Evaluate the model
184	:param x: simple value
185	:return: I value
186	:Use this runXY() for the computation
187	"""
188	if x.__class__.__name__ == 'list':
189	i_out = numpy.zeros_like(x[0])
190	out = self._gen(x[0], x[1], i_out)
191	return out
192	else:
193	msg = "Q must be given as list of qx's and qy's"
194	raise ValueError, msg
195
196	def evalDistribution(self, qdist):
197	"""
198	Evaluate a distribution of q-values.
199
200	:param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy]
201	where qx,qy are 1D ndarrays (for 2D).
202	"""
203	if qdist.__class__.__name__ == 'list':
204	if len(qdist[1]) < 1:
205	out = self.run(qdist)
206	else:
207	out = self.runXY(qdist)
208	return out
209	else:
210	mesg = "evalDistribution is expecting an ndarray of "
211	mesg += "a list [qx,qy] where qx,qy are arrays."
212	raise RuntimeError, mesg
213
214	class OMF2SLD(object):
215	"""
216	Convert OMFData to MAgData
217	"""
218	def __init__(self):
219	"""
220	Init
221	"""
222	self.pos_x = None
223	self.pos_y = None
224	self.pos_z = None
225	self.mx = None
226	self.my = None
227	self.mz = None
228	self.sld_n = None
229	self.vol_pix = None
230	self.output = None
231	self.omfdata = None
232
233	def set_data(self, omfdata, shape='rectangular'):
234	"""
235	Set all data
236	"""
237	self.omfdata = omfdata
238	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
239	pos_x = numpy.arange(omfdata.xmin,
240	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
241	omfdata.xstepsize)
242	pos_y = numpy.arange(omfdata.ymin,
243	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
244	omfdata.ystepsize)
245	pos_z = numpy.arange(omfdata.zmin,
246	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
247	omfdata.zstepsize)
248	self.pos_x = numpy.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
249	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
250	self.pos_y = numpy.tile(self.pos_y, int(omfdata.znodes))
251	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
252	self.mx = omfdata.mx
253	self.my = omfdata.my
254	self.mz = omfdata.mz
255	self.sld_n = numpy.zeros(length)
256
257	if omfdata.mx == None:
258	self.mx = numpy.zeros(length)
259	if omfdata.my == None:
260	self.my = numpy.zeros(length)
261	if omfdata.mz == None:
262	self.mz = numpy.zeros(length)
263
264	self._check_data_length(length)
265	self.remove_null_points(False, False)
266	mask = numpy.ones(len(self.sld_n), dtype=bool)
267	if shape.lower() == 'ellipsoid':
268	try:
269	# Pixel (step) size included
270	x_c = max(self.pos_x) + min(self.pos_x)
271	y_c = max(self.pos_y) + min(self.pos_y)
272	z_c = max(self.pos_z) + min(self.pos_z)
273	x_d = max(self.pos_x) - min(self.pos_x)
274	y_d = max(self.pos_y) - min(self.pos_y)
275	z_d = max(self.pos_z) - min(self.pos_z)
276	x_r = (x_d + omfdata.xstepsize) / 2.0
277	y_r = (y_d + omfdata.ystepsize) / 2.0
278	z_r = (z_d + omfdata.zstepsize) / 2.0
279	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
280	x_dir2 *= x_dir2
281	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
282	y_dir2 *= y_dir2
283	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
284	z_dir2 *= z_dir2
285	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
286	except:
287	logging.error(sys.exc_value)
288	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
289	self.pos_z[mask], self.sld_n[mask],
290	self.mx[mask], self.my[mask], self.mz[mask])
291	self.output.set_pix_type('pixel')
292	self.output.set_pixel_symbols('pixel')
293
294	def get_omfdata(self):
295	"""
296	Return all data
297	"""
298	return self.omfdata
299
300	def get_output(self):
301	"""
302	Return output
303	"""
304	return self.output
305
306	def _check_data_length(self, length):
307	"""
308	Check if the data lengths are consistent
309	:Params length: data length
310	"""
311	msg = "Error: Inconsistent data length."
312	if len(self.pos_x) != length:
313	raise ValueError, msg
314	if len(self.pos_y) != length:
315	raise ValueError, msg
316	if len(self.pos_z) != length:
317	raise ValueError, msg
318	if len(self.mx) != length:
319	raise ValueError, msg
320	if len(self.my) != length:
321	raise ValueError, msg
322	if len(self.mz) != length:
323	raise ValueError, msg
324
325	def remove_null_points(self, remove=False, recenter=False):
326	"""
327	Removes any mx, my, and mz = 0 points
328	"""
329	if remove:
330	is_nonzero = (numpy.fabs(self.mx) + numpy.fabs(self.my) +
331	numpy.fabs(self.mz)).nonzero()
332	if len(is_nonzero[0]) > 0:
333	self.pos_x = self.pos_x[is_nonzero]
334	self.pos_y = self.pos_y[is_nonzero]
335	self.pos_z = self.pos_z[is_nonzero]
336	self.sld_n = self.sld_n[is_nonzero]
337	self.mx = self.mx[is_nonzero]
338	self.my = self.my[is_nonzero]
339	self.mz = self.mz[is_nonzero]
340	if recenter:
341	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
342	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
343	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
344
345	def get_magsld(self):
346	"""
347	return MagSLD
348	"""
349	return self.output
350
351
352	class OMFReader(object):
353	"""
354	Class to load omf/ascii files (3 columns w/header).
355	"""
356	## File type
357	type_name = "OMF ASCII"
358
359	## Wildcards
360	type = ["OMF files (.OMF, .omf)\|*.omf"]
361	## List of allowed extensions
362	ext = ['.omf', '.OMF']
363
364	def read(self, path):
365	"""
366	Load data file
367	:param path: file path
368	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
369	"""
370	desc = ""
371	mx = numpy.zeros(0)
372	my = numpy.zeros(0)
373	mz = numpy.zeros(0)
374	try:
375	input_f = open(path, 'rb')
376	buff = input_f.read()
377	lines = buff.split('\n')
378	input_f.close()
379	output = OMFData()
380	valueunit = None
381	for line in lines:
382	toks = line.split()
383	# Read data
384	try:
385	_mx = float(toks[0])
386	_my = float(toks[1])
387	_mz = float(toks[2])
388	_mx = mag2sld(_mx, valueunit)
389	_my = mag2sld(_my, valueunit)
390	_mz = mag2sld(_mz, valueunit)
391	mx = numpy.append(mx, _mx)
392	my = numpy.append(my, _my)
393	mz = numpy.append(mz, _mz)
394	except:
395	# Skip non-data lines
396	logging.error(sys.exc_value)
397	#Reading Header; Segment count ignored
398	s_line = line.split(":", 1)
399	if s_line[0].lower().count("oommf") > 0:
400	oommf = s_line[1].lstrip()
401	if s_line[0].lower().count("title") > 0:
402	title = s_line[1].lstrip()
403	if s_line[0].lower().count("desc") > 0:
404	desc += s_line[1].lstrip()
405	desc += '\n'
406	if s_line[0].lower().count("meshtype") > 0:
407	meshtype = s_line[1].lstrip()
408	if s_line[0].lower().count("meshunit") > 0:
409	meshunit = s_line[1].lstrip()
410	if meshunit.count("m") < 1:
411	msg = "Error: \n"
412	msg += "We accept only m as meshunit"
413	raise ValueError, msg
414	if s_line[0].lower().count("xbase") > 0:
415	xbase = s_line[1].lstrip()
416	if s_line[0].lower().count("ybase") > 0:
417	ybase = s_line[1].lstrip()
418	if s_line[0].lower().count("zbase") > 0:
419	zbase = s_line[1].lstrip()
420	if s_line[0].lower().count("xstepsize") > 0:
421	xstepsize = s_line[1].lstrip()
422	if s_line[0].lower().count("ystepsize") > 0:
423	ystepsize = s_line[1].lstrip()
424	if s_line[0].lower().count("zstepsize") > 0:
425	zstepsize = s_line[1].lstrip()
426	if s_line[0].lower().count("xnodes") > 0:
427	xnodes = s_line[1].lstrip()
428	if s_line[0].lower().count("ynodes") > 0:
429	ynodes = s_line[1].lstrip()
430	if s_line[0].lower().count("znodes") > 0:
431	znodes = s_line[1].lstrip()
432	if s_line[0].lower().count("xmin") > 0:
433	xmin = s_line[1].lstrip()
434	if s_line[0].lower().count("ymin") > 0:
435	ymin = s_line[1].lstrip()
436	if s_line[0].lower().count("zmin") > 0:
437	zmin = s_line[1].lstrip()
438	if s_line[0].lower().count("xmax") > 0:
439	xmax = s_line[1].lstrip()
440	if s_line[0].lower().count("ymax") > 0:
441	ymax = s_line[1].lstrip()
442	if s_line[0].lower().count("zmax") > 0:
443	zmax = s_line[1].lstrip()
444	if s_line[0].lower().count("valueunit") > 0:
445	valueunit = s_line[1].lstrip().rstrip()
446	if s_line[0].lower().count("valuemultiplier") > 0:
447	valuemultiplier = s_line[1].lstrip()
448	if s_line[0].lower().count("valuerangeminmag") > 0:
449	valuerangeminmag = s_line[1].lstrip()
450	if s_line[0].lower().count("valuerangemaxmag") > 0:
451	valuerangemaxmag = s_line[1].lstrip()
452	if s_line[0].lower().count("end") > 0:
453	output.filename = os.path.basename(path)
454	output.oommf = oommf
455	output.title = title
456	output.desc = desc
457	output.meshtype = meshtype
458	output.xbase = float(xbase) * METER2ANG
459	output.ybase = float(ybase) * METER2ANG
460	output.zbase = float(zbase) * METER2ANG
461	output.xstepsize = float(xstepsize) * METER2ANG
462	output.ystepsize = float(ystepsize) * METER2ANG
463	output.zstepsize = float(zstepsize) * METER2ANG
464	output.xnodes = float(xnodes)
465	output.ynodes = float(ynodes)
466	output.znodes = float(znodes)
467	output.xmin = float(xmin) * METER2ANG
468	output.ymin = float(ymin) * METER2ANG
469	output.zmin = float(zmin) * METER2ANG
470	output.xmax = float(xmax) * METER2ANG
471	output.ymax = float(ymax) * METER2ANG
472	output.zmax = float(zmax) * METER2ANG
473	output.valuemultiplier = valuemultiplier
474	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
475	valueunit)
476	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
477	valueunit)
478	output.set_m(mx, my, mz)
479	return output
480	except:
481	msg = "%s is not supported: \n" % path
482	msg += "We accept only Text format OMF file."
483	raise RuntimeError, msg
484
485	class PDBReader(object):
486	"""
487	PDB reader class: limited for reading the lines starting with 'ATOM'
488	"""
489	type_name = "PDB"
490	## Wildcards
491	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
492	## List of allowed extensions
493	ext = ['.pdb', '.PDB']
494
495	def read(self, path):
496	"""
497	Load data file
498
499	:param path: file path
500	:return: MagSLD
501	:raise RuntimeError: when the file can't be opened
502	"""
503	pos_x = numpy.zeros(0)
504	pos_y = numpy.zeros(0)
505	pos_z = numpy.zeros(0)
506	sld_n = numpy.zeros(0)
507	sld_mx = numpy.zeros(0)
508	sld_my = numpy.zeros(0)
509	sld_mz = numpy.zeros(0)
510	vol_pix = numpy.zeros(0)
511	pix_symbol = numpy.zeros(0)
512	x_line = []
513	y_line = []
514	z_line = []
515	x_lines = []
516	y_lines = []
517	z_lines = []
518	try:
519	input_f = open(path, 'rb')
520	buff = input_f.read()
521	lines = buff.split('\n')
522	input_f.close()
523	num = 0
524	for line in lines:
525	try:
526	# check if line starts with "ATOM"
527	if line[0:6].strip().count('ATM') > 0 or \
528	line[0:6].strip() == 'ATOM':
529	# define fields of interest
530	atom_name = line[12:16].strip()
531	try:
532	float(line[12])
533	atom_name = atom_name[1].upper()
534	except:
535	if len(atom_name) == 4:
536	atom_name = atom_name[0].upper()
537	elif line[12] != ' ':
538	atom_name = atom_name[0].upper() + \
539	atom_name[1].lower()
540	else:
541	atom_name = atom_name[0].upper()
542	_pos_x = float(line[30:38].strip())
543	_pos_y = float(line[38:46].strip())
544	_pos_z = float(line[46:54].strip())
545	pos_x = numpy.append(pos_x, _pos_x)
546	pos_y = numpy.append(pos_y, _pos_y)
547	pos_z = numpy.append(pos_z, _pos_z)
548	try:
549	val = nsf.neutron_sld(atom_name)[0]
550	# sld in Ang^-2 unit
551	val *= 1.0e-6
552	sld_n = numpy.append(sld_n, val)
553	atom = formula(atom_name)
554	# cm to A units
555	vol = 1.0e+24 * atom.mass / atom.density / NA
556	vol_pix = numpy.append(vol_pix, vol)
557	except:
558	print "Error: set the sld of %s to zero"% atom_name
559	sld_n = numpy.append(sld_n, 0.0)
560	sld_mx = numpy.append(sld_mx, 0)
561	sld_my = numpy.append(sld_my, 0)
562	sld_mz = numpy.append(sld_mz, 0)
563	pix_symbol = numpy.append(pix_symbol, atom_name)
564	elif line[0:6].strip().count('CONECT') > 0:
565	toks = line.split()
566	num = int(toks[1]) - 1
567	val_list = []
568	for val in toks[2:]:
569	try:
570	int_val = int(val)
571	except:
572	break
573	if int_val == 0:
574	break
575	val_list.append(int_val)
576	#need val_list ordered
577	for val in val_list:
578	index = val - 1
579	if (pos_x[index], pos_x[num]) in x_line and \
580	(pos_y[index], pos_y[num]) in y_line and \
581	(pos_z[index], pos_z[num]) in z_line:
582	continue
583	x_line.append((pos_x[num], pos_x[index]))
584	y_line.append((pos_y[num], pos_y[index]))
585	z_line.append((pos_z[num], pos_z[index]))
586	if len(x_line) > 0:
587	x_lines.append(x_line)
588	y_lines.append(y_line)
589	z_lines.append(z_line)
590	except:
591	logging.error(sys.exc_value)
592
593	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
594	output.set_conect_lines(x_line, y_line, z_line)
595	output.filename = os.path.basename(path)
596	output.set_pix_type('atom')
597	output.set_pixel_symbols(pix_symbol)
598	output.set_nodes()
599	output.set_pixel_volumes(vol_pix)
600	output.sld_unit = '1/A^(2)'
601	return output
602	except:
603	raise RuntimeError, "%s is not a sld file" % path
604
605	def write(self, path, data):
606	"""
607	Write
608	"""
609	print "Not implemented... "
610
611	class SLDReader(object):
612	"""
613	Class to load ascii files (7 columns).
614	"""
615	## File type
616	type_name = "SLD ASCII"
617	## Wildcards
618	type = ["sld files (.SLD, .sld)\|*.sld",
619	"txt files (.TXT, .txt)\|*.txt",
620	"all files (.)\|."]
621	## List of allowed extensions
622	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
623	def read(self, path):
624	"""
625	Load data file
626	:param path: file path
627	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
628	:raise RuntimeError: when the file can't be opened
629	:raise ValueError: when the length of the data vectors are inconsistent
630	"""
631	try:
632	pos_x = numpy.zeros(0)
633	pos_y = numpy.zeros(0)
634	pos_z = numpy.zeros(0)
635	sld_n = numpy.zeros(0)
636	sld_mx = numpy.zeros(0)
637	sld_my = numpy.zeros(0)
638	sld_mz = numpy.zeros(0)
639	try:
640	# Use numpy to speed up loading
641	input_f = numpy.loadtxt(path, dtype='float', skiprows=1,
642	ndmin=1, unpack=True)
643	pos_x = numpy.array(input_f[0])
644	pos_y = numpy.array(input_f[1])
645	pos_z = numpy.array(input_f[2])
646	sld_n = numpy.array(input_f[3])
647	sld_mx = numpy.array(input_f[4])
648	sld_my = numpy.array(input_f[5])
649	sld_mz = numpy.array(input_f[6])
650	ncols = len(input_f)
651	if ncols == 8:
652	vol_pix = numpy.array(input_f[7])
653	elif ncols == 7:
654	vol_pix = None
655	except:
656	# For older version of numpy
657	input_f = open(path, 'rb')
658	buff = input_f.read()
659	lines = buff.split('\n')
660	input_f.close()
661	for line in lines:
662	toks = line.split()
663	try:
664	_pos_x = float(toks[0])
665	_pos_y = float(toks[1])
666	_pos_z = float(toks[2])
667	_sld_n = float(toks[3])
668	_sld_mx = float(toks[4])
669	_sld_my = float(toks[5])
670	_sld_mz = float(toks[6])
671	pos_x = numpy.append(pos_x, _pos_x)
672	pos_y = numpy.append(pos_y, _pos_y)
673	pos_z = numpy.append(pos_z, _pos_z)
674	sld_n = numpy.append(sld_n, _sld_n)
675	sld_mx = numpy.append(sld_mx, _sld_mx)
676	sld_my = numpy.append(sld_my, _sld_my)
677	sld_mz = numpy.append(sld_mz, _sld_mz)
678	try:
679	_vol_pix = float(toks[7])
680	vol_pix = numpy.append(vol_pix, _vol_pix)
681	except:
682	vol_pix = None
683	except:
684	# Skip non-data lines
685	logging.error(sys.exc_value)
686	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
687	sld_mx, sld_my, sld_mz)
688	output.filename = os.path.basename(path)
689	output.set_pix_type('pixel')
690	output.set_pixel_symbols('pixel')
691	if vol_pix != None:
692	output.set_pixel_volumes(vol_pix)
693	return output
694	except:
695	raise RuntimeError, "%s is not a sld file" % path
696
697	def write(self, path, data):
698	"""
699	Write sld file
700	:Param path: file path
701	:Param data: MagSLD data object
702	"""
703	if path == None:
704	raise ValueError, "Missing the file path."
705	if data == None:
706	raise ValueError, "Missing the data to save."
707	x_val = data.pos_x
708	y_val = data.pos_y
709	z_val = data.pos_z
710	vol_pix = data.vol_pix
711	length = len(x_val)
712	sld_n = data.sld_n
713	if sld_n == None:
714	sld_n = numpy.zeros(length)
715	sld_mx = data.sld_mx
716	if sld_mx == None:
717	sld_mx = numpy.zeros(length)
718	sld_my = numpy.zeros(length)
719	sld_mz = numpy.zeros(length)
720	else:
721	sld_my = data.sld_my
722	sld_mz = data.sld_mz
723	out = open(path, 'w')
724	# First Line: Column names
725	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
726	for ind in range(length):
727	out.write("\n%g %g %g %g %g %g %g %g" % \
728	(x_val[ind], y_val[ind], z_val[ind], sld_n[ind],
729	sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind]))
730	out.close()
731
732
733	class OMFData(object):
734	"""
735	OMF Data.
736	"""
737	_meshunit = "A"
738	_valueunit = "A^(-2)"
739	def __init__(self):
740	"""
741	Init for mag SLD
742	"""
743	self.filename = 'default'
744	self.oommf = ''
745	self.title = ''
746	self.desc = ''
747	self.meshtype = ''
748	self.meshunit = self._meshunit
749	self.valueunit = self._valueunit
750	self.xbase = 0.0
751	self.ybase = 0.0
752	self.zbase = 0.0
753	self.xstepsize = 6.0
754	self.ystepsize = 6.0
755	self.zstepsize = 6.0
756	self.xnodes = 10.0
757	self.ynodes = 10.0
758	self.znodes = 10.0
759	self.xmin = 0.0
760	self.ymin = 0.0
761	self.zmin = 0.0
762	self.xmax = 60.0
763	self.ymax = 60.0
764	self.zmax = 60.0
765	self.mx = None
766	self.my = None
767	self.mz = None
768	self.valuemultiplier = 1.
769	self.valuerangeminmag = 0
770	self.valuerangemaxmag = 0
771
772	def __str__(self):
773	"""
774	doc strings
775	"""
776	_str = "Type: %s\n" % self.__class__.__name__
777	_str += "File: %s\n" % self.filename
778	_str += "OOMMF: %s\n" % self.oommf
779	_str += "Title: %s\n" % self.title
780	_str += "Desc: %s\n" % self.desc
781	_str += "meshtype: %s\n" % self.meshtype
782	_str += "meshunit: %s\n" % str(self.meshunit)
783	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
784	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
785	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
786	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
787	self.meshunit)
788	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
789	self.meshunit)
790	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
791	self.meshunit)
792	_str += "xnodes: %s\n" % str(self.xnodes)
793	_str += "ynodes: %s\n" % str(self.ynodes)
794	_str += "znodes: %s\n" % str(self.znodes)
795	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
796	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
797	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
798	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
799	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
800	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
801	_str += "valueunit: %s\n" % self.valueunit
802	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
803	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
804	self.valueunit)
805	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
806	self.valueunit)
807	return _str
808
809	def set_m(self, mx, my, mz):
810	"""
811	Set the Mx, My, Mz values
812	"""
813	self.mx = mx
814	self.my = my
815	self.mz = mz
816
817	class MagSLD(object):
818	"""
819	Magnetic SLD.
820	"""
821	pos_x = None
822	pos_y = None
823	pos_z = None
824	sld_n = None
825	sld_mx = None
826	sld_my = None
827	sld_mz = None
828	# Units
829	_pos_unit = 'A'
830	_sld_unit = '1/A^(2)'
831	_pix_type = 'pixel'
832
833	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
834	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
835	"""
836	Init for mag SLD
837	:params : All should be numpy 1D array
838	"""
839	self.is_data = True
840	self.filename = ''
841	self.xstepsize = 6.0
842	self.ystepsize = 6.0
843	self.zstepsize = 6.0
844	self.xnodes = 10.0
845	self.ynodes = 10.0
846	self.znodes = 10.0
847	self.has_stepsize = False
848	self.has_conect = False
849	self.pos_unit = self._pos_unit
850	self.sld_unit = self._sld_unit
851	self.pix_type = 'pixel'
852	self.pos_x = pos_x
853	self.pos_y = pos_y
854	self.pos_z = pos_z
855	self.sld_n = sld_n
856	self.line_x = None
857	self.line_y = None
858	self.line_z = None
859	self.sld_mx = sld_mx
860	self.sld_my = sld_my
861	self.sld_mz = sld_mz
862	self.vol_pix = vol_pix
863	self.sld_m = None
864	self.sld_phi = None
865	self.sld_theta = None
866	self.pix_symbol = None
867	if sld_mx != None and sld_my != None and sld_mz != None:
868	self.set_sldms(sld_mx, sld_my, sld_mz)
869	self.set_nodes()
870
871	def __str__(self):
872	"""
873	doc strings
874	"""
875	_str = "Type: %s\n" % self.__class__.__name__
876	_str += "File: %s\n" % self.filename
877	_str += "Axis_unit: %s\n" % self.pos_unit
878	_str += "SLD_unit: %s\n" % self.sld_unit
879	return _str
880
881	def set_pix_type(self, pix_type):
882	"""
883	Set pixel type
884	:Param pix_type: string, 'pixel' or 'atom'
885	"""
886	self.pix_type = pix_type
887
888	def set_sldn(self, sld_n):
889	"""
890	Sets neutron SLD
891	"""
892	if sld_n.__class__.__name__ == 'float':
893	if self.is_data:
894	# For data, put the value to only the pixels w non-zero M
895	is_nonzero = (numpy.fabs(self.sld_mx) +
896	numpy.fabs(self.sld_my) +
897	numpy.fabs(self.sld_mz)).nonzero()
898	self.sld_n = numpy.zeros(len(self.pos_x))
899	if len(self.sld_n[is_nonzero]) > 0:
900	self.sld_n[is_nonzero] = sld_n
901	else:
902	self.sld_n.fill(sld_n)
903	else:
904	# For non-data, put the value to all the pixels
905	self.sld_n = numpy.ones(len(self.pos_x)) * sld_n
906	else:
907	self.sld_n = sld_n
908
909	def set_sldms(self, sld_mx, sld_my, sld_mz):
910	r"""
911	Sets (\\|m\\|, m_theta, m_phi)
912	"""
913	if sld_mx.__class__.__name__ == 'float':
914	self.sld_mx = numpy.ones(len(self.pos_x)) * sld_mx
915	else:
916	self.sld_mx = sld_mx
917	if sld_my.__class__.__name__ == 'float':
918	self.sld_my = numpy.ones(len(self.pos_x)) * sld_my
919	else:
920	self.sld_my = sld_my
921	if sld_mz.__class__.__name__ == 'float':
922	self.sld_mz = numpy.ones(len(self.pos_x)) * sld_mz
923	else:
924	self.sld_mz = sld_mz
925
926	sld_m = numpy.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
927	sld_mz * sld_mz)
928	self.sld_m = sld_m
929
930	def set_pixel_symbols(self, symbol='pixel'):
931	"""
932	Set pixel
933	:Params pixel: str; pixel or atomic symbol, or array of strings
934	"""
935	if self.sld_n == None:
936	return
937	if symbol.__class__.__name__ == 'str':
938	self.pix_symbol = numpy.repeat(symbol, len(self.sld_n))
939	else:
940	self.pix_symbol = symbol
941
942	def set_pixel_volumes(self, vol):
943	"""
944	Set pixel volumes
945	:Params pixel: str; pixel or atomic symbol, or array of strings
946	"""
947	if self.sld_n == None:
948	return
949	if vol.__class__.__name__ == 'ndarray':
950	self.vol_pix = vol
951	elif vol.__class__.__name__.count('float') > 0:
952	self.vol_pix = numpy.repeat(vol, len(self.sld_n))
953	else:
954	self.vol_pix = None
955
956	def get_sldn(self):
957	"""
958	Returns nuclear sld
959	"""
960	return self.sld_n
961
962	def set_nodes(self):
963	"""
964	Set xnodes, ynodes, and znodes
965	"""
966	self.set_stepsize()
967	if self.pix_type == 'pixel':
968	try:
969	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
970	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
971	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
972	self.xnodes = int(xdist) + 1
973	self.ynodes = int(ydist) + 1
974	self.znodes = int(zdist) + 1
975	except:
976	self.xnodes = None
977	self.ynodes = None
978	self.znodes = None
979	else:
980	self.xnodes = None
981	self.ynodes = None
982	self.znodes = None
983
984	def set_stepsize(self):
985	"""
986	Set xtepsize, ystepsize, and zstepsize
987	"""
988	if self.pix_type == 'pixel':
989	try:
990	xpos_pre = self.pos_x[0]
991	ypos_pre = self.pos_y[0]
992	zpos_pre = self.pos_z[0]
993	for x_pos in self.pos_x:
994	if xpos_pre != x_pos:
995	self.xstepsize = numpy.fabs(x_pos - xpos_pre)
996	break
997	for y_pos in self.pos_y:
998	if ypos_pre != y_pos:
999	self.ystepsize = numpy.fabs(y_pos - ypos_pre)
1000	break
1001	for z_pos in self.pos_z:
1002	if zpos_pre != z_pos:
1003	self.zstepsize = numpy.fabs(z_pos - zpos_pre)
1004	break
1005	#default pix volume
1006	self.vol_pix = numpy.ones(len(self.pos_x))
1007	vol = self.xstepsize * self.ystepsize * self.zstepsize
1008	self.set_pixel_volumes(vol)
1009	self.has_stepsize = True
1010	except:
1011	self.xstepsize = None
1012	self.ystepsize = None
1013	self.zstepsize = None
1014	self.vol_pix = None
1015	self.has_stepsize = False
1016	else:
1017	self.xstepsize = None
1018	self.ystepsize = None
1019	self.zstepsize = None
1020	self.has_stepsize = True
1021	return self.xstepsize, self.ystepsize, self.zstepsize
1022
1023	def set_conect_lines(self, line_x, line_y, line_z):
1024	"""
1025	Set bonding line data if taken from pdb
1026	"""
1027	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
1028	return
1029	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
1030	return
1031	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
1032	return
1033	self.has_conect = True
1034	self.line_x = line_x
1035	self.line_y = line_y
1036	self.line_z = line_z
1037
1038	def test_load():
1039	"""
1040	Test code
1041	"""
1042	from sas.plottools.arrow3d import Arrow3D
1043	current_dir = os.path.abspath(os.path.curdir)
1044	print current_dir
1045	for i in range(6):
1046	current_dir, _ = os.path.split(current_dir)
1047	tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt")
1048	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
1049	if os.path.isfile(tfile):
1050	tfpath = tfile
1051	ofpath = ofile
1052	break
1053	reader = SLDReader()
1054	oreader = OMFReader()
1055	output = reader.read(tfpath)
1056	ooutput = oreader.read(ofpath)
1057	foutput = OMF2SLD()
1058	foutput.set_data(ooutput)
1059
1060	import matplotlib.pyplot as plt
1061	fig = plt.figure()
1062	ax = fig.gca(projection='3d')
1063	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
1064	alpha=0.7, markeredgecolor='gray', rasterized=True)
1065	gap = 7
1066	max_mx = max(output.sld_mx)
1067	max_my = max(output.sld_my)
1068	max_mz = max(output.sld_mz)
1069	max_m = max(max_mx, max_my, max_mz)
1070	x2 = output.pos_x+output.sld_mx/max_m * gap
1071	y2 = output.pos_y+output.sld_my/max_m * gap
1072	z2 = output.pos_z+output.sld_mz/max_m * gap
1073	x_arrow = numpy.column_stack((output.pos_x, x2))
1074	y_arrow = numpy.column_stack((output.pos_y, y2))
1075	z_arrow = numpy.column_stack((output.pos_z, z2))
1076	unit_x2 = output.sld_mx / max_m
1077	unit_y2 = output.sld_my / max_m
1078	unit_z2 = output.sld_mz / max_m
1079	color_x = numpy.fabs(unit_x2 * 0.8)
1080	color_y = numpy.fabs(unit_y2 * 0.8)
1081	color_z = numpy.fabs(unit_z2 * 0.8)
1082	colors = numpy.column_stack((color_x, color_y, color_z))
1083	a = Arrow3D(None, x_arrow, y_arrow, z_arrow, colors,
1084	mutation_scale=10, lw=1, arrowstyle="->",
1085	color="y", alpha=0.5)
1086	ax.add_artist(a)
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 = numpy.arange(1000)/10000. + 1e-5
1110	y = numpy.arange(1000)/10000. + 1e-5
1111	i = numpy.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/calculator/sas_gen.py @ ac7be54

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