sas_gen.py @ 5f0be1f

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 5f0be1f was b6627d9, checked in by Doucet, Mathieu <doucetm@…>, 10 years ago
pylint fixes
Property mode set to `100644`
File size: 40.0 KB

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	* For 1D, a numpy array is expected as input:
200	evalDistribution(q) where q is a numpy array.
201	* For 2D, a list of numpy arrays are expected:
202	[qx_prime,qy_prime], where 1D arrays.
203	:param qdist: ndarray of scalar q-values or list [qx,qy]
204	where qx,qy are 1D ndarrays
205	"""
206	if qdist.__class__.__name__ == 'list':
207	if len(qdist[1]) < 1:
208	out = self.run(qdist)
209	else:
210	out = self.runXY(qdist)
211	return out
212	else:
213	mesg = "evalDistribution is expecting an ndarray of "
214	mesg += "a list [qx,qy] where qx,qy are arrays."
215	raise RuntimeError, mesg
216
217	class OMF2SLD(object):
218	"""
219	Convert OMFData to MAgData
220	"""
221	def __init__(self):
222	"""
223	Init
224	"""
225	self.pos_x = None
226	self.pos_y = None
227	self.pos_z = None
228	self.mx = None
229	self.my = None
230	self.mz = None
231	self.sld_n = None
232	self.vol_pix = None
233	self.output = None
234	self.omfdata = None
235
236	def set_data(self, omfdata, shape='rectangular'):
237	"""
238	Set all data
239	"""
240	self.omfdata = omfdata
241	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
242	pos_x = numpy.arange(omfdata.xmin,
243	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
244	omfdata.xstepsize)
245	pos_y = numpy.arange(omfdata.ymin,
246	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
247	omfdata.ystepsize)
248	pos_z = numpy.arange(omfdata.zmin,
249	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
250	omfdata.zstepsize)
251	self.pos_x = numpy.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
252	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
253	self.pos_y = numpy.tile(self.pos_y, int(omfdata.znodes))
254	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
255	self.mx = omfdata.mx
256	self.my = omfdata.my
257	self.mz = omfdata.mz
258	self.sld_n = numpy.zeros(length)
259
260	if omfdata.mx == None:
261	self.mx = numpy.zeros(length)
262	if omfdata.my == None:
263	self.my = numpy.zeros(length)
264	if omfdata.mz == None:
265	self.mz = numpy.zeros(length)
266
267	self._check_data_length(length)
268	self.remove_null_points(False, False)
269	mask = numpy.ones(len(self.sld_n), dtype=bool)
270	if shape.lower() == 'ellipsoid':
271	try:
272	# Pixel (step) size included
273	x_c = max(self.pos_x) + min(self.pos_x)
274	y_c = max(self.pos_y) + min(self.pos_y)
275	z_c = max(self.pos_z) + min(self.pos_z)
276	x_d = max(self.pos_x) - min(self.pos_x)
277	y_d = max(self.pos_y) - min(self.pos_y)
278	z_d = max(self.pos_z) - min(self.pos_z)
279	x_r = (x_d + omfdata.xstepsize) / 2.0
280	y_r = (y_d + omfdata.ystepsize) / 2.0
281	z_r = (z_d + omfdata.zstepsize) / 2.0
282	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
283	x_dir2 *= x_dir2
284	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
285	y_dir2 *= y_dir2
286	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
287	z_dir2 *= z_dir2
288	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
289	except:
290	logging.error(sys.exc_value)
291	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
292	self.pos_z[mask], self.sld_n[mask],
293	self.mx[mask], self.my[mask], self.mz[mask])
294	self.output.set_pix_type('pixel')
295	self.output.set_pixel_symbols('pixel')
296
297	def get_omfdata(self):
298	"""
299	Return all data
300	"""
301	return self.omfdata
302
303	def get_output(self):
304	"""
305	Return output
306	"""
307	return self.output
308
309	def _check_data_length(self, length):
310	"""
311	Check if the data lengths are consistent
312	:Params length: data length
313	"""
314	msg = "Error: Inconsistent data length."
315	if len(self.pos_x) != length:
316	raise ValueError, msg
317	if len(self.pos_y) != length:
318	raise ValueError, msg
319	if len(self.pos_z) != length:
320	raise ValueError, msg
321	if len(self.mx) != length:
322	raise ValueError, msg
323	if len(self.my) != length:
324	raise ValueError, msg
325	if len(self.mz) != length:
326	raise ValueError, msg
327
328	def remove_null_points(self, remove=False, recenter=False):
329	"""
330	Removes any mx, my, and mz = 0 points
331	"""
332	if remove:
333	is_nonzero = (numpy.fabs(self.mx) + numpy.fabs(self.my) +
334	numpy.fabs(self.mz)).nonzero()
335	if len(is_nonzero[0]) > 0:
336	self.pos_x = self.pos_x[is_nonzero]
337	self.pos_y = self.pos_y[is_nonzero]
338	self.pos_z = self.pos_z[is_nonzero]
339	self.sld_n = self.sld_n[is_nonzero]
340	self.mx = self.mx[is_nonzero]
341	self.my = self.my[is_nonzero]
342	self.mz = self.mz[is_nonzero]
343	if recenter:
344	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
345	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
346	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
347
348	def get_magsld(self):
349	"""
350	return MagSLD
351	"""
352	return self.output
353
354
355	class OMFReader(object):
356	"""
357	Class to load omf/ascii files (3 columns w/header).
358	"""
359	## File type
360	type_name = "OMF ASCII"
361
362	## Wildcards
363	type = ["OMF files (.OMF, .omf)\|*.omf"]
364	## List of allowed extensions
365	ext = ['.omf', '.OMF']
366
367	def read(self, path):
368	"""
369	Load data file
370	:param path: file path
371	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
372	"""
373	desc = ""
374	mx = numpy.zeros(0)
375	my = numpy.zeros(0)
376	mz = numpy.zeros(0)
377	try:
378	input_f = open(path, 'rb')
379	buff = input_f.read()
380	lines = buff.split('\n')
381	input_f.close()
382	output = OMFData()
383	valueunit = None
384	for line in lines:
385	toks = line.split()
386	# Read data
387	try:
388	_mx = float(toks[0])
389	_my = float(toks[1])
390	_mz = float(toks[2])
391	_mx = mag2sld(_mx, valueunit)
392	_my = mag2sld(_my, valueunit)
393	_mz = mag2sld(_mz, valueunit)
394	mx = numpy.append(mx, _mx)
395	my = numpy.append(my, _my)
396	mz = numpy.append(mz, _mz)
397	except:
398	# Skip non-data lines
399	logging.error(sys.exc_value)
400	#Reading Header; Segment count ignored
401	s_line = line.split(":", 1)
402	if s_line[0].lower().count("oommf") > 0:
403	oommf = s_line[1].lstrip()
404	if s_line[0].lower().count("title") > 0:
405	title = s_line[1].lstrip()
406	if s_line[0].lower().count("desc") > 0:
407	desc += s_line[1].lstrip()
408	desc += '\n'
409	if s_line[0].lower().count("meshtype") > 0:
410	meshtype = s_line[1].lstrip()
411	if s_line[0].lower().count("meshunit") > 0:
412	meshunit = s_line[1].lstrip()
413	if meshunit.count("m") < 1:
414	msg = "Error: \n"
415	msg += "We accept only m as meshunit"
416	raise ValueError, msg
417	if s_line[0].lower().count("xbase") > 0:
418	xbase = s_line[1].lstrip()
419	if s_line[0].lower().count("ybase") > 0:
420	ybase = s_line[1].lstrip()
421	if s_line[0].lower().count("zbase") > 0:
422	zbase = s_line[1].lstrip()
423	if s_line[0].lower().count("xstepsize") > 0:
424	xstepsize = s_line[1].lstrip()
425	if s_line[0].lower().count("ystepsize") > 0:
426	ystepsize = s_line[1].lstrip()
427	if s_line[0].lower().count("zstepsize") > 0:
428	zstepsize = s_line[1].lstrip()
429	if s_line[0].lower().count("xnodes") > 0:
430	xnodes = s_line[1].lstrip()
431	if s_line[0].lower().count("ynodes") > 0:
432	ynodes = s_line[1].lstrip()
433	if s_line[0].lower().count("znodes") > 0:
434	znodes = s_line[1].lstrip()
435	if s_line[0].lower().count("xmin") > 0:
436	xmin = s_line[1].lstrip()
437	if s_line[0].lower().count("ymin") > 0:
438	ymin = s_line[1].lstrip()
439	if s_line[0].lower().count("zmin") > 0:
440	zmin = s_line[1].lstrip()
441	if s_line[0].lower().count("xmax") > 0:
442	xmax = s_line[1].lstrip()
443	if s_line[0].lower().count("ymax") > 0:
444	ymax = s_line[1].lstrip()
445	if s_line[0].lower().count("zmax") > 0:
446	zmax = s_line[1].lstrip()
447	if s_line[0].lower().count("valueunit") > 0:
448	valueunit = s_line[1].lstrip().rstrip()
449	if s_line[0].lower().count("valuemultiplier") > 0:
450	valuemultiplier = s_line[1].lstrip()
451	if s_line[0].lower().count("valuerangeminmag") > 0:
452	valuerangeminmag = s_line[1].lstrip()
453	if s_line[0].lower().count("valuerangemaxmag") > 0:
454	valuerangemaxmag = s_line[1].lstrip()
455	if s_line[0].lower().count("end") > 0:
456	output.filename = os.path.basename(path)
457	output.oommf = oommf
458	output.title = title
459	output.desc = desc
460	output.meshtype = meshtype
461	output.xbase = float(xbase) * METER2ANG
462	output.ybase = float(ybase) * METER2ANG
463	output.zbase = float(zbase) * METER2ANG
464	output.xstepsize = float(xstepsize) * METER2ANG
465	output.ystepsize = float(ystepsize) * METER2ANG
466	output.zstepsize = float(zstepsize) * METER2ANG
467	output.xnodes = float(xnodes)
468	output.ynodes = float(ynodes)
469	output.znodes = float(znodes)
470	output.xmin = float(xmin) * METER2ANG
471	output.ymin = float(ymin) * METER2ANG
472	output.zmin = float(zmin) * METER2ANG
473	output.xmax = float(xmax) * METER2ANG
474	output.ymax = float(ymax) * METER2ANG
475	output.zmax = float(zmax) * METER2ANG
476	output.valuemultiplier = valuemultiplier
477	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
478	valueunit)
479	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
480	valueunit)
481	output.set_m(mx, my, mz)
482	return output
483	except:
484	msg = "%s is not supported: \n" % path
485	msg += "We accept only Text format OMF file."
486	raise RuntimeError, msg
487
488	class PDBReader(object):
489	"""
490	PDB reader class: limited for reading the lines starting with 'ATOM'
491	"""
492	type_name = "PDB"
493	## Wildcards
494	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
495	## List of allowed extensions
496	ext = ['.pdb', '.PDB']
497
498	def read(self, path):
499	"""
500	Load data file
501
502	:param path: file path
503	:return: MagSLD
504	:raise RuntimeError: when the file can't be opened
505	"""
506	pos_x = numpy.zeros(0)
507	pos_y = numpy.zeros(0)
508	pos_z = numpy.zeros(0)
509	sld_n = numpy.zeros(0)
510	sld_mx = numpy.zeros(0)
511	sld_my = numpy.zeros(0)
512	sld_mz = numpy.zeros(0)
513	vol_pix = numpy.zeros(0)
514	pix_symbol = numpy.zeros(0)
515	x_line = []
516	y_line = []
517	z_line = []
518	x_lines = []
519	y_lines = []
520	z_lines = []
521	try:
522	input_f = open(path, 'rb')
523	buff = input_f.read()
524	lines = buff.split('\n')
525	input_f.close()
526	num = 0
527	for line in lines:
528	try:
529	# check if line starts with "ATOM"
530	if line[0:6].strip().count('ATM') > 0 or \
531	line[0:6].strip() == 'ATOM':
532	# define fields of interest
533	atom_name = line[12:16].strip()
534	try:
535	float(line[12])
536	atom_name = atom_name[1].upper()
537	except:
538	if len(atom_name) == 4:
539	atom_name = atom_name[0].upper()
540	elif line[12] != ' ':
541	atom_name = atom_name[0].upper() + \
542	atom_name[1].lower()
543	else:
544	atom_name = atom_name[0].upper()
545	_pos_x = float(line[30:38].strip())
546	_pos_y = float(line[38:46].strip())
547	_pos_z = float(line[46:54].strip())
548	pos_x = numpy.append(pos_x, _pos_x)
549	pos_y = numpy.append(pos_y, _pos_y)
550	pos_z = numpy.append(pos_z, _pos_z)
551	try:
552	val = nsf.neutron_sld(atom_name)[0]
553	# sld in Ang^-2 unit
554	val *= 1.0e-6
555	sld_n = numpy.append(sld_n, val)
556	atom = formula(atom_name)
557	# cm to A units
558	vol = 1.0e+24 * atom.mass / atom.density / NA
559	vol_pix = numpy.append(vol_pix, vol)
560	except:
561	print "Error: set the sld of %s to zero"% atom_name
562	sld_n = numpy.append(sld_n, 0.0)
563	sld_mx = numpy.append(sld_mx, 0)
564	sld_my = numpy.append(sld_my, 0)
565	sld_mz = numpy.append(sld_mz, 0)
566	pix_symbol = numpy.append(pix_symbol, atom_name)
567	elif line[0:6].strip().count('CONECT') > 0:
568	toks = line.split()
569	num = int(toks[1]) - 1
570	val_list = []
571	for val in toks[2:]:
572	try:
573	int_val = int(val)
574	except:
575	break
576	if int_val == 0:
577	break
578	val_list.append(int_val)
579	#need val_list ordered
580	for val in val_list:
581	index = val - 1
582	if (pos_x[index], pos_x[num]) in x_line and \
583	(pos_y[index], pos_y[num]) in y_line and \
584	(pos_z[index], pos_z[num]) in z_line:
585	continue
586	x_line.append((pos_x[num], pos_x[index]))
587	y_line.append((pos_y[num], pos_y[index]))
588	z_line.append((pos_z[num], pos_z[index]))
589	if len(x_line) > 0:
590	x_lines.append(x_line)
591	y_lines.append(y_line)
592	z_lines.append(z_line)
593	except:
594	logging.error(sys.exc_value)
595
596	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
597	output.set_conect_lines(x_line, y_line, z_line)
598	output.filename = os.path.basename(path)
599	output.set_pix_type('atom')
600	output.set_pixel_symbols(pix_symbol)
601	output.set_nodes()
602	output.set_pixel_volumes(vol_pix)
603	output.sld_unit = '1/A^(2)'
604	return output
605	except:
606	raise RuntimeError, "%s is not a sld file" % path
607
608	def write(self, path, data):
609	"""
610	Write
611	"""
612	print "Not implemented... "
613
614	class SLDReader(object):
615	"""
616	Class to load ascii files (7 columns).
617	"""
618	## File type
619	type_name = "SLD ASCII"
620	## Wildcards
621	type = ["sld files (.SLD, .sld)\|*.sld",
622	"txt files (.TXT, .txt)\|*.txt",
623	"all files (.)\|."]
624	## List of allowed extensions
625	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
626	def read(self, path):
627	"""
628	Load data file
629	:param path: file path
630	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
631	:raise RuntimeError: when the file can't be opened
632	:raise ValueError: when the length of the data vectors are inconsistent
633	"""
634	try:
635	pos_x = numpy.zeros(0)
636	pos_y = numpy.zeros(0)
637	pos_z = numpy.zeros(0)
638	sld_n = numpy.zeros(0)
639	sld_mx = numpy.zeros(0)
640	sld_my = numpy.zeros(0)
641	sld_mz = numpy.zeros(0)
642	try:
643	# Use numpy to speed up loading
644	input_f = numpy.loadtxt(path, dtype='float', skiprows=1,
645	ndmin=1, unpack=True)
646	pos_x = numpy.array(input_f[0])
647	pos_y = numpy.array(input_f[1])
648	pos_z = numpy.array(input_f[2])
649	sld_n = numpy.array(input_f[3])
650	sld_mx = numpy.array(input_f[4])
651	sld_my = numpy.array(input_f[5])
652	sld_mz = numpy.array(input_f[6])
653	ncols = len(input_f)
654	if ncols == 8:
655	vol_pix = numpy.array(input_f[7])
656	elif ncols == 7:
657	vol_pix = None
658	except:
659	# For older version of numpy
660	input_f = open(path, 'rb')
661	buff = input_f.read()
662	lines = buff.split('\n')
663	input_f.close()
664	for line in lines:
665	toks = line.split()
666	try:
667	_pos_x = float(toks[0])
668	_pos_y = float(toks[1])
669	_pos_z = float(toks[2])
670	_sld_n = float(toks[3])
671	_sld_mx = float(toks[4])
672	_sld_my = float(toks[5])
673	_sld_mz = float(toks[6])
674	pos_x = numpy.append(pos_x, _pos_x)
675	pos_y = numpy.append(pos_y, _pos_y)
676	pos_z = numpy.append(pos_z, _pos_z)
677	sld_n = numpy.append(sld_n, _sld_n)
678	sld_mx = numpy.append(sld_mx, _sld_mx)
679	sld_my = numpy.append(sld_my, _sld_my)
680	sld_mz = numpy.append(sld_mz, _sld_mz)
681	try:
682	_vol_pix = float(toks[7])
683	vol_pix = numpy.append(vol_pix, _vol_pix)
684	except:
685	vol_pix = None
686	except:
687	# Skip non-data lines
688	logging.error(sys.exc_value)
689	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
690	sld_mx, sld_my, sld_mz)
691	output.filename = os.path.basename(path)
692	output.set_pix_type('pixel')
693	output.set_pixel_symbols('pixel')
694	if vol_pix != None:
695	output.set_pixel_volumes(vol_pix)
696	return output
697	except:
698	raise RuntimeError, "%s is not a sld file" % path
699
700	def write(self, path, data):
701	"""
702	Write sld file
703	:Param path: file path
704	:Param data: MagSLD data object
705	"""
706	if path == None:
707	raise ValueError, "Missing the file path."
708	if data == None:
709	raise ValueError, "Missing the data to save."
710	x_val = data.pos_x
711	y_val = data.pos_y
712	z_val = data.pos_z
713	vol_pix = data.vol_pix
714	length = len(x_val)
715	sld_n = data.sld_n
716	if sld_n == None:
717	sld_n = numpy.zeros(length)
718	sld_mx = data.sld_mx
719	if sld_mx == None:
720	sld_mx = numpy.zeros(length)
721	sld_my = numpy.zeros(length)
722	sld_mz = numpy.zeros(length)
723	else:
724	sld_my = data.sld_my
725	sld_mz = data.sld_mz
726	out = open(path, 'w')
727	# First Line: Column names
728	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
729	for ind in range(length):
730	out.write("\n%g %g %g %g %g %g %g %g" % \
731	(x_val[ind], y_val[ind], z_val[ind], sld_n[ind],
732	sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind]))
733	out.close()
734
735
736	class OMFData(object):
737	"""
738	OMF Data.
739	"""
740	_meshunit = "A"
741	_valueunit = "A^(-2)"
742	def __init__(self):
743	"""
744	Init for mag SLD
745	"""
746	self.filename = 'default'
747	self.oommf = ''
748	self.title = ''
749	self.desc = ''
750	self.meshtype = ''
751	self.meshunit = self._meshunit
752	self.valueunit = self._valueunit
753	self.xbase = 0.0
754	self.ybase = 0.0
755	self.zbase = 0.0
756	self.xstepsize = 6.0
757	self.ystepsize = 6.0
758	self.zstepsize = 6.0
759	self.xnodes = 10.0
760	self.ynodes = 10.0
761	self.znodes = 10.0
762	self.xmin = 0.0
763	self.ymin = 0.0
764	self.zmin = 0.0
765	self.xmax = 60.0
766	self.ymax = 60.0
767	self.zmax = 60.0
768	self.mx = None
769	self.my = None
770	self.mz = None
771	self.valuemultiplier = 1.
772	self.valuerangeminmag = 0
773	self.valuerangemaxmag = 0
774
775	def __str__(self):
776	"""
777	doc strings
778	"""
779	_str = "Type: %s\n" % self.__class__.__name__
780	_str += "File: %s\n" % self.filename
781	_str += "OOMMF: %s\n" % self.oommf
782	_str += "Title: %s\n" % self.title
783	_str += "Desc: %s\n" % self.desc
784	_str += "meshtype: %s\n" % self.meshtype
785	_str += "meshunit: %s\n" % str(self.meshunit)
786	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
787	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
788	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
789	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
790	self.meshunit)
791	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
792	self.meshunit)
793	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
794	self.meshunit)
795	_str += "xnodes: %s\n" % str(self.xnodes)
796	_str += "ynodes: %s\n" % str(self.ynodes)
797	_str += "znodes: %s\n" % str(self.znodes)
798	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
799	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
800	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
801	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
802	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
803	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
804	_str += "valueunit: %s\n" % self.valueunit
805	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
806	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
807	self.valueunit)
808	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
809	self.valueunit)
810	return _str
811
812	def set_m(self, mx, my, mz):
813	"""
814	Set the Mx, My, Mz values
815	"""
816	self.mx = mx
817	self.my = my
818	self.mz = mz
819
820	class MagSLD(object):
821	"""
822	Magnetic SLD.
823	"""
824	pos_x = None
825	pos_y = None
826	pos_z = None
827	sld_n = None
828	sld_mx = None
829	sld_my = None
830	sld_mz = None
831	# Units
832	_pos_unit = 'A'
833	_sld_unit = '1/A^(2)'
834	_pix_type = 'pixel'
835
836	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
837	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
838	"""
839	Init for mag SLD
840	:params : All should be numpy 1D array
841	"""
842	self.is_data = True
843	self.filename = ''
844	self.xstepsize = 6.0
845	self.ystepsize = 6.0
846	self.zstepsize = 6.0
847	self.xnodes = 10.0
848	self.ynodes = 10.0
849	self.znodes = 10.0
850	self.has_stepsize = False
851	self.has_conect = False
852	self.pos_unit = self._pos_unit
853	self.sld_unit = self._sld_unit
854	self.pix_type = 'pixel'
855	self.pos_x = pos_x
856	self.pos_y = pos_y
857	self.pos_z = pos_z
858	self.sld_n = sld_n
859	self.line_x = None
860	self.line_y = None
861	self.line_z = None
862	self.sld_mx = sld_mx
863	self.sld_my = sld_my
864	self.sld_mz = sld_mz
865	self.vol_pix = vol_pix
866	self.sld_m = None
867	self.sld_phi = None
868	self.sld_theta = None
869	self.pix_symbol = None
870	if sld_mx != None and sld_my != None and sld_mz != None:
871	self.set_sldms(sld_mx, sld_my, sld_mz)
872	self.set_nodes()
873
874	def __str__(self):
875	"""
876	doc strings
877	"""
878	_str = "Type: %s\n" % self.__class__.__name__
879	_str += "File: %s\n" % self.filename
880	_str += "Axis_unit: %s\n" % self.pos_unit
881	_str += "SLD_unit: %s\n" % self.sld_unit
882	return _str
883
884	def set_pix_type(self, pix_type):
885	"""
886	Set pixel type
887	:Param pix_type: string, 'pixel' or 'atom'
888	"""
889	self.pix_type = pix_type
890
891	def set_sldn(self, sld_n):
892	"""
893	Sets neutron SLD
894	"""
895	if sld_n.__class__.__name__ == 'float':
896	if self.is_data:
897	# For data, put the value to only the pixels w non-zero M
898	is_nonzero = (numpy.fabs(self.sld_mx) +
899	numpy.fabs(self.sld_my) +
900	numpy.fabs(self.sld_mz)).nonzero()
901	self.sld_n = numpy.zeros(len(self.pos_x))
902	if len(self.sld_n[is_nonzero]) > 0:
903	self.sld_n[is_nonzero] = sld_n
904	else:
905	self.sld_n.fill(sld_n)
906	else:
907	# For non-data, put the value to all the pixels
908	self.sld_n = numpy.ones(len(self.pos_x)) * sld_n
909	else:
910	self.sld_n = sld_n
911
912	def set_sldms(self, sld_mx, sld_my, sld_mz):
913	"""
914	Sets (\|m\|, m_theta, m_phi)
915	"""
916	if sld_mx.__class__.__name__ == 'float':
917	self.sld_mx = numpy.ones(len(self.pos_x)) * sld_mx
918	else:
919	self.sld_mx = sld_mx
920	if sld_my.__class__.__name__ == 'float':
921	self.sld_my = numpy.ones(len(self.pos_x)) * sld_my
922	else:
923	self.sld_my = sld_my
924	if sld_mz.__class__.__name__ == 'float':
925	self.sld_mz = numpy.ones(len(self.pos_x)) * sld_mz
926	else:
927	self.sld_mz = sld_mz
928
929	sld_m = numpy.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
930	sld_mz * sld_mz)
931	self.sld_m = sld_m
932
933	def set_pixel_symbols(self, symbol='pixel'):
934	"""
935	Set pixel
936	:Params pixel: str; pixel or atomic symbol, or array of strings
937	"""
938	if self.sld_n == None:
939	return
940	if symbol.__class__.__name__ == 'str':
941	self.pix_symbol = numpy.repeat(symbol, len(self.sld_n))
942	else:
943	self.pix_symbol = symbol
944
945	def set_pixel_volumes(self, vol):
946	"""
947	Set pixel volumes
948	:Params pixel: str; pixel or atomic symbol, or array of strings
949	"""
950	if self.sld_n == None:
951	return
952	if vol.__class__.__name__ == 'ndarray':
953	self.vol_pix = vol
954	elif vol.__class__.__name__.count('float') > 0:
955	self.vol_pix = numpy.repeat(vol, len(self.sld_n))
956	else:
957	self.vol_pix = None
958
959	def get_sldn(self):
960	"""
961	Returns nuclear sld
962	"""
963	return self.sld_n
964
965	def set_nodes(self):
966	"""
967	Set xnodes, ynodes, and znodes
968	"""
969	self.set_stepsize()
970	if self.pix_type == 'pixel':
971	try:
972	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
973	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
974	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
975	self.xnodes = int(xdist) + 1
976	self.ynodes = int(ydist) + 1
977	self.znodes = int(zdist) + 1
978	except:
979	self.xnodes = None
980	self.ynodes = None
981	self.znodes = None
982	else:
983	self.xnodes = None
984	self.ynodes = None
985	self.znodes = None
986
987	def set_stepsize(self):
988	"""
989	Set xtepsize, ystepsize, and zstepsize
990	"""
991	if self.pix_type == 'pixel':
992	try:
993	xpos_pre = self.pos_x[0]
994	ypos_pre = self.pos_y[0]
995	zpos_pre = self.pos_z[0]
996	for x_pos in self.pos_x:
997	if xpos_pre != x_pos:
998	self.xstepsize = numpy.fabs(x_pos - xpos_pre)
999	break
1000	for y_pos in self.pos_y:
1001	if ypos_pre != y_pos:
1002	self.ystepsize = numpy.fabs(y_pos - ypos_pre)
1003	break
1004	for z_pos in self.pos_z:
1005	if zpos_pre != z_pos:
1006	self.zstepsize = numpy.fabs(z_pos - zpos_pre)
1007	break
1008	#default pix volume
1009	self.vol_pix = numpy.ones(len(self.pos_x))
1010	vol = self.xstepsize * self.ystepsize * self.zstepsize
1011	self.set_pixel_volumes(vol)
1012	self.has_stepsize = True
1013	except:
1014	self.xstepsize = None
1015	self.ystepsize = None
1016	self.zstepsize = None
1017	self.vol_pix = None
1018	self.has_stepsize = False
1019	else:
1020	self.xstepsize = None
1021	self.ystepsize = None
1022	self.zstepsize = None
1023	self.has_stepsize = True
1024	return self.xstepsize, self.ystepsize, self.zstepsize
1025
1026	def set_conect_lines(self, line_x, line_y, line_z):
1027	"""
1028	Set bonding line data if taken from pdb
1029	"""
1030	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
1031	return
1032	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
1033	return
1034	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
1035	return
1036	self.has_conect = True
1037	self.line_x = line_x
1038	self.line_y = line_y
1039	self.line_z = line_z
1040
1041	def test_load():
1042	"""
1043	Test code
1044	"""
1045	from sas.plottools.arrow3d import Arrow3D
1046	current_dir = os.path.abspath(os.path.curdir)
1047	print current_dir
1048	for i in range(6):
1049	current_dir, _ = os.path.split(current_dir)
1050	tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt")
1051	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
1052	if os.path.isfile(tfile):
1053	tfpath = tfile
1054	ofpath = ofile
1055	break
1056	reader = SLDReader()
1057	oreader = OMFReader()
1058	output = reader.read(tfpath)
1059	ooutput = oreader.read(ofpath)
1060	foutput = OMF2SLD()
1061	foutput.set_data(ooutput)
1062
1063	import matplotlib.pyplot as plt
1064	fig = plt.figure()
1065	ax = fig.gca(projection='3d')
1066	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
1067	alpha=0.7, markeredgecolor='gray', rasterized=True)
1068	gap = 7
1069	max_mx = max(output.sld_mx)
1070	max_my = max(output.sld_my)
1071	max_mz = max(output.sld_mz)
1072	max_m = max(max_mx, max_my, max_mz)
1073	x2 = output.pos_x+output.sld_mx/max_m * gap
1074	y2 = output.pos_y+output.sld_my/max_m * gap
1075	z2 = output.pos_z+output.sld_mz/max_m * gap
1076	x_arrow = numpy.column_stack((output.pos_x, x2))
1077	y_arrow = numpy.column_stack((output.pos_y, y2))
1078	z_arrow = numpy.column_stack((output.pos_z, z2))
1079	unit_x2 = output.sld_mx / max_m
1080	unit_y2 = output.sld_my / max_m
1081	unit_z2 = output.sld_mz / max_m
1082	color_x = numpy.fabs(unit_x2 * 0.8)
1083	color_y = numpy.fabs(unit_y2 * 0.8)
1084	color_z = numpy.fabs(unit_z2 * 0.8)
1085	colors = numpy.column_stack((color_x, color_y, color_z))
1086	a = Arrow3D(None, x_arrow, y_arrow, z_arrow, colors,
1087	mutation_scale=10, lw=1, arrowstyle="->",
1088	color="y", alpha=0.5)
1089	ax.add_artist(a)
1090	plt.show()
1091
1092	def test():
1093	"""
1094	Test code
1095	"""
1096	current_dir = os.path.abspath(os.path.curdir)
1097	for i in range(3):
1098	current_dir, _ = os.path.split(current_dir)
1099	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
1100	if os.path.isfile(ofile):
1101	ofpath = ofile
1102	break
1103	oreader = OMFReader()
1104	ooutput = oreader.read(ofpath)
1105	foutput = OMF2SLD()
1106	foutput.set_data(ooutput)
1107	writer = SLDReader()
1108	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
1109	foutput.output)
1110	model = GenSAS()
1111	model.set_sld_data(foutput.output)
1112	x = numpy.arange(1000)/10000. + 1e-5
1113	y = numpy.arange(1000)/10000. + 1e-5
1114	i = numpy.zeros(1000)
1115	model.runXY([x, y, i])
1116
1117	if __name__ == "__main__":
1118	test()
1119	test_load()

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SasView

source: sasview/src/sas/calculator/sas_gen.py @ 5f0be1f

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