sans_gen.py @ f468791

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 f468791 was f468791, checked in by Mathieu Doucet <doucetm@…>, 11 years ago
Move plottools under sans
Property mode set to `100644`
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1	"""
2	SANS generic computation and sld file readers
3	"""
4	from sans.models.BaseComponent import BaseComponent
5	import sans.models.sans_extension.sld2i as mod
6	from periodictable import formula
7	from periodictable import nsf
8	import numpy
9	import os
10	import copy
11
12	MFactor_AM = 2.853E-12
13	MFactor_mT = 2.3164E-9
14	METER2ANG = 1.0E+10
15	#Avogadro constant [1/mol]
16	NA = 6.02214129e+23
17
18	def mag2sld(mag, v_unit=None):
19	"""
20	Convert magnetization to magnatic SLD
21	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
22	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
23	"""
24	if v_unit == "A/m":
25	factor = MFactor_AM
26	elif v_unit == "mT":
27	factor = MFactor_mT
28	else:
29	raise ValueError, "Invalid valueunit"
30	sld_m = factor * mag
31	return sld_m
32
33	def transform_center(pos_x, pos_y, pos_z):
34	"""
35	re-center
36
37	:return: posx, posy, posz [arrays]
38	"""
39	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
40	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
41	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
42	return posx, posy, posz
43
44	class GenSAS(BaseComponent):
45	"""
46	Generic SAS computation Model based on sld (n & m) arrays
47	"""
48	def __init__(self):
49	"""
50	Init
51
52	:Params sld_data: MagSLD object
53	"""
54	# Initialize BaseComponent
55	BaseComponent.__init__(self)
56	self.sld_data = None
57	self.data_pos_unit = None
58	self.data_x = None
59	self.data_y = None
60	self.data_z = None
61	self.data_sldn = None
62	self.data_mx = None
63	self.data_my = None
64	self.data_mz = None
65	self.data_vol = None #[A^3]
66	self.is_avg = False
67	## Name of the model
68	self.name = "GenSAS"
69	## Define parameters
70	self.params = {}
71	self.params['scale'] = 1.0
72	self.params['background'] = 0.0
73	self.params['solvent_SLD'] = 0.0
74	self.params['total_volume'] = 1.0
75	self.params['Up_frac_in'] = 1.0
76	self.params['Up_frac_out'] = 1.0
77	self.params['Up_theta'] = 0.0
78	self.description = 'GenSAS'
79	## Parameter details [units, min, max]
80	self.details = {}
81	self.details['scale'] = ['', None, None]
82	self.details['background'] = ['[1/cm]', None, None]
83	self.details['solvent_SLD'] = ['1/A^(2)', None, None]
84	self.details['total_volume'] = ['A^(3)', None, None]
85	self.details['Up_frac_in'] = ['[u/(u+d)]', None, None]
86	self.details['Up_frac_out'] = ['[u/(u+d)]', None, None]
87	self.details['Up_theta'] = ['[deg]', None, None]
88	# fixed parameters
89	self.fixed = []
90
91	def set_pixel_volumes(self, volume):
92	"""
93	Set the volume of a pixel in (A^3) unit
94	:Param volume: pixel volume [float]
95	"""
96	if self.data_vol == None:
97	raise
98	self.data_vol = volume
99
100	def set_is_avg(self, is_avg=False):
101	"""
102	Sets is_avg: [bool]
103	"""
104	self.is_avg = is_avg
105
106	def _gen(self, x, y, i):
107	"""
108	Evaluate the function
109	:Param x: array of x-values
110	:Param y: array of y-values
111	:Param i: array of initial i-value
112	:return: function value
113	"""
114	pos_x = self.data_x
115	pos_y = self.data_y
116	pos_z = self.data_z
117	len_x = len(pos_x)
118	if self.is_avg == None:
119	len_x *= -1
120	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
121	len_q = len(x)
122	sldn = copy.deepcopy(self.data_sldn)
123	sldn -= self.params['solvent_SLD']
124	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
125	sldn, self.data_mx, self.data_my,
126	self.data_mz, self.data_vol,
127	self.params['Up_frac_in'],
128	self.params['Up_frac_out'],
129	self.params['Up_theta'])
130	if y == []:
131	mod.genicom(model, len_q, x, i)
132	else:
133	mod.genicomXY(model, len_q, x, y, i)
134	vol_correction = self.data_total_volume / self.params['total_volume']
135	return self.params['scale'] * vol_correction * i + \
136	self.params['background']
137
138	def set_sld_data(self, sld_data=None):
139	"""
140	Sets sld_data
141	"""
142	self.sld_data = sld_data
143	self.data_pos_unit = sld_data.pos_unit
144	self.data_x = sld_data.pos_x
145	self.data_y = sld_data.pos_y
146	self.data_z = sld_data.pos_z
147	self.data_sldn = sld_data.sld_n
148	self.data_mx = sld_data.sld_mx
149	self.data_my = sld_data.sld_my
150	self.data_mz = sld_data.sld_mz
151	self.data_vol = sld_data.vol_pix
152	self.data_total_volume = sum(sld_data.vol_pix)
153	self.params['total_volume'] = sum(sld_data.vol_pix)
154
155	def getProfile(self):
156	"""
157	Get SLD profile
158
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)
201	where q is a numpy array.
202	* For 2D, a list of numpy arrays are expected: [qx_prime,qy_prime],
203	where 1D arrays,
204	:param qdist: ndarray of scalar q-values or list [qx,qy]
205	where qx,qy are 1D ndarrays
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:
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 = numpy.arange(omfdata.xmin,
244	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
245	omfdata.xstepsize)
246	pos_y = numpy.arange(omfdata.ymin,
247	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
248	omfdata.ystepsize)
249	pos_z = numpy.arange(omfdata.zmin,
250	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
251	omfdata.zstepsize)
252	self.pos_x = numpy.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
253	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
254	self.pos_y = numpy.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 = numpy.zeros(length)
260
261	if omfdata.mx == None:
262	self.mx = numpy.zeros(length)
263	if omfdata.my == None:
264	self.my = numpy.zeros(length)
265	if omfdata.mz == None:
266	self.mz = numpy.zeros(length)
267
268	self._check_data_length(length)
269	self.remove_null_points(False, False)
270	mask = numpy.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	pass
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 = (numpy.fabs(self.mx) + numpy.fabs(self.my) +
335	numpy.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:
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	#data_conv_m = None
375	desc = ""
376	mx = numpy.zeros(0)
377	my = numpy.zeros(0)
378	mz = numpy.zeros(0)
379	try:
380	data_conv_val = None
381	data_conv_mesh = None
382	input_f = open(path, 'rb')
383	buff = input_f.read()
384	lines = buff.split('\n')
385	input_f.close()
386	output = OMFData()
387	valueunit = None
388	for line in lines:
389	toks = line.split()
390	# Read data
391	try:
392	_mx = float(toks[0])
393	_my = float(toks[1])
394	_mz = float(toks[2])
395	_mx = mag2sld(_mx, valueunit)
396	_my = mag2sld(_my, valueunit)
397	_mz = mag2sld(_mz, valueunit)
398	mx = numpy.append(mx, _mx)
399	my = numpy.append(my, _my)
400	mz = numpy.append(mz, _mz)
401	except:
402	# Skip non-data lines
403	pass
404	#Reading Header; Segment count ignored
405	s_line = line.split(":", 1)
406	if s_line[0].lower().count("oommf") > 0:
407	oommf = s_line[1].lstrip()
408	if s_line[0].lower().count("title") > 0:
409	title = s_line[1].lstrip()
410	if s_line[0].lower().count("desc") > 0:
411	desc += s_line[1].lstrip()
412	desc += '\n'
413	if s_line[0].lower().count("meshtype") > 0:
414	meshtype = s_line[1].lstrip()
415	if s_line[0].lower().count("meshunit") > 0:
416	meshunit = s_line[1].lstrip()
417	if meshunit.count("m") < 1:
418	msg = "Error: \n"
419	msg += "We accept only m as meshunit"
420	raise ValueError, msg
421	if s_line[0].lower().count("xbase") > 0:
422	xbase = s_line[1].lstrip()
423	if s_line[0].lower().count("ybase") > 0:
424	ybase = s_line[1].lstrip()
425	if s_line[0].lower().count("zbase") > 0:
426	zbase = s_line[1].lstrip()
427	if s_line[0].lower().count("xstepsize") > 0:
428	xstepsize = s_line[1].lstrip()
429	if s_line[0].lower().count("ystepsize") > 0:
430	ystepsize = s_line[1].lstrip()
431	if s_line[0].lower().count("zstepsize") > 0:
432	zstepsize = s_line[1].lstrip()
433	if s_line[0].lower().count("xnodes") > 0:
434	xnodes = s_line[1].lstrip()
435	if s_line[0].lower().count("ynodes") > 0:
436	ynodes = s_line[1].lstrip()
437	if s_line[0].lower().count("znodes") > 0:
438	znodes = s_line[1].lstrip()
439	if s_line[0].lower().count("xmin") > 0:
440	xmin = s_line[1].lstrip()
441	if s_line[0].lower().count("ymin") > 0:
442	ymin = s_line[1].lstrip()
443	if s_line[0].lower().count("zmin") > 0:
444	zmin = s_line[1].lstrip()
445	if s_line[0].lower().count("xmax") > 0:
446	xmax = s_line[1].lstrip()
447	if s_line[0].lower().count("ymax") > 0:
448	ymax = s_line[1].lstrip()
449	if s_line[0].lower().count("zmax") > 0:
450	zmax = s_line[1].lstrip()
451	if s_line[0].lower().count("valueunit") > 0:
452	valueunit = s_line[1].lstrip().rstrip()
453	if s_line[0].lower().count("valuemultiplier") > 0:
454	valuemultiplier = s_line[1].lstrip()
455	if s_line[0].lower().count("valuerangeminmag") > 0:
456	valuerangeminmag = s_line[1].lstrip()
457	if s_line[0].lower().count("valuerangemaxmag") > 0:
458	valuerangemaxmag = s_line[1].lstrip()
459	if s_line[0].lower().count("end") > 0:
460	#output.set_sldms(mx, my, mz)
461	output.filename = os.path.basename(path)
462	output.oommf = oommf
463	output.title = title
464	output.desc = desc
465	output.meshtype = meshtype
466	output.xbase = float(xbase) * METER2ANG
467	output.ybase = float(ybase) * METER2ANG
468	output.zbase = float(zbase) * METER2ANG
469	output.xstepsize = float(xstepsize) * METER2ANG
470	output.ystepsize = float(ystepsize) * METER2ANG
471	output.zstepsize = float(zstepsize) * METER2ANG
472	output.xnodes = float(xnodes)
473	output.ynodes = float(ynodes)
474	output.znodes = float(znodes)
475	output.xmin = float(xmin) * METER2ANG
476	output.ymin = float(ymin) * METER2ANG
477	output.zmin = float(zmin) * METER2ANG
478	output.xmax = float(xmax) * METER2ANG
479	output.ymax = float(ymax) * METER2ANG
480	output.zmax = float(zmax) * METER2ANG
481	output.valuemultiplier = valuemultiplier
482	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
483	valueunit)
484	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
485	valueunit)
486	output.set_m(mx, my, mz)
487	return output
488	except:
489	msg = "%s is not supported: \n" % path
490	msg += "We accept only Text format OMF file."
491	raise RuntimeError, msg
492
493	class PDBReader:
494	"""
495	PDB reader class: limited for reading the lines starting with 'ATOM'
496	"""
497	type_name = "PDB"
498	## Wildcards
499	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
500	## List of allowed extensions
501	ext = ['.pdb', '.PDB']
502
503	def read(self, path):
504	"""
505	Load data file
506
507	:param path: file path
508
509	:return: MagSLD
510
511	:raise RuntimeError: when the file can't be opened
512	"""
513	pos_x = numpy.zeros(0)
514	pos_y = numpy.zeros(0)
515	pos_z = numpy.zeros(0)
516	sld_n = numpy.zeros(0)
517	sld_mx = numpy.zeros(0)
518	sld_my = numpy.zeros(0)
519	sld_mz = numpy.zeros(0)
520	vol_pix = numpy.zeros(0)
521	pix_symbol = numpy.zeros(0)
522	x_line = []
523	y_line = []
524	z_line = []
525	x_lines = []
526	y_lines = []
527	z_lines = []
528	try:
529	input_f = open(path, 'rb')
530	buff = input_f.read()
531	lines = buff.split('\n')
532	input_f.close()
533	pre_num = 0
534	num = 0
535	for line in lines:
536	try:
537	# check if line starts with "ATOM"
538	if line[0:6].strip().count('ATM') > 0 or \
539	line[0:6].strip() == 'ATOM':
540	# define fields of interest
541	atom_id = line[6:11].strip()
542	atom_name = line[12:16].strip()
543	try:
544	float(line[12])
545	atom_name = atom_name[1].upper()
546	except:
547	if len(atom_name) == 4:
548	atom_name = atom_name[0].upper()
549	elif line[12] != ' ':
550	atom_name = atom_name[0].upper() + \
551	atom_name[1].lower()
552	else:
553	atom_name = atom_name[0].upper()
554	#res_name = line[17:20].strip()
555	#chain_name = line[21:22].strip()
556	_pos_x = float(line[30:38].strip())
557	_pos_y = float(line[38:46].strip())
558	_pos_z = float(line[46:54].strip())
559
560	pos_x = numpy.append(pos_x, _pos_x)
561	pos_y = numpy.append(pos_y, _pos_y)
562	pos_z = numpy.append(pos_z, _pos_z)
563	try:
564	# sld in Ang unit (from fm)
565	#val = formula(atom_name).atoms.keys()[0].neutron.b_c
566	#val *= 1.0e-5
567	val = nsf.neutron_sld(atom_name)[0]
568	# sld in Ang^-2 unit
569	val *= 1.0e-6
570	sld_n = numpy.append(sld_n, val)
571	atom = formula(atom_name)
572	# cm to A units
573	vol = 1.0e+24 * atom.mass / atom.density / NA
574	vol_pix = numpy.append(vol_pix, vol)
575	except:
576	print "Error: set the sld of %s to zero"% atom_name
577	sld_n = numpy.append(sld_n, 0.0)
578	sld_mx = numpy.append(sld_mx, 0)
579	sld_my = numpy.append(sld_my, 0)
580	sld_mz = numpy.append(sld_mz, 0)
581	pix_symbol = numpy.append(pix_symbol, atom_name)
582	elif line[0:6].strip().count('CONECT') > 0 :
583	toks = line.split()
584	num = int(toks[1]) - 1
585	val_list = []
586	for val in toks[2:]:
587	try:
588	int_val = int(val)
589	except:
590	break
591	if int_val == 0:
592	break
593	val_list.append(int_val)
594	#need val_list ordered
595	for val in val_list:
596	index = val - 1
597	if (pos_x[index], pos_x[num]) in x_line and \
598	(pos_y[index], pos_y[num]) in y_line and \
599	(pos_z[index], pos_z[num]) in z_line:
600	continue
601	x_line.append((pos_x[num], pos_x[index]))
602	y_line.append((pos_y[num], pos_y[index]))
603	z_line.append((pos_z[num], pos_z[index]))
604	if len(x_line) > 0:
605	x_lines.append(x_line)
606	y_lines.append(y_line)
607	z_lines.append(z_line)
608	except:
609	pass
610	#re-centering
611	#pos_x -= (min(pos_x) + max(pos_x)) / 2.0
612	#pos_y -= (min(pos_y) + max(pos_y)) / 2.0
613	#pos_z -= (min(pos_z) + max(pos_z)) / 2.0
614
615	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
616	output.set_conect_lines(x_line, y_line, z_line)
617	output.filename = os.path.basename(path)
618	output.set_pix_type('atom')
619	output.set_pixel_symbols(pix_symbol)
620	output.set_nodes()
621	output.set_pixel_volumes(vol_pix)
622	output.sld_unit = '1/A^(2)'
623	return output
624	except:
625	RuntimeError, "%s is not a sld file" % path
626
627	def write(self, path, data):
628	"""
629	Write
630	"""
631	#Not implemented
632	print "Not implemented... "
633
634	class SLDReader:
635	"""
636	Class to load ascii files (7 columns).
637	"""
638	## File type
639	type_name = "SLD ASCII"
640
641	## Wildcards
642	type = ["sld files (.SLD, .sld)\|*.sld",
643	"txt files (.TXT, .txt)\|*.txt",
644	"all files (.)\|."]
645	## List of allowed extensions
646	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
647
648	def read(self, path):
649	"""
650	Load data file
651
652	:param path: file path
653
654	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
655
656	:raise RuntimeError: when the file can't be opened
657	:raise ValueError: when the length of the data vectors are inconsistent
658	"""
659	try:
660	pos_x = numpy.zeros(0)
661	pos_y = numpy.zeros(0)
662	pos_z = numpy.zeros(0)
663	sld_n = numpy.zeros(0)
664	sld_mx = numpy.zeros(0)
665	sld_my = numpy.zeros(0)
666	sld_mz = numpy.zeros(0)
667	try:
668	# Use numpy to speed up loading
669	input_f = numpy.loadtxt(path, dtype='float', skiprows=1,
670	ndmin=1, unpack=True)
671	pos_x = numpy.array(input_f[0])
672	pos_y = numpy.array(input_f[1])
673	pos_z = numpy.array(input_f[2])
674	sld_n = numpy.array(input_f[3])
675	sld_mx = numpy.array(input_f[4])
676	sld_my = numpy.array(input_f[5])
677	sld_mz = numpy.array(input_f[6])
678	ncols = len(input_f)
679	if ncols == 8:
680	vol_pix = numpy.array(input_f[7])
681	elif ncols == 7:
682	vol_pix = None
683	except:
684	# For older version of numpy
685	input_f = open(path, 'rb')
686	buff = input_f.read()
687	lines = buff.split('\n')
688	input_f.close()
689	for line in lines:
690	toks = line.split()
691	try:
692	_pos_x = float(toks[0])
693	_pos_y = float(toks[1])
694	_pos_z = float(toks[2])
695	_sld_n = float(toks[3])
696	_sld_mx = float(toks[4])
697	_sld_my = float(toks[5])
698	_sld_mz = float(toks[6])
699
700	pos_x = numpy.append(pos_x, _pos_x)
701	pos_y = numpy.append(pos_y, _pos_y)
702	pos_z = numpy.append(pos_z, _pos_z)
703	sld_n = numpy.append(sld_n, _sld_n)
704	sld_mx = numpy.append(sld_mx, _sld_mx)
705	sld_my = numpy.append(sld_my, _sld_my)
706	sld_mz = numpy.append(sld_mz, _sld_mz)
707	try:
708	_vol_pix = float(toks[7])
709	vol_pix = numpy.append(vol_pix, _vol_pix)
710	except:
711	vol_pix = None
712	except:
713	# Skip non-data lines
714	pass
715
716	# re-center
717	#pos_x -= (min(pos_x) + max(pos_x)) / 2.0
718	#pos_y -= (min(pos_y) + max(pos_y)) / 2.0
719	#pos_z -= (min(pos_z) + max(pos_z)) / 2.0
720
721	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
722	sld_mx, sld_my, sld_mz)
723
724	output.filename = os.path.basename(path)
725	output.set_pix_type('pixel')
726	output.set_pixel_symbols('pixel')
727	if vol_pix != None:
728	output.set_pixel_volumes(vol_pix)
729	return output
730	except:
731	RuntimeError, "%s is not a sld file" % path
732
733	def write(self, path, data):
734	"""
735	Write sld file
736
737	:Param path: file path
738	:Param data: MagSLD data object
739	"""
740	if path == None:
741	raise ValueError, "Missing the file path."
742	if data == None:
743	raise ValueError, "Missing the data to save."
744
745	x_val = data.pos_x
746	y_val = data.pos_y
747	z_val = data.pos_z
748	vol_pix = data.vol_pix
749
750	length = len(x_val)
751
752	sld_n = data.sld_n
753	if sld_n == None:
754	sld_n = numpy.zerros(length)
755
756	sld_mx = data.sld_mx
757	if sld_mx == None:
758	sld_mx = numpy.zerros(length)
759	sld_my = numpy.zerros(length)
760	sld_mz = numpy.zerros(length)
761	else:
762	sld_my = data.sld_my
763	sld_mz = data.sld_mz
764
765	out = open(path, 'w')
766	# First Line: Column names
767	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
768	for ind in range(length):
769	out.write("\n%g %g %g %g %g %g %g %g" % (x_val[ind], y_val[ind],
770	z_val[ind], sld_n[ind],
771	sld_mx[ind], sld_my[ind],
772	sld_mz[ind], vol_pix[ind]))
773	out.close()
774
775
776	class OMFData:
777	"""
778	OMF Data.
779	"""
780	_meshunit = "A"
781	_valueunit = "A^(-2)"
782	def __init__(self):
783	"""
784	Init for mag SLD
785	"""
786	self.filename = 'default'
787	self.oommf = ''
788	self.title = ''
789	self.desc = ''
790	self.meshtype = ''
791	self.meshunit = self._meshunit
792	self.valueunit = self._valueunit
793	self.xbase = 0.0
794	self.ybase = 0.0
795	self.zbase = 0.0
796	self.xstepsize = 6.0
797	self.ystepsize = 6.0
798	self.zstepsize = 6.0
799	self.xnodes = 10.0
800	self.ynodes = 10.0
801	self.znodes = 10.0
802	self.xmin = 0.0
803	self.ymin = 0.0
804	self.zmin = 0.0
805	self.xmax = 60.0
806	self.ymax = 60.0
807	self.zmax = 60.0
808	self.mx = None
809	self.my = None
810	self.mz = None
811	self.valuemultiplier = 1.
812	self.valuerangeminmag = 0
813	self.valuerangemaxmag = 0
814
815	def __str__(self):
816	"""
817	doc strings
818	"""
819	_str = "Type: %s\n" % self.__class__.__name__
820	_str += "File: %s\n" % self.filename
821	_str += "OOMMF: %s\n" % self.oommf
822	_str += "Title: %s\n" % self.title
823	_str += "Desc: %s\n" % self.desc
824	_str += "meshtype: %s\n" % self.meshtype
825	_str += "meshunit: %s\n" % str(self.meshunit)
826	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
827	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
828	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
829	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
830	self.meshunit)
831	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
832	self.meshunit)
833	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
834	self.meshunit)
835	_str += "xnodes: %s\n" % str(self.xnodes)
836	_str += "ynodes: %s\n" % str(self.ynodes)
837	_str += "znodes: %s\n" % str(self.znodes)
838	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
839	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
840	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
841	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
842	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
843	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
844	_str += "valueunit: %s\n" % self.valueunit
845	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
846	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
847	self.valueunit)
848	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
849	self.valueunit)
850	return _str
851
852	def set_m(self, mx, my, mz):
853	"""
854	Set the Mx, My, Mz values
855	"""
856	self.mx = mx
857	self.my = my
858	self.mz = mz
859
860	class MagSLD:
861	"""
862	Magnetic SLD.
863	"""
864	pos_x = None
865	pos_y = None
866	pos_z = None
867	sld_n = None
868	sld_mx = None
869	sld_my = None
870	sld_mz = None
871	# Units
872	_pos_unit = 'A'
873	_sld_unit = '1/A^(2)'
874	_pix_type = 'pixel'
875
876	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
877	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
878	"""
879	Init for mag SLD
880	:params : All should be numpy 1D array
881	"""
882	self.is_data = True
883	self.filename = ''
884	self.xstepsize = 6.0
885	self.ystepsize = 6.0
886	self.zstepsize = 6.0
887	self.xnodes = 10.0
888	self.ynodes = 10.0
889	self.znodes = 10.0
890	self.has_stepsize = False
891	self.has_conect = False
892	self.pos_unit = self._pos_unit
893	self.sld_unit = self._sld_unit
894	self.pix_type = 'pixel'
895	self.pos_x = pos_x
896	self.pos_y = pos_y
897	self.pos_z = pos_z
898	self.sld_n = sld_n
899	self.line_x = None
900	self.line_y = None
901	self.line_z = None
902	self.sld_mx = sld_mx
903	self.sld_my = sld_my
904	self.sld_mz = sld_mz
905	self.vol_pix = vol_pix
906	self.sld_m = None
907	self.sld_phi = None
908	self.sld_theta = None
909	self.pix_symbol = None
910	if sld_mx != None and sld_my != None and sld_mz != None:
911	self.set_sldms(sld_mx, sld_my, sld_mz)
912	self.set_nodes()
913
914	def __str__(self):
915	"""
916	doc strings
917	"""
918	_str = "Type: %s\n" % self.__class__.__name__
919	_str += "File: %s\n" % self.filename
920	_str += "Axis_unit: %s\n" % self.pos_unit
921	_str += "SLD_unit: %s\n" % self.sld_unit
922	return _str
923
924	def set_pix_type(self, pix_type):
925	"""
926	Set pixel type
927	:Param pix_type: string, 'pixel' or 'atom'
928	"""
929	self.pix_type = pix_type
930
931	def set_sldn(self, sld_n):
932	"""
933	Sets neutron SLD
934	"""
935	if sld_n.__class__.__name__ == 'float':
936	if self.is_data:
937	# For data, put the value to only the pixels w non-zero M
938	is_nonzero = (numpy.fabs(self.sld_mx) +
939	numpy.fabs(self.sld_my) +
940	numpy.fabs(self.sld_mz)).nonzero()
941	self.sld_n = numpy.zeros(len(self.pos_x))
942	if len(self.sld_n[is_nonzero]) > 0:
943	self.sld_n[is_nonzero] = sld_n
944	else:
945	self.sld_n.fill(sld_n)
946	else:
947	# For non-data, put the value to all the pixels
948	self.sld_n = numpy.ones(len(self.pos_x)) * sld_n
949	else:
950	self.sld_n = sld_n
951
952	def set_sldms(self, sld_mx, sld_my, sld_mz):
953	"""
954	Sets (\|m\|, m_theta, m_phi)
955	"""
956	if sld_mx.__class__.__name__ == 'float':
957	self.sld_mx = numpy.ones(len(self.pos_x)) * sld_mx
958	else:
959	self.sld_mx = sld_mx
960	if sld_my.__class__.__name__ == 'float':
961	self.sld_my = numpy.ones(len(self.pos_x)) * sld_my
962	else:
963	self.sld_my = sld_my
964	if sld_mz.__class__.__name__ == 'float':
965	self.sld_mz = numpy.ones(len(self.pos_x)) * sld_mz
966	else:
967	self.sld_mz = sld_mz
968
969	sld_m = numpy.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
970	sld_mz * sld_mz)
971	self.sld_m = sld_m
972
973	def set_pixel_symbols(self, symbol='pixel'):
974	"""
975	Set pixel
976	:Params pixel: str; pixel or atomic symbol, or array of strings
977	"""
978	if self.sld_n == None:
979	return
980	if symbol.__class__.__name__ == 'str':
981	self.pix_symbol = numpy.repeat(symbol, len(self.sld_n))
982	else:
983	self.pix_symbol = symbol
984
985	def set_pixel_volumes(self, vol):
986	"""
987	Set pixel volumes
988	:Params pixel: str; pixel or atomic symbol, or array of strings
989	"""
990	if self.sld_n == None:
991	return
992	if vol.__class__.__name__ == 'ndarray':
993	self.vol_pix = vol
994	elif vol.__class__.__name__.count('float') > 0:
995	self.vol_pix = numpy.repeat(vol, len(self.sld_n))
996	else:
997	self.vol_pix = None
998
999	def get_sldn(self):
1000	"""
1001	Returns nuclear sld
1002	"""
1003	return self.sld_n
1004
1005	def get_sld_mxyz(self):
1006	"""
1007	Returns (sld_mx, sldmy, sld_mz)
1008	"""
1009	return (self.sld_mx, self.sldmy, self.sld_mz)
1010
1011	def get_sld_m(self):
1012	"""
1013	Returns (sldm, sld_theta, sld_phi)
1014	"""
1015	return (self.sldm, self.sld_theta, self.sld_phi)
1016
1017	def set_nodes(self):
1018	"""
1019	Set xnodes, ynodes, and znodes
1020	"""
1021	self.set_stepsize()
1022	if self.pix_type == 'pixel':
1023	try:
1024	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
1025	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
1026	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
1027	self.xnodes = int(xdist) + 1
1028	self.ynodes = int(ydist) + 1
1029	self.znodes = int(zdist) + 1
1030	except:
1031	self.xnodes = None
1032	self.ynodes = None
1033	self.znodes = None
1034	else:
1035	self.xnodes = None
1036	self.ynodes = None
1037	self.znodes = None
1038
1039	def set_stepsize(self):
1040	"""
1041	Set xtepsize, ystepsize, and zstepsize
1042	"""
1043	if self.pix_type == 'pixel':
1044	try:
1045	xpos_pre = self.pos_x[0]
1046	ypos_pre = self.pos_y[0]
1047	zpos_pre = self.pos_z[0]
1048	for x_pos in self.pos_x:
1049	if xpos_pre != x_pos:
1050	self.xstepsize = numpy.fabs(x_pos - xpos_pre)
1051	break
1052	for y_pos in self.pos_y:
1053	if ypos_pre != y_pos:
1054	self.ystepsize = numpy.fabs(y_pos - ypos_pre)
1055	break
1056	for z_pos in self.pos_z:
1057	if zpos_pre != z_pos:
1058	self.zstepsize = numpy.fabs(z_pos - zpos_pre)
1059	break
1060	#default pix volume
1061	self.vol_pix = numpy.ones(len(self.pos_x))
1062	vol = self.xstepsize * self.ystepsize * self.zstepsize
1063	self.set_pixel_volumes(vol)
1064	self.has_stepsize = True
1065	except:
1066	self.xstepsize = None
1067	self.ystepsize = None
1068	self.zstepsize = None
1069	self.vol_pix = None
1070	self.has_stepsize = False
1071	else:
1072	self.xstepsize = None
1073	self.ystepsize = None
1074	self.zstepsize = None
1075	self.has_stepsize = True
1076	return self.xstepsize, self.ystepsize, self.zstepsize
1077
1078	def set_conect_lines(self, line_x, line_y, line_z):
1079	"""
1080	Set bonding line data if taken from pdb
1081	"""
1082	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
1083	return
1084	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
1085	return
1086	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
1087	return
1088	self.has_conect = True
1089	self.line_x = line_x
1090	self.line_y = line_y
1091	self.line_z = line_z
1092
1093
1094	def test_load():
1095	from sans.plottools.arrow3d import Arrow3D
1096	import os
1097	dir = os.path.abspath(os.path.curdir)
1098	print dir
1099	for i in range(6):
1100	dir, _ = os.path.split(dir)
1101	tfile = os.path.join(dir, "test", "CoreXY_ShellZ.txt")
1102	ofile = os.path.join(dir, "test", "A_Raw_Example-1.omf")
1103	if os.path.isfile(tfile):
1104	tfpath = tfile
1105	ofpath = ofile
1106	break
1107	reader = SLDReader()
1108	oreader = OMFReader()
1109	output = reader.read(tfpath)
1110	ooutput = oreader.read(ofpath)
1111	foutput = OMF2SLD()
1112	foutput.set_data(ooutput)
1113
1114	import matplotlib.pyplot as plt
1115	from mpl_toolkits.mplot3d import Axes3D
1116	fig = plt.figure()
1117	ax = fig.gca(projection='3d')
1118	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
1119	alpha = 0.7, markeredgecolor='gray',rasterized=True)
1120	gap = 7
1121	max_mx = max(output.sld_mx)
1122	max_my = max(output.sld_my)
1123	max_mz = max(output.sld_mz)
1124	max_m = max(max_mx,max_my,max_mz)
1125	x2 = output.pos_x+output.sld_mx/max_m * gap
1126	y2 = output.pos_y+output.sld_my/max_m * gap
1127	z2 = output.pos_z+output.sld_mz/max_m * gap
1128	x_arrow = numpy.column_stack((output.pos_x,x2))
1129	y_arrow = numpy.column_stack((output.pos_y,y2))
1130	z_arrow = numpy.column_stack((output.pos_z,z2))
1131	unit_x2 = output.sld_mx / max_m
1132	unit_y2 = output.sld_my / max_m
1133	unit_z2 = output.sld_mz / max_m
1134	color_x = numpy.fabs(unit_x2 * 0.8)
1135	color_y = numpy.fabs(unit_y2 * 0.8)
1136	color_z = numpy.fabs(unit_z2 * 0.8)
1137	colors = numpy.column_stack((color_x, color_y, color_z))
1138	a = Arrow3D(None, x_arrow,y_arrow,z_arrow, colors, mutation_scale=10, lw=1,
1139	arrowstyle="->", color="y", alpha = 0.5)
1140
1141	ax.add_artist(a)
1142	plt.show()
1143
1144	def test():
1145	import os
1146	dir = os.path.abspath(os.path.curdir)
1147	for i in range(3):
1148	dir, _ = os.path.split(dir)
1149	#tfile = os.path.join(dir, "test", "C_Example_Converted.txt")
1150	ofile = os.path.join(dir, "test", "A_Raw_Example-1.omf")
1151	if os.path.isfile(ofile):
1152	#tfpath = tfile
1153	ofpath = ofile
1154	break
1155	#reader = SLDReader()
1156	oreader = OMFReader()
1157	#output = reader.read(tfpath)
1158	ooutput = oreader.read(ofpath)
1159	foutput = OMF2SLD()
1160	foutput.set_data(ooutput)
1161	writer = SLDReader()
1162	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
1163	foutput.output)
1164	model = GenSAS()
1165	model.set_sld_data(foutput.output)
1166	x = numpy.arange(1000)/10000. + 1e-5
1167	y = numpy.arange(1000)/10000. + 1e-5
1168	#z = numpy.arange(1000)/10000. + 1e-5
1169	i = numpy.zeros(1000)
1170	out = model.runXY([x,y,i])
1171
1172	if __name__ == "__main__":
1173	test()
1174	test_load()

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SasView

source: sasview/src/sans/calculator/sans_gen.py @ f468791

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