sas_gen.py @ 59dfb53

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalcmagnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 59dfb53 was b58265c3, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
use logger rather than print for error notifications
Property mode set to `100644`
File size: 39.7 KB

Line
1	# pylint: disable=invalid-name
2	"""
3	SAS generic computation and sld file readers
4	"""
5	from __future__ import print_function
6
7	import os
8	import sys
9	import copy
10	import logging
11
12	from periodictable import formula
13	from periodictable import nsf
14	import numpy as np
15
16	from .core import sld2i as mod
17	from .BaseComponent import BaseComponent
18
19	logger = logging.getLogger(__name__)
20
21	if sys.version_info[0] < 3:
22	def decode(s):
23	return s
24	else:
25	def decode(s):
26	return s.decode() if isinstance(s, bytes) else s
27
28	MFACTOR_AM = 2.853E-12
29	MFACTOR_MT = 2.3164E-9
30	METER2ANG = 1.0E+10
31	#Avogadro constant [1/mol]
32	NA = 6.02214129e+23
33
34	def mag2sld(mag, v_unit=None):
35	"""
36	Convert magnetization to magnatic SLD
37	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
38	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
39	"""
40	if v_unit == "A/m":
41	factor = MFACTOR_AM
42	elif v_unit == "mT":
43	factor = MFACTOR_MT
44	else:
45	raise ValueError("Invalid valueunit")
46	sld_m = factor * mag
47	return sld_m
48
49	def transform_center(pos_x, pos_y, pos_z):
50	"""
51	re-center
52	:return: posx, posy, posz [arrays]
53	"""
54	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
55	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
56	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
57	return posx, posy, posz
58
59	class GenSAS(BaseComponent):
60	"""
61	Generic SAS computation Model based on sld (n & m) arrays
62	"""
63	def __init__(self):
64	"""
65	Init
66	:Params sld_data: MagSLD object
67	"""
68	# Initialize BaseComponent
69	BaseComponent.__init__(self)
70	self.sld_data = None
71	self.data_pos_unit = None
72	self.data_x = None
73	self.data_y = None
74	self.data_z = None
75	self.data_sldn = None
76	self.data_mx = None
77	self.data_my = None
78	self.data_mz = None
79	self.data_vol = None #[A^3]
80	self.is_avg = False
81	## Name of the model
82	self.name = "GenSAS"
83	## Define parameters
84	self.params = {}
85	self.params['scale'] = 1.0
86	self.params['background'] = 0.0
87	self.params['solvent_SLD'] = 0.0
88	self.params['total_volume'] = 1.0
89	self.params['Up_frac_in'] = 1.0
90	self.params['Up_frac_out'] = 1.0
91	self.params['Up_theta'] = 0.0
92	self.description = 'GenSAS'
93	## Parameter details [units, min, max]
94	self.details = {}
95	self.details['scale'] = ['', 0.0, np.inf]
96	self.details['background'] = ['[1/cm]', 0.0, np.inf]
97	self.details['solvent_SLD'] = ['1/A^(2)', -np.inf, np.inf]
98	self.details['total_volume'] = ['A^(3)', 0.0, np.inf]
99	self.details['Up_frac_in'] = ['[u/(u+d)]', 0.0, 1.0]
100	self.details['Up_frac_out'] = ['[u/(u+d)]', 0.0, 1.0]
101	self.details['Up_theta'] = ['[deg]', -np.inf, np.inf]
102	# fixed parameters
103	self.fixed = []
104
105	def set_pixel_volumes(self, volume):
106	"""
107	Set the volume of a pixel in (A^3) unit
108	:Param volume: pixel volume [float]
109	"""
110	if self.data_vol is None:
111	raise TypeError("data_vol is missing")
112	self.data_vol = volume
113
114	def set_is_avg(self, is_avg=False):
115	"""
116	Sets is_avg: [bool]
117	"""
118	self.is_avg = is_avg
119
120	def _gen(self, x, y, i):
121	"""
122	Evaluate the function
123	:Param x: array of x-values
124	:Param y: array of y-values
125	:Param i: array of initial i-value
126	:return: function value
127	"""
128	pos_x = self.data_x
129	pos_y = self.data_y
130	pos_z = self.data_z
131	len_x = len(pos_x)
132	if self.is_avg is None:
133	len_x *= -1
134	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
135	len_q = len(x)
136	sldn = copy.deepcopy(self.data_sldn)
137	sldn -= self.params['solvent_SLD']
138	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
139	sldn, self.data_mx, self.data_my,
140	self.data_mz, self.data_vol,
141	self.params['Up_frac_in'],
142	self.params['Up_frac_out'],
143	self.params['Up_theta'])
144	if y == []:
145	mod.genicom(model, len_q, x, i)
146	else:
147	mod.genicomXY(model, len_q, x, y, i)
148	vol_correction = self.data_total_volume / self.params['total_volume']
149	return self.params['scale'] * vol_correction * i + \
150	self.params['background']
151
152	def set_sld_data(self, sld_data=None):
153	"""
154	Sets sld_data
155	"""
156	self.sld_data = sld_data
157	self.data_pos_unit = sld_data.pos_unit
158	self.data_x = sld_data.pos_x
159	self.data_y = sld_data.pos_y
160	self.data_z = sld_data.pos_z
161	self.data_sldn = sld_data.sld_n
162	self.data_mx = sld_data.sld_mx
163	self.data_my = sld_data.sld_my
164	self.data_mz = sld_data.sld_mz
165	self.data_vol = sld_data.vol_pix
166	self.data_total_volume = sum(sld_data.vol_pix)
167	self.params['total_volume'] = sum(sld_data.vol_pix)
168
169	def getProfile(self):
170	"""
171	Get SLD profile
172	: return: sld_data
173	"""
174	return self.sld_data
175
176	def run(self, x=0.0):
177	"""
178	Evaluate the model
179	:param x: simple value
180	:return: (I value)
181	"""
182	if x.__class__.__name__ == 'list':
183	if len(x[1]) > 0:
184	msg = "Not a 1D."
185	raise ValueError(msg)
186	i_out = np.zeros_like(x[0])
187	# 1D I is found at y =0 in the 2D pattern
188	out = self._gen(x[0], [], i_out)
189	return out
190	else:
191	msg = "Q must be given as list of qx's and qy's"
192	raise ValueError(msg)
193
194	def runXY(self, x=0.0):
195	"""
196	Evaluate the model
197	:param x: simple value
198	:return: I value
199	:Use this runXY() for the computation
200	"""
201	if x.__class__.__name__ == 'list':
202	i_out = np.zeros_like(x[0])
203	out = self._gen(x[0], x[1], i_out)
204	return out
205	else:
206	msg = "Q must be given as list of qx's and qy's"
207	raise ValueError(msg)
208
209	def evalDistribution(self, qdist):
210	"""
211	Evaluate a distribution of q-values.
212
213	:param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy]
214	where qx,qy are 1D ndarrays (for 2D).
215	"""
216	if qdist.__class__.__name__ == 'list':
217	if len(qdist[1]) < 1:
218	out = self.run(qdist)
219	else:
220	out = self.runXY(qdist)
221	return out
222	else:
223	mesg = "evalDistribution is expecting an ndarray of "
224	mesg += "a list [qx,qy] where qx,qy are arrays."
225	raise RuntimeError(mesg)
226
227	class OMF2SLD(object):
228	"""
229	Convert OMFData to MAgData
230	"""
231	def __init__(self):
232	"""
233	Init
234	"""
235	self.pos_x = None
236	self.pos_y = None
237	self.pos_z = None
238	self.mx = None
239	self.my = None
240	self.mz = None
241	self.sld_n = None
242	self.vol_pix = None
243	self.output = None
244	self.omfdata = None
245
246	def set_data(self, omfdata, shape='rectangular'):
247	"""
248	Set all data
249	"""
250	self.omfdata = omfdata
251	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
252	pos_x = np.arange(omfdata.xmin,
253	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
254	omfdata.xstepsize)
255	pos_y = np.arange(omfdata.ymin,
256	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
257	omfdata.ystepsize)
258	pos_z = np.arange(omfdata.zmin,
259	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
260	omfdata.zstepsize)
261	self.pos_x = np.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
262	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
263	self.pos_y = np.tile(self.pos_y, int(omfdata.znodes))
264	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
265	self.mx = omfdata.mx
266	self.my = omfdata.my
267	self.mz = omfdata.mz
268	self.sld_n = np.zeros(length)
269
270	if omfdata.mx is None:
271	self.mx = np.zeros(length)
272	if omfdata.my is None:
273	self.my = np.zeros(length)
274	if omfdata.mz is None:
275	self.mz = np.zeros(length)
276
277	self._check_data_length(length)
278	self.remove_null_points(False, False)
279	mask = np.ones(len(self.sld_n), dtype=bool)
280	if shape.lower() == 'ellipsoid':
281	try:
282	# Pixel (step) size included
283	x_c = max(self.pos_x) + min(self.pos_x)
284	y_c = max(self.pos_y) + min(self.pos_y)
285	z_c = max(self.pos_z) + min(self.pos_z)
286	x_d = max(self.pos_x) - min(self.pos_x)
287	y_d = max(self.pos_y) - min(self.pos_y)
288	z_d = max(self.pos_z) - min(self.pos_z)
289	x_r = (x_d + omfdata.xstepsize) / 2.0
290	y_r = (y_d + omfdata.ystepsize) / 2.0
291	z_r = (z_d + omfdata.zstepsize) / 2.0
292	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
293	x_dir2 *= x_dir2
294	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
295	y_dir2 *= y_dir2
296	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
297	z_dir2 *= z_dir2
298	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
299	except Exception:
300	logger.error(sys.exc_value)
301	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
302	self.pos_z[mask], self.sld_n[mask],
303	self.mx[mask], self.my[mask], self.mz[mask])
304	self.output.set_pix_type('pixel')
305	self.output.set_pixel_symbols('pixel')
306
307	def get_omfdata(self):
308	"""
309	Return all data
310	"""
311	return self.omfdata
312
313	def get_output(self):
314	"""
315	Return output
316	"""
317	return self.output
318
319	def _check_data_length(self, length):
320	"""
321	Check if the data lengths are consistent
322	:Params length: data length
323	"""
324	parts = (self.pos_x, self.pos_y, self.pos_z, self.mx, self.my, self.mz)
325	if any(len(v) != length for v in parts):
326	raise ValueError("Error: Inconsistent data length.")
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 = (np.fabs(self.mx) + np.fabs(self.my) +
334	np.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 = np.zeros(0)
375	my = np.zeros(0)
376	mz = np.zeros(0)
377	try:
378	input_f = open(path, 'rb')
379	buff = decode(input_f.read())
380	lines = buff.split('\n')
381	input_f.close()
382	output = OMFData()
383	valueunit = None
384	for line in lines:
385	line = line.strip()
386	# Read data
387	if line and not line.startswith('#'):
388	try:
389	toks = line.split()
390	_mx = float(toks[0])
391	_my = float(toks[1])
392	_mz = float(toks[2])
393	_mx = mag2sld(_mx, valueunit)
394	_my = mag2sld(_my, valueunit)
395	_mz = mag2sld(_mz, valueunit)
396	mx = np.append(mx, _mx)
397	my = np.append(my, _my)
398	mz = np.append(mz, _mz)
399	except Exception as exc:
400	# Skip non-data lines
401	logger.error(str(exc)+" when processing %r"%line)
402	#Reading Header; Segment count ignored
403	s_line = line.split(":", 1)
404	if s_line[0].lower().count("oommf") > 0:
405	oommf = s_line[1].lstrip()
406	if s_line[0].lower().count("title") > 0:
407	title = s_line[1].lstrip()
408	if s_line[0].lower().count("desc") > 0:
409	desc += s_line[1].lstrip()
410	desc += '\n'
411	if s_line[0].lower().count("meshtype") > 0:
412	meshtype = s_line[1].lstrip()
413	if s_line[0].lower().count("meshunit") > 0:
414	meshunit = s_line[1].lstrip()
415	if meshunit.count("m") < 1:
416	msg = "Error: \n"
417	msg += "We accept only m as meshunit"
418	raise ValueError(msg)
419	if s_line[0].lower().count("xbase") > 0:
420	xbase = s_line[1].lstrip()
421	if s_line[0].lower().count("ybase") > 0:
422	ybase = s_line[1].lstrip()
423	if s_line[0].lower().count("zbase") > 0:
424	zbase = s_line[1].lstrip()
425	if s_line[0].lower().count("xstepsize") > 0:
426	xstepsize = s_line[1].lstrip()
427	if s_line[0].lower().count("ystepsize") > 0:
428	ystepsize = s_line[1].lstrip()
429	if s_line[0].lower().count("zstepsize") > 0:
430	zstepsize = s_line[1].lstrip()
431	if s_line[0].lower().count("xnodes") > 0:
432	xnodes = s_line[1].lstrip()
433	if s_line[0].lower().count("ynodes") > 0:
434	ynodes = s_line[1].lstrip()
435	if s_line[0].lower().count("znodes") > 0:
436	znodes = s_line[1].lstrip()
437	if s_line[0].lower().count("xmin") > 0:
438	xmin = s_line[1].lstrip()
439	if s_line[0].lower().count("ymin") > 0:
440	ymin = s_line[1].lstrip()
441	if s_line[0].lower().count("zmin") > 0:
442	zmin = s_line[1].lstrip()
443	if s_line[0].lower().count("xmax") > 0:
444	xmax = s_line[1].lstrip()
445	if s_line[0].lower().count("ymax") > 0:
446	ymax = s_line[1].lstrip()
447	if s_line[0].lower().count("zmax") > 0:
448	zmax = s_line[1].lstrip()
449	if s_line[0].lower().count("valueunit") > 0:
450	valueunit = s_line[1].lstrip().rstrip()
451	if s_line[0].lower().count("valuemultiplier") > 0:
452	valuemultiplier = s_line[1].lstrip()
453	if s_line[0].lower().count("valuerangeminmag") > 0:
454	valuerangeminmag = s_line[1].lstrip()
455	if s_line[0].lower().count("valuerangemaxmag") > 0:
456	valuerangemaxmag = s_line[1].lstrip()
457	if s_line[0].lower().count("end") > 0:
458	output.filename = os.path.basename(path)
459	output.oommf = oommf
460	output.title = title
461	output.desc = desc
462	output.meshtype = meshtype
463	output.xbase = float(xbase) * METER2ANG
464	output.ybase = float(ybase) * METER2ANG
465	output.zbase = float(zbase) * METER2ANG
466	output.xstepsize = float(xstepsize) * METER2ANG
467	output.ystepsize = float(ystepsize) * METER2ANG
468	output.zstepsize = float(zstepsize) * METER2ANG
469	output.xnodes = float(xnodes)
470	output.ynodes = float(ynodes)
471	output.znodes = float(znodes)
472	output.xmin = float(xmin) * METER2ANG
473	output.ymin = float(ymin) * METER2ANG
474	output.zmin = float(zmin) * METER2ANG
475	output.xmax = float(xmax) * METER2ANG
476	output.ymax = float(ymax) * METER2ANG
477	output.zmax = float(zmax) * METER2ANG
478	output.valuemultiplier = valuemultiplier
479	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
480	valueunit)
481	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
482	valueunit)
483	output.set_m(mx, my, mz)
484	return output
485	except Exception:
486	msg = "%s is not supported: \n" % path
487	msg += "We accept only Text format OMF file."
488	raise RuntimeError(msg)
489
490	class PDBReader(object):
491	"""
492	PDB reader class: limited for reading the lines starting with 'ATOM'
493	"""
494	type_name = "PDB"
495	## Wildcards
496	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
497	## List of allowed extensions
498	ext = ['.pdb', '.PDB']
499
500	def read(self, path):
501	"""
502	Load data file
503
504	:param path: file path
505	:return: MagSLD
506	:raise RuntimeError: when the file can't be opened
507	"""
508	pos_x = np.zeros(0)
509	pos_y = np.zeros(0)
510	pos_z = np.zeros(0)
511	sld_n = np.zeros(0)
512	sld_mx = np.zeros(0)
513	sld_my = np.zeros(0)
514	sld_mz = np.zeros(0)
515	vol_pix = np.zeros(0)
516	pix_symbol = np.zeros(0)
517	x_line = []
518	y_line = []
519	z_line = []
520	x_lines = []
521	y_lines = []
522	z_lines = []
523	try:
524	input_f = open(path, 'rb')
525	buff = decode(input_f.read())
526	lines = buff.split('\n')
527	input_f.close()
528	num = 0
529	for line in lines:
530	try:
531	# check if line starts with "ATOM"
532	if line[0:6].strip().count('ATM') > 0 or \
533	line[0:6].strip() == 'ATOM':
534	# define fields of interest
535	atom_name = line[12:16].strip()
536	try:
537	float(line[12])
538	atom_name = atom_name[1].upper()
539	except Exception:
540	if len(atom_name) == 4:
541	atom_name = atom_name[0].upper()
542	elif line[12] != ' ':
543	atom_name = atom_name[0].upper() + \
544	atom_name[1].lower()
545	else:
546	atom_name = atom_name[0].upper()
547	_pos_x = float(line[30:38].strip())
548	_pos_y = float(line[38:46].strip())
549	_pos_z = float(line[46:54].strip())
550	pos_x = np.append(pos_x, _pos_x)
551	pos_y = np.append(pos_y, _pos_y)
552	pos_z = np.append(pos_z, _pos_z)
553	try:
554	val = nsf.neutron_sld(atom_name)[0]
555	# sld in Ang^-2 unit
556	val *= 1.0e-6
557	sld_n = np.append(sld_n, val)
558	atom = formula(atom_name)
559	# cm to A units
560	vol = 1.0e+24 * atom.mass / atom.density / NA
561	vol_pix = np.append(vol_pix, vol)
562	except Exception:
563	logger.error("Error: set the sld of %s to zero"% atom_name)
564	sld_n = np.append(sld_n, 0.0)
565	sld_mx = np.append(sld_mx, 0)
566	sld_my = np.append(sld_my, 0)
567	sld_mz = np.append(sld_mz, 0)
568	pix_symbol = np.append(pix_symbol, atom_name)
569	elif line[0:6].strip().count('CONECT') > 0:
570	toks = line.split()
571	num = int(toks[1]) - 1
572	val_list = []
573	for val in toks[2:]:
574	try:
575	int_val = int(val)
576	except Exception:
577	break
578	if int_val == 0:
579	break
580	val_list.append(int_val)
581	#need val_list ordered
582	for val in val_list:
583	index = val - 1
584	if (pos_x[index], pos_x[num]) in x_line and \
585	(pos_y[index], pos_y[num]) in y_line and \
586	(pos_z[index], pos_z[num]) in z_line:
587	continue
588	x_line.append((pos_x[num], pos_x[index]))
589	y_line.append((pos_y[num], pos_y[index]))
590	z_line.append((pos_z[num], pos_z[index]))
591	if len(x_line) > 0:
592	x_lines.append(x_line)
593	y_lines.append(y_line)
594	z_lines.append(z_line)
595	except Exception:
596	logger.error(sys.exc_value)
597
598	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
599	output.set_conect_lines(x_line, y_line, z_line)
600	output.filename = os.path.basename(path)
601	output.set_pix_type('atom')
602	output.set_pixel_symbols(pix_symbol)
603	output.set_nodes()
604	output.set_pixel_volumes(vol_pix)
605	output.sld_unit = '1/A^(2)'
606	return output
607	except Exception:
608	raise RuntimeError("%s is not a sld file" % path)
609
610	def write(self, path, data):
611	"""
612	Write
613	"""
614	print("Not implemented... ")
615
616	class SLDReader(object):
617	"""
618	Class to load ascii files (7 columns).
619	"""
620	## File type
621	type_name = "SLD ASCII"
622	## Wildcards
623	type = ["sld files (.SLD, .sld)\|*.sld",
624	"txt files (.TXT, .txt)\|*.txt",
625	"all files (.)\|."]
626	## List of allowed extensions
627	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
628	def read(self, path):
629	"""
630	Load data file
631	:param path: file path
632	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
633	:raise RuntimeError: when the file can't be opened
634	:raise ValueError: when the length of the data vectors are inconsistent
635	"""
636	try:
637	pos_x = np.zeros(0)
638	pos_y = np.zeros(0)
639	pos_z = np.zeros(0)
640	sld_n = np.zeros(0)
641	sld_mx = np.zeros(0)
642	sld_my = np.zeros(0)
643	sld_mz = np.zeros(0)
644	try:
645	# Use numpy to speed up loading
646	input_f = np.loadtxt(path, dtype='float', skiprows=1,
647	ndmin=1, unpack=True)
648	pos_x = np.array(input_f[0])
649	pos_y = np.array(input_f[1])
650	pos_z = np.array(input_f[2])
651	sld_n = np.array(input_f[3])
652	sld_mx = np.array(input_f[4])
653	sld_my = np.array(input_f[5])
654	sld_mz = np.array(input_f[6])
655	ncols = len(input_f)
656	if ncols == 8:
657	vol_pix = np.array(input_f[7])
658	elif ncols == 7:
659	vol_pix = None
660	except Exception:
661	# For older version of numpy
662	input_f = open(path, 'rb')
663	buff = decode(input_f.read())
664	lines = buff.split('\n')
665	input_f.close()
666	for line in lines:
667	toks = line.split()
668	try:
669	_pos_x = float(toks[0])
670	_pos_y = float(toks[1])
671	_pos_z = float(toks[2])
672	_sld_n = float(toks[3])
673	_sld_mx = float(toks[4])
674	_sld_my = float(toks[5])
675	_sld_mz = float(toks[6])
676	pos_x = np.append(pos_x, _pos_x)
677	pos_y = np.append(pos_y, _pos_y)
678	pos_z = np.append(pos_z, _pos_z)
679	sld_n = np.append(sld_n, _sld_n)
680	sld_mx = np.append(sld_mx, _sld_mx)
681	sld_my = np.append(sld_my, _sld_my)
682	sld_mz = np.append(sld_mz, _sld_mz)
683	try:
684	_vol_pix = float(toks[7])
685	vol_pix = np.append(vol_pix, _vol_pix)
686	except Exception:
687	vol_pix = None
688	except Exception:
689	# Skip non-data lines
690	logger.error(sys.exc_value)
691	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
692	sld_mx, sld_my, sld_mz)
693	output.filename = os.path.basename(path)
694	output.set_pix_type('pixel')
695	output.set_pixel_symbols('pixel')
696	if vol_pix is not None:
697	output.set_pixel_volumes(vol_pix)
698	return output
699	except Exception:
700	raise RuntimeError("%s is not a sld file" % path)
701
702	def write(self, path, data):
703	"""
704	Write sld file
705	:Param path: file path
706	:Param data: MagSLD data object
707	"""
708	if path is None:
709	raise ValueError("Missing the file path.")
710	if data is None:
711	raise ValueError("Missing the data to save.")
712	x_val = data.pos_x
713	y_val = data.pos_y
714	z_val = data.pos_z
715	vol_pix = data.vol_pix
716	length = len(x_val)
717	sld_n = data.sld_n
718	if sld_n is None:
719	sld_n = np.zeros(length)
720	sld_mx = data.sld_mx
721	if sld_mx is None:
722	sld_mx = np.zeros(length)
723	sld_my = np.zeros(length)
724	sld_mz = np.zeros(length)
725	else:
726	sld_my = data.sld_my
727	sld_mz = data.sld_mz
728	out = open(path, 'w')
729	# First Line: Column names
730	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
731	for ind in range(length):
732	out.write("\n%g %g %g %g %g %g %g %g" % \
733	(x_val[ind], y_val[ind], z_val[ind], sld_n[ind],
734	sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind]))
735	out.close()
736
737
738	class OMFData(object):
739	"""
740	OMF Data.
741	"""
742	_meshunit = "A"
743	_valueunit = "A^(-2)"
744	def __init__(self):
745	"""
746	Init for mag SLD
747	"""
748	self.filename = 'default'
749	self.oommf = ''
750	self.title = ''
751	self.desc = ''
752	self.meshtype = ''
753	self.meshunit = self._meshunit
754	self.valueunit = self._valueunit
755	self.xbase = 0.0
756	self.ybase = 0.0
757	self.zbase = 0.0
758	self.xstepsize = 6.0
759	self.ystepsize = 6.0
760	self.zstepsize = 6.0
761	self.xnodes = 10.0
762	self.ynodes = 10.0
763	self.znodes = 10.0
764	self.xmin = 0.0
765	self.ymin = 0.0
766	self.zmin = 0.0
767	self.xmax = 60.0
768	self.ymax = 60.0
769	self.zmax = 60.0
770	self.mx = None
771	self.my = None
772	self.mz = None
773	self.valuemultiplier = 1.
774	self.valuerangeminmag = 0
775	self.valuerangemaxmag = 0
776
777	def __str__(self):
778	"""
779	doc strings
780	"""
781	_str = "Type: %s\n" % self.__class__.__name__
782	_str += "File: %s\n" % self.filename
783	_str += "OOMMF: %s\n" % self.oommf
784	_str += "Title: %s\n" % self.title
785	_str += "Desc: %s\n" % self.desc
786	_str += "meshtype: %s\n" % self.meshtype
787	_str += "meshunit: %s\n" % str(self.meshunit)
788	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
789	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
790	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
791	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
792	self.meshunit)
793	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
794	self.meshunit)
795	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
796	self.meshunit)
797	_str += "xnodes: %s\n" % str(self.xnodes)
798	_str += "ynodes: %s\n" % str(self.ynodes)
799	_str += "znodes: %s\n" % str(self.znodes)
800	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
801	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
802	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
803	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
804	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
805	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
806	_str += "valueunit: %s\n" % self.valueunit
807	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
808	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
809	self.valueunit)
810	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
811	self.valueunit)
812	return _str
813
814	def set_m(self, mx, my, mz):
815	"""
816	Set the Mx, My, Mz values
817	"""
818	self.mx = mx
819	self.my = my
820	self.mz = mz
821
822	class MagSLD(object):
823	"""
824	Magnetic SLD.
825	"""
826	pos_x = None
827	pos_y = None
828	pos_z = None
829	sld_n = None
830	sld_mx = None
831	sld_my = None
832	sld_mz = None
833	# Units
834	_pos_unit = 'A'
835	_sld_unit = '1/A^(2)'
836	_pix_type = 'pixel'
837
838	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
839	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
840	"""
841	Init for mag SLD
842	:params : All should be numpy 1D array
843	"""
844	self.is_data = True
845	self.filename = ''
846	self.xstepsize = 6.0
847	self.ystepsize = 6.0
848	self.zstepsize = 6.0
849	self.xnodes = 10.0
850	self.ynodes = 10.0
851	self.znodes = 10.0
852	self.has_stepsize = False
853	self.has_conect = False
854	self.pos_unit = self._pos_unit
855	self.sld_unit = self._sld_unit
856	self.pix_type = 'pixel'
857	self.pos_x = pos_x
858	self.pos_y = pos_y
859	self.pos_z = pos_z
860	self.sld_n = sld_n
861	self.line_x = None
862	self.line_y = None
863	self.line_z = None
864	self.sld_mx = sld_mx
865	self.sld_my = sld_my
866	self.sld_mz = sld_mz
867	self.vol_pix = vol_pix
868	self.sld_m = None
869	self.sld_phi = None
870	self.sld_theta = None
871	self.pix_symbol = None
872	if sld_mx is not None and sld_my is not None and sld_mz is not None:
873	self.set_sldms(sld_mx, sld_my, sld_mz)
874	self.set_nodes()
875
876	def __str__(self):
877	"""
878	doc strings
879	"""
880	_str = "Type: %s\n" % self.__class__.__name__
881	_str += "File: %s\n" % self.filename
882	_str += "Axis_unit: %s\n" % self.pos_unit
883	_str += "SLD_unit: %s\n" % self.sld_unit
884	return _str
885
886	def set_pix_type(self, pix_type):
887	"""
888	Set pixel type
889	:Param pix_type: string, 'pixel' or 'atom'
890	"""
891	self.pix_type = pix_type
892
893	def set_sldn(self, sld_n):
894	"""
895	Sets neutron SLD
896	"""
897	if sld_n.__class__.__name__ == 'float':
898	if self.is_data:
899	# For data, put the value to only the pixels w non-zero M
900	is_nonzero = (np.fabs(self.sld_mx) +
901	np.fabs(self.sld_my) +
902	np.fabs(self.sld_mz)).nonzero()
903	self.sld_n = np.zeros(len(self.pos_x))
904	if len(self.sld_n[is_nonzero]) > 0:
905	self.sld_n[is_nonzero] = sld_n
906	else:
907	self.sld_n.fill(sld_n)
908	else:
909	# For non-data, put the value to all the pixels
910	self.sld_n = np.ones(len(self.pos_x)) * sld_n
911	else:
912	self.sld_n = sld_n
913
914	def set_sldms(self, sld_mx, sld_my, sld_mz):
915	r"""
916	Sets mx, my, mz and abs(m).
917	""" # Note: escaping
918	if sld_mx.__class__.__name__ == 'float':
919	self.sld_mx = np.ones(len(self.pos_x)) * sld_mx
920	else:
921	self.sld_mx = sld_mx
922	if sld_my.__class__.__name__ == 'float':
923	self.sld_my = np.ones(len(self.pos_x)) * sld_my
924	else:
925	self.sld_my = sld_my
926	if sld_mz.__class__.__name__ == 'float':
927	self.sld_mz = np.ones(len(self.pos_x)) * sld_mz
928	else:
929	self.sld_mz = sld_mz
930
931	sld_m = np.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
932	sld_mz * sld_mz)
933	self.sld_m = sld_m
934
935	def set_pixel_symbols(self, symbol='pixel'):
936	"""
937	Set pixel
938	:Params pixel: str; pixel or atomic symbol, or array of strings
939	"""
940	if self.sld_n is None:
941	return
942	if symbol.__class__.__name__ == 'str':
943	self.pix_symbol = np.repeat(symbol, len(self.sld_n))
944	else:
945	self.pix_symbol = symbol
946
947	def set_pixel_volumes(self, vol):
948	"""
949	Set pixel volumes
950	:Params pixel: str; pixel or atomic symbol, or array of strings
951	"""
952	if self.sld_n is None:
953	return
954	if vol.__class__.__name__ == 'ndarray':
955	self.vol_pix = vol
956	elif vol.__class__.__name__.count('float') > 0:
957	self.vol_pix = np.repeat(vol, len(self.sld_n))
958	else:
959	self.vol_pix = None
960
961	def get_sldn(self):
962	"""
963	Returns nuclear sld
964	"""
965	return self.sld_n
966
967	def set_nodes(self):
968	"""
969	Set xnodes, ynodes, and znodes
970	"""
971	self.set_stepsize()
972	if self.pix_type == 'pixel':
973	try:
974	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
975	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
976	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
977	self.xnodes = int(xdist) + 1
978	self.ynodes = int(ydist) + 1
979	self.znodes = int(zdist) + 1
980	except Exception:
981	self.xnodes = None
982	self.ynodes = None
983	self.znodes = None
984	else:
985	self.xnodes = None
986	self.ynodes = None
987	self.znodes = None
988
989	def set_stepsize(self):
990	"""
991	Set xtepsize, ystepsize, and zstepsize
992	"""
993	if self.pix_type == 'pixel':
994	try:
995	xpos_pre = self.pos_x[0]
996	ypos_pre = self.pos_y[0]
997	zpos_pre = self.pos_z[0]
998	for x_pos in self.pos_x:
999	if xpos_pre != x_pos:
1000	self.xstepsize = np.fabs(x_pos - xpos_pre)
1001	break
1002	for y_pos in self.pos_y:
1003	if ypos_pre != y_pos:
1004	self.ystepsize = np.fabs(y_pos - ypos_pre)
1005	break
1006	for z_pos in self.pos_z:
1007	if zpos_pre != z_pos:
1008	self.zstepsize = np.fabs(z_pos - zpos_pre)
1009	break
1010	#default pix volume
1011	self.vol_pix = np.ones(len(self.pos_x))
1012	vol = self.xstepsize * self.ystepsize * self.zstepsize
1013	self.set_pixel_volumes(vol)
1014	self.has_stepsize = True
1015	except Exception:
1016	self.xstepsize = None
1017	self.ystepsize = None
1018	self.zstepsize = None
1019	self.vol_pix = None
1020	self.has_stepsize = False
1021	else:
1022	self.xstepsize = None
1023	self.ystepsize = None
1024	self.zstepsize = None
1025	self.has_stepsize = True
1026	return self.xstepsize, self.ystepsize, self.zstepsize
1027
1028	def set_conect_lines(self, line_x, line_y, line_z):
1029	"""
1030	Set bonding line data if taken from pdb
1031	"""
1032	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
1033	return
1034	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
1035	return
1036	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
1037	return
1038	self.has_conect = True
1039	self.line_x = line_x
1040	self.line_y = line_y
1041	self.line_z = line_z
1042
1043	def test_load():
1044	"""
1045	Test code
1046	"""
1047	from mpl_toolkits.mplot3d import Axes3D
1048	current_dir = os.path.abspath(os.path.curdir)
1049	print(current_dir)
1050	for i in range(6):
1051	current_dir, _ = os.path.split(current_dir)
1052	tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt")
1053	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
1054	if os.path.isfile(tfile):
1055	tfpath = tfile
1056	ofpath = ofile
1057	break
1058	reader = SLDReader()
1059	oreader = OMFReader()
1060	output = decode(reader.read(tfpath))
1061	ooutput = decode(oreader.read(ofpath))
1062	foutput = OMF2SLD()
1063	foutput.set_data(ooutput)
1064
1065	import matplotlib.pyplot as plt
1066	fig = plt.figure()
1067	ax = Axes3D(fig)
1068	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
1069	alpha=0.7, markeredgecolor='gray', rasterized=True)
1070	gap = 7
1071	max_mx = max(output.sld_mx)
1072	max_my = max(output.sld_my)
1073	max_mz = max(output.sld_mz)
1074	max_m = max(max_mx, max_my, max_mz)
1075	x2 = output.pos_x+output.sld_mx/max_m * gap
1076	y2 = output.pos_y+output.sld_my/max_m * gap
1077	z2 = output.pos_z+output.sld_mz/max_m * gap
1078	x_arrow = np.column_stack((output.pos_x, x2))
1079	y_arrow = np.column_stack((output.pos_y, y2))
1080	z_arrow = np.column_stack((output.pos_z, z2))
1081	unit_x2 = output.sld_mx / max_m
1082	unit_y2 = output.sld_my / max_m
1083	unit_z2 = output.sld_mz / max_m
1084	color_x = np.fabs(unit_x2 * 0.8)
1085	color_y = np.fabs(unit_y2 * 0.8)
1086	color_z = np.fabs(unit_z2 * 0.8)
1087	colors = np.column_stack((color_x, color_y, color_z))
1088	plt.show()
1089
1090	def test():
1091	"""
1092	Test code
1093	"""
1094	current_dir = os.path.abspath(os.path.curdir)
1095	for i in range(3):
1096	current_dir, _ = os.path.split(current_dir)
1097	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
1098	if os.path.isfile(ofile):
1099	ofpath = ofile
1100	break
1101	oreader = OMFReader()
1102	ooutput = decode(oreader.read(ofpath))
1103	foutput = OMF2SLD()
1104	foutput.set_data(ooutput)
1105	writer = SLDReader()
1106	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
1107	foutput.output)
1108	model = GenSAS()
1109	model.set_sld_data(foutput.output)
1110	x = np.arange(1000)/10000. + 1e-5
1111	y = np.arange(1000)/10000. + 1e-5
1112	i = np.zeros(1000)
1113	model.runXY([x, y, i])
1114
1115	if __name__ == "__main__":
1116	test()
1117	test_load()

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SasView

source: sasview/src/sas/sascalc/calculator/sas_gen.py @ 59dfb53

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