sas_gen.py @ 59b1b92

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 59b1b92 was fd5ac0d, checked in by krzywon, 10 years ago
I have completed the removal of all SANS references. I will build, run, and run all unit tests before pushing.
Property mode set to `100644`
File size: 41.8 KB

Line
1	"""
2	SAS generic computation and sld file readers
3	"""
4	from sas.models.BaseComponent import BaseComponent
5	import sas.models.sas_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: evalDistribution(q) where q is a numpy array.
200	* For 2D, a list of numpy arrays are expected: [qx_prime,qy_prime], where 1D arrays.
201	:param qdist: ndarray of scalar q-values or list [qx,qy] where qx,qy are 1D ndarrays
202	"""
203	if qdist.__class__.__name__ == 'list':
204	if len(qdist[1]) < 1:
205	out = self.run(qdist)
206	else:
207	out = self.runXY(qdist)
208	return out
209	else:
210	mesg = "evalDistribution is expecting an ndarray of "
211	mesg += "a list [qx,qy] where qx,qy are arrays."
212	raise RuntimeError, mesg
213
214	class OMF2SLD:
215	"""
216	Convert OMFData to MAgData
217	"""
218	def __init__(self):
219	"""
220	Init
221	"""
222	self.pos_x = None
223	self.pos_y = None
224	self.pos_z = None
225	self.mx = None
226	self.my = None
227	self.mz = None
228	self.sld_n = None
229	self.vol_pix = None
230	self.output = None
231	self.omfdata = None
232
233	def set_data(self, omfdata, shape='rectangular'):
234	"""
235	Set all data
236	"""
237	self.omfdata = omfdata
238	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
239	pos_x = numpy.arange(omfdata.xmin,
240	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
241	omfdata.xstepsize)
242	pos_y = numpy.arange(omfdata.ymin,
243	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
244	omfdata.ystepsize)
245	pos_z = numpy.arange(omfdata.zmin,
246	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
247	omfdata.zstepsize)
248	self.pos_x = numpy.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
249	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
250	self.pos_y = numpy.tile(self.pos_y, int(omfdata.znodes))
251	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
252	self.mx = omfdata.mx
253	self.my = omfdata.my
254	self.mz = omfdata.mz
255	self.sld_n = numpy.zeros(length)
256
257	if omfdata.mx == None:
258	self.mx = numpy.zeros(length)
259	if omfdata.my == None:
260	self.my = numpy.zeros(length)
261	if omfdata.mz == None:
262	self.mz = numpy.zeros(length)
263
264	self._check_data_length(length)
265	self.remove_null_points(False, False)
266	mask = numpy.ones(len(self.sld_n), dtype=bool)
267	if shape.lower() == 'ellipsoid':
268	try:
269	# Pixel (step) size included
270	x_c = max(self.pos_x) + min(self.pos_x)
271	y_c = max(self.pos_y) + min(self.pos_y)
272	z_c = max(self.pos_z) + min(self.pos_z)
273	x_d = max(self.pos_x) - min(self.pos_x)
274	y_d = max(self.pos_y) - min(self.pos_y)
275	z_d = max(self.pos_z) - min(self.pos_z)
276	x_r = (x_d + omfdata.xstepsize) / 2.0
277	y_r = (y_d + omfdata.ystepsize) / 2.0
278	z_r = (z_d + omfdata.zstepsize) / 2.0
279	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
280	x_dir2 *= x_dir2
281	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
282	y_dir2 *= y_dir2
283	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
284	z_dir2 *= z_dir2
285	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
286	except:
287	pass
288	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
289	self.pos_z[mask], self.sld_n[mask],
290	self.mx[mask], self.my[mask], self.mz[mask])
291	self.output.set_pix_type('pixel')
292	self.output.set_pixel_symbols('pixel')
293
294	def get_omfdata(self):
295	"""
296	Return all data
297	"""
298	return self.omfdata
299
300	def get_output(self):
301	"""
302	Return output
303	"""
304	return self.output
305
306	def _check_data_length(self, length):
307	"""
308	Check if the data lengths are consistent
309	:Params length: data length
310	"""
311	msg = "Error: Inconsistent data length."
312	if len(self.pos_x) != length:
313	raise ValueError, msg
314	if len(self.pos_y) != length:
315	raise ValueError, msg
316	if len(self.pos_z) != length:
317	raise ValueError, msg
318	if len(self.mx) != length:
319	raise ValueError, msg
320	if len(self.my) != length:
321	raise ValueError, msg
322	if len(self.mz) != length:
323	raise ValueError, msg
324
325	def remove_null_points(self, remove=False, recenter=False):
326	"""
327	Removes any mx, my, and mz = 0 points
328	"""
329	if remove:
330	is_nonzero = (numpy.fabs(self.mx) + numpy.fabs(self.my) +
331	numpy.fabs(self.mz)).nonzero()
332	if len(is_nonzero[0]) > 0:
333	self.pos_x = self.pos_x[is_nonzero]
334	self.pos_y = self.pos_y[is_nonzero]
335	self.pos_z = self.pos_z[is_nonzero]
336	self.sld_n = self.sld_n[is_nonzero]
337	self.mx = self.mx[is_nonzero]
338	self.my = self.my[is_nonzero]
339	self.mz = self.mz[is_nonzero]
340	if recenter:
341	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
342	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
343	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
344
345	def get_magsld(self):
346	"""
347	return MagSLD
348	"""
349	return self.output
350
351
352	class OMFReader:
353	"""
354	Class to load omf/ascii files (3 columns w/header).
355	"""
356	## File type
357	type_name = "OMF ASCII"
358
359	## Wildcards
360	type = ["OMF files (.OMF, .omf)\|*.omf"]
361	## List of allowed extensions
362	ext = ['.omf', '.OMF']
363
364	def read(self, path):
365	"""
366	Load data file
367	:param path: file path
368	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
369	"""
370	#data_conv_m = None
371	desc = ""
372	mx = numpy.zeros(0)
373	my = numpy.zeros(0)
374	mz = numpy.zeros(0)
375	try:
376	data_conv_val = None
377	data_conv_mesh = None
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	pass
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.set_sldms(mx, my, mz)
457	output.filename = os.path.basename(path)
458	output.oommf = oommf
459	output.title = title
460	output.desc = desc
461	output.meshtype = meshtype
462	output.xbase = float(xbase) * METER2ANG
463	output.ybase = float(ybase) * METER2ANG
464	output.zbase = float(zbase) * METER2ANG
465	output.xstepsize = float(xstepsize) * METER2ANG
466	output.ystepsize = float(ystepsize) * METER2ANG
467	output.zstepsize = float(zstepsize) * METER2ANG
468	output.xnodes = float(xnodes)
469	output.ynodes = float(ynodes)
470	output.znodes = float(znodes)
471	output.xmin = float(xmin) * METER2ANG
472	output.ymin = float(ymin) * METER2ANG
473	output.zmin = float(zmin) * METER2ANG
474	output.xmax = float(xmax) * METER2ANG
475	output.ymax = float(ymax) * METER2ANG
476	output.zmax = float(zmax) * METER2ANG
477	output.valuemultiplier = valuemultiplier
478	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
479	valueunit)
480	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
481	valueunit)
482	output.set_m(mx, my, mz)
483	return output
484	except:
485	msg = "%s is not supported: \n" % path
486	msg += "We accept only Text format OMF file."
487	raise RuntimeError, msg
488
489	class PDBReader:
490	"""
491	PDB reader class: limited for reading the lines starting with 'ATOM'
492	"""
493	type_name = "PDB"
494	## Wildcards
495	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
496	## List of allowed extensions
497	ext = ['.pdb', '.PDB']
498
499	def read(self, path):
500	"""
501	Load data file
502
503	:param path: file path
504
505	:return: MagSLD
506
507	:raise RuntimeError: when the file can't be opened
508	"""
509	pos_x = numpy.zeros(0)
510	pos_y = numpy.zeros(0)
511	pos_z = numpy.zeros(0)
512	sld_n = numpy.zeros(0)
513	sld_mx = numpy.zeros(0)
514	sld_my = numpy.zeros(0)
515	sld_mz = numpy.zeros(0)
516	vol_pix = numpy.zeros(0)
517	pix_symbol = numpy.zeros(0)
518	x_line = []
519	y_line = []
520	z_line = []
521	x_lines = []
522	y_lines = []
523	z_lines = []
524	try:
525	input_f = open(path, 'rb')
526	buff = input_f.read()
527	lines = buff.split('\n')
528	input_f.close()
529	pre_num = 0
530	num = 0
531	for line in lines:
532	try:
533	# check if line starts with "ATOM"
534	if line[0:6].strip().count('ATM') > 0 or \
535	line[0:6].strip() == 'ATOM':
536	# define fields of interest
537	atom_id = line[6:11].strip()
538	atom_name = line[12:16].strip()
539	try:
540	float(line[12])
541	atom_name = atom_name[1].upper()
542	except:
543	if len(atom_name) == 4:
544	atom_name = atom_name[0].upper()
545	elif line[12] != ' ':
546	atom_name = atom_name[0].upper() + \
547	atom_name[1].lower()
548	else:
549	atom_name = atom_name[0].upper()
550	#res_name = line[17:20].strip()
551	#chain_name = line[21:22].strip()
552	_pos_x = float(line[30:38].strip())
553	_pos_y = float(line[38:46].strip())
554	_pos_z = float(line[46:54].strip())
555
556	pos_x = numpy.append(pos_x, _pos_x)
557	pos_y = numpy.append(pos_y, _pos_y)
558	pos_z = numpy.append(pos_z, _pos_z)
559	try:
560	# sld in Ang unit (from fm)
561	#val = formula(atom_name).atoms.keys()[0].neutron.b_c
562	#val *= 1.0e-5
563	val = nsf.neutron_sld(atom_name)[0]
564	# sld in Ang^-2 unit
565	val *= 1.0e-6
566	sld_n = numpy.append(sld_n, val)
567	atom = formula(atom_name)
568	# cm to A units
569	vol = 1.0e+24 * atom.mass / atom.density / NA
570	vol_pix = numpy.append(vol_pix, vol)
571	except:
572	print "Error: set the sld of %s to zero"% atom_name
573	sld_n = numpy.append(sld_n, 0.0)
574	sld_mx = numpy.append(sld_mx, 0)
575	sld_my = numpy.append(sld_my, 0)
576	sld_mz = numpy.append(sld_mz, 0)
577	pix_symbol = numpy.append(pix_symbol, atom_name)
578	elif line[0:6].strip().count('CONECT') > 0 :
579	toks = line.split()
580	num = int(toks[1]) - 1
581	val_list = []
582	for val in toks[2:]:
583	try:
584	int_val = int(val)
585	except:
586	break
587	if int_val == 0:
588	break
589	val_list.append(int_val)
590	#need val_list ordered
591	for val in val_list:
592	index = val - 1
593	if (pos_x[index], pos_x[num]) in x_line and \
594	(pos_y[index], pos_y[num]) in y_line and \
595	(pos_z[index], pos_z[num]) in z_line:
596	continue
597	x_line.append((pos_x[num], pos_x[index]))
598	y_line.append((pos_y[num], pos_y[index]))
599	z_line.append((pos_z[num], pos_z[index]))
600	if len(x_line) > 0:
601	x_lines.append(x_line)
602	y_lines.append(y_line)
603	z_lines.append(z_line)
604	except:
605	pass
606	#re-centering
607	#pos_x -= (min(pos_x) + max(pos_x)) / 2.0
608	#pos_y -= (min(pos_y) + max(pos_y)) / 2.0
609	#pos_z -= (min(pos_z) + max(pos_z)) / 2.0
610
611	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
612	output.set_conect_lines(x_line, y_line, z_line)
613	output.filename = os.path.basename(path)
614	output.set_pix_type('atom')
615	output.set_pixel_symbols(pix_symbol)
616	output.set_nodes()
617	output.set_pixel_volumes(vol_pix)
618	output.sld_unit = '1/A^(2)'
619	return output
620	except:
621	RuntimeError, "%s is not a sld file" % path
622
623	def write(self, path, data):
624	"""
625	Write
626	"""
627	#Not implemented
628	print "Not implemented... "
629
630	class SLDReader:
631	"""
632	Class to load ascii files (7 columns).
633	"""
634	## File type
635	type_name = "SLD ASCII"
636
637	## Wildcards
638	type = ["sld files (.SLD, .sld)\|*.sld",
639	"txt files (.TXT, .txt)\|*.txt",
640	"all files (.)\|."]
641	## List of allowed extensions
642	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
643
644	def read(self, path):
645	"""
646	Load data file
647
648	:param path: file path
649
650	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
651
652	:raise RuntimeError: when the file can't be opened
653	:raise ValueError: when the length of the data vectors are inconsistent
654	"""
655	try:
656	pos_x = numpy.zeros(0)
657	pos_y = numpy.zeros(0)
658	pos_z = numpy.zeros(0)
659	sld_n = numpy.zeros(0)
660	sld_mx = numpy.zeros(0)
661	sld_my = numpy.zeros(0)
662	sld_mz = numpy.zeros(0)
663	try:
664	# Use numpy to speed up loading
665	input_f = numpy.loadtxt(path, dtype='float', skiprows=1,
666	ndmin=1, unpack=True)
667	pos_x = numpy.array(input_f[0])
668	pos_y = numpy.array(input_f[1])
669	pos_z = numpy.array(input_f[2])
670	sld_n = numpy.array(input_f[3])
671	sld_mx = numpy.array(input_f[4])
672	sld_my = numpy.array(input_f[5])
673	sld_mz = numpy.array(input_f[6])
674	ncols = len(input_f)
675	if ncols == 8:
676	vol_pix = numpy.array(input_f[7])
677	elif ncols == 7:
678	vol_pix = None
679	except:
680	# For older version of numpy
681	input_f = open(path, 'rb')
682	buff = input_f.read()
683	lines = buff.split('\n')
684	input_f.close()
685	for line in lines:
686	toks = line.split()
687	try:
688	_pos_x = float(toks[0])
689	_pos_y = float(toks[1])
690	_pos_z = float(toks[2])
691	_sld_n = float(toks[3])
692	_sld_mx = float(toks[4])
693	_sld_my = float(toks[5])
694	_sld_mz = float(toks[6])
695
696	pos_x = numpy.append(pos_x, _pos_x)
697	pos_y = numpy.append(pos_y, _pos_y)
698	pos_z = numpy.append(pos_z, _pos_z)
699	sld_n = numpy.append(sld_n, _sld_n)
700	sld_mx = numpy.append(sld_mx, _sld_mx)
701	sld_my = numpy.append(sld_my, _sld_my)
702	sld_mz = numpy.append(sld_mz, _sld_mz)
703	try:
704	_vol_pix = float(toks[7])
705	vol_pix = numpy.append(vol_pix, _vol_pix)
706	except:
707	vol_pix = None
708	except:
709	# Skip non-data lines
710	pass
711
712	# re-center
713	#pos_x -= (min(pos_x) + max(pos_x)) / 2.0
714	#pos_y -= (min(pos_y) + max(pos_y)) / 2.0
715	#pos_z -= (min(pos_z) + max(pos_z)) / 2.0
716
717	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
718	sld_mx, sld_my, sld_mz)
719
720	output.filename = os.path.basename(path)
721	output.set_pix_type('pixel')
722	output.set_pixel_symbols('pixel')
723	if vol_pix != None:
724	output.set_pixel_volumes(vol_pix)
725	return output
726	except:
727	RuntimeError, "%s is not a sld file" % path
728
729	def write(self, path, data):
730	"""
731	Write sld file
732
733	:Param path: file path
734	:Param data: MagSLD data object
735	"""
736	if path == None:
737	raise ValueError, "Missing the file path."
738	if data == None:
739	raise ValueError, "Missing the data to save."
740
741	x_val = data.pos_x
742	y_val = data.pos_y
743	z_val = data.pos_z
744	vol_pix = data.vol_pix
745
746	length = len(x_val)
747
748	sld_n = data.sld_n
749	if sld_n == None:
750	sld_n = numpy.zerros(length)
751
752	sld_mx = data.sld_mx
753	if sld_mx == None:
754	sld_mx = numpy.zerros(length)
755	sld_my = numpy.zerros(length)
756	sld_mz = numpy.zerros(length)
757	else:
758	sld_my = data.sld_my
759	sld_mz = data.sld_mz
760
761	out = open(path, 'w')
762	# First Line: Column names
763	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
764	for ind in range(length):
765	out.write("\n%g %g %g %g %g %g %g %g" % (x_val[ind], y_val[ind],
766	z_val[ind], sld_n[ind],
767	sld_mx[ind], sld_my[ind],
768	sld_mz[ind], vol_pix[ind]))
769	out.close()
770
771
772	class OMFData:
773	"""
774	OMF Data.
775	"""
776	_meshunit = "A"
777	_valueunit = "A^(-2)"
778	def __init__(self):
779	"""
780	Init for mag SLD
781	"""
782	self.filename = 'default'
783	self.oommf = ''
784	self.title = ''
785	self.desc = ''
786	self.meshtype = ''
787	self.meshunit = self._meshunit
788	self.valueunit = self._valueunit
789	self.xbase = 0.0
790	self.ybase = 0.0
791	self.zbase = 0.0
792	self.xstepsize = 6.0
793	self.ystepsize = 6.0
794	self.zstepsize = 6.0
795	self.xnodes = 10.0
796	self.ynodes = 10.0
797	self.znodes = 10.0
798	self.xmin = 0.0
799	self.ymin = 0.0
800	self.zmin = 0.0
801	self.xmax = 60.0
802	self.ymax = 60.0
803	self.zmax = 60.0
804	self.mx = None
805	self.my = None
806	self.mz = None
807	self.valuemultiplier = 1.
808	self.valuerangeminmag = 0
809	self.valuerangemaxmag = 0
810
811	def __str__(self):
812	"""
813	doc strings
814	"""
815	_str = "Type: %s\n" % self.__class__.__name__
816	_str += "File: %s\n" % self.filename
817	_str += "OOMMF: %s\n" % self.oommf
818	_str += "Title: %s\n" % self.title
819	_str += "Desc: %s\n" % self.desc
820	_str += "meshtype: %s\n" % self.meshtype
821	_str += "meshunit: %s\n" % str(self.meshunit)
822	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
823	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
824	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
825	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
826	self.meshunit)
827	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
828	self.meshunit)
829	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
830	self.meshunit)
831	_str += "xnodes: %s\n" % str(self.xnodes)
832	_str += "ynodes: %s\n" % str(self.ynodes)
833	_str += "znodes: %s\n" % str(self.znodes)
834	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
835	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
836	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
837	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
838	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
839	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
840	_str += "valueunit: %s\n" % self.valueunit
841	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
842	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
843	self.valueunit)
844	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
845	self.valueunit)
846	return _str
847
848	def set_m(self, mx, my, mz):
849	"""
850	Set the Mx, My, Mz values
851	"""
852	self.mx = mx
853	self.my = my
854	self.mz = mz
855
856	class MagSLD:
857	"""
858	Magnetic SLD.
859	"""
860	pos_x = None
861	pos_y = None
862	pos_z = None
863	sld_n = None
864	sld_mx = None
865	sld_my = None
866	sld_mz = None
867	# Units
868	_pos_unit = 'A'
869	_sld_unit = '1/A^(2)'
870	_pix_type = 'pixel'
871
872	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
873	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
874	"""
875	Init for mag SLD
876	:params : All should be numpy 1D array
877	"""
878	self.is_data = True
879	self.filename = ''
880	self.xstepsize = 6.0
881	self.ystepsize = 6.0
882	self.zstepsize = 6.0
883	self.xnodes = 10.0
884	self.ynodes = 10.0
885	self.znodes = 10.0
886	self.has_stepsize = False
887	self.has_conect = False
888	self.pos_unit = self._pos_unit
889	self.sld_unit = self._sld_unit
890	self.pix_type = 'pixel'
891	self.pos_x = pos_x
892	self.pos_y = pos_y
893	self.pos_z = pos_z
894	self.sld_n = sld_n
895	self.line_x = None
896	self.line_y = None
897	self.line_z = None
898	self.sld_mx = sld_mx
899	self.sld_my = sld_my
900	self.sld_mz = sld_mz
901	self.vol_pix = vol_pix
902	self.sld_m = None
903	self.sld_phi = None
904	self.sld_theta = None
905	self.pix_symbol = None
906	if sld_mx != None and sld_my != None and sld_mz != None:
907	self.set_sldms(sld_mx, sld_my, sld_mz)
908	self.set_nodes()
909
910	def __str__(self):
911	"""
912	doc strings
913	"""
914	_str = "Type: %s\n" % self.__class__.__name__
915	_str += "File: %s\n" % self.filename
916	_str += "Axis_unit: %s\n" % self.pos_unit
917	_str += "SLD_unit: %s\n" % self.sld_unit
918	return _str
919
920	def set_pix_type(self, pix_type):
921	"""
922	Set pixel type
923	:Param pix_type: string, 'pixel' or 'atom'
924	"""
925	self.pix_type = pix_type
926
927	def set_sldn(self, sld_n):
928	"""
929	Sets neutron SLD
930	"""
931	if sld_n.__class__.__name__ == 'float':
932	if self.is_data:
933	# For data, put the value to only the pixels w non-zero M
934	is_nonzero = (numpy.fabs(self.sld_mx) +
935	numpy.fabs(self.sld_my) +
936	numpy.fabs(self.sld_mz)).nonzero()
937	self.sld_n = numpy.zeros(len(self.pos_x))
938	if len(self.sld_n[is_nonzero]) > 0:
939	self.sld_n[is_nonzero] = sld_n
940	else:
941	self.sld_n.fill(sld_n)
942	else:
943	# For non-data, put the value to all the pixels
944	self.sld_n = numpy.ones(len(self.pos_x)) * sld_n
945	else:
946	self.sld_n = sld_n
947
948	def set_sldms(self, sld_mx, sld_my, sld_mz):
949	"""
950	Sets (\\|m\\|, m_theta, m_phi)
951	"""
952	if sld_mx.__class__.__name__ == 'float':
953	self.sld_mx = numpy.ones(len(self.pos_x)) * sld_mx
954	else:
955	self.sld_mx = sld_mx
956	if sld_my.__class__.__name__ == 'float':
957	self.sld_my = numpy.ones(len(self.pos_x)) * sld_my
958	else:
959	self.sld_my = sld_my
960	if sld_mz.__class__.__name__ == 'float':
961	self.sld_mz = numpy.ones(len(self.pos_x)) * sld_mz
962	else:
963	self.sld_mz = sld_mz
964
965	sld_m = numpy.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
966	sld_mz * sld_mz)
967	self.sld_m = sld_m
968
969	def set_pixel_symbols(self, symbol='pixel'):
970	"""
971	Set pixel
972	:Params pixel: str; pixel or atomic symbol, or array of strings
973	"""
974	if self.sld_n == None:
975	return
976	if symbol.__class__.__name__ == 'str':
977	self.pix_symbol = numpy.repeat(symbol, len(self.sld_n))
978	else:
979	self.pix_symbol = symbol
980
981	def set_pixel_volumes(self, vol):
982	"""
983	Set pixel volumes
984	:Params pixel: str; pixel or atomic symbol, or array of strings
985	"""
986	if self.sld_n == None:
987	return
988	if vol.__class__.__name__ == 'ndarray':
989	self.vol_pix = vol
990	elif vol.__class__.__name__.count('float') > 0:
991	self.vol_pix = numpy.repeat(vol, len(self.sld_n))
992	else:
993	self.vol_pix = None
994
995	def get_sldn(self):
996	"""
997	Returns nuclear sld
998	"""
999	return self.sld_n
1000
1001	def get_sld_mxyz(self):
1002	"""
1003	Returns (sld_mx, sldmy, sld_mz)
1004	"""
1005	return (self.sld_mx, self.sldmy, self.sld_mz)
1006
1007	def get_sld_m(self):
1008	"""
1009	Returns (sldm, sld_theta, sld_phi)
1010	"""
1011	return (self.sldm, self.sld_theta, self.sld_phi)
1012
1013	def set_nodes(self):
1014	"""
1015	Set xnodes, ynodes, and znodes
1016	"""
1017	self.set_stepsize()
1018	if self.pix_type == 'pixel':
1019	try:
1020	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
1021	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
1022	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
1023	self.xnodes = int(xdist) + 1
1024	self.ynodes = int(ydist) + 1
1025	self.znodes = int(zdist) + 1
1026	except:
1027	self.xnodes = None
1028	self.ynodes = None
1029	self.znodes = None
1030	else:
1031	self.xnodes = None
1032	self.ynodes = None
1033	self.znodes = None
1034
1035	def set_stepsize(self):
1036	"""
1037	Set xtepsize, ystepsize, and zstepsize
1038	"""
1039	if self.pix_type == 'pixel':
1040	try:
1041	xpos_pre = self.pos_x[0]
1042	ypos_pre = self.pos_y[0]
1043	zpos_pre = self.pos_z[0]
1044	for x_pos in self.pos_x:
1045	if xpos_pre != x_pos:
1046	self.xstepsize = numpy.fabs(x_pos - xpos_pre)
1047	break
1048	for y_pos in self.pos_y:
1049	if ypos_pre != y_pos:
1050	self.ystepsize = numpy.fabs(y_pos - ypos_pre)
1051	break
1052	for z_pos in self.pos_z:
1053	if zpos_pre != z_pos:
1054	self.zstepsize = numpy.fabs(z_pos - zpos_pre)
1055	break
1056	#default pix volume
1057	self.vol_pix = numpy.ones(len(self.pos_x))
1058	vol = self.xstepsize * self.ystepsize * self.zstepsize
1059	self.set_pixel_volumes(vol)
1060	self.has_stepsize = True
1061	except:
1062	self.xstepsize = None
1063	self.ystepsize = None
1064	self.zstepsize = None
1065	self.vol_pix = None
1066	self.has_stepsize = False
1067	else:
1068	self.xstepsize = None
1069	self.ystepsize = None
1070	self.zstepsize = None
1071	self.has_stepsize = True
1072	return self.xstepsize, self.ystepsize, self.zstepsize
1073
1074	def set_conect_lines(self, line_x, line_y, line_z):
1075	"""
1076	Set bonding line data if taken from pdb
1077	"""
1078	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
1079	return
1080	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
1081	return
1082	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
1083	return
1084	self.has_conect = True
1085	self.line_x = line_x
1086	self.line_y = line_y
1087	self.line_z = line_z
1088
1089
1090	def test_load():
1091	from sas.plottools.arrow3d import Arrow3D
1092	import os
1093	dir = os.path.abspath(os.path.curdir)
1094	print dir
1095	for i in range(6):
1096	dir, _ = os.path.split(dir)
1097	tfile = os.path.join(dir, "test", "CoreXY_ShellZ.txt")
1098	ofile = os.path.join(dir, "test", "A_Raw_Example-1.omf")
1099	if os.path.isfile(tfile):
1100	tfpath = tfile
1101	ofpath = ofile
1102	break
1103	reader = SLDReader()
1104	oreader = OMFReader()
1105	output = reader.read(tfpath)
1106	ooutput = oreader.read(ofpath)
1107	foutput = OMF2SLD()
1108	foutput.set_data(ooutput)
1109
1110	import matplotlib.pyplot as plt
1111	from mpl_toolkits.mplot3d import Axes3D
1112	fig = plt.figure()
1113	ax = fig.gca(projection='3d')
1114	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
1115	alpha = 0.7, markeredgecolor='gray',rasterized=True)
1116	gap = 7
1117	max_mx = max(output.sld_mx)
1118	max_my = max(output.sld_my)
1119	max_mz = max(output.sld_mz)
1120	max_m = max(max_mx,max_my,max_mz)
1121	x2 = output.pos_x+output.sld_mx/max_m * gap
1122	y2 = output.pos_y+output.sld_my/max_m * gap
1123	z2 = output.pos_z+output.sld_mz/max_m * gap
1124	x_arrow = numpy.column_stack((output.pos_x,x2))
1125	y_arrow = numpy.column_stack((output.pos_y,y2))
1126	z_arrow = numpy.column_stack((output.pos_z,z2))
1127	unit_x2 = output.sld_mx / max_m
1128	unit_y2 = output.sld_my / max_m
1129	unit_z2 = output.sld_mz / max_m
1130	color_x = numpy.fabs(unit_x2 * 0.8)
1131	color_y = numpy.fabs(unit_y2 * 0.8)
1132	color_z = numpy.fabs(unit_z2 * 0.8)
1133	colors = numpy.column_stack((color_x, color_y, color_z))
1134	a = Arrow3D(None, x_arrow,y_arrow,z_arrow, colors, mutation_scale=10, lw=1,
1135	arrowstyle="->", color="y", alpha = 0.5)
1136
1137	ax.add_artist(a)
1138	plt.show()
1139
1140	def test():
1141	import os
1142	dir = os.path.abspath(os.path.curdir)
1143	for i in range(3):
1144	dir, _ = os.path.split(dir)
1145	#tfile = os.path.join(dir, "test", "C_Example_Converted.txt")
1146	ofile = os.path.join(dir, "test", "A_Raw_Example-1.omf")
1147	if os.path.isfile(ofile):
1148	#tfpath = tfile
1149	ofpath = ofile
1150	break
1151	#reader = SLDReader()
1152	oreader = OMFReader()
1153	#output = reader.read(tfpath)
1154	ooutput = oreader.read(ofpath)
1155	foutput = OMF2SLD()
1156	foutput.set_data(ooutput)
1157	writer = SLDReader()
1158	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
1159	foutput.output)
1160	model = GenSAS()
1161	model.set_sld_data(foutput.output)
1162	x = numpy.arange(1000)/10000. + 1e-5
1163	y = numpy.arange(1000)/10000. + 1e-5
1164	#z = numpy.arange(1000)/10000. + 1e-5
1165	i = numpy.zeros(1000)
1166	out = model.runXY([x,y,i])
1167
1168	if __name__ == "__main__":
1169	test()
1170	test_load()

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SasView

source: sasview/src/sas/calculator/sas_gen.py @ 59b1b92

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