sas_gen.py @ 6d6832e

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 6d6832e was 5ed76f8, checked in by Paul Kienzle <pkienzle@…>, 8 years ago
docs: use latex in equations rather than unicode + rst markup
Property mode set to `100644`
File size: 39.4 KB

Rev	Line
[b6627d9]	1	# pylint: disable=invalid-name
[51f14603]	2	"""
[fd5ac0d]	3	SAS generic computation and sld file readers
[51f14603]	4	"""
[9e531f2]	5	import sas.sascalc.calculator.core.sld2i as mod
[d2fd8fc]	6	from sas.sascalc.calculator.BaseComponent import BaseComponent
[51f14603]	7	from periodictable import formula
	8	from periodictable import nsf
[9a5097c]	9	import numpy as np
[51f14603]	10	import os
	11	import copy
[b6627d9]	12	import sys
	13	import logging
[51f14603]	14
[e3f77d8b]	15	MFACTOR_AM = 2.853E-12
	16	MFACTOR_MT = 2.3164E-9
[51f14603]	17	METER2ANG = 1.0E+10
	18	#Avogadro constant [1/mol]
	19	NA = 6.02214129e+23
	20
	21	def mag2sld(mag, v_unit=None):
	22	"""
	23	Convert magnetization to magnatic SLD
	24	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
	25	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
[e3f77d8b]	26	"""
[51f14603]	27	if v_unit == "A/m":
[e3f77d8b]	28	factor = MFACTOR_AM
[51f14603]	29	elif v_unit == "mT":
[e3f77d8b]	30	factor = MFACTOR_MT
[51f14603]	31	else:
	32	raise ValueError, "Invalid valueunit"
	33	sld_m = factor * mag
	34	return sld_m
	35
	36	def transform_center(pos_x, pos_y, pos_z):
	37	"""
[e3f77d8b]	38	re-center
[51f14603]	39	:return: posx, posy, posz [arrays]
[e3f77d8b]	40	"""
[51f14603]	41	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
	42	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
[e3f77d8b]	43	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
	44	return posx, posy, posz
[51f14603]	45
	46	class GenSAS(BaseComponent):
	47	"""
	48	Generic SAS computation Model based on sld (n & m) arrays
	49	"""
	50	def __init__(self):
	51	"""
	52	Init
	53	:Params sld_data: MagSLD object
	54	"""
	55	# Initialize BaseComponent
	56	BaseComponent.__init__(self)
	57	self.sld_data = None
	58	self.data_pos_unit = None
	59	self.data_x = None
	60	self.data_y = None
	61	self.data_z = None
	62	self.data_sldn = None
	63	self.data_mx = None
	64	self.data_my = None
	65	self.data_mz = None
	66	self.data_vol = None #[A^3]
	67	self.is_avg = False
	68	## Name of the model
	69	self.name = "GenSAS"
	70	## Define parameters
	71	self.params = {}
[e3f77d8b]	72	self.params['scale'] = 1.0
	73	self.params['background'] = 0.0
	74	self.params['solvent_SLD'] = 0.0
[51f14603]	75	self.params['total_volume'] = 1.0
[e3f77d8b]	76	self.params['Up_frac_in'] = 1.0
	77	self.params['Up_frac_out'] = 1.0
	78	self.params['Up_theta'] = 0.0
[51f14603]	79	self.description = 'GenSAS'
	80	## Parameter details [units, min, max]
	81	self.details = {}
[9a5097c]	82	self.details['scale'] = ['', 0.0, np.inf]
	83	self.details['background'] = ['[1/cm]', 0.0, np.inf]
	84	self.details['solvent_SLD'] = ['1/A^(2)', -np.inf, np.inf]
	85	self.details['total_volume'] = ['A^(3)', 0.0, np.inf]
[cb4ef58]	86	self.details['Up_frac_in'] = ['[u/(u+d)]', 0.0, 1.0]
	87	self.details['Up_frac_out'] = ['[u/(u+d)]', 0.0, 1.0]
[9a5097c]	88	self.details['Up_theta'] = ['[deg]', -np.inf, np.inf]
[51f14603]	89	# fixed parameters
	90	self.fixed = []
[e3f77d8b]	91
	92	def set_pixel_volumes(self, volume):
[51f14603]	93	"""
	94	Set the volume of a pixel in (A^3) unit
	95	:Param volume: pixel volume [float]
	96	"""
	97	if self.data_vol == None:
	98	raise
	99	self.data_vol = volume
[e3f77d8b]	100
	101	def set_is_avg(self, is_avg=False):
[51f14603]	102	"""
	103	Sets is_avg: [bool]
	104	"""
	105	self.is_avg = is_avg
[e3f77d8b]	106
[51f14603]	107	def _gen(self, x, y, i):
	108	"""
	109	Evaluate the function
	110	:Param x: array of x-values
	111	:Param y: array of y-values
[e3f77d8b]	112	:Param i: array of initial i-value
[51f14603]	113	:return: function value
	114	"""
	115	pos_x = self.data_x
	116	pos_y = self.data_y
	117	pos_z = self.data_z
	118	len_x = len(pos_x)
	119	if self.is_avg == None:
	120	len_x *= -1
	121	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
	122	len_q = len(x)
	123	sldn = copy.deepcopy(self.data_sldn)
	124	sldn -= self.params['solvent_SLD']
[e3f77d8b]	125	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
	126	sldn, self.data_mx, self.data_my,
[51f14603]	127	self.data_mz, self.data_vol,
[e3f77d8b]	128	self.params['Up_frac_in'],
	129	self.params['Up_frac_out'],
[51f14603]	130	self.params['Up_theta'])
	131	if y == []:
	132	mod.genicom(model, len_q, x, i)
	133	else:
	134	mod.genicomXY(model, len_q, x, y, i)
	135	vol_correction = self.data_total_volume / self.params['total_volume']
	136	return self.params['scale'] * vol_correction * i + \
	137	self.params['background']
[e3f77d8b]	138
	139	def set_sld_data(self, sld_data=None):
[51f14603]	140	"""
	141	Sets sld_data
	142	"""
	143	self.sld_data = sld_data
	144	self.data_pos_unit = sld_data.pos_unit
	145	self.data_x = sld_data.pos_x
	146	self.data_y = sld_data.pos_y
	147	self.data_z = sld_data.pos_z
	148	self.data_sldn = sld_data.sld_n
	149	self.data_mx = sld_data.sld_mx
	150	self.data_my = sld_data.sld_my
	151	self.data_mz = sld_data.sld_mz
	152	self.data_vol = sld_data.vol_pix
	153	self.data_total_volume = sum(sld_data.vol_pix)
	154	self.params['total_volume'] = sum(sld_data.vol_pix)
[e3f77d8b]	155
[51f14603]	156	def getProfile(self):
	157	"""
[e3f77d8b]	158	Get SLD profile
[51f14603]	159	: return: sld_data
	160	"""
	161	return self.sld_data
[e3f77d8b]	162
	163	def run(self, x=0.0):
	164	"""
[51f14603]	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
[9a5097c]	173	i_out = np.zeros_like(x[0])
[51f14603]	174	# 1D I is found at y =0 in the 2D pattern
[e3f77d8b]	175	out = self._gen(x[0], [], i_out)
[51f14603]	176	return out
	177	else:
	178	msg = "Q must be given as list of qx's and qy's"
	179	raise ValueError, msg
[e3f77d8b]	180
	181	def runXY(self, x=0.0):
	182	"""
[51f14603]	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':
[9a5097c]	189	i_out = np.zeros_like(x[0])
[51f14603]	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
[e3f77d8b]	195
[51f14603]	196	def evalDistribution(self, qdist):
	197	"""
	198	Evaluate a distribution of q-values.
[ac7be54]	199
	200	:param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy]
	201	where qx,qy are 1D ndarrays (for 2D).
[51f14603]	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
[e3f77d8b]	213
	214	class OMF2SLD(object):
[51f14603]	215	"""
	216	Convert OMFData to MAgData
	217	"""
[e3f77d8b]	218	def __init__(self):
[51f14603]	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
[e3f77d8b]	232
[51f14603]	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)
[9a5097c]	239	pos_x = np.arange(omfdata.xmin,
[e3f77d8b]	240	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
[51f14603]	241	omfdata.xstepsize)
[9a5097c]	242	pos_y = np.arange(omfdata.ymin,
[e3f77d8b]	243	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
[51f14603]	244	omfdata.ystepsize)
[9a5097c]	245	pos_z = np.arange(omfdata.zmin,
[e3f77d8b]	246	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
[51f14603]	247	omfdata.zstepsize)
[9a5097c]	248	self.pos_x = np.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
[51f14603]	249	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
[9a5097c]	250	self.pos_y = np.tile(self.pos_y, int(omfdata.znodes))
[51f14603]	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
[9a5097c]	255	self.sld_n = np.zeros(length)
[e3f77d8b]	256
[51f14603]	257	if omfdata.mx == None:
[9a5097c]	258	self.mx = np.zeros(length)
[51f14603]	259	if omfdata.my == None:
[9a5097c]	260	self.my = np.zeros(length)
[51f14603]	261	if omfdata.mz == None:
[9a5097c]	262	self.mz = np.zeros(length)
[e3f77d8b]	263
[51f14603]	264	self._check_data_length(length)
	265	self.remove_null_points(False, False)
[9a5097c]	266	mask = np.ones(len(self.sld_n), dtype=bool)
[51f14603]	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:
[b6627d9]	287	logging.error(sys.exc_value)
[e3f77d8b]	288	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
	289	self.pos_z[mask], self.sld_n[mask],
[51f14603]	290	self.mx[mask], self.my[mask], self.mz[mask])
	291	self.output.set_pix_type('pixel')
	292	self.output.set_pixel_symbols('pixel')
[e3f77d8b]	293
[51f14603]	294	def get_omfdata(self):
	295	"""
	296	Return all data
	297	"""
	298	return self.omfdata
[e3f77d8b]	299
[51f14603]	300	def get_output(self):
	301	"""
	302	Return output
	303	"""
	304	return self.output
[e3f77d8b]	305
[51f14603]	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
[e3f77d8b]	324
[51f14603]	325	def remove_null_points(self, remove=False, recenter=False):
	326	"""
	327	Removes any mx, my, and mz = 0 points
	328	"""
	329	if remove:
[9a5097c]	330	is_nonzero = (np.fabs(self.mx) + np.fabs(self.my) +
	331	np.fabs(self.mz)).nonzero()
[e3f77d8b]	332	if len(is_nonzero[0]) > 0:
[51f14603]	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
[e3f77d8b]	344
[51f14603]	345	def get_magsld(self):
	346	"""
	347	return MagSLD
	348	"""
	349	return self.output
[e3f77d8b]	350
	351
	352	class OMFReader(object):
[51f14603]	353	"""
	354	Class to load omf/ascii files (3 columns w/header).
	355	"""
	356	## File type
	357	type_name = "OMF ASCII"
[e3f77d8b]	358
[51f14603]	359	## Wildcards
	360	type = ["OMF files (.OMF, .omf)\|*.omf"]
	361	## List of allowed extensions
	362	ext = ['.omf', '.OMF']
[e3f77d8b]	363
[51f14603]	364	def read(self, path):
	365	"""
	366	Load data file
	367	:param path: file path
	368	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	369	"""
	370	desc = ""
[9a5097c]	371	mx = np.zeros(0)
	372	my = np.zeros(0)
	373	mz = np.zeros(0)
[51f14603]	374	try:
	375	input_f = open(path, 'rb')
	376	buff = input_f.read()
	377	lines = buff.split('\n')
	378	input_f.close()
	379	output = OMFData()
	380	valueunit = None
	381	for line in lines:
	382	toks = line.split()
	383	# Read data
	384	try:
	385	_mx = float(toks[0])
	386	_my = float(toks[1])
	387	_mz = float(toks[2])
	388	_mx = mag2sld(_mx, valueunit)
	389	_my = mag2sld(_my, valueunit)
	390	_mz = mag2sld(_mz, valueunit)
[9a5097c]	391	mx = np.append(mx, _mx)
	392	my = np.append(my, _my)
	393	mz = np.append(mz, _mz)
[51f14603]	394	except:
	395	# Skip non-data lines
[b6627d9]	396	logging.error(sys.exc_value)
[51f14603]	397	#Reading Header; Segment count ignored
	398	s_line = line.split(":", 1)
	399	if s_line[0].lower().count("oommf") > 0:
	400	oommf = s_line[1].lstrip()
	401	if s_line[0].lower().count("title") > 0:
	402	title = s_line[1].lstrip()
	403	if s_line[0].lower().count("desc") > 0:
	404	desc += s_line[1].lstrip()
	405	desc += '\n'
	406	if s_line[0].lower().count("meshtype") > 0:
	407	meshtype = s_line[1].lstrip()
	408	if s_line[0].lower().count("meshunit") > 0:
	409	meshunit = s_line[1].lstrip()
	410	if meshunit.count("m") < 1:
	411	msg = "Error: \n"
	412	msg += "We accept only m as meshunit"
	413	raise ValueError, msg
	414	if s_line[0].lower().count("xbase") > 0:
	415	xbase = s_line[1].lstrip()
	416	if s_line[0].lower().count("ybase") > 0:
	417	ybase = s_line[1].lstrip()
	418	if s_line[0].lower().count("zbase") > 0:
	419	zbase = s_line[1].lstrip()
	420	if s_line[0].lower().count("xstepsize") > 0:
	421	xstepsize = s_line[1].lstrip()
	422	if s_line[0].lower().count("ystepsize") > 0:
	423	ystepsize = s_line[1].lstrip()
	424	if s_line[0].lower().count("zstepsize") > 0:
	425	zstepsize = s_line[1].lstrip()
	426	if s_line[0].lower().count("xnodes") > 0:
	427	xnodes = s_line[1].lstrip()
	428	if s_line[0].lower().count("ynodes") > 0:
	429	ynodes = s_line[1].lstrip()
	430	if s_line[0].lower().count("znodes") > 0:
	431	znodes = s_line[1].lstrip()
	432	if s_line[0].lower().count("xmin") > 0:
	433	xmin = s_line[1].lstrip()
	434	if s_line[0].lower().count("ymin") > 0:
	435	ymin = s_line[1].lstrip()
	436	if s_line[0].lower().count("zmin") > 0:
	437	zmin = s_line[1].lstrip()
	438	if s_line[0].lower().count("xmax") > 0:
	439	xmax = s_line[1].lstrip()
	440	if s_line[0].lower().count("ymax") > 0:
	441	ymax = s_line[1].lstrip()
	442	if s_line[0].lower().count("zmax") > 0:
	443	zmax = s_line[1].lstrip()
	444	if s_line[0].lower().count("valueunit") > 0:
	445	valueunit = s_line[1].lstrip().rstrip()
	446	if s_line[0].lower().count("valuemultiplier") > 0:
	447	valuemultiplier = s_line[1].lstrip()
	448	if s_line[0].lower().count("valuerangeminmag") > 0:
	449	valuerangeminmag = s_line[1].lstrip()
	450	if s_line[0].lower().count("valuerangemaxmag") > 0:
	451	valuerangemaxmag = s_line[1].lstrip()
	452	if s_line[0].lower().count("end") > 0:
	453	output.filename = os.path.basename(path)
	454	output.oommf = oommf
	455	output.title = title
	456	output.desc = desc
	457	output.meshtype = meshtype
	458	output.xbase = float(xbase) * METER2ANG
	459	output.ybase = float(ybase) * METER2ANG
	460	output.zbase = float(zbase) * METER2ANG
	461	output.xstepsize = float(xstepsize) * METER2ANG
	462	output.ystepsize = float(ystepsize) * METER2ANG
	463	output.zstepsize = float(zstepsize) * METER2ANG
	464	output.xnodes = float(xnodes)
	465	output.ynodes = float(ynodes)
	466	output.znodes = float(znodes)
	467	output.xmin = float(xmin) * METER2ANG
	468	output.ymin = float(ymin) * METER2ANG
	469	output.zmin = float(zmin) * METER2ANG
	470	output.xmax = float(xmax) * METER2ANG
	471	output.ymax = float(ymax) * METER2ANG
	472	output.zmax = float(zmax) * METER2ANG
	473	output.valuemultiplier = valuemultiplier
	474	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
	475	valueunit)
	476	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
	477	valueunit)
	478	output.set_m(mx, my, mz)
	479	return output
	480	except:
	481	msg = "%s is not supported: \n" % path
	482	msg += "We accept only Text format OMF file."
	483	raise RuntimeError, msg
	484
[e3f77d8b]	485	class PDBReader(object):
[51f14603]	486	"""
	487	PDB reader class: limited for reading the lines starting with 'ATOM'
	488	"""
	489	type_name = "PDB"
	490	## Wildcards
	491	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
	492	## List of allowed extensions
[e3f77d8b]	493	ext = ['.pdb', '.PDB']
	494
[51f14603]	495	def read(self, path):
	496	"""
	497	Load data file
[e3f77d8b]	498
[51f14603]	499	:param path: file path
	500	:return: MagSLD
	501	:raise RuntimeError: when the file can't be opened
	502	"""
[9a5097c]	503	pos_x = np.zeros(0)
	504	pos_y = np.zeros(0)
	505	pos_z = np.zeros(0)
	506	sld_n = np.zeros(0)
	507	sld_mx = np.zeros(0)
	508	sld_my = np.zeros(0)
	509	sld_mz = np.zeros(0)
	510	vol_pix = np.zeros(0)
	511	pix_symbol = np.zeros(0)
[51f14603]	512	x_line = []
	513	y_line = []
	514	z_line = []
	515	x_lines = []
	516	y_lines = []
[e3f77d8b]	517	z_lines = []
[51f14603]	518	try:
	519	input_f = open(path, 'rb')
	520	buff = input_f.read()
	521	lines = buff.split('\n')
	522	input_f.close()
	523	num = 0
	524	for line in lines:
	525	try:
	526	# check if line starts with "ATOM"
	527	if line[0:6].strip().count('ATM') > 0 or \
	528	line[0:6].strip() == 'ATOM':
	529	# define fields of interest
	530	atom_name = line[12:16].strip()
	531	try:
	532	float(line[12])
	533	atom_name = atom_name[1].upper()
	534	except:
	535	if len(atom_name) == 4:
	536	atom_name = atom_name[0].upper()
[e3f77d8b]	537	elif line[12] != ' ':
[51f14603]	538	atom_name = atom_name[0].upper() + \
[e3f77d8b]	539	atom_name[1].lower()
[51f14603]	540	else:
	541	atom_name = atom_name[0].upper()
	542	_pos_x = float(line[30:38].strip())
	543	_pos_y = float(line[38:46].strip())
	544	_pos_z = float(line[46:54].strip())
[9a5097c]	545	pos_x = np.append(pos_x, _pos_x)
	546	pos_y = np.append(pos_y, _pos_y)
	547	pos_z = np.append(pos_z, _pos_z)
[51f14603]	548	try:
	549	val = nsf.neutron_sld(atom_name)[0]
	550	# sld in Ang^-2 unit
	551	val *= 1.0e-6
[9a5097c]	552	sld_n = np.append(sld_n, val)
[51f14603]	553	atom = formula(atom_name)
	554	# cm to A units
	555	vol = 1.0e+24 * atom.mass / atom.density / NA
[9a5097c]	556	vol_pix = np.append(vol_pix, vol)
[51f14603]	557	except:
	558	print "Error: set the sld of %s to zero"% atom_name
[9a5097c]	559	sld_n = np.append(sld_n, 0.0)
	560	sld_mx = np.append(sld_mx, 0)
	561	sld_my = np.append(sld_my, 0)
	562	sld_mz = np.append(sld_mz, 0)
	563	pix_symbol = np.append(pix_symbol, atom_name)
[e3f77d8b]	564	elif line[0:6].strip().count('CONECT') > 0:
[51f14603]	565	toks = line.split()
[e3f77d8b]	566	num = int(toks[1]) - 1
	567	val_list = []
[51f14603]	568	for val in toks[2:]:
	569	try:
	570	int_val = int(val)
	571	except:
	572	break
	573	if int_val == 0:
	574	break
	575	val_list.append(int_val)
[e3f77d8b]	576	#need val_list ordered
[51f14603]	577	for val in val_list:
	578	index = val - 1
	579	if (pos_x[index], pos_x[num]) in x_line and \
	580	(pos_y[index], pos_y[num]) in y_line and \
	581	(pos_z[index], pos_z[num]) in z_line:
	582	continue
	583	x_line.append((pos_x[num], pos_x[index]))
	584	y_line.append((pos_y[num], pos_y[index]))
	585	z_line.append((pos_z[num], pos_z[index]))
	586	if len(x_line) > 0:
[e3f77d8b]	587	x_lines.append(x_line)
[51f14603]	588	y_lines.append(y_line)
[e3f77d8b]	589	z_lines.append(z_line)
[51f14603]	590	except:
[b6627d9]	591	logging.error(sys.exc_value)
[e3f77d8b]	592
[51f14603]	593	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
	594	output.set_conect_lines(x_line, y_line, z_line)
	595	output.filename = os.path.basename(path)
	596	output.set_pix_type('atom')
	597	output.set_pixel_symbols(pix_symbol)
	598	output.set_nodes()
	599	output.set_pixel_volumes(vol_pix)
	600	output.sld_unit = '1/A^(2)'
	601	return output
	602	except:
[e3f77d8b]	603	raise RuntimeError, "%s is not a sld file" % path
[51f14603]	604
	605	def write(self, path, data):
	606	"""
	607	Write
	608	"""
	609	print "Not implemented... "
	610
[e3f77d8b]	611	class SLDReader(object):
[51f14603]	612	"""
	613	Class to load ascii files (7 columns).
	614	"""
	615	## File type
	616	type_name = "SLD ASCII"
	617	## Wildcards
	618	type = ["sld files (.SLD, .sld)\|*.sld",
	619	"txt files (.TXT, .txt)\|*.txt",
	620	"all files (.)\|."]
	621	## List of allowed extensions
	622	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
	623	def read(self, path):
	624	"""
	625	Load data file
	626	:param path: file path
	627	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	628	:raise RuntimeError: when the file can't be opened
	629	:raise ValueError: when the length of the data vectors are inconsistent
	630	"""
	631	try:
[9a5097c]	632	pos_x = np.zeros(0)
	633	pos_y = np.zeros(0)
	634	pos_z = np.zeros(0)
	635	sld_n = np.zeros(0)
	636	sld_mx = np.zeros(0)
	637	sld_my = np.zeros(0)
	638	sld_mz = np.zeros(0)
[51f14603]	639	try:
	640	# Use numpy to speed up loading
[9a5097c]	641	input_f = np.loadtxt(path, dtype='float', skiprows=1,
[51f14603]	642	ndmin=1, unpack=True)
[9a5097c]	643	pos_x = np.array(input_f[0])
	644	pos_y = np.array(input_f[1])
	645	pos_z = np.array(input_f[2])
	646	sld_n = np.array(input_f[3])
	647	sld_mx = np.array(input_f[4])
	648	sld_my = np.array(input_f[5])
	649	sld_mz = np.array(input_f[6])
[51f14603]	650	ncols = len(input_f)
	651	if ncols == 8:
[9a5097c]	652	vol_pix = np.array(input_f[7])
[51f14603]	653	elif ncols == 7:
[e3f77d8b]	654	vol_pix = None
[51f14603]	655	except:
	656	# For older version of numpy
	657	input_f = open(path, 'rb')
	658	buff = input_f.read()
	659	lines = buff.split('\n')
	660	input_f.close()
	661	for line in lines:
	662	toks = line.split()
	663	try:
	664	_pos_x = float(toks[0])
	665	_pos_y = float(toks[1])
	666	_pos_z = float(toks[2])
	667	_sld_n = float(toks[3])
	668	_sld_mx = float(toks[4])
	669	_sld_my = float(toks[5])
	670	_sld_mz = float(toks[6])
[9a5097c]	671	pos_x = np.append(pos_x, _pos_x)
	672	pos_y = np.append(pos_y, _pos_y)
	673	pos_z = np.append(pos_z, _pos_z)
	674	sld_n = np.append(sld_n, _sld_n)
	675	sld_mx = np.append(sld_mx, _sld_mx)
	676	sld_my = np.append(sld_my, _sld_my)
	677	sld_mz = np.append(sld_mz, _sld_mz)
[51f14603]	678	try:
[e3f77d8b]	679	_vol_pix = float(toks[7])
[9a5097c]	680	vol_pix = np.append(vol_pix, _vol_pix)
[51f14603]	681	except:
	682	vol_pix = None
	683	except:
	684	# Skip non-data lines
[b6627d9]	685	logging.error(sys.exc_value)
[e3f77d8b]	686	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
[51f14603]	687	sld_mx, sld_my, sld_mz)
	688	output.filename = os.path.basename(path)
	689	output.set_pix_type('pixel')
	690	output.set_pixel_symbols('pixel')
	691	if vol_pix != None:
	692	output.set_pixel_volumes(vol_pix)
	693	return output
	694	except:
[e3f77d8b]	695	raise RuntimeError, "%s is not a sld file" % path
	696
[51f14603]	697	def write(self, path, data):
	698	"""
	699	Write sld file
[e3f77d8b]	700	:Param path: file path
[51f14603]	701	:Param data: MagSLD data object
	702	"""
	703	if path == None:
	704	raise ValueError, "Missing the file path."
	705	if data == None:
	706	raise ValueError, "Missing the data to save."
	707	x_val = data.pos_x
	708	y_val = data.pos_y
	709	z_val = data.pos_z
	710	vol_pix = data.vol_pix
	711	length = len(x_val)
	712	sld_n = data.sld_n
	713	if sld_n == None:
[9a5097c]	714	sld_n = np.zeros(length)
[51f14603]	715	sld_mx = data.sld_mx
	716	if sld_mx == None:
[9a5097c]	717	sld_mx = np.zeros(length)
	718	sld_my = np.zeros(length)
	719	sld_mz = np.zeros(length)
[51f14603]	720	else:
	721	sld_my = data.sld_my
	722	sld_mz = data.sld_mz
	723	out = open(path, 'w')
	724	# First Line: Column names
	725	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
	726	for ind in range(length):
[e3f77d8b]	727	out.write("\n%g %g %g %g %g %g %g %g" % \
	728	(x_val[ind], y_val[ind], z_val[ind], sld_n[ind],
	729	sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind]))
	730	out.close()
	731
	732
	733	class OMFData(object):
[51f14603]	734	"""
	735	OMF Data.
	736	"""
	737	_meshunit = "A"
	738	_valueunit = "A^(-2)"
	739	def __init__(self):
	740	"""
	741	Init for mag SLD
	742	"""
	743	self.filename = 'default'
	744	self.oommf = ''
	745	self.title = ''
	746	self.desc = ''
	747	self.meshtype = ''
	748	self.meshunit = self._meshunit
	749	self.valueunit = self._valueunit
	750	self.xbase = 0.0
	751	self.ybase = 0.0
	752	self.zbase = 0.0
	753	self.xstepsize = 6.0
	754	self.ystepsize = 6.0
	755	self.zstepsize = 6.0
	756	self.xnodes = 10.0
	757	self.ynodes = 10.0
	758	self.znodes = 10.0
	759	self.xmin = 0.0
	760	self.ymin = 0.0
	761	self.zmin = 0.0
	762	self.xmax = 60.0
	763	self.ymax = 60.0
	764	self.zmax = 60.0
	765	self.mx = None
	766	self.my = None
	767	self.mz = None
	768	self.valuemultiplier = 1.
	769	self.valuerangeminmag = 0
	770	self.valuerangemaxmag = 0
[e3f77d8b]	771
[51f14603]	772	def __str__(self):
	773	"""
	774	doc strings
	775	"""
[e3f77d8b]	776	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	777	_str += "File: %s\n" % self.filename
	778	_str += "OOMMF: %s\n" % self.oommf
	779	_str += "Title: %s\n" % self.title
	780	_str += "Desc: %s\n" % self.desc
	781	_str += "meshtype: %s\n" % self.meshtype
	782	_str += "meshunit: %s\n" % str(self.meshunit)
	783	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
	784	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
	785	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
[e3f77d8b]	786	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
[51f14603]	787	self.meshunit)
[e3f77d8b]	788	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
[51f14603]	789	self.meshunit)
[e3f77d8b]	790	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
[51f14603]	791	self.meshunit)
	792	_str += "xnodes: %s\n" % str(self.xnodes)
	793	_str += "ynodes: %s\n" % str(self.ynodes)
	794	_str += "znodes: %s\n" % str(self.znodes)
	795	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
	796	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
	797	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
	798	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
	799	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
	800	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
	801	_str += "valueunit: %s\n" % self.valueunit
	802	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
[e3f77d8b]	803	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
	804	self.valueunit)
	805	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
	806	self.valueunit)
[51f14603]	807	return _str
[e3f77d8b]	808
[51f14603]	809	def set_m(self, mx, my, mz):
	810	"""
	811	Set the Mx, My, Mz values
	812	"""
	813	self.mx = mx
	814	self.my = my
	815	self.mz = mz
[e3f77d8b]	816
	817	class MagSLD(object):
[51f14603]	818	"""
	819	Magnetic SLD.
	820	"""
	821	pos_x = None
	822	pos_y = None
	823	pos_z = None
	824	sld_n = None
	825	sld_mx = None
	826	sld_my = None
	827	sld_mz = None
	828	# Units
	829	_pos_unit = 'A'
	830	_sld_unit = '1/A^(2)'
	831	_pix_type = 'pixel'
[e3f77d8b]	832
	833	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
[51f14603]	834	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
	835	"""
	836	Init for mag SLD
	837	:params : All should be numpy 1D array
	838	"""
	839	self.is_data = True
	840	self.filename = ''
	841	self.xstepsize = 6.0
	842	self.ystepsize = 6.0
	843	self.zstepsize = 6.0
	844	self.xnodes = 10.0
	845	self.ynodes = 10.0
	846	self.znodes = 10.0
	847	self.has_stepsize = False
	848	self.has_conect = False
	849	self.pos_unit = self._pos_unit
	850	self.sld_unit = self._sld_unit
	851	self.pix_type = 'pixel'
	852	self.pos_x = pos_x
	853	self.pos_y = pos_y
	854	self.pos_z = pos_z
	855	self.sld_n = sld_n
	856	self.line_x = None
	857	self.line_y = None
	858	self.line_z = None
	859	self.sld_mx = sld_mx
	860	self.sld_my = sld_my
	861	self.sld_mz = sld_mz
	862	self.vol_pix = vol_pix
	863	self.sld_m = None
	864	self.sld_phi = None
	865	self.sld_theta = None
	866	self.pix_symbol = None
	867	if sld_mx != None and sld_my != None and sld_mz != None:
	868	self.set_sldms(sld_mx, sld_my, sld_mz)
	869	self.set_nodes()
[e3f77d8b]	870
[51f14603]	871	def __str__(self):
	872	"""
	873	doc strings
	874	"""
[e3f77d8b]	875	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	876	_str += "File: %s\n" % self.filename
	877	_str += "Axis_unit: %s\n" % self.pos_unit
	878	_str += "SLD_unit: %s\n" % self.sld_unit
	879	return _str
[e3f77d8b]	880
[51f14603]	881	def set_pix_type(self, pix_type):
	882	"""
	883	Set pixel type
	884	:Param pix_type: string, 'pixel' or 'atom'
	885	"""
	886	self.pix_type = pix_type
[e3f77d8b]	887
[51f14603]	888	def set_sldn(self, sld_n):
	889	"""
	890	Sets neutron SLD
	891	"""
	892	if sld_n.__class__.__name__ == 'float':
	893	if self.is_data:
[e3f77d8b]	894	# For data, put the value to only the pixels w non-zero M
[9a5097c]	895	is_nonzero = (np.fabs(self.sld_mx) +
	896	np.fabs(self.sld_my) +
	897	np.fabs(self.sld_mz)).nonzero()
	898	self.sld_n = np.zeros(len(self.pos_x))
[51f14603]	899	if len(self.sld_n[is_nonzero]) > 0:
	900	self.sld_n[is_nonzero] = sld_n
	901	else:
	902	self.sld_n.fill(sld_n)
	903	else:
	904	# For non-data, put the value to all the pixels
[9a5097c]	905	self.sld_n = np.ones(len(self.pos_x)) * sld_n
[51f14603]	906	else:
	907	self.sld_n = sld_n
[e3f77d8b]	908
[51f14603]	909	def set_sldms(self, sld_mx, sld_my, sld_mz):
[ac7be54]	910	r"""
[5ed76f8]	911	Sets mx, my, mz and abs(m).
	912	""" # Note: escaping
[51f14603]	913	if sld_mx.__class__.__name__ == 'float':
[9a5097c]	914	self.sld_mx = np.ones(len(self.pos_x)) * sld_mx
[51f14603]	915	else:
	916	self.sld_mx = sld_mx
	917	if sld_my.__class__.__name__ == 'float':
[9a5097c]	918	self.sld_my = np.ones(len(self.pos_x)) * sld_my
[51f14603]	919	else:
	920	self.sld_my = sld_my
	921	if sld_mz.__class__.__name__ == 'float':
[9a5097c]	922	self.sld_mz = np.ones(len(self.pos_x)) * sld_mz
[51f14603]	923	else:
	924	self.sld_mz = sld_mz
	925
[9a5097c]	926	sld_m = np.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
[e3f77d8b]	927	sld_mz * sld_mz)
[51f14603]	928	self.sld_m = sld_m
[e3f77d8b]	929
	930	def set_pixel_symbols(self, symbol='pixel'):
[51f14603]	931	"""
	932	Set pixel
	933	:Params pixel: str; pixel or atomic symbol, or array of strings
	934	"""
	935	if self.sld_n == None:
	936	return
	937	if symbol.__class__.__name__ == 'str':
[9a5097c]	938	self.pix_symbol = np.repeat(symbol, len(self.sld_n))
[51f14603]	939	else:
	940	self.pix_symbol = symbol
[e3f77d8b]	941
	942	def set_pixel_volumes(self, vol):
[51f14603]	943	"""
	944	Set pixel volumes
	945	:Params pixel: str; pixel or atomic symbol, or array of strings
	946	"""
	947	if self.sld_n == None:
	948	return
	949	if vol.__class__.__name__ == 'ndarray':
	950	self.vol_pix = vol
	951	elif vol.__class__.__name__.count('float') > 0:
[9a5097c]	952	self.vol_pix = np.repeat(vol, len(self.sld_n))
[51f14603]	953	else:
	954	self.vol_pix = None
	955
	956	def get_sldn(self):
	957	"""
	958	Returns nuclear sld
	959	"""
	960	return self.sld_n
[e3f77d8b]	961
[51f14603]	962	def set_nodes(self):
	963	"""
	964	Set xnodes, ynodes, and znodes
	965	"""
	966	self.set_stepsize()
	967	if self.pix_type == 'pixel':
	968	try:
	969	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
	970	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
	971	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
	972	self.xnodes = int(xdist) + 1
	973	self.ynodes = int(ydist) + 1
	974	self.znodes = int(zdist) + 1
	975	except:
	976	self.xnodes = None
	977	self.ynodes = None
	978	self.znodes = None
	979	else:
	980	self.xnodes = None
	981	self.ynodes = None
	982	self.znodes = None
[e3f77d8b]	983
[51f14603]	984	def set_stepsize(self):
	985	"""
	986	Set xtepsize, ystepsize, and zstepsize
	987	"""
	988	if self.pix_type == 'pixel':
	989	try:
	990	xpos_pre = self.pos_x[0]
	991	ypos_pre = self.pos_y[0]
	992	zpos_pre = self.pos_z[0]
	993	for x_pos in self.pos_x:
	994	if xpos_pre != x_pos:
[9a5097c]	995	self.xstepsize = np.fabs(x_pos - xpos_pre)
[51f14603]	996	break
	997	for y_pos in self.pos_y:
	998	if ypos_pre != y_pos:
[9a5097c]	999	self.ystepsize = np.fabs(y_pos - ypos_pre)
[51f14603]	1000	break
	1001	for z_pos in self.pos_z:
	1002	if zpos_pre != z_pos:
[9a5097c]	1003	self.zstepsize = np.fabs(z_pos - zpos_pre)
[51f14603]	1004	break
	1005	#default pix volume
[9a5097c]	1006	self.vol_pix = np.ones(len(self.pos_x))
[51f14603]	1007	vol = self.xstepsize * self.ystepsize * self.zstepsize
	1008	self.set_pixel_volumes(vol)
	1009	self.has_stepsize = True
	1010	except:
	1011	self.xstepsize = None
	1012	self.ystepsize = None
	1013	self.zstepsize = None
	1014	self.vol_pix = None
	1015	self.has_stepsize = False
	1016	else:
	1017	self.xstepsize = None
	1018	self.ystepsize = None
	1019	self.zstepsize = None
	1020	self.has_stepsize = True
	1021	return self.xstepsize, self.ystepsize, self.zstepsize
	1022
	1023	def set_conect_lines(self, line_x, line_y, line_z):
	1024	"""
	1025	Set bonding line data if taken from pdb
	1026	"""
	1027	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
	1028	return
	1029	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
	1030	return
	1031	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
	1032	return
	1033	self.has_conect = True
[e3f77d8b]	1034	self.line_x = line_x
	1035	self.line_y = line_y
[51f14603]	1036	self.line_z = line_z
	1037
	1038	def test_load():
[b6627d9]	1039	"""
	1040	Test code
	1041	"""
[06aaa75d]	1042	from mpl_toolkits.mplot3d import Axes3D
[e3f77d8b]	1043	current_dir = os.path.abspath(os.path.curdir)
	1044	print current_dir
[51f14603]	1045	for i in range(6):
[e3f77d8b]	1046	current_dir, _ = os.path.split(current_dir)
	1047	tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt")
	1048	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
[51f14603]	1049	if os.path.isfile(tfile):
	1050	tfpath = tfile
	1051	ofpath = ofile
	1052	break
	1053	reader = SLDReader()
	1054	oreader = OMFReader()
	1055	output = reader.read(tfpath)
	1056	ooutput = oreader.read(ofpath)
	1057	foutput = OMF2SLD()
	1058	foutput.set_data(ooutput)
	1059
	1060	import matplotlib.pyplot as plt
	1061	fig = plt.figure()
[06aaa75d]	1062	ax = Axes3D(fig)
[e3f77d8b]	1063	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
	1064	alpha=0.7, markeredgecolor='gray', rasterized=True)
[51f14603]	1065	gap = 7
	1066	max_mx = max(output.sld_mx)
	1067	max_my = max(output.sld_my)
	1068	max_mz = max(output.sld_mz)
[e3f77d8b]	1069	max_m = max(max_mx, max_my, max_mz)
[51f14603]	1070	x2 = output.pos_x+output.sld_mx/max_m * gap
	1071	y2 = output.pos_y+output.sld_my/max_m * gap
	1072	z2 = output.pos_z+output.sld_mz/max_m * gap
[9a5097c]	1073	x_arrow = np.column_stack((output.pos_x, x2))
	1074	y_arrow = np.column_stack((output.pos_y, y2))
	1075	z_arrow = np.column_stack((output.pos_z, z2))
[51f14603]	1076	unit_x2 = output.sld_mx / max_m
	1077	unit_y2 = output.sld_my / max_m
	1078	unit_z2 = output.sld_mz / max_m
[9a5097c]	1079	color_x = np.fabs(unit_x2 * 0.8)
	1080	color_y = np.fabs(unit_y2 * 0.8)
	1081	color_z = np.fabs(unit_z2 * 0.8)
	1082	colors = np.column_stack((color_x, color_y, color_z))
[51f14603]	1083	plt.show()
[b6627d9]	1084
[51f14603]	1085	def test():
[b6627d9]	1086	"""
	1087	Test code
	1088	"""
[e3f77d8b]	1089	current_dir = os.path.abspath(os.path.curdir)
[51f14603]	1090	for i in range(3):
[e3f77d8b]	1091	current_dir, _ = os.path.split(current_dir)
	1092	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
[51f14603]	1093	if os.path.isfile(ofile):
	1094	ofpath = ofile
	1095	break
	1096	oreader = OMFReader()
	1097	ooutput = oreader.read(ofpath)
[e3f77d8b]	1098	foutput = OMF2SLD()
	1099	foutput.set_data(ooutput)
	1100	writer = SLDReader()
	1101	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
[51f14603]	1102	foutput.output)
	1103	model = GenSAS()
[e3f77d8b]	1104	model.set_sld_data(foutput.output)
[9a5097c]	1105	x = np.arange(1000)/10000. + 1e-5
	1106	y = np.arange(1000)/10000. + 1e-5
	1107	i = np.zeros(1000)
[e3f77d8b]	1108	model.runXY([x, y, i])
	1109
	1110	if __name__ == "__main__":
[51f14603]	1111	test()
	1112	test_load()

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SasView

source: sasview/src/sas/sascalc/calculator/sas_gen.py @ 6d6832e

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