sas_gen.py @ c6fb57c

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc

Last change on this file since c6fb57c 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

Rev	Line
[b6627d9]	1	# pylint: disable=invalid-name
[51f14603]	2	"""
[fd5ac0d]	3	SAS generic computation and sld file readers
[51f14603]	4	"""
[a1b8fee]	5	from __future__ import print_function
	6
[51f14603]	7	import os
[b6627d9]	8	import sys
[1d014cb]	9	import copy
[b6627d9]	10	import logging
[51f14603]	11
[1d014cb]	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
[463e7ffc]	19	logger = logging.getLogger(__name__)
[c155a16]	20
[1d014cb]	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
[e3f77d8b]	28	MFACTOR_AM = 2.853E-12
	29	MFACTOR_MT = 2.3164E-9
[51f14603]	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)]???
[e3f77d8b]	39	"""
[51f14603]	40	if v_unit == "A/m":
[e3f77d8b]	41	factor = MFACTOR_AM
[51f14603]	42	elif v_unit == "mT":
[e3f77d8b]	43	factor = MFACTOR_MT
[51f14603]	44	else:
[574adc7]	45	raise ValueError("Invalid valueunit")
[51f14603]	46	sld_m = factor * mag
	47	return sld_m
	48
	49	def transform_center(pos_x, pos_y, pos_z):
	50	"""
[e3f77d8b]	51	re-center
[51f14603]	52	:return: posx, posy, posz [arrays]
[e3f77d8b]	53	"""
[51f14603]	54	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
	55	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
[e3f77d8b]	56	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
	57	return posx, posy, posz
[51f14603]	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 = {}
[e3f77d8b]	85	self.params['scale'] = 1.0
	86	self.params['background'] = 0.0
	87	self.params['solvent_SLD'] = 0.0
[51f14603]	88	self.params['total_volume'] = 1.0
[e3f77d8b]	89	self.params['Up_frac_in'] = 1.0
	90	self.params['Up_frac_out'] = 1.0
	91	self.params['Up_theta'] = 0.0
[51f14603]	92	self.description = 'GenSAS'
	93	## Parameter details [units, min, max]
	94	self.details = {}
[9a5097c]	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]
[cb4ef58]	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]
[9a5097c]	101	self.details['Up_theta'] = ['[deg]', -np.inf, np.inf]
[51f14603]	102	# fixed parameters
	103	self.fixed = []
[e3f77d8b]	104
	105	def set_pixel_volumes(self, volume):
[51f14603]	106	"""
	107	Set the volume of a pixel in (A^3) unit
	108	:Param volume: pixel volume [float]
	109	"""
[235f514]	110	if self.data_vol is None:
[574adc7]	111	raise TypeError("data_vol is missing")
[51f14603]	112	self.data_vol = volume
[e3f77d8b]	113
	114	def set_is_avg(self, is_avg=False):
[51f14603]	115	"""
	116	Sets is_avg: [bool]
	117	"""
	118	self.is_avg = is_avg
[e3f77d8b]	119
[51f14603]	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
[e3f77d8b]	125	:Param i: array of initial i-value
[51f14603]	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)
[235f514]	132	if self.is_avg is None:
[51f14603]	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']
[e3f77d8b]	138	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
	139	sldn, self.data_mx, self.data_my,
[51f14603]	140	self.data_mz, self.data_vol,
[e3f77d8b]	141	self.params['Up_frac_in'],
	142	self.params['Up_frac_out'],
[51f14603]	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']
[e3f77d8b]	151
	152	def set_sld_data(self, sld_data=None):
[51f14603]	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)
[e3f77d8b]	168
[51f14603]	169	def getProfile(self):
	170	"""
[e3f77d8b]	171	Get SLD profile
[51f14603]	172	: return: sld_data
	173	"""
	174	return self.sld_data
[e3f77d8b]	175
	176	def run(self, x=0.0):
	177	"""
[51f14603]	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."
[574adc7]	185	raise ValueError(msg)
[9a5097c]	186	i_out = np.zeros_like(x[0])
[51f14603]	187	# 1D I is found at y =0 in the 2D pattern
[e3f77d8b]	188	out = self._gen(x[0], [], i_out)
[51f14603]	189	return out
	190	else:
	191	msg = "Q must be given as list of qx's and qy's"
[574adc7]	192	raise ValueError(msg)
[e3f77d8b]	193
	194	def runXY(self, x=0.0):
	195	"""
[51f14603]	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':
[9a5097c]	202	i_out = np.zeros_like(x[0])
[51f14603]	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"
[574adc7]	207	raise ValueError(msg)
[e3f77d8b]	208
[51f14603]	209	def evalDistribution(self, qdist):
	210	"""
	211	Evaluate a distribution of q-values.
[ac7be54]	212
	213	:param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy]
	214	where qx,qy are 1D ndarrays (for 2D).
[51f14603]	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."
[574adc7]	225	raise RuntimeError(mesg)
[e3f77d8b]	226
	227	class OMF2SLD(object):
[51f14603]	228	"""
	229	Convert OMFData to MAgData
	230	"""
[e3f77d8b]	231	def __init__(self):
[51f14603]	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
[e3f77d8b]	245
[51f14603]	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)
[9a5097c]	252	pos_x = np.arange(omfdata.xmin,
[e3f77d8b]	253	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
[51f14603]	254	omfdata.xstepsize)
[9a5097c]	255	pos_y = np.arange(omfdata.ymin,
[e3f77d8b]	256	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
[51f14603]	257	omfdata.ystepsize)
[9a5097c]	258	pos_z = np.arange(omfdata.zmin,
[e3f77d8b]	259	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
[51f14603]	260	omfdata.zstepsize)
[9a5097c]	261	self.pos_x = np.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
[51f14603]	262	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
[9a5097c]	263	self.pos_y = np.tile(self.pos_y, int(omfdata.znodes))
[51f14603]	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
[9a5097c]	268	self.sld_n = np.zeros(length)
[e3f77d8b]	269
[235f514]	270	if omfdata.mx is None:
[9a5097c]	271	self.mx = np.zeros(length)
[235f514]	272	if omfdata.my is None:
[9a5097c]	273	self.my = np.zeros(length)
[235f514]	274	if omfdata.mz is None:
[9a5097c]	275	self.mz = np.zeros(length)
[e3f77d8b]	276
[51f14603]	277	self._check_data_length(length)
	278	self.remove_null_points(False, False)
[9a5097c]	279	mask = np.ones(len(self.sld_n), dtype=bool)
[51f14603]	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
[1d014cb]	299	except Exception:
[c155a16]	300	logger.error(sys.exc_value)
[e3f77d8b]	301	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
	302	self.pos_z[mask], self.sld_n[mask],
[51f14603]	303	self.mx[mask], self.my[mask], self.mz[mask])
	304	self.output.set_pix_type('pixel')
	305	self.output.set_pixel_symbols('pixel')
[e3f77d8b]	306
[51f14603]	307	def get_omfdata(self):
	308	"""
	309	Return all data
	310	"""
	311	return self.omfdata
[e3f77d8b]	312
[51f14603]	313	def get_output(self):
	314	"""
	315	Return output
	316	"""
	317	return self.output
[e3f77d8b]	318
[51f14603]	319	def _check_data_length(self, length):
	320	"""
	321	Check if the data lengths are consistent
	322	:Params length: data length
	323	"""
[574adc7]	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.")
[e3f77d8b]	327
[51f14603]	328	def remove_null_points(self, remove=False, recenter=False):
	329	"""
	330	Removes any mx, my, and mz = 0 points
	331	"""
	332	if remove:
[9a5097c]	333	is_nonzero = (np.fabs(self.mx) + np.fabs(self.my) +
	334	np.fabs(self.mz)).nonzero()
[e3f77d8b]	335	if len(is_nonzero[0]) > 0:
[51f14603]	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
[e3f77d8b]	347
[51f14603]	348	def get_magsld(self):
	349	"""
	350	return MagSLD
	351	"""
	352	return self.output
[e3f77d8b]	353
	354
	355	class OMFReader(object):
[51f14603]	356	"""
	357	Class to load omf/ascii files (3 columns w/header).
	358	"""
	359	## File type
	360	type_name = "OMF ASCII"
[e3f77d8b]	361
[51f14603]	362	## Wildcards
	363	type = ["OMF files (.OMF, .omf)\|*.omf"]
	364	## List of allowed extensions
	365	ext = ['.omf', '.OMF']
[e3f77d8b]	366
[51f14603]	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 = ""
[9a5097c]	374	mx = np.zeros(0)
	375	my = np.zeros(0)
	376	mz = np.zeros(0)
[51f14603]	377	try:
	378	input_f = open(path, 'rb')
[1d014cb]	379	buff = decode(input_f.read())
[51f14603]	380	lines = buff.split('\n')
	381	input_f.close()
	382	output = OMFData()
	383	valueunit = None
	384	for line in lines:
[1d014cb]	385	line = line.strip()
[51f14603]	386	# Read data
[1d014cb]	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)
[51f14603]	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"
[574adc7]	418	raise ValueError(msg)
[51f14603]	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
[1d014cb]	485	except Exception:
[51f14603]	486	msg = "%s is not supported: \n" % path
	487	msg += "We accept only Text format OMF file."
[574adc7]	488	raise RuntimeError(msg)
[51f14603]	489
[e3f77d8b]	490	class PDBReader(object):
[51f14603]	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
[e3f77d8b]	498	ext = ['.pdb', '.PDB']
	499
[51f14603]	500	def read(self, path):
	501	"""
	502	Load data file
[e3f77d8b]	503
[51f14603]	504	:param path: file path
	505	:return: MagSLD
	506	:raise RuntimeError: when the file can't be opened
	507	"""
[9a5097c]	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)
[51f14603]	517	x_line = []
	518	y_line = []
	519	z_line = []
	520	x_lines = []
	521	y_lines = []
[e3f77d8b]	522	z_lines = []
[51f14603]	523	try:
	524	input_f = open(path, 'rb')
[1d014cb]	525	buff = decode(input_f.read())
[51f14603]	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()
[1d014cb]	539	except Exception:
[51f14603]	540	if len(atom_name) == 4:
	541	atom_name = atom_name[0].upper()
[e3f77d8b]	542	elif line[12] != ' ':
[51f14603]	543	atom_name = atom_name[0].upper() + \
[e3f77d8b]	544	atom_name[1].lower()
[51f14603]	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())
[9a5097c]	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)
[51f14603]	553	try:
	554	val = nsf.neutron_sld(atom_name)[0]
	555	# sld in Ang^-2 unit
	556	val *= 1.0e-6
[9a5097c]	557	sld_n = np.append(sld_n, val)
[51f14603]	558	atom = formula(atom_name)
	559	# cm to A units
	560	vol = 1.0e+24 * atom.mass / atom.density / NA
[9a5097c]	561	vol_pix = np.append(vol_pix, vol)
[1d014cb]	562	except Exception:
[b58265c3]	563	logger.error("Error: set the sld of %s to zero"% atom_name)
[9a5097c]	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)
[e3f77d8b]	569	elif line[0:6].strip().count('CONECT') > 0:
[51f14603]	570	toks = line.split()
[e3f77d8b]	571	num = int(toks[1]) - 1
	572	val_list = []
[51f14603]	573	for val in toks[2:]:
	574	try:
	575	int_val = int(val)
[1d014cb]	576	except Exception:
[51f14603]	577	break
	578	if int_val == 0:
	579	break
	580	val_list.append(int_val)
[e3f77d8b]	581	#need val_list ordered
[51f14603]	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:
[e3f77d8b]	592	x_lines.append(x_line)
[51f14603]	593	y_lines.append(y_line)
[e3f77d8b]	594	z_lines.append(z_line)
[1d014cb]	595	except Exception:
[c155a16]	596	logger.error(sys.exc_value)
[e3f77d8b]	597
[51f14603]	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
[1d014cb]	607	except Exception:
[574adc7]	608	raise RuntimeError("%s is not a sld file" % path)
[51f14603]	609
	610	def write(self, path, data):
	611	"""
	612	Write
	613	"""
[9c3d784]	614	print("Not implemented... ")
[51f14603]	615
[e3f77d8b]	616	class SLDReader(object):
[51f14603]	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:
[9a5097c]	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)
[51f14603]	644	try:
	645	# Use numpy to speed up loading
[9a5097c]	646	input_f = np.loadtxt(path, dtype='float', skiprows=1,
[51f14603]	647	ndmin=1, unpack=True)
[9a5097c]	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])
[51f14603]	655	ncols = len(input_f)
	656	if ncols == 8:
[9a5097c]	657	vol_pix = np.array(input_f[7])
[51f14603]	658	elif ncols == 7:
[e3f77d8b]	659	vol_pix = None
[1d014cb]	660	except Exception:
[51f14603]	661	# For older version of numpy
	662	input_f = open(path, 'rb')
[1d014cb]	663	buff = decode(input_f.read())
[51f14603]	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])
[9a5097c]	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)
[51f14603]	683	try:
[e3f77d8b]	684	_vol_pix = float(toks[7])
[9a5097c]	685	vol_pix = np.append(vol_pix, _vol_pix)
[1d014cb]	686	except Exception:
[51f14603]	687	vol_pix = None
[1d014cb]	688	except Exception:
[51f14603]	689	# Skip non-data lines
[c155a16]	690	logger.error(sys.exc_value)
[e3f77d8b]	691	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
[51f14603]	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')
[7432acb]	696	if vol_pix is not None:
[51f14603]	697	output.set_pixel_volumes(vol_pix)
	698	return output
[1d014cb]	699	except Exception:
[574adc7]	700	raise RuntimeError("%s is not a sld file" % path)
[e3f77d8b]	701
[51f14603]	702	def write(self, path, data):
	703	"""
	704	Write sld file
[e3f77d8b]	705	:Param path: file path
[51f14603]	706	:Param data: MagSLD data object
	707	"""
[235f514]	708	if path is None:
[574adc7]	709	raise ValueError("Missing the file path.")
[235f514]	710	if data is None:
[574adc7]	711	raise ValueError("Missing the data to save.")
[51f14603]	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
[235f514]	718	if sld_n is None:
[9a5097c]	719	sld_n = np.zeros(length)
[51f14603]	720	sld_mx = data.sld_mx
[235f514]	721	if sld_mx is None:
[9a5097c]	722	sld_mx = np.zeros(length)
	723	sld_my = np.zeros(length)
	724	sld_mz = np.zeros(length)
[51f14603]	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):
[e3f77d8b]	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):
[51f14603]	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
[e3f77d8b]	776
[51f14603]	777	def __str__(self):
	778	"""
	779	doc strings
	780	"""
[e3f77d8b]	781	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	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)
[e3f77d8b]	791	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
[51f14603]	792	self.meshunit)
[e3f77d8b]	793	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
[51f14603]	794	self.meshunit)
[e3f77d8b]	795	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
[51f14603]	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)
[e3f77d8b]	808	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
	809	self.valueunit)
	810	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
	811	self.valueunit)
[51f14603]	812	return _str
[e3f77d8b]	813
[51f14603]	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
[e3f77d8b]	821
	822	class MagSLD(object):
[51f14603]	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'
[e3f77d8b]	837
	838	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
[51f14603]	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
[7432acb]	872	if sld_mx is not None and sld_my is not None and sld_mz is not None:
[51f14603]	873	self.set_sldms(sld_mx, sld_my, sld_mz)
	874	self.set_nodes()
[e3f77d8b]	875
[51f14603]	876	def __str__(self):
	877	"""
	878	doc strings
	879	"""
[e3f77d8b]	880	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	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
[e3f77d8b]	885
[51f14603]	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
[e3f77d8b]	892
[51f14603]	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:
[e3f77d8b]	899	# For data, put the value to only the pixels w non-zero M
[9a5097c]	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))
[51f14603]	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
[9a5097c]	910	self.sld_n = np.ones(len(self.pos_x)) * sld_n
[51f14603]	911	else:
	912	self.sld_n = sld_n
[e3f77d8b]	913
[51f14603]	914	def set_sldms(self, sld_mx, sld_my, sld_mz):
[ac7be54]	915	r"""
[5ed76f8]	916	Sets mx, my, mz and abs(m).
	917	""" # Note: escaping
[51f14603]	918	if sld_mx.__class__.__name__ == 'float':
[9a5097c]	919	self.sld_mx = np.ones(len(self.pos_x)) * sld_mx
[51f14603]	920	else:
	921	self.sld_mx = sld_mx
	922	if sld_my.__class__.__name__ == 'float':
[9a5097c]	923	self.sld_my = np.ones(len(self.pos_x)) * sld_my
[51f14603]	924	else:
	925	self.sld_my = sld_my
	926	if sld_mz.__class__.__name__ == 'float':
[9a5097c]	927	self.sld_mz = np.ones(len(self.pos_x)) * sld_mz
[51f14603]	928	else:
	929	self.sld_mz = sld_mz
	930
[9a5097c]	931	sld_m = np.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
[e3f77d8b]	932	sld_mz * sld_mz)
[51f14603]	933	self.sld_m = sld_m
[e3f77d8b]	934
	935	def set_pixel_symbols(self, symbol='pixel'):
[51f14603]	936	"""
	937	Set pixel
	938	:Params pixel: str; pixel or atomic symbol, or array of strings
	939	"""
[235f514]	940	if self.sld_n is None:
[51f14603]	941	return
	942	if symbol.__class__.__name__ == 'str':
[9a5097c]	943	self.pix_symbol = np.repeat(symbol, len(self.sld_n))
[51f14603]	944	else:
	945	self.pix_symbol = symbol
[e3f77d8b]	946
	947	def set_pixel_volumes(self, vol):
[51f14603]	948	"""
	949	Set pixel volumes
	950	:Params pixel: str; pixel or atomic symbol, or array of strings
	951	"""
[235f514]	952	if self.sld_n is None:
[51f14603]	953	return
	954	if vol.__class__.__name__ == 'ndarray':
	955	self.vol_pix = vol
	956	elif vol.__class__.__name__.count('float') > 0:
[9a5097c]	957	self.vol_pix = np.repeat(vol, len(self.sld_n))
[51f14603]	958	else:
	959	self.vol_pix = None
	960
	961	def get_sldn(self):
	962	"""
	963	Returns nuclear sld
	964	"""
	965	return self.sld_n
[e3f77d8b]	966
[51f14603]	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
[1d014cb]	980	except Exception:
[51f14603]	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
[e3f77d8b]	988
[51f14603]	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:
[9a5097c]	1000	self.xstepsize = np.fabs(x_pos - xpos_pre)
[51f14603]	1001	break
	1002	for y_pos in self.pos_y:
	1003	if ypos_pre != y_pos:
[9a5097c]	1004	self.ystepsize = np.fabs(y_pos - ypos_pre)
[51f14603]	1005	break
	1006	for z_pos in self.pos_z:
	1007	if zpos_pre != z_pos:
[9a5097c]	1008	self.zstepsize = np.fabs(z_pos - zpos_pre)
[51f14603]	1009	break
	1010	#default pix volume
[9a5097c]	1011	self.vol_pix = np.ones(len(self.pos_x))
[51f14603]	1012	vol = self.xstepsize * self.ystepsize * self.zstepsize
	1013	self.set_pixel_volumes(vol)
	1014	self.has_stepsize = True
[1d014cb]	1015	except Exception:
[51f14603]	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
[e3f77d8b]	1039	self.line_x = line_x
	1040	self.line_y = line_y
[51f14603]	1041	self.line_z = line_z
	1042
	1043	def test_load():
[b6627d9]	1044	"""
	1045	Test code
	1046	"""
[06aaa75d]	1047	from mpl_toolkits.mplot3d import Axes3D
[e3f77d8b]	1048	current_dir = os.path.abspath(os.path.curdir)
[9c3d784]	1049	print(current_dir)
[51f14603]	1050	for i in range(6):
[e3f77d8b]	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")
[51f14603]	1054	if os.path.isfile(tfile):
	1055	tfpath = tfile
	1056	ofpath = ofile
	1057	break
	1058	reader = SLDReader()
	1059	oreader = OMFReader()
[1d014cb]	1060	output = decode(reader.read(tfpath))
	1061	ooutput = decode(oreader.read(ofpath))
[51f14603]	1062	foutput = OMF2SLD()
	1063	foutput.set_data(ooutput)
	1064
	1065	import matplotlib.pyplot as plt
	1066	fig = plt.figure()
[06aaa75d]	1067	ax = Axes3D(fig)
[e3f77d8b]	1068	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
	1069	alpha=0.7, markeredgecolor='gray', rasterized=True)
[51f14603]	1070	gap = 7
	1071	max_mx = max(output.sld_mx)
	1072	max_my = max(output.sld_my)
	1073	max_mz = max(output.sld_mz)
[e3f77d8b]	1074	max_m = max(max_mx, max_my, max_mz)
[51f14603]	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
[9a5097c]	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))
[51f14603]	1081	unit_x2 = output.sld_mx / max_m
	1082	unit_y2 = output.sld_my / max_m
	1083	unit_z2 = output.sld_mz / max_m
[9a5097c]	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))
[51f14603]	1088	plt.show()
[b6627d9]	1089
[51f14603]	1090	def test():
[b6627d9]	1091	"""
	1092	Test code
	1093	"""
[e3f77d8b]	1094	current_dir = os.path.abspath(os.path.curdir)
[51f14603]	1095	for i in range(3):
[e3f77d8b]	1096	current_dir, _ = os.path.split(current_dir)
	1097	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
[51f14603]	1098	if os.path.isfile(ofile):
	1099	ofpath = ofile
	1100	break
	1101	oreader = OMFReader()
[1d014cb]	1102	ooutput = decode(oreader.read(ofpath))
[e3f77d8b]	1103	foutput = OMF2SLD()
	1104	foutput.set_data(ooutput)
	1105	writer = SLDReader()
	1106	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
[51f14603]	1107	foutput.output)
	1108	model = GenSAS()
[e3f77d8b]	1109	model.set_sld_data(foutput.output)
[9a5097c]	1110	x = np.arange(1000)/10000. + 1e-5
	1111	y = np.arange(1000)/10000. + 1e-5
	1112	i = np.zeros(1000)
[e3f77d8b]	1113	model.runXY([x, y, i])
	1114
	1115	if __name__ == "__main__":
[51f14603]	1116	test()
	1117	test_load()

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SasView

source: sasview/src/sas/sascalc/calculator/sas_gen.py @ c6fb57c

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