sas_gen.py @ 0657b10

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 0657b10 was 7432acb, checked in by andyfaff, 8 years ago
MAINT: search+replace '!= None' by 'is not None'
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
[463e7ffc]	15	logger = logging.getLogger(__name__)
[c155a16]	16
[e3f77d8b]	17	MFACTOR_AM = 2.853E-12
	18	MFACTOR_MT = 2.3164E-9
[51f14603]	19	METER2ANG = 1.0E+10
	20	#Avogadro constant [1/mol]
	21	NA = 6.02214129e+23
	22
	23	def mag2sld(mag, v_unit=None):
	24	"""
	25	Convert magnetization to magnatic SLD
	26	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
	27	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
[e3f77d8b]	28	"""
[51f14603]	29	if v_unit == "A/m":
[e3f77d8b]	30	factor = MFACTOR_AM
[51f14603]	31	elif v_unit == "mT":
[e3f77d8b]	32	factor = MFACTOR_MT
[51f14603]	33	else:
	34	raise ValueError, "Invalid valueunit"
	35	sld_m = factor * mag
	36	return sld_m
	37
	38	def transform_center(pos_x, pos_y, pos_z):
	39	"""
[e3f77d8b]	40	re-center
[51f14603]	41	:return: posx, posy, posz [arrays]
[e3f77d8b]	42	"""
[51f14603]	43	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
	44	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
[e3f77d8b]	45	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
	46	return posx, posy, posz
[51f14603]	47
	48	class GenSAS(BaseComponent):
	49	"""
	50	Generic SAS computation Model based on sld (n & m) arrays
	51	"""
	52	def __init__(self):
	53	"""
	54	Init
	55	:Params sld_data: MagSLD object
	56	"""
	57	# Initialize BaseComponent
	58	BaseComponent.__init__(self)
	59	self.sld_data = None
	60	self.data_pos_unit = None
	61	self.data_x = None
	62	self.data_y = None
	63	self.data_z = None
	64	self.data_sldn = None
	65	self.data_mx = None
	66	self.data_my = None
	67	self.data_mz = None
	68	self.data_vol = None #[A^3]
	69	self.is_avg = False
	70	## Name of the model
	71	self.name = "GenSAS"
	72	## Define parameters
	73	self.params = {}
[e3f77d8b]	74	self.params['scale'] = 1.0
	75	self.params['background'] = 0.0
	76	self.params['solvent_SLD'] = 0.0
[51f14603]	77	self.params['total_volume'] = 1.0
[e3f77d8b]	78	self.params['Up_frac_in'] = 1.0
	79	self.params['Up_frac_out'] = 1.0
	80	self.params['Up_theta'] = 0.0
[51f14603]	81	self.description = 'GenSAS'
	82	## Parameter details [units, min, max]
	83	self.details = {}
[9a5097c]	84	self.details['scale'] = ['', 0.0, np.inf]
	85	self.details['background'] = ['[1/cm]', 0.0, np.inf]
	86	self.details['solvent_SLD'] = ['1/A^(2)', -np.inf, np.inf]
	87	self.details['total_volume'] = ['A^(3)', 0.0, np.inf]
[cb4ef58]	88	self.details['Up_frac_in'] = ['[u/(u+d)]', 0.0, 1.0]
	89	self.details['Up_frac_out'] = ['[u/(u+d)]', 0.0, 1.0]
[9a5097c]	90	self.details['Up_theta'] = ['[deg]', -np.inf, np.inf]
[51f14603]	91	# fixed parameters
	92	self.fixed = []
[e3f77d8b]	93
	94	def set_pixel_volumes(self, volume):
[51f14603]	95	"""
	96	Set the volume of a pixel in (A^3) unit
	97	:Param volume: pixel volume [float]
	98	"""
[235f514]	99	if self.data_vol is None:
[51f14603]	100	raise
	101	self.data_vol = volume
[e3f77d8b]	102
	103	def set_is_avg(self, is_avg=False):
[51f14603]	104	"""
	105	Sets is_avg: [bool]
	106	"""
	107	self.is_avg = is_avg
[e3f77d8b]	108
[51f14603]	109	def _gen(self, x, y, i):
	110	"""
	111	Evaluate the function
	112	:Param x: array of x-values
	113	:Param y: array of y-values
[e3f77d8b]	114	:Param i: array of initial i-value
[51f14603]	115	:return: function value
	116	"""
	117	pos_x = self.data_x
	118	pos_y = self.data_y
	119	pos_z = self.data_z
	120	len_x = len(pos_x)
[235f514]	121	if self.is_avg is None:
[51f14603]	122	len_x *= -1
	123	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
	124	len_q = len(x)
	125	sldn = copy.deepcopy(self.data_sldn)
	126	sldn -= self.params['solvent_SLD']
[e3f77d8b]	127	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
	128	sldn, self.data_mx, self.data_my,
[51f14603]	129	self.data_mz, self.data_vol,
[e3f77d8b]	130	self.params['Up_frac_in'],
	131	self.params['Up_frac_out'],
[51f14603]	132	self.params['Up_theta'])
	133	if y == []:
	134	mod.genicom(model, len_q, x, i)
	135	else:
	136	mod.genicomXY(model, len_q, x, y, i)
	137	vol_correction = self.data_total_volume / self.params['total_volume']
	138	return self.params['scale'] * vol_correction * i + \
	139	self.params['background']
[e3f77d8b]	140
	141	def set_sld_data(self, sld_data=None):
[51f14603]	142	"""
	143	Sets sld_data
	144	"""
	145	self.sld_data = sld_data
	146	self.data_pos_unit = sld_data.pos_unit
	147	self.data_x = sld_data.pos_x
	148	self.data_y = sld_data.pos_y
	149	self.data_z = sld_data.pos_z
	150	self.data_sldn = sld_data.sld_n
	151	self.data_mx = sld_data.sld_mx
	152	self.data_my = sld_data.sld_my
	153	self.data_mz = sld_data.sld_mz
	154	self.data_vol = sld_data.vol_pix
	155	self.data_total_volume = sum(sld_data.vol_pix)
	156	self.params['total_volume'] = sum(sld_data.vol_pix)
[e3f77d8b]	157
[51f14603]	158	def getProfile(self):
	159	"""
[e3f77d8b]	160	Get SLD profile
[51f14603]	161	: return: sld_data
	162	"""
	163	return self.sld_data
[e3f77d8b]	164
	165	def run(self, x=0.0):
	166	"""
[51f14603]	167	Evaluate the model
	168	:param x: simple value
	169	:return: (I value)
	170	"""
	171	if x.__class__.__name__ == 'list':
	172	if len(x[1]) > 0:
	173	msg = "Not a 1D."
	174	raise ValueError, msg
[9a5097c]	175	i_out = np.zeros_like(x[0])
[51f14603]	176	# 1D I is found at y =0 in the 2D pattern
[e3f77d8b]	177	out = self._gen(x[0], [], i_out)
[51f14603]	178	return out
	179	else:
	180	msg = "Q must be given as list of qx's and qy's"
	181	raise ValueError, msg
[e3f77d8b]	182
	183	def runXY(self, x=0.0):
	184	"""
[51f14603]	185	Evaluate the model
	186	:param x: simple value
	187	:return: I value
	188	:Use this runXY() for the computation
	189	"""
	190	if x.__class__.__name__ == 'list':
[9a5097c]	191	i_out = np.zeros_like(x[0])
[51f14603]	192	out = self._gen(x[0], x[1], i_out)
	193	return out
	194	else:
	195	msg = "Q must be given as list of qx's and qy's"
	196	raise ValueError, msg
[e3f77d8b]	197
[51f14603]	198	def evalDistribution(self, qdist):
	199	"""
	200	Evaluate a distribution of q-values.
[ac7be54]	201
	202	:param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy]
	203	where qx,qy are 1D ndarrays (for 2D).
[51f14603]	204	"""
	205	if qdist.__class__.__name__ == 'list':
	206	if len(qdist[1]) < 1:
	207	out = self.run(qdist)
	208	else:
	209	out = self.runXY(qdist)
	210	return out
	211	else:
	212	mesg = "evalDistribution is expecting an ndarray of "
	213	mesg += "a list [qx,qy] where qx,qy are arrays."
	214	raise RuntimeError, mesg
[e3f77d8b]	215
	216	class OMF2SLD(object):
[51f14603]	217	"""
	218	Convert OMFData to MAgData
	219	"""
[e3f77d8b]	220	def __init__(self):
[51f14603]	221	"""
	222	Init
	223	"""
	224	self.pos_x = None
	225	self.pos_y = None
	226	self.pos_z = None
	227	self.mx = None
	228	self.my = None
	229	self.mz = None
	230	self.sld_n = None
	231	self.vol_pix = None
	232	self.output = None
	233	self.omfdata = None
[e3f77d8b]	234
[51f14603]	235	def set_data(self, omfdata, shape='rectangular'):
	236	"""
	237	Set all data
	238	"""
	239	self.omfdata = omfdata
	240	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
[9a5097c]	241	pos_x = np.arange(omfdata.xmin,
[e3f77d8b]	242	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
[51f14603]	243	omfdata.xstepsize)
[9a5097c]	244	pos_y = np.arange(omfdata.ymin,
[e3f77d8b]	245	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
[51f14603]	246	omfdata.ystepsize)
[9a5097c]	247	pos_z = np.arange(omfdata.zmin,
[e3f77d8b]	248	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
[51f14603]	249	omfdata.zstepsize)
[9a5097c]	250	self.pos_x = np.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
[51f14603]	251	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
[9a5097c]	252	self.pos_y = np.tile(self.pos_y, int(omfdata.znodes))
[51f14603]	253	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
	254	self.mx = omfdata.mx
	255	self.my = omfdata.my
	256	self.mz = omfdata.mz
[9a5097c]	257	self.sld_n = np.zeros(length)
[e3f77d8b]	258
[235f514]	259	if omfdata.mx is None:
[9a5097c]	260	self.mx = np.zeros(length)
[235f514]	261	if omfdata.my is None:
[9a5097c]	262	self.my = np.zeros(length)
[235f514]	263	if omfdata.mz is None:
[9a5097c]	264	self.mz = np.zeros(length)
[e3f77d8b]	265
[51f14603]	266	self._check_data_length(length)
	267	self.remove_null_points(False, False)
[9a5097c]	268	mask = np.ones(len(self.sld_n), dtype=bool)
[51f14603]	269	if shape.lower() == 'ellipsoid':
	270	try:
	271	# Pixel (step) size included
	272	x_c = max(self.pos_x) + min(self.pos_x)
	273	y_c = max(self.pos_y) + min(self.pos_y)
	274	z_c = max(self.pos_z) + min(self.pos_z)
	275	x_d = max(self.pos_x) - min(self.pos_x)
	276	y_d = max(self.pos_y) - min(self.pos_y)
	277	z_d = max(self.pos_z) - min(self.pos_z)
	278	x_r = (x_d + omfdata.xstepsize) / 2.0
	279	y_r = (y_d + omfdata.ystepsize) / 2.0
	280	z_r = (z_d + omfdata.zstepsize) / 2.0
	281	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
	282	x_dir2 *= x_dir2
	283	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
	284	y_dir2 *= y_dir2
	285	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
	286	z_dir2 *= z_dir2
	287	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
	288	except:
[c155a16]	289	logger.error(sys.exc_value)
[e3f77d8b]	290	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
	291	self.pos_z[mask], self.sld_n[mask],
[51f14603]	292	self.mx[mask], self.my[mask], self.mz[mask])
	293	self.output.set_pix_type('pixel')
	294	self.output.set_pixel_symbols('pixel')
[e3f77d8b]	295
[51f14603]	296	def get_omfdata(self):
	297	"""
	298	Return all data
	299	"""
	300	return self.omfdata
[e3f77d8b]	301
[51f14603]	302	def get_output(self):
	303	"""
	304	Return output
	305	"""
	306	return self.output
[e3f77d8b]	307
[51f14603]	308	def _check_data_length(self, length):
	309	"""
	310	Check if the data lengths are consistent
	311	:Params length: data length
	312	"""
	313	msg = "Error: Inconsistent data length."
	314	if len(self.pos_x) != length:
	315	raise ValueError, msg
	316	if len(self.pos_y) != length:
	317	raise ValueError, msg
	318	if len(self.pos_z) != length:
	319	raise ValueError, msg
	320	if len(self.mx) != length:
	321	raise ValueError, msg
	322	if len(self.my) != length:
	323	raise ValueError, msg
	324	if len(self.mz) != length:
	325	raise ValueError, msg
[e3f77d8b]	326
[51f14603]	327	def remove_null_points(self, remove=False, recenter=False):
	328	"""
	329	Removes any mx, my, and mz = 0 points
	330	"""
	331	if remove:
[9a5097c]	332	is_nonzero = (np.fabs(self.mx) + np.fabs(self.my) +
	333	np.fabs(self.mz)).nonzero()
[e3f77d8b]	334	if len(is_nonzero[0]) > 0:
[51f14603]	335	self.pos_x = self.pos_x[is_nonzero]
	336	self.pos_y = self.pos_y[is_nonzero]
	337	self.pos_z = self.pos_z[is_nonzero]
	338	self.sld_n = self.sld_n[is_nonzero]
	339	self.mx = self.mx[is_nonzero]
	340	self.my = self.my[is_nonzero]
	341	self.mz = self.mz[is_nonzero]
	342	if recenter:
	343	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
	344	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
	345	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
[e3f77d8b]	346
[51f14603]	347	def get_magsld(self):
	348	"""
	349	return MagSLD
	350	"""
	351	return self.output
[e3f77d8b]	352
	353
	354	class OMFReader(object):
[51f14603]	355	"""
	356	Class to load omf/ascii files (3 columns w/header).
	357	"""
	358	## File type
	359	type_name = "OMF ASCII"
[e3f77d8b]	360
[51f14603]	361	## Wildcards
	362	type = ["OMF files (.OMF, .omf)\|*.omf"]
	363	## List of allowed extensions
	364	ext = ['.omf', '.OMF']
[e3f77d8b]	365
[51f14603]	366	def read(self, path):
	367	"""
	368	Load data file
	369	:param path: file path
	370	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	371	"""
	372	desc = ""
[9a5097c]	373	mx = np.zeros(0)
	374	my = np.zeros(0)
	375	mz = np.zeros(0)
[51f14603]	376	try:
	377	input_f = open(path, 'rb')
	378	buff = input_f.read()
	379	lines = buff.split('\n')
	380	input_f.close()
	381	output = OMFData()
	382	valueunit = None
	383	for line in lines:
	384	toks = line.split()
	385	# Read data
	386	try:
	387	_mx = float(toks[0])
	388	_my = float(toks[1])
	389	_mz = float(toks[2])
	390	_mx = mag2sld(_mx, valueunit)
	391	_my = mag2sld(_my, valueunit)
	392	_mz = mag2sld(_mz, valueunit)
[9a5097c]	393	mx = np.append(mx, _mx)
	394	my = np.append(my, _my)
	395	mz = np.append(mz, _mz)
[51f14603]	396	except:
	397	# Skip non-data lines
[c155a16]	398	logger.error(sys.exc_value)
[51f14603]	399	#Reading Header; Segment count ignored
	400	s_line = line.split(":", 1)
	401	if s_line[0].lower().count("oommf") > 0:
	402	oommf = s_line[1].lstrip()
	403	if s_line[0].lower().count("title") > 0:
	404	title = s_line[1].lstrip()
	405	if s_line[0].lower().count("desc") > 0:
	406	desc += s_line[1].lstrip()
	407	desc += '\n'
	408	if s_line[0].lower().count("meshtype") > 0:
	409	meshtype = s_line[1].lstrip()
	410	if s_line[0].lower().count("meshunit") > 0:
	411	meshunit = s_line[1].lstrip()
	412	if meshunit.count("m") < 1:
	413	msg = "Error: \n"
	414	msg += "We accept only m as meshunit"
	415	raise ValueError, msg
	416	if s_line[0].lower().count("xbase") > 0:
	417	xbase = s_line[1].lstrip()
	418	if s_line[0].lower().count("ybase") > 0:
	419	ybase = s_line[1].lstrip()
	420	if s_line[0].lower().count("zbase") > 0:
	421	zbase = s_line[1].lstrip()
	422	if s_line[0].lower().count("xstepsize") > 0:
	423	xstepsize = s_line[1].lstrip()
	424	if s_line[0].lower().count("ystepsize") > 0:
	425	ystepsize = s_line[1].lstrip()
	426	if s_line[0].lower().count("zstepsize") > 0:
	427	zstepsize = s_line[1].lstrip()
	428	if s_line[0].lower().count("xnodes") > 0:
	429	xnodes = s_line[1].lstrip()
	430	if s_line[0].lower().count("ynodes") > 0:
	431	ynodes = s_line[1].lstrip()
	432	if s_line[0].lower().count("znodes") > 0:
	433	znodes = s_line[1].lstrip()
	434	if s_line[0].lower().count("xmin") > 0:
	435	xmin = s_line[1].lstrip()
	436	if s_line[0].lower().count("ymin") > 0:
	437	ymin = s_line[1].lstrip()
	438	if s_line[0].lower().count("zmin") > 0:
	439	zmin = s_line[1].lstrip()
	440	if s_line[0].lower().count("xmax") > 0:
	441	xmax = s_line[1].lstrip()
	442	if s_line[0].lower().count("ymax") > 0:
	443	ymax = s_line[1].lstrip()
	444	if s_line[0].lower().count("zmax") > 0:
	445	zmax = s_line[1].lstrip()
	446	if s_line[0].lower().count("valueunit") > 0:
	447	valueunit = s_line[1].lstrip().rstrip()
	448	if s_line[0].lower().count("valuemultiplier") > 0:
	449	valuemultiplier = s_line[1].lstrip()
	450	if s_line[0].lower().count("valuerangeminmag") > 0:
	451	valuerangeminmag = s_line[1].lstrip()
	452	if s_line[0].lower().count("valuerangemaxmag") > 0:
	453	valuerangemaxmag = s_line[1].lstrip()
	454	if s_line[0].lower().count("end") > 0:
	455	output.filename = os.path.basename(path)
	456	output.oommf = oommf
	457	output.title = title
	458	output.desc = desc
	459	output.meshtype = meshtype
	460	output.xbase = float(xbase) * METER2ANG
	461	output.ybase = float(ybase) * METER2ANG
	462	output.zbase = float(zbase) * METER2ANG
	463	output.xstepsize = float(xstepsize) * METER2ANG
	464	output.ystepsize = float(ystepsize) * METER2ANG
	465	output.zstepsize = float(zstepsize) * METER2ANG
	466	output.xnodes = float(xnodes)
	467	output.ynodes = float(ynodes)
	468	output.znodes = float(znodes)
	469	output.xmin = float(xmin) * METER2ANG
	470	output.ymin = float(ymin) * METER2ANG
	471	output.zmin = float(zmin) * METER2ANG
	472	output.xmax = float(xmax) * METER2ANG
	473	output.ymax = float(ymax) * METER2ANG
	474	output.zmax = float(zmax) * METER2ANG
	475	output.valuemultiplier = valuemultiplier
	476	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
	477	valueunit)
	478	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
	479	valueunit)
	480	output.set_m(mx, my, mz)
	481	return output
	482	except:
	483	msg = "%s is not supported: \n" % path
	484	msg += "We accept only Text format OMF file."
	485	raise RuntimeError, msg
	486
[e3f77d8b]	487	class PDBReader(object):
[51f14603]	488	"""
	489	PDB reader class: limited for reading the lines starting with 'ATOM'
	490	"""
	491	type_name = "PDB"
	492	## Wildcards
	493	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
	494	## List of allowed extensions
[e3f77d8b]	495	ext = ['.pdb', '.PDB']
	496
[51f14603]	497	def read(self, path):
	498	"""
	499	Load data file
[e3f77d8b]	500
[51f14603]	501	:param path: file path
	502	:return: MagSLD
	503	:raise RuntimeError: when the file can't be opened
	504	"""
[9a5097c]	505	pos_x = np.zeros(0)
	506	pos_y = np.zeros(0)
	507	pos_z = np.zeros(0)
	508	sld_n = np.zeros(0)
	509	sld_mx = np.zeros(0)
	510	sld_my = np.zeros(0)
	511	sld_mz = np.zeros(0)
	512	vol_pix = np.zeros(0)
	513	pix_symbol = np.zeros(0)
[51f14603]	514	x_line = []
	515	y_line = []
	516	z_line = []
	517	x_lines = []
	518	y_lines = []
[e3f77d8b]	519	z_lines = []
[51f14603]	520	try:
	521	input_f = open(path, 'rb')
	522	buff = input_f.read()
	523	lines = buff.split('\n')
	524	input_f.close()
	525	num = 0
	526	for line in lines:
	527	try:
	528	# check if line starts with "ATOM"
	529	if line[0:6].strip().count('ATM') > 0 or \
	530	line[0:6].strip() == 'ATOM':
	531	# define fields of interest
	532	atom_name = line[12:16].strip()
	533	try:
	534	float(line[12])
	535	atom_name = atom_name[1].upper()
	536	except:
	537	if len(atom_name) == 4:
	538	atom_name = atom_name[0].upper()
[e3f77d8b]	539	elif line[12] != ' ':
[51f14603]	540	atom_name = atom_name[0].upper() + \
[e3f77d8b]	541	atom_name[1].lower()
[51f14603]	542	else:
	543	atom_name = atom_name[0].upper()
	544	_pos_x = float(line[30:38].strip())
	545	_pos_y = float(line[38:46].strip())
	546	_pos_z = float(line[46:54].strip())
[9a5097c]	547	pos_x = np.append(pos_x, _pos_x)
	548	pos_y = np.append(pos_y, _pos_y)
	549	pos_z = np.append(pos_z, _pos_z)
[51f14603]	550	try:
	551	val = nsf.neutron_sld(atom_name)[0]
	552	# sld in Ang^-2 unit
	553	val *= 1.0e-6
[9a5097c]	554	sld_n = np.append(sld_n, val)
[51f14603]	555	atom = formula(atom_name)
	556	# cm to A units
	557	vol = 1.0e+24 * atom.mass / atom.density / NA
[9a5097c]	558	vol_pix = np.append(vol_pix, vol)
[51f14603]	559	except:
	560	print "Error: set the sld of %s to zero"% atom_name
[9a5097c]	561	sld_n = np.append(sld_n, 0.0)
	562	sld_mx = np.append(sld_mx, 0)
	563	sld_my = np.append(sld_my, 0)
	564	sld_mz = np.append(sld_mz, 0)
	565	pix_symbol = np.append(pix_symbol, atom_name)
[e3f77d8b]	566	elif line[0:6].strip().count('CONECT') > 0:
[51f14603]	567	toks = line.split()
[e3f77d8b]	568	num = int(toks[1]) - 1
	569	val_list = []
[51f14603]	570	for val in toks[2:]:
	571	try:
	572	int_val = int(val)
	573	except:
	574	break
	575	if int_val == 0:
	576	break
	577	val_list.append(int_val)
[e3f77d8b]	578	#need val_list ordered
[51f14603]	579	for val in val_list:
	580	index = val - 1
	581	if (pos_x[index], pos_x[num]) in x_line and \
	582	(pos_y[index], pos_y[num]) in y_line and \
	583	(pos_z[index], pos_z[num]) in z_line:
	584	continue
	585	x_line.append((pos_x[num], pos_x[index]))
	586	y_line.append((pos_y[num], pos_y[index]))
	587	z_line.append((pos_z[num], pos_z[index]))
	588	if len(x_line) > 0:
[e3f77d8b]	589	x_lines.append(x_line)
[51f14603]	590	y_lines.append(y_line)
[e3f77d8b]	591	z_lines.append(z_line)
[51f14603]	592	except:
[c155a16]	593	logger.error(sys.exc_value)
[e3f77d8b]	594
[51f14603]	595	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
	596	output.set_conect_lines(x_line, y_line, z_line)
	597	output.filename = os.path.basename(path)
	598	output.set_pix_type('atom')
	599	output.set_pixel_symbols(pix_symbol)
	600	output.set_nodes()
	601	output.set_pixel_volumes(vol_pix)
	602	output.sld_unit = '1/A^(2)'
	603	return output
	604	except:
[e3f77d8b]	605	raise RuntimeError, "%s is not a sld file" % path
[51f14603]	606
	607	def write(self, path, data):
	608	"""
	609	Write
	610	"""
	611	print "Not implemented... "
	612
[e3f77d8b]	613	class SLDReader(object):
[51f14603]	614	"""
	615	Class to load ascii files (7 columns).
	616	"""
	617	## File type
	618	type_name = "SLD ASCII"
	619	## Wildcards
	620	type = ["sld files (.SLD, .sld)\|*.sld",
	621	"txt files (.TXT, .txt)\|*.txt",
	622	"all files (.)\|."]
	623	## List of allowed extensions
	624	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
	625	def read(self, path):
	626	"""
	627	Load data file
	628	:param path: file path
	629	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	630	:raise RuntimeError: when the file can't be opened
	631	:raise ValueError: when the length of the data vectors are inconsistent
	632	"""
	633	try:
[9a5097c]	634	pos_x = np.zeros(0)
	635	pos_y = np.zeros(0)
	636	pos_z = np.zeros(0)
	637	sld_n = np.zeros(0)
	638	sld_mx = np.zeros(0)
	639	sld_my = np.zeros(0)
	640	sld_mz = np.zeros(0)
[51f14603]	641	try:
	642	# Use numpy to speed up loading
[9a5097c]	643	input_f = np.loadtxt(path, dtype='float', skiprows=1,
[51f14603]	644	ndmin=1, unpack=True)
[9a5097c]	645	pos_x = np.array(input_f[0])
	646	pos_y = np.array(input_f[1])
	647	pos_z = np.array(input_f[2])
	648	sld_n = np.array(input_f[3])
	649	sld_mx = np.array(input_f[4])
	650	sld_my = np.array(input_f[5])
	651	sld_mz = np.array(input_f[6])
[51f14603]	652	ncols = len(input_f)
	653	if ncols == 8:
[9a5097c]	654	vol_pix = np.array(input_f[7])
[51f14603]	655	elif ncols == 7:
[e3f77d8b]	656	vol_pix = None
[51f14603]	657	except:
	658	# For older version of numpy
	659	input_f = open(path, 'rb')
	660	buff = input_f.read()
	661	lines = buff.split('\n')
	662	input_f.close()
	663	for line in lines:
	664	toks = line.split()
	665	try:
	666	_pos_x = float(toks[0])
	667	_pos_y = float(toks[1])
	668	_pos_z = float(toks[2])
	669	_sld_n = float(toks[3])
	670	_sld_mx = float(toks[4])
	671	_sld_my = float(toks[5])
	672	_sld_mz = float(toks[6])
[9a5097c]	673	pos_x = np.append(pos_x, _pos_x)
	674	pos_y = np.append(pos_y, _pos_y)
	675	pos_z = np.append(pos_z, _pos_z)
	676	sld_n = np.append(sld_n, _sld_n)
	677	sld_mx = np.append(sld_mx, _sld_mx)
	678	sld_my = np.append(sld_my, _sld_my)
	679	sld_mz = np.append(sld_mz, _sld_mz)
[51f14603]	680	try:
[e3f77d8b]	681	_vol_pix = float(toks[7])
[9a5097c]	682	vol_pix = np.append(vol_pix, _vol_pix)
[51f14603]	683	except:
	684	vol_pix = None
	685	except:
	686	# Skip non-data lines
[c155a16]	687	logger.error(sys.exc_value)
[e3f77d8b]	688	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
[51f14603]	689	sld_mx, sld_my, sld_mz)
	690	output.filename = os.path.basename(path)
	691	output.set_pix_type('pixel')
	692	output.set_pixel_symbols('pixel')
[7432acb]	693	if vol_pix is not None:
[51f14603]	694	output.set_pixel_volumes(vol_pix)
	695	return output
	696	except:
[e3f77d8b]	697	raise RuntimeError, "%s is not a sld file" % path
	698
[51f14603]	699	def write(self, path, data):
	700	"""
	701	Write sld file
[e3f77d8b]	702	:Param path: file path
[51f14603]	703	:Param data: MagSLD data object
	704	"""
[235f514]	705	if path is None:
[51f14603]	706	raise ValueError, "Missing the file path."
[235f514]	707	if data is None:
[51f14603]	708	raise ValueError, "Missing the data to save."
	709	x_val = data.pos_x
	710	y_val = data.pos_y
	711	z_val = data.pos_z
	712	vol_pix = data.vol_pix
	713	length = len(x_val)
	714	sld_n = data.sld_n
[235f514]	715	if sld_n is None:
[9a5097c]	716	sld_n = np.zeros(length)
[51f14603]	717	sld_mx = data.sld_mx
[235f514]	718	if sld_mx is None:
[9a5097c]	719	sld_mx = np.zeros(length)
	720	sld_my = np.zeros(length)
	721	sld_mz = np.zeros(length)
[51f14603]	722	else:
	723	sld_my = data.sld_my
	724	sld_mz = data.sld_mz
	725	out = open(path, 'w')
	726	# First Line: Column names
	727	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
	728	for ind in range(length):
[e3f77d8b]	729	out.write("\n%g %g %g %g %g %g %g %g" % \
	730	(x_val[ind], y_val[ind], z_val[ind], sld_n[ind],
	731	sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind]))
	732	out.close()
	733
	734
	735	class OMFData(object):
[51f14603]	736	"""
	737	OMF Data.
	738	"""
	739	_meshunit = "A"
	740	_valueunit = "A^(-2)"
	741	def __init__(self):
	742	"""
	743	Init for mag SLD
	744	"""
	745	self.filename = 'default'
	746	self.oommf = ''
	747	self.title = ''
	748	self.desc = ''
	749	self.meshtype = ''
	750	self.meshunit = self._meshunit
	751	self.valueunit = self._valueunit
	752	self.xbase = 0.0
	753	self.ybase = 0.0
	754	self.zbase = 0.0
	755	self.xstepsize = 6.0
	756	self.ystepsize = 6.0
	757	self.zstepsize = 6.0
	758	self.xnodes = 10.0
	759	self.ynodes = 10.0
	760	self.znodes = 10.0
	761	self.xmin = 0.0
	762	self.ymin = 0.0
	763	self.zmin = 0.0
	764	self.xmax = 60.0
	765	self.ymax = 60.0
	766	self.zmax = 60.0
	767	self.mx = None
	768	self.my = None
	769	self.mz = None
	770	self.valuemultiplier = 1.
	771	self.valuerangeminmag = 0
	772	self.valuerangemaxmag = 0
[e3f77d8b]	773
[51f14603]	774	def __str__(self):
	775	"""
	776	doc strings
	777	"""
[e3f77d8b]	778	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	779	_str += "File: %s\n" % self.filename
	780	_str += "OOMMF: %s\n" % self.oommf
	781	_str += "Title: %s\n" % self.title
	782	_str += "Desc: %s\n" % self.desc
	783	_str += "meshtype: %s\n" % self.meshtype
	784	_str += "meshunit: %s\n" % str(self.meshunit)
	785	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
	786	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
	787	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
[e3f77d8b]	788	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
[51f14603]	789	self.meshunit)
[e3f77d8b]	790	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
[51f14603]	791	self.meshunit)
[e3f77d8b]	792	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
[51f14603]	793	self.meshunit)
	794	_str += "xnodes: %s\n" % str(self.xnodes)
	795	_str += "ynodes: %s\n" % str(self.ynodes)
	796	_str += "znodes: %s\n" % str(self.znodes)
	797	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
	798	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
	799	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
	800	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
	801	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
	802	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
	803	_str += "valueunit: %s\n" % self.valueunit
	804	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
[e3f77d8b]	805	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
	806	self.valueunit)
	807	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
	808	self.valueunit)
[51f14603]	809	return _str
[e3f77d8b]	810
[51f14603]	811	def set_m(self, mx, my, mz):
	812	"""
	813	Set the Mx, My, Mz values
	814	"""
	815	self.mx = mx
	816	self.my = my
	817	self.mz = mz
[e3f77d8b]	818
	819	class MagSLD(object):
[51f14603]	820	"""
	821	Magnetic SLD.
	822	"""
	823	pos_x = None
	824	pos_y = None
	825	pos_z = None
	826	sld_n = None
	827	sld_mx = None
	828	sld_my = None
	829	sld_mz = None
	830	# Units
	831	_pos_unit = 'A'
	832	_sld_unit = '1/A^(2)'
	833	_pix_type = 'pixel'
[e3f77d8b]	834
	835	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
[51f14603]	836	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
	837	"""
	838	Init for mag SLD
	839	:params : All should be numpy 1D array
	840	"""
	841	self.is_data = True
	842	self.filename = ''
	843	self.xstepsize = 6.0
	844	self.ystepsize = 6.0
	845	self.zstepsize = 6.0
	846	self.xnodes = 10.0
	847	self.ynodes = 10.0
	848	self.znodes = 10.0
	849	self.has_stepsize = False
	850	self.has_conect = False
	851	self.pos_unit = self._pos_unit
	852	self.sld_unit = self._sld_unit
	853	self.pix_type = 'pixel'
	854	self.pos_x = pos_x
	855	self.pos_y = pos_y
	856	self.pos_z = pos_z
	857	self.sld_n = sld_n
	858	self.line_x = None
	859	self.line_y = None
	860	self.line_z = None
	861	self.sld_mx = sld_mx
	862	self.sld_my = sld_my
	863	self.sld_mz = sld_mz
	864	self.vol_pix = vol_pix
	865	self.sld_m = None
	866	self.sld_phi = None
	867	self.sld_theta = None
	868	self.pix_symbol = None
[7432acb]	869	if sld_mx is not None and sld_my is not None and sld_mz is not None:
[51f14603]	870	self.set_sldms(sld_mx, sld_my, sld_mz)
	871	self.set_nodes()
[e3f77d8b]	872
[51f14603]	873	def __str__(self):
	874	"""
	875	doc strings
	876	"""
[e3f77d8b]	877	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	878	_str += "File: %s\n" % self.filename
	879	_str += "Axis_unit: %s\n" % self.pos_unit
	880	_str += "SLD_unit: %s\n" % self.sld_unit
	881	return _str
[e3f77d8b]	882
[51f14603]	883	def set_pix_type(self, pix_type):
	884	"""
	885	Set pixel type
	886	:Param pix_type: string, 'pixel' or 'atom'
	887	"""
	888	self.pix_type = pix_type
[e3f77d8b]	889
[51f14603]	890	def set_sldn(self, sld_n):
	891	"""
	892	Sets neutron SLD
	893	"""
	894	if sld_n.__class__.__name__ == 'float':
	895	if self.is_data:
[e3f77d8b]	896	# For data, put the value to only the pixels w non-zero M
[9a5097c]	897	is_nonzero = (np.fabs(self.sld_mx) +
	898	np.fabs(self.sld_my) +
	899	np.fabs(self.sld_mz)).nonzero()
	900	self.sld_n = np.zeros(len(self.pos_x))
[51f14603]	901	if len(self.sld_n[is_nonzero]) > 0:
	902	self.sld_n[is_nonzero] = sld_n
	903	else:
	904	self.sld_n.fill(sld_n)
	905	else:
	906	# For non-data, put the value to all the pixels
[9a5097c]	907	self.sld_n = np.ones(len(self.pos_x)) * sld_n
[51f14603]	908	else:
	909	self.sld_n = sld_n
[e3f77d8b]	910
[51f14603]	911	def set_sldms(self, sld_mx, sld_my, sld_mz):
[ac7be54]	912	r"""
	913	Sets (\\|m\\|, m_theta, m_phi)
[51f14603]	914	"""
	915	if sld_mx.__class__.__name__ == 'float':
[9a5097c]	916	self.sld_mx = np.ones(len(self.pos_x)) * sld_mx
[51f14603]	917	else:
	918	self.sld_mx = sld_mx
	919	if sld_my.__class__.__name__ == 'float':
[9a5097c]	920	self.sld_my = np.ones(len(self.pos_x)) * sld_my
[51f14603]	921	else:
	922	self.sld_my = sld_my
	923	if sld_mz.__class__.__name__ == 'float':
[9a5097c]	924	self.sld_mz = np.ones(len(self.pos_x)) * sld_mz
[51f14603]	925	else:
	926	self.sld_mz = sld_mz
	927
[9a5097c]	928	sld_m = np.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
[e3f77d8b]	929	sld_mz * sld_mz)
[51f14603]	930	self.sld_m = sld_m
[e3f77d8b]	931
	932	def set_pixel_symbols(self, symbol='pixel'):
[51f14603]	933	"""
	934	Set pixel
	935	:Params pixel: str; pixel or atomic symbol, or array of strings
	936	"""
[235f514]	937	if self.sld_n is None:
[51f14603]	938	return
	939	if symbol.__class__.__name__ == 'str':
[9a5097c]	940	self.pix_symbol = np.repeat(symbol, len(self.sld_n))
[51f14603]	941	else:
	942	self.pix_symbol = symbol
[e3f77d8b]	943
	944	def set_pixel_volumes(self, vol):
[51f14603]	945	"""
	946	Set pixel volumes
	947	:Params pixel: str; pixel or atomic symbol, or array of strings
	948	"""
[235f514]	949	if self.sld_n is None:
[51f14603]	950	return
	951	if vol.__class__.__name__ == 'ndarray':
	952	self.vol_pix = vol
	953	elif vol.__class__.__name__.count('float') > 0:
[9a5097c]	954	self.vol_pix = np.repeat(vol, len(self.sld_n))
[51f14603]	955	else:
	956	self.vol_pix = None
	957
	958	def get_sldn(self):
	959	"""
	960	Returns nuclear sld
	961	"""
	962	return self.sld_n
[e3f77d8b]	963
[51f14603]	964	def set_nodes(self):
	965	"""
	966	Set xnodes, ynodes, and znodes
	967	"""
	968	self.set_stepsize()
	969	if self.pix_type == 'pixel':
	970	try:
	971	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
	972	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
	973	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
	974	self.xnodes = int(xdist) + 1
	975	self.ynodes = int(ydist) + 1
	976	self.znodes = int(zdist) + 1
	977	except:
	978	self.xnodes = None
	979	self.ynodes = None
	980	self.znodes = None
	981	else:
	982	self.xnodes = None
	983	self.ynodes = None
	984	self.znodes = None
[e3f77d8b]	985
[51f14603]	986	def set_stepsize(self):
	987	"""
	988	Set xtepsize, ystepsize, and zstepsize
	989	"""
	990	if self.pix_type == 'pixel':
	991	try:
	992	xpos_pre = self.pos_x[0]
	993	ypos_pre = self.pos_y[0]
	994	zpos_pre = self.pos_z[0]
	995	for x_pos in self.pos_x:
	996	if xpos_pre != x_pos:
[9a5097c]	997	self.xstepsize = np.fabs(x_pos - xpos_pre)
[51f14603]	998	break
	999	for y_pos in self.pos_y:
	1000	if ypos_pre != y_pos:
[9a5097c]	1001	self.ystepsize = np.fabs(y_pos - ypos_pre)
[51f14603]	1002	break
	1003	for z_pos in self.pos_z:
	1004	if zpos_pre != z_pos:
[9a5097c]	1005	self.zstepsize = np.fabs(z_pos - zpos_pre)
[51f14603]	1006	break
	1007	#default pix volume
[9a5097c]	1008	self.vol_pix = np.ones(len(self.pos_x))
[51f14603]	1009	vol = self.xstepsize * self.ystepsize * self.zstepsize
	1010	self.set_pixel_volumes(vol)
	1011	self.has_stepsize = True
	1012	except:
	1013	self.xstepsize = None
	1014	self.ystepsize = None
	1015	self.zstepsize = None
	1016	self.vol_pix = None
	1017	self.has_stepsize = False
	1018	else:
	1019	self.xstepsize = None
	1020	self.ystepsize = None
	1021	self.zstepsize = None
	1022	self.has_stepsize = True
	1023	return self.xstepsize, self.ystepsize, self.zstepsize
	1024
	1025	def set_conect_lines(self, line_x, line_y, line_z):
	1026	"""
	1027	Set bonding line data if taken from pdb
	1028	"""
	1029	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
	1030	return
	1031	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
	1032	return
	1033	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
	1034	return
	1035	self.has_conect = True
[e3f77d8b]	1036	self.line_x = line_x
	1037	self.line_y = line_y
[51f14603]	1038	self.line_z = line_z
	1039
	1040	def test_load():
[b6627d9]	1041	"""
	1042	Test code
	1043	"""
[06aaa75d]	1044	from mpl_toolkits.mplot3d import Axes3D
[e3f77d8b]	1045	current_dir = os.path.abspath(os.path.curdir)
	1046	print current_dir
[51f14603]	1047	for i in range(6):
[e3f77d8b]	1048	current_dir, _ = os.path.split(current_dir)
	1049	tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt")
	1050	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
[51f14603]	1051	if os.path.isfile(tfile):
	1052	tfpath = tfile
	1053	ofpath = ofile
	1054	break
	1055	reader = SLDReader()
	1056	oreader = OMFReader()
	1057	output = reader.read(tfpath)
	1058	ooutput = oreader.read(ofpath)
	1059	foutput = OMF2SLD()
	1060	foutput.set_data(ooutput)
	1061
	1062	import matplotlib.pyplot as plt
	1063	fig = plt.figure()
[06aaa75d]	1064	ax = Axes3D(fig)
[e3f77d8b]	1065	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
	1066	alpha=0.7, markeredgecolor='gray', rasterized=True)
[51f14603]	1067	gap = 7
	1068	max_mx = max(output.sld_mx)
	1069	max_my = max(output.sld_my)
	1070	max_mz = max(output.sld_mz)
[e3f77d8b]	1071	max_m = max(max_mx, max_my, max_mz)
[51f14603]	1072	x2 = output.pos_x+output.sld_mx/max_m * gap
	1073	y2 = output.pos_y+output.sld_my/max_m * gap
	1074	z2 = output.pos_z+output.sld_mz/max_m * gap
[9a5097c]	1075	x_arrow = np.column_stack((output.pos_x, x2))
	1076	y_arrow = np.column_stack((output.pos_y, y2))
	1077	z_arrow = np.column_stack((output.pos_z, z2))
[51f14603]	1078	unit_x2 = output.sld_mx / max_m
	1079	unit_y2 = output.sld_my / max_m
	1080	unit_z2 = output.sld_mz / max_m
[9a5097c]	1081	color_x = np.fabs(unit_x2 * 0.8)
	1082	color_y = np.fabs(unit_y2 * 0.8)
	1083	color_z = np.fabs(unit_z2 * 0.8)
	1084	colors = np.column_stack((color_x, color_y, color_z))
[51f14603]	1085	plt.show()
[b6627d9]	1086
[51f14603]	1087	def test():
[b6627d9]	1088	"""
	1089	Test code
	1090	"""
[e3f77d8b]	1091	current_dir = os.path.abspath(os.path.curdir)
[51f14603]	1092	for i in range(3):
[e3f77d8b]	1093	current_dir, _ = os.path.split(current_dir)
	1094	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
[51f14603]	1095	if os.path.isfile(ofile):
	1096	ofpath = ofile
	1097	break
	1098	oreader = OMFReader()
	1099	ooutput = oreader.read(ofpath)
[e3f77d8b]	1100	foutput = OMF2SLD()
	1101	foutput.set_data(ooutput)
	1102	writer = SLDReader()
	1103	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
[51f14603]	1104	foutput.output)
	1105	model = GenSAS()
[e3f77d8b]	1106	model.set_sld_data(foutput.output)
[9a5097c]	1107	x = np.arange(1000)/10000. + 1e-5
	1108	y = np.arange(1000)/10000. + 1e-5
	1109	i = np.zeros(1000)
[e3f77d8b]	1110	model.runXY([x, y, i])
	1111
	1112	if __name__ == "__main__":
[51f14603]	1113	test()
	1114	test_load()

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SasView

source: sasview/src/sas/sascalc/calculator/sas_gen.py @ 0657b10

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