sas_gen.py @ afb311e

Last change on this file since afb311e was 144e032a, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
tinycc doesn't return structures, so must pass return structure as pointer
Property mode set to `100644`
File size: 40.2 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
[54b0650]	120	def _gen(self, qx, qy):
[51f14603]	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
[235f514]	131	if self.is_avg is None:
[51f14603]	132	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
	133	sldn = copy.deepcopy(self.data_sldn)
	134	sldn -= self.params['solvent_SLD']
[144e032a]	135	# ** WARNING ** new_GenI holds pointers to numpy vectors
	136	# be sure that they are contiguous double precision arrays and make
	137	# sure the GC doesn't eat them before genicom is called.
	138	# TODO: rewrite so that the parameters are passed directly to genicom
	139	args = (
	140	(1 if self.is_avg else 0),
	141	pos_x, pos_y, pos_z,
	142	sldn, self.data_mx, self.data_my,
	143	self.data_mz, self.data_vol,
	144	self.params['Up_frac_in'],
	145	self.params['Up_frac_out'],
	146	self.params['Up_theta'])
	147	model = mod.new_GenI(*args)
[54b0650]	148	if len(qy):
	149	qx, qy = _vec(qx), _vec(qy)
	150	I_out = np.empty_like(qx)
[a1daf86]	151	#print("npoints", qx.shape, "npixels", pos_x.shape)
[54b0650]	152	mod.genicomXY(model, qx, qy, I_out)
[a1daf86]	153	#print("I_out after", I_out)
[51f14603]	154	else:
[54b0650]	155	qx = _vec(qx)
	156	I_out = np.empty_like(qx)
	157	mod.genicom(model, qx, I_out)
[51f14603]	158	vol_correction = self.data_total_volume / self.params['total_volume']
[54b0650]	159	result = (self.params['scale'] * vol_correction * I_out
	160	+ self.params['background'])
	161	return result
[e3f77d8b]	162
	163	def set_sld_data(self, sld_data=None):
[51f14603]	164	"""
	165	Sets sld_data
	166	"""
	167	self.sld_data = sld_data
	168	self.data_pos_unit = sld_data.pos_unit
[54b0650]	169	self.data_x = _vec(sld_data.pos_x)
	170	self.data_y = _vec(sld_data.pos_y)
	171	self.data_z = _vec(sld_data.pos_z)
	172	self.data_sldn = _vec(sld_data.sld_n)
	173	self.data_mx = _vec(sld_data.sld_mx)
	174	self.data_my = _vec(sld_data.sld_my)
	175	self.data_mz = _vec(sld_data.sld_mz)
	176	self.data_vol = _vec(sld_data.vol_pix)
[51f14603]	177	self.data_total_volume = sum(sld_data.vol_pix)
	178	self.params['total_volume'] = sum(sld_data.vol_pix)
[e3f77d8b]	179
[51f14603]	180	def getProfile(self):
	181	"""
[e3f77d8b]	182	Get SLD profile
[51f14603]	183	: return: sld_data
	184	"""
	185	return self.sld_data
[e3f77d8b]	186
	187	def run(self, x=0.0):
	188	"""
[51f14603]	189	Evaluate the model
	190	:param x: simple value
	191	:return: (I value)
	192	"""
[54b0650]	193	if isinstance(x, list):
[51f14603]	194	if len(x[1]) > 0:
	195	msg = "Not a 1D."
[574adc7]	196	raise ValueError(msg)
[51f14603]	197	# 1D I is found at y =0 in the 2D pattern
[54b0650]	198	out = self._gen(x[0], [])
[51f14603]	199	return out
	200	else:
	201	msg = "Q must be given as list of qx's and qy's"
[574adc7]	202	raise ValueError(msg)
[e3f77d8b]	203
	204	def runXY(self, x=0.0):
	205	"""
[51f14603]	206	Evaluate the model
	207	:param x: simple value
	208	:return: I value
	209	:Use this runXY() for the computation
	210	"""
[54b0650]	211	if isinstance(x, list):
	212	return self._gen(x[0], x[1])
[51f14603]	213	else:
	214	msg = "Q must be given as list of qx's and qy's"
[574adc7]	215	raise ValueError(msg)
[e3f77d8b]	216
[51f14603]	217	def evalDistribution(self, qdist):
	218	"""
	219	Evaluate a distribution of q-values.
[ac7be54]	220
	221	:param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy]
	222	where qx,qy are 1D ndarrays (for 2D).
[51f14603]	223	"""
[54b0650]	224	if isinstance(qdist, list):
	225	return self.run(qdist) if len(qdist[1]) < 1 else self.runXY(qdist)
[51f14603]	226	else:
	227	mesg = "evalDistribution is expecting an ndarray of "
	228	mesg += "a list [qx,qy] where qx,qy are arrays."
[574adc7]	229	raise RuntimeError(mesg)
[e3f77d8b]	230
[54b0650]	231	def _vec(v):
	232	return np.ascontiguousarray(v, 'd')
	233
[e3f77d8b]	234	class OMF2SLD(object):
[51f14603]	235	"""
	236	Convert OMFData to MAgData
	237	"""
[e3f77d8b]	238	def __init__(self):
[51f14603]	239	"""
	240	Init
	241	"""
	242	self.pos_x = None
	243	self.pos_y = None
	244	self.pos_z = None
	245	self.mx = None
	246	self.my = None
	247	self.mz = None
	248	self.sld_n = None
	249	self.vol_pix = None
	250	self.output = None
	251	self.omfdata = None
[e3f77d8b]	252
[51f14603]	253	def set_data(self, omfdata, shape='rectangular'):
	254	"""
	255	Set all data
	256	"""
	257	self.omfdata = omfdata
	258	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
[9a5097c]	259	pos_x = np.arange(omfdata.xmin,
[e3f77d8b]	260	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
[51f14603]	261	omfdata.xstepsize)
[9a5097c]	262	pos_y = np.arange(omfdata.ymin,
[e3f77d8b]	263	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
[51f14603]	264	omfdata.ystepsize)
[9a5097c]	265	pos_z = np.arange(omfdata.zmin,
[e3f77d8b]	266	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
[51f14603]	267	omfdata.zstepsize)
[9a5097c]	268	self.pos_x = np.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
[51f14603]	269	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
[9a5097c]	270	self.pos_y = np.tile(self.pos_y, int(omfdata.znodes))
[51f14603]	271	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
	272	self.mx = omfdata.mx
	273	self.my = omfdata.my
	274	self.mz = omfdata.mz
[9a5097c]	275	self.sld_n = np.zeros(length)
[e3f77d8b]	276
[235f514]	277	if omfdata.mx is None:
[9a5097c]	278	self.mx = np.zeros(length)
[235f514]	279	if omfdata.my is None:
[9a5097c]	280	self.my = np.zeros(length)
[235f514]	281	if omfdata.mz is None:
[9a5097c]	282	self.mz = np.zeros(length)
[e3f77d8b]	283
[51f14603]	284	self._check_data_length(length)
	285	self.remove_null_points(False, False)
[9a5097c]	286	mask = np.ones(len(self.sld_n), dtype=bool)
[51f14603]	287	if shape.lower() == 'ellipsoid':
	288	try:
	289	# Pixel (step) size included
	290	x_c = max(self.pos_x) + min(self.pos_x)
	291	y_c = max(self.pos_y) + min(self.pos_y)
	292	z_c = max(self.pos_z) + min(self.pos_z)
	293	x_d = max(self.pos_x) - min(self.pos_x)
	294	y_d = max(self.pos_y) - min(self.pos_y)
	295	z_d = max(self.pos_z) - min(self.pos_z)
	296	x_r = (x_d + omfdata.xstepsize) / 2.0
	297	y_r = (y_d + omfdata.ystepsize) / 2.0
	298	z_r = (z_d + omfdata.zstepsize) / 2.0
	299	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
	300	x_dir2 *= x_dir2
	301	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
	302	y_dir2 *= y_dir2
	303	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
	304	z_dir2 *= z_dir2
	305	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
[1d014cb]	306	except Exception:
[c155a16]	307	logger.error(sys.exc_value)
[e3f77d8b]	308	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
	309	self.pos_z[mask], self.sld_n[mask],
[51f14603]	310	self.mx[mask], self.my[mask], self.mz[mask])
	311	self.output.set_pix_type('pixel')
	312	self.output.set_pixel_symbols('pixel')
[e3f77d8b]	313
[51f14603]	314	def get_omfdata(self):
	315	"""
	316	Return all data
	317	"""
	318	return self.omfdata
[e3f77d8b]	319
[51f14603]	320	def get_output(self):
	321	"""
	322	Return output
	323	"""
	324	return self.output
[e3f77d8b]	325
[51f14603]	326	def _check_data_length(self, length):
	327	"""
	328	Check if the data lengths are consistent
	329	:Params length: data length
	330	"""
[574adc7]	331	parts = (self.pos_x, self.pos_y, self.pos_z, self.mx, self.my, self.mz)
	332	if any(len(v) != length for v in parts):
	333	raise ValueError("Error: Inconsistent data length.")
[e3f77d8b]	334
[51f14603]	335	def remove_null_points(self, remove=False, recenter=False):
	336	"""
	337	Removes any mx, my, and mz = 0 points
	338	"""
	339	if remove:
[9a5097c]	340	is_nonzero = (np.fabs(self.mx) + np.fabs(self.my) +
	341	np.fabs(self.mz)).nonzero()
[e3f77d8b]	342	if len(is_nonzero[0]) > 0:
[51f14603]	343	self.pos_x = self.pos_x[is_nonzero]
	344	self.pos_y = self.pos_y[is_nonzero]
	345	self.pos_z = self.pos_z[is_nonzero]
	346	self.sld_n = self.sld_n[is_nonzero]
	347	self.mx = self.mx[is_nonzero]
	348	self.my = self.my[is_nonzero]
	349	self.mz = self.mz[is_nonzero]
	350	if recenter:
	351	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
	352	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
	353	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
[e3f77d8b]	354
[51f14603]	355	def get_magsld(self):
	356	"""
	357	return MagSLD
	358	"""
	359	return self.output
[e3f77d8b]	360
	361
	362	class OMFReader(object):
[51f14603]	363	"""
	364	Class to load omf/ascii files (3 columns w/header).
	365	"""
	366	## File type
	367	type_name = "OMF ASCII"
[e3f77d8b]	368
[51f14603]	369	## Wildcards
	370	type = ["OMF files (.OMF, .omf)\|*.omf"]
	371	## List of allowed extensions
	372	ext = ['.omf', '.OMF']
[e3f77d8b]	373
[51f14603]	374	def read(self, path):
	375	"""
	376	Load data file
	377	:param path: file path
	378	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	379	"""
	380	desc = ""
[9a5097c]	381	mx = np.zeros(0)
	382	my = np.zeros(0)
	383	mz = np.zeros(0)
[51f14603]	384	try:
	385	input_f = open(path, 'rb')
[1d014cb]	386	buff = decode(input_f.read())
[51f14603]	387	lines = buff.split('\n')
	388	input_f.close()
	389	output = OMFData()
	390	valueunit = None
	391	for line in lines:
[1d014cb]	392	line = line.strip()
[51f14603]	393	# Read data
[1d014cb]	394	if line and not line.startswith('#'):
	395	try:
	396	toks = line.split()
	397	_mx = float(toks[0])
	398	_my = float(toks[1])
	399	_mz = float(toks[2])
	400	_mx = mag2sld(_mx, valueunit)
	401	_my = mag2sld(_my, valueunit)
	402	_mz = mag2sld(_mz, valueunit)
	403	mx = np.append(mx, _mx)
	404	my = np.append(my, _my)
	405	mz = np.append(mz, _mz)
	406	except Exception as exc:
	407	# Skip non-data lines
	408	logger.error(str(exc)+" when processing %r"%line)
[51f14603]	409	#Reading Header; Segment count ignored
	410	s_line = line.split(":", 1)
	411	if s_line[0].lower().count("oommf") > 0:
	412	oommf = s_line[1].lstrip()
	413	if s_line[0].lower().count("title") > 0:
	414	title = s_line[1].lstrip()
	415	if s_line[0].lower().count("desc") > 0:
	416	desc += s_line[1].lstrip()
	417	desc += '\n'
	418	if s_line[0].lower().count("meshtype") > 0:
	419	meshtype = s_line[1].lstrip()
	420	if s_line[0].lower().count("meshunit") > 0:
	421	meshunit = s_line[1].lstrip()
	422	if meshunit.count("m") < 1:
	423	msg = "Error: \n"
	424	msg += "We accept only m as meshunit"
[574adc7]	425	raise ValueError(msg)
[51f14603]	426	if s_line[0].lower().count("xbase") > 0:
	427	xbase = s_line[1].lstrip()
	428	if s_line[0].lower().count("ybase") > 0:
	429	ybase = s_line[1].lstrip()
	430	if s_line[0].lower().count("zbase") > 0:
	431	zbase = s_line[1].lstrip()
	432	if s_line[0].lower().count("xstepsize") > 0:
	433	xstepsize = s_line[1].lstrip()
	434	if s_line[0].lower().count("ystepsize") > 0:
	435	ystepsize = s_line[1].lstrip()
	436	if s_line[0].lower().count("zstepsize") > 0:
	437	zstepsize = s_line[1].lstrip()
	438	if s_line[0].lower().count("xnodes") > 0:
	439	xnodes = s_line[1].lstrip()
	440	if s_line[0].lower().count("ynodes") > 0:
	441	ynodes = s_line[1].lstrip()
	442	if s_line[0].lower().count("znodes") > 0:
	443	znodes = s_line[1].lstrip()
	444	if s_line[0].lower().count("xmin") > 0:
	445	xmin = s_line[1].lstrip()
	446	if s_line[0].lower().count("ymin") > 0:
	447	ymin = s_line[1].lstrip()
	448	if s_line[0].lower().count("zmin") > 0:
	449	zmin = s_line[1].lstrip()
	450	if s_line[0].lower().count("xmax") > 0:
	451	xmax = s_line[1].lstrip()
	452	if s_line[0].lower().count("ymax") > 0:
	453	ymax = s_line[1].lstrip()
	454	if s_line[0].lower().count("zmax") > 0:
	455	zmax = s_line[1].lstrip()
	456	if s_line[0].lower().count("valueunit") > 0:
	457	valueunit = s_line[1].lstrip().rstrip()
	458	if s_line[0].lower().count("valuemultiplier") > 0:
	459	valuemultiplier = s_line[1].lstrip()
	460	if s_line[0].lower().count("valuerangeminmag") > 0:
	461	valuerangeminmag = s_line[1].lstrip()
	462	if s_line[0].lower().count("valuerangemaxmag") > 0:
	463	valuerangemaxmag = s_line[1].lstrip()
	464	if s_line[0].lower().count("end") > 0:
	465	output.filename = os.path.basename(path)
	466	output.oommf = oommf
	467	output.title = title
	468	output.desc = desc
	469	output.meshtype = meshtype
	470	output.xbase = float(xbase) * METER2ANG
	471	output.ybase = float(ybase) * METER2ANG
	472	output.zbase = float(zbase) * METER2ANG
	473	output.xstepsize = float(xstepsize) * METER2ANG
	474	output.ystepsize = float(ystepsize) * METER2ANG
	475	output.zstepsize = float(zstepsize) * METER2ANG
	476	output.xnodes = float(xnodes)
	477	output.ynodes = float(ynodes)
	478	output.znodes = float(znodes)
	479	output.xmin = float(xmin) * METER2ANG
	480	output.ymin = float(ymin) * METER2ANG
	481	output.zmin = float(zmin) * METER2ANG
	482	output.xmax = float(xmax) * METER2ANG
	483	output.ymax = float(ymax) * METER2ANG
	484	output.zmax = float(zmax) * METER2ANG
	485	output.valuemultiplier = valuemultiplier
	486	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
	487	valueunit)
	488	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
	489	valueunit)
	490	output.set_m(mx, my, mz)
	491	return output
[1d014cb]	492	except Exception:
[51f14603]	493	msg = "%s is not supported: \n" % path
	494	msg += "We accept only Text format OMF file."
[574adc7]	495	raise RuntimeError(msg)
[51f14603]	496
[e3f77d8b]	497	class PDBReader(object):
[51f14603]	498	"""
	499	PDB reader class: limited for reading the lines starting with 'ATOM'
	500	"""
	501	type_name = "PDB"
	502	## Wildcards
	503	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
	504	## List of allowed extensions
[e3f77d8b]	505	ext = ['.pdb', '.PDB']
	506
[51f14603]	507	def read(self, path):
	508	"""
	509	Load data file
[e3f77d8b]	510
[51f14603]	511	:param path: file path
	512	:return: MagSLD
	513	:raise RuntimeError: when the file can't be opened
	514	"""
[9a5097c]	515	pos_x = np.zeros(0)
	516	pos_y = np.zeros(0)
	517	pos_z = np.zeros(0)
	518	sld_n = np.zeros(0)
	519	sld_mx = np.zeros(0)
	520	sld_my = np.zeros(0)
	521	sld_mz = np.zeros(0)
	522	vol_pix = np.zeros(0)
	523	pix_symbol = np.zeros(0)
[51f14603]	524	x_line = []
	525	y_line = []
	526	z_line = []
	527	x_lines = []
	528	y_lines = []
[e3f77d8b]	529	z_lines = []
[51f14603]	530	try:
	531	input_f = open(path, 'rb')
[1d014cb]	532	buff = decode(input_f.read())
[51f14603]	533	lines = buff.split('\n')
	534	input_f.close()
	535	num = 0
	536	for line in lines:
	537	try:
	538	# check if line starts with "ATOM"
	539	if line[0:6].strip().count('ATM') > 0 or \
	540	line[0:6].strip() == 'ATOM':
	541	# define fields of interest
	542	atom_name = line[12:16].strip()
	543	try:
	544	float(line[12])
	545	atom_name = atom_name[1].upper()
[1d014cb]	546	except Exception:
[51f14603]	547	if len(atom_name) == 4:
	548	atom_name = atom_name[0].upper()
[e3f77d8b]	549	elif line[12] != ' ':
[51f14603]	550	atom_name = atom_name[0].upper() + \
[e3f77d8b]	551	atom_name[1].lower()
[51f14603]	552	else:
	553	atom_name = atom_name[0].upper()
	554	_pos_x = float(line[30:38].strip())
	555	_pos_y = float(line[38:46].strip())
	556	_pos_z = float(line[46:54].strip())
[9a5097c]	557	pos_x = np.append(pos_x, _pos_x)
	558	pos_y = np.append(pos_y, _pos_y)
	559	pos_z = np.append(pos_z, _pos_z)
[51f14603]	560	try:
	561	val = nsf.neutron_sld(atom_name)[0]
	562	# sld in Ang^-2 unit
	563	val *= 1.0e-6
[9a5097c]	564	sld_n = np.append(sld_n, val)
[51f14603]	565	atom = formula(atom_name)
	566	# cm to A units
	567	vol = 1.0e+24 * atom.mass / atom.density / NA
[9a5097c]	568	vol_pix = np.append(vol_pix, vol)
[1d014cb]	569	except Exception:
[b58265c3]	570	logger.error("Error: set the sld of %s to zero"% atom_name)
[9a5097c]	571	sld_n = np.append(sld_n, 0.0)
	572	sld_mx = np.append(sld_mx, 0)
	573	sld_my = np.append(sld_my, 0)
	574	sld_mz = np.append(sld_mz, 0)
	575	pix_symbol = np.append(pix_symbol, atom_name)
[e3f77d8b]	576	elif line[0:6].strip().count('CONECT') > 0:
[51f14603]	577	toks = line.split()
[e3f77d8b]	578	num = int(toks[1]) - 1
	579	val_list = []
[51f14603]	580	for val in toks[2:]:
	581	try:
	582	int_val = int(val)
[1d014cb]	583	except Exception:
[51f14603]	584	break
	585	if int_val == 0:
	586	break
	587	val_list.append(int_val)
[e3f77d8b]	588	#need val_list ordered
[51f14603]	589	for val in val_list:
	590	index = val - 1
	591	if (pos_x[index], pos_x[num]) in x_line and \
	592	(pos_y[index], pos_y[num]) in y_line and \
	593	(pos_z[index], pos_z[num]) in z_line:
	594	continue
	595	x_line.append((pos_x[num], pos_x[index]))
	596	y_line.append((pos_y[num], pos_y[index]))
	597	z_line.append((pos_z[num], pos_z[index]))
	598	if len(x_line) > 0:
[e3f77d8b]	599	x_lines.append(x_line)
[51f14603]	600	y_lines.append(y_line)
[e3f77d8b]	601	z_lines.append(z_line)
[1d014cb]	602	except Exception:
[c155a16]	603	logger.error(sys.exc_value)
[e3f77d8b]	604
[51f14603]	605	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
	606	output.set_conect_lines(x_line, y_line, z_line)
	607	output.filename = os.path.basename(path)
	608	output.set_pix_type('atom')
	609	output.set_pixel_symbols(pix_symbol)
	610	output.set_nodes()
	611	output.set_pixel_volumes(vol_pix)
	612	output.sld_unit = '1/A^(2)'
	613	return output
[1d014cb]	614	except Exception:
[574adc7]	615	raise RuntimeError("%s is not a sld file" % path)
[51f14603]	616
	617	def write(self, path, data):
	618	"""
	619	Write
	620	"""
[9c3d784]	621	print("Not implemented... ")
[51f14603]	622
[e3f77d8b]	623	class SLDReader(object):
[51f14603]	624	"""
	625	Class to load ascii files (7 columns).
	626	"""
	627	## File type
	628	type_name = "SLD ASCII"
	629	## Wildcards
	630	type = ["sld files (.SLD, .sld)\|*.sld",
	631	"txt files (.TXT, .txt)\|*.txt",
	632	"all files (.)\|."]
	633	## List of allowed extensions
	634	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
	635	def read(self, path):
	636	"""
	637	Load data file
	638	:param path: file path
	639	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	640	:raise RuntimeError: when the file can't be opened
	641	:raise ValueError: when the length of the data vectors are inconsistent
	642	"""
	643	try:
[9a5097c]	644	pos_x = np.zeros(0)
	645	pos_y = np.zeros(0)
	646	pos_z = np.zeros(0)
	647	sld_n = np.zeros(0)
	648	sld_mx = np.zeros(0)
	649	sld_my = np.zeros(0)
	650	sld_mz = np.zeros(0)
[51f14603]	651	try:
	652	# Use numpy to speed up loading
[9a5097c]	653	input_f = np.loadtxt(path, dtype='float', skiprows=1,
[51f14603]	654	ndmin=1, unpack=True)
[9a5097c]	655	pos_x = np.array(input_f[0])
	656	pos_y = np.array(input_f[1])
	657	pos_z = np.array(input_f[2])
	658	sld_n = np.array(input_f[3])
	659	sld_mx = np.array(input_f[4])
	660	sld_my = np.array(input_f[5])
	661	sld_mz = np.array(input_f[6])
[51f14603]	662	ncols = len(input_f)
	663	if ncols == 8:
[9a5097c]	664	vol_pix = np.array(input_f[7])
[51f14603]	665	elif ncols == 7:
[e3f77d8b]	666	vol_pix = None
[1d014cb]	667	except Exception:
[51f14603]	668	# For older version of numpy
	669	input_f = open(path, 'rb')
[1d014cb]	670	buff = decode(input_f.read())
[51f14603]	671	lines = buff.split('\n')
	672	input_f.close()
	673	for line in lines:
	674	toks = line.split()
	675	try:
	676	_pos_x = float(toks[0])
	677	_pos_y = float(toks[1])
	678	_pos_z = float(toks[2])
	679	_sld_n = float(toks[3])
	680	_sld_mx = float(toks[4])
	681	_sld_my = float(toks[5])
	682	_sld_mz = float(toks[6])
[9a5097c]	683	pos_x = np.append(pos_x, _pos_x)
	684	pos_y = np.append(pos_y, _pos_y)
	685	pos_z = np.append(pos_z, _pos_z)
	686	sld_n = np.append(sld_n, _sld_n)
	687	sld_mx = np.append(sld_mx, _sld_mx)
	688	sld_my = np.append(sld_my, _sld_my)
	689	sld_mz = np.append(sld_mz, _sld_mz)
[51f14603]	690	try:
[e3f77d8b]	691	_vol_pix = float(toks[7])
[9a5097c]	692	vol_pix = np.append(vol_pix, _vol_pix)
[1d014cb]	693	except Exception:
[51f14603]	694	vol_pix = None
[1d014cb]	695	except Exception:
[51f14603]	696	# Skip non-data lines
[c155a16]	697	logger.error(sys.exc_value)
[e3f77d8b]	698	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
[51f14603]	699	sld_mx, sld_my, sld_mz)
	700	output.filename = os.path.basename(path)
	701	output.set_pix_type('pixel')
	702	output.set_pixel_symbols('pixel')
[7432acb]	703	if vol_pix is not None:
[51f14603]	704	output.set_pixel_volumes(vol_pix)
	705	return output
[1d014cb]	706	except Exception:
[574adc7]	707	raise RuntimeError("%s is not a sld file" % path)
[e3f77d8b]	708
[51f14603]	709	def write(self, path, data):
	710	"""
	711	Write sld file
[e3f77d8b]	712	:Param path: file path
[51f14603]	713	:Param data: MagSLD data object
	714	"""
[235f514]	715	if path is None:
[574adc7]	716	raise ValueError("Missing the file path.")
[235f514]	717	if data is None:
[574adc7]	718	raise ValueError("Missing the data to save.")
[51f14603]	719	x_val = data.pos_x
	720	y_val = data.pos_y
	721	z_val = data.pos_z
	722	vol_pix = data.vol_pix
	723	length = len(x_val)
	724	sld_n = data.sld_n
[235f514]	725	if sld_n is None:
[9a5097c]	726	sld_n = np.zeros(length)
[51f14603]	727	sld_mx = data.sld_mx
[235f514]	728	if sld_mx is None:
[9a5097c]	729	sld_mx = np.zeros(length)
	730	sld_my = np.zeros(length)
	731	sld_mz = np.zeros(length)
[51f14603]	732	else:
	733	sld_my = data.sld_my
	734	sld_mz = data.sld_mz
	735	out = open(path, 'w')
	736	# First Line: Column names
	737	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
	738	for ind in range(length):
[e3f77d8b]	739	out.write("\n%g %g %g %g %g %g %g %g" % \
	740	(x_val[ind], y_val[ind], z_val[ind], sld_n[ind],
	741	sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind]))
	742	out.close()
	743
	744
	745	class OMFData(object):
[51f14603]	746	"""
	747	OMF Data.
	748	"""
	749	_meshunit = "A"
	750	_valueunit = "A^(-2)"
	751	def __init__(self):
	752	"""
	753	Init for mag SLD
	754	"""
	755	self.filename = 'default'
	756	self.oommf = ''
	757	self.title = ''
	758	self.desc = ''
	759	self.meshtype = ''
	760	self.meshunit = self._meshunit
	761	self.valueunit = self._valueunit
	762	self.xbase = 0.0
	763	self.ybase = 0.0
	764	self.zbase = 0.0
	765	self.xstepsize = 6.0
	766	self.ystepsize = 6.0
	767	self.zstepsize = 6.0
	768	self.xnodes = 10.0
	769	self.ynodes = 10.0
	770	self.znodes = 10.0
	771	self.xmin = 0.0
	772	self.ymin = 0.0
	773	self.zmin = 0.0
	774	self.xmax = 60.0
	775	self.ymax = 60.0
	776	self.zmax = 60.0
	777	self.mx = None
	778	self.my = None
	779	self.mz = None
	780	self.valuemultiplier = 1.
	781	self.valuerangeminmag = 0
	782	self.valuerangemaxmag = 0
[e3f77d8b]	783
[51f14603]	784	def __str__(self):
	785	"""
	786	doc strings
	787	"""
[e3f77d8b]	788	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	789	_str += "File: %s\n" % self.filename
	790	_str += "OOMMF: %s\n" % self.oommf
	791	_str += "Title: %s\n" % self.title
	792	_str += "Desc: %s\n" % self.desc
	793	_str += "meshtype: %s\n" % self.meshtype
	794	_str += "meshunit: %s\n" % str(self.meshunit)
	795	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
	796	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
	797	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
[e3f77d8b]	798	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
[51f14603]	799	self.meshunit)
[e3f77d8b]	800	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
[51f14603]	801	self.meshunit)
[e3f77d8b]	802	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
[51f14603]	803	self.meshunit)
	804	_str += "xnodes: %s\n" % str(self.xnodes)
	805	_str += "ynodes: %s\n" % str(self.ynodes)
	806	_str += "znodes: %s\n" % str(self.znodes)
	807	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
	808	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
	809	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
	810	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
	811	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
	812	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
	813	_str += "valueunit: %s\n" % self.valueunit
	814	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
[e3f77d8b]	815	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
	816	self.valueunit)
	817	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
	818	self.valueunit)
[51f14603]	819	return _str
[e3f77d8b]	820
[51f14603]	821	def set_m(self, mx, my, mz):
	822	"""
	823	Set the Mx, My, Mz values
	824	"""
	825	self.mx = mx
	826	self.my = my
	827	self.mz = mz
[e3f77d8b]	828
	829	class MagSLD(object):
[51f14603]	830	"""
	831	Magnetic SLD.
	832	"""
	833	pos_x = None
	834	pos_y = None
	835	pos_z = None
	836	sld_n = None
	837	sld_mx = None
	838	sld_my = None
	839	sld_mz = None
	840	# Units
	841	_pos_unit = 'A'
	842	_sld_unit = '1/A^(2)'
	843	_pix_type = 'pixel'
[e3f77d8b]	844
	845	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
[51f14603]	846	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
	847	"""
	848	Init for mag SLD
	849	:params : All should be numpy 1D array
	850	"""
	851	self.is_data = True
	852	self.filename = ''
	853	self.xstepsize = 6.0
	854	self.ystepsize = 6.0
	855	self.zstepsize = 6.0
	856	self.xnodes = 10.0
	857	self.ynodes = 10.0
	858	self.znodes = 10.0
	859	self.has_stepsize = False
	860	self.has_conect = False
	861	self.pos_unit = self._pos_unit
	862	self.sld_unit = self._sld_unit
	863	self.pix_type = 'pixel'
	864	self.pos_x = pos_x
	865	self.pos_y = pos_y
	866	self.pos_z = pos_z
	867	self.sld_n = sld_n
	868	self.line_x = None
	869	self.line_y = None
	870	self.line_z = None
	871	self.sld_mx = sld_mx
	872	self.sld_my = sld_my
	873	self.sld_mz = sld_mz
	874	self.vol_pix = vol_pix
	875	self.sld_m = None
	876	self.sld_phi = None
	877	self.sld_theta = None
	878	self.pix_symbol = None
[7432acb]	879	if sld_mx is not None and sld_my is not None and sld_mz is not None:
[51f14603]	880	self.set_sldms(sld_mx, sld_my, sld_mz)
	881	self.set_nodes()
[e3f77d8b]	882
[51f14603]	883	def __str__(self):
	884	"""
	885	doc strings
	886	"""
[e3f77d8b]	887	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	888	_str += "File: %s\n" % self.filename
	889	_str += "Axis_unit: %s\n" % self.pos_unit
	890	_str += "SLD_unit: %s\n" % self.sld_unit
	891	return _str
[e3f77d8b]	892
[51f14603]	893	def set_pix_type(self, pix_type):
	894	"""
	895	Set pixel type
	896	:Param pix_type: string, 'pixel' or 'atom'
	897	"""
	898	self.pix_type = pix_type
[e3f77d8b]	899
[51f14603]	900	def set_sldn(self, sld_n):
	901	"""
	902	Sets neutron SLD
	903	"""
	904	if sld_n.__class__.__name__ == 'float':
	905	if self.is_data:
[e3f77d8b]	906	# For data, put the value to only the pixels w non-zero M
[9a5097c]	907	is_nonzero = (np.fabs(self.sld_mx) +
	908	np.fabs(self.sld_my) +
	909	np.fabs(self.sld_mz)).nonzero()
	910	self.sld_n = np.zeros(len(self.pos_x))
[51f14603]	911	if len(self.sld_n[is_nonzero]) > 0:
	912	self.sld_n[is_nonzero] = sld_n
	913	else:
	914	self.sld_n.fill(sld_n)
	915	else:
	916	# For non-data, put the value to all the pixels
[9a5097c]	917	self.sld_n = np.ones(len(self.pos_x)) * sld_n
[51f14603]	918	else:
	919	self.sld_n = sld_n
[e3f77d8b]	920
[51f14603]	921	def set_sldms(self, sld_mx, sld_my, sld_mz):
[ac7be54]	922	r"""
[5ed76f8]	923	Sets mx, my, mz and abs(m).
	924	""" # Note: escaping
[51f14603]	925	if sld_mx.__class__.__name__ == 'float':
[9a5097c]	926	self.sld_mx = np.ones(len(self.pos_x)) * sld_mx
[51f14603]	927	else:
	928	self.sld_mx = sld_mx
	929	if sld_my.__class__.__name__ == 'float':
[9a5097c]	930	self.sld_my = np.ones(len(self.pos_x)) * sld_my
[51f14603]	931	else:
	932	self.sld_my = sld_my
	933	if sld_mz.__class__.__name__ == 'float':
[9a5097c]	934	self.sld_mz = np.ones(len(self.pos_x)) * sld_mz
[51f14603]	935	else:
	936	self.sld_mz = sld_mz
	937
[9a5097c]	938	sld_m = np.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
[e3f77d8b]	939	sld_mz * sld_mz)
[51f14603]	940	self.sld_m = sld_m
[e3f77d8b]	941
	942	def set_pixel_symbols(self, symbol='pixel'):
[51f14603]	943	"""
	944	Set pixel
	945	:Params pixel: str; pixel or atomic symbol, or array of strings
	946	"""
[235f514]	947	if self.sld_n is None:
[51f14603]	948	return
	949	if symbol.__class__.__name__ == 'str':
[9a5097c]	950	self.pix_symbol = np.repeat(symbol, len(self.sld_n))
[51f14603]	951	else:
	952	self.pix_symbol = symbol
[e3f77d8b]	953
	954	def set_pixel_volumes(self, vol):
[51f14603]	955	"""
	956	Set pixel volumes
	957	:Params pixel: str; pixel or atomic symbol, or array of strings
	958	"""
[235f514]	959	if self.sld_n is None:
[51f14603]	960	return
	961	if vol.__class__.__name__ == 'ndarray':
	962	self.vol_pix = vol
	963	elif vol.__class__.__name__.count('float') > 0:
[9a5097c]	964	self.vol_pix = np.repeat(vol, len(self.sld_n))
[51f14603]	965	else:
	966	self.vol_pix = None
	967
	968	def get_sldn(self):
	969	"""
	970	Returns nuclear sld
	971	"""
	972	return self.sld_n
[e3f77d8b]	973
[51f14603]	974	def set_nodes(self):
	975	"""
	976	Set xnodes, ynodes, and znodes
	977	"""
	978	self.set_stepsize()
	979	if self.pix_type == 'pixel':
	980	try:
	981	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
	982	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
	983	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
	984	self.xnodes = int(xdist) + 1
	985	self.ynodes = int(ydist) + 1
	986	self.znodes = int(zdist) + 1
[1d014cb]	987	except Exception:
[51f14603]	988	self.xnodes = None
	989	self.ynodes = None
	990	self.znodes = None
	991	else:
	992	self.xnodes = None
	993	self.ynodes = None
	994	self.znodes = None
[e3f77d8b]	995
[51f14603]	996	def set_stepsize(self):
	997	"""
	998	Set xtepsize, ystepsize, and zstepsize
	999	"""
	1000	if self.pix_type == 'pixel':
	1001	try:
	1002	xpos_pre = self.pos_x[0]
	1003	ypos_pre = self.pos_y[0]
	1004	zpos_pre = self.pos_z[0]
	1005	for x_pos in self.pos_x:
	1006	if xpos_pre != x_pos:
[9a5097c]	1007	self.xstepsize = np.fabs(x_pos - xpos_pre)
[51f14603]	1008	break
	1009	for y_pos in self.pos_y:
	1010	if ypos_pre != y_pos:
[9a5097c]	1011	self.ystepsize = np.fabs(y_pos - ypos_pre)
[51f14603]	1012	break
	1013	for z_pos in self.pos_z:
	1014	if zpos_pre != z_pos:
[9a5097c]	1015	self.zstepsize = np.fabs(z_pos - zpos_pre)
[51f14603]	1016	break
	1017	#default pix volume
[9a5097c]	1018	self.vol_pix = np.ones(len(self.pos_x))
[51f14603]	1019	vol = self.xstepsize * self.ystepsize * self.zstepsize
	1020	self.set_pixel_volumes(vol)
	1021	self.has_stepsize = True
[1d014cb]	1022	except Exception:
[51f14603]	1023	self.xstepsize = None
	1024	self.ystepsize = None
	1025	self.zstepsize = None
	1026	self.vol_pix = None
	1027	self.has_stepsize = False
	1028	else:
	1029	self.xstepsize = None
	1030	self.ystepsize = None
	1031	self.zstepsize = None
	1032	self.has_stepsize = True
	1033	return self.xstepsize, self.ystepsize, self.zstepsize
	1034
	1035	def set_conect_lines(self, line_x, line_y, line_z):
	1036	"""
	1037	Set bonding line data if taken from pdb
	1038	"""
	1039	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
	1040	return
	1041	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
	1042	return
	1043	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
	1044	return
	1045	self.has_conect = True
[e3f77d8b]	1046	self.line_x = line_x
	1047	self.line_y = line_y
[51f14603]	1048	self.line_z = line_z
	1049
[54b0650]	1050	def _get_data_path(*path_parts):
	1051	from os.path import realpath, join as joinpath, dirname, abspath
	1052	# in sas/sascalc/calculator; want sas/sasview/test
	1053	return joinpath(dirname(realpath(__file__)),
	1054	'..', '..', 'sasview', 'test', *path_parts)
	1055
[51f14603]	1056	def test_load():
[b6627d9]	1057	"""
	1058	Test code
	1059	"""
[06aaa75d]	1060	from mpl_toolkits.mplot3d import Axes3D
[54b0650]	1061	tfpath = _get_data_path("1d_data", "CoreXY_ShellZ.txt")
	1062	ofpath = _get_data_path("coordinate_data", "A_Raw_Example-1.omf")
	1063	if not os.path.isfile(tfpath) or not os.path.isfile(ofpath):
	1064	raise ValueError("file(s) not found: %r, %r"%(tfpath, ofpath))
[51f14603]	1065	reader = SLDReader()
	1066	oreader = OMFReader()
[f926abb]	1067	output = reader.read(tfpath)
	1068	ooutput = oreader.read(ofpath)
[51f14603]	1069	foutput = OMF2SLD()
	1070	foutput.set_data(ooutput)
	1071
	1072	import matplotlib.pyplot as plt
	1073	fig = plt.figure()
[06aaa75d]	1074	ax = Axes3D(fig)
[e3f77d8b]	1075	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
	1076	alpha=0.7, markeredgecolor='gray', rasterized=True)
[51f14603]	1077	gap = 7
	1078	max_mx = max(output.sld_mx)
	1079	max_my = max(output.sld_my)
	1080	max_mz = max(output.sld_mz)
[e3f77d8b]	1081	max_m = max(max_mx, max_my, max_mz)
[51f14603]	1082	x2 = output.pos_x+output.sld_mx/max_m * gap
	1083	y2 = output.pos_y+output.sld_my/max_m * gap
	1084	z2 = output.pos_z+output.sld_mz/max_m * gap
[9a5097c]	1085	x_arrow = np.column_stack((output.pos_x, x2))
	1086	y_arrow = np.column_stack((output.pos_y, y2))
	1087	z_arrow = np.column_stack((output.pos_z, z2))
[51f14603]	1088	unit_x2 = output.sld_mx / max_m
	1089	unit_y2 = output.sld_my / max_m
	1090	unit_z2 = output.sld_mz / max_m
[9a5097c]	1091	color_x = np.fabs(unit_x2 * 0.8)
	1092	color_y = np.fabs(unit_y2 * 0.8)
	1093	color_z = np.fabs(unit_z2 * 0.8)
	1094	colors = np.column_stack((color_x, color_y, color_z))
[51f14603]	1095	plt.show()
[b6627d9]	1096
[f926abb]	1097	def test_save():
	1098	ofpath = _get_data_path("coordinate_data", "A_Raw_Example-1.omf")
	1099	if not os.path.isfile(ofpath):
	1100	raise ValueError("file(s) not found: %r"%(ofpath,))
	1101	oreader = OMFReader()
	1102	omfdata = oreader.read(ofpath)
	1103	omf2sld = OMF2SLD()
	1104	omf2sld.set_data(omfdata)
	1105	writer = SLDReader()
	1106	writer.write("out.txt", omf2sld.output)
	1107
[51f14603]	1108	def test():
[b6627d9]	1109	"""
	1110	Test code
	1111	"""
[54b0650]	1112	ofpath = _get_data_path("coordinate_data", "A_Raw_Example-1.omf")
	1113	if not os.path.isfile(ofpath):
	1114	raise ValueError("file(s) not found: %r"%(ofpath,))
[51f14603]	1115	oreader = OMFReader()
[f926abb]	1116	omfdata = oreader.read(ofpath)
	1117	omf2sld = OMF2SLD()
	1118	omf2sld.set_data(omfdata)
[51f14603]	1119	model = GenSAS()
[f926abb]	1120	model.set_sld_data(omf2sld.output)
	1121	x = np.linspace(0, 0.1, 11)[1:]
[a1daf86]	1122	return model.runXY([x, x])
[e3f77d8b]	1123
	1124	if __name__ == "__main__":
[54b0650]	1125	#test_load()
[f926abb]	1126	#test_save()
[a1daf86]	1127	#print(test())
[51f14603]	1128	test()

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SasView

source: sasview/src/sas/sascalc/calculator/sas_gen.py @ afb311e

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