sas_gen.py @ 457f735

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Last change on this file since 457f735 was a1b8fee, checked in by andyfaff, 8 years ago
MAINT: from future import print_function
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	"""
[a1b8fee]	5	from __future__ import print_function
	6
[9e531f2]	7	import sas.sascalc.calculator.core.sld2i as mod
[d2fd8fc]	8	from sas.sascalc.calculator.BaseComponent import BaseComponent
[51f14603]	9	from periodictable import formula
	10	from periodictable import nsf
[9a5097c]	11	import numpy as np
[51f14603]	12	import os
	13	import copy
[b6627d9]	14	import sys
	15	import logging
[51f14603]	16
[463e7ffc]	17	logger = logging.getLogger(__name__)
[c155a16]	18
[e3f77d8b]	19	MFACTOR_AM = 2.853E-12
	20	MFACTOR_MT = 2.3164E-9
[51f14603]	21	METER2ANG = 1.0E+10
	22	#Avogadro constant [1/mol]
	23	NA = 6.02214129e+23
	24
	25	def mag2sld(mag, v_unit=None):
	26	"""
	27	Convert magnetization to magnatic SLD
	28	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
	29	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
[e3f77d8b]	30	"""
[51f14603]	31	if v_unit == "A/m":
[e3f77d8b]	32	factor = MFACTOR_AM
[51f14603]	33	elif v_unit == "mT":
[e3f77d8b]	34	factor = MFACTOR_MT
[51f14603]	35	else:
	36	raise ValueError, "Invalid valueunit"
	37	sld_m = factor * mag
	38	return sld_m
	39
	40	def transform_center(pos_x, pos_y, pos_z):
	41	"""
[e3f77d8b]	42	re-center
[51f14603]	43	:return: posx, posy, posz [arrays]
[e3f77d8b]	44	"""
[51f14603]	45	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
	46	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
[e3f77d8b]	47	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
	48	return posx, posy, posz
[51f14603]	49
	50	class GenSAS(BaseComponent):
	51	"""
	52	Generic SAS computation Model based on sld (n & m) arrays
	53	"""
	54	def __init__(self):
	55	"""
	56	Init
	57	:Params sld_data: MagSLD object
	58	"""
	59	# Initialize BaseComponent
	60	BaseComponent.__init__(self)
	61	self.sld_data = None
	62	self.data_pos_unit = None
	63	self.data_x = None
	64	self.data_y = None
	65	self.data_z = None
	66	self.data_sldn = None
	67	self.data_mx = None
	68	self.data_my = None
	69	self.data_mz = None
	70	self.data_vol = None #[A^3]
	71	self.is_avg = False
	72	## Name of the model
	73	self.name = "GenSAS"
	74	## Define parameters
	75	self.params = {}
[e3f77d8b]	76	self.params['scale'] = 1.0
	77	self.params['background'] = 0.0
	78	self.params['solvent_SLD'] = 0.0
[51f14603]	79	self.params['total_volume'] = 1.0
[e3f77d8b]	80	self.params['Up_frac_in'] = 1.0
	81	self.params['Up_frac_out'] = 1.0
	82	self.params['Up_theta'] = 0.0
[51f14603]	83	self.description = 'GenSAS'
	84	## Parameter details [units, min, max]
	85	self.details = {}
[9a5097c]	86	self.details['scale'] = ['', 0.0, np.inf]
	87	self.details['background'] = ['[1/cm]', 0.0, np.inf]
	88	self.details['solvent_SLD'] = ['1/A^(2)', -np.inf, np.inf]
	89	self.details['total_volume'] = ['A^(3)', 0.0, np.inf]
[cb4ef58]	90	self.details['Up_frac_in'] = ['[u/(u+d)]', 0.0, 1.0]
	91	self.details['Up_frac_out'] = ['[u/(u+d)]', 0.0, 1.0]
[9a5097c]	92	self.details['Up_theta'] = ['[deg]', -np.inf, np.inf]
[51f14603]	93	# fixed parameters
	94	self.fixed = []
[e3f77d8b]	95
	96	def set_pixel_volumes(self, volume):
[51f14603]	97	"""
	98	Set the volume of a pixel in (A^3) unit
	99	:Param volume: pixel volume [float]
	100	"""
[235f514]	101	if self.data_vol is None:
[51f14603]	102	raise
	103	self.data_vol = volume
[e3f77d8b]	104
	105	def set_is_avg(self, is_avg=False):
[51f14603]	106	"""
	107	Sets is_avg: [bool]
	108	"""
	109	self.is_avg = is_avg
[e3f77d8b]	110
[51f14603]	111	def _gen(self, x, y, i):
	112	"""
	113	Evaluate the function
	114	:Param x: array of x-values
	115	:Param y: array of y-values
[e3f77d8b]	116	:Param i: array of initial i-value
[51f14603]	117	:return: function value
	118	"""
	119	pos_x = self.data_x
	120	pos_y = self.data_y
	121	pos_z = self.data_z
	122	len_x = len(pos_x)
[235f514]	123	if self.is_avg is None:
[51f14603]	124	len_x *= -1
	125	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
	126	len_q = len(x)
	127	sldn = copy.deepcopy(self.data_sldn)
	128	sldn -= self.params['solvent_SLD']
[e3f77d8b]	129	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
	130	sldn, self.data_mx, self.data_my,
[51f14603]	131	self.data_mz, self.data_vol,
[e3f77d8b]	132	self.params['Up_frac_in'],
	133	self.params['Up_frac_out'],
[51f14603]	134	self.params['Up_theta'])
	135	if y == []:
	136	mod.genicom(model, len_q, x, i)
	137	else:
	138	mod.genicomXY(model, len_q, x, y, i)
	139	vol_correction = self.data_total_volume / self.params['total_volume']
	140	return self.params['scale'] * vol_correction * i + \
	141	self.params['background']
[e3f77d8b]	142
	143	def set_sld_data(self, sld_data=None):
[51f14603]	144	"""
	145	Sets sld_data
	146	"""
	147	self.sld_data = sld_data
	148	self.data_pos_unit = sld_data.pos_unit
	149	self.data_x = sld_data.pos_x
	150	self.data_y = sld_data.pos_y
	151	self.data_z = sld_data.pos_z
	152	self.data_sldn = sld_data.sld_n
	153	self.data_mx = sld_data.sld_mx
	154	self.data_my = sld_data.sld_my
	155	self.data_mz = sld_data.sld_mz
	156	self.data_vol = sld_data.vol_pix
	157	self.data_total_volume = sum(sld_data.vol_pix)
	158	self.params['total_volume'] = sum(sld_data.vol_pix)
[e3f77d8b]	159
[51f14603]	160	def getProfile(self):
	161	"""
[e3f77d8b]	162	Get SLD profile
[51f14603]	163	: return: sld_data
	164	"""
	165	return self.sld_data
[e3f77d8b]	166
	167	def run(self, x=0.0):
	168	"""
[51f14603]	169	Evaluate the model
	170	:param x: simple value
	171	:return: (I value)
	172	"""
	173	if x.__class__.__name__ == 'list':
	174	if len(x[1]) > 0:
	175	msg = "Not a 1D."
	176	raise ValueError, msg
[9a5097c]	177	i_out = np.zeros_like(x[0])
[51f14603]	178	# 1D I is found at y =0 in the 2D pattern
[e3f77d8b]	179	out = self._gen(x[0], [], i_out)
[51f14603]	180	return out
	181	else:
	182	msg = "Q must be given as list of qx's and qy's"
	183	raise ValueError, msg
[e3f77d8b]	184
	185	def runXY(self, x=0.0):
	186	"""
[51f14603]	187	Evaluate the model
	188	:param x: simple value
	189	:return: I value
	190	:Use this runXY() for the computation
	191	"""
	192	if x.__class__.__name__ == 'list':
[9a5097c]	193	i_out = np.zeros_like(x[0])
[51f14603]	194	out = self._gen(x[0], x[1], i_out)
	195	return out
	196	else:
	197	msg = "Q must be given as list of qx's and qy's"
	198	raise ValueError, msg
[e3f77d8b]	199
[51f14603]	200	def evalDistribution(self, qdist):
	201	"""
	202	Evaluate a distribution of q-values.
[ac7be54]	203
	204	:param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy]
	205	where qx,qy are 1D ndarrays (for 2D).
[51f14603]	206	"""
	207	if qdist.__class__.__name__ == 'list':
	208	if len(qdist[1]) < 1:
	209	out = self.run(qdist)
	210	else:
	211	out = self.runXY(qdist)
	212	return out
	213	else:
	214	mesg = "evalDistribution is expecting an ndarray of "
	215	mesg += "a list [qx,qy] where qx,qy are arrays."
	216	raise RuntimeError, mesg
[e3f77d8b]	217
	218	class OMF2SLD(object):
[51f14603]	219	"""
	220	Convert OMFData to MAgData
	221	"""
[e3f77d8b]	222	def __init__(self):
[51f14603]	223	"""
	224	Init
	225	"""
	226	self.pos_x = None
	227	self.pos_y = None
	228	self.pos_z = None
	229	self.mx = None
	230	self.my = None
	231	self.mz = None
	232	self.sld_n = None
	233	self.vol_pix = None
	234	self.output = None
	235	self.omfdata = None
[e3f77d8b]	236
[51f14603]	237	def set_data(self, omfdata, shape='rectangular'):
	238	"""
	239	Set all data
	240	"""
	241	self.omfdata = omfdata
	242	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
[9a5097c]	243	pos_x = np.arange(omfdata.xmin,
[e3f77d8b]	244	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
[51f14603]	245	omfdata.xstepsize)
[9a5097c]	246	pos_y = np.arange(omfdata.ymin,
[e3f77d8b]	247	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
[51f14603]	248	omfdata.ystepsize)
[9a5097c]	249	pos_z = np.arange(omfdata.zmin,
[e3f77d8b]	250	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
[51f14603]	251	omfdata.zstepsize)
[9a5097c]	252	self.pos_x = np.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
[51f14603]	253	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
[9a5097c]	254	self.pos_y = np.tile(self.pos_y, int(omfdata.znodes))
[51f14603]	255	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
	256	self.mx = omfdata.mx
	257	self.my = omfdata.my
	258	self.mz = omfdata.mz
[9a5097c]	259	self.sld_n = np.zeros(length)
[e3f77d8b]	260
[235f514]	261	if omfdata.mx is None:
[9a5097c]	262	self.mx = np.zeros(length)
[235f514]	263	if omfdata.my is None:
[9a5097c]	264	self.my = np.zeros(length)
[235f514]	265	if omfdata.mz is None:
[9a5097c]	266	self.mz = np.zeros(length)
[e3f77d8b]	267
[51f14603]	268	self._check_data_length(length)
	269	self.remove_null_points(False, False)
[9a5097c]	270	mask = np.ones(len(self.sld_n), dtype=bool)
[51f14603]	271	if shape.lower() == 'ellipsoid':
	272	try:
	273	# Pixel (step) size included
	274	x_c = max(self.pos_x) + min(self.pos_x)
	275	y_c = max(self.pos_y) + min(self.pos_y)
	276	z_c = max(self.pos_z) + min(self.pos_z)
	277	x_d = max(self.pos_x) - min(self.pos_x)
	278	y_d = max(self.pos_y) - min(self.pos_y)
	279	z_d = max(self.pos_z) - min(self.pos_z)
	280	x_r = (x_d + omfdata.xstepsize) / 2.0
	281	y_r = (y_d + omfdata.ystepsize) / 2.0
	282	z_r = (z_d + omfdata.zstepsize) / 2.0
	283	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
	284	x_dir2 *= x_dir2
	285	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
	286	y_dir2 *= y_dir2
	287	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
	288	z_dir2 *= z_dir2
	289	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
	290	except:
[c155a16]	291	logger.error(sys.exc_value)
[e3f77d8b]	292	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
	293	self.pos_z[mask], self.sld_n[mask],
[51f14603]	294	self.mx[mask], self.my[mask], self.mz[mask])
	295	self.output.set_pix_type('pixel')
	296	self.output.set_pixel_symbols('pixel')
[e3f77d8b]	297
[51f14603]	298	def get_omfdata(self):
	299	"""
	300	Return all data
	301	"""
	302	return self.omfdata
[e3f77d8b]	303
[51f14603]	304	def get_output(self):
	305	"""
	306	Return output
	307	"""
	308	return self.output
[e3f77d8b]	309
[51f14603]	310	def _check_data_length(self, length):
	311	"""
	312	Check if the data lengths are consistent
	313	:Params length: data length
	314	"""
	315	msg = "Error: Inconsistent data length."
	316	if len(self.pos_x) != length:
	317	raise ValueError, msg
	318	if len(self.pos_y) != length:
	319	raise ValueError, msg
	320	if len(self.pos_z) != length:
	321	raise ValueError, msg
	322	if len(self.mx) != length:
	323	raise ValueError, msg
	324	if len(self.my) != length:
	325	raise ValueError, msg
	326	if len(self.mz) != length:
	327	raise ValueError, msg
[e3f77d8b]	328
[51f14603]	329	def remove_null_points(self, remove=False, recenter=False):
	330	"""
	331	Removes any mx, my, and mz = 0 points
	332	"""
	333	if remove:
[9a5097c]	334	is_nonzero = (np.fabs(self.mx) + np.fabs(self.my) +
	335	np.fabs(self.mz)).nonzero()
[e3f77d8b]	336	if len(is_nonzero[0]) > 0:
[51f14603]	337	self.pos_x = self.pos_x[is_nonzero]
	338	self.pos_y = self.pos_y[is_nonzero]
	339	self.pos_z = self.pos_z[is_nonzero]
	340	self.sld_n = self.sld_n[is_nonzero]
	341	self.mx = self.mx[is_nonzero]
	342	self.my = self.my[is_nonzero]
	343	self.mz = self.mz[is_nonzero]
	344	if recenter:
	345	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
	346	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
	347	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
[e3f77d8b]	348
[51f14603]	349	def get_magsld(self):
	350	"""
	351	return MagSLD
	352	"""
	353	return self.output
[e3f77d8b]	354
	355
	356	class OMFReader(object):
[51f14603]	357	"""
	358	Class to load omf/ascii files (3 columns w/header).
	359	"""
	360	## File type
	361	type_name = "OMF ASCII"
[e3f77d8b]	362
[51f14603]	363	## Wildcards
	364	type = ["OMF files (.OMF, .omf)\|*.omf"]
	365	## List of allowed extensions
	366	ext = ['.omf', '.OMF']
[e3f77d8b]	367
[51f14603]	368	def read(self, path):
	369	"""
	370	Load data file
	371	:param path: file path
	372	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	373	"""
	374	desc = ""
[9a5097c]	375	mx = np.zeros(0)
	376	my = np.zeros(0)
	377	mz = np.zeros(0)
[51f14603]	378	try:
	379	input_f = open(path, 'rb')
	380	buff = input_f.read()
	381	lines = buff.split('\n')
	382	input_f.close()
	383	output = OMFData()
	384	valueunit = None
	385	for line in lines:
	386	toks = line.split()
	387	# Read data
	388	try:
	389	_mx = float(toks[0])
	390	_my = float(toks[1])
	391	_mz = float(toks[2])
	392	_mx = mag2sld(_mx, valueunit)
	393	_my = mag2sld(_my, valueunit)
	394	_mz = mag2sld(_mz, valueunit)
[9a5097c]	395	mx = np.append(mx, _mx)
	396	my = np.append(my, _my)
	397	mz = np.append(mz, _mz)
[51f14603]	398	except:
	399	# Skip non-data lines
[c155a16]	400	logger.error(sys.exc_value)
[51f14603]	401	#Reading Header; Segment count ignored
	402	s_line = line.split(":", 1)
	403	if s_line[0].lower().count("oommf") > 0:
	404	oommf = s_line[1].lstrip()
	405	if s_line[0].lower().count("title") > 0:
	406	title = s_line[1].lstrip()
	407	if s_line[0].lower().count("desc") > 0:
	408	desc += s_line[1].lstrip()
	409	desc += '\n'
	410	if s_line[0].lower().count("meshtype") > 0:
	411	meshtype = s_line[1].lstrip()
	412	if s_line[0].lower().count("meshunit") > 0:
	413	meshunit = s_line[1].lstrip()
	414	if meshunit.count("m") < 1:
	415	msg = "Error: \n"
	416	msg += "We accept only m as meshunit"
	417	raise ValueError, msg
	418	if s_line[0].lower().count("xbase") > 0:
	419	xbase = s_line[1].lstrip()
	420	if s_line[0].lower().count("ybase") > 0:
	421	ybase = s_line[1].lstrip()
	422	if s_line[0].lower().count("zbase") > 0:
	423	zbase = s_line[1].lstrip()
	424	if s_line[0].lower().count("xstepsize") > 0:
	425	xstepsize = s_line[1].lstrip()
	426	if s_line[0].lower().count("ystepsize") > 0:
	427	ystepsize = s_line[1].lstrip()
	428	if s_line[0].lower().count("zstepsize") > 0:
	429	zstepsize = s_line[1].lstrip()
	430	if s_line[0].lower().count("xnodes") > 0:
	431	xnodes = s_line[1].lstrip()
	432	if s_line[0].lower().count("ynodes") > 0:
	433	ynodes = s_line[1].lstrip()
	434	if s_line[0].lower().count("znodes") > 0:
	435	znodes = s_line[1].lstrip()
	436	if s_line[0].lower().count("xmin") > 0:
	437	xmin = s_line[1].lstrip()
	438	if s_line[0].lower().count("ymin") > 0:
	439	ymin = s_line[1].lstrip()
	440	if s_line[0].lower().count("zmin") > 0:
	441	zmin = s_line[1].lstrip()
	442	if s_line[0].lower().count("xmax") > 0:
	443	xmax = s_line[1].lstrip()
	444	if s_line[0].lower().count("ymax") > 0:
	445	ymax = s_line[1].lstrip()
	446	if s_line[0].lower().count("zmax") > 0:
	447	zmax = s_line[1].lstrip()
	448	if s_line[0].lower().count("valueunit") > 0:
	449	valueunit = s_line[1].lstrip().rstrip()
	450	if s_line[0].lower().count("valuemultiplier") > 0:
	451	valuemultiplier = s_line[1].lstrip()
	452	if s_line[0].lower().count("valuerangeminmag") > 0:
	453	valuerangeminmag = s_line[1].lstrip()
	454	if s_line[0].lower().count("valuerangemaxmag") > 0:
	455	valuerangemaxmag = s_line[1].lstrip()
	456	if s_line[0].lower().count("end") > 0:
	457	output.filename = os.path.basename(path)
	458	output.oommf = oommf
	459	output.title = title
	460	output.desc = desc
	461	output.meshtype = meshtype
	462	output.xbase = float(xbase) * METER2ANG
	463	output.ybase = float(ybase) * METER2ANG
	464	output.zbase = float(zbase) * METER2ANG
	465	output.xstepsize = float(xstepsize) * METER2ANG
	466	output.ystepsize = float(ystepsize) * METER2ANG
	467	output.zstepsize = float(zstepsize) * METER2ANG
	468	output.xnodes = float(xnodes)
	469	output.ynodes = float(ynodes)
	470	output.znodes = float(znodes)
	471	output.xmin = float(xmin) * METER2ANG
	472	output.ymin = float(ymin) * METER2ANG
	473	output.zmin = float(zmin) * METER2ANG
	474	output.xmax = float(xmax) * METER2ANG
	475	output.ymax = float(ymax) * METER2ANG
	476	output.zmax = float(zmax) * METER2ANG
	477	output.valuemultiplier = valuemultiplier
	478	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
	479	valueunit)
	480	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
	481	valueunit)
	482	output.set_m(mx, my, mz)
	483	return output
	484	except:
	485	msg = "%s is not supported: \n" % path
	486	msg += "We accept only Text format OMF file."
	487	raise RuntimeError, msg
	488
[e3f77d8b]	489	class PDBReader(object):
[51f14603]	490	"""
	491	PDB reader class: limited for reading the lines starting with 'ATOM'
	492	"""
	493	type_name = "PDB"
	494	## Wildcards
	495	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
	496	## List of allowed extensions
[e3f77d8b]	497	ext = ['.pdb', '.PDB']
	498
[51f14603]	499	def read(self, path):
	500	"""
	501	Load data file
[e3f77d8b]	502
[51f14603]	503	:param path: file path
	504	:return: MagSLD
	505	:raise RuntimeError: when the file can't be opened
	506	"""
[9a5097c]	507	pos_x = np.zeros(0)
	508	pos_y = np.zeros(0)
	509	pos_z = np.zeros(0)
	510	sld_n = np.zeros(0)
	511	sld_mx = np.zeros(0)
	512	sld_my = np.zeros(0)
	513	sld_mz = np.zeros(0)
	514	vol_pix = np.zeros(0)
	515	pix_symbol = np.zeros(0)
[51f14603]	516	x_line = []
	517	y_line = []
	518	z_line = []
	519	x_lines = []
	520	y_lines = []
[e3f77d8b]	521	z_lines = []
[51f14603]	522	try:
	523	input_f = open(path, 'rb')
	524	buff = input_f.read()
	525	lines = buff.split('\n')
	526	input_f.close()
	527	num = 0
	528	for line in lines:
	529	try:
	530	# check if line starts with "ATOM"
	531	if line[0:6].strip().count('ATM') > 0 or \
	532	line[0:6].strip() == 'ATOM':
	533	# define fields of interest
	534	atom_name = line[12:16].strip()
	535	try:
	536	float(line[12])
	537	atom_name = atom_name[1].upper()
	538	except:
	539	if len(atom_name) == 4:
	540	atom_name = atom_name[0].upper()
[e3f77d8b]	541	elif line[12] != ' ':
[51f14603]	542	atom_name = atom_name[0].upper() + \
[e3f77d8b]	543	atom_name[1].lower()
[51f14603]	544	else:
	545	atom_name = atom_name[0].upper()
	546	_pos_x = float(line[30:38].strip())
	547	_pos_y = float(line[38:46].strip())
	548	_pos_z = float(line[46:54].strip())
[9a5097c]	549	pos_x = np.append(pos_x, _pos_x)
	550	pos_y = np.append(pos_y, _pos_y)
	551	pos_z = np.append(pos_z, _pos_z)
[51f14603]	552	try:
	553	val = nsf.neutron_sld(atom_name)[0]
	554	# sld in Ang^-2 unit
	555	val *= 1.0e-6
[9a5097c]	556	sld_n = np.append(sld_n, val)
[51f14603]	557	atom = formula(atom_name)
	558	# cm to A units
	559	vol = 1.0e+24 * atom.mass / atom.density / NA
[9a5097c]	560	vol_pix = np.append(vol_pix, vol)
[51f14603]	561	except:
[9c3d784]	562	print("Error: set the sld of %s to zero"% atom_name)
[9a5097c]	563	sld_n = np.append(sld_n, 0.0)
	564	sld_mx = np.append(sld_mx, 0)
	565	sld_my = np.append(sld_my, 0)
	566	sld_mz = np.append(sld_mz, 0)
	567	pix_symbol = np.append(pix_symbol, atom_name)
[e3f77d8b]	568	elif line[0:6].strip().count('CONECT') > 0:
[51f14603]	569	toks = line.split()
[e3f77d8b]	570	num = int(toks[1]) - 1
	571	val_list = []
[51f14603]	572	for val in toks[2:]:
	573	try:
	574	int_val = int(val)
	575	except:
	576	break
	577	if int_val == 0:
	578	break
	579	val_list.append(int_val)
[e3f77d8b]	580	#need val_list ordered
[51f14603]	581	for val in val_list:
	582	index = val - 1
	583	if (pos_x[index], pos_x[num]) in x_line and \
	584	(pos_y[index], pos_y[num]) in y_line and \
	585	(pos_z[index], pos_z[num]) in z_line:
	586	continue
	587	x_line.append((pos_x[num], pos_x[index]))
	588	y_line.append((pos_y[num], pos_y[index]))
	589	z_line.append((pos_z[num], pos_z[index]))
	590	if len(x_line) > 0:
[e3f77d8b]	591	x_lines.append(x_line)
[51f14603]	592	y_lines.append(y_line)
[e3f77d8b]	593	z_lines.append(z_line)
[51f14603]	594	except:
[c155a16]	595	logger.error(sys.exc_value)
[e3f77d8b]	596
[51f14603]	597	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
	598	output.set_conect_lines(x_line, y_line, z_line)
	599	output.filename = os.path.basename(path)
	600	output.set_pix_type('atom')
	601	output.set_pixel_symbols(pix_symbol)
	602	output.set_nodes()
	603	output.set_pixel_volumes(vol_pix)
	604	output.sld_unit = '1/A^(2)'
	605	return output
	606	except:
[e3f77d8b]	607	raise RuntimeError, "%s is not a sld file" % path
[51f14603]	608
	609	def write(self, path, data):
	610	"""
	611	Write
	612	"""
[9c3d784]	613	print("Not implemented... ")
[51f14603]	614
[e3f77d8b]	615	class SLDReader(object):
[51f14603]	616	"""
	617	Class to load ascii files (7 columns).
	618	"""
	619	## File type
	620	type_name = "SLD ASCII"
	621	## Wildcards
	622	type = ["sld files (.SLD, .sld)\|*.sld",
	623	"txt files (.TXT, .txt)\|*.txt",
	624	"all files (.)\|."]
	625	## List of allowed extensions
	626	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
	627	def read(self, path):
	628	"""
	629	Load data file
	630	:param path: file path
	631	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	632	:raise RuntimeError: when the file can't be opened
	633	:raise ValueError: when the length of the data vectors are inconsistent
	634	"""
	635	try:
[9a5097c]	636	pos_x = np.zeros(0)
	637	pos_y = np.zeros(0)
	638	pos_z = np.zeros(0)
	639	sld_n = np.zeros(0)
	640	sld_mx = np.zeros(0)
	641	sld_my = np.zeros(0)
	642	sld_mz = np.zeros(0)
[51f14603]	643	try:
	644	# Use numpy to speed up loading
[9a5097c]	645	input_f = np.loadtxt(path, dtype='float', skiprows=1,
[51f14603]	646	ndmin=1, unpack=True)
[9a5097c]	647	pos_x = np.array(input_f[0])
	648	pos_y = np.array(input_f[1])
	649	pos_z = np.array(input_f[2])
	650	sld_n = np.array(input_f[3])
	651	sld_mx = np.array(input_f[4])
	652	sld_my = np.array(input_f[5])
	653	sld_mz = np.array(input_f[6])
[51f14603]	654	ncols = len(input_f)
	655	if ncols == 8:
[9a5097c]	656	vol_pix = np.array(input_f[7])
[51f14603]	657	elif ncols == 7:
[e3f77d8b]	658	vol_pix = None
[51f14603]	659	except:
	660	# For older version of numpy
	661	input_f = open(path, 'rb')
	662	buff = input_f.read()
	663	lines = buff.split('\n')
	664	input_f.close()
	665	for line in lines:
	666	toks = line.split()
	667	try:
	668	_pos_x = float(toks[0])
	669	_pos_y = float(toks[1])
	670	_pos_z = float(toks[2])
	671	_sld_n = float(toks[3])
	672	_sld_mx = float(toks[4])
	673	_sld_my = float(toks[5])
	674	_sld_mz = float(toks[6])
[9a5097c]	675	pos_x = np.append(pos_x, _pos_x)
	676	pos_y = np.append(pos_y, _pos_y)
	677	pos_z = np.append(pos_z, _pos_z)
	678	sld_n = np.append(sld_n, _sld_n)
	679	sld_mx = np.append(sld_mx, _sld_mx)
	680	sld_my = np.append(sld_my, _sld_my)
	681	sld_mz = np.append(sld_mz, _sld_mz)
[51f14603]	682	try:
[e3f77d8b]	683	_vol_pix = float(toks[7])
[9a5097c]	684	vol_pix = np.append(vol_pix, _vol_pix)
[51f14603]	685	except:
	686	vol_pix = None
	687	except:
	688	# Skip non-data lines
[c155a16]	689	logger.error(sys.exc_value)
[e3f77d8b]	690	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
[51f14603]	691	sld_mx, sld_my, sld_mz)
	692	output.filename = os.path.basename(path)
	693	output.set_pix_type('pixel')
	694	output.set_pixel_symbols('pixel')
[7432acb]	695	if vol_pix is not None:
[51f14603]	696	output.set_pixel_volumes(vol_pix)
	697	return output
	698	except:
[e3f77d8b]	699	raise RuntimeError, "%s is not a sld file" % path
	700
[51f14603]	701	def write(self, path, data):
	702	"""
	703	Write sld file
[e3f77d8b]	704	:Param path: file path
[51f14603]	705	:Param data: MagSLD data object
	706	"""
[235f514]	707	if path is None:
[51f14603]	708	raise ValueError, "Missing the file path."
[235f514]	709	if data is None:
[51f14603]	710	raise ValueError, "Missing the data to save."
	711	x_val = data.pos_x
	712	y_val = data.pos_y
	713	z_val = data.pos_z
	714	vol_pix = data.vol_pix
	715	length = len(x_val)
	716	sld_n = data.sld_n
[235f514]	717	if sld_n is None:
[9a5097c]	718	sld_n = np.zeros(length)
[51f14603]	719	sld_mx = data.sld_mx
[235f514]	720	if sld_mx is None:
[9a5097c]	721	sld_mx = np.zeros(length)
	722	sld_my = np.zeros(length)
	723	sld_mz = np.zeros(length)
[51f14603]	724	else:
	725	sld_my = data.sld_my
	726	sld_mz = data.sld_mz
	727	out = open(path, 'w')
	728	# First Line: Column names
	729	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
	730	for ind in range(length):
[e3f77d8b]	731	out.write("\n%g %g %g %g %g %g %g %g" % \
	732	(x_val[ind], y_val[ind], z_val[ind], sld_n[ind],
	733	sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind]))
	734	out.close()
	735
	736
	737	class OMFData(object):
[51f14603]	738	"""
	739	OMF Data.
	740	"""
	741	_meshunit = "A"
	742	_valueunit = "A^(-2)"
	743	def __init__(self):
	744	"""
	745	Init for mag SLD
	746	"""
	747	self.filename = 'default'
	748	self.oommf = ''
	749	self.title = ''
	750	self.desc = ''
	751	self.meshtype = ''
	752	self.meshunit = self._meshunit
	753	self.valueunit = self._valueunit
	754	self.xbase = 0.0
	755	self.ybase = 0.0
	756	self.zbase = 0.0
	757	self.xstepsize = 6.0
	758	self.ystepsize = 6.0
	759	self.zstepsize = 6.0
	760	self.xnodes = 10.0
	761	self.ynodes = 10.0
	762	self.znodes = 10.0
	763	self.xmin = 0.0
	764	self.ymin = 0.0
	765	self.zmin = 0.0
	766	self.xmax = 60.0
	767	self.ymax = 60.0
	768	self.zmax = 60.0
	769	self.mx = None
	770	self.my = None
	771	self.mz = None
	772	self.valuemultiplier = 1.
	773	self.valuerangeminmag = 0
	774	self.valuerangemaxmag = 0
[e3f77d8b]	775
[51f14603]	776	def __str__(self):
	777	"""
	778	doc strings
	779	"""
[e3f77d8b]	780	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	781	_str += "File: %s\n" % self.filename
	782	_str += "OOMMF: %s\n" % self.oommf
	783	_str += "Title: %s\n" % self.title
	784	_str += "Desc: %s\n" % self.desc
	785	_str += "meshtype: %s\n" % self.meshtype
	786	_str += "meshunit: %s\n" % str(self.meshunit)
	787	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
	788	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
	789	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
[e3f77d8b]	790	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
[51f14603]	791	self.meshunit)
[e3f77d8b]	792	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
[51f14603]	793	self.meshunit)
[e3f77d8b]	794	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
[51f14603]	795	self.meshunit)
	796	_str += "xnodes: %s\n" % str(self.xnodes)
	797	_str += "ynodes: %s\n" % str(self.ynodes)
	798	_str += "znodes: %s\n" % str(self.znodes)
	799	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
	800	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
	801	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
	802	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
	803	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
	804	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
	805	_str += "valueunit: %s\n" % self.valueunit
	806	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
[e3f77d8b]	807	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
	808	self.valueunit)
	809	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
	810	self.valueunit)
[51f14603]	811	return _str
[e3f77d8b]	812
[51f14603]	813	def set_m(self, mx, my, mz):
	814	"""
	815	Set the Mx, My, Mz values
	816	"""
	817	self.mx = mx
	818	self.my = my
	819	self.mz = mz
[e3f77d8b]	820
	821	class MagSLD(object):
[51f14603]	822	"""
	823	Magnetic SLD.
	824	"""
	825	pos_x = None
	826	pos_y = None
	827	pos_z = None
	828	sld_n = None
	829	sld_mx = None
	830	sld_my = None
	831	sld_mz = None
	832	# Units
	833	_pos_unit = 'A'
	834	_sld_unit = '1/A^(2)'
	835	_pix_type = 'pixel'
[e3f77d8b]	836
	837	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
[51f14603]	838	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
	839	"""
	840	Init for mag SLD
	841	:params : All should be numpy 1D array
	842	"""
	843	self.is_data = True
	844	self.filename = ''
	845	self.xstepsize = 6.0
	846	self.ystepsize = 6.0
	847	self.zstepsize = 6.0
	848	self.xnodes = 10.0
	849	self.ynodes = 10.0
	850	self.znodes = 10.0
	851	self.has_stepsize = False
	852	self.has_conect = False
	853	self.pos_unit = self._pos_unit
	854	self.sld_unit = self._sld_unit
	855	self.pix_type = 'pixel'
	856	self.pos_x = pos_x
	857	self.pos_y = pos_y
	858	self.pos_z = pos_z
	859	self.sld_n = sld_n
	860	self.line_x = None
	861	self.line_y = None
	862	self.line_z = None
	863	self.sld_mx = sld_mx
	864	self.sld_my = sld_my
	865	self.sld_mz = sld_mz
	866	self.vol_pix = vol_pix
	867	self.sld_m = None
	868	self.sld_phi = None
	869	self.sld_theta = None
	870	self.pix_symbol = None
[7432acb]	871	if sld_mx is not None and sld_my is not None and sld_mz is not None:
[51f14603]	872	self.set_sldms(sld_mx, sld_my, sld_mz)
	873	self.set_nodes()
[e3f77d8b]	874
[51f14603]	875	def __str__(self):
	876	"""
	877	doc strings
	878	"""
[e3f77d8b]	879	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	880	_str += "File: %s\n" % self.filename
	881	_str += "Axis_unit: %s\n" % self.pos_unit
	882	_str += "SLD_unit: %s\n" % self.sld_unit
	883	return _str
[e3f77d8b]	884
[51f14603]	885	def set_pix_type(self, pix_type):
	886	"""
	887	Set pixel type
	888	:Param pix_type: string, 'pixel' or 'atom'
	889	"""
	890	self.pix_type = pix_type
[e3f77d8b]	891
[51f14603]	892	def set_sldn(self, sld_n):
	893	"""
	894	Sets neutron SLD
	895	"""
	896	if sld_n.__class__.__name__ == 'float':
	897	if self.is_data:
[e3f77d8b]	898	# For data, put the value to only the pixels w non-zero M
[9a5097c]	899	is_nonzero = (np.fabs(self.sld_mx) +
	900	np.fabs(self.sld_my) +
	901	np.fabs(self.sld_mz)).nonzero()
	902	self.sld_n = np.zeros(len(self.pos_x))
[51f14603]	903	if len(self.sld_n[is_nonzero]) > 0:
	904	self.sld_n[is_nonzero] = sld_n
	905	else:
	906	self.sld_n.fill(sld_n)
	907	else:
	908	# For non-data, put the value to all the pixels
[9a5097c]	909	self.sld_n = np.ones(len(self.pos_x)) * sld_n
[51f14603]	910	else:
	911	self.sld_n = sld_n
[e3f77d8b]	912
[51f14603]	913	def set_sldms(self, sld_mx, sld_my, sld_mz):
[ac7be54]	914	r"""
	915	Sets (\\|m\\|, m_theta, m_phi)
[51f14603]	916	"""
	917	if sld_mx.__class__.__name__ == 'float':
[9a5097c]	918	self.sld_mx = np.ones(len(self.pos_x)) * sld_mx
[51f14603]	919	else:
	920	self.sld_mx = sld_mx
	921	if sld_my.__class__.__name__ == 'float':
[9a5097c]	922	self.sld_my = np.ones(len(self.pos_x)) * sld_my
[51f14603]	923	else:
	924	self.sld_my = sld_my
	925	if sld_mz.__class__.__name__ == 'float':
[9a5097c]	926	self.sld_mz = np.ones(len(self.pos_x)) * sld_mz
[51f14603]	927	else:
	928	self.sld_mz = sld_mz
	929
[9a5097c]	930	sld_m = np.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
[e3f77d8b]	931	sld_mz * sld_mz)
[51f14603]	932	self.sld_m = sld_m
[e3f77d8b]	933
	934	def set_pixel_symbols(self, symbol='pixel'):
[51f14603]	935	"""
	936	Set pixel
	937	:Params pixel: str; pixel or atomic symbol, or array of strings
	938	"""
[235f514]	939	if self.sld_n is None:
[51f14603]	940	return
	941	if symbol.__class__.__name__ == 'str':
[9a5097c]	942	self.pix_symbol = np.repeat(symbol, len(self.sld_n))
[51f14603]	943	else:
	944	self.pix_symbol = symbol
[e3f77d8b]	945
	946	def set_pixel_volumes(self, vol):
[51f14603]	947	"""
	948	Set pixel volumes
	949	:Params pixel: str; pixel or atomic symbol, or array of strings
	950	"""
[235f514]	951	if self.sld_n is None:
[51f14603]	952	return
	953	if vol.__class__.__name__ == 'ndarray':
	954	self.vol_pix = vol
	955	elif vol.__class__.__name__.count('float') > 0:
[9a5097c]	956	self.vol_pix = np.repeat(vol, len(self.sld_n))
[51f14603]	957	else:
	958	self.vol_pix = None
	959
	960	def get_sldn(self):
	961	"""
	962	Returns nuclear sld
	963	"""
	964	return self.sld_n
[e3f77d8b]	965
[51f14603]	966	def set_nodes(self):
	967	"""
	968	Set xnodes, ynodes, and znodes
	969	"""
	970	self.set_stepsize()
	971	if self.pix_type == 'pixel':
	972	try:
	973	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
	974	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
	975	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
	976	self.xnodes = int(xdist) + 1
	977	self.ynodes = int(ydist) + 1
	978	self.znodes = int(zdist) + 1
	979	except:
	980	self.xnodes = None
	981	self.ynodes = None
	982	self.znodes = None
	983	else:
	984	self.xnodes = None
	985	self.ynodes = None
	986	self.znodes = None
[e3f77d8b]	987
[51f14603]	988	def set_stepsize(self):
	989	"""
	990	Set xtepsize, ystepsize, and zstepsize
	991	"""
	992	if self.pix_type == 'pixel':
	993	try:
	994	xpos_pre = self.pos_x[0]
	995	ypos_pre = self.pos_y[0]
	996	zpos_pre = self.pos_z[0]
	997	for x_pos in self.pos_x:
	998	if xpos_pre != x_pos:
[9a5097c]	999	self.xstepsize = np.fabs(x_pos - xpos_pre)
[51f14603]	1000	break
	1001	for y_pos in self.pos_y:
	1002	if ypos_pre != y_pos:
[9a5097c]	1003	self.ystepsize = np.fabs(y_pos - ypos_pre)
[51f14603]	1004	break
	1005	for z_pos in self.pos_z:
	1006	if zpos_pre != z_pos:
[9a5097c]	1007	self.zstepsize = np.fabs(z_pos - zpos_pre)
[51f14603]	1008	break
	1009	#default pix volume
[9a5097c]	1010	self.vol_pix = np.ones(len(self.pos_x))
[51f14603]	1011	vol = self.xstepsize * self.ystepsize * self.zstepsize
	1012	self.set_pixel_volumes(vol)
	1013	self.has_stepsize = True
	1014	except:
	1015	self.xstepsize = None
	1016	self.ystepsize = None
	1017	self.zstepsize = None
	1018	self.vol_pix = None
	1019	self.has_stepsize = False
	1020	else:
	1021	self.xstepsize = None
	1022	self.ystepsize = None
	1023	self.zstepsize = None
	1024	self.has_stepsize = True
	1025	return self.xstepsize, self.ystepsize, self.zstepsize
	1026
	1027	def set_conect_lines(self, line_x, line_y, line_z):
	1028	"""
	1029	Set bonding line data if taken from pdb
	1030	"""
	1031	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
	1032	return
	1033	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
	1034	return
	1035	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
	1036	return
	1037	self.has_conect = True
[e3f77d8b]	1038	self.line_x = line_x
	1039	self.line_y = line_y
[51f14603]	1040	self.line_z = line_z
	1041
	1042	def test_load():
[b6627d9]	1043	"""
	1044	Test code
	1045	"""
[06aaa75d]	1046	from mpl_toolkits.mplot3d import Axes3D
[e3f77d8b]	1047	current_dir = os.path.abspath(os.path.curdir)
[9c3d784]	1048	print(current_dir)
[51f14603]	1049	for i in range(6):
[e3f77d8b]	1050	current_dir, _ = os.path.split(current_dir)
	1051	tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt")
	1052	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
[51f14603]	1053	if os.path.isfile(tfile):
	1054	tfpath = tfile
	1055	ofpath = ofile
	1056	break
	1057	reader = SLDReader()
	1058	oreader = OMFReader()
	1059	output = reader.read(tfpath)
	1060	ooutput = oreader.read(ofpath)
	1061	foutput = OMF2SLD()
	1062	foutput.set_data(ooutput)
	1063
	1064	import matplotlib.pyplot as plt
	1065	fig = plt.figure()
[06aaa75d]	1066	ax = Axes3D(fig)
[e3f77d8b]	1067	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
	1068	alpha=0.7, markeredgecolor='gray', rasterized=True)
[51f14603]	1069	gap = 7
	1070	max_mx = max(output.sld_mx)
	1071	max_my = max(output.sld_my)
	1072	max_mz = max(output.sld_mz)
[e3f77d8b]	1073	max_m = max(max_mx, max_my, max_mz)
[51f14603]	1074	x2 = output.pos_x+output.sld_mx/max_m * gap
	1075	y2 = output.pos_y+output.sld_my/max_m * gap
	1076	z2 = output.pos_z+output.sld_mz/max_m * gap
[9a5097c]	1077	x_arrow = np.column_stack((output.pos_x, x2))
	1078	y_arrow = np.column_stack((output.pos_y, y2))
	1079	z_arrow = np.column_stack((output.pos_z, z2))
[51f14603]	1080	unit_x2 = output.sld_mx / max_m
	1081	unit_y2 = output.sld_my / max_m
	1082	unit_z2 = output.sld_mz / max_m
[9a5097c]	1083	color_x = np.fabs(unit_x2 * 0.8)
	1084	color_y = np.fabs(unit_y2 * 0.8)
	1085	color_z = np.fabs(unit_z2 * 0.8)
	1086	colors = np.column_stack((color_x, color_y, color_z))
[51f14603]	1087	plt.show()
[b6627d9]	1088
[51f14603]	1089	def test():
[b6627d9]	1090	"""
	1091	Test code
	1092	"""
[e3f77d8b]	1093	current_dir = os.path.abspath(os.path.curdir)
[51f14603]	1094	for i in range(3):
[e3f77d8b]	1095	current_dir, _ = os.path.split(current_dir)
	1096	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
[51f14603]	1097	if os.path.isfile(ofile):
	1098	ofpath = ofile
	1099	break
	1100	oreader = OMFReader()
	1101	ooutput = oreader.read(ofpath)
[e3f77d8b]	1102	foutput = OMF2SLD()
	1103	foutput.set_data(ooutput)
	1104	writer = SLDReader()
	1105	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
[51f14603]	1106	foutput.output)
	1107	model = GenSAS()
[e3f77d8b]	1108	model.set_sld_data(foutput.output)
[9a5097c]	1109	x = np.arange(1000)/10000. + 1e-5
	1110	y = np.arange(1000)/10000. + 1e-5
	1111	i = np.zeros(1000)
[e3f77d8b]	1112	model.runXY([x, y, i])
	1113
	1114	if __name__ == "__main__":
[51f14603]	1115	test()
	1116	test_load()

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SasView

source: sasview/src/sas/sascalc/calculator/sas_gen.py @ 457f735

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