sas_gen.py @ b9dbd6b

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2release_4.0.1ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since b9dbd6b was b6627d9, checked in by Doucet, Mathieu <doucetm@…>, 10 years ago
pylint fixes
Property mode set to `100644`
File size: 40.0 KB

Rev	Line
[b6627d9]	1	# pylint: disable=invalid-name
[51f14603]	2	"""
[fd5ac0d]	3	SAS generic computation and sld file readers
[51f14603]	4	"""
[79492222]	5	from sas.models.BaseComponent import BaseComponent
	6	import sas.models.sas_extension.sld2i as mod
[51f14603]	7	from periodictable import formula
	8	from periodictable import nsf
	9	import numpy
	10	import os
	11	import copy
[b6627d9]	12	import sys
	13	import logging
[51f14603]	14
[e3f77d8b]	15	MFACTOR_AM = 2.853E-12
	16	MFACTOR_MT = 2.3164E-9
[51f14603]	17	METER2ANG = 1.0E+10
	18	#Avogadro constant [1/mol]
	19	NA = 6.02214129e+23
	20
	21	def mag2sld(mag, v_unit=None):
	22	"""
	23	Convert magnetization to magnatic SLD
	24	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
	25	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
[e3f77d8b]	26	"""
[51f14603]	27	if v_unit == "A/m":
[e3f77d8b]	28	factor = MFACTOR_AM
[51f14603]	29	elif v_unit == "mT":
[e3f77d8b]	30	factor = MFACTOR_MT
[51f14603]	31	else:
	32	raise ValueError, "Invalid valueunit"
	33	sld_m = factor * mag
	34	return sld_m
	35
	36	def transform_center(pos_x, pos_y, pos_z):
	37	"""
[e3f77d8b]	38	re-center
[51f14603]	39	:return: posx, posy, posz [arrays]
[e3f77d8b]	40	"""
[51f14603]	41	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
	42	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
[e3f77d8b]	43	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
	44	return posx, posy, posz
[51f14603]	45
	46	class GenSAS(BaseComponent):
	47	"""
	48	Generic SAS computation Model based on sld (n & m) arrays
	49	"""
	50	def __init__(self):
	51	"""
	52	Init
	53	:Params sld_data: MagSLD object
	54	"""
	55	# Initialize BaseComponent
	56	BaseComponent.__init__(self)
	57	self.sld_data = None
	58	self.data_pos_unit = None
	59	self.data_x = None
	60	self.data_y = None
	61	self.data_z = None
	62	self.data_sldn = None
	63	self.data_mx = None
	64	self.data_my = None
	65	self.data_mz = None
	66	self.data_vol = None #[A^3]
	67	self.is_avg = False
	68	## Name of the model
	69	self.name = "GenSAS"
	70	## Define parameters
	71	self.params = {}
[e3f77d8b]	72	self.params['scale'] = 1.0
	73	self.params['background'] = 0.0
	74	self.params['solvent_SLD'] = 0.0
[51f14603]	75	self.params['total_volume'] = 1.0
[e3f77d8b]	76	self.params['Up_frac_in'] = 1.0
	77	self.params['Up_frac_out'] = 1.0
	78	self.params['Up_theta'] = 0.0
[51f14603]	79	self.description = 'GenSAS'
	80	## Parameter details [units, min, max]
	81	self.details = {}
[e3f77d8b]	82	self.details['scale'] = ['', None, None]
[51f14603]	83	self.details['background'] = ['[1/cm]', None, None]
[e3f77d8b]	84	self.details['solvent_SLD'] = ['1/A^(2)', None, None]
	85	self.details['total_volume'] = ['A^(3)', None, None]
	86	self.details['Up_frac_in'] = ['[u/(u+d)]', None, None]
	87	self.details['Up_frac_out'] = ['[u/(u+d)]', None, None]
[51f14603]	88	self.details['Up_theta'] = ['[deg]', None, None]
	89	# fixed parameters
	90	self.fixed = []
[e3f77d8b]	91
	92	def set_pixel_volumes(self, volume):
[51f14603]	93	"""
	94	Set the volume of a pixel in (A^3) unit
	95	:Param volume: pixel volume [float]
	96	"""
	97	if self.data_vol == None:
	98	raise
	99	self.data_vol = volume
[e3f77d8b]	100
	101	def set_is_avg(self, is_avg=False):
[51f14603]	102	"""
	103	Sets is_avg: [bool]
	104	"""
	105	self.is_avg = is_avg
[e3f77d8b]	106
[51f14603]	107	def _gen(self, x, y, i):
	108	"""
	109	Evaluate the function
	110	:Param x: array of x-values
	111	:Param y: array of y-values
[e3f77d8b]	112	:Param i: array of initial i-value
[51f14603]	113	:return: function value
	114	"""
	115	pos_x = self.data_x
	116	pos_y = self.data_y
	117	pos_z = self.data_z
	118	len_x = len(pos_x)
	119	if self.is_avg == None:
	120	len_x *= -1
	121	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
	122	len_q = len(x)
	123	sldn = copy.deepcopy(self.data_sldn)
	124	sldn -= self.params['solvent_SLD']
[e3f77d8b]	125	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
	126	sldn, self.data_mx, self.data_my,
[51f14603]	127	self.data_mz, self.data_vol,
[e3f77d8b]	128	self.params['Up_frac_in'],
	129	self.params['Up_frac_out'],
[51f14603]	130	self.params['Up_theta'])
	131	if y == []:
	132	mod.genicom(model, len_q, x, i)
	133	else:
	134	mod.genicomXY(model, len_q, x, y, i)
	135	vol_correction = self.data_total_volume / self.params['total_volume']
	136	return self.params['scale'] * vol_correction * i + \
	137	self.params['background']
[e3f77d8b]	138
	139	def set_sld_data(self, sld_data=None):
[51f14603]	140	"""
	141	Sets sld_data
	142	"""
	143	self.sld_data = sld_data
	144	self.data_pos_unit = sld_data.pos_unit
	145	self.data_x = sld_data.pos_x
	146	self.data_y = sld_data.pos_y
	147	self.data_z = sld_data.pos_z
	148	self.data_sldn = sld_data.sld_n
	149	self.data_mx = sld_data.sld_mx
	150	self.data_my = sld_data.sld_my
	151	self.data_mz = sld_data.sld_mz
	152	self.data_vol = sld_data.vol_pix
	153	self.data_total_volume = sum(sld_data.vol_pix)
	154	self.params['total_volume'] = sum(sld_data.vol_pix)
[e3f77d8b]	155
[51f14603]	156	def getProfile(self):
	157	"""
[e3f77d8b]	158	Get SLD profile
[51f14603]	159	: return: sld_data
	160	"""
	161	return self.sld_data
[e3f77d8b]	162
	163	def run(self, x=0.0):
	164	"""
[51f14603]	165	Evaluate the model
	166	:param x: simple value
	167	:return: (I value)
	168	"""
	169	if x.__class__.__name__ == 'list':
	170	if len(x[1]) > 0:
	171	msg = "Not a 1D."
	172	raise ValueError, msg
	173	i_out = numpy.zeros_like(x[0])
	174	# 1D I is found at y =0 in the 2D pattern
[e3f77d8b]	175	out = self._gen(x[0], [], i_out)
[51f14603]	176	return out
	177	else:
	178	msg = "Q must be given as list of qx's and qy's"
	179	raise ValueError, msg
[e3f77d8b]	180
	181	def runXY(self, x=0.0):
	182	"""
[51f14603]	183	Evaluate the model
	184	:param x: simple value
	185	:return: I value
	186	:Use this runXY() for the computation
	187	"""
	188	if x.__class__.__name__ == 'list':
	189	i_out = numpy.zeros_like(x[0])
	190	out = self._gen(x[0], x[1], i_out)
	191	return out
	192	else:
	193	msg = "Q must be given as list of qx's and qy's"
	194	raise ValueError, msg
[e3f77d8b]	195
[51f14603]	196	def evalDistribution(self, qdist):
	197	"""
	198	Evaluate a distribution of q-values.
[e3f77d8b]	199	* For 1D, a numpy array is expected as input:
	200	evalDistribution(q) where q is a numpy array.
	201	* For 2D, a list of numpy arrays are expected:
	202	[qx_prime,qy_prime], where 1D arrays.
	203	:param qdist: ndarray of scalar q-values or list [qx,qy]
	204	where qx,qy are 1D ndarrays
[51f14603]	205	"""
	206	if qdist.__class__.__name__ == 'list':
	207	if len(qdist[1]) < 1:
	208	out = self.run(qdist)
	209	else:
	210	out = self.runXY(qdist)
	211	return out
	212	else:
	213	mesg = "evalDistribution is expecting an ndarray of "
	214	mesg += "a list [qx,qy] where qx,qy are arrays."
	215	raise RuntimeError, mesg
[e3f77d8b]	216
	217	class OMF2SLD(object):
[51f14603]	218	"""
	219	Convert OMFData to MAgData
	220	"""
[e3f77d8b]	221	def __init__(self):
[51f14603]	222	"""
	223	Init
	224	"""
	225	self.pos_x = None
	226	self.pos_y = None
	227	self.pos_z = None
	228	self.mx = None
	229	self.my = None
	230	self.mz = None
	231	self.sld_n = None
	232	self.vol_pix = None
	233	self.output = None
	234	self.omfdata = None
[e3f77d8b]	235
[51f14603]	236	def set_data(self, omfdata, shape='rectangular'):
	237	"""
	238	Set all data
	239	"""
	240	self.omfdata = omfdata
	241	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
[e3f77d8b]	242	pos_x = numpy.arange(omfdata.xmin,
	243	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
[51f14603]	244	omfdata.xstepsize)
[e3f77d8b]	245	pos_y = numpy.arange(omfdata.ymin,
	246	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
[51f14603]	247	omfdata.ystepsize)
[e3f77d8b]	248	pos_z = numpy.arange(omfdata.zmin,
	249	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
[51f14603]	250	omfdata.zstepsize)
	251	self.pos_x = numpy.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
	252	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
	253	self.pos_y = numpy.tile(self.pos_y, int(omfdata.znodes))
	254	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
	255	self.mx = omfdata.mx
	256	self.my = omfdata.my
	257	self.mz = omfdata.mz
	258	self.sld_n = numpy.zeros(length)
[e3f77d8b]	259
[51f14603]	260	if omfdata.mx == None:
	261	self.mx = numpy.zeros(length)
	262	if omfdata.my == None:
	263	self.my = numpy.zeros(length)
	264	if omfdata.mz == None:
	265	self.mz = numpy.zeros(length)
[e3f77d8b]	266
[51f14603]	267	self._check_data_length(length)
	268	self.remove_null_points(False, False)
	269	mask = numpy.ones(len(self.sld_n), dtype=bool)
	270	if shape.lower() == 'ellipsoid':
	271	try:
	272	# Pixel (step) size included
	273	x_c = max(self.pos_x) + min(self.pos_x)
	274	y_c = max(self.pos_y) + min(self.pos_y)
	275	z_c = max(self.pos_z) + min(self.pos_z)
	276	x_d = max(self.pos_x) - min(self.pos_x)
	277	y_d = max(self.pos_y) - min(self.pos_y)
	278	z_d = max(self.pos_z) - min(self.pos_z)
	279	x_r = (x_d + omfdata.xstepsize) / 2.0
	280	y_r = (y_d + omfdata.ystepsize) / 2.0
	281	z_r = (z_d + omfdata.zstepsize) / 2.0
	282	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
	283	x_dir2 *= x_dir2
	284	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
	285	y_dir2 *= y_dir2
	286	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
	287	z_dir2 *= z_dir2
	288	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
	289	except:
[b6627d9]	290	logging.error(sys.exc_value)
[e3f77d8b]	291	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
	292	self.pos_z[mask], self.sld_n[mask],
[51f14603]	293	self.mx[mask], self.my[mask], self.mz[mask])
	294	self.output.set_pix_type('pixel')
	295	self.output.set_pixel_symbols('pixel')
[e3f77d8b]	296
[51f14603]	297	def get_omfdata(self):
	298	"""
	299	Return all data
	300	"""
	301	return self.omfdata
[e3f77d8b]	302
[51f14603]	303	def get_output(self):
	304	"""
	305	Return output
	306	"""
	307	return self.output
[e3f77d8b]	308
[51f14603]	309	def _check_data_length(self, length):
	310	"""
	311	Check if the data lengths are consistent
	312	:Params length: data length
	313	"""
	314	msg = "Error: Inconsistent data length."
	315	if len(self.pos_x) != length:
	316	raise ValueError, msg
	317	if len(self.pos_y) != length:
	318	raise ValueError, msg
	319	if len(self.pos_z) != length:
	320	raise ValueError, msg
	321	if len(self.mx) != length:
	322	raise ValueError, msg
	323	if len(self.my) != length:
	324	raise ValueError, msg
	325	if len(self.mz) != length:
	326	raise ValueError, msg
[e3f77d8b]	327
[51f14603]	328	def remove_null_points(self, remove=False, recenter=False):
	329	"""
	330	Removes any mx, my, and mz = 0 points
	331	"""
	332	if remove:
[e3f77d8b]	333	is_nonzero = (numpy.fabs(self.mx) + numpy.fabs(self.my) +
	334	numpy.fabs(self.mz)).nonzero()
	335	if len(is_nonzero[0]) > 0:
[51f14603]	336	self.pos_x = self.pos_x[is_nonzero]
	337	self.pos_y = self.pos_y[is_nonzero]
	338	self.pos_z = self.pos_z[is_nonzero]
	339	self.sld_n = self.sld_n[is_nonzero]
	340	self.mx = self.mx[is_nonzero]
	341	self.my = self.my[is_nonzero]
	342	self.mz = self.mz[is_nonzero]
	343	if recenter:
	344	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
	345	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
	346	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
[e3f77d8b]	347
[51f14603]	348	def get_magsld(self):
	349	"""
	350	return MagSLD
	351	"""
	352	return self.output
[e3f77d8b]	353
	354
	355	class OMFReader(object):
[51f14603]	356	"""
	357	Class to load omf/ascii files (3 columns w/header).
	358	"""
	359	## File type
	360	type_name = "OMF ASCII"
[e3f77d8b]	361
[51f14603]	362	## Wildcards
	363	type = ["OMF files (.OMF, .omf)\|*.omf"]
	364	## List of allowed extensions
	365	ext = ['.omf', '.OMF']
[e3f77d8b]	366
[51f14603]	367	def read(self, path):
	368	"""
	369	Load data file
	370	:param path: file path
	371	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	372	"""
	373	desc = ""
	374	mx = numpy.zeros(0)
	375	my = numpy.zeros(0)
	376	mz = numpy.zeros(0)
	377	try:
	378	input_f = open(path, 'rb')
	379	buff = input_f.read()
	380	lines = buff.split('\n')
	381	input_f.close()
	382	output = OMFData()
	383	valueunit = None
	384	for line in lines:
	385	toks = line.split()
	386	# Read data
	387	try:
	388	_mx = float(toks[0])
	389	_my = float(toks[1])
	390	_mz = float(toks[2])
	391	_mx = mag2sld(_mx, valueunit)
	392	_my = mag2sld(_my, valueunit)
	393	_mz = mag2sld(_mz, valueunit)
	394	mx = numpy.append(mx, _mx)
	395	my = numpy.append(my, _my)
	396	mz = numpy.append(mz, _mz)
	397	except:
	398	# Skip non-data lines
[b6627d9]	399	logging.error(sys.exc_value)
[51f14603]	400	#Reading Header; Segment count ignored
	401	s_line = line.split(":", 1)
	402	if s_line[0].lower().count("oommf") > 0:
	403	oommf = s_line[1].lstrip()
	404	if s_line[0].lower().count("title") > 0:
	405	title = s_line[1].lstrip()
	406	if s_line[0].lower().count("desc") > 0:
	407	desc += s_line[1].lstrip()
	408	desc += '\n'
	409	if s_line[0].lower().count("meshtype") > 0:
	410	meshtype = s_line[1].lstrip()
	411	if s_line[0].lower().count("meshunit") > 0:
	412	meshunit = s_line[1].lstrip()
	413	if meshunit.count("m") < 1:
	414	msg = "Error: \n"
	415	msg += "We accept only m as meshunit"
	416	raise ValueError, msg
	417	if s_line[0].lower().count("xbase") > 0:
	418	xbase = s_line[1].lstrip()
	419	if s_line[0].lower().count("ybase") > 0:
	420	ybase = s_line[1].lstrip()
	421	if s_line[0].lower().count("zbase") > 0:
	422	zbase = s_line[1].lstrip()
	423	if s_line[0].lower().count("xstepsize") > 0:
	424	xstepsize = s_line[1].lstrip()
	425	if s_line[0].lower().count("ystepsize") > 0:
	426	ystepsize = s_line[1].lstrip()
	427	if s_line[0].lower().count("zstepsize") > 0:
	428	zstepsize = s_line[1].lstrip()
	429	if s_line[0].lower().count("xnodes") > 0:
	430	xnodes = s_line[1].lstrip()
	431	if s_line[0].lower().count("ynodes") > 0:
	432	ynodes = s_line[1].lstrip()
	433	if s_line[0].lower().count("znodes") > 0:
	434	znodes = s_line[1].lstrip()
	435	if s_line[0].lower().count("xmin") > 0:
	436	xmin = s_line[1].lstrip()
	437	if s_line[0].lower().count("ymin") > 0:
	438	ymin = s_line[1].lstrip()
	439	if s_line[0].lower().count("zmin") > 0:
	440	zmin = s_line[1].lstrip()
	441	if s_line[0].lower().count("xmax") > 0:
	442	xmax = s_line[1].lstrip()
	443	if s_line[0].lower().count("ymax") > 0:
	444	ymax = s_line[1].lstrip()
	445	if s_line[0].lower().count("zmax") > 0:
	446	zmax = s_line[1].lstrip()
	447	if s_line[0].lower().count("valueunit") > 0:
	448	valueunit = s_line[1].lstrip().rstrip()
	449	if s_line[0].lower().count("valuemultiplier") > 0:
	450	valuemultiplier = s_line[1].lstrip()
	451	if s_line[0].lower().count("valuerangeminmag") > 0:
	452	valuerangeminmag = s_line[1].lstrip()
	453	if s_line[0].lower().count("valuerangemaxmag") > 0:
	454	valuerangemaxmag = s_line[1].lstrip()
	455	if s_line[0].lower().count("end") > 0:
	456	output.filename = os.path.basename(path)
	457	output.oommf = oommf
	458	output.title = title
	459	output.desc = desc
	460	output.meshtype = meshtype
	461	output.xbase = float(xbase) * METER2ANG
	462	output.ybase = float(ybase) * METER2ANG
	463	output.zbase = float(zbase) * METER2ANG
	464	output.xstepsize = float(xstepsize) * METER2ANG
	465	output.ystepsize = float(ystepsize) * METER2ANG
	466	output.zstepsize = float(zstepsize) * METER2ANG
	467	output.xnodes = float(xnodes)
	468	output.ynodes = float(ynodes)
	469	output.znodes = float(znodes)
	470	output.xmin = float(xmin) * METER2ANG
	471	output.ymin = float(ymin) * METER2ANG
	472	output.zmin = float(zmin) * METER2ANG
	473	output.xmax = float(xmax) * METER2ANG
	474	output.ymax = float(ymax) * METER2ANG
	475	output.zmax = float(zmax) * METER2ANG
	476	output.valuemultiplier = valuemultiplier
	477	output.valuerangeminmag = mag2sld(float(valuerangeminmag), \
	478	valueunit)
	479	output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \
	480	valueunit)
	481	output.set_m(mx, my, mz)
	482	return output
	483	except:
	484	msg = "%s is not supported: \n" % path
	485	msg += "We accept only Text format OMF file."
	486	raise RuntimeError, msg
	487
[e3f77d8b]	488	class PDBReader(object):
[51f14603]	489	"""
	490	PDB reader class: limited for reading the lines starting with 'ATOM'
	491	"""
	492	type_name = "PDB"
	493	## Wildcards
	494	type = ["pdb files (.PDB, .pdb)\|*.pdb"]
	495	## List of allowed extensions
[e3f77d8b]	496	ext = ['.pdb', '.PDB']
	497
[51f14603]	498	def read(self, path):
	499	"""
	500	Load data file
[e3f77d8b]	501
[51f14603]	502	:param path: file path
	503	:return: MagSLD
	504	:raise RuntimeError: when the file can't be opened
	505	"""
	506	pos_x = numpy.zeros(0)
	507	pos_y = numpy.zeros(0)
	508	pos_z = numpy.zeros(0)
	509	sld_n = numpy.zeros(0)
	510	sld_mx = numpy.zeros(0)
	511	sld_my = numpy.zeros(0)
	512	sld_mz = numpy.zeros(0)
	513	vol_pix = numpy.zeros(0)
	514	pix_symbol = numpy.zeros(0)
	515	x_line = []
	516	y_line = []
	517	z_line = []
	518	x_lines = []
	519	y_lines = []
[e3f77d8b]	520	z_lines = []
[51f14603]	521	try:
	522	input_f = open(path, 'rb')
	523	buff = input_f.read()
	524	lines = buff.split('\n')
	525	input_f.close()
	526	num = 0
	527	for line in lines:
	528	try:
	529	# check if line starts with "ATOM"
	530	if line[0:6].strip().count('ATM') > 0 or \
	531	line[0:6].strip() == 'ATOM':
	532	# define fields of interest
	533	atom_name = line[12:16].strip()
	534	try:
	535	float(line[12])
	536	atom_name = atom_name[1].upper()
	537	except:
	538	if len(atom_name) == 4:
	539	atom_name = atom_name[0].upper()
[e3f77d8b]	540	elif line[12] != ' ':
[51f14603]	541	atom_name = atom_name[0].upper() + \
[e3f77d8b]	542	atom_name[1].lower()
[51f14603]	543	else:
	544	atom_name = atom_name[0].upper()
	545	_pos_x = float(line[30:38].strip())
	546	_pos_y = float(line[38:46].strip())
	547	_pos_z = float(line[46:54].strip())
	548	pos_x = numpy.append(pos_x, _pos_x)
	549	pos_y = numpy.append(pos_y, _pos_y)
	550	pos_z = numpy.append(pos_z, _pos_z)
	551	try:
	552	val = nsf.neutron_sld(atom_name)[0]
	553	# sld in Ang^-2 unit
	554	val *= 1.0e-6
	555	sld_n = numpy.append(sld_n, val)
	556	atom = formula(atom_name)
	557	# cm to A units
	558	vol = 1.0e+24 * atom.mass / atom.density / NA
	559	vol_pix = numpy.append(vol_pix, vol)
	560	except:
	561	print "Error: set the sld of %s to zero"% atom_name
[e3f77d8b]	562	sld_n = numpy.append(sld_n, 0.0)
[51f14603]	563	sld_mx = numpy.append(sld_mx, 0)
	564	sld_my = numpy.append(sld_my, 0)
	565	sld_mz = numpy.append(sld_mz, 0)
	566	pix_symbol = numpy.append(pix_symbol, atom_name)
[e3f77d8b]	567	elif line[0:6].strip().count('CONECT') > 0:
[51f14603]	568	toks = line.split()
[e3f77d8b]	569	num = int(toks[1]) - 1
	570	val_list = []
[51f14603]	571	for val in toks[2:]:
	572	try:
	573	int_val = int(val)
	574	except:
	575	break
	576	if int_val == 0:
	577	break
	578	val_list.append(int_val)
[e3f77d8b]	579	#need val_list ordered
[51f14603]	580	for val in val_list:
	581	index = val - 1
	582	if (pos_x[index], pos_x[num]) in x_line and \
	583	(pos_y[index], pos_y[num]) in y_line and \
	584	(pos_z[index], pos_z[num]) in z_line:
	585	continue
	586	x_line.append((pos_x[num], pos_x[index]))
	587	y_line.append((pos_y[num], pos_y[index]))
	588	z_line.append((pos_z[num], pos_z[index]))
	589	if len(x_line) > 0:
[e3f77d8b]	590	x_lines.append(x_line)
[51f14603]	591	y_lines.append(y_line)
[e3f77d8b]	592	z_lines.append(z_line)
[51f14603]	593	except:
[b6627d9]	594	logging.error(sys.exc_value)
[e3f77d8b]	595
[51f14603]	596	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
	597	output.set_conect_lines(x_line, y_line, z_line)
	598	output.filename = os.path.basename(path)
	599	output.set_pix_type('atom')
	600	output.set_pixel_symbols(pix_symbol)
	601	output.set_nodes()
	602	output.set_pixel_volumes(vol_pix)
	603	output.sld_unit = '1/A^(2)'
	604	return output
	605	except:
[e3f77d8b]	606	raise RuntimeError, "%s is not a sld file" % path
[51f14603]	607
	608	def write(self, path, data):
	609	"""
	610	Write
	611	"""
	612	print "Not implemented... "
	613
[e3f77d8b]	614	class SLDReader(object):
[51f14603]	615	"""
	616	Class to load ascii files (7 columns).
	617	"""
	618	## File type
	619	type_name = "SLD ASCII"
	620	## Wildcards
	621	type = ["sld files (.SLD, .sld)\|*.sld",
	622	"txt files (.TXT, .txt)\|*.txt",
	623	"all files (.)\|."]
	624	## List of allowed extensions
	625	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
	626	def read(self, path):
	627	"""
	628	Load data file
	629	:param path: file path
	630	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	631	:raise RuntimeError: when the file can't be opened
	632	:raise ValueError: when the length of the data vectors are inconsistent
	633	"""
	634	try:
	635	pos_x = numpy.zeros(0)
	636	pos_y = numpy.zeros(0)
	637	pos_z = numpy.zeros(0)
	638	sld_n = numpy.zeros(0)
	639	sld_mx = numpy.zeros(0)
	640	sld_my = numpy.zeros(0)
	641	sld_mz = numpy.zeros(0)
	642	try:
	643	# Use numpy to speed up loading
[e3f77d8b]	644	input_f = numpy.loadtxt(path, dtype='float', skiprows=1,
[51f14603]	645	ndmin=1, unpack=True)
	646	pos_x = numpy.array(input_f[0])
	647	pos_y = numpy.array(input_f[1])
	648	pos_z = numpy.array(input_f[2])
	649	sld_n = numpy.array(input_f[3])
	650	sld_mx = numpy.array(input_f[4])
	651	sld_my = numpy.array(input_f[5])
	652	sld_mz = numpy.array(input_f[6])
	653	ncols = len(input_f)
	654	if ncols == 8:
	655	vol_pix = numpy.array(input_f[7])
	656	elif ncols == 7:
[e3f77d8b]	657	vol_pix = None
[51f14603]	658	except:
	659	# For older version of numpy
	660	input_f = open(path, 'rb')
	661	buff = input_f.read()
	662	lines = buff.split('\n')
	663	input_f.close()
	664	for line in lines:
	665	toks = line.split()
	666	try:
	667	_pos_x = float(toks[0])
	668	_pos_y = float(toks[1])
	669	_pos_z = float(toks[2])
	670	_sld_n = float(toks[3])
	671	_sld_mx = float(toks[4])
	672	_sld_my = float(toks[5])
	673	_sld_mz = float(toks[6])
	674	pos_x = numpy.append(pos_x, _pos_x)
	675	pos_y = numpy.append(pos_y, _pos_y)
	676	pos_z = numpy.append(pos_z, _pos_z)
	677	sld_n = numpy.append(sld_n, _sld_n)
	678	sld_mx = numpy.append(sld_mx, _sld_mx)
	679	sld_my = numpy.append(sld_my, _sld_my)
	680	sld_mz = numpy.append(sld_mz, _sld_mz)
	681	try:
[e3f77d8b]	682	_vol_pix = float(toks[7])
[51f14603]	683	vol_pix = numpy.append(vol_pix, _vol_pix)
	684	except:
	685	vol_pix = None
	686	except:
	687	# Skip non-data lines
[b6627d9]	688	logging.error(sys.exc_value)
[e3f77d8b]	689	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
[51f14603]	690	sld_mx, sld_my, sld_mz)
	691	output.filename = os.path.basename(path)
	692	output.set_pix_type('pixel')
	693	output.set_pixel_symbols('pixel')
	694	if vol_pix != None:
	695	output.set_pixel_volumes(vol_pix)
	696	return output
	697	except:
[e3f77d8b]	698	raise RuntimeError, "%s is not a sld file" % path
	699
[51f14603]	700	def write(self, path, data):
	701	"""
	702	Write sld file
[e3f77d8b]	703	:Param path: file path
[51f14603]	704	:Param data: MagSLD data object
	705	"""
	706	if path == None:
	707	raise ValueError, "Missing the file path."
	708	if data == None:
	709	raise ValueError, "Missing the data to save."
	710	x_val = data.pos_x
	711	y_val = data.pos_y
	712	z_val = data.pos_z
	713	vol_pix = data.vol_pix
	714	length = len(x_val)
	715	sld_n = data.sld_n
	716	if sld_n == None:
[e3f77d8b]	717	sld_n = numpy.zeros(length)
[51f14603]	718	sld_mx = data.sld_mx
	719	if sld_mx == None:
[e3f77d8b]	720	sld_mx = numpy.zeros(length)
	721	sld_my = numpy.zeros(length)
	722	sld_mz = numpy.zeros(length)
[51f14603]	723	else:
	724	sld_my = data.sld_my
	725	sld_mz = data.sld_mz
	726	out = open(path, 'w')
	727	# First Line: Column names
	728	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
	729	for ind in range(length):
[e3f77d8b]	730	out.write("\n%g %g %g %g %g %g %g %g" % \
	731	(x_val[ind], y_val[ind], z_val[ind], sld_n[ind],
	732	sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind]))
	733	out.close()
	734
	735
	736	class OMFData(object):
[51f14603]	737	"""
	738	OMF Data.
	739	"""
	740	_meshunit = "A"
	741	_valueunit = "A^(-2)"
	742	def __init__(self):
	743	"""
	744	Init for mag SLD
	745	"""
	746	self.filename = 'default'
	747	self.oommf = ''
	748	self.title = ''
	749	self.desc = ''
	750	self.meshtype = ''
	751	self.meshunit = self._meshunit
	752	self.valueunit = self._valueunit
	753	self.xbase = 0.0
	754	self.ybase = 0.0
	755	self.zbase = 0.0
	756	self.xstepsize = 6.0
	757	self.ystepsize = 6.0
	758	self.zstepsize = 6.0
	759	self.xnodes = 10.0
	760	self.ynodes = 10.0
	761	self.znodes = 10.0
	762	self.xmin = 0.0
	763	self.ymin = 0.0
	764	self.zmin = 0.0
	765	self.xmax = 60.0
	766	self.ymax = 60.0
	767	self.zmax = 60.0
	768	self.mx = None
	769	self.my = None
	770	self.mz = None
	771	self.valuemultiplier = 1.
	772	self.valuerangeminmag = 0
	773	self.valuerangemaxmag = 0
[e3f77d8b]	774
[51f14603]	775	def __str__(self):
	776	"""
	777	doc strings
	778	"""
[e3f77d8b]	779	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	780	_str += "File: %s\n" % self.filename
	781	_str += "OOMMF: %s\n" % self.oommf
	782	_str += "Title: %s\n" % self.title
	783	_str += "Desc: %s\n" % self.desc
	784	_str += "meshtype: %s\n" % self.meshtype
	785	_str += "meshunit: %s\n" % str(self.meshunit)
	786	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
	787	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
	788	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
[e3f77d8b]	789	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
[51f14603]	790	self.meshunit)
[e3f77d8b]	791	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
[51f14603]	792	self.meshunit)
[e3f77d8b]	793	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
[51f14603]	794	self.meshunit)
	795	_str += "xnodes: %s\n" % str(self.xnodes)
	796	_str += "ynodes: %s\n" % str(self.ynodes)
	797	_str += "znodes: %s\n" % str(self.znodes)
	798	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
	799	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
	800	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
	801	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
	802	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
	803	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
	804	_str += "valueunit: %s\n" % self.valueunit
	805	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
[e3f77d8b]	806	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
	807	self.valueunit)
	808	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
	809	self.valueunit)
[51f14603]	810	return _str
[e3f77d8b]	811
[51f14603]	812	def set_m(self, mx, my, mz):
	813	"""
	814	Set the Mx, My, Mz values
	815	"""
	816	self.mx = mx
	817	self.my = my
	818	self.mz = mz
[e3f77d8b]	819
	820	class MagSLD(object):
[51f14603]	821	"""
	822	Magnetic SLD.
	823	"""
	824	pos_x = None
	825	pos_y = None
	826	pos_z = None
	827	sld_n = None
	828	sld_mx = None
	829	sld_my = None
	830	sld_mz = None
	831	# Units
	832	_pos_unit = 'A'
	833	_sld_unit = '1/A^(2)'
	834	_pix_type = 'pixel'
[e3f77d8b]	835
	836	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
[51f14603]	837	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
	838	"""
	839	Init for mag SLD
	840	:params : All should be numpy 1D array
	841	"""
	842	self.is_data = True
	843	self.filename = ''
	844	self.xstepsize = 6.0
	845	self.ystepsize = 6.0
	846	self.zstepsize = 6.0
	847	self.xnodes = 10.0
	848	self.ynodes = 10.0
	849	self.znodes = 10.0
	850	self.has_stepsize = False
	851	self.has_conect = False
	852	self.pos_unit = self._pos_unit
	853	self.sld_unit = self._sld_unit
	854	self.pix_type = 'pixel'
	855	self.pos_x = pos_x
	856	self.pos_y = pos_y
	857	self.pos_z = pos_z
	858	self.sld_n = sld_n
	859	self.line_x = None
	860	self.line_y = None
	861	self.line_z = None
	862	self.sld_mx = sld_mx
	863	self.sld_my = sld_my
	864	self.sld_mz = sld_mz
	865	self.vol_pix = vol_pix
	866	self.sld_m = None
	867	self.sld_phi = None
	868	self.sld_theta = None
	869	self.pix_symbol = None
	870	if sld_mx != None and sld_my != None and sld_mz != None:
	871	self.set_sldms(sld_mx, sld_my, sld_mz)
	872	self.set_nodes()
[e3f77d8b]	873
[51f14603]	874	def __str__(self):
	875	"""
	876	doc strings
	877	"""
[e3f77d8b]	878	_str = "Type: %s\n" % self.__class__.__name__
[51f14603]	879	_str += "File: %s\n" % self.filename
	880	_str += "Axis_unit: %s\n" % self.pos_unit
	881	_str += "SLD_unit: %s\n" % self.sld_unit
	882	return _str
[e3f77d8b]	883
[51f14603]	884	def set_pix_type(self, pix_type):
	885	"""
	886	Set pixel type
	887	:Param pix_type: string, 'pixel' or 'atom'
	888	"""
	889	self.pix_type = pix_type
[e3f77d8b]	890
[51f14603]	891	def set_sldn(self, sld_n):
	892	"""
	893	Sets neutron SLD
	894	"""
	895	if sld_n.__class__.__name__ == 'float':
	896	if self.is_data:
[e3f77d8b]	897	# For data, put the value to only the pixels w non-zero M
	898	is_nonzero = (numpy.fabs(self.sld_mx) +
	899	numpy.fabs(self.sld_my) +
	900	numpy.fabs(self.sld_mz)).nonzero()
[51f14603]	901	self.sld_n = numpy.zeros(len(self.pos_x))
	902	if len(self.sld_n[is_nonzero]) > 0:
	903	self.sld_n[is_nonzero] = sld_n
	904	else:
	905	self.sld_n.fill(sld_n)
	906	else:
	907	# For non-data, put the value to all the pixels
	908	self.sld_n = numpy.ones(len(self.pos_x)) * sld_n
	909	else:
	910	self.sld_n = sld_n
[e3f77d8b]	911
[51f14603]	912	def set_sldms(self, sld_mx, sld_my, sld_mz):
	913	"""
[e3f77d8b]	914	Sets (\|m\|, m_theta, m_phi)
[51f14603]	915	"""
	916	if sld_mx.__class__.__name__ == 'float':
	917	self.sld_mx = numpy.ones(len(self.pos_x)) * sld_mx
	918	else:
	919	self.sld_mx = sld_mx
	920	if sld_my.__class__.__name__ == 'float':
	921	self.sld_my = numpy.ones(len(self.pos_x)) * sld_my
	922	else:
	923	self.sld_my = sld_my
	924	if sld_mz.__class__.__name__ == 'float':
	925	self.sld_mz = numpy.ones(len(self.pos_x)) * sld_mz
	926	else:
	927	self.sld_mz = sld_mz
	928
	929	sld_m = numpy.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
[e3f77d8b]	930	sld_mz * sld_mz)
[51f14603]	931	self.sld_m = sld_m
[e3f77d8b]	932
	933	def set_pixel_symbols(self, symbol='pixel'):
[51f14603]	934	"""
	935	Set pixel
	936	:Params pixel: str; pixel or atomic symbol, or array of strings
	937	"""
	938	if self.sld_n == None:
	939	return
	940	if symbol.__class__.__name__ == 'str':
	941	self.pix_symbol = numpy.repeat(symbol, len(self.sld_n))
	942	else:
	943	self.pix_symbol = symbol
[e3f77d8b]	944
	945	def set_pixel_volumes(self, vol):
[51f14603]	946	"""
	947	Set pixel volumes
	948	:Params pixel: str; pixel or atomic symbol, or array of strings
	949	"""
	950	if self.sld_n == None:
	951	return
	952	if vol.__class__.__name__ == 'ndarray':
	953	self.vol_pix = vol
	954	elif vol.__class__.__name__.count('float') > 0:
	955	self.vol_pix = numpy.repeat(vol, len(self.sld_n))
	956	else:
	957	self.vol_pix = None
	958
	959	def get_sldn(self):
	960	"""
	961	Returns nuclear sld
	962	"""
	963	return self.sld_n
[e3f77d8b]	964
[51f14603]	965	def set_nodes(self):
	966	"""
	967	Set xnodes, ynodes, and znodes
	968	"""
	969	self.set_stepsize()
	970	if self.pix_type == 'pixel':
	971	try:
	972	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
	973	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
	974	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
	975	self.xnodes = int(xdist) + 1
	976	self.ynodes = int(ydist) + 1
	977	self.znodes = int(zdist) + 1
	978	except:
	979	self.xnodes = None
	980	self.ynodes = None
	981	self.znodes = None
	982	else:
	983	self.xnodes = None
	984	self.ynodes = None
	985	self.znodes = None
[e3f77d8b]	986
[51f14603]	987	def set_stepsize(self):
	988	"""
	989	Set xtepsize, ystepsize, and zstepsize
	990	"""
	991	if self.pix_type == 'pixel':
	992	try:
	993	xpos_pre = self.pos_x[0]
	994	ypos_pre = self.pos_y[0]
	995	zpos_pre = self.pos_z[0]
	996	for x_pos in self.pos_x:
	997	if xpos_pre != x_pos:
	998	self.xstepsize = numpy.fabs(x_pos - xpos_pre)
	999	break
	1000	for y_pos in self.pos_y:
	1001	if ypos_pre != y_pos:
	1002	self.ystepsize = numpy.fabs(y_pos - ypos_pre)
	1003	break
	1004	for z_pos in self.pos_z:
	1005	if zpos_pre != z_pos:
	1006	self.zstepsize = numpy.fabs(z_pos - zpos_pre)
	1007	break
	1008	#default pix volume
	1009	self.vol_pix = numpy.ones(len(self.pos_x))
	1010	vol = self.xstepsize * self.ystepsize * self.zstepsize
	1011	self.set_pixel_volumes(vol)
	1012	self.has_stepsize = True
	1013	except:
	1014	self.xstepsize = None
	1015	self.ystepsize = None
	1016	self.zstepsize = None
	1017	self.vol_pix = None
	1018	self.has_stepsize = False
	1019	else:
	1020	self.xstepsize = None
	1021	self.ystepsize = None
	1022	self.zstepsize = None
	1023	self.has_stepsize = True
	1024	return self.xstepsize, self.ystepsize, self.zstepsize
	1025
	1026	def set_conect_lines(self, line_x, line_y, line_z):
	1027	"""
	1028	Set bonding line data if taken from pdb
	1029	"""
	1030	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
	1031	return
	1032	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
	1033	return
	1034	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
	1035	return
	1036	self.has_conect = True
[e3f77d8b]	1037	self.line_x = line_x
	1038	self.line_y = line_y
[51f14603]	1039	self.line_z = line_z
	1040
	1041	def test_load():
[b6627d9]	1042	"""
	1043	Test code
	1044	"""
[79492222]	1045	from sas.plottools.arrow3d import Arrow3D
[e3f77d8b]	1046	current_dir = os.path.abspath(os.path.curdir)
	1047	print current_dir
[51f14603]	1048	for i in range(6):
[e3f77d8b]	1049	current_dir, _ = os.path.split(current_dir)
	1050	tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt")
	1051	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
[51f14603]	1052	if os.path.isfile(tfile):
	1053	tfpath = tfile
	1054	ofpath = ofile
	1055	break
	1056	reader = SLDReader()
	1057	oreader = OMFReader()
	1058	output = reader.read(tfpath)
	1059	ooutput = oreader.read(ofpath)
	1060	foutput = OMF2SLD()
	1061	foutput.set_data(ooutput)
	1062
	1063	import matplotlib.pyplot as plt
	1064	fig = plt.figure()
	1065	ax = fig.gca(projection='3d')
[e3f77d8b]	1066	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
	1067	alpha=0.7, markeredgecolor='gray', rasterized=True)
[51f14603]	1068	gap = 7
	1069	max_mx = max(output.sld_mx)
	1070	max_my = max(output.sld_my)
	1071	max_mz = max(output.sld_mz)
[e3f77d8b]	1072	max_m = max(max_mx, max_my, max_mz)
[51f14603]	1073	x2 = output.pos_x+output.sld_mx/max_m * gap
	1074	y2 = output.pos_y+output.sld_my/max_m * gap
	1075	z2 = output.pos_z+output.sld_mz/max_m * gap
[e3f77d8b]	1076	x_arrow = numpy.column_stack((output.pos_x, x2))
	1077	y_arrow = numpy.column_stack((output.pos_y, y2))
	1078	z_arrow = numpy.column_stack((output.pos_z, z2))
[51f14603]	1079	unit_x2 = output.sld_mx / max_m
	1080	unit_y2 = output.sld_my / max_m
	1081	unit_z2 = output.sld_mz / max_m
	1082	color_x = numpy.fabs(unit_x2 * 0.8)
	1083	color_y = numpy.fabs(unit_y2 * 0.8)
	1084	color_z = numpy.fabs(unit_z2 * 0.8)
[e3f77d8b]	1085	colors = numpy.column_stack((color_x, color_y, color_z))
	1086	a = Arrow3D(None, x_arrow, y_arrow, z_arrow, colors,
	1087	mutation_scale=10, lw=1, arrowstyle="->",
	1088	color="y", alpha=0.5)
[51f14603]	1089	ax.add_artist(a)
	1090	plt.show()
[b6627d9]	1091
[51f14603]	1092	def test():
[b6627d9]	1093	"""
	1094	Test code
	1095	"""
[e3f77d8b]	1096	current_dir = os.path.abspath(os.path.curdir)
[51f14603]	1097	for i in range(3):
[e3f77d8b]	1098	current_dir, _ = os.path.split(current_dir)
	1099	ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf")
[51f14603]	1100	if os.path.isfile(ofile):
	1101	ofpath = ofile
	1102	break
	1103	oreader = OMFReader()
	1104	ooutput = oreader.read(ofpath)
[e3f77d8b]	1105	foutput = OMF2SLD()
	1106	foutput.set_data(ooutput)
	1107	writer = SLDReader()
	1108	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
[51f14603]	1109	foutput.output)
	1110	model = GenSAS()
[e3f77d8b]	1111	model.set_sld_data(foutput.output)
[51f14603]	1112	x = numpy.arange(1000)/10000. + 1e-5
	1113	y = numpy.arange(1000)/10000. + 1e-5
	1114	i = numpy.zeros(1000)
[e3f77d8b]	1115	model.runXY([x, y, i])
	1116
	1117	if __name__ == "__main__":
[51f14603]	1118	test()
	1119	test_load()

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SasView

source: sasview/src/sas/calculator/sas_gen.py @ b9dbd6b

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