sas_gen.py @ 379b87a

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 379b87a was fd5ac0d, checked in by krzywon, 10 years ago
I have completed the removal of all SANS references. I will build, run, and run all unit tests before pushing.
Property mode set to `100644`
File size: 41.8 KB

Rev	Line
[51f14603]	1	"""
[fd5ac0d]	2	SAS generic computation and sld file readers
[51f14603]	3	"""
[79492222]	4	from sas.models.BaseComponent import BaseComponent
	5	import sas.models.sas_extension.sld2i as mod
[51f14603]	6	from periodictable import formula
	7	from periodictable import nsf
	8	import numpy
	9	import os
	10	import copy
	11
	12	MFactor_AM = 2.853E-12
	13	MFactor_mT = 2.3164E-9
	14	METER2ANG = 1.0E+10
	15	#Avogadro constant [1/mol]
	16	NA = 6.02214129e+23
	17
	18	def mag2sld(mag, v_unit=None):
	19	"""
	20	Convert magnetization to magnatic SLD
	21	sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)
	22	Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???
	23	"""
	24	if v_unit == "A/m":
	25	factor = MFactor_AM
	26	elif v_unit == "mT":
	27	factor = MFactor_mT
	28	else:
	29	raise ValueError, "Invalid valueunit"
	30	sld_m = factor * mag
	31	return sld_m
	32
	33	def transform_center(pos_x, pos_y, pos_z):
	34	"""
	35	re-center
	36
	37	:return: posx, posy, posz [arrays]
	38	"""
	39	posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0
	40	posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0
	41	posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0
	42	return posx, posy, posz
	43
	44	class GenSAS(BaseComponent):
	45	"""
	46	Generic SAS computation Model based on sld (n & m) arrays
	47	"""
	48	def __init__(self):
	49	"""
	50	Init
	51
	52	:Params sld_data: MagSLD object
	53	"""
	54	# Initialize BaseComponent
	55	BaseComponent.__init__(self)
	56	self.sld_data = None
	57	self.data_pos_unit = None
	58	self.data_x = None
	59	self.data_y = None
	60	self.data_z = None
	61	self.data_sldn = None
	62	self.data_mx = None
	63	self.data_my = None
	64	self.data_mz = None
	65	self.data_vol = None #[A^3]
	66	self.is_avg = False
	67	## Name of the model
	68	self.name = "GenSAS"
	69	## Define parameters
	70	self.params = {}
	71	self.params['scale'] = 1.0
	72	self.params['background'] = 0.0
	73	self.params['solvent_SLD'] = 0.0
	74	self.params['total_volume'] = 1.0
	75	self.params['Up_frac_in'] = 1.0
	76	self.params['Up_frac_out'] = 1.0
	77	self.params['Up_theta'] = 0.0
	78	self.description = 'GenSAS'
	79	## Parameter details [units, min, max]
	80	self.details = {}
	81	self.details['scale'] = ['', None, None]
	82	self.details['background'] = ['[1/cm]', None, None]
	83	self.details['solvent_SLD'] = ['1/A^(2)', None, None]
	84	self.details['total_volume'] = ['A^(3)', None, None]
	85	self.details['Up_frac_in'] = ['[u/(u+d)]', None, None]
	86	self.details['Up_frac_out'] = ['[u/(u+d)]', None, None]
	87	self.details['Up_theta'] = ['[deg]', None, None]
	88	# fixed parameters
	89	self.fixed = []
	90
	91	def set_pixel_volumes(self, volume):
	92	"""
	93	Set the volume of a pixel in (A^3) unit
	94	:Param volume: pixel volume [float]
	95	"""
	96	if self.data_vol == None:
	97	raise
	98	self.data_vol = volume
	99
	100	def set_is_avg(self, is_avg=False):
	101	"""
	102	Sets is_avg: [bool]
	103	"""
	104	self.is_avg = is_avg
	105
	106	def _gen(self, x, y, i):
	107	"""
	108	Evaluate the function
	109	:Param x: array of x-values
	110	:Param y: array of y-values
	111	:Param i: array of initial i-value
	112	:return: function value
	113	"""
	114	pos_x = self.data_x
	115	pos_y = self.data_y
	116	pos_z = self.data_z
	117	len_x = len(pos_x)
	118	if self.is_avg == None:
	119	len_x *= -1
	120	pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z)
	121	len_q = len(x)
	122	sldn = copy.deepcopy(self.data_sldn)
	123	sldn -= self.params['solvent_SLD']
	124	model = mod.new_GenI(len_x, pos_x, pos_y, pos_z,
	125	sldn, self.data_mx, self.data_my,
	126	self.data_mz, self.data_vol,
	127	self.params['Up_frac_in'],
	128	self.params['Up_frac_out'],
	129	self.params['Up_theta'])
	130	if y == []:
	131	mod.genicom(model, len_q, x, i)
	132	else:
	133	mod.genicomXY(model, len_q, x, y, i)
	134	vol_correction = self.data_total_volume / self.params['total_volume']
	135	return self.params['scale'] * vol_correction * i + \
	136	self.params['background']
	137
	138	def set_sld_data(self, sld_data=None):
	139	"""
	140	Sets sld_data
	141	"""
	142	self.sld_data = sld_data
	143	self.data_pos_unit = sld_data.pos_unit
	144	self.data_x = sld_data.pos_x
	145	self.data_y = sld_data.pos_y
	146	self.data_z = sld_data.pos_z
	147	self.data_sldn = sld_data.sld_n
	148	self.data_mx = sld_data.sld_mx
	149	self.data_my = sld_data.sld_my
	150	self.data_mz = sld_data.sld_mz
	151	self.data_vol = sld_data.vol_pix
	152	self.data_total_volume = sum(sld_data.vol_pix)
	153	self.params['total_volume'] = sum(sld_data.vol_pix)
	154
	155	def getProfile(self):
	156	"""
	157	Get SLD profile
	158
	159	: return: sld_data
	160	"""
	161	return self.sld_data
	162
	163	def run(self, x = 0.0):
	164	"""
	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
	175	out = self._gen(x[0], [], i_out )
	176	return out
	177	else:
	178	msg = "Q must be given as list of qx's and qy's"
	179	raise ValueError, msg
	180
	181	def runXY(self, x = 0.0):
	182	"""
	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
	195
	196	def evalDistribution(self, qdist):
	197	"""
	198	Evaluate a distribution of q-values.
	199	* For 1D, a numpy array is expected as input: evalDistribution(q) where q is a numpy array.
	200	* For 2D, a list of numpy arrays are expected: [qx_prime,qy_prime], where 1D arrays.
	201	:param qdist: ndarray of scalar q-values or list [qx,qy] where qx,qy are 1D ndarrays
	202	"""
	203	if qdist.__class__.__name__ == 'list':
	204	if len(qdist[1]) < 1:
	205	out = self.run(qdist)
	206	else:
	207	out = self.runXY(qdist)
	208	return out
	209	else:
	210	mesg = "evalDistribution is expecting an ndarray of "
	211	mesg += "a list [qx,qy] where qx,qy are arrays."
	212	raise RuntimeError, mesg
	213
	214	class OMF2SLD:
	215	"""
	216	Convert OMFData to MAgData
	217	"""
	218	def __init__(self):
	219	"""
	220	Init
	221	"""
	222	self.pos_x = None
	223	self.pos_y = None
	224	self.pos_z = None
	225	self.mx = None
	226	self.my = None
	227	self.mz = None
	228	self.sld_n = None
	229	self.vol_pix = None
	230	self.output = None
	231	self.omfdata = None
	232
	233	def set_data(self, omfdata, shape='rectangular'):
	234	"""
	235	Set all data
	236	"""
	237	self.omfdata = omfdata
	238	length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes)
	239	pos_x = numpy.arange(omfdata.xmin,
	240	omfdata.xnodes*omfdata.xstepsize + omfdata.xmin,
	241	omfdata.xstepsize)
	242	pos_y = numpy.arange(omfdata.ymin,
	243	omfdata.ynodes*omfdata.ystepsize + omfdata.ymin,
	244	omfdata.ystepsize)
	245	pos_z = numpy.arange(omfdata.zmin,
	246	omfdata.znodes*omfdata.zstepsize + omfdata.zmin,
	247	omfdata.zstepsize)
	248	self.pos_x = numpy.tile(pos_x, int(omfdata.ynodes * omfdata.znodes))
	249	self.pos_y = pos_y.repeat(int(omfdata.xnodes))
	250	self.pos_y = numpy.tile(self.pos_y, int(omfdata.znodes))
	251	self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes))
	252	self.mx = omfdata.mx
	253	self.my = omfdata.my
	254	self.mz = omfdata.mz
	255	self.sld_n = numpy.zeros(length)
	256
	257	if omfdata.mx == None:
	258	self.mx = numpy.zeros(length)
	259	if omfdata.my == None:
	260	self.my = numpy.zeros(length)
	261	if omfdata.mz == None:
	262	self.mz = numpy.zeros(length)
	263
	264	self._check_data_length(length)
	265	self.remove_null_points(False, False)
	266	mask = numpy.ones(len(self.sld_n), dtype=bool)
	267	if shape.lower() == 'ellipsoid':
	268	try:
	269	# Pixel (step) size included
	270	x_c = max(self.pos_x) + min(self.pos_x)
	271	y_c = max(self.pos_y) + min(self.pos_y)
	272	z_c = max(self.pos_z) + min(self.pos_z)
	273	x_d = max(self.pos_x) - min(self.pos_x)
	274	y_d = max(self.pos_y) - min(self.pos_y)
	275	z_d = max(self.pos_z) - min(self.pos_z)
	276	x_r = (x_d + omfdata.xstepsize) / 2.0
	277	y_r = (y_d + omfdata.ystepsize) / 2.0
	278	z_r = (z_d + omfdata.zstepsize) / 2.0
	279	x_dir2 = ((self.pos_x - x_c / 2.0) / x_r)
	280	x_dir2 *= x_dir2
	281	y_dir2 = ((self.pos_y - y_c / 2.0) / y_r)
	282	y_dir2 *= y_dir2
	283	z_dir2 = ((self.pos_z - z_c / 2.0) / z_r)
	284	z_dir2 *= z_dir2
	285	mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
	286	except:
	287	pass
	288	self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
	289	self.pos_z[mask], self.sld_n[mask],
	290	self.mx[mask], self.my[mask], self.mz[mask])
	291	self.output.set_pix_type('pixel')
	292	self.output.set_pixel_symbols('pixel')
	293
	294	def get_omfdata(self):
	295	"""
	296	Return all data
	297	"""
	298	return self.omfdata
	299
	300	def get_output(self):
	301	"""
	302	Return output
	303	"""
	304	return self.output
	305
	306	def _check_data_length(self, length):
	307	"""
	308	Check if the data lengths are consistent
	309	:Params length: data length
	310	"""
	311	msg = "Error: Inconsistent data length."
	312	if len(self.pos_x) != length:
	313	raise ValueError, msg
	314	if len(self.pos_y) != length:
	315	raise ValueError, msg
	316	if len(self.pos_z) != length:
	317	raise ValueError, msg
	318	if len(self.mx) != length:
	319	raise ValueError, msg
	320	if len(self.my) != length:
	321	raise ValueError, msg
	322	if len(self.mz) != length:
	323	raise ValueError, msg
	324
	325	def remove_null_points(self, remove=False, recenter=False):
	326	"""
	327	Removes any mx, my, and mz = 0 points
	328	"""
	329	if remove:
	330	is_nonzero = (numpy.fabs(self.mx) + numpy.fabs(self.my) +
	331	numpy.fabs(self.mz)).nonzero()
	332	if len(is_nonzero[0]) > 0:
	333	self.pos_x = self.pos_x[is_nonzero]
	334	self.pos_y = self.pos_y[is_nonzero]
	335	self.pos_z = self.pos_z[is_nonzero]
	336	self.sld_n = self.sld_n[is_nonzero]
	337	self.mx = self.mx[is_nonzero]
	338	self.my = self.my[is_nonzero]
	339	self.mz = self.mz[is_nonzero]
	340	if recenter:
	341	self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0
	342	self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0
	343	self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
	344
	345	def get_magsld(self):
	346	"""
	347	return MagSLD
	348	"""
	349	return self.output
	350
	351
	352	class OMFReader:
	353	"""
	354	Class to load omf/ascii files (3 columns w/header).
	355	"""
	356	## File type
	357	type_name = "OMF ASCII"
	358
	359	## Wildcards
	360	type = ["OMF files (.OMF, .omf)\|*.omf"]
	361	## List of allowed extensions
	362	ext = ['.omf', '.OMF']
	363
	364	def read(self, path):
	365	"""
	366	Load data file
	367	:param path: file path
	368	:return: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	369	"""
	370	#data_conv_m = None
	371	desc = ""
	372	mx = numpy.zeros(0)
	373	my = numpy.zeros(0)
	374	mz = numpy.zeros(0)
	375	try:
	376	data_conv_val = None
	377	data_conv_mesh = None
	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
	399	pass
	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.set_sldms(mx, my, mz)
	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
	489	class PDBReader:
	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
	497	ext = ['.pdb', '.PDB']
	498
	499	def read(self, path):
	500	"""
	501	Load data file
	502
	503	:param path: file path
	504
	505	:return: MagSLD
	506
	507	:raise RuntimeError: when the file can't be opened
	508	"""
	509	pos_x = numpy.zeros(0)
	510	pos_y = numpy.zeros(0)
	511	pos_z = numpy.zeros(0)
	512	sld_n = numpy.zeros(0)
	513	sld_mx = numpy.zeros(0)
	514	sld_my = numpy.zeros(0)
	515	sld_mz = numpy.zeros(0)
	516	vol_pix = numpy.zeros(0)
	517	pix_symbol = numpy.zeros(0)
	518	x_line = []
	519	y_line = []
	520	z_line = []
	521	x_lines = []
	522	y_lines = []
	523	z_lines = []
	524	try:
	525	input_f = open(path, 'rb')
	526	buff = input_f.read()
	527	lines = buff.split('\n')
	528	input_f.close()
	529	pre_num = 0
	530	num = 0
	531	for line in lines:
	532	try:
	533	# check if line starts with "ATOM"
	534	if line[0:6].strip().count('ATM') > 0 or \
	535	line[0:6].strip() == 'ATOM':
	536	# define fields of interest
	537	atom_id = line[6:11].strip()
	538	atom_name = line[12:16].strip()
	539	try:
	540	float(line[12])
	541	atom_name = atom_name[1].upper()
	542	except:
	543	if len(atom_name) == 4:
	544	atom_name = atom_name[0].upper()
	545	elif line[12] != ' ':
	546	atom_name = atom_name[0].upper() + \
	547	atom_name[1].lower()
	548	else:
	549	atom_name = atom_name[0].upper()
	550	#res_name = line[17:20].strip()
	551	#chain_name = line[21:22].strip()
	552	_pos_x = float(line[30:38].strip())
	553	_pos_y = float(line[38:46].strip())
	554	_pos_z = float(line[46:54].strip())
	555
	556	pos_x = numpy.append(pos_x, _pos_x)
	557	pos_y = numpy.append(pos_y, _pos_y)
	558	pos_z = numpy.append(pos_z, _pos_z)
	559	try:
	560	# sld in Ang unit (from fm)
	561	#val = formula(atom_name).atoms.keys()[0].neutron.b_c
	562	#val *= 1.0e-5
	563	val = nsf.neutron_sld(atom_name)[0]
	564	# sld in Ang^-2 unit
	565	val *= 1.0e-6
	566	sld_n = numpy.append(sld_n, val)
	567	atom = formula(atom_name)
	568	# cm to A units
	569	vol = 1.0e+24 * atom.mass / atom.density / NA
	570	vol_pix = numpy.append(vol_pix, vol)
	571	except:
	572	print "Error: set the sld of %s to zero"% atom_name
	573	sld_n = numpy.append(sld_n, 0.0)
	574	sld_mx = numpy.append(sld_mx, 0)
	575	sld_my = numpy.append(sld_my, 0)
	576	sld_mz = numpy.append(sld_mz, 0)
	577	pix_symbol = numpy.append(pix_symbol, atom_name)
	578	elif line[0:6].strip().count('CONECT') > 0 :
	579	toks = line.split()
	580	num = int(toks[1]) - 1
	581	val_list = []
	582	for val in toks[2:]:
	583	try:
	584	int_val = int(val)
	585	except:
	586	break
	587	if int_val == 0:
	588	break
	589	val_list.append(int_val)
	590	#need val_list ordered
	591	for val in val_list:
	592	index = val - 1
	593	if (pos_x[index], pos_x[num]) in x_line and \
	594	(pos_y[index], pos_y[num]) in y_line and \
	595	(pos_z[index], pos_z[num]) in z_line:
	596	continue
	597	x_line.append((pos_x[num], pos_x[index]))
	598	y_line.append((pos_y[num], pos_y[index]))
	599	z_line.append((pos_z[num], pos_z[index]))
	600	if len(x_line) > 0:
	601	x_lines.append(x_line)
	602	y_lines.append(y_line)
	603	z_lines.append(z_line)
	604	except:
	605	pass
	606	#re-centering
	607	#pos_x -= (min(pos_x) + max(pos_x)) / 2.0
	608	#pos_y -= (min(pos_y) + max(pos_y)) / 2.0
	609	#pos_z -= (min(pos_z) + max(pos_z)) / 2.0
	610
	611	output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
	612	output.set_conect_lines(x_line, y_line, z_line)
	613	output.filename = os.path.basename(path)
	614	output.set_pix_type('atom')
	615	output.set_pixel_symbols(pix_symbol)
	616	output.set_nodes()
	617	output.set_pixel_volumes(vol_pix)
	618	output.sld_unit = '1/A^(2)'
	619	return output
	620	except:
	621	RuntimeError, "%s is not a sld file" % path
	622
	623	def write(self, path, data):
	624	"""
	625	Write
	626	"""
	627	#Not implemented
	628	print "Not implemented... "
	629
	630	class SLDReader:
	631	"""
	632	Class to load ascii files (7 columns).
	633	"""
	634	## File type
	635	type_name = "SLD ASCII"
	636
	637	## Wildcards
	638	type = ["sld files (.SLD, .sld)\|*.sld",
	639	"txt files (.TXT, .txt)\|*.txt",
	640	"all files (.)\|."]
	641	## List of allowed extensions
	642	ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
	643
	644	def read(self, path):
	645	"""
	646	Load data file
	647
	648	:param path: file path
	649
	650	:return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz
	651
	652	:raise RuntimeError: when the file can't be opened
	653	:raise ValueError: when the length of the data vectors are inconsistent
	654	"""
	655	try:
	656	pos_x = numpy.zeros(0)
	657	pos_y = numpy.zeros(0)
	658	pos_z = numpy.zeros(0)
	659	sld_n = numpy.zeros(0)
	660	sld_mx = numpy.zeros(0)
	661	sld_my = numpy.zeros(0)
	662	sld_mz = numpy.zeros(0)
	663	try:
	664	# Use numpy to speed up loading
	665	input_f = numpy.loadtxt(path, dtype='float', skiprows=1,
	666	ndmin=1, unpack=True)
	667	pos_x = numpy.array(input_f[0])
	668	pos_y = numpy.array(input_f[1])
	669	pos_z = numpy.array(input_f[2])
	670	sld_n = numpy.array(input_f[3])
	671	sld_mx = numpy.array(input_f[4])
	672	sld_my = numpy.array(input_f[5])
	673	sld_mz = numpy.array(input_f[6])
	674	ncols = len(input_f)
	675	if ncols == 8:
	676	vol_pix = numpy.array(input_f[7])
	677	elif ncols == 7:
	678	vol_pix = None
	679	except:
	680	# For older version of numpy
	681	input_f = open(path, 'rb')
	682	buff = input_f.read()
	683	lines = buff.split('\n')
	684	input_f.close()
	685	for line in lines:
	686	toks = line.split()
	687	try:
	688	_pos_x = float(toks[0])
	689	_pos_y = float(toks[1])
	690	_pos_z = float(toks[2])
	691	_sld_n = float(toks[3])
	692	_sld_mx = float(toks[4])
	693	_sld_my = float(toks[5])
	694	_sld_mz = float(toks[6])
	695
	696	pos_x = numpy.append(pos_x, _pos_x)
	697	pos_y = numpy.append(pos_y, _pos_y)
	698	pos_z = numpy.append(pos_z, _pos_z)
	699	sld_n = numpy.append(sld_n, _sld_n)
	700	sld_mx = numpy.append(sld_mx, _sld_mx)
	701	sld_my = numpy.append(sld_my, _sld_my)
	702	sld_mz = numpy.append(sld_mz, _sld_mz)
	703	try:
	704	_vol_pix = float(toks[7])
	705	vol_pix = numpy.append(vol_pix, _vol_pix)
	706	except:
	707	vol_pix = None
	708	except:
	709	# Skip non-data lines
	710	pass
	711
	712	# re-center
	713	#pos_x -= (min(pos_x) + max(pos_x)) / 2.0
	714	#pos_y -= (min(pos_y) + max(pos_y)) / 2.0
	715	#pos_z -= (min(pos_z) + max(pos_z)) / 2.0
	716
	717	output = MagSLD(pos_x, pos_y, pos_z, sld_n,
	718	sld_mx, sld_my, sld_mz)
	719
	720	output.filename = os.path.basename(path)
	721	output.set_pix_type('pixel')
	722	output.set_pixel_symbols('pixel')
	723	if vol_pix != None:
	724	output.set_pixel_volumes(vol_pix)
	725	return output
	726	except:
	727	RuntimeError, "%s is not a sld file" % path
	728
	729	def write(self, path, data):
	730	"""
	731	Write sld file
	732
	733	:Param path: file path
	734	:Param data: MagSLD data object
	735	"""
	736	if path == None:
	737	raise ValueError, "Missing the file path."
	738	if data == None:
	739	raise ValueError, "Missing the data to save."
	740
	741	x_val = data.pos_x
	742	y_val = data.pos_y
	743	z_val = data.pos_z
	744	vol_pix = data.vol_pix
	745
	746	length = len(x_val)
	747
	748	sld_n = data.sld_n
	749	if sld_n == None:
	750	sld_n = numpy.zerros(length)
	751
	752	sld_mx = data.sld_mx
	753	if sld_mx == None:
	754	sld_mx = numpy.zerros(length)
	755	sld_my = numpy.zerros(length)
	756	sld_mz = numpy.zerros(length)
	757	else:
	758	sld_my = data.sld_my
	759	sld_mz = data.sld_mz
	760
	761	out = open(path, 'w')
	762	# First Line: Column names
	763	out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix")
	764	for ind in range(length):
	765	out.write("\n%g %g %g %g %g %g %g %g" % (x_val[ind], y_val[ind],
	766	z_val[ind], sld_n[ind],
	767	sld_mx[ind], sld_my[ind],
	768	sld_mz[ind], vol_pix[ind]))
	769	out.close()
	770
	771
	772	class OMFData:
	773	"""
	774	OMF Data.
	775	"""
	776	_meshunit = "A"
	777	_valueunit = "A^(-2)"
	778	def __init__(self):
	779	"""
	780	Init for mag SLD
	781	"""
	782	self.filename = 'default'
	783	self.oommf = ''
	784	self.title = ''
	785	self.desc = ''
	786	self.meshtype = ''
	787	self.meshunit = self._meshunit
	788	self.valueunit = self._valueunit
	789	self.xbase = 0.0
	790	self.ybase = 0.0
	791	self.zbase = 0.0
	792	self.xstepsize = 6.0
	793	self.ystepsize = 6.0
	794	self.zstepsize = 6.0
	795	self.xnodes = 10.0
	796	self.ynodes = 10.0
	797	self.znodes = 10.0
	798	self.xmin = 0.0
	799	self.ymin = 0.0
	800	self.zmin = 0.0
	801	self.xmax = 60.0
	802	self.ymax = 60.0
	803	self.zmax = 60.0
	804	self.mx = None
	805	self.my = None
	806	self.mz = None
	807	self.valuemultiplier = 1.
	808	self.valuerangeminmag = 0
	809	self.valuerangemaxmag = 0
	810
	811	def __str__(self):
	812	"""
	813	doc strings
	814	"""
	815	_str = "Type: %s\n" % self.__class__.__name__
	816	_str += "File: %s\n" % self.filename
	817	_str += "OOMMF: %s\n" % self.oommf
	818	_str += "Title: %s\n" % self.title
	819	_str += "Desc: %s\n" % self.desc
	820	_str += "meshtype: %s\n" % self.meshtype
	821	_str += "meshunit: %s\n" % str(self.meshunit)
	822	_str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit)
	823	_str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit)
	824	_str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit)
	825	_str += "xstepsize: %s [%s]\n" % (str(self.xstepsize),
	826	self.meshunit)
	827	_str += "ystepsize: %s [%s]\n" % (str(self.ystepsize),
	828	self.meshunit)
	829	_str += "zstepsize: %s [%s]\n" % (str(self.zstepsize),
	830	self.meshunit)
	831	_str += "xnodes: %s\n" % str(self.xnodes)
	832	_str += "ynodes: %s\n" % str(self.ynodes)
	833	_str += "znodes: %s\n" % str(self.znodes)
	834	_str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit)
	835	_str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit)
	836	_str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit)
	837	_str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit)
	838	_str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit)
	839	_str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit)
	840	_str += "valueunit: %s\n" % self.valueunit
	841	_str += "valuemultiplier: %s\n" % str(self.valuemultiplier)
	842	_str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag),
	843	self.valueunit)
	844	_str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag),
	845	self.valueunit)
	846	return _str
	847
	848	def set_m(self, mx, my, mz):
	849	"""
	850	Set the Mx, My, Mz values
	851	"""
	852	self.mx = mx
	853	self.my = my
	854	self.mz = mz
	855
	856	class MagSLD:
	857	"""
	858	Magnetic SLD.
	859	"""
	860	pos_x = None
	861	pos_y = None
	862	pos_z = None
	863	sld_n = None
	864	sld_mx = None
	865	sld_my = None
	866	sld_mz = None
	867	# Units
	868	_pos_unit = 'A'
	869	_sld_unit = '1/A^(2)'
	870	_pix_type = 'pixel'
	871
	872	def __init__(self, pos_x, pos_y, pos_z, sld_n=None,
	873	sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None):
	874	"""
	875	Init for mag SLD
	876	:params : All should be numpy 1D array
	877	"""
	878	self.is_data = True
	879	self.filename = ''
	880	self.xstepsize = 6.0
	881	self.ystepsize = 6.0
	882	self.zstepsize = 6.0
	883	self.xnodes = 10.0
	884	self.ynodes = 10.0
	885	self.znodes = 10.0
	886	self.has_stepsize = False
	887	self.has_conect = False
	888	self.pos_unit = self._pos_unit
	889	self.sld_unit = self._sld_unit
	890	self.pix_type = 'pixel'
	891	self.pos_x = pos_x
	892	self.pos_y = pos_y
	893	self.pos_z = pos_z
	894	self.sld_n = sld_n
	895	self.line_x = None
	896	self.line_y = None
	897	self.line_z = None
	898	self.sld_mx = sld_mx
	899	self.sld_my = sld_my
	900	self.sld_mz = sld_mz
	901	self.vol_pix = vol_pix
	902	self.sld_m = None
	903	self.sld_phi = None
	904	self.sld_theta = None
	905	self.pix_symbol = None
	906	if sld_mx != None and sld_my != None and sld_mz != None:
	907	self.set_sldms(sld_mx, sld_my, sld_mz)
	908	self.set_nodes()
	909
	910	def __str__(self):
	911	"""
	912	doc strings
	913	"""
	914	_str = "Type: %s\n" % self.__class__.__name__
	915	_str += "File: %s\n" % self.filename
	916	_str += "Axis_unit: %s\n" % self.pos_unit
	917	_str += "SLD_unit: %s\n" % self.sld_unit
	918	return _str
	919
	920	def set_pix_type(self, pix_type):
	921	"""
	922	Set pixel type
	923	:Param pix_type: string, 'pixel' or 'atom'
	924	"""
	925	self.pix_type = pix_type
	926
	927	def set_sldn(self, sld_n):
	928	"""
	929	Sets neutron SLD
	930	"""
	931	if sld_n.__class__.__name__ == 'float':
	932	if self.is_data:
	933	# For data, put the value to only the pixels w non-zero M
	934	is_nonzero = (numpy.fabs(self.sld_mx) +
	935	numpy.fabs(self.sld_my) +
	936	numpy.fabs(self.sld_mz)).nonzero()
	937	self.sld_n = numpy.zeros(len(self.pos_x))
	938	if len(self.sld_n[is_nonzero]) > 0:
	939	self.sld_n[is_nonzero] = sld_n
	940	else:
	941	self.sld_n.fill(sld_n)
	942	else:
	943	# For non-data, put the value to all the pixels
	944	self.sld_n = numpy.ones(len(self.pos_x)) * sld_n
	945	else:
	946	self.sld_n = sld_n
	947
	948	def set_sldms(self, sld_mx, sld_my, sld_mz):
	949	"""
	950	Sets (\\|m\\|, m_theta, m_phi)
	951	"""
	952	if sld_mx.__class__.__name__ == 'float':
	953	self.sld_mx = numpy.ones(len(self.pos_x)) * sld_mx
	954	else:
	955	self.sld_mx = sld_mx
	956	if sld_my.__class__.__name__ == 'float':
	957	self.sld_my = numpy.ones(len(self.pos_x)) * sld_my
	958	else:
	959	self.sld_my = sld_my
	960	if sld_mz.__class__.__name__ == 'float':
	961	self.sld_mz = numpy.ones(len(self.pos_x)) * sld_mz
	962	else:
	963	self.sld_mz = sld_mz
	964
	965	sld_m = numpy.sqrt(sld_mx * sld_mx + sld_my * sld_my + \
	966	sld_mz * sld_mz)
	967	self.sld_m = sld_m
	968
	969	def set_pixel_symbols(self, symbol='pixel'):
	970	"""
	971	Set pixel
	972	:Params pixel: str; pixel or atomic symbol, or array of strings
	973	"""
	974	if self.sld_n == None:
	975	return
	976	if symbol.__class__.__name__ == 'str':
	977	self.pix_symbol = numpy.repeat(symbol, len(self.sld_n))
	978	else:
	979	self.pix_symbol = symbol
	980
	981	def set_pixel_volumes(self, vol):
	982	"""
	983	Set pixel volumes
	984	:Params pixel: str; pixel or atomic symbol, or array of strings
	985	"""
	986	if self.sld_n == None:
	987	return
	988	if vol.__class__.__name__ == 'ndarray':
	989	self.vol_pix = vol
	990	elif vol.__class__.__name__.count('float') > 0:
	991	self.vol_pix = numpy.repeat(vol, len(self.sld_n))
	992	else:
	993	self.vol_pix = None
	994
	995	def get_sldn(self):
	996	"""
	997	Returns nuclear sld
	998	"""
	999	return self.sld_n
	1000
	1001	def get_sld_mxyz(self):
	1002	"""
	1003	Returns (sld_mx, sldmy, sld_mz)
	1004	"""
	1005	return (self.sld_mx, self.sldmy, self.sld_mz)
	1006
	1007	def get_sld_m(self):
	1008	"""
	1009	Returns (sldm, sld_theta, sld_phi)
	1010	"""
	1011	return (self.sldm, self.sld_theta, self.sld_phi)
	1012
	1013	def set_nodes(self):
	1014	"""
	1015	Set xnodes, ynodes, and znodes
	1016	"""
	1017	self.set_stepsize()
	1018	if self.pix_type == 'pixel':
	1019	try:
	1020	xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize
	1021	ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize
	1022	zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize
	1023	self.xnodes = int(xdist) + 1
	1024	self.ynodes = int(ydist) + 1
	1025	self.znodes = int(zdist) + 1
	1026	except:
	1027	self.xnodes = None
	1028	self.ynodes = None
	1029	self.znodes = None
	1030	else:
	1031	self.xnodes = None
	1032	self.ynodes = None
	1033	self.znodes = None
	1034
	1035	def set_stepsize(self):
	1036	"""
	1037	Set xtepsize, ystepsize, and zstepsize
	1038	"""
	1039	if self.pix_type == 'pixel':
	1040	try:
	1041	xpos_pre = self.pos_x[0]
	1042	ypos_pre = self.pos_y[0]
	1043	zpos_pre = self.pos_z[0]
	1044	for x_pos in self.pos_x:
	1045	if xpos_pre != x_pos:
	1046	self.xstepsize = numpy.fabs(x_pos - xpos_pre)
	1047	break
	1048	for y_pos in self.pos_y:
	1049	if ypos_pre != y_pos:
	1050	self.ystepsize = numpy.fabs(y_pos - ypos_pre)
	1051	break
	1052	for z_pos in self.pos_z:
	1053	if zpos_pre != z_pos:
	1054	self.zstepsize = numpy.fabs(z_pos - zpos_pre)
	1055	break
	1056	#default pix volume
	1057	self.vol_pix = numpy.ones(len(self.pos_x))
	1058	vol = self.xstepsize * self.ystepsize * self.zstepsize
	1059	self.set_pixel_volumes(vol)
	1060	self.has_stepsize = True
	1061	except:
	1062	self.xstepsize = None
	1063	self.ystepsize = None
	1064	self.zstepsize = None
	1065	self.vol_pix = None
	1066	self.has_stepsize = False
	1067	else:
	1068	self.xstepsize = None
	1069	self.ystepsize = None
	1070	self.zstepsize = None
	1071	self.has_stepsize = True
	1072	return self.xstepsize, self.ystepsize, self.zstepsize
	1073
	1074	def set_conect_lines(self, line_x, line_y, line_z):
	1075	"""
	1076	Set bonding line data if taken from pdb
	1077	"""
	1078	if line_x.__class__.__name__ != 'list' or len(line_x) < 1:
	1079	return
	1080	if line_y.__class__.__name__ != 'list' or len(line_y) < 1:
	1081	return
	1082	if line_z.__class__.__name__ != 'list' or len(line_z) < 1:
	1083	return
	1084	self.has_conect = True
	1085	self.line_x = line_x
	1086	self.line_y = line_y
	1087	self.line_z = line_z
	1088
	1089
	1090	def test_load():
[79492222]	1091	from sas.plottools.arrow3d import Arrow3D
[51f14603]	1092	import os
	1093	dir = os.path.abspath(os.path.curdir)
	1094	print dir
	1095	for i in range(6):
	1096	dir, _ = os.path.split(dir)
	1097	tfile = os.path.join(dir, "test", "CoreXY_ShellZ.txt")
	1098	ofile = os.path.join(dir, "test", "A_Raw_Example-1.omf")
	1099	if os.path.isfile(tfile):
	1100	tfpath = tfile
	1101	ofpath = ofile
	1102	break
	1103	reader = SLDReader()
	1104	oreader = OMFReader()
	1105	output = reader.read(tfpath)
	1106	ooutput = oreader.read(ofpath)
	1107	foutput = OMF2SLD()
	1108	foutput.set_data(ooutput)
	1109
	1110	import matplotlib.pyplot as plt
	1111	from mpl_toolkits.mplot3d import Axes3D
	1112	fig = plt.figure()
	1113	ax = fig.gca(projection='3d')
	1114	ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g",
	1115	alpha = 0.7, markeredgecolor='gray',rasterized=True)
	1116	gap = 7
	1117	max_mx = max(output.sld_mx)
	1118	max_my = max(output.sld_my)
	1119	max_mz = max(output.sld_mz)
	1120	max_m = max(max_mx,max_my,max_mz)
	1121	x2 = output.pos_x+output.sld_mx/max_m * gap
	1122	y2 = output.pos_y+output.sld_my/max_m * gap
	1123	z2 = output.pos_z+output.sld_mz/max_m * gap
	1124	x_arrow = numpy.column_stack((output.pos_x,x2))
	1125	y_arrow = numpy.column_stack((output.pos_y,y2))
	1126	z_arrow = numpy.column_stack((output.pos_z,z2))
	1127	unit_x2 = output.sld_mx / max_m
	1128	unit_y2 = output.sld_my / max_m
	1129	unit_z2 = output.sld_mz / max_m
	1130	color_x = numpy.fabs(unit_x2 * 0.8)
	1131	color_y = numpy.fabs(unit_y2 * 0.8)
	1132	color_z = numpy.fabs(unit_z2 * 0.8)
	1133	colors = numpy.column_stack((color_x, color_y, color_z))
	1134	a = Arrow3D(None, x_arrow,y_arrow,z_arrow, colors, mutation_scale=10, lw=1,
	1135	arrowstyle="->", color="y", alpha = 0.5)
	1136
	1137	ax.add_artist(a)
	1138	plt.show()
	1139
	1140	def test():
	1141	import os
	1142	dir = os.path.abspath(os.path.curdir)
	1143	for i in range(3):
	1144	dir, _ = os.path.split(dir)
	1145	#tfile = os.path.join(dir, "test", "C_Example_Converted.txt")
	1146	ofile = os.path.join(dir, "test", "A_Raw_Example-1.omf")
	1147	if os.path.isfile(ofile):
	1148	#tfpath = tfile
	1149	ofpath = ofile
	1150	break
	1151	#reader = SLDReader()
	1152	oreader = OMFReader()
	1153	#output = reader.read(tfpath)
	1154	ooutput = oreader.read(ofpath)
	1155	foutput = OMF2SLD()
	1156	foutput.set_data(ooutput)
	1157	writer = SLDReader()
	1158	writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"),
	1159	foutput.output)
	1160	model = GenSAS()
	1161	model.set_sld_data(foutput.output)
	1162	x = numpy.arange(1000)/10000. + 1e-5
	1163	y = numpy.arange(1000)/10000. + 1e-5
	1164	#z = numpy.arange(1000)/10000. + 1e-5
	1165	i = numpy.zeros(1000)
	1166	out = model.runXY([x,y,i])
	1167
	1168	if __name__ == "__main__":
	1169	test()
	1170	test_load()

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SasView

source: sasview/src/sas/calculator/sas_gen.py @ 379b87a

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