pagestate.py @ 845144e

magnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249unittest-saveload

Last change on this file since 845144e was 863ac2c, checked in by butler, 6 years ago

Update fix to pagestate.py for ticket-1179 branch as per P. Kienzle

Use global already defined in pagestate.py instead of recreating it as
suggested by Paul Kienzle.

Property mode set to 100644

File size: 55.3 KB

Rev	Line
[959eb01]	1	"""
[ba8d326]	2	Class that holds a fit page state
[959eb01]	3	"""
	4	# TODO: Refactor code so we don't need to use getattr/setattr
	5	################################################################################
	6	# This software was developed by the University of Tennessee as part of the
	7	# Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	8	# project funded by the US National Science Foundation.
	9	#
	10	# See the license text in license.txt
	11	#
	12	# copyright 2009, University of Tennessee
	13	################################################################################
	14	import time
[59873e1]	15	import re
[959eb01]	16	import os
	17	import sys
	18	import copy
	19	import logging
	20	import numpy as np
	21	import traceback
	22
	23	import xml.dom.minidom
	24	from xml.dom.minidom import parseString
[00f7ff1]	25	from xml.dom.minidom import getDOMImplementation
[959eb01]	26	from lxml import etree
	27
	28	from sasmodels import convert
	29	import sasmodels.weights
	30
[00f7ff1]	31	from sas.sasview import __version__ as SASVIEW_VERSION
	32
[959eb01]	33	import sas.sascalc.dataloader
	34	from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader
	35	from sas.sascalc.dataloader.readers.cansas_reader import get_content, write_node
	36	from sas.sascalc.dataloader.data_info import Data2D, Collimation, Detector
	37	from sas.sascalc.dataloader.data_info import Process, Aperture
	38
	39	logger = logging.getLogger(__name__)
	40
	41	# Information to read/write state as xml
	42	FITTING_NODE_NAME = 'fitting_plug_in'
[ba8d326]	43	CANSAS_NS = {"ns": "cansas1d/1.0"}
[959eb01]	44
	45	CUSTOM_MODEL = 'Plugin Models'
	46	CUSTOM_MODEL_OLD = 'Customized Models'
	47
	48	LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"],
	49	["group_id", "data_group_id", "string"],
	50	["data_name", "data_name", "string"],
	51	["data_id", "data_id", "string"],
	52	["name", "name", "string"],
	53	["data_name", "data_name", "string"]]
	54	LIST_OF_STATE_ATTRIBUTES = [["qmin", "qmin", "float"],
	55	["qmax", "qmax", "float"],
	56	["npts", "npts", "float"],
	57	["categorycombobox", "categorycombobox", "string"],
	58	["formfactorcombobox", "formfactorcombobox",
	59	"string"],
	60	["structurecombobox", "structurecombobox",
	61	"string"],
	62	["multi_factor", "multi_factor", "float"],
	63	["magnetic_on", "magnetic_on", "bool"],
	64	["enable_smearer", "enable_smearer", "bool"],
	65	["disable_smearer", "disable_smearer", "bool"],
	66	["pinhole_smearer", "pinhole_smearer", "bool"],
	67	["slit_smearer", "slit_smearer", "bool"],
	68	["enable_disp", "enable_disp", "bool"],
	69	["disable_disp", "disable_disp", "bool"],
	70	["dI_noweight", "dI_noweight", "bool"],
	71	["dI_didata", "dI_didata", "bool"],
	72	["dI_sqrdata", "dI_sqrdata", "bool"],
	73	["dI_idata", "dI_idata", "bool"],
	74	["enable2D", "enable2D", "bool"],
	75	["cb1", "cb1", "bool"],
	76	["tcChi", "tcChi", "float"],
	77	["dq_l", "dq_l", "float"],
	78	["dq_r", "dq_r", "float"],
	79	["dx_percent", "dx_percent", "float"],
	80	["dxl", "dxl", "float"],
	81	["dxw", "dxw", "float"]]
	82
	83	LIST_OF_MODEL_ATTRIBUTES = [["values", "values"],
	84	["weights", "weights"]]
	85
[ba8d326]	86	DISPERSION_LIST = [["disp_obj_dict", "disp_obj_dict", "string"]]
[959eb01]	87
	88	LIST_OF_STATE_PARAMETERS = [["parameters", "parameters"],
	89	["str_parameters", "str_parameters"],
	90	["orientation_parameters", "orientation_params"],
	91	["dispersity_parameters",
	92	"orientation_params_disp"],
	93	["fixed_param", "fixed_param"],
	94	["fittable_param", "fittable_param"]]
	95	LIST_OF_DATA_2D_ATTR = [["xmin", "xmin", "float"],
	96	["xmax", "xmax", "float"],
	97	["ymin", "ymin", "float"],
	98	["ymax", "ymax", "float"],
	99	["_xaxis", "_xaxis", "string"],
	100	["_xunit", "_xunit", "string"],
	101	["_yaxis", "_yaxis", "string"],
	102	["_yunit", "_yunit", "string"],
	103	["_zaxis", "_zaxis", "string"],
	104	["_zunit", "_zunit", "string"]]
	105	LIST_OF_DATA_2D_VALUES = [["qx_data", "qx_data", "float"],
	106	["qy_data", "qy_data", "float"],
	107	["dqx_data", "dqx_data", "float"],
	108	["dqy_data", "dqy_data", "float"],
	109	["data", "data", "float"],
	110	["q_data", "q_data", "float"],
	111	["err_data", "err_data", "float"],
	112	["mask", "mask", "bool"]]
	113
	114
	115	def parse_entry_helper(node, item):
	116	"""
	117	Create a numpy list from value extrated from the node
	118
	119	:param node: node from each the value is stored
	120	:param item: list name of three strings.the two first are name of data
	121	attribute and the third one is the type of the value of that
	122	attribute. type can be string, float, bool, etc.
	123
	124	: return: numpy array
	125	"""
	126	if node is not None:
	127	if item[2] == "string":
	128	return str(node.get(item[0]).strip())
	129	elif item[2] == "bool":
	130	try:
	131	return node.get(item[0]).strip() == "True"
	132	except Exception:
	133	return None
	134	else:
	135	try:
	136	return float(node.get(item[0]))
	137	except Exception:
	138	return None
	139
	140
	141	class PageState(object):
	142	"""
	143	Contains information to reconstruct a page of the fitpanel.
	144	"""
[00f7ff1]	145	def __init__(self, model=None, data=None):
[959eb01]	146	"""
	147	Initialize the current state
	148
	149	:param model: a selected model within a page
	150	:param data:
	151
	152	"""
	153	self.file = None
	154	# Time of state creation
	155	self.timestamp = time.time()
	156	# Data member to store the dispersion object created
[ba8d326]	157	self.disp_obj_dict = {}
[959eb01]	158	# ------------------------
	159	# Data used for fitting
	160	self.data = data
	161	# model data
	162	self.theory_data = None
	163	# Is 2D
	164	self.is_2D = False
	165	self.images = None
	166
	167	# save additional information on data that dataloader.reader
	168	# does not read
	169	self.is_data = None
	170	self.data_name = ""
	171
	172	if self.data is not None:
	173	self.data_name = self.data.name
	174	self.data_id = None
	175	if self.data is not None and hasattr(self.data, "id"):
	176	self.data_id = self.data.id
	177	self.data_group_id = None
	178	if self.data is not None and hasattr(self.data, "group_id"):
	179	self.data_group_id = self.data.group_id
	180
	181	# reset True change the state of existing button
	182	self.reset = False
	183
	184	# flag to allow data2D plot
	185	self.enable2D = False
	186	# model on which the fit would be performed
	187	self.model = model
	188	self.m_name = None
	189	# list of process done to model
	190	self.process = []
	191	# fit page manager
	192	self.manager = None
	193	# Event_owner is the owner of model event
	194	self.event_owner = None
	195	# page name
	196	self.page_name = ""
	197	# Contains link between model, its parameters, and panel organization
	198	self.parameters = []
	199	# String parameter list that can not be fitted
	200	self.str_parameters = []
	201	# Contains list of parameters that cannot be fitted and reference to
	202	# panel objects
	203	self.fixed_param = []
	204	# Contains list of parameters with dispersity and reference to
	205	# panel objects
	206	self.fittable_param = []
	207	# orientation parameters
	208	self.orientation_params = []
	209	# orientation parameters for gaussian dispersity
	210	self.orientation_params_disp = []
	211	self.dq_l = None
	212	self.dq_r = None
	213	self.dx_percent = None
	214	self.dx_old = False
	215	self.dxl = None
	216	self.dxw = None
	217	# list of dispersion parameters
	218	self.disp_list = []
	219	if self.model is not None:
	220	self.disp_list = self.model.getDispParamList()
	221
	222	self.disp_cb_dict = {}
	223	self.values = {}
	224	self.weights = {}
	225
	226	# contains link between a model and selected parameters to fit
	227	self.param_toFit = []
	228	# save the state of the context menu
	229	self.saved_states = {}
	230	# save selection of combobox
	231	self.formfactorcombobox = None
	232	self.categorycombobox = None
	233	self.structurecombobox = None
	234
	235	# radio box to select type of model
	236	# self.shape_rbutton = False
	237	# self.shape_indep_rbutton = False
	238	# self.struct_rbutton = False
	239	# self.plugin_rbutton = False
	240	# the indice of the current selection
	241	self.disp_box = 0
	242	# Qrange
	243	# Q range
	244	self.qmin = 0.001
	245	self.qmax = 0.1
	246	# reset data range
	247	self.qmax_x = None
	248	self.qmin_x = None
	249
	250	self.npts = None
	251	self.name = ""
	252	self.multi_factor = None
	253	self.magnetic_on = False
	254	# enable smearering state
	255	self.enable_smearer = False
	256	self.disable_smearer = True
	257	self.pinhole_smearer = False
	258	self.slit_smearer = False
	259	# weighting options
	260	self.dI_noweight = False
	261	self.dI_didata = True
	262	self.dI_sqrdata = False
	263	self.dI_idata = False
	264	# disperity selection
	265	self.enable_disp = False
	266	self.disable_disp = True
	267
	268	# state of selected all check button
	269	self.cb1 = False
	270	# store value of chisqr
	271	self.tcChi = None
[ba8d326]	272	self.version = (1, 0, 0)
[959eb01]	273
	274	def clone(self):
	275	"""
	276	Create a new copy of the current object
	277	"""
	278	model = None
	279	if self.model is not None:
	280	model = self.model.clone()
	281	model.name = self.model.name
[00f7ff1]	282	obj = PageState(model=model)
[959eb01]	283	obj.file = copy.deepcopy(self.file)
	284	obj.data = copy.deepcopy(self.data)
	285	if self.data is not None:
	286	self.data_name = self.data.name
	287	obj.data_name = self.data_name
	288	obj.is_data = self.is_data
	289
	290	obj.categorycombobox = self.categorycombobox
	291	obj.formfactorcombobox = self.formfactorcombobox
	292	obj.structurecombobox = self.structurecombobox
	293
	294	# obj.shape_rbutton = self.shape_rbutton
	295	# obj.shape_indep_rbutton = self.shape_indep_rbutton
	296	# obj.struct_rbutton = self.struct_rbutton
	297	# obj.plugin_rbutton = self.plugin_rbutton
	298
	299	obj.manager = self.manager
	300	obj.event_owner = self.event_owner
	301	obj.disp_list = copy.deepcopy(self.disp_list)
	302
	303	obj.enable2D = copy.deepcopy(self.enable2D)
	304	obj.parameters = copy.deepcopy(self.parameters)
	305	obj.str_parameters = copy.deepcopy(self.str_parameters)
	306	obj.fixed_param = copy.deepcopy(self.fixed_param)
	307	obj.fittable_param = copy.deepcopy(self.fittable_param)
	308	obj.orientation_params = copy.deepcopy(self.orientation_params)
	309	obj.orientation_params_disp = \
	310	copy.deepcopy(self.orientation_params_disp)
	311	obj.enable_disp = copy.deepcopy(self.enable_disp)
	312	obj.disable_disp = copy.deepcopy(self.disable_disp)
	313	obj.tcChi = self.tcChi
	314
[ba8d326]	315	if len(self.disp_obj_dict) > 0:
[574adc7]	316	for k, v in self.disp_obj_dict.items():
[ba8d326]	317	obj.disp_obj_dict[k] = v
[959eb01]	318	if len(self.disp_cb_dict) > 0:
[574adc7]	319	for k, v in self.disp_cb_dict.items():
[959eb01]	320	obj.disp_cb_dict[k] = v
	321	if len(self.values) > 0:
[574adc7]	322	for k, v in self.values.items():
[959eb01]	323	obj.values[k] = v
	324	if len(self.weights) > 0:
[574adc7]	325	for k, v in self.weights.items():
[959eb01]	326	obj.weights[k] = v
	327	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
	328	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
	329	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
	330	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
	331	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
	332	obj.dI_didata = copy.deepcopy(self.dI_didata)
	333	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
	334	obj.dI_idata = copy.deepcopy(self.dI_idata)
	335	obj.dq_l = copy.deepcopy(self.dq_l)
	336	obj.dq_r = copy.deepcopy(self.dq_r)
	337	obj.dx_percent = copy.deepcopy(self.dx_percent)
	338	obj.dx_old = copy.deepcopy(self.dx_old)
	339	obj.dxl = copy.deepcopy(self.dxl)
	340	obj.dxw = copy.deepcopy(self.dxw)
	341	obj.disp_box = copy.deepcopy(self.disp_box)
	342	obj.qmin = copy.deepcopy(self.qmin)
	343	obj.qmax = copy.deepcopy(self.qmax)
	344	obj.multi_factor = self.multi_factor
	345	obj.magnetic_on = self.magnetic_on
	346	obj.npts = copy.deepcopy(self.npts)
	347	obj.cb1 = copy.deepcopy(self.cb1)
	348	obj.version = copy.deepcopy(self.version)
	349
[574adc7]	350	for name, state in self.saved_states.items():
[959eb01]	351	copy_name = copy.deepcopy(name)
	352	copy_state = state.clone()
	353	obj.saved_states[copy_name] = copy_state
	354	return obj
	355
	356	def _old_first_model(self):
	357	"""
	358	Handle save states from 4.0.1 and before where the first item in the
	359	selection boxes of category, formfactor and structurefactor were not
	360	saved.
	361	:return: None
	362	"""
	363	if self.categorycombobox == CUSTOM_MODEL_OLD:
	364	self.categorycombobox = CUSTOM_MODEL
	365	if self.formfactorcombobox == '':
	366	FIRST_FORM = {
	367	'Shapes' : 'BCCrystalModel',
	368	'Uncategorized' : 'LineModel',
	369	'StructureFactor' : 'HardsphereStructure',
	370	'Ellipsoid' : 'core_shell_ellipsoid',
	371	'Lamellae' : 'lamellar',
	372	'Paracrystal' : 'bcc_paracrystal',
	373	'Parallelepiped' : 'core_shell_parallelepiped',
	374	'Shape Independent' : 'be_polyelectrolyte',
	375	'Sphere' : 'adsorbed_layer',
	376	'Structure Factor' : 'hardsphere',
	377	CUSTOM_MODEL : ''
	378	}
	379	if self.categorycombobox == '':
	380	if len(self.parameters) == 3:
	381	self.categorycombobox = "Shape-Independent"
	382	self.formfactorcombobox = 'PowerLawAbsModel'
	383	elif len(self.parameters) == 9:
	384	self.categorycombobox = 'Cylinder'
	385	self.formfactorcombobox = 'barbell'
	386	else:
	387	msg = "Save state does not have enough information to load"
	388	msg += " the all of the data."
	389	logger.warning(msg=msg)
	390	else:
	391	self.formfactorcombobox = FIRST_FORM[self.categorycombobox]
	392
	393	@staticmethod
	394	def param_remap_to_sasmodels_convert(params, is_string=False):
	395	"""
	396	Remaps the parameters for sasmodels conversion
	397
	398	:param params: list of parameters (likely self.parameters)
	399	:return: remapped dictionary of parameters
	400	"""
	401	p = dict()
	402	for fittable, name, value, _, uncert, lower, upper, units in params:
	403	if not value:
	404	value = np.nan
	405	if not uncert or uncert[1] == '' or uncert[1] == 'None':
	406	uncert[0] = False
	407	uncert[1] = np.nan
	408	if not upper or upper[1] == '' or upper[1] == 'None':
	409	upper[0] = False
	410	upper[1] = np.nan
	411	if not lower or lower[1] == '' or lower[1] == 'None':
	412	lower[0] = False
	413	lower[1] = np.nan
	414	if is_string:
	415	p[name] = str(value)
	416	else:
	417	p[name] = float(value)
	418	p[name + ".fittable"] = bool(fittable)
	419	p[name + ".std"] = float(uncert[1])
	420	p[name + ".upper"] = float(upper[1])
	421	p[name + ".lower"] = float(lower[1])
	422	p[name + ".units"] = units
	423	return p
	424
	425	@staticmethod
	426	def param_remap_from_sasmodels_convert(params):
	427	"""
	428	Converts {name : value} map back to [] param list
	429	:param params: parameter map returned from sasmodels
	430	:return: None
	431	"""
	432	p_map = []
[574adc7]	433	for name, info in params.items():
[959eb01]	434	if ".fittable" in name or ".std" in name or ".upper" in name or \
	435	".lower" in name or ".units" in name:
	436	pass
	437	else:
	438	fittable = params.get(name + ".fittable", True)
	439	std = params.get(name + ".std", '0.0')
	440	upper = params.get(name + ".upper", 'inf')
	441	lower = params.get(name + ".lower", '-inf')
	442	units = params.get(name + ".units")
	443	if std is not None and std is not np.nan:
	444	std = [True, str(std)]
	445	else:
	446	std = [False, '']
	447	if lower is not None and lower is not np.nan:
	448	lower = [True, str(lower)]
	449	else:
	450	lower = [True, '-inf']
	451	if upper is not None and upper is not np.nan:
	452	upper = [True, str(upper)]
	453	else:
	454	upper = [True, 'inf']
	455	param_list = [bool(fittable), str(name), str(info),
	456	"+/-", std, lower, upper, str(units)]
	457	p_map.append(param_list)
	458	return p_map
	459
	460	def _convert_to_sasmodels(self):
	461	"""
	462	Convert parameters to a form usable by sasmodels converter
	463
	464	:return: None
	465	"""
	466	# Create conversion dictionary to send to sasmodels
	467	self._old_first_model()
	468	p = self.param_remap_to_sasmodels_convert(self.parameters)
	469	structurefactor, params = convert.convert_model(self.structurecombobox,
	470	p, False, self.version)
	471	formfactor, params = convert.convert_model(self.formfactorcombobox,
	472	params, False, self.version)
	473	if len(self.str_parameters) > 0:
	474	str_pars = self.param_remap_to_sasmodels_convert(
	475	self.str_parameters, True)
	476	formfactor, str_params = convert.convert_model(
	477	self.formfactorcombobox, str_pars, False, self.version)
[574adc7]	478	for key, value in str_params.items():
[959eb01]	479	params[key] = value
	480
	481	if self.formfactorcombobox == 'SphericalSLDModel':
	482	self.multi_factor += 1
	483	self.formfactorcombobox = formfactor
	484	self.structurecombobox = structurefactor
	485	self.parameters = []
	486	self.parameters = self.param_remap_from_sasmodels_convert(params)
	487
	488	def _repr_helper(self, list, rep):
	489	"""
	490	Helper method to print a state
	491	"""
	492	for item in list:
	493	rep += "parameter name: %s \n" % str(item[1])
	494	rep += "value: %s\n" % str(item[2])
	495	rep += "selected: %s\n" % str(item[0])
	496	rep += "error displayed : %s \n" % str(item[4][0])
	497	rep += "error value:%s \n" % str(item[4][1])
	498	rep += "minimum displayed : %s \n" % str(item[5][0])
	499	rep += "minimum value : %s \n" % str(item[5][1])
	500	rep += "maximum displayed : %s \n" % str(item[6][0])
	501	rep += "maximum value : %s \n" % str(item[6][1])
	502	rep += "parameter unit: %s\n\n" % str(item[7])
	503	return rep
	504
	505	def __repr__(self):
	506	"""
	507	output string for printing
	508	"""
	509	rep = "\nState name: %s\n" % self.file
	510	t = time.localtime(self.timestamp)
[78312f7]	511	time_str = time.strftime("%b %d %Y %H:%M:%S ", t)
[959eb01]	512
	513	rep += "State created: %s\n" % time_str
	514	rep += "State form factor combobox selection: %s\n" % \
	515	self.formfactorcombobox
	516	rep += "State structure factor combobox selection: %s\n" % \
	517	self.structurecombobox
	518	rep += "is data : %s\n" % self.is_data
	519	rep += "data's name : %s\n" % self.data_name
	520	rep += "data's id : %s\n" % self.data_id
	521	if self.model is not None:
	522	m_name = self.model.__class__.__name__
	523	if m_name == 'Model':
	524	m_name = self.m_name
	525	rep += "model name : %s\n" % m_name
	526	else:
	527	rep += "model name : None\n"
	528	rep += "multi_factor : %s\n" % str(self.multi_factor)
	529	rep += "magnetic_on : %s\n" % str(self.magnetic_on)
	530	rep += "model type (Category) selected: %s\n" % self.categorycombobox
	531	rep += "data : %s\n" % str(self.data)
	532	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % \
	533	(str(self.qmin), str(self.qmax), str(self.npts))
	534	rep += "Dispersion selection : %s\n" % str(self.disp_box)
	535	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
	536	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
	537	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
	538	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
	539	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
	540	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
	541	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
	542
	543	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
	544	rep += "dI_didata : %s\n" % str(self.dI_didata)
	545	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
	546	rep += "dI_idata : %s\n" % str(self.dI_idata)
	547
	548	rep += "2D enable : %s\n" % str(self.enable2D)
	549	rep += "All parameters checkbox selected: %s\n" % self.cb1
	550	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
	551	rep += "dq_l : %s\n" % self.dq_l
	552	rep += "dq_r : %s\n" % self.dq_r
	553	rep += "dx_percent : %s\n" % str(self.dx_percent)
	554	rep += "dxl : %s\n" % str(self.dxl)
	555	rep += "dxw : %s\n" % str(self.dxw)
	556	rep += "model : %s\n\n" % str(self.model)
	557	temp_parameters = []
	558	temp_fittable_param = []
	559	if self.data.__class__.__name__ == "Data2D":
	560	self.is_2D = True
	561	else:
	562	self.is_2D = False
	563	if self.data is not None:
	564	if not self.is_2D:
	565	for item in self.parameters:
	566	if item not in self.orientation_params:
	567	temp_parameters.append(item)
	568	for item in self.fittable_param:
	569	if item not in self.orientation_params_disp:
	570	temp_fittable_param.append(item)
	571	else:
	572	temp_parameters = self.parameters
	573	temp_fittable_param = self.fittable_param
	574
	575	rep += "number parameters(self.parameters): %s\n" % \
	576	len(temp_parameters)
	577	rep = self._repr_helper(list=temp_parameters, rep=rep)
	578	rep += "number str_parameters(self.str_parameters): %s\n" % \
	579	len(self.str_parameters)
	580	rep = self._repr_helper(list=self.str_parameters, rep=rep)
	581	rep += "number fittable_param(self.fittable_param): %s\n" % \
	582	len(temp_fittable_param)
	583	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
	584	return rep
	585
[78312f7]	586	def _get_report_string(self):
[959eb01]	587	"""
	588	Get the values (strings) from __str__ for report
	589	"""
	590	# Dictionary of the report strings
	591	repo_time = ""
	592	model_name = ""
	593	title = ""
	594	title_name = ""
	595	file_name = ""
	596	param_string = ""
	597	paramval_string = ""
	598	chi2_string = ""
	599	q_range = ""
	600	strings = self.__repr__()
[78312f7]	601	fixed_parameter = False
[959eb01]	602	lines = strings.split('\n')
	603	# get all string values from __str__()
	604	for line in lines:
[78312f7]	605	# Skip lines which are not key: value pairs, which includes
	606	# blank lines and freeform notes in SASNotes fields.
	607	if not ':' in line:
	608	#msg = "Report string expected 'name: value' but got %r" % line
	609	#logger.error(msg)
	610	continue
	611
	612	name, value = [s.strip() for s in line.split(":", 1)]
	613	if name == "State created":
	614	repo_time = value
	615	elif name == "parameter name":
[959eb01]	616	val_name = value.split(".")
	617	if len(val_name) > 1:
	618	if val_name[1].count("width"):
	619	param_string += value + ','
	620	else:
	621	continue
	622	else:
	623	param_string += value + ','
[78312f7]	624	elif name == "value":
[959eb01]	625	param_string += value + ','
[78312f7]	626	elif name == "selected":
	627	# remember if it is fixed when reporting error value
	628	fixed_parameter = (value == u'False')
	629	elif name == "error value":
[959eb01]	630	if fixed_parameter:
	631	param_string += '(fixed),'
	632	else:
	633	param_string += value + ','
[78312f7]	634	elif name == "parameter unit":
[959eb01]	635	param_string += value + ':'
[78312f7]	636	elif name == "Value of Chisqr":
[959eb01]	637	chi2 = ("Chi2/Npts = " + value)
	638	chi2_string = CENTRE % chi2
[78312f7]	639	elif name == "Title":
[959eb01]	640	if len(value.strip()) == 0:
	641	continue
[e9920cd]	642	title = (value + " [" + repo_time + "] [SasView v" +
[863ac2c]	643	SASVIEW_VERSION + "]")
[959eb01]	644	title_name = HEADER % title
[78312f7]	645	elif name == "data":
[959eb01]	646	try:
[78312f7]	647	# parsing "data : File: filename [mmm dd hh:mm]"
	648	name = value.split(':', 1)[1].strip()
	649	file_value = "File name:" + name
[47c44f0]	650	#Truncating string so print doesn't complain of being outside margins
	651	if sys.platform != "win32":
	652	MAX_STRING_LENGHT = 50
	653	if len(file_value) > MAX_STRING_LENGHT:
	654	file_value = "File name:.."+file_value[-MAX_STRING_LENGHT+10:]
[959eb01]	655	file_name = CENTRE % file_value
	656	if len(title) == 0:
[78312f7]	657	title = name + " [" + repo_time + "]"
[959eb01]	658	title_name = HEADER % title
	659	except Exception:
	660	msg = "While parsing 'data: ...'\n"
	661	logger.error(msg + traceback.format_exc())
[78312f7]	662	elif name == "model name":
[959eb01]	663	try:
[78312f7]	664	modelname = "Model name:" + value
	665	except Exception:
[959eb01]	666	modelname = "Model name:" + " NAN"
	667	model_name = CENTRE % modelname
	668
[78312f7]	669	elif name == "Plotting Range":
[959eb01]	670	try:
[78312f7]	671	parts = value.split(':')
	672	q_range = parts[0] + " = " + parts[1] \
	673	+ " = " + parts[2].split(",")[0]
[959eb01]	674	q_name = ("Q Range: " + q_range)
	675	q_range = CENTRE % q_name
	676	except Exception:
	677	msg = "While parsing 'Plotting Range: ...'\n"
	678	logger.error(msg + traceback.format_exc())
[78312f7]	679
[959eb01]	680	paramval = ""
	681	for lines in param_string.split(":"):
	682	line = lines.split(",")
	683	if len(lines) > 0:
	684	param = line[0]
	685	param += " = " + line[1]
	686	if len(line[2].split()) > 0 and not line[2].count("None"):
	687	param += " +- " + line[2]
	688	if len(line[3].split()) > 0 and not line[3].count("None"):
	689	param += " " + line[3]
	690	if not paramval.count(param):
	691	paramval += param + "\n"
	692	paramval_string += CENTRE % param + "\n"
	693
	694	text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % \
	695	(title, file, q_name, chi2, paramval)
	696
	697	title_name = self._check_html_format(title_name)
	698	file_name = self._check_html_format(file_name)
	699	title = self._check_html_format(title)
	700
	701	html_string = title_name + "\n" + file_name + \
	702	"\n" + model_name + \
	703	"\n" + q_range + \
	704	"\n" + chi2_string + \
	705	"\n" + ELINE + \
	706	"\n" + paramval_string + \
	707	"\n" + ELINE + \
[78312f7]	708	"\n" + FEET_1 % title
[959eb01]	709
	710	return html_string, text_string, title
	711
	712	def _check_html_format(self, name):
	713	"""
	714	Check string '%' for html format
	715	"""
	716	if name.count('%'):
	717	name = name.replace('%', '&#37')
	718
	719	return name
	720
[78312f7]	721	def report(self, fig_urls):
[959eb01]	722	"""
	723	Invoke report dialog panel
	724
	725	: param figs: list of pylab figures [list]
	726	"""
	727	# get the strings for report
[78312f7]	728	html_str, text_str, title = self._get_report_string()
[959eb01]	729	# Allow 2 figures to append
[47c44f0]	730	#Constraining image width for OSX and linux, so print doesn't complain of being outside margins
	731	if sys.platform == "win32":
	732	image_links = [FEET_2%fig for fig in fig_urls]
	733	else:
	734	image_links = [FEET_2_unix%fig for fig in fig_urls]
[959eb01]	735	# final report html strings
[78312f7]	736	report_str = html_str + ELINE.join(image_links)
[5818dae]	737	report_str += FEET_3
[78312f7]	738	return report_str, text_str
[959eb01]	739
	740	def _to_xml_helper(self, thelist, element, newdoc):
	741	"""
	742	Helper method to create xml file for saving state
	743	"""
	744	for item in thelist:
	745	sub_element = newdoc.createElement('parameter')
	746	sub_element.setAttribute('name', str(item[1]))
	747	sub_element.setAttribute('value', str(item[2]))
	748	sub_element.setAttribute('selected_to_fit', str(item[0]))
	749	sub_element.setAttribute('error_displayed', str(item[4][0]))
	750	sub_element.setAttribute('error_value', str(item[4][1]))
	751	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
	752	sub_element.setAttribute('minimum_value', str(item[5][1]))
	753	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
	754	sub_element.setAttribute('maximum_value', str(item[6][1]))
	755	sub_element.setAttribute('unit', str(item[7]))
	756	element.appendChild(sub_element)
	757
	758	def to_xml(self, file="fitting_state.fitv", doc=None,
	759	entry_node=None, batch_fit_state=None):
	760	"""
	761	Writes the state of the fit panel to file, as XML.
	762
	763	Compatible with standalone writing, or appending to an
	764	already existing XML document. In that case, the XML document is
	765	required. An optional entry node in the XML document may also be given.
	766
	767	:param file: file to write to
	768	:param doc: XML document object [optional]
	769	:param entry_node: XML node within the XML document at which we
	770	will append the data [optional]
	771	:param batch_fit_state: simultaneous fit state
	772	"""
	773	# Check whether we have to write a standalone XML file
	774	if doc is None:
	775	impl = getDOMImplementation()
	776	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
	777	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
	778	top_element = newdoc.documentElement
	779	else:
	780	# We are appending to an existing document
	781	newdoc = doc
	782	try:
	783	top_element = newdoc.createElement(FITTING_NODE_NAME)
[78312f7]	784	except Exception:
[959eb01]	785	string = etree.tostring(doc, pretty_print=True)
	786	newdoc = parseString(string)
	787	top_element = newdoc.createElement(FITTING_NODE_NAME)
	788	if entry_node is None:
	789	newdoc.documentElement.appendChild(top_element)
	790	else:
	791	try:
	792	entry_node.appendChild(top_element)
[78312f7]	793	except Exception:
[959eb01]	794	node_name = entry_node.tag
	795	node_list = newdoc.getElementsByTagName(node_name)
	796	entry_node = node_list.item(0)
	797	entry_node.appendChild(top_element)
	798
	799	attr = newdoc.createAttribute("version")
[00f7ff1]	800	attr.nodeValue = SASVIEW_VERSION
[959eb01]	801	# attr.nodeValue = '1.0'
	802	top_element.setAttributeNode(attr)
	803
	804	# File name
	805	element = newdoc.createElement("filename")
	806	if self.file is not None:
	807	element.appendChild(newdoc.createTextNode(str(self.file)))
	808	else:
	809	element.appendChild(newdoc.createTextNode(str(file)))
	810	top_element.appendChild(element)
	811
	812	element = newdoc.createElement("timestamp")
	813	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
	814	attr = newdoc.createAttribute("epoch")
	815	attr.nodeValue = str(self.timestamp)
	816	element.setAttributeNode(attr)
	817	top_element.appendChild(element)
	818
	819	# Inputs
	820	inputs = newdoc.createElement("Attributes")
	821	top_element.appendChild(inputs)
	822
	823	if self.data is not None and hasattr(self.data, "group_id"):
	824	self.data_group_id = self.data.group_id
	825	if self.data is not None and hasattr(self.data, "is_data"):
	826	self.is_data = self.data.is_data
	827	if self.data is not None:
	828	self.data_name = self.data.name
	829	if self.data is not None and hasattr(self.data, "id"):
	830	self.data_id = self.data.id
	831
	832	for item in LIST_OF_DATA_ATTRIBUTES:
	833	element = newdoc.createElement(item[0])
	834	element.setAttribute(item[0], str(getattr(self, item[1])))
	835	inputs.appendChild(element)
	836
	837	for item in LIST_OF_STATE_ATTRIBUTES:
	838	element = newdoc.createElement(item[0])
	839	element.setAttribute(item[0], str(getattr(self, item[1])))
	840	inputs.appendChild(element)
	841
	842	# For self.values ={ disp_param_name: [vals,...],...}
	843	# and for self.weights ={ disp_param_name: [weights,...],...}
	844	for item in LIST_OF_MODEL_ATTRIBUTES:
	845	element = newdoc.createElement(item[0])
	846	value_list = getattr(self, item[1])
[574adc7]	847	for key, value in value_list.items():
[959eb01]	848	sub_element = newdoc.createElement(key)
	849	sub_element.setAttribute('name', str(key))
	850	for val in value:
	851	sub_element.appendChild(newdoc.createTextNode(str(val)))
	852
	853	element.appendChild(sub_element)
	854	inputs.appendChild(element)
	855
[ba8d326]	856	# Create doc for the dictionary of self.disp_obj_dic
[959eb01]	857	for tagname, varname, tagtype in DISPERSION_LIST:
	858	element = newdoc.createElement(tagname)
	859	value_list = getattr(self, varname)
[574adc7]	860	for key, value in value_list.items():
[959eb01]	861	sub_element = newdoc.createElement(key)
	862	sub_element.setAttribute('name', str(key))
	863	sub_element.setAttribute('value', str(value))
	864	element.appendChild(sub_element)
	865	inputs.appendChild(element)
	866
	867	for item in LIST_OF_STATE_PARAMETERS:
	868	element = newdoc.createElement(item[0])
	869	self._to_xml_helper(thelist=getattr(self, item[1]),
	870	element=element, newdoc=newdoc)
	871	inputs.appendChild(element)
	872
	873	# Combined and Simultaneous Fit Parameters
	874	if batch_fit_state is not None:
	875	batch_combo = newdoc.createElement('simultaneous_fit')
	876	top_element.appendChild(batch_combo)
	877
	878	# Simultaneous Fit Number For Linking Later
	879	element = newdoc.createElement('sim_fit_number')
	880	element.setAttribute('fit_number', str(batch_fit_state.fit_page_no))
	881	batch_combo.appendChild(element)
	882
	883	# Save constraints
	884	constraints = newdoc.createElement('constraints')
	885	batch_combo.appendChild(constraints)
	886	for constraint in batch_fit_state.constraints_list:
	887	if constraint.model_cbox.GetValue() != "":
	888	# model_cbox, param_cbox, egal_txt, constraint,
	889	# btRemove, sizer
	890	doc_cons = newdoc.createElement('constraint')
	891	doc_cons.setAttribute('model_cbox',
	892	str(constraint.model_cbox.GetValue()))
	893	doc_cons.setAttribute('param_cbox',
	894	str(constraint.param_cbox.GetValue()))
	895	doc_cons.setAttribute('egal_txt',
	896	str(constraint.egal_txt.GetLabel()))
	897	doc_cons.setAttribute('constraint',
	898	str(constraint.constraint.GetValue()))
	899	constraints.appendChild(doc_cons)
	900
	901	# Save all models
	902	models = newdoc.createElement('model_list')
	903	batch_combo.appendChild(models)
	904	for model in batch_fit_state.model_list:
	905	doc_model = newdoc.createElement('model_list_item')
	906	doc_model.setAttribute('checked', str(model[0].GetValue()))
	907	keys = model[1].keys()
	908	doc_model.setAttribute('name', str(keys[0]))
	909	values = model[1].get(keys[0])
	910	doc_model.setAttribute('fit_number', str(model[2]))
	911	doc_model.setAttribute('fit_page_source', str(model[3]))
	912	doc_model.setAttribute('model_name', str(values.model.id))
	913	models.appendChild(doc_model)
	914
	915	# Select All Checkbox
	916	element = newdoc.createElement('select_all')
	917	if batch_fit_state.select_all:
	918	element.setAttribute('checked', 'True')
	919	else:
	920	element.setAttribute('checked', 'False')
	921	batch_combo.appendChild(element)
	922
	923	# Save the file
	924	if doc is None:
	925	fd = open(file, 'w')
	926	fd.write(newdoc.toprettyxml())
	927	fd.close()
	928	return None
	929	else:
	930	return newdoc
	931
	932	def _from_xml_helper(self, node, list):
	933	"""
	934	Helper function to write state to xml
	935	"""
	936	for item in node:
[ba8d326]	937	name = item.get('name')
	938	value = item.get('value')
	939	selected_to_fit = (item.get('selected_to_fit') == "True")
	940	error_displayed = (item.get('error_displayed') == "True")
	941	error_value = item.get('error_value')
	942	minimum_displayed = (item.get('minimum_displayed') == "True")
	943	minimum_value = item.get('minimum_value')
	944	maximum_displayed = (item.get('maximum_displayed') == "True")
	945	maximum_value = item.get('maximum_value')
	946	unit = item.get('unit')
[959eb01]	947	list.append([selected_to_fit, name, value, "+/-",
	948	[error_displayed, error_value],
	949	[minimum_displayed, minimum_value],
	950	[maximum_displayed, maximum_value], unit])
	951
	952	def from_xml(self, file=None, node=None):
	953	"""
	954	Load fitting state from a file
	955
	956	:param file: .fitv file
	957	:param node: node of a XML document to read from
	958	"""
	959	if file is not None:
	960	msg = "PageState no longer supports non-CanSAS"
	961	msg += " format for fitting files"
[574adc7]	962	raise RuntimeError(msg)
[959eb01]	963
	964	if node.get('version'):
	965	# Get the version for model conversion purposes
[59873e1]	966	x = re.sub('[^\d.]', '', node.get('version'))
	967	self.version = tuple(int(e) for e in str.split(x, "."))
[959eb01]	968	# The tuple must be at least 3 items long
	969	while len(self.version) < 3:
	970	ver_list = list(self.version)
	971	ver_list.append(0)
	972	self.version = tuple(ver_list)
	973
	974	# Get file name
	975	entry = get_content('ns:filename', node)
[277257f]	976	if entry is not None and entry.text:
[959eb01]	977	self.file = entry.text.strip()
[277257f]	978	else:
	979	self.file = ''
[959eb01]	980
	981	# Get time stamp
	982	entry = get_content('ns:timestamp', node)
	983	if entry is not None and entry.get('epoch'):
	984	try:
	985	self.timestamp = float(entry.get('epoch'))
[78312f7]	986	except Exception:
[959eb01]	987	msg = "PageState.fromXML: Could not"
	988	msg += " read timestamp\n %s" % sys.exc_value
	989	logger.error(msg)
	990
	991	if entry is not None:
	992	# Parse fitting attributes
	993	entry = get_content('ns:Attributes', node)
	994	for item in LIST_OF_DATA_ATTRIBUTES:
	995	node = get_content('ns:%s' % item[0], entry)
	996	setattr(self, item[0], parse_entry_helper(node, item))
	997
	998	dx_old_node = get_content('ns:%s' % 'dx_min', entry)
	999	for item in LIST_OF_STATE_ATTRIBUTES:
	1000	if item[0] == "dx_percent" and dx_old_node is not None:
	1001	dxmin = ["dx_min", "dx_min", "float"]
	1002	setattr(self, item[0], parse_entry_helper(dx_old_node,
	1003	dxmin))
	1004	self.dx_old = True
	1005	else:
	1006	node = get_content('ns:%s' % item[0], entry)
	1007	setattr(self, item[0], parse_entry_helper(node, item))
	1008
	1009	for item in LIST_OF_STATE_PARAMETERS:
	1010	node = get_content("ns:%s" % item[0], entry)
	1011	self._from_xml_helper(node=node,
	1012	list=getattr(self, item[1]))
	1013
[ba8d326]	1014	# Recover disp_obj_dict from xml file
	1015	self.disp_obj_dict = {}
[959eb01]	1016	for tagname, varname, tagtype in DISPERSION_LIST:
	1017	node = get_content("ns:%s" % tagname, entry)
	1018	for attr in node:
	1019	parameter = str(attr.get('name'))
	1020	value = attr.get('value')
	1021	if value.startswith("<"):
	1022	try:
	1023	# <path.to.NamedDistribution object/instance...>
	1024	cls_name = value[1:].split()[0].split('.')[-1]
	1025	cls = getattr(sasmodels.weights, cls_name)
	1026	value = cls.type
	1027	except Exception:
	1028	base = "unable to load distribution %r for %s"
[ba8d326]	1029	logger.error(base, value, parameter)
[959eb01]	1030	continue
[ba8d326]	1031	disp_obj_dict = getattr(self, varname)
	1032	disp_obj_dict[parameter] = value
[959eb01]	1033
	1034	# get self.values and self.weights dic. if exists
	1035	for tagname, varname in LIST_OF_MODEL_ATTRIBUTES:
	1036	node = get_content("ns:%s" % tagname, entry)
	1037	dic = {}
	1038	value_list = []
	1039	for par in node:
	1040	name = par.get('name')
	1041	values = par.text.split()
	1042	# Get lines only with numbers
	1043	for line in values:
	1044	try:
	1045	val = float(line)
	1046	value_list.append(val)
	1047	except Exception:
	1048	# pass if line is empty (it happens)
	1049	msg = ("Error reading %r from %s %s\n"
	1050	% (line, tagname, name))
	1051	logger.error(msg + traceback.format_exc())
	1052	dic[name] = np.array(value_list)
	1053	setattr(self, varname, dic)
	1054
[ba8d326]	1055	class SimFitPageState(object):
[00f7ff1]	1056	"""
	1057	State of the simultaneous fit page for saving purposes
	1058	"""
	1059
	1060	def __init__(self):
	1061	# Sim Fit Page Number
	1062	self.fit_page_no = None
	1063	# Select all data
	1064	self.select_all = False
	1065	# Data sets sent to fit page
	1066	self.model_list = []
	1067	# Data sets to be fit
	1068	self.model_to_fit = []
	1069	# Number of constraints
	1070	self.no_constraint = 0
	1071	# Dictionary of constraints
	1072	self.constraint_dict = {}
	1073	# List of constraints
	1074	self.constraints_list = []
[959eb01]	1075
[ba8d326]	1076	def __repr__(self):
	1077	# TODO: should use __str__, not __repr__ (similarly for PageState)
	1078	# TODO: could use a nicer representation
	1079	repr = """\
	1080	fit page number : %(fit_page_no)s
	1081	select all : %(select_all)s
	1082	model_list : %(model_list)s
	1083	model to fit : %(model_to_fit)s
	1084	number of construsts : %(no_constraint)s
	1085	constraint dict : %(constraint_dict)s
	1086	constraints list : %(constraints_list)s
	1087	"""%self.__dict__
	1088	return repr
	1089
[959eb01]	1090	class Reader(CansasReader):
	1091	"""
	1092	Class to load a .fitv fitting file
	1093	"""
	1094	# File type
	1095	type_name = "Fitting"
	1096
	1097	# Wildcards
	1098	type = ["Fitting files (.fitv)\|.fitv"
	1099	"SASView file (.svs)\|.svs"]
	1100	# List of allowed extensions
	1101	ext = ['.fitv', '.FITV', '.svs', 'SVS']
	1102
	1103	def __init__(self, call_back=None, cansas=True):
	1104	CansasReader.__init__(self)
	1105	"""
	1106	Initialize the call-back method to be called
	1107	after we load a file
	1108
	1109	:param call_back: call-back method
	1110	:param cansas: True = files will be written/read in CanSAS format
	1111	False = write CanSAS format
	1112
	1113	"""
	1114	# Call back method to be executed after a file is read
	1115	self.call_back = call_back
	1116	# CanSAS format flag
	1117	self.cansas = cansas
	1118	self.state = None
	1119	# batch fitting params for saving
	1120	self.batchfit_params = []
	1121
	1122	def get_state(self):
	1123	return self.state
	1124
	1125	def read(self, path):
	1126	"""
	1127	Load a new P(r) inversion state from file
	1128
	1129	:param path: file path
	1130
	1131	"""
	1132	if self.cansas:
	1133	return self._read_cansas(path)
	1134
	1135	def _parse_state(self, entry):
	1136	"""
	1137	Read a fit result from an XML node
	1138
	1139	:param entry: XML node to read from
	1140	:return: PageState object
	1141	"""
	1142	# Create an empty state
	1143	state = None
	1144	# Locate the P(r) node
	1145	try:
	1146	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
[ba8d326]	1147	namespaces=CANSAS_NS)
[959eb01]	1148	if nodes:
	1149	# Create an empty state
	1150	state = PageState()
	1151	state.from_xml(node=nodes[0])
	1152
[ba8d326]	1153	except Exception:
[959eb01]	1154	logger.info("XML document does not contain fitting information.\n"
[ba8d326]	1155	+ traceback.format_exc())
[959eb01]	1156
	1157	return state
	1158
	1159	def _parse_simfit_state(self, entry):
	1160	"""
	1161	Parses the saved data for a simultaneous fit
	1162	:param entry: XML object to read from
	1163	:return: XML object for a simultaneous fit or None
	1164	"""
	1165	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
[ba8d326]	1166	namespaces=CANSAS_NS)
[959eb01]	1167	if nodes:
	1168	simfitstate = nodes[0].xpath('ns:simultaneous_fit',
[ba8d326]	1169	namespaces=CANSAS_NS)
[959eb01]	1170	if simfitstate:
	1171	sim_fit_state = SimFitPageState()
	1172	simfitstate_0 = simfitstate[0]
	1173	all = simfitstate_0.xpath('ns:select_all',
[ba8d326]	1174	namespaces=CANSAS_NS)
[959eb01]	1175	atts = all[0].attrib
	1176	checked = atts.get('checked')
	1177	sim_fit_state.select_all = bool(checked)
	1178	model_list = simfitstate_0.xpath('ns:model_list',
[ba8d326]	1179	namespaces=CANSAS_NS)
[959eb01]	1180	model_list_items = model_list[0].xpath('ns:model_list_item',
[ba8d326]	1181	namespaces=CANSAS_NS)
[959eb01]	1182	for model in model_list_items:
	1183	attrs = model.attrib
	1184	sim_fit_state.model_list.append(attrs)
	1185
	1186	constraints = simfitstate_0.xpath('ns:constraints',
[ba8d326]	1187	namespaces=CANSAS_NS)
[959eb01]	1188	constraint_list = constraints[0].xpath('ns:constraint',
[ba8d326]	1189	namespaces=CANSAS_NS)
[959eb01]	1190	for constraint in constraint_list:
	1191	attrs = constraint.attrib
	1192	sim_fit_state.constraints_list.append(attrs)
	1193
	1194	return sim_fit_state
	1195	else:
	1196	return None
	1197
	1198	def _parse_save_state_entry(self, dom):
	1199	"""
	1200	Parse a SASentry
	1201
	1202	:param node: SASentry node
	1203
	1204	:return: Data1D/Data2D object
	1205
	1206	"""
[ba8d326]	1207	node = dom.xpath('ns:data_class', namespaces=CANSAS_NS)
[959eb01]	1208	return_value, _ = self._parse_entry(dom)
	1209	return return_value, _
	1210
	1211	def _read_cansas(self, path):
	1212	"""
	1213	Load data and fitting information from a CanSAS XML file.
	1214
	1215	:param path: file path
	1216	:return: Data1D object if a single SASentry was found,
	1217	or a list of Data1D objects if multiple entries were found,
	1218	or None of nothing was found
	1219	:raise RuntimeError: when the file can't be opened
	1220	:raise ValueError: when the length of the data vectors are inconsistent
	1221	"""
	1222	output = []
	1223	simfitstate = None
	1224	basename = os.path.basename(path)
	1225	root, extension = os.path.splitext(basename)
	1226	ext = extension.lower()
	1227	try:
	1228	if os.path.isfile(path):
	1229	if ext in self.ext or ext == '.xml':
	1230	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
	1231	# Check the format version number
	1232	# Specifying the namespace will take care of the file
	1233	# format version
	1234	root = tree.getroot()
	1235	entry_list = root.xpath('ns:SASentry',
[ba8d326]	1236	namespaces=CANSAS_NS)
[959eb01]	1237	for entry in entry_list:
	1238	fitstate = self._parse_state(entry)
	1239	# state could be None when .svs file is loaded
	1240	# in this case, skip appending to output
	1241	if fitstate is not None:
[1fa4f736]	1242	try:
	1243	sas_entry, _ = self._parse_save_state_entry(
	1244	entry)
	1245	except:
	1246	raise
[959eb01]	1247	sas_entry.meta_data['fitstate'] = fitstate
	1248	sas_entry.filename = fitstate.file
	1249	output.append(sas_entry)
	1250
	1251	else:
	1252	self.call_back(format=ext)
[574adc7]	1253	raise RuntimeError("%s is not a file" % path)
[959eb01]	1254
	1255	# Return output consistent with the loader's api
	1256	if len(output) == 0:
	1257	self.call_back(state=None, datainfo=None, format=ext)
	1258	return None
	1259	else:
[ba8d326]	1260	for data in output:
[959eb01]	1261	# Call back to post the new state
[ba8d326]	1262	state = data.meta_data['fitstate']
[959eb01]	1263	t = time.localtime(state.timestamp)
	1264	time_str = time.strftime("%b %d %H:%M", t)
	1265	# Check that no time stamp is already appended
	1266	max_char = state.file.find("[")
	1267	if max_char < 0:
	1268	max_char = len(state.file)
	1269	original_fname = state.file[0:max_char]
	1270	state.file = original_fname + ' [' + time_str + ']'
	1271
	1272	if state is not None and state.is_data is not None:
[ba8d326]	1273	data.is_data = state.is_data
[959eb01]	1274
[ba8d326]	1275	data.filename = state.file
	1276	state.data = data
	1277	state.data.name = data.filename # state.data_name
[959eb01]	1278	state.data.id = state.data_id
	1279	if state.is_data is not None:
	1280	state.data.is_data = state.is_data
[ba8d326]	1281	if data.run_name is not None and len(data.run_name) != 0:
	1282	if isinstance(data.run_name, dict):
	1283	# Note: key order in dict is not guaranteed, so sort
	1284	name = data.run_name.keys()[0]
[959eb01]	1285	else:
[ba8d326]	1286	name = data.run_name
[959eb01]	1287	else:
	1288	name = original_fname
	1289	state.data.group_id = name
	1290	state.version = fitstate.version
	1291	# store state in fitting
[ba8d326]	1292	self.call_back(state=state, datainfo=data, format=ext)
[959eb01]	1293	self.state = state
	1294	simfitstate = self._parse_simfit_state(entry)
	1295	if simfitstate is not None:
	1296	self.call_back(state=simfitstate)
	1297
	1298	return output
	1299	except:
	1300	self.call_back(format=ext)
	1301	raise
	1302
	1303	def write(self, filename, datainfo=None, fitstate=None):
	1304	"""
	1305	Write the content of a Data1D as a CanSAS XML file only for standalone
	1306
	1307	:param filename: name of the file to write
	1308	:param datainfo: Data1D object
	1309	:param fitstate: PageState object
	1310
	1311	"""
	1312	# Sanity check
	1313	if self.cansas:
	1314	# Add fitting information to the XML document
	1315	doc = self.write_toXML(datainfo, fitstate)
	1316	# Write the XML document
	1317	else:
	1318	doc = fitstate.to_xml(file=filename)
	1319
	1320	# Save the document no matter the type
	1321	fd = open(filename, 'w')
	1322	fd.write(doc.toprettyxml())
	1323	fd.close()
	1324
	1325	def write_toXML(self, datainfo=None, state=None, batchfit=None):
	1326	"""
	1327	Write toXML, a helper for write(),
	1328	could be used by guimanager._on_save()
	1329
	1330	: return: xml doc
	1331	"""
	1332
	1333	self.batchfit_params = batchfit
	1334	if state.data is None or not state.data.is_data:
	1335	return None
	1336	# make sure title and data run are filled.
	1337	if state.data.title is None or state.data.title == '':
	1338	state.data.title = state.data.name
	1339	if state.data.run_name is None or state.data.run_name == {}:
	1340	state.data.run = [str(state.data.name)]
	1341	state.data.run_name[0] = state.data.name
	1342
	1343	data = state.data
	1344	doc, sasentry = self._to_xml_doc(data)
	1345
	1346	if state is not None:
	1347	doc = state.to_xml(doc=doc, file=data.filename, entry_node=sasentry,
	1348	batch_fit_state=self.batchfit_params)
	1349
	1350	return doc
	1351
[78312f7]	1352	# Simple html report template
[959eb01]	1353	HEADER = "<html>\n"
	1354	HEADER += "<head>\n"
	1355	HEADER += "<meta http-equiv=Content-Type content='text/html; "
	1356	HEADER += "charset=windows-1252'> \n"
	1357	HEADER += "<meta name=Generator >\n"
	1358	HEADER += "</head>\n"
	1359	HEADER += "<body lang=EN-US>\n"
	1360	HEADER += "<div class=WordSection1>\n"
	1361	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
	1362	HEADER += "%s</font></center></span></center></b></p>"
	1363	HEADER += "<p class=MsoNormal> </p>"
	1364	PARA = "<p class=MsoNormal><font size='4' > %s \n"
	1365	PARA += "</font></p>"
	1366	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
	1367	CENTRE += "</font></center></p>"
	1368	FEET_1 = \
	1369	"""
	1370	<p class=MsoNormal> </p>
	1371	<br>
	1372	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
	1373	</font></span></center></b></p>
	1374	<p class=MsoNormal> </p>
	1375	<center>
	1376	<br><font size='4' >Model Computation</font>
	1377	<br><font size='4' >Data: "%s"</font><br>
	1378	"""
	1379	FEET_2 = \
[3b070a0]	1380	"""<img src="%s"></img>
[959eb01]	1381	"""
[47c44f0]	1382	FEET_2_unix = \
	1383	"""<img src="%s" width="540"></img>
	1384	"""
[959eb01]	1385	FEET_3 = \
[78312f7]	1386	"""</center>
[959eb01]	1387	</div>
	1388	</body>
	1389	</html>
	1390	"""
[78312f7]	1391	ELINE = """<p class=MsoNormal> </p>
	1392	"""

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SasView

source: sasview/src/sas/sascalc/fit/pagestate.py @ 845144e

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