pagestate.py @ 009abcc

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

Last change on this file since 009abcc was 59873e1, checked in by krzywon, 6 years ago
Remove any non-numeric characters from the version number when loading projects.
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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
	642	title = value + " [" + repo_time + "]"
	643	title_name = HEADER % title
[78312f7]	644	elif name == "data":
[959eb01]	645	try:
[78312f7]	646	# parsing "data : File: filename [mmm dd hh:mm]"
	647	name = value.split(':', 1)[1].strip()
	648	file_value = "File name:" + name
[47c44f0]	649	#Truncating string so print doesn't complain of being outside margins
	650	if sys.platform != "win32":
	651	MAX_STRING_LENGHT = 50
	652	if len(file_value) > MAX_STRING_LENGHT:
	653	file_value = "File name:.."+file_value[-MAX_STRING_LENGHT+10:]
[959eb01]	654	file_name = CENTRE % file_value
	655	if len(title) == 0:
[78312f7]	656	title = name + " [" + repo_time + "]"
[959eb01]	657	title_name = HEADER % title
	658	except Exception:
	659	msg = "While parsing 'data: ...'\n"
	660	logger.error(msg + traceback.format_exc())
[78312f7]	661	elif name == "model name":
[959eb01]	662	try:
[78312f7]	663	modelname = "Model name:" + value
	664	except Exception:
[959eb01]	665	modelname = "Model name:" + " NAN"
	666	model_name = CENTRE % modelname
	667
[78312f7]	668	elif name == "Plotting Range":
[959eb01]	669	try:
[78312f7]	670	parts = value.split(':')
	671	q_range = parts[0] + " = " + parts[1] \
	672	+ " = " + parts[2].split(",")[0]
[959eb01]	673	q_name = ("Q Range: " + q_range)
	674	q_range = CENTRE % q_name
	675	except Exception:
	676	msg = "While parsing 'Plotting Range: ...'\n"
	677	logger.error(msg + traceback.format_exc())
[78312f7]	678
[959eb01]	679	paramval = ""
	680	for lines in param_string.split(":"):
	681	line = lines.split(",")
	682	if len(lines) > 0:
	683	param = line[0]
	684	param += " = " + line[1]
	685	if len(line[2].split()) > 0 and not line[2].count("None"):
	686	param += " +- " + line[2]
	687	if len(line[3].split()) > 0 and not line[3].count("None"):
	688	param += " " + line[3]
	689	if not paramval.count(param):
	690	paramval += param + "\n"
	691	paramval_string += CENTRE % param + "\n"
	692
	693	text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % \
	694	(title, file, q_name, chi2, paramval)
	695
	696	title_name = self._check_html_format(title_name)
	697	file_name = self._check_html_format(file_name)
	698	title = self._check_html_format(title)
	699
	700	html_string = title_name + "\n" + file_name + \
	701	"\n" + model_name + \
	702	"\n" + q_range + \
	703	"\n" + chi2_string + \
	704	"\n" + ELINE + \
	705	"\n" + paramval_string + \
	706	"\n" + ELINE + \
[78312f7]	707	"\n" + FEET_1 % title
[959eb01]	708
	709	return html_string, text_string, title
	710
	711	def _check_html_format(self, name):
	712	"""
	713	Check string '%' for html format
	714	"""
	715	if name.count('%'):
	716	name = name.replace('%', '&#37')
	717
	718	return name
	719
[78312f7]	720	def report(self, fig_urls):
[959eb01]	721	"""
	722	Invoke report dialog panel
	723
	724	: param figs: list of pylab figures [list]
	725	"""
	726	# get the strings for report
[78312f7]	727	html_str, text_str, title = self._get_report_string()
[959eb01]	728	# Allow 2 figures to append
[47c44f0]	729	#Constraining image width for OSX and linux, so print doesn't complain of being outside margins
	730	if sys.platform == "win32":
	731	image_links = [FEET_2%fig for fig in fig_urls]
	732	else:
	733	image_links = [FEET_2_unix%fig for fig in fig_urls]
[959eb01]	734	# final report html strings
[78312f7]	735	report_str = html_str + ELINE.join(image_links)
[5818dae]	736	report_str += FEET_3
[78312f7]	737	return report_str, text_str
[959eb01]	738
	739	def _to_xml_helper(self, thelist, element, newdoc):
	740	"""
	741	Helper method to create xml file for saving state
	742	"""
	743	for item in thelist:
	744	sub_element = newdoc.createElement('parameter')
	745	sub_element.setAttribute('name', str(item[1]))
	746	sub_element.setAttribute('value', str(item[2]))
	747	sub_element.setAttribute('selected_to_fit', str(item[0]))
	748	sub_element.setAttribute('error_displayed', str(item[4][0]))
	749	sub_element.setAttribute('error_value', str(item[4][1]))
	750	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
	751	sub_element.setAttribute('minimum_value', str(item[5][1]))
	752	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
	753	sub_element.setAttribute('maximum_value', str(item[6][1]))
	754	sub_element.setAttribute('unit', str(item[7]))
	755	element.appendChild(sub_element)
	756
	757	def to_xml(self, file="fitting_state.fitv", doc=None,
	758	entry_node=None, batch_fit_state=None):
	759	"""
	760	Writes the state of the fit panel to file, as XML.
	761
	762	Compatible with standalone writing, or appending to an
	763	already existing XML document. In that case, the XML document is
	764	required. An optional entry node in the XML document may also be given.
	765
	766	:param file: file to write to
	767	:param doc: XML document object [optional]
	768	:param entry_node: XML node within the XML document at which we
	769	will append the data [optional]
	770	:param batch_fit_state: simultaneous fit state
	771	"""
	772	# Check whether we have to write a standalone XML file
	773	if doc is None:
	774	impl = getDOMImplementation()
	775	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
	776	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
	777	top_element = newdoc.documentElement
	778	else:
	779	# We are appending to an existing document
	780	newdoc = doc
	781	try:
	782	top_element = newdoc.createElement(FITTING_NODE_NAME)
[78312f7]	783	except Exception:
[959eb01]	784	string = etree.tostring(doc, pretty_print=True)
	785	newdoc = parseString(string)
	786	top_element = newdoc.createElement(FITTING_NODE_NAME)
	787	if entry_node is None:
	788	newdoc.documentElement.appendChild(top_element)
	789	else:
	790	try:
	791	entry_node.appendChild(top_element)
[78312f7]	792	except Exception:
[959eb01]	793	node_name = entry_node.tag
	794	node_list = newdoc.getElementsByTagName(node_name)
	795	entry_node = node_list.item(0)
	796	entry_node.appendChild(top_element)
	797
	798	attr = newdoc.createAttribute("version")
[00f7ff1]	799	attr.nodeValue = SASVIEW_VERSION
[959eb01]	800	# attr.nodeValue = '1.0'
	801	top_element.setAttributeNode(attr)
	802
	803	# File name
	804	element = newdoc.createElement("filename")
	805	if self.file is not None:
	806	element.appendChild(newdoc.createTextNode(str(self.file)))
	807	else:
	808	element.appendChild(newdoc.createTextNode(str(file)))
	809	top_element.appendChild(element)
	810
	811	element = newdoc.createElement("timestamp")
	812	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
	813	attr = newdoc.createAttribute("epoch")
	814	attr.nodeValue = str(self.timestamp)
	815	element.setAttributeNode(attr)
	816	top_element.appendChild(element)
	817
	818	# Inputs
	819	inputs = newdoc.createElement("Attributes")
	820	top_element.appendChild(inputs)
	821
	822	if self.data is not None and hasattr(self.data, "group_id"):
	823	self.data_group_id = self.data.group_id
	824	if self.data is not None and hasattr(self.data, "is_data"):
	825	self.is_data = self.data.is_data
	826	if self.data is not None:
	827	self.data_name = self.data.name
	828	if self.data is not None and hasattr(self.data, "id"):
	829	self.data_id = self.data.id
	830
	831	for item in LIST_OF_DATA_ATTRIBUTES:
	832	element = newdoc.createElement(item[0])
	833	element.setAttribute(item[0], str(getattr(self, item[1])))
	834	inputs.appendChild(element)
	835
	836	for item in LIST_OF_STATE_ATTRIBUTES:
	837	element = newdoc.createElement(item[0])
	838	element.setAttribute(item[0], str(getattr(self, item[1])))
	839	inputs.appendChild(element)
	840
	841	# For self.values ={ disp_param_name: [vals,...],...}
	842	# and for self.weights ={ disp_param_name: [weights,...],...}
	843	for item in LIST_OF_MODEL_ATTRIBUTES:
	844	element = newdoc.createElement(item[0])
	845	value_list = getattr(self, item[1])
[574adc7]	846	for key, value in value_list.items():
[959eb01]	847	sub_element = newdoc.createElement(key)
	848	sub_element.setAttribute('name', str(key))
	849	for val in value:
	850	sub_element.appendChild(newdoc.createTextNode(str(val)))
	851
	852	element.appendChild(sub_element)
	853	inputs.appendChild(element)
	854
[ba8d326]	855	# Create doc for the dictionary of self.disp_obj_dic
[959eb01]	856	for tagname, varname, tagtype in DISPERSION_LIST:
	857	element = newdoc.createElement(tagname)
	858	value_list = getattr(self, varname)
[574adc7]	859	for key, value in value_list.items():
[959eb01]	860	sub_element = newdoc.createElement(key)
	861	sub_element.setAttribute('name', str(key))
	862	sub_element.setAttribute('value', str(value))
	863	element.appendChild(sub_element)
	864	inputs.appendChild(element)
	865
	866	for item in LIST_OF_STATE_PARAMETERS:
	867	element = newdoc.createElement(item[0])
	868	self._to_xml_helper(thelist=getattr(self, item[1]),
	869	element=element, newdoc=newdoc)
	870	inputs.appendChild(element)
	871
	872	# Combined and Simultaneous Fit Parameters
	873	if batch_fit_state is not None:
	874	batch_combo = newdoc.createElement('simultaneous_fit')
	875	top_element.appendChild(batch_combo)
	876
	877	# Simultaneous Fit Number For Linking Later
	878	element = newdoc.createElement('sim_fit_number')
	879	element.setAttribute('fit_number', str(batch_fit_state.fit_page_no))
	880	batch_combo.appendChild(element)
	881
	882	# Save constraints
	883	constraints = newdoc.createElement('constraints')
	884	batch_combo.appendChild(constraints)
	885	for constraint in batch_fit_state.constraints_list:
	886	if constraint.model_cbox.GetValue() != "":
	887	# model_cbox, param_cbox, egal_txt, constraint,
	888	# btRemove, sizer
	889	doc_cons = newdoc.createElement('constraint')
	890	doc_cons.setAttribute('model_cbox',
	891	str(constraint.model_cbox.GetValue()))
	892	doc_cons.setAttribute('param_cbox',
	893	str(constraint.param_cbox.GetValue()))
	894	doc_cons.setAttribute('egal_txt',
	895	str(constraint.egal_txt.GetLabel()))
	896	doc_cons.setAttribute('constraint',
	897	str(constraint.constraint.GetValue()))
	898	constraints.appendChild(doc_cons)
	899
	900	# Save all models
	901	models = newdoc.createElement('model_list')
	902	batch_combo.appendChild(models)
	903	for model in batch_fit_state.model_list:
	904	doc_model = newdoc.createElement('model_list_item')
	905	doc_model.setAttribute('checked', str(model[0].GetValue()))
	906	keys = model[1].keys()
	907	doc_model.setAttribute('name', str(keys[0]))
	908	values = model[1].get(keys[0])
	909	doc_model.setAttribute('fit_number', str(model[2]))
	910	doc_model.setAttribute('fit_page_source', str(model[3]))
	911	doc_model.setAttribute('model_name', str(values.model.id))
	912	models.appendChild(doc_model)
	913
	914	# Select All Checkbox
	915	element = newdoc.createElement('select_all')
	916	if batch_fit_state.select_all:
	917	element.setAttribute('checked', 'True')
	918	else:
	919	element.setAttribute('checked', 'False')
	920	batch_combo.appendChild(element)
	921
	922	# Save the file
	923	if doc is None:
	924	fd = open(file, 'w')
	925	fd.write(newdoc.toprettyxml())
	926	fd.close()
	927	return None
	928	else:
	929	return newdoc
	930
	931	def _from_xml_helper(self, node, list):
	932	"""
	933	Helper function to write state to xml
	934	"""
	935	for item in node:
[ba8d326]	936	name = item.get('name')
	937	value = item.get('value')
	938	selected_to_fit = (item.get('selected_to_fit') == "True")
	939	error_displayed = (item.get('error_displayed') == "True")
	940	error_value = item.get('error_value')
	941	minimum_displayed = (item.get('minimum_displayed') == "True")
	942	minimum_value = item.get('minimum_value')
	943	maximum_displayed = (item.get('maximum_displayed') == "True")
	944	maximum_value = item.get('maximum_value')
	945	unit = item.get('unit')
[959eb01]	946	list.append([selected_to_fit, name, value, "+/-",
	947	[error_displayed, error_value],
	948	[minimum_displayed, minimum_value],
	949	[maximum_displayed, maximum_value], unit])
	950
	951	def from_xml(self, file=None, node=None):
	952	"""
	953	Load fitting state from a file
	954
	955	:param file: .fitv file
	956	:param node: node of a XML document to read from
	957	"""
	958	if file is not None:
	959	msg = "PageState no longer supports non-CanSAS"
	960	msg += " format for fitting files"
[574adc7]	961	raise RuntimeError(msg)
[959eb01]	962
	963	if node.get('version'):
	964	# Get the version for model conversion purposes
[59873e1]	965	x = re.sub('[^\d.]', '', node.get('version'))
	966	self.version = tuple(int(e) for e in str.split(x, "."))
[959eb01]	967	# The tuple must be at least 3 items long
	968	while len(self.version) < 3:
	969	ver_list = list(self.version)
	970	ver_list.append(0)
	971	self.version = tuple(ver_list)
	972
	973	# Get file name
	974	entry = get_content('ns:filename', node)
[277257f]	975	if entry is not None and entry.text:
[959eb01]	976	self.file = entry.text.strip()
[277257f]	977	else:
	978	self.file = ''
[959eb01]	979
	980	# Get time stamp
	981	entry = get_content('ns:timestamp', node)
	982	if entry is not None and entry.get('epoch'):
	983	try:
	984	self.timestamp = float(entry.get('epoch'))
[78312f7]	985	except Exception:
[959eb01]	986	msg = "PageState.fromXML: Could not"
	987	msg += " read timestamp\n %s" % sys.exc_value
	988	logger.error(msg)
	989
	990	if entry is not None:
	991	# Parse fitting attributes
	992	entry = get_content('ns:Attributes', node)
	993	for item in LIST_OF_DATA_ATTRIBUTES:
	994	node = get_content('ns:%s' % item[0], entry)
	995	setattr(self, item[0], parse_entry_helper(node, item))
	996
	997	dx_old_node = get_content('ns:%s' % 'dx_min', entry)
	998	for item in LIST_OF_STATE_ATTRIBUTES:
	999	if item[0] == "dx_percent" and dx_old_node is not None:
	1000	dxmin = ["dx_min", "dx_min", "float"]
	1001	setattr(self, item[0], parse_entry_helper(dx_old_node,
	1002	dxmin))
	1003	self.dx_old = True
	1004	else:
	1005	node = get_content('ns:%s' % item[0], entry)
	1006	setattr(self, item[0], parse_entry_helper(node, item))
	1007
	1008	for item in LIST_OF_STATE_PARAMETERS:
	1009	node = get_content("ns:%s" % item[0], entry)
	1010	self._from_xml_helper(node=node,
	1011	list=getattr(self, item[1]))
	1012
[ba8d326]	1013	# Recover disp_obj_dict from xml file
	1014	self.disp_obj_dict = {}
[959eb01]	1015	for tagname, varname, tagtype in DISPERSION_LIST:
	1016	node = get_content("ns:%s" % tagname, entry)
	1017	for attr in node:
	1018	parameter = str(attr.get('name'))
	1019	value = attr.get('value')
	1020	if value.startswith("<"):
	1021	try:
	1022	# <path.to.NamedDistribution object/instance...>
	1023	cls_name = value[1:].split()[0].split('.')[-1]
	1024	cls = getattr(sasmodels.weights, cls_name)
	1025	value = cls.type
	1026	except Exception:
	1027	base = "unable to load distribution %r for %s"
[ba8d326]	1028	logger.error(base, value, parameter)
[959eb01]	1029	continue
[ba8d326]	1030	disp_obj_dict = getattr(self, varname)
	1031	disp_obj_dict[parameter] = value
[959eb01]	1032
	1033	# get self.values and self.weights dic. if exists
	1034	for tagname, varname in LIST_OF_MODEL_ATTRIBUTES:
	1035	node = get_content("ns:%s" % tagname, entry)
	1036	dic = {}
	1037	value_list = []
	1038	for par in node:
	1039	name = par.get('name')
	1040	values = par.text.split()
	1041	# Get lines only with numbers
	1042	for line in values:
	1043	try:
	1044	val = float(line)
	1045	value_list.append(val)
	1046	except Exception:
	1047	# pass if line is empty (it happens)
	1048	msg = ("Error reading %r from %s %s\n"
	1049	% (line, tagname, name))
	1050	logger.error(msg + traceback.format_exc())
	1051	dic[name] = np.array(value_list)
	1052	setattr(self, varname, dic)
	1053
[ba8d326]	1054	class SimFitPageState(object):
[00f7ff1]	1055	"""
	1056	State of the simultaneous fit page for saving purposes
	1057	"""
	1058
	1059	def __init__(self):
	1060	# Sim Fit Page Number
	1061	self.fit_page_no = None
	1062	# Select all data
	1063	self.select_all = False
	1064	# Data sets sent to fit page
	1065	self.model_list = []
	1066	# Data sets to be fit
	1067	self.model_to_fit = []
	1068	# Number of constraints
	1069	self.no_constraint = 0
	1070	# Dictionary of constraints
	1071	self.constraint_dict = {}
	1072	# List of constraints
	1073	self.constraints_list = []
[959eb01]	1074
[ba8d326]	1075	def __repr__(self):
	1076	# TODO: should use __str__, not __repr__ (similarly for PageState)
	1077	# TODO: could use a nicer representation
	1078	repr = """\
	1079	fit page number : %(fit_page_no)s
	1080	select all : %(select_all)s
	1081	model_list : %(model_list)s
	1082	model to fit : %(model_to_fit)s
	1083	number of construsts : %(no_constraint)s
	1084	constraint dict : %(constraint_dict)s
	1085	constraints list : %(constraints_list)s
	1086	"""%self.__dict__
	1087	return repr
	1088
[959eb01]	1089	class Reader(CansasReader):
	1090	"""
	1091	Class to load a .fitv fitting file
	1092	"""
	1093	# File type
	1094	type_name = "Fitting"
	1095
	1096	# Wildcards
	1097	type = ["Fitting files (.fitv)\|.fitv"
	1098	"SASView file (.svs)\|.svs"]
	1099	# List of allowed extensions
	1100	ext = ['.fitv', '.FITV', '.svs', 'SVS']
	1101
	1102	def __init__(self, call_back=None, cansas=True):
	1103	CansasReader.__init__(self)
	1104	"""
	1105	Initialize the call-back method to be called
	1106	after we load a file
	1107
	1108	:param call_back: call-back method
	1109	:param cansas: True = files will be written/read in CanSAS format
	1110	False = write CanSAS format
	1111
	1112	"""
	1113	# Call back method to be executed after a file is read
	1114	self.call_back = call_back
	1115	# CanSAS format flag
	1116	self.cansas = cansas
	1117	self.state = None
	1118	# batch fitting params for saving
	1119	self.batchfit_params = []
	1120
	1121	def get_state(self):
	1122	return self.state
	1123
	1124	def read(self, path):
	1125	"""
	1126	Load a new P(r) inversion state from file
	1127
	1128	:param path: file path
	1129
	1130	"""
	1131	if self.cansas:
	1132	return self._read_cansas(path)
	1133
	1134	def _parse_state(self, entry):
	1135	"""
	1136	Read a fit result from an XML node
	1137
	1138	:param entry: XML node to read from
	1139	:return: PageState object
	1140	"""
	1141	# Create an empty state
	1142	state = None
	1143	# Locate the P(r) node
	1144	try:
	1145	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
[ba8d326]	1146	namespaces=CANSAS_NS)
[959eb01]	1147	if nodes:
	1148	# Create an empty state
	1149	state = PageState()
	1150	state.from_xml(node=nodes[0])
	1151
[ba8d326]	1152	except Exception:
[959eb01]	1153	logger.info("XML document does not contain fitting information.\n"
[ba8d326]	1154	+ traceback.format_exc())
[959eb01]	1155
	1156	return state
	1157
	1158	def _parse_simfit_state(self, entry):
	1159	"""
	1160	Parses the saved data for a simultaneous fit
	1161	:param entry: XML object to read from
	1162	:return: XML object for a simultaneous fit or None
	1163	"""
	1164	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
[ba8d326]	1165	namespaces=CANSAS_NS)
[959eb01]	1166	if nodes:
	1167	simfitstate = nodes[0].xpath('ns:simultaneous_fit',
[ba8d326]	1168	namespaces=CANSAS_NS)
[959eb01]	1169	if simfitstate:
	1170	sim_fit_state = SimFitPageState()
	1171	simfitstate_0 = simfitstate[0]
	1172	all = simfitstate_0.xpath('ns:select_all',
[ba8d326]	1173	namespaces=CANSAS_NS)
[959eb01]	1174	atts = all[0].attrib
	1175	checked = atts.get('checked')
	1176	sim_fit_state.select_all = bool(checked)
	1177	model_list = simfitstate_0.xpath('ns:model_list',
[ba8d326]	1178	namespaces=CANSAS_NS)
[959eb01]	1179	model_list_items = model_list[0].xpath('ns:model_list_item',
[ba8d326]	1180	namespaces=CANSAS_NS)
[959eb01]	1181	for model in model_list_items:
	1182	attrs = model.attrib
	1183	sim_fit_state.model_list.append(attrs)
	1184
	1185	constraints = simfitstate_0.xpath('ns:constraints',
[ba8d326]	1186	namespaces=CANSAS_NS)
[959eb01]	1187	constraint_list = constraints[0].xpath('ns:constraint',
[ba8d326]	1188	namespaces=CANSAS_NS)
[959eb01]	1189	for constraint in constraint_list:
	1190	attrs = constraint.attrib
	1191	sim_fit_state.constraints_list.append(attrs)
	1192
	1193	return sim_fit_state
	1194	else:
	1195	return None
	1196
	1197	def _parse_save_state_entry(self, dom):
	1198	"""
	1199	Parse a SASentry
	1200
	1201	:param node: SASentry node
	1202
	1203	:return: Data1D/Data2D object
	1204
	1205	"""
[ba8d326]	1206	node = dom.xpath('ns:data_class', namespaces=CANSAS_NS)
[959eb01]	1207	return_value, _ = self._parse_entry(dom)
	1208	return return_value, _
	1209
	1210	def _read_cansas(self, path):
	1211	"""
	1212	Load data and fitting information from a CanSAS XML file.
	1213
	1214	:param path: file path
	1215	:return: Data1D object if a single SASentry was found,
	1216	or a list of Data1D objects if multiple entries were found,
	1217	or None of nothing was found
	1218	:raise RuntimeError: when the file can't be opened
	1219	:raise ValueError: when the length of the data vectors are inconsistent
	1220	"""
	1221	output = []
	1222	simfitstate = None
	1223	basename = os.path.basename(path)
	1224	root, extension = os.path.splitext(basename)
	1225	ext = extension.lower()
	1226	try:
	1227	if os.path.isfile(path):
	1228	if ext in self.ext or ext == '.xml':
	1229	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
	1230	# Check the format version number
	1231	# Specifying the namespace will take care of the file
	1232	# format version
	1233	root = tree.getroot()
	1234	entry_list = root.xpath('ns:SASentry',
[ba8d326]	1235	namespaces=CANSAS_NS)
[959eb01]	1236	for entry in entry_list:
	1237	fitstate = self._parse_state(entry)
	1238	# state could be None when .svs file is loaded
	1239	# in this case, skip appending to output
	1240	if fitstate is not None:
[1fa4f736]	1241	try:
	1242	sas_entry, _ = self._parse_save_state_entry(
	1243	entry)
	1244	except:
	1245	raise
[959eb01]	1246	sas_entry.meta_data['fitstate'] = fitstate
	1247	sas_entry.filename = fitstate.file
	1248	output.append(sas_entry)
	1249
	1250	else:
	1251	self.call_back(format=ext)
[574adc7]	1252	raise RuntimeError("%s is not a file" % path)
[959eb01]	1253
	1254	# Return output consistent with the loader's api
	1255	if len(output) == 0:
	1256	self.call_back(state=None, datainfo=None, format=ext)
	1257	return None
	1258	else:
[ba8d326]	1259	for data in output:
[959eb01]	1260	# Call back to post the new state
[ba8d326]	1261	state = data.meta_data['fitstate']
[959eb01]	1262	t = time.localtime(state.timestamp)
	1263	time_str = time.strftime("%b %d %H:%M", t)
	1264	# Check that no time stamp is already appended
	1265	max_char = state.file.find("[")
	1266	if max_char < 0:
	1267	max_char = len(state.file)
	1268	original_fname = state.file[0:max_char]
	1269	state.file = original_fname + ' [' + time_str + ']'
	1270
	1271	if state is not None and state.is_data is not None:
[ba8d326]	1272	data.is_data = state.is_data
[959eb01]	1273
[ba8d326]	1274	data.filename = state.file
	1275	state.data = data
	1276	state.data.name = data.filename # state.data_name
[959eb01]	1277	state.data.id = state.data_id
	1278	if state.is_data is not None:
	1279	state.data.is_data = state.is_data
[ba8d326]	1280	if data.run_name is not None and len(data.run_name) != 0:
	1281	if isinstance(data.run_name, dict):
	1282	# Note: key order in dict is not guaranteed, so sort
	1283	name = data.run_name.keys()[0]
[959eb01]	1284	else:
[ba8d326]	1285	name = data.run_name
[959eb01]	1286	else:
	1287	name = original_fname
	1288	state.data.group_id = name
	1289	state.version = fitstate.version
	1290	# store state in fitting
[ba8d326]	1291	self.call_back(state=state, datainfo=data, format=ext)
[959eb01]	1292	self.state = state
	1293	simfitstate = self._parse_simfit_state(entry)
	1294	if simfitstate is not None:
	1295	self.call_back(state=simfitstate)
	1296
	1297	return output
	1298	except:
	1299	self.call_back(format=ext)
	1300	raise
	1301
	1302	def write(self, filename, datainfo=None, fitstate=None):
	1303	"""
	1304	Write the content of a Data1D as a CanSAS XML file only for standalone
	1305
	1306	:param filename: name of the file to write
	1307	:param datainfo: Data1D object
	1308	:param fitstate: PageState object
	1309
	1310	"""
	1311	# Sanity check
	1312	if self.cansas:
	1313	# Add fitting information to the XML document
	1314	doc = self.write_toXML(datainfo, fitstate)
	1315	# Write the XML document
	1316	else:
	1317	doc = fitstate.to_xml(file=filename)
	1318
	1319	# Save the document no matter the type
	1320	fd = open(filename, 'w')
	1321	fd.write(doc.toprettyxml())
	1322	fd.close()
	1323
	1324	def write_toXML(self, datainfo=None, state=None, batchfit=None):
	1325	"""
	1326	Write toXML, a helper for write(),
	1327	could be used by guimanager._on_save()
	1328
	1329	: return: xml doc
	1330	"""
	1331
	1332	self.batchfit_params = batchfit
	1333	if state.data is None or not state.data.is_data:
	1334	return None
	1335	# make sure title and data run are filled.
	1336	if state.data.title is None or state.data.title == '':
	1337	state.data.title = state.data.name
	1338	if state.data.run_name is None or state.data.run_name == {}:
	1339	state.data.run = [str(state.data.name)]
	1340	state.data.run_name[0] = state.data.name
	1341
	1342	data = state.data
	1343	doc, sasentry = self._to_xml_doc(data)
	1344
	1345	if state is not None:
	1346	doc = state.to_xml(doc=doc, file=data.filename, entry_node=sasentry,
	1347	batch_fit_state=self.batchfit_params)
	1348
	1349	return doc
	1350
[78312f7]	1351	# Simple html report template
[959eb01]	1352	HEADER = "<html>\n"
	1353	HEADER += "<head>\n"
	1354	HEADER += "<meta http-equiv=Content-Type content='text/html; "
	1355	HEADER += "charset=windows-1252'> \n"
	1356	HEADER += "<meta name=Generator >\n"
	1357	HEADER += "</head>\n"
	1358	HEADER += "<body lang=EN-US>\n"
	1359	HEADER += "<div class=WordSection1>\n"
	1360	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
	1361	HEADER += "%s</font></center></span></center></b></p>"
	1362	HEADER += "<p class=MsoNormal> </p>"
	1363	PARA = "<p class=MsoNormal><font size='4' > %s \n"
	1364	PARA += "</font></p>"
	1365	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
	1366	CENTRE += "</font></center></p>"
	1367	FEET_1 = \
	1368	"""
	1369	<p class=MsoNormal> </p>
	1370	<br>
	1371	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
	1372	</font></span></center></b></p>
	1373	<p class=MsoNormal> </p>
	1374	<center>
	1375	<br><font size='4' >Model Computation</font>
	1376	<br><font size='4' >Data: "%s"</font><br>
	1377	"""
	1378	FEET_2 = \
[3b070a0]	1379	"""<img src="%s"></img>
[959eb01]	1380	"""
[47c44f0]	1381	FEET_2_unix = \
	1382	"""<img src="%s" width="540"></img>
	1383	"""
[959eb01]	1384	FEET_3 = \
[78312f7]	1385	"""</center>
[959eb01]	1386	</div>
	1387	</body>
	1388	</html>
	1389	"""
[78312f7]	1390	ELINE = """<p class=MsoNormal> </p>
	1391	"""

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SasView

source: sasview/src/sas/sascalc/fit/pagestate.py @ 009abcc

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