pagestate.py @ f21d496

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

Last change on this file since f21d496 was 0e33a8d, checked in by Doucet, Mathieu <doucetm@…>, 9 years ago
Minor fixes to state loading
Property mode set to `100644`
File size: 69.9 KB

Rev	Line
[f32d144]	1	"""
	2	Class that holds a fit page state
	3	"""
[b1e609c]	4	#TODO: Refactor code so we don't need to use getattr/setattr
[5062bbf]	5	################################################################################
	6	#This software was developed by the University of Tennessee as part of the
	7	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
[f32d144]	8	#project funded by the US National Science Foundation.
[5062bbf]	9	#
	10	#See the license text in license.txt
	11	#
	12	#copyright 2009, University of Tennessee
	13	################################################################################
[11a7e11]	14	import time
	15	import os
	16	import sys
[6f023e8]	17	import copy
[11a7e11]	18	import logging
[df7ed14]	19	import numpy
[eddb6ec]	20	import string
[c77d859]	21
[35b556d]	22	import xml.dom.minidom
[ac5b69d]	23	from xml.dom.minidom import parseString
[11a7e11]	24	from lxml import etree
	25
[79492222]	26	import sas.dataloader
	27	from sas.dataloader.readers.cansas_reader import Reader as CansasReader
	28	from sas.dataloader.readers.cansas_reader import get_content, write_node
	29	from sas.dataloader.data_info import Data2D
	30	from sas.dataloader.data_info import Collimation
	31	from sas.dataloader.data_info import Detector
	32	from sas.dataloader.data_info import Process
	33	from sas.dataloader.data_info import Aperture
[11a7e11]	34	#Information to read/write state as xml
[61cada5]	35	FITTING_NODE_NAME = 'fitting_plug_in'
	36	CANSAS_NS = "cansas1d/1.0"
	37
[b1e609c]	38	LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"],
	39	["group_id", "data_group_id", "string"],
	40	["data_name", "data_name", "string"],
	41	["data_id", "data_id", "string"],
	42	["name", "name", "string"],
	43	["data_name", "data_name", "string"]]
[acf8e4a5]	44	LIST_OF_STATE_ATTRIBUTES = [["qmin", "qmin", "float"],
[b1e609c]	45	["qmax", "qmax", "float"],
	46	["npts", "npts", "float"],
	47	["categorycombobox", "categorycombobox", "string"],
	48	["formfactorcombobox", "formfactorcombobox", "string"],
	49	["structurecombobox", "structurecombobox", "string"],
	50	["multi_factor", "multi_factor", "float"],
	51	["magnetic_on", "magnetic_on", "bool"],
	52	["enable_smearer", "enable_smearer", "bool"],
	53	["disable_smearer", "disable_smearer", "bool"],
	54	["pinhole_smearer", "pinhole_smearer", "bool"],
	55	["slit_smearer", "slit_smearer", "bool"],
	56	["enable_disp", "enable_disp", "bool"],
	57	["disable_disp", "disable_disp", "bool"],
	58	["dI_noweight", "dI_noweight", "bool"],
	59	["dI_didata", "dI_didata", "bool"],
	60	["dI_sqrdata", "dI_sqrdata", "bool"],
	61	["dI_idata", "dI_idata", "bool"],
	62	["enable2D", "enable2D", "bool"],
	63	["cb1", "cb1", "bool"],
	64	["tcChi", "tcChi", "float"],
	65	["smearer", "smearer", "float"],
	66	["smear_type", "smear_type", "string"],
	67	["dq_l", "dq_l", "string"],
	68	["dq_r", "dq_r", "string"],
	69	["dx_max", "dx_max", "float"],
	70	["dx_min", "dx_min", "float"],
	71	["dxl", "dxl", "float"],
	72	["dxw", "dxw", "float"]]
	73
	74	LIST_OF_MODEL_ATTRIBUTES = [["values", "values"],
[11a7e11]	75	["weights", "weights"]]
	76
[b1e609c]	77	DISPERSION_LIST = [["disp_obj_dict", "_disp_obj_dict", "string"]]
[2296316]	78
[b1e609c]	79	LIST_OF_STATE_PARAMETERS = [["parameters", "parameters"],
[f32d144]	80	["str_parameters", "str_parameters"],
[61cada5]	81	["orientation_parameters", "orientation_params"],
	82	["dispersity_parameters", "orientation_params_disp"],
[f32d144]	83	["fixed_param", "fixed_param"],
	84	["fittable_param", "fittable_param"]]
[b1e609c]	85	LIST_OF_DATA_2D_ATTR = [["xmin", "xmin", "float"],
[f32d144]	86	["xmax", "xmax", "float"],
	87	["ymin", "ymin", "float"],
	88	["ymax", "ymax", "float"],
	89	["_xaxis", "_xaxis", "string"],
[df7ed14]	90	["_xunit", "_xunit", "string"],
[f32d144]	91	["_yaxis", "_yaxis", "string"],
	92	["_yunit", "_yunit", "string"],
	93	["_zaxis", "_zaxis", "string"],
	94	["_zunit", "_zunit", "string"]]
[b1e609c]	95	LIST_OF_DATA_2D_VALUES = [["qx_data", "qx_data", "float"],
	96	["qy_data", "qy_data", "float"],
	97	["dqx_data", "dqx_data", "float"],
	98	["dqy_data", "dqy_data", "float"],
	99	["data", "data", "float"],
	100	["q_data", "q_data", "float"],
	101	["err_data", "err_data", "float"],
	102	["mask", "mask", "bool"]]
[61cada5]	103
[f32d144]	104
	105	def parse_entry_helper(node, item):
[0b12abb5]	106	"""
	107	Create a numpy list from value extrated from the node
[2f4b430]	108
[0b12abb5]	109	:param node: node from each the value is stored
	110	:param item: list name of three strings.the two first are name of data
[f32d144]	111	attribute and the third one is the type of the value of that
[0b12abb5]	112	attribute. type can be string, float, bool, etc.
[2f4b430]	113
[0b12abb5]	114	: return: numpy array
	115	"""
	116	if node is not None:
	117	if item[2] == "string":
	118	return str(node.get(item[0]).strip())
	119	elif item[2] == "bool":
	120	try:
[e3d1423]	121	return node.get(item[0]).strip() == "True"
[2f4b430]	122
[0b12abb5]	123	except:
	124	return None
	125	else:
	126	try:
	127	return float(node.get(item[0]))
	128	except:
	129	return None
[2f4b430]	130
	131
[cfc0913]	132	class PageState(object):
[c77d859]	133	"""
[5062bbf]	134	Contains information to reconstruct a page of the fitpanel.
[c77d859]	135	"""
[61cada5]	136	def __init__(self, parent=None, model=None, data=None):
[f32d144]	137	"""
[5062bbf]	138	Initialize the current state
[2f4b430]	139
[5062bbf]	140	:param model: a selected model within a page
[f32d144]	141	:param data:
[2f4b430]	142
[c77d859]	143	"""
[61cada5]	144	self.file = None
[11a7e11]	145	#Time of state creation
	146	self.timestamp = time.time()
[c77d859]	147	## Data member to store the dispersion object created
	148	self._disp_obj_dict = {}
[61cada5]	149	#------------------------
[f32d144]	150	#Data used for fitting
[c77d859]	151	self.data = data
[2296316]	152	# model data
	153	self.theory_data = None
	154	#Is 2D
	155	self.is_2D = False
	156	self.images = None
[2f4b430]	157
[61cada5]	158	#save additional information on data that dataloader.reader does not read
	159	self.is_data = None
	160	self.data_name = ""
[c0ff8cc]	161
[61cada5]	162	if self.data is not None:
	163	self.data_name = self.data.name
	164	self.data_id = None
	165	if self.data is not None and hasattr(self.data, "id"):
	166	self.data_id = self.data.id
	167	self.data_group_id = None
	168	if self.data is not None and hasattr(self.data, "group_id"):
	169	self.data_group_id = self.data.group_id
[2f4b430]	170
[61cada5]	171	## reset True change the state of exsiting button
	172	self.reset = False
[2f4b430]	173
[c77d859]	174	# flag to allow data2D plot
[cfc0913]	175	self.enable2D = False
[c77d859]	176	# model on which the fit would be performed
	177	self.model = model
[93f0a862]	178	self.m_name = None
[dce84c0]	179	#list of process done to model
	180	self.process = []
[f32d144]	181	#fit page manager
[c77d859]	182	self.manager = None
	183	#Store the parent of this panel parent
	184	# For this application fitpanel is the parent
[f32d144]	185	self.parent = parent
[c77d859]	186	# Event_owner is the owner of model event
	187	self.event_owner = None
[c9a4377]	188	##page name
[cfc0913]	189	self.page_name = ""
[eddb6ec]	190	# Contains link between model, all its parameters, and panel organization
[61cada5]	191	self.parameters = []
[fb59ed9]	192	# String parameter list that can not be fitted
	193	self.str_parameters = []
[f32d144]	194	# Contains list of parameters that cannot be fitted and reference to
	195	#panel objects
[61cada5]	196	self.fixed_param = []
[f32d144]	197	# Contains list of parameters with dispersity and reference to
	198	#panel objects
[61cada5]	199	self.fittable_param = []
[60132ef]	200	## orientation parameters
[61cada5]	201	self.orientation_params = []
[eddb6ec]	202	## orientation parameters for gaussian dispersity
[61cada5]	203	self.orientation_params_disp = []
[3370922]	204	## smearer info
[61cada5]	205	self.smearer = None
[7609f1a]	206	self.smear_type = None
	207	self.dq_l = None
	208	self.dq_r = None
[db8fd5b]	209	self.dx_max = None
	210	self.dx_min = None
	211	self.dxl = None
	212	self.dxw = None
[eddb6ec]	213	#list of dispersion parameters
[f32d144]	214	self.disp_list = []
[61cada5]	215	if self.model is not None:
[71f0373]	216	self.disp_list = self.model.getDispParamList()
[2296316]	217
[61cada5]	218	self.disp_cb_dict = {}
[2296316]	219	self.values = {}
	220	self.weights = {}
[2f4b430]	221
[f32d144]	222	#contains link between a model and selected parameters to fit
[61cada5]	223	self.param_toFit = []
[a074145]	224	##dictionary of model type and model class
[cfc0913]	225	self.model_list_box = None
[a074145]	226	## save the state of the context menu
[61cada5]	227	self.saved_states = {}
[240b9966]	228	## save selection of combobox
[3b9e023]	229	self.formfactorcombobox = None
[ea5fa58]	230	self.categorycombobox = None
[f32d144]	231	self.structurecombobox = None
[c0ff8cc]	232
[240b9966]	233	## radio box to select type of model
[ea5fa58]	234	#self.shape_rbutton = False
	235	#self.shape_indep_rbutton = False
	236	#self.struct_rbutton = False
	237	#self.plugin_rbutton = False
[b787e68c]	238	## the indice of the current selection
	239	self.disp_box = 0
[c77d859]	240	## Qrange
[cfc0913]	241	## Q range
[61cada5]	242	self.qmin = 0.001
	243	self.qmax = 0.1
[0b12abb5]	244	#reset data range
	245	self.qmax_x = None
	246	self.qmin_x = None
[2f4b430]	247
[cfc0913]	248	self.npts = None
[61cada5]	249	self.name = ""
[4523b68]	250	self.multi_factor = None
[318b5bbb]	251	self.magnetic_on = False
[cfc0913]	252	## enable smearering state
	253	self.enable_smearer = False
[fc6ea43]	254	self.disable_smearer = True
[7609f1a]	255	self.pinhole_smearer = False
[f32d144]	256	self.slit_smearer = False
[55bb249c]	257	# weighting options
	258	self.dI_noweight = False
	259	self.dI_didata = True
	260	self.dI_sqrdata = False
[f32d144]	261	self.dI_idata = False
[cfc0913]	262	## disperity selection
[61cada5]	263	self.enable_disp = False
	264	self.disable_disp = True
[2f4b430]	265
[cfc0913]	266	## state of selected all check button
	267	self.cb1 = False
[0aeabc6]	268	## store value of chisqr
[61cada5]	269	self.tcChi = None
[2f4b430]	270
[6f023e8]	271	def clone(self):
[61cada5]	272	"""
[5062bbf]	273	Create a new copy of the current object
[61cada5]	274	"""
	275	model = None
	276	if self.model is not None:
[6f023e8]	277	model = self.model.clone()
[bb70474]	278	model.name = self.model.name
[61cada5]	279	obj = PageState(self.parent, model=model)
	280	obj.file = copy.deepcopy(self.file)
[6f023e8]	281	obj.data = copy.deepcopy(self.data)
[61cada5]	282	if self.data is not None:
	283	self.data_name = self.data.name
	284	obj.data_name = self.data_name
	285	obj.is_data = self.is_data
[dcf29d7]	286	obj.model_list_box = copy.deepcopy(self.model_list_box)
[2f4b430]	287
[ea5fa58]	288	obj.categorycombobox = self.categorycombobox
[61cada5]	289	obj.formfactorcombobox = self.formfactorcombobox
[f32d144]	290	obj.structurecombobox = self.structurecombobox
[2f4b430]	291
[ea5fa58]	292	#obj.shape_rbutton = self.shape_rbutton
	293	#obj.shape_indep_rbutton = self.shape_indep_rbutton
	294	#obj.struct_rbutton = self.struct_rbutton
	295	#obj.plugin_rbutton = self.plugin_rbutton
[2f4b430]	296
[dcf29d7]	297	obj.manager = self.manager
	298	obj.event_owner = self.event_owner
[71f0373]	299	obj.disp_list = copy.deepcopy(self.disp_list)
[2f4b430]	300
[c477b31]	301	obj.enable2D = copy.deepcopy(self.enable2D)
[cfc0913]	302	obj.parameters = copy.deepcopy(self.parameters)
[fb59ed9]	303	obj.str_parameters = copy.deepcopy(self.str_parameters)
[cfc0913]	304	obj.fixed_param = copy.deepcopy(self.fixed_param)
	305	obj.fittable_param = copy.deepcopy(self.fittable_param)
[f32d144]	306	obj.orientation_params = copy.deepcopy(self.orientation_params)
	307	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
[b787e68c]	308	obj.enable_disp = copy.deepcopy(self.enable_disp)
[fc6ea43]	309	obj.disable_disp = copy.deepcopy(self.disable_disp)
[0aeabc6]	310	obj.tcChi = self.tcChi
[2f4b430]	311
[f32d144]	312	if len(self._disp_obj_dict) > 0:
	313	for k, v in self._disp_obj_dict.iteritems():
	314	obj._disp_obj_dict[k] = v
	315	if len(self.disp_cb_dict) > 0:
	316	for k, v in self.disp_cb_dict.iteritems():
	317	obj.disp_cb_dict[k] = v
	318	if len(self.values) > 0:
	319	for k, v in self.values.iteritems():
[2296316]	320	obj.values[k] = v
[f32d144]	321	if len(self.weights) > 0:
	322	for k, v in self.weights.iteritems():
[2296316]	323	obj.weights[k] = v
[b787e68c]	324	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
[fc6ea43]	325	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
[7609f1a]	326	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
	327	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
	328	obj.smear_type = copy.deepcopy(self.smear_type)
[55bb249c]	329	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
	330	obj.dI_didata = copy.deepcopy(self.dI_didata)
	331	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
	332	obj.dI_idata = copy.deepcopy(self.dI_idata)
[7609f1a]	333	obj.dq_l = copy.deepcopy(self.dq_l)
	334	obj.dq_r = copy.deepcopy(self.dq_r)
[db8fd5b]	335	obj.dx_max = copy.deepcopy(self.dx_max)
	336	obj.dx_min = copy.deepcopy(self.dx_min)
	337	obj.dxl = copy.deepcopy(self.dxl)
[2f4b430]	338	obj.dxw = copy.deepcopy(self.dxw)
[b787e68c]	339	obj.disp_box = copy.deepcopy(self.disp_box)
	340	obj.qmin = copy.deepcopy(self.qmin)
	341	obj.qmax = copy.deepcopy(self.qmax)
[c0ff8cc]	342	obj.multi_factor = self.multi_factor
[318b5bbb]	343	obj.magnetic_on = self.magnetic_on
[f32d144]	344	obj.npts = copy.deepcopy(self.npts)
[b787e68c]	345	obj.cb1 = copy.deepcopy(self.cb1)
[3370922]	346	obj.smearer = copy.deepcopy(self.smearer)
[2f4b430]	347
[a074145]	348	for name, state in self.saved_states.iteritems():
	349	copy_name = copy.deepcopy(name)
	350	copy_state = state.clone()
[f32d144]	351	obj.saved_states[copy_name] = copy_state
[6f023e8]	352	return obj
[2f4b430]	353
[61cada5]	354	def _repr_helper(self, list, rep):
	355	"""
[5062bbf]	356	Helper method to print a state
[61cada5]	357	"""
	358	for item in list:
[f32d144]	359	rep += "parameter name: %s \n" % str(item[1])
	360	rep += "value: %s\n" % str(item[2])
	361	rep += "selected: %s\n" % str(item[0])
	362	rep += "error displayed : %s \n" % str(item[4][0])
	363	rep += "error value:%s \n" % str(item[4][1])
	364	rep += "minimum displayed : %s \n" % str(item[5][0])
	365	rep += "minimum value : %s \n" % str(item[5][1])
	366	rep += "maximum displayed : %s \n" % str(item[6][0])
	367	rep += "maximum value : %s \n" % str(item[6][1])
	368	rep += "parameter unit: %s\n\n" % str(item[7])
[240b9966]	369	return rep
[2f4b430]	370
[61cada5]	371	def __repr__(self):
[f32d144]	372	"""
[5062bbf]	373	output string for printing
[11a7e11]	374	"""
[f32d144]	375	rep = "\nState name: %s\n" % self.file
[11a7e11]	376	t = time.localtime(self.timestamp)
[deff488]	377	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
[c0ff8cc]	378
[f32d144]	379	rep += "State created: %s\n" % time_str
	380	rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
	381	rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
	382	rep += "is data : %s\n" % self.is_data
	383	rep += "data's name : %s\n" % self.data_name
	384	rep += "data's id : %s\n" % self.data_id
[74dc0a4]	385	if self.model != None:
[93f0a862]	386	m_name = self.model.__class__.__name__
	387	if m_name == 'Model':
	388	m_name = self.m_name
[f32d144]	389	rep += "model name : %s\n" % m_name
[74dc0a4]	390	else:
	391	rep += "model name : None\n"
[f32d144]	392	rep += "multi_factor : %s\n" % str(self.multi_factor)
[2f4b430]	393	rep += "magnetic_on : %s\n" % str(self.magnetic_on)
[ea5fa58]	394	rep += "model type (Category) selected: %s\n" % self.categorycombobox
[f32d144]	395	rep += "data : %s\n" % str(self.data)
	396	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
[b1e609c]	397	str(self.qmax), str(self.npts))
[f32d144]	398	rep += "Dispersion selection : %s\n" % str(self.disp_box)
	399	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
	400	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
	401	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
	402	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
	403	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
	404	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
	405	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
[2f4b430]	406
[f32d144]	407	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
	408	rep += "dI_didata : %s\n" % str(self.dI_didata)
	409	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
	410	rep += "dI_idata : %s\n" % str(self.dI_idata)
[2f4b430]	411
[f32d144]	412	rep += "2D enable : %s\n" % str(self.enable2D)
	413	rep += "All parameters checkbox selected: %s\n" % (self.cb1)
	414	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
	415	rep += "Smear object : %s\n" % str(self.smearer)
	416	rep += "Smear type : %s\n" % (self.smear_type)
	417	rep += "dq_l : %s\n" % self.dq_l
	418	rep += "dq_r : %s\n" % self.dq_r
[db8fd5b]	419	rep += "dx_max : %s\n" % str(self.dx_max)
[2f4b430]	420	rep += "dx_min : %s\n" % str(self.dx_min)
[db8fd5b]	421	rep += "dxl : %s\n" % str(self.dxl)
[2f4b430]	422	rep += "dxw : %s\n" % str(self.dxw)
[f32d144]	423	rep += "model : %s\n\n" % str(self.model)
[2296316]	424	temp_parameters = []
	425	temp_fittable_param = []
	426	if self.data.__class__.__name__ == "Data2D":
	427	self.is_2D = True
	428	else:
	429	self.is_2D = False
	430	if self.data is not None:
	431	if not self.is_2D:
	432	for item in self.parameters:
	433	if not item in self.orientation_params:
	434	temp_parameters.append(item)
	435	for item in self.fittable_param:
	436	if not item in self.orientation_params_disp:
	437	temp_fittable_param.append(item)
	438	else:
	439	temp_parameters = self.parameters
	440	temp_fittable_param = self.fittable_param
[2f4b430]	441
[f32d144]	442	rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
	443	rep = self._repr_helper(list=temp_parameters, rep=rep)
	444	rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
	445	rep = self._repr_helper(list=self.str_parameters, rep=rep)
	446	rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
	447	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
[61cada5]	448	return rep
[2296316]	449
	450	def set_report_string(self):
	451	"""
[f32d144]	452	Get the values (strings) from __str__ for report
[2296316]	453	"""
[d06ae30]	454	# Dictionary of the report strings
[2296316]	455	repo_time = ""
	456	model_name = ""
	457	title = ""
	458	title_name = ""
	459	file_name = ""
	460	param_string = ""
	461	paramval_string = ""
	462	chi2_string = ""
	463	q_range = ""
	464	strings = self.__repr__()
	465	lines = strings.split('\n')
	466
	467	# get all string values from __str__()
	468	for line in lines:
	469	value = ""
	470	content = line.split(":")
	471	name = content[0]
	472	try:
	473	value = content[1]
	474	except:
[b1e609c]	475	logging.error(sys.exc_value)
[b7c6a4a]	476	if name.count("State created"):
	477	repo_time = "" + value
[2296316]	478	if name.count("parameter name"):
	479	val_name = value.split(".")
	480	if len(val_name) > 1:
	481	if val_name[1].count("width"):
	482	param_string += value + ','
	483	else:
	484	continue
	485	else:
	486	param_string += value + ','
	487	if name == "value":
	488	param_string += value + ','
[b1e609c]	489	if name == "selected":
	490	if value == u' False':
	491	fixed_parameter = True
	492	else:
	493	fixed_parameter = False
[2296316]	494	if name == "error value":
[b1e609c]	495	if fixed_parameter:
	496	param_string += '(fixed),'
	497	else:
[d06ae30]	498	param_string += value + ','
[2296316]	499	if name == "parameter unit":
[f32d144]	500	param_string += value + ':'
[2296316]	501	if name == "Value of Chisqr ":
	502	chi2 = ("Chi2/Npts = " + value)
	503	chi2_string = CENTRE % chi2
	504	if name == "Title":
	505	if len(value.strip()) == 0:
	506	continue
	507	title = value + " [" + repo_time + "]"
	508	title_name = HEADER % title
	509	if name == "data ":
	510	try:
[b1e609c]	511	file_value = ("File name:" + content[2])
	512	file_name = CENTRE % file_value
[2296316]	513	if len(title) == 0:
	514	title = content[2] + " [" + repo_time + "]"
	515	title_name = HEADER % title
	516	except:
[b1e609c]	517	logging.error(sys.exc_value)
[74dc0a4]	518	if name == "model name ":
	519	try:
	520	modelname = "Model name:" + content[1]
	521	except:
	522	modelname = "Model name:" + " NAN"
[f32d144]	523	model_name = CENTRE % modelname
[2f4b430]	524
[2296316]	525	if name == "Plotting Range":
	526	try:
	527	q_range = content[1] + " = " + content[2] \
	528	+ " = " + content[3].split(",")[0]
	529	q_name = ("Q Range: " + q_range)
	530	q_range = CENTRE % q_name
	531	except:
[b1e609c]	532	logging.error(sys.exc_value)
[2296316]	533	paramval = ""
[f32d144]	534	for lines in param_string.split(":"):
[2296316]	535	line = lines.split(",")
[f32d144]	536	if len(lines) > 0:
	537	param = line[0]
[2296316]	538	param += " = " + line[1]
	539	if len(line[2].split()) > 0 and not line[2].count("None"):
	540	param += " +- " + line[2]
	541	if len(line[3].split()) > 0 and not line[3].count("None"):
	542	param += " " + line[3]
	543	if not paramval.count(param):
[f32d144]	544	paramval += param + "\n"
[2296316]	545	paramval_string += CENTRE % param + "\n"
[2f4b430]	546
[a15e754]	547	text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % (title, file, q_name, chi2, paramval)
[2f4b430]	548
[f5bdb4a]	549	title_name = self._check_html_format(title_name)
	550	file_name = self._check_html_format(file_name)
	551	title = self._check_html_format(title)
[2f4b430]	552
[2296316]	553	html_string = title_name + "\n" + file_name + \
[f32d144]	554	"\n" + model_name + \
[2296316]	555	"\n" + q_range + \
	556	"\n" + chi2_string + \
	557	"\n" + ELINE + \
	558	"\n" + paramval_string + \
	559	"\n" + ELINE + \
	560	"\n" + FEET_1 % title + \
[f32d144]	561	"\n" + FEET_2
[2f4b430]	562
[2296316]	563	return html_string, text_string, title
[2f4b430]	564
[f5bdb4a]	565	def _check_html_format(self, name):
	566	"""
	567	Check string '%' for html format
	568	"""
	569	if name.count('%'):
	570	name = name.replace('%', '&#37')
[2f4b430]	571
[f5bdb4a]	572	return name
[2f4b430]	573
[2296316]	574	def report(self, figs=None, canvases=None):
	575	"""
	576	Invoke report dialog panel
[2f4b430]	577
[2296316]	578	: param figs: list of pylab figures [list]
	579	"""
[79492222]	580	from sas.perspectives.fitting.report_dialog import ReportDialog
[2296316]	581	# get the strings for report
	582	html_str, text_str, title = self.set_report_string()
	583	# Allow 2 figures to append
	584	if len(figs) == 1:
[f32d144]	585	add_str = FEET_3
[2296316]	586	elif len(figs) == 2:
[f32d144]	587	add_str = ELINE
	588	add_str += FEET_2 % ("%s")
	589	add_str += ELINE
	590	add_str += FEET_3
[2296316]	591	elif len(figs) > 2:
[f32d144]	592	add_str = ELINE
	593	add_str += FEET_2 % ("%s")
	594	add_str += ELINE
	595	add_str += FEET_2 % ("%s")
	596	add_str += ELINE
	597	add_str += FEET_3
[2296316]	598	else:
	599	add_str = ""
[c0ff8cc]	600
[2296316]	601	# final report html strings
	602	report_str = html_str % ("%s") + add_str
	603
	604	# make plot image
	605	images = self.set_plot_state(figs, canvases)
[f32d144]	606	report_list = [report_str, text_str, images]
[2296316]	607	dialog = ReportDialog(report_list, None, -1, "")
[d838715]	608	dialog.Show()
[2f4b430]	609
[eddb6ec]	610	def _toXML_helper(self, thelist, element, newdoc):
[61cada5]	611	"""
[5062bbf]	612	Helper method to create xml file for saving state
[61cada5]	613	"""
[eddb6ec]	614	for item in thelist:
[61cada5]	615	sub_element = newdoc.createElement('parameter')
	616	sub_element.setAttribute('name', str(item[1]))
	617	sub_element.setAttribute('value', str(item[2]))
	618	sub_element.setAttribute('selected_to_fit', str(item[0]))
	619	sub_element.setAttribute('error_displayed', str(item[4][0]))
	620	sub_element.setAttribute('error_value', str(item[4][1]))
	621	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
	622	sub_element.setAttribute('minimum_value', str(item[5][1]))
	623	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
	624	sub_element.setAttribute('maximum_value', str(item[6][1]))
	625	sub_element.setAttribute('unit', str(item[7]))
	626	element.appendChild(sub_element)
[2f4b430]	627
[61cada5]	628	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
	629	"""
[5062bbf]	630	Writes the state of the InversionControl panel to file, as XML.
[2f4b430]	631
[5062bbf]	632	Compatible with standalone writing, or appending to an
	633	already existing XML document. In that case, the XML document
	634	is required. An optional entry node in the XML document may also be given.
[2f4b430]	635
[5062bbf]	636	:param file: file to write to
	637	:param doc: XML document object [optional]
	638	:param entry_node: XML node within the XML document at which we will append the data [optional]
[2f4b430]	639
[61cada5]	640	"""
	641	from xml.dom.minidom import getDOMImplementation
[71f0373]	642
[61cada5]	643	# Check whether we have to write a standalone XML file
	644	if doc is None:
	645	impl = getDOMImplementation()
[f32d144]	646	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
[61cada5]	647	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
	648	top_element = newdoc.documentElement
	649	else:
	650	# We are appending to an existing document
	651	newdoc = doc
[ac5b69d]	652	try:
	653	top_element = newdoc.createElement(FITTING_NODE_NAME)
	654	except:
	655	string = etree.tostring(doc, pretty_print=True)
	656	newdoc = parseString(string)
	657	top_element = newdoc.createElement(FITTING_NODE_NAME)
[61cada5]	658	if entry_node is None:
	659	newdoc.documentElement.appendChild(top_element)
	660	else:
[ac5b69d]	661	try:
	662	entry_node.appendChild(top_element)
	663	except:
	664	node_name = entry_node.tag
	665	node_list = newdoc.getElementsByTagName(node_name)
	666	entry_node = node_list.item(0)
	667	entry_node.appendChild(top_element)
[2f4b430]	668
[61cada5]	669	attr = newdoc.createAttribute("version")
	670	attr.nodeValue = '1.0'
	671	top_element.setAttributeNode(attr)
[2f4b430]	672
[61cada5]	673	# File name
	674	element = newdoc.createElement("filename")
	675	if self.file is not None:
	676	element.appendChild(newdoc.createTextNode(str(self.file)))
	677	else:
	678	element.appendChild(newdoc.createTextNode(str(file)))
	679	top_element.appendChild(element)
[2f4b430]	680
[11a7e11]	681	element = newdoc.createElement("timestamp")
	682	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
	683	attr = newdoc.createAttribute("epoch")
	684	attr.nodeValue = str(self.timestamp)
	685	element.setAttributeNode(attr)
	686	top_element.appendChild(element)
[61cada5]	687	# Inputs
	688	inputs = newdoc.createElement("Attributes")
	689	top_element.appendChild(inputs)
[2f4b430]	690
[61cada5]	691	if self.data is not None and hasattr(self.data, "group_id"):
	692	self.data_group_id = self.data.group_id
	693	if self.data is not None and hasattr(self.data, "is_data"):
	694	self.is_data = self.data.is_data
	695	if self.data is not None:
	696	self.data_name = self.data.name
	697	if self.data is not None and hasattr(self.data, "id"):
	698	self.data_id = self.data.id
[2f4b430]	699
[b1e609c]	700	for item in LIST_OF_DATA_ATTRIBUTES:
[0b12abb5]	701	element = newdoc.createElement(item[0])
[b1e609c]	702	element.setAttribute(item[0], str(getattr(self, item[1])))
[f32d144]	703	inputs.appendChild(element)
[2f4b430]	704
[b1e609c]	705	for item in LIST_OF_STATE_ATTRIBUTES:
[26f3dd5]	706	element = newdoc.createElement(item[0])
[b1e609c]	707	element.setAttribute(item[0], str(getattr(self, item[1])))
[26f3dd5]	708	inputs.appendChild(element)
[2f4b430]	709
[f32d144]	710	# For self.values ={ disp_param_name: [vals,...],...}
	711	# and for self.weights ={ disp_param_name: [weights,...],...}
[b1e609c]	712	value_list = {}
	713	for item in LIST_OF_MODEL_ATTRIBUTES:
[11a7e11]	714	element = newdoc.createElement(item[0])
[b1e609c]	715	value_list = getattr(self, item[1])
	716	for key, value in value_list.iteritems():
[2296316]	717	sub_element = newdoc.createElement(key)
	718	sub_element.setAttribute('name', str(key))
	719	for val in value:
[b1e609c]	720	sub_element.appendChild(newdoc.createTextNode(str(val)))
[2f4b430]	721
[f32d144]	722	element.appendChild(sub_element)
[11a7e11]	723	inputs.appendChild(element)
[2f4b430]	724
[2296316]	725	# Create doc for the dictionary of self._disp_obj_dic
[b1e609c]	726	for item in DISPERSION_LIST:
[f32d144]	727	element = newdoc.createElement(item[0])
[b1e609c]	728	value_list = getattr(self, item[1])
	729	for key, val in value_list.iteritems():
[f32d144]	730	value = repr(val)
	731	sub_element = newdoc.createElement(key)
	732	sub_element.setAttribute('name', str(key))
	733	sub_element.setAttribute('value', str(value))
	734	element.appendChild(sub_element)
	735	inputs.appendChild(element)
[2f4b430]	736
[b1e609c]	737	for item in LIST_OF_STATE_PARAMETERS:
[61cada5]	738	element = newdoc.createElement(item[0])
[b1e609c]	739	self._toXML_helper(thelist=getattr(self, item[1]), element=element, newdoc=newdoc)
[61cada5]	740	inputs.appendChild(element)
[2f4b430]	741
[61cada5]	742	# Save the file
	743	if doc is None:
	744	fd = open(file, 'w')
	745	fd.write(newdoc.toprettyxml())
	746	fd.close()
	747	return None
	748	else:
[ac5b69d]	749	return newdoc
[2f4b430]	750
[61cada5]	751	def _fromXML_helper(self, node, list):
	752	"""
[5062bbf]	753	Helper function to write state to xml
[61cada5]	754	"""
	755	for item in node:
[0b12abb5]	756	try:
	757	name = item.get('name')
	758	except:
	759	name = None
	760	try:
	761	value = item.get('value')
	762	except:
	763	value = None
	764	try:
[3ad91de]	765	selected_to_fit = (item.get('selected_to_fit') == "True")
[0b12abb5]	766	except:
	767	selected_to_fit = None
	768	try:
[3ad91de]	769	error_displayed = (item.get('error_displayed') == "True")
[0b12abb5]	770	except:
	771	error_displayed = None
[f32d144]	772	try:
[0b12abb5]	773	error_value = item.get('error_value')
	774	except:
	775	error_value = None
	776	try:
[f32d144]	777	minimum_displayed = (item.get('minimum_displayed') == "True")
[0b12abb5]	778	except:
	779	minimum_displayed = None
	780	try:
	781	minimum_value = item.get('minimum_value')
	782	except:
	783	minimum_value = None
	784	try:
[3ad91de]	785	maximum_displayed = (item.get('maximum_displayed') == "True")
[0b12abb5]	786	except:
	787	maximum_displayed = None
	788	try:
	789	maximum_value = item.get('maximum_value')
	790	except:
	791	maximum_value = None
	792	try:
	793	unit = item.get('unit')
	794	except:
	795	unit = None
[2296316]	796	list.append([selected_to_fit, name, value, "+/-",
	797	[error_displayed, error_value],
[f32d144]	798	[minimum_displayed, minimum_value],
	799	[maximum_displayed, maximum_value], unit])
[2f4b430]	800
[61cada5]	801	def fromXML(self, file=None, node=None):
	802	"""
[5062bbf]	803	Load fitting state from a file
[2f4b430]	804
[5062bbf]	805	:param file: .fitv file
	806	:param node: node of a XML document to read from
[2f4b430]	807
[61cada5]	808	"""
	809	if file is not None:
[11a7e11]	810	msg = "PageState no longer supports non-CanSAS"
	811	msg += " format for fitting files"
	812	raise RuntimeError, msg
[2f4b430]	813
[11a7e11]	814	if node.get('version')and node.get('version') == '1.0':
[2f4b430]	815
[61cada5]	816	# Get file name
	817	entry = get_content('ns:filename', node)
	818	if entry is not None:
	819	self.file = entry.text.strip()
[2f4b430]	820
[11a7e11]	821	# Get time stamp
	822	entry = get_content('ns:timestamp', node)
	823	if entry is not None and entry.get('epoch'):
	824	try:
	825	self.timestamp = float(entry.get('epoch'))
	826	except:
	827	msg = "PageState.fromXML: Could not"
	828	msg += " read timestamp\n %s" % sys.exc_value
	829	logging.error(msg)
[2f4b430]	830
[61cada5]	831	# Parse fitting attributes
	832	entry = get_content('ns:Attributes', node)
[b1e609c]	833	for item in LIST_OF_DATA_ATTRIBUTES:
[f32d144]	834	node = get_content('ns:%s' % item[0], entry)
[b1e609c]	835	setattr(self, item[0], parse_entry_helper(node, item))
[2296316]	836
[61cada5]	837	if entry is not None:
[b1e609c]	838	for item in LIST_OF_STATE_ATTRIBUTES:
[2296316]	839	node = get_content('ns:%s' % item[0], entry)
[b1e609c]	840	setattr(self, item[0], parse_entry_helper(node, item))
[2f4b430]	841
[b1e609c]	842	for item in LIST_OF_STATE_PARAMETERS:
[2296316]	843	node = get_content("ns:%s" % item[0], entry)
[b1e609c]	844	self._fromXML_helper(node=node, list=getattr(self, item[1]))
[2f4b430]	845
[f32d144]	846	# Recover _disp_obj_dict from xml file
	847	self._disp_obj_dict = {}
[b1e609c]	848	for item in DISPERSION_LIST:
[2296316]	849	# Get node
	850	node = get_content("ns:%s" % item[0], entry)
	851	for attr in node:
[b1e609c]	852	name = str(attr.get('name'))
[f32d144]	853	val = attr.get('value')
[2296316]	854	value = val.split(" instance")[0]
	855	disp_name = value.split("<")[1]
[11a7e11]	856	try:
[2296316]	857	# Try to recover disp_model object from strings
[79492222]	858	com = "from sas.models.dispersion_models "
[2c44cf8]	859	com += "import %s as disp"
[2296316]	860	com_name = disp_name.split(".")[3]
	861	exec com % com_name
[2c44cf8]	862	disp_model = disp()
[b1e609c]	863	attribute = getattr(self, item[1])
	864	attribute[name] = com_name
[11a7e11]	865	except:
[b1e609c]	866	logging.error(sys.exc_value)
[2f4b430]	867
[f32d144]	868	# get self.values and self.weights dic. if exists
[b1e609c]	869	for item in LIST_OF_MODEL_ATTRIBUTES:
[2296316]	870	node = get_content("ns:%s" % item[0], entry)
	871	dic = {}
[b1e609c]	872	value_list = []
[2296316]	873	for par in node:
	874	name = par.get('name')
	875	values = par.text.split('\n')
	876	# Get lines only with numbers
	877	for line in values:
	878	try:
[f32d144]	879	val = float(line)
[b1e609c]	880	value_list.append(val)
[2296316]	881	except:
	882	# pass if line is empty (it happens)
[b1e609c]	883	logging.error(sys.exc_value)
[0e33a8d]	884	dic[name] = numpy.array(value_list)
[b1e609c]	885	setattr(self, item[1], dic)
[2f4b430]	886
[2296316]	887	def set_plot_state(self, figs, canvases):
	888	"""
	889	Build image state that wx.html understand
	890	by plotting, putting it into wx.FileSystem image object
	891
	892	"""
	893	images = []
	894	# some imports
	895	import wx
	896
	897	# Reset memory
	898	self.imgRAM = None
	899	wx.MemoryFSHandler()
[2f4b430]	900
[2296316]	901	# For no figures in the list, prepare empty plot
	902	if figs == None or len(figs) == 0:
	903	figs = [None]
[2f4b430]	904
[f32d144]	905	# Loop over the list of figures
[2296316]	906	# use wx.MemoryFSHandler
[f32d144]	907	self.imgRAM = wx.MemoryFSHandler()
[2296316]	908	for fig in figs:
	909	if figs != None:
	910	ind = figs.index(fig)
	911	canvas = canvases[ind]
[2f4b430]	912
[b1e609c]	913	#store the image in wx.FileSystem Object
[2296316]	914	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
[2f4b430]	915
[2296316]	916	# index of the fig
	917	ind = figs.index(fig)
[2f4b430]	918
[2296316]	919	#AddFile, image can be retrieved with 'memory:filename'
[f32d144]	920	self.imgRAM.AddFile('img_fit%s.png' % ind,
[2296316]	921	canvas.bitmap, wx.BITMAP_TYPE_PNG)
[2f4b430]	922
[2296316]	923	#append figs
	924	images.append(fig)
[2f4b430]	925
[c0ff8cc]	926	return images
[61cada5]	927
[f32d144]	928
[61cada5]	929	class Reader(CansasReader):
	930	"""
[5062bbf]	931	Class to load a .fitv fitting file
[61cada5]	932	"""
	933	## File type
	934	type_name = "Fitting"
[2f4b430]	935
[61cada5]	936	## Wildcards
[b35d3d1]	937	type = ["Fitting files (.fitv)\|.fitv"
[b9a5f0e]	938	"SASView file (.svs)\|.svs"]
[61cada5]	939	## List of allowed extensions
[f32d144]	940	ext = ['.fitv', '.FITV', '.svs', 'SVS']
[2f4b430]	941
[61cada5]	942	def __init__(self, call_back=None, cansas=True):
[df7ed14]	943	CansasReader.__init__(self)
[61cada5]	944	"""
[5062bbf]	945	Initialize the call-back method to be called
	946	after we load a file
[2f4b430]	947
[5062bbf]	948	:param call_back: call-back method
	949	:param cansas: True = files will be written/read in CanSAS format
	950	False = write CanSAS format
[2f4b430]	951
[61cada5]	952	"""
	953	## Call back method to be executed after a file is read
	954	self.call_back = call_back
	955	## CanSAS format flag
	956	self.cansas = cansas
[75fbd17]	957	self.state = None
[2f4b430]	958
[75fbd17]	959	def get_state(self):
	960	return self.state
[2f4b430]	961
[61cada5]	962	def read(self, path):
[f32d144]	963	"""
[5062bbf]	964	Load a new P(r) inversion state from file
[2f4b430]	965
[5062bbf]	966	:param path: file path
[2f4b430]	967
[61cada5]	968	"""
[e9b12eaf]	969	if self.cansas == True:
[61cada5]	970	return self._read_cansas(path)
[2f4b430]	971
[e9b12eaf]	972	def _data2d_to_xml_doc(self, datainfo):
[61cada5]	973	"""
[5062bbf]	974	Create an XML document to contain the content of a Data2D
[2f4b430]	975
[5062bbf]	976	:param datainfo: Data2D object
[2f4b430]	977
[61cada5]	978	"""
	979	if not issubclass(datainfo.__class__, Data2D):
	980	raise RuntimeError, "The cansas writer expects a Data2D instance"
[2f4b430]	981
[61cada5]	982	doc = xml.dom.minidom.Document()
	983	main_node = doc.createElement("SASroot")
	984	main_node.setAttribute("version", self.version)
[df7ed14]	985	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
	986	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
[b1e609c]	987	main_node.setAttribute("xsi:schemaLocation",
	988	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
[2f4b430]	989
[61cada5]	990	doc.appendChild(main_node)
[2f4b430]	991
[61cada5]	992	entry_node = doc.createElement("SASentry")
	993	main_node.appendChild(entry_node)
[2f4b430]	994
[61cada5]	995	write_node(doc, entry_node, "Title", datainfo.title)
[df7ed14]	996	if datainfo is not None:
	997	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
[61cada5]	998	for item in datainfo.run:
	999	runname = {}
[2f4b430]	1000	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item])) > 1:
[b1e609c]	1001	runname = {'name': datainfo.run_name[item]}
[61cada5]	1002	write_node(doc, entry_node, "Run", item, runname)
	1003	# Data info
[df7ed14]	1004	new_node = doc.createElement("SASdata")
	1005	entry_node.appendChild(new_node)
[b1e609c]	1006	for item in LIST_OF_DATA_2D_ATTR:
[e9b12eaf]	1007	element = doc.createElement(item[0])
[b1e609c]	1008	element.setAttribute(item[0], str(getattr(datainfo, item[1])))
[df7ed14]	1009	new_node.appendChild(element)
[2f4b430]	1010
[b1e609c]	1011	for item in LIST_OF_DATA_2D_VALUES:
[df7ed14]	1012	root_node = doc.createElement(item[0])
	1013	new_node.appendChild(root_node)
[38226d26]	1014	temp_list = None
[b1e609c]	1015	temp_list = getattr(datainfo, item[1])
[df7ed14]	1016
[2f4b430]	1017	if temp_list is None or len(temp_list) == 0:
[df7ed14]	1018	element = doc.createElement(item[0])
[b1e609c]	1019	element.appendChild(doc.createTextNode(str(temp_list)))
[df7ed14]	1020	root_node.appendChild(element)
[35b556d]	1021	else:
	1022	for value in temp_list:
[df7ed14]	1023	element = doc.createElement(item[0])
[b1e609c]	1024	element.setAttribute(item[0], str(value))
[df7ed14]	1025	root_node.appendChild(element)
[2f4b430]	1026
[61cada5]	1027	# Sample info
	1028	sample = doc.createElement("SASsample")
	1029	if datainfo.sample.name is not None:
	1030	sample.setAttribute("name", str(datainfo.sample.name))
	1031	entry_node.appendChild(sample)
	1032	write_node(doc, sample, "ID", str(datainfo.sample.ID))
[f32d144]	1033	write_node(doc, sample, "thickness", datainfo.sample.thickness,
	1034	{"unit": datainfo.sample.thickness_unit})
[61cada5]	1035	write_node(doc, sample, "transmission", datainfo.sample.transmission)
[f32d144]	1036	write_node(doc, sample, "temperature", datainfo.sample.temperature,
	1037	{"unit": datainfo.sample.temperature_unit})
[2f4b430]	1038
[61cada5]	1039	for item in datainfo.sample.details:
	1040	write_node(doc, sample, "details", item)
[2f4b430]	1041
[61cada5]	1042	pos = doc.createElement("position")
[f32d144]	1043	written = write_node(doc, pos, "x", datainfo.sample.position.x,
	1044	{"unit": datainfo.sample.position_unit})
	1045	written = written \| write_node(doc, pos, "y",
	1046	datainfo.sample.position.y,
	1047	{"unit": datainfo.sample.position_unit})
	1048	written = written \| write_node(doc, pos, "z",
	1049	datainfo.sample.position.z,
	1050	{"unit": datainfo.sample.position_unit})
[61cada5]	1051	if written == True:
	1052	sample.appendChild(pos)
[2f4b430]	1053
[61cada5]	1054	ori = doc.createElement("orientation")
[f32d144]	1055	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
	1056	{"unit": datainfo.sample.orientation_unit})
	1057	written = written \| write_node(doc, ori, "pitch",
	1058	datainfo.sample.orientation.y,
	1059	{"unit": datainfo.sample.orientation_unit})
	1060	written = written \| write_node(doc, ori, "yaw",
	1061	datainfo.sample.orientation.z,
	1062	{"unit": datainfo.sample.orientation_unit})
[61cada5]	1063	if written == True:
	1064	sample.appendChild(ori)
[2f4b430]	1065
[61cada5]	1066	# Instrument info
	1067	instr = doc.createElement("SASinstrument")
	1068	entry_node.appendChild(instr)
[2f4b430]	1069
[61cada5]	1070	write_node(doc, instr, "name", datainfo.instrument)
[2f4b430]	1071
[61cada5]	1072	# Source
	1073	source = doc.createElement("SASsource")
	1074	if datainfo.source.name is not None:
	1075	source.setAttribute("name", str(datainfo.source.name))
	1076	instr.appendChild(source)
[2f4b430]	1077
[61cada5]	1078	write_node(doc, source, "radiation", datainfo.source.radiation)
	1079	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
	1080	size = doc.createElement("beam_size")
	1081	if datainfo.source.beam_size_name is not None:
	1082	size.setAttribute("name", str(datainfo.source.beam_size_name))
[f32d144]	1083	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
	1084	{"unit": datainfo.source.beam_size_unit})
	1085	written = written \| write_node(doc, size, "y",
	1086	datainfo.source.beam_size.y,
	1087	{"unit": datainfo.source.beam_size_unit})
	1088	written = written \| write_node(doc, size, "z",
	1089	datainfo.source.beam_size.z,
	1090	{"unit": datainfo.source.beam_size_unit})
[61cada5]	1091	if written == True:
	1092	source.appendChild(size)
[2f4b430]	1093
[f32d144]	1094	write_node(doc, source, "wavelength", datainfo.source.wavelength,
	1095	{"unit": datainfo.source.wavelength_unit})
	1096	write_node(doc, source, "wavelength_min",
	1097	datainfo.source.wavelength_min,
	1098	{"unit": datainfo.source.wavelength_min_unit})
	1099	write_node(doc, source, "wavelength_max",
	1100	datainfo.source.wavelength_max,
	1101	{"unit": datainfo.source.wavelength_max_unit})
	1102	write_node(doc, source, "wavelength_spread",
	1103	datainfo.source.wavelength_spread,
	1104	{"unit": datainfo.source.wavelength_spread_unit})
[2f4b430]	1105
[61cada5]	1106	# Collimation
	1107	for item in datainfo.collimation:
	1108	coll = doc.createElement("SAScollimation")
	1109	if item.name is not None:
	1110	coll.setAttribute("name", str(item.name))
	1111	instr.appendChild(coll)
[2f4b430]	1112
[f32d144]	1113	write_node(doc, coll, "length", item.length,
	1114	{"unit": item.length_unit})
[2f4b430]	1115
[61cada5]	1116	for apert in item.aperture:
	1117	ap = doc.createElement("aperture")
	1118	if apert.name is not None:
	1119	ap.setAttribute("name", str(apert.name))
	1120	if apert.type is not None:
	1121	ap.setAttribute("type", str(apert.type))
	1122	coll.appendChild(ap)
[2f4b430]	1123
[f32d144]	1124	write_node(doc, ap, "distance", apert.distance,
	1125	{"unit": apert.distance_unit})
[2f4b430]	1126
[61cada5]	1127	size = doc.createElement("size")
	1128	if apert.size_name is not None:
	1129	size.setAttribute("name", str(apert.size_name))
[f32d144]	1130	written = write_node(doc, size, "x", apert.size.x,
	1131	{"unit": apert.size_unit})
	1132	written = written \| write_node(doc, size, "y", apert.size.y,
	1133	{"unit": apert.size_unit})
	1134	written = written \| write_node(doc, size, "z", apert.size.z,
	1135	{"unit": apert.size_unit})
[61cada5]	1136	if written == True:
	1137	ap.appendChild(size)
	1138
	1139	# Detectors
	1140	for item in datainfo.detector:
	1141	det = doc.createElement("SASdetector")
	1142	written = write_node(doc, det, "name", item.name)
[f32d144]	1143	written = written \| write_node(doc, det, "SDD", item.distance,
	1144	{"unit": item.distance_unit})
	1145	written = written \| write_node(doc, det, "slit_length",
	1146	item.slit_length,
	1147	{"unit": item.slit_length_unit})
[61cada5]	1148	if written == True:
	1149	instr.appendChild(det)
[2f4b430]	1150
[61cada5]	1151	off = doc.createElement("offset")
[f32d144]	1152	written = write_node(doc, off, "x", item.offset.x,
	1153	{"unit": item.offset_unit})
	1154	written = written \| write_node(doc, off, "y", item.offset.y,
	1155	{"unit": item.offset_unit})
	1156	written = written \| write_node(doc, off, "z", item.offset.z,
	1157	{"unit": item.offset_unit})
[61cada5]	1158	if written == True:
	1159	det.appendChild(off)
[2f4b430]	1160
[61cada5]	1161	center = doc.createElement("beam_center")
[f32d144]	1162	written = write_node(doc, center, "x", item.beam_center.x,
	1163	{"unit": item.beam_center_unit})
	1164	written = written \| write_node(doc, center, "y",
	1165	item.beam_center.y,
	1166	{"unit": item.beam_center_unit})
	1167	written = written \| write_node(doc, center, "z",
	1168	item.beam_center.z,
	1169	{"unit": item.beam_center_unit})
[61cada5]	1170	if written == True:
	1171	det.appendChild(center)
[2f4b430]	1172
[61cada5]	1173	pix = doc.createElement("pixel_size")
[f32d144]	1174	written = write_node(doc, pix, "x", item.pixel_size.x,
	1175	{"unit": item.pixel_size_unit})
	1176	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
	1177	{"unit": item.pixel_size_unit})
	1178	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
	1179	{"unit": item.pixel_size_unit})
[61cada5]	1180	if written == True:
	1181	det.appendChild(pix)
[2f4b430]	1182
[61cada5]	1183	ori = doc.createElement("orientation")
[f32d144]	1184	written = write_node(doc, ori, "roll", item.orientation.x,
	1185	{"unit": item.orientation_unit})
	1186	written = written \| write_node(doc, ori, "pitch",
	1187	item.orientation.y,
	1188	{"unit": item.orientation_unit})
	1189	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
	1190	{"unit": item.orientation_unit})
[61cada5]	1191	if written == True:
	1192	det.appendChild(ori)
[2f4b430]	1193
[61cada5]	1194	# Processes info
	1195	for item in datainfo.process:
	1196	node = doc.createElement("SASprocess")
	1197	entry_node.appendChild(node)
	1198
	1199	write_node(doc, node, "name", item.name)
	1200	write_node(doc, node, "date", item.date)
	1201	write_node(doc, node, "description", item.description)
	1202	for term in item.term:
	1203	value = term['value']
	1204	del term['value']
	1205	write_node(doc, node, "term", value, term)
	1206	for note in item.notes:
	1207	write_node(doc, node, "SASprocessnote", note)
	1208	# Return the document, and the SASentry node associated with
	1209	# the data we just wrote
	1210	return doc, entry_node
[2f4b430]	1211
[61cada5]	1212	def _parse_state(self, entry):
	1213	"""
[5062bbf]	1214	Read a fit result from an XML node
[2f4b430]	1215
[f32d144]	1216	:param entry: XML node to read from
[2f4b430]	1217
[5062bbf]	1218	:return: PageState object
[61cada5]	1219	"""
	1220	# Create an empty state
[2f4b430]	1221	state = None
[61cada5]	1222	# Locate the P(r) node
	1223	try:
[f32d144]	1224	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
	1225	namespaces={'ns': CANSAS_NS})
	1226	if nodes != []:
[b35d3d1]	1227	# Create an empty state
[f32d144]	1228	state = PageState()
[b35d3d1]	1229	state.fromXML(node=nodes[0])
[2f4b430]	1230
[61cada5]	1231	except:
	1232	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
[2f4b430]	1233
[61cada5]	1234	return state
[2f4b430]	1235
[ac5b69d]	1236	def _parse_save_state_entry(self, dom):
[e9b12eaf]	1237	"""
[5062bbf]	1238	Parse a SASentry
[2f4b430]	1239
[5062bbf]	1240	:param node: SASentry node
[2f4b430]	1241
[df7ed14]	1242	:return: Data1D/Data2D object
[2f4b430]	1243
[e9b12eaf]	1244	"""
[df7ed14]	1245	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
	1246	if not node or node[0].text.lstrip().rstrip() != "Data2D":
[ac5b69d]	1247	return_value, _ = self._parse_entry(dom)
	1248	numpy.trim_zeros(return_value.x)
	1249	numpy.trim_zeros(return_value.y)
	1250	numpy.trim_zeros(return_value.dy)
	1251	size_dx = return_value.dx.size
	1252	size_dxl = return_value.dxl.size
	1253	size_dxw = return_value.dxw.size
	1254	if size_dxl == 0 and size_dxw == 0:
	1255	return_value.dxl = None
	1256	return_value.dxw = None
	1257	numpy.trim_zeros(return_value.dx)
	1258	elif size_dx == 0:
	1259	return_value.dx = None
	1260	size_dx = size_dxl
	1261	numpy.trim_zeros(return_value.dxl)
	1262	numpy.trim_zeros(return_value.dxw)
[2f4b430]	1263
[ac5b69d]	1264	return return_value, _
[2f4b430]	1265
[df7ed14]	1266	#Parse 2D
[e9b12eaf]	1267	data_info = Data2D()
[2f4b430]	1268
[f32d144]	1269	# Look up title
[e9b12eaf]	1270	self._store_content('ns:Title', dom, 'title', data_info)
[2f4b430]	1271
[f32d144]	1272	# Look up run number
[e9b12eaf]	1273	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
[f32d144]	1274	for item in nodes:
[e9b12eaf]	1275	if item.text is not None:
	1276	value = item.text.strip()
	1277	if len(value) > 0:
	1278	data_info.run.append(value)
	1279	if item.get('name') is not None:
	1280	data_info.run_name[value] = item.get('name')
[2f4b430]	1281
[f32d144]	1282	# Look up instrument name
	1283	self._store_content('ns:SASinstrument/ns:name', dom,
	1284	'instrument', data_info)
[e9b12eaf]	1285
	1286	# Notes
	1287	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
	1288	for note in note_list:
	1289	try:
	1290	if note.text is not None:
	1291	note_value = note.text.strip()
	1292	if len(note_value) > 0:
	1293	data_info.notes.append(note_value)
	1294	except:
	1295	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
	1296	self.errors.append(err_mess)
	1297	logging.error(err_mess)
[2f4b430]	1298
[e9b12eaf]	1299	# Sample info ###################
	1300	entry = get_content('ns:SASsample', dom)
	1301	if entry is not None:
	1302	data_info.sample.name = entry.get('name')
[2f4b430]	1303
[b1e609c]	1304	self._store_content('ns:SASsample/ns:ID', dom, 'ID', data_info.sample)
	1305	self._store_float('ns:SASsample/ns:thickness', dom, 'thickness', data_info.sample)
	1306	self._store_float('ns:SASsample/ns:transmission', dom, 'transmission', data_info.sample)
	1307	self._store_float('ns:SASsample/ns:temperature', dom, 'temperature', data_info.sample)
[2f4b430]	1308
[b1e609c]	1309	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1310	for item in nodes:
	1311	try:
	1312	if item.text is not None:
	1313	detail_value = item.text.strip()
	1314	if len(detail_value) > 0:
	1315	data_info.sample.details.append(detail_value)
	1316	except:
	1317	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
	1318	self.errors.append(err_mess)
	1319	logging.error(err_mess)
[2f4b430]	1320
[e9b12eaf]	1321	# Position (as a vector)
[b1e609c]	1322	self._store_float('ns:SASsample/ns:position/ns:x', dom, 'position.x', data_info.sample)
	1323	self._store_float('ns:SASsample/ns:position/ns:y', dom, 'position.y', data_info.sample)
	1324	self._store_float('ns:SASsample/ns:position/ns:z', dom, 'position.z', data_info.sample)
[2f4b430]	1325
[e9b12eaf]	1326	# Orientation (as a vector)
[f32d144]	1327	self._store_float('ns:SASsample/ns:orientation/ns:roll',
[b1e609c]	1328	dom, 'orientation.x', data_info.sample)
[f32d144]	1329	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
[b1e609c]	1330	dom, 'orientation.y', data_info.sample)
[f32d144]	1331	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
[b1e609c]	1332	dom, 'orientation.z', data_info.sample)
[2f4b430]	1333
[e9b12eaf]	1334	# Source info ###################
	1335	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
	1336	if entry is not None:
	1337	data_info.source.name = entry.get('name')
[2f4b430]	1338
[f32d144]	1339	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
[b1e609c]	1340	dom, 'radiation', data_info.source)
[f32d144]	1341	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
[b1e609c]	1342	dom, 'beam_shape', data_info.source)
[f32d144]	1343	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
[b1e609c]	1344	dom, 'wavelength', data_info.source)
[f32d144]	1345	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
[b1e609c]	1346	dom, 'wavelength_min', data_info.source)
[f32d144]	1347	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
[b1e609c]	1348	dom, 'wavelength_max', data_info.source)
[f32d144]	1349	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
[b1e609c]	1350	dom, 'wavelength_spread', data_info.source)
[2f4b430]	1351
[f32d144]	1352	# Beam size (as a vector)
[e9b12eaf]	1353	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
	1354	if entry is not None:
	1355	data_info.source.beam_size_name = entry.get('name')
[2f4b430]	1356
[f32d144]	1357	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
[b1e609c]	1358	dom, 'beam_size.x', data_info.source)
[f32d144]	1359	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
[b1e609c]	1360	dom, 'beam_size.y', data_info.source)
[f32d144]	1361	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
[b1e609c]	1362	dom, 'beam_size.z', data_info.source)
[2f4b430]	1363
[e9b12eaf]	1364	# Collimation info ###################
[f32d144]	1365	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
	1366	namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1367	for item in nodes:
	1368	collim = Collimation()
	1369	if item.get('name') is not None:
	1370	collim.name = item.get('name')
[f32d144]	1371	self._store_float('ns:length', item, 'length', collim)
[2f4b430]	1372
[e9b12eaf]	1373	# Look for apertures
[f32d144]	1374	apert_list = item.xpath('ns:aperture',
	1375	namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1376	for apert in apert_list:
[f32d144]	1377	aperture = Aperture()
[2f4b430]	1378
[e9b12eaf]	1379	# Get the name and type of the aperture
	1380	aperture.name = apert.get('name')
	1381	aperture.type = apert.get('type')
[2f4b430]	1382
[f32d144]	1383	self._store_float('ns:distance', apert, 'distance', aperture)
[2f4b430]	1384
[e9b12eaf]	1385	entry = get_content('ns:size', apert)
	1386	if entry is not None:
	1387	aperture.size_name = entry.get('name')
[2f4b430]	1388
[f32d144]	1389	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
	1390	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
[e9b12eaf]	1391	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
[2f4b430]	1392
[e9b12eaf]	1393	collim.aperture.append(aperture)
[2f4b430]	1394
[e9b12eaf]	1395	data_info.collimation.append(collim)
[2f4b430]	1396
[e9b12eaf]	1397	# Detector info ######################
[f32d144]	1398	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
	1399	namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1400	for item in nodes:
[2f4b430]	1401
[e9b12eaf]	1402	detector = Detector()
[2f4b430]	1403
[e9b12eaf]	1404	self._store_content('ns:name', item, 'name', detector)
[f32d144]	1405	self._store_float('ns:SDD', item, 'distance', detector)
[2f4b430]	1406
[e9b12eaf]	1407	# Detector offset (as a vector)
[f32d144]	1408	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
	1409	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
	1410	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
[2f4b430]	1411
[e9b12eaf]	1412	# Detector orientation (as a vector)
[f32d144]	1413	self._store_float('ns:orientation/ns:roll', item,
	1414	'orientation.x', detector)
	1415	self._store_float('ns:orientation/ns:pitch', item,
	1416	'orientation.y', detector)
	1417	self._store_float('ns:orientation/ns:yaw', item,
	1418	'orientation.z', detector)
[2f4b430]	1419
[e9b12eaf]	1420	# Beam center (as a vector)
[f32d144]	1421	self._store_float('ns:beam_center/ns:x', item,
	1422	'beam_center.x', detector)
	1423	self._store_float('ns:beam_center/ns:y', item,
	1424	'beam_center.y', detector)
	1425	self._store_float('ns:beam_center/ns:z', item,
	1426	'beam_center.z', detector)
[2f4b430]	1427
[e9b12eaf]	1428	# Pixel size (as a vector)
[f32d144]	1429	self._store_float('ns:pixel_size/ns:x', item,
	1430	'pixel_size.x', detector)
	1431	self._store_float('ns:pixel_size/ns:y', item,
	1432	'pixel_size.y', detector)
	1433	self._store_float('ns:pixel_size/ns:z', item,
	1434	'pixel_size.z', detector)
[2f4b430]	1435
[e9b12eaf]	1436	self._store_float('ns:slit_length', item, 'slit_length', detector)
[2f4b430]	1437
[f32d144]	1438	data_info.detector.append(detector)
[e9b12eaf]	1439
	1440	# Processes info ######################
	1441	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
	1442	for item in nodes:
	1443	process = Process()
	1444	self._store_content('ns:name', item, 'name', process)
	1445	self._store_content('ns:date', item, 'date', process)
	1446	self._store_content('ns:description', item, 'description', process)
[2f4b430]	1447
[e9b12eaf]	1448	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
	1449	for term in term_list:
	1450	try:
	1451	term_attr = {}
	1452	for attr in term.keys():
	1453	term_attr[attr] = term.get(attr).strip()
	1454	if term.text is not None:
	1455	term_attr['value'] = term.text.strip()
	1456	process.term.append(term_attr)
	1457	except:
	1458	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
	1459	self.errors.append(err_mess)
	1460	logging.error(err_mess)
[2f4b430]	1461
[f32d144]	1462	note_list = item.xpath('ns:SASprocessnote',
	1463	namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1464	for note in note_list:
	1465	if note.text is not None:
	1466	process.notes.append(note.text.strip())
[2f4b430]	1467
[e9b12eaf]	1468	data_info.process.append(process)
[2f4b430]	1469
[e9b12eaf]	1470	# Data info ######################
	1471	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
[f32d144]	1472	if len(nodes) > 1:
[e9b12eaf]	1473	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
[2f4b430]	1474
[df7ed14]	1475	for entry in nodes:
[b1e609c]	1476	for item in LIST_OF_DATA_2D_ATTR:
[df7ed14]	1477	#get node
[f32d144]	1478	node = get_content('ns:%s' % item[0], entry)
[b1e609c]	1479	setattr(data_info, item[1], parse_entry_helper(node, item))
[2f4b430]	1480
[b1e609c]	1481	for item in LIST_OF_DATA_2D_VALUES:
[f32d144]	1482	field = get_content('ns:%s' % item[0], entry)
[b1e609c]	1483	value_list = []
[df7ed14]	1484	if field is not None:
[b1e609c]	1485	value_list = [parse_entry_helper(node, item) for node in field]
	1486	if len(value_list) < 2:
	1487	setattr(data_info, item[0], None)
[44f7c1b]	1488	else:
[b1e609c]	1489	setattr(data_info, item[0], numpy.array(value_list))
[2f4b430]	1490
[e9b12eaf]	1491	return data_info
	1492
[61cada5]	1493	def _read_cansas(self, path):
[f32d144]	1494	"""
[5062bbf]	1495	Load data and P(r) information from a CanSAS XML file.
[2f4b430]	1496
[5062bbf]	1497	:param path: file path
[2f4b430]	1498
[f32d144]	1499	:return: Data1D object if a single SASentry was found,
[5062bbf]	1500	or a list of Data1D objects if multiple entries were found,
	1501	or None of nothing was found
[2f4b430]	1502
[5062bbf]	1503	:raise RuntimeError: when the file can't be opened
	1504	:raise ValueError: when the length of the data vectors are inconsistent
[2f4b430]	1505
[61cada5]	1506	"""
	1507	output = []
[f32d144]	1508	basename = os.path.basename(path)
[b63dc6e]	1509	root, extension = os.path.splitext(basename)
	1510	ext = extension.lower()
[61cada5]	1511	try:
	1512	if os.path.isfile(path):
[2f4b430]	1513
[61cada5]	1514	#TODO: eventually remove the check for .xml once
	1515	# the P(r) writer/reader is truly complete.
[b63dc6e]	1516	if ext in self.ext or \
	1517	ext == '.xml':
[2f4b430]	1518
[61cada5]	1519	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
	1520	# Check the format version number
[f32d144]	1521	# Specifying the namespace will take care of the file format version
[61cada5]	1522	root = tree.getroot()
[f32d144]	1523	entry_list = root.xpath('ns:SASentry',
	1524	namespaces={'ns': CANSAS_NS})
	1525	for entry in entry_list:
[e9b12eaf]	1526	try:
[ac5b69d]	1527	sas_entry, _ = self._parse_save_state_entry(entry)
[e9b12eaf]	1528	except:
[df7ed14]	1529	raise
[61cada5]	1530	fitstate = self._parse_state(entry)
[2f4b430]	1531
[b35d3d1]	1532	#state could be None when .svs file is loaded
	1533	#in this case, skip appending to output
	1534	if fitstate != None:
	1535	sas_entry.meta_data['fitstate'] = fitstate
	1536	sas_entry.filename = fitstate.file
	1537	output.append(sas_entry)
[61cada5]	1538	else:
[b63dc6e]	1539	self.call_back(format=ext)
[61cada5]	1540	raise RuntimeError, "%s is not a file" % path
[b35d3d1]	1541
[61cada5]	1542	# Return output consistent with the loader's api
[f32d144]	1543	if len(output) == 0:
	1544	self.call_back(state=None, datainfo=None, format=ext)
[61cada5]	1545	return None
	1546	else:
[b35d3d1]	1547	for ind in range(len(output)):
	1548	# Call back to post the new state
	1549	state = output[ind].meta_data['fitstate']
	1550	t = time.localtime(state.timestamp)
	1551	time_str = time.strftime("%b %d %H:%M", t)
	1552	# Check that no time stamp is already appended
	1553	max_char = state.file.find("[")
	1554	if max_char < 0:
	1555	max_char = len(state.file)
[ef16f59]	1556	original_fname = state.file[0:max_char]
[f32d144]	1557	state.file = original_fname + ' [' + time_str + ']'
[2f4b430]	1558
[b35d3d1]	1559	if state is not None and state.is_data is not None:
[b1e609c]	1560	output[ind].is_data = state.is_data
[2f4b430]	1561
[b35d3d1]	1562	output[ind].filename = state.file
	1563	state.data = output[ind]
[f32d144]	1564	state.data.name = output[ind].filename # state.data_name
[b35d3d1]	1565	state.data.id = state.data_id
	1566	if state.is_data is not None:
	1567	state.data.is_data = state.is_data
[f32d144]	1568	if output[ind].run_name is not None\
	1569	and len(output[ind].run_name) != 0:
[ef16f59]	1570	name = output[ind].run_name
[f32d144]	1571	else:
	1572	name = original_fname
[ef16f59]	1573	state.data.group_id = name
	1574	#store state in fitting
[f32d144]	1575	self.call_back(state=state,
	1576	datainfo=output[ind], format=ext)
	1577	self.state = state
[ef16f59]	1578	return output
[61cada5]	1579	except:
[4bee68d]	1580	self.call_back(format=ext)
[61cada5]	1581	raise
[2f4b430]	1582
[61cada5]	1583	def write(self, filename, datainfo=None, fitstate=None):
	1584	"""
[b35d3d1]	1585	Write the content of a Data1D as a CanSAS XML file only for standalone
[2f4b430]	1586
[5062bbf]	1587	:param filename: name of the file to write
	1588	:param datainfo: Data1D object
	1589	:param fitstate: PageState object
[2f4b430]	1590
[61cada5]	1591	"""
	1592	# Sanity check
	1593	if self.cansas == True:
	1594	# Add fitting information to the XML document
[ef16f59]	1595	doc = self.write_toXML(datainfo, fitstate)
[61cada5]	1596	# Write the XML document
	1597	else:
[ac5b69d]	1598	doc = fitstate.toXML(file=filename)
[2f4b430]	1599
[ac5b69d]	1600	# Save the document no matter the type
	1601	fd = open(filename, 'w')
	1602	fd.write(doc.toprettyxml())
	1603	fd.close()
[2f4b430]	1604
[b35d3d1]	1605	def write_toXML(self, datainfo=None, state=None):
	1606	"""
[f32d144]	1607	Write toXML, a helper for write(),
	1608	could be used by guimanager._on_save()
[2f4b430]	1609
[b35d3d1]	1610	: return: xml doc
	1611	"""
[3c44c66]	1612
[b35d3d1]	1613	if state.data is None:
[79492222]	1614	data = sas.dataloader.data_info.Data1D(x=[], y=[])
[a805118]	1615	return None
[3b148c3]	1616	elif not state.data.is_data:
	1617	return None
[f32d144]	1618	else:
[b35d3d1]	1619	#make sure title and data run is filled up.
[f32d144]	1620	if state.data.title == None or state.data.title == '':
	1621	state.data.title = state.data.name
	1622	if state.data.run_name == None or state.data.run_name == {}:
[028a0e8]	1623	state.data.run = [str(state.data.name)]
	1624	state.data.run_name[0] = state.data.name
[2f4b430]	1625
[f32d144]	1626	if issubclass(state.data.__class__,
[79492222]	1627	sas.dataloader.data_info.Data1D):
[b35d3d1]	1628	data = state.data
	1629	doc, sasentry = self._to_xml_doc(data)
	1630	else:
	1631	data = state.data
	1632	doc, sasentry = self._data2d_to_xml_doc(data)
[2f4b430]	1633
[b35d3d1]	1634	if state is not None:
[ac5b69d]	1635	doc = state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
[2f4b430]	1636
[f32d144]	1637	return doc
[2f4b430]	1638
[f32d144]	1639	# Simple html report templet
[2296316]	1640	HEADER = "<html>\n"
	1641	HEADER += "<head>\n"
	1642	HEADER += "<meta http-equiv=Content-Type content='text/html; "
	1643	HEADER += "charset=windows-1252'> \n"
	1644	HEADER += "<meta name=Generator >\n"
	1645	HEADER += "</head>\n"
	1646	HEADER += "<body lang=EN-US>\n"
	1647	HEADER += "<div class=WordSection1>\n"
[14d2daa]	1648	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
	1649	HEADER += "%s</font></center></span></center></b></p>"
[2296316]	1650	HEADER += "<p class=MsoNormal> </p>"
[14d2daa]	1651	PARA = "<p class=MsoNormal><font size='4' > %s \n"
	1652	PARA += "</font></p>"
	1653	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
	1654	CENTRE += "</font></center></p>"
[2296316]	1655	FEET_1 = \
	1656	"""
[3a3dd9c]	1657	<p class=MsoNormal> </p>
[14d2daa]	1658	<br>
	1659	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
[f32d144]	1660	</font></span></center></b></p>
	1661	<p class=MsoNormal> </p>
	1662	<center>
[14d2daa]	1663	<br><font size='4' >Model Computation</font>
[f32d144]	1664	<br><font size='4' >Data: "%s"</font><br>
[2296316]	1665	"""
	1666	FEET_2 = \
	1667	"""
[f32d144]	1668	<img src="%s" >
[2296316]	1669	</img>
	1670	"""
	1671	FEET_3 = \
	1672	"""
[f32d144]	1673	</center>
[2296316]	1674	</div>
	1675	</body>
	1676	</html>
	1677	"""
	1678	ELINE = "<p class=MsoNormal> </p>"
	1679
[3c44c66]	1680	if __name__ == "__main__":
	1681	state = PageState(parent=None)
	1682	#state.toXML()
	1683	"""
[2f4b430]	1684
[3c44c66]	1685	file = open("test_state", "w")
	1686	pickle.dump(state, file)
	1687	print pickle.dumps(state)
	1688	state.data_name = "hello---->"
	1689	pickle.dump(state, file)
	1690	file = open("test_state", "r")
	1691	new_state= pickle.load(file)
	1692	print "new state", new_state
	1693	new_state= pickle.load(file)
	1694	print "new state", new_state
	1695	#print "state", state
	1696	"""
	1697	import bsddb
	1698	import pickle
[f32d144]	1699	db = bsddb.btopen('file_state.db', 'c')
[3c44c66]	1700	val = (pickle.dumps(state), "hello", "hi")
[f32d144]	1701	db['state1'] = pickle.dumps(val)
[3c44c66]	1702	print pickle.loads(db['state1'])
	1703	state.data_name = "hello---->22"
[f32d144]	1704	db['state2'] = pickle.dumps(state)
[3c44c66]	1705	state.data_name = "hello---->2"
[f32d144]	1706	db['state3'] = pickle.dumps(state)
[3c44c66]	1707	del db['state3']
	1708	state.data_name = "hello---->3"
[f32d144]	1709	db['state4'] = pickle.dumps(state)
[3c44c66]	1710	new_state = pickle.loads(db['state1'])
	1711	#print db.last()
	1712	db.set_location('state2')
	1713	state.data_name = "hello---->5"
[f32d144]	1714	db['aastate5'] = pickle.dumps(state)
[3c44c66]	1715	db.keys().sort()
	1716	print pickle.loads(db['state2'])
[2f4b430]	1717
[f32d144]	1718	db.close()

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SasView

source: sasview/src/sas/perspectives/fitting/pagestate.py @ f21d496

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