pagestate.py @ ce94504

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since ce94504 was 654e8e0, checked in by krzywon, 8 years ago
Resolves #644 and #642: Improved loading performance for cansas XML data. Loading invariants and fits from save states no longer throw errors or open multiple windows.
Property mode set to `100644`
File size: 70.3 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
[abcbe09]	17	import wx
[6f023e8]	18	import copy
[11a7e11]	19	import logging
[df7ed14]	20	import numpy
[7673ecd]	21	import traceback
[c77d859]	22
[35b556d]	23	import xml.dom.minidom
[ac5b69d]	24	from xml.dom.minidom import parseString
[11a7e11]	25	from lxml import etree
	26
[b699768]	27	import sas.sascalc.dataloader
	28	from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader
	29	from sas.sascalc.dataloader.readers.cansas_reader import get_content, write_node
	30	from sas.sascalc.dataloader.data_info import Data2D
	31	from sas.sascalc.dataloader.data_info import Collimation
	32	from sas.sascalc.dataloader.data_info import Detector
	33	from sas.sascalc.dataloader.data_info import Process
	34	from sas.sascalc.dataloader.data_info import Aperture
[11a7e11]	35	#Information to read/write state as xml
[61cada5]	36	FITTING_NODE_NAME = 'fitting_plug_in'
	37	CANSAS_NS = "cansas1d/1.0"
	38
[b1e609c]	39	LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"],
	40	["group_id", "data_group_id", "string"],
	41	["data_name", "data_name", "string"],
	42	["data_id", "data_id", "string"],
	43	["name", "name", "string"],
	44	["data_name", "data_name", "string"]]
[acf8e4a5]	45	LIST_OF_STATE_ATTRIBUTES = [["qmin", "qmin", "float"],
[b1e609c]	46	["qmax", "qmax", "float"],
	47	["npts", "npts", "float"],
	48	["categorycombobox", "categorycombobox", "string"],
	49	["formfactorcombobox", "formfactorcombobox", "string"],
	50	["structurecombobox", "structurecombobox", "string"],
	51	["multi_factor", "multi_factor", "float"],
	52	["magnetic_on", "magnetic_on", "bool"],
	53	["enable_smearer", "enable_smearer", "bool"],
	54	["disable_smearer", "disable_smearer", "bool"],
	55	["pinhole_smearer", "pinhole_smearer", "bool"],
	56	["slit_smearer", "slit_smearer", "bool"],
	57	["enable_disp", "enable_disp", "bool"],
	58	["disable_disp", "disable_disp", "bool"],
	59	["dI_noweight", "dI_noweight", "bool"],
	60	["dI_didata", "dI_didata", "bool"],
	61	["dI_sqrdata", "dI_sqrdata", "bool"],
	62	["dI_idata", "dI_idata", "bool"],
	63	["enable2D", "enable2D", "bool"],
	64	["cb1", "cb1", "bool"],
	65	["tcChi", "tcChi", "float"],
	66	["smearer", "smearer", "float"],
	67	["smear_type", "smear_type", "string"],
	68	["dq_l", "dq_l", "string"],
	69	["dq_r", "dq_r", "string"],
	70	["dx_max", "dx_max", "float"],
	71	["dx_min", "dx_min", "float"],
	72	["dxl", "dxl", "float"],
	73	["dxw", "dxw", "float"]]
	74
	75	LIST_OF_MODEL_ATTRIBUTES = [["values", "values"],
[11a7e11]	76	["weights", "weights"]]
	77
[b1e609c]	78	DISPERSION_LIST = [["disp_obj_dict", "_disp_obj_dict", "string"]]
[2296316]	79
[b1e609c]	80	LIST_OF_STATE_PARAMETERS = [["parameters", "parameters"],
[f32d144]	81	["str_parameters", "str_parameters"],
[61cada5]	82	["orientation_parameters", "orientation_params"],
	83	["dispersity_parameters", "orientation_params_disp"],
[f32d144]	84	["fixed_param", "fixed_param"],
	85	["fittable_param", "fittable_param"]]
[b1e609c]	86	LIST_OF_DATA_2D_ATTR = [["xmin", "xmin", "float"],
[f32d144]	87	["xmax", "xmax", "float"],
	88	["ymin", "ymin", "float"],
	89	["ymax", "ymax", "float"],
	90	["_xaxis", "_xaxis", "string"],
[df7ed14]	91	["_xunit", "_xunit", "string"],
[f32d144]	92	["_yaxis", "_yaxis", "string"],
	93	["_yunit", "_yunit", "string"],
	94	["_zaxis", "_zaxis", "string"],
	95	["_zunit", "_zunit", "string"]]
[b1e609c]	96	LIST_OF_DATA_2D_VALUES = [["qx_data", "qx_data", "float"],
	97	["qy_data", "qy_data", "float"],
	98	["dqx_data", "dqx_data", "float"],
	99	["dqy_data", "dqy_data", "float"],
	100	["data", "data", "float"],
	101	["q_data", "q_data", "float"],
	102	["err_data", "err_data", "float"],
	103	["mask", "mask", "bool"]]
[61cada5]	104
[f32d144]	105
	106	def parse_entry_helper(node, item):
[0b12abb5]	107	"""
	108	Create a numpy list from value extrated from the node
[2f4b430]	109
[0b12abb5]	110	:param node: node from each the value is stored
	111	:param item: list name of three strings.the two first are name of data
[f32d144]	112	attribute and the third one is the type of the value of that
[0b12abb5]	113	attribute. type can be string, float, bool, etc.
[2f4b430]	114
[0b12abb5]	115	: return: numpy array
	116	"""
	117	if node is not None:
	118	if item[2] == "string":
	119	return str(node.get(item[0]).strip())
	120	elif item[2] == "bool":
	121	try:
[e3d1423]	122	return node.get(item[0]).strip() == "True"
[2f4b430]	123
[0b12abb5]	124	except:
	125	return None
	126	else:
	127	try:
	128	return float(node.get(item[0]))
	129	except:
	130	return None
[2f4b430]	131
	132
[cfc0913]	133	class PageState(object):
[c77d859]	134	"""
[5062bbf]	135	Contains information to reconstruct a page of the fitpanel.
[c77d859]	136	"""
[61cada5]	137	def __init__(self, parent=None, model=None, data=None):
[f32d144]	138	"""
[5062bbf]	139	Initialize the current state
[2f4b430]	140
[5062bbf]	141	:param model: a selected model within a page
[f32d144]	142	:param data:
[2f4b430]	143
[c77d859]	144	"""
[61cada5]	145	self.file = None
[11a7e11]	146	#Time of state creation
	147	self.timestamp = time.time()
[c77d859]	148	## Data member to store the dispersion object created
	149	self._disp_obj_dict = {}
[61cada5]	150	#------------------------
[f32d144]	151	#Data used for fitting
[c77d859]	152	self.data = data
[2296316]	153	# model data
	154	self.theory_data = None
	155	#Is 2D
	156	self.is_2D = False
	157	self.images = None
[2f4b430]	158
[61cada5]	159	#save additional information on data that dataloader.reader does not read
	160	self.is_data = None
	161	self.data_name = ""
[c0ff8cc]	162
[61cada5]	163	if self.data is not None:
	164	self.data_name = self.data.name
	165	self.data_id = None
	166	if self.data is not None and hasattr(self.data, "id"):
	167	self.data_id = self.data.id
	168	self.data_group_id = None
	169	if self.data is not None and hasattr(self.data, "group_id"):
	170	self.data_group_id = self.data.group_id
[2f4b430]	171
[61cada5]	172	## reset True change the state of exsiting button
	173	self.reset = False
[2f4b430]	174
[c77d859]	175	# flag to allow data2D plot
[cfc0913]	176	self.enable2D = False
[c77d859]	177	# model on which the fit would be performed
	178	self.model = model
[93f0a862]	179	self.m_name = None
[dce84c0]	180	#list of process done to model
	181	self.process = []
[f32d144]	182	#fit page manager
[c77d859]	183	self.manager = None
	184	#Store the parent of this panel parent
	185	# For this application fitpanel is the parent
[f32d144]	186	self.parent = parent
[c77d859]	187	# Event_owner is the owner of model event
	188	self.event_owner = None
[c9a4377]	189	##page name
[cfc0913]	190	self.page_name = ""
[eddb6ec]	191	# Contains link between model, all its parameters, and panel organization
[61cada5]	192	self.parameters = []
[fb59ed9]	193	# String parameter list that can not be fitted
	194	self.str_parameters = []
[f32d144]	195	# Contains list of parameters that cannot be fitted and reference to
	196	#panel objects
[61cada5]	197	self.fixed_param = []
[f32d144]	198	# Contains list of parameters with dispersity and reference to
	199	#panel objects
[61cada5]	200	self.fittable_param = []
[60132ef]	201	## orientation parameters
[61cada5]	202	self.orientation_params = []
[eddb6ec]	203	## orientation parameters for gaussian dispersity
[61cada5]	204	self.orientation_params_disp = []
[3370922]	205	## smearer info
[61cada5]	206	self.smearer = None
[7609f1a]	207	self.smear_type = None
	208	self.dq_l = None
	209	self.dq_r = None
[db8fd5b]	210	self.dx_max = None
	211	self.dx_min = None
	212	self.dxl = None
	213	self.dxw = None
[eddb6ec]	214	#list of dispersion parameters
[f32d144]	215	self.disp_list = []
[61cada5]	216	if self.model is not None:
[71f0373]	217	self.disp_list = self.model.getDispParamList()
[2296316]	218
[61cada5]	219	self.disp_cb_dict = {}
[2296316]	220	self.values = {}
	221	self.weights = {}
[2f4b430]	222
[f32d144]	223	#contains link between a model and selected parameters to fit
[61cada5]	224	self.param_toFit = []
[a074145]	225	##dictionary of model type and model class
[cfc0913]	226	self.model_list_box = None
[a074145]	227	## save the state of the context menu
[61cada5]	228	self.saved_states = {}
[240b9966]	229	## save selection of combobox
[3b9e023]	230	self.formfactorcombobox = None
[ea5fa58]	231	self.categorycombobox = None
[f32d144]	232	self.structurecombobox = None
[c0ff8cc]	233
[240b9966]	234	## radio box to select type of model
[ea5fa58]	235	#self.shape_rbutton = False
	236	#self.shape_indep_rbutton = False
	237	#self.struct_rbutton = False
	238	#self.plugin_rbutton = False
[b787e68c]	239	## the indice of the current selection
	240	self.disp_box = 0
[c77d859]	241	## Qrange
[cfc0913]	242	## Q range
[61cada5]	243	self.qmin = 0.001
	244	self.qmax = 0.1
[0b12abb5]	245	#reset data range
	246	self.qmax_x = None
	247	self.qmin_x = None
[2f4b430]	248
[cfc0913]	249	self.npts = None
[61cada5]	250	self.name = ""
[4523b68]	251	self.multi_factor = None
[318b5bbb]	252	self.magnetic_on = False
[cfc0913]	253	## enable smearering state
	254	self.enable_smearer = False
[fc6ea43]	255	self.disable_smearer = True
[7609f1a]	256	self.pinhole_smearer = False
[f32d144]	257	self.slit_smearer = False
[55bb249c]	258	# weighting options
	259	self.dI_noweight = False
	260	self.dI_didata = True
	261	self.dI_sqrdata = False
[f32d144]	262	self.dI_idata = False
[cfc0913]	263	## disperity selection
[61cada5]	264	self.enable_disp = False
	265	self.disable_disp = True
[2f4b430]	266
[cfc0913]	267	## state of selected all check button
	268	self.cb1 = False
[0aeabc6]	269	## store value of chisqr
[61cada5]	270	self.tcChi = None
[2f4b430]	271
[6f023e8]	272	def clone(self):
[61cada5]	273	"""
[5062bbf]	274	Create a new copy of the current object
[61cada5]	275	"""
	276	model = None
	277	if self.model is not None:
[6f023e8]	278	model = self.model.clone()
[bb70474]	279	model.name = self.model.name
[61cada5]	280	obj = PageState(self.parent, model=model)
	281	obj.file = copy.deepcopy(self.file)
[6f023e8]	282	obj.data = copy.deepcopy(self.data)
[61cada5]	283	if self.data is not None:
	284	self.data_name = self.data.name
	285	obj.data_name = self.data_name
	286	obj.is_data = self.is_data
[dcf29d7]	287	obj.model_list_box = copy.deepcopy(self.model_list_box)
[2f4b430]	288
[ea5fa58]	289	obj.categorycombobox = self.categorycombobox
[61cada5]	290	obj.formfactorcombobox = self.formfactorcombobox
[f32d144]	291	obj.structurecombobox = self.structurecombobox
[2f4b430]	292
[ea5fa58]	293	#obj.shape_rbutton = self.shape_rbutton
	294	#obj.shape_indep_rbutton = self.shape_indep_rbutton
	295	#obj.struct_rbutton = self.struct_rbutton
	296	#obj.plugin_rbutton = self.plugin_rbutton
[2f4b430]	297
[dcf29d7]	298	obj.manager = self.manager
	299	obj.event_owner = self.event_owner
[71f0373]	300	obj.disp_list = copy.deepcopy(self.disp_list)
[2f4b430]	301
[c477b31]	302	obj.enable2D = copy.deepcopy(self.enable2D)
[cfc0913]	303	obj.parameters = copy.deepcopy(self.parameters)
[fb59ed9]	304	obj.str_parameters = copy.deepcopy(self.str_parameters)
[cfc0913]	305	obj.fixed_param = copy.deepcopy(self.fixed_param)
	306	obj.fittable_param = copy.deepcopy(self.fittable_param)
[f32d144]	307	obj.orientation_params = copy.deepcopy(self.orientation_params)
	308	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
[b787e68c]	309	obj.enable_disp = copy.deepcopy(self.enable_disp)
[fc6ea43]	310	obj.disable_disp = copy.deepcopy(self.disable_disp)
[0aeabc6]	311	obj.tcChi = self.tcChi
[2f4b430]	312
[f32d144]	313	if len(self._disp_obj_dict) > 0:
	314	for k, v in self._disp_obj_dict.iteritems():
	315	obj._disp_obj_dict[k] = v
	316	if len(self.disp_cb_dict) > 0:
	317	for k, v in self.disp_cb_dict.iteritems():
	318	obj.disp_cb_dict[k] = v
	319	if len(self.values) > 0:
	320	for k, v in self.values.iteritems():
[2296316]	321	obj.values[k] = v
[f32d144]	322	if len(self.weights) > 0:
	323	for k, v in self.weights.iteritems():
[2296316]	324	obj.weights[k] = v
[b787e68c]	325	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
[fc6ea43]	326	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
[7609f1a]	327	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
	328	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
	329	obj.smear_type = copy.deepcopy(self.smear_type)
[55bb249c]	330	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
	331	obj.dI_didata = copy.deepcopy(self.dI_didata)
	332	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
	333	obj.dI_idata = copy.deepcopy(self.dI_idata)
[7609f1a]	334	obj.dq_l = copy.deepcopy(self.dq_l)
	335	obj.dq_r = copy.deepcopy(self.dq_r)
[db8fd5b]	336	obj.dx_max = copy.deepcopy(self.dx_max)
	337	obj.dx_min = copy.deepcopy(self.dx_min)
	338	obj.dxl = copy.deepcopy(self.dxl)
[2f4b430]	339	obj.dxw = copy.deepcopy(self.dxw)
[b787e68c]	340	obj.disp_box = copy.deepcopy(self.disp_box)
	341	obj.qmin = copy.deepcopy(self.qmin)
	342	obj.qmax = copy.deepcopy(self.qmax)
[c0ff8cc]	343	obj.multi_factor = self.multi_factor
[318b5bbb]	344	obj.magnetic_on = self.magnetic_on
[f32d144]	345	obj.npts = copy.deepcopy(self.npts)
[b787e68c]	346	obj.cb1 = copy.deepcopy(self.cb1)
[3370922]	347	obj.smearer = copy.deepcopy(self.smearer)
[2f4b430]	348
[a074145]	349	for name, state in self.saved_states.iteritems():
	350	copy_name = copy.deepcopy(name)
	351	copy_state = state.clone()
[f32d144]	352	obj.saved_states[copy_name] = copy_state
[6f023e8]	353	return obj
[2f4b430]	354
[61cada5]	355	def _repr_helper(self, list, rep):
	356	"""
[5062bbf]	357	Helper method to print a state
[61cada5]	358	"""
	359	for item in list:
[f32d144]	360	rep += "parameter name: %s \n" % str(item[1])
	361	rep += "value: %s\n" % str(item[2])
	362	rep += "selected: %s\n" % str(item[0])
	363	rep += "error displayed : %s \n" % str(item[4][0])
	364	rep += "error value:%s \n" % str(item[4][1])
	365	rep += "minimum displayed : %s \n" % str(item[5][0])
	366	rep += "minimum value : %s \n" % str(item[5][1])
	367	rep += "maximum displayed : %s \n" % str(item[6][0])
	368	rep += "maximum value : %s \n" % str(item[6][1])
	369	rep += "parameter unit: %s\n\n" % str(item[7])
[240b9966]	370	return rep
[2f4b430]	371
[61cada5]	372	def __repr__(self):
[f32d144]	373	"""
[5062bbf]	374	output string for printing
[11a7e11]	375	"""
[f32d144]	376	rep = "\nState name: %s\n" % self.file
[11a7e11]	377	t = time.localtime(self.timestamp)
[deff488]	378	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
[c0ff8cc]	379
[f32d144]	380	rep += "State created: %s\n" % time_str
	381	rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
	382	rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
	383	rep += "is data : %s\n" % self.is_data
	384	rep += "data's name : %s\n" % self.data_name
	385	rep += "data's id : %s\n" % self.data_id
[74dc0a4]	386	if self.model != None:
[93f0a862]	387	m_name = self.model.__class__.__name__
	388	if m_name == 'Model':
	389	m_name = self.m_name
[f32d144]	390	rep += "model name : %s\n" % m_name
[74dc0a4]	391	else:
	392	rep += "model name : None\n"
[f32d144]	393	rep += "multi_factor : %s\n" % str(self.multi_factor)
[2f4b430]	394	rep += "magnetic_on : %s\n" % str(self.magnetic_on)
[ea5fa58]	395	rep += "model type (Category) selected: %s\n" % self.categorycombobox
[f32d144]	396	rep += "data : %s\n" % str(self.data)
	397	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
[b1e609c]	398	str(self.qmax), str(self.npts))
[f32d144]	399	rep += "Dispersion selection : %s\n" % str(self.disp_box)
	400	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
	401	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
	402	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
	403	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
	404	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
	405	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
	406	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
[2f4b430]	407
[f32d144]	408	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
	409	rep += "dI_didata : %s\n" % str(self.dI_didata)
	410	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
	411	rep += "dI_idata : %s\n" % str(self.dI_idata)
[2f4b430]	412
[f32d144]	413	rep += "2D enable : %s\n" % str(self.enable2D)
	414	rep += "All parameters checkbox selected: %s\n" % (self.cb1)
	415	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
	416	rep += "Smear object : %s\n" % str(self.smearer)
	417	rep += "Smear type : %s\n" % (self.smear_type)
	418	rep += "dq_l : %s\n" % self.dq_l
	419	rep += "dq_r : %s\n" % self.dq_r
[db8fd5b]	420	rep += "dx_max : %s\n" % str(self.dx_max)
[2f4b430]	421	rep += "dx_min : %s\n" % str(self.dx_min)
[db8fd5b]	422	rep += "dxl : %s\n" % str(self.dxl)
[2f4b430]	423	rep += "dxw : %s\n" % str(self.dxw)
[f32d144]	424	rep += "model : %s\n\n" % str(self.model)
[2296316]	425	temp_parameters = []
	426	temp_fittable_param = []
	427	if self.data.__class__.__name__ == "Data2D":
	428	self.is_2D = True
	429	else:
	430	self.is_2D = False
	431	if self.data is not None:
	432	if not self.is_2D:
	433	for item in self.parameters:
	434	if not item in self.orientation_params:
	435	temp_parameters.append(item)
	436	for item in self.fittable_param:
	437	if not item in self.orientation_params_disp:
	438	temp_fittable_param.append(item)
	439	else:
	440	temp_parameters = self.parameters
	441	temp_fittable_param = self.fittable_param
[2f4b430]	442
[f32d144]	443	rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
	444	rep = self._repr_helper(list=temp_parameters, rep=rep)
	445	rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
	446	rep = self._repr_helper(list=self.str_parameters, rep=rep)
	447	rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
	448	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
[61cada5]	449	return rep
[2296316]	450
	451	def set_report_string(self):
	452	"""
[f32d144]	453	Get the values (strings) from __str__ for report
[2296316]	454	"""
[d06ae30]	455	# Dictionary of the report strings
[2296316]	456	repo_time = ""
	457	model_name = ""
	458	title = ""
	459	title_name = ""
	460	file_name = ""
	461	param_string = ""
	462	paramval_string = ""
	463	chi2_string = ""
	464	q_range = ""
	465	strings = self.__repr__()
	466	lines = strings.split('\n')
	467
	468	# get all string values from __str__()
	469	for line in lines:
	470	value = ""
	471	content = line.split(":")
	472	name = content[0]
	473	try:
	474	value = content[1]
[7673ecd]	475	except Exception:
	476	logging.error(traceback.format_exc())
[b7c6a4a]	477	if name.count("State created"):
	478	repo_time = "" + value
[2296316]	479	if name.count("parameter name"):
	480	val_name = value.split(".")
	481	if len(val_name) > 1:
	482	if val_name[1].count("width"):
	483	param_string += value + ','
	484	else:
	485	continue
	486	else:
	487	param_string += value + ','
	488	if name == "value":
	489	param_string += value + ','
[b1e609c]	490	if name == "selected":
	491	if value == u' False':
	492	fixed_parameter = True
	493	else:
	494	fixed_parameter = False
[2296316]	495	if name == "error value":
[b1e609c]	496	if fixed_parameter:
	497	param_string += '(fixed),'
	498	else:
[d06ae30]	499	param_string += value + ','
[2296316]	500	if name == "parameter unit":
[f32d144]	501	param_string += value + ':'
[2296316]	502	if name == "Value of Chisqr ":
	503	chi2 = ("Chi2/Npts = " + value)
	504	chi2_string = CENTRE % chi2
	505	if name == "Title":
	506	if len(value.strip()) == 0:
	507	continue
	508	title = value + " [" + repo_time + "]"
	509	title_name = HEADER % title
	510	if name == "data ":
	511	try:
[b1e609c]	512	file_value = ("File name:" + content[2])
	513	file_name = CENTRE % file_value
[2296316]	514	if len(title) == 0:
	515	title = content[2] + " [" + repo_time + "]"
	516	title_name = HEADER % title
[7673ecd]	517	except Exception:
	518	logging.error(traceback.format_exc())
[74dc0a4]	519	if name == "model name ":
	520	try:
	521	modelname = "Model name:" + content[1]
	522	except:
	523	modelname = "Model name:" + " NAN"
[f32d144]	524	model_name = CENTRE % modelname
[2f4b430]	525
[2296316]	526	if name == "Plotting Range":
	527	try:
	528	q_range = content[1] + " = " + content[2] \
	529	+ " = " + content[3].split(",")[0]
	530	q_name = ("Q Range: " + q_range)
	531	q_range = CENTRE % q_name
[7673ecd]	532	except Exception:
	533	logging.error(traceback.format_exc())
[2296316]	534	paramval = ""
[f32d144]	535	for lines in param_string.split(":"):
[2296316]	536	line = lines.split(",")
[f32d144]	537	if len(lines) > 0:
	538	param = line[0]
[2296316]	539	param += " = " + line[1]
	540	if len(line[2].split()) > 0 and not line[2].count("None"):
	541	param += " +- " + line[2]
	542	if len(line[3].split()) > 0 and not line[3].count("None"):
	543	param += " " + line[3]
	544	if not paramval.count(param):
[f32d144]	545	paramval += param + "\n"
[2296316]	546	paramval_string += CENTRE % param + "\n"
[2f4b430]	547
[a15e754]	548	text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % (title, file, q_name, chi2, paramval)
[2f4b430]	549
[f5bdb4a]	550	title_name = self._check_html_format(title_name)
	551	file_name = self._check_html_format(file_name)
	552	title = self._check_html_format(title)
[2f4b430]	553
[2296316]	554	html_string = title_name + "\n" + file_name + \
[f32d144]	555	"\n" + model_name + \
[2296316]	556	"\n" + q_range + \
	557	"\n" + chi2_string + \
	558	"\n" + ELINE + \
	559	"\n" + paramval_string + \
	560	"\n" + ELINE + \
	561	"\n" + FEET_1 % title + \
[f32d144]	562	"\n" + FEET_2
[2f4b430]	563
[2296316]	564	return html_string, text_string, title
[2f4b430]	565
[f5bdb4a]	566	def _check_html_format(self, name):
	567	"""
	568	Check string '%' for html format
	569	"""
	570	if name.count('%'):
	571	name = name.replace('%', '&#37')
[2f4b430]	572
[f5bdb4a]	573	return name
[2f4b430]	574
[2296316]	575	def report(self, figs=None, canvases=None):
	576	"""
	577	Invoke report dialog panel
[2f4b430]	578
[2296316]	579	: param figs: list of pylab figures [list]
	580	"""
[d85c194]	581	from sas.sasgui.perspectives.fitting.report_dialog import ReportDialog
[2296316]	582	# get the strings for report
	583	html_str, text_str, title = self.set_report_string()
	584	# Allow 2 figures to append
	585	if len(figs) == 1:
[f32d144]	586	add_str = FEET_3
[2296316]	587	elif len(figs) == 2:
[f32d144]	588	add_str = ELINE
	589	add_str += FEET_2 % ("%s")
	590	add_str += ELINE
	591	add_str += FEET_3
[2296316]	592	elif len(figs) > 2:
[f32d144]	593	add_str = ELINE
	594	add_str += FEET_2 % ("%s")
	595	add_str += ELINE
	596	add_str += FEET_2 % ("%s")
	597	add_str += ELINE
	598	add_str += FEET_3
[2296316]	599	else:
	600	add_str = ""
[c0ff8cc]	601
[2296316]	602	# final report html strings
	603	report_str = html_str % ("%s") + add_str
	604
	605	# make plot image
	606	images = self.set_plot_state(figs, canvases)
[f32d144]	607	report_list = [report_str, text_str, images]
[6f16e25]	608	dialog = ReportDialog(report_list, None, wx.ID_ANY, "")
[d838715]	609	dialog.Show()
[2f4b430]	610
[eddb6ec]	611	def _toXML_helper(self, thelist, element, newdoc):
[61cada5]	612	"""
[5062bbf]	613	Helper method to create xml file for saving state
[61cada5]	614	"""
[eddb6ec]	615	for item in thelist:
[61cada5]	616	sub_element = newdoc.createElement('parameter')
	617	sub_element.setAttribute('name', str(item[1]))
	618	sub_element.setAttribute('value', str(item[2]))
	619	sub_element.setAttribute('selected_to_fit', str(item[0]))
	620	sub_element.setAttribute('error_displayed', str(item[4][0]))
	621	sub_element.setAttribute('error_value', str(item[4][1]))
	622	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
	623	sub_element.setAttribute('minimum_value', str(item[5][1]))
	624	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
	625	sub_element.setAttribute('maximum_value', str(item[6][1]))
	626	sub_element.setAttribute('unit', str(item[7]))
	627	element.appendChild(sub_element)
[2f4b430]	628
[61cada5]	629	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
	630	"""
[5062bbf]	631	Writes the state of the InversionControl panel to file, as XML.
[2f4b430]	632
[5062bbf]	633	Compatible with standalone writing, or appending to an
	634	already existing XML document. In that case, the XML document
	635	is required. An optional entry node in the XML document may also be given.
[2f4b430]	636
[5062bbf]	637	:param file: file to write to
	638	:param doc: XML document object [optional]
	639	:param entry_node: XML node within the XML document at which we will append the data [optional]
[2f4b430]	640
[61cada5]	641	"""
	642	from xml.dom.minidom import getDOMImplementation
[71f0373]	643
[61cada5]	644	# Check whether we have to write a standalone XML file
	645	if doc is None:
	646	impl = getDOMImplementation()
[f32d144]	647	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
[61cada5]	648	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
	649	top_element = newdoc.documentElement
	650	else:
	651	# We are appending to an existing document
	652	newdoc = doc
[ac5b69d]	653	try:
	654	top_element = newdoc.createElement(FITTING_NODE_NAME)
	655	except:
	656	string = etree.tostring(doc, pretty_print=True)
	657	newdoc = parseString(string)
	658	top_element = newdoc.createElement(FITTING_NODE_NAME)
[61cada5]	659	if entry_node is None:
	660	newdoc.documentElement.appendChild(top_element)
	661	else:
[ac5b69d]	662	try:
	663	entry_node.appendChild(top_element)
	664	except:
	665	node_name = entry_node.tag
	666	node_list = newdoc.getElementsByTagName(node_name)
	667	entry_node = node_list.item(0)
	668	entry_node.appendChild(top_element)
[2f4b430]	669
[61cada5]	670	attr = newdoc.createAttribute("version")
	671	attr.nodeValue = '1.0'
	672	top_element.setAttributeNode(attr)
[2f4b430]	673
[61cada5]	674	# File name
	675	element = newdoc.createElement("filename")
	676	if self.file is not None:
	677	element.appendChild(newdoc.createTextNode(str(self.file)))
	678	else:
	679	element.appendChild(newdoc.createTextNode(str(file)))
	680	top_element.appendChild(element)
[2f4b430]	681
[11a7e11]	682	element = newdoc.createElement("timestamp")
	683	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
	684	attr = newdoc.createAttribute("epoch")
	685	attr.nodeValue = str(self.timestamp)
	686	element.setAttributeNode(attr)
	687	top_element.appendChild(element)
[61cada5]	688	# Inputs
	689	inputs = newdoc.createElement("Attributes")
	690	top_element.appendChild(inputs)
[2f4b430]	691
[61cada5]	692	if self.data is not None and hasattr(self.data, "group_id"):
	693	self.data_group_id = self.data.group_id
	694	if self.data is not None and hasattr(self.data, "is_data"):
	695	self.is_data = self.data.is_data
	696	if self.data is not None:
	697	self.data_name = self.data.name
	698	if self.data is not None and hasattr(self.data, "id"):
	699	self.data_id = self.data.id
[2f4b430]	700
[b1e609c]	701	for item in LIST_OF_DATA_ATTRIBUTES:
[0b12abb5]	702	element = newdoc.createElement(item[0])
[b1e609c]	703	element.setAttribute(item[0], str(getattr(self, item[1])))
[f32d144]	704	inputs.appendChild(element)
[2f4b430]	705
[b1e609c]	706	for item in LIST_OF_STATE_ATTRIBUTES:
[26f3dd5]	707	element = newdoc.createElement(item[0])
[b1e609c]	708	element.setAttribute(item[0], str(getattr(self, item[1])))
[26f3dd5]	709	inputs.appendChild(element)
[2f4b430]	710
[f32d144]	711	# For self.values ={ disp_param_name: [vals,...],...}
	712	# and for self.weights ={ disp_param_name: [weights,...],...}
[b1e609c]	713	value_list = {}
	714	for item in LIST_OF_MODEL_ATTRIBUTES:
[11a7e11]	715	element = newdoc.createElement(item[0])
[b1e609c]	716	value_list = getattr(self, item[1])
	717	for key, value in value_list.iteritems():
[2296316]	718	sub_element = newdoc.createElement(key)
	719	sub_element.setAttribute('name', str(key))
	720	for val in value:
[b1e609c]	721	sub_element.appendChild(newdoc.createTextNode(str(val)))
[2f4b430]	722
[f32d144]	723	element.appendChild(sub_element)
[11a7e11]	724	inputs.appendChild(element)
[2f4b430]	725
[2296316]	726	# Create doc for the dictionary of self._disp_obj_dic
[b1e609c]	727	for item in DISPERSION_LIST:
[f32d144]	728	element = newdoc.createElement(item[0])
[b1e609c]	729	value_list = getattr(self, item[1])
	730	for key, val in value_list.iteritems():
[f32d144]	731	value = repr(val)
	732	sub_element = newdoc.createElement(key)
	733	sub_element.setAttribute('name', str(key))
	734	sub_element.setAttribute('value', str(value))
	735	element.appendChild(sub_element)
	736	inputs.appendChild(element)
[2f4b430]	737
[b1e609c]	738	for item in LIST_OF_STATE_PARAMETERS:
[61cada5]	739	element = newdoc.createElement(item[0])
[b1e609c]	740	self._toXML_helper(thelist=getattr(self, item[1]), element=element, newdoc=newdoc)
[61cada5]	741	inputs.appendChild(element)
[2f4b430]	742
[61cada5]	743	# Save the file
	744	if doc is None:
	745	fd = open(file, 'w')
	746	fd.write(newdoc.toprettyxml())
	747	fd.close()
	748	return None
	749	else:
[ac5b69d]	750	return newdoc
[2f4b430]	751
[61cada5]	752	def _fromXML_helper(self, node, list):
	753	"""
[5062bbf]	754	Helper function to write state to xml
[61cada5]	755	"""
	756	for item in node:
[0b12abb5]	757	try:
	758	name = item.get('name')
	759	except:
	760	name = None
	761	try:
	762	value = item.get('value')
	763	except:
	764	value = None
	765	try:
[3ad91de]	766	selected_to_fit = (item.get('selected_to_fit') == "True")
[0b12abb5]	767	except:
	768	selected_to_fit = None
	769	try:
[3ad91de]	770	error_displayed = (item.get('error_displayed') == "True")
[0b12abb5]	771	except:
	772	error_displayed = None
[f32d144]	773	try:
[0b12abb5]	774	error_value = item.get('error_value')
	775	except:
	776	error_value = None
	777	try:
[f32d144]	778	minimum_displayed = (item.get('minimum_displayed') == "True")
[0b12abb5]	779	except:
	780	minimum_displayed = None
	781	try:
	782	minimum_value = item.get('minimum_value')
	783	except:
	784	minimum_value = None
	785	try:
[3ad91de]	786	maximum_displayed = (item.get('maximum_displayed') == "True")
[0b12abb5]	787	except:
	788	maximum_displayed = None
	789	try:
	790	maximum_value = item.get('maximum_value')
	791	except:
	792	maximum_value = None
	793	try:
	794	unit = item.get('unit')
	795	except:
	796	unit = None
[2296316]	797	list.append([selected_to_fit, name, value, "+/-",
	798	[error_displayed, error_value],
[f32d144]	799	[minimum_displayed, minimum_value],
	800	[maximum_displayed, maximum_value], unit])
[2f4b430]	801
[61cada5]	802	def fromXML(self, file=None, node=None):
	803	"""
[5062bbf]	804	Load fitting state from a file
[2f4b430]	805
[5062bbf]	806	:param file: .fitv file
	807	:param node: node of a XML document to read from
[2f4b430]	808
[61cada5]	809	"""
	810	if file is not None:
[11a7e11]	811	msg = "PageState no longer supports non-CanSAS"
	812	msg += " format for fitting files"
	813	raise RuntimeError, msg
[2f4b430]	814
[11a7e11]	815	if node.get('version')and node.get('version') == '1.0':
[2f4b430]	816
[61cada5]	817	# Get file name
	818	entry = get_content('ns:filename', node)
	819	if entry is not None:
	820	self.file = entry.text.strip()
[2f4b430]	821
[11a7e11]	822	# Get time stamp
	823	entry = get_content('ns:timestamp', node)
	824	if entry is not None and entry.get('epoch'):
	825	try:
	826	self.timestamp = float(entry.get('epoch'))
	827	except:
	828	msg = "PageState.fromXML: Could not"
	829	msg += " read timestamp\n %s" % sys.exc_value
	830	logging.error(msg)
[2f4b430]	831
[61cada5]	832	# Parse fitting attributes
	833	entry = get_content('ns:Attributes', node)
[b1e609c]	834	for item in LIST_OF_DATA_ATTRIBUTES:
[f32d144]	835	node = get_content('ns:%s' % item[0], entry)
[b1e609c]	836	setattr(self, item[0], parse_entry_helper(node, item))
[2296316]	837
[61cada5]	838	if entry is not None:
[b1e609c]	839	for item in LIST_OF_STATE_ATTRIBUTES:
[2296316]	840	node = get_content('ns:%s' % item[0], entry)
[b1e609c]	841	setattr(self, item[0], parse_entry_helper(node, item))
[2f4b430]	842
[b1e609c]	843	for item in LIST_OF_STATE_PARAMETERS:
[2296316]	844	node = get_content("ns:%s" % item[0], entry)
[b1e609c]	845	self._fromXML_helper(node=node, list=getattr(self, item[1]))
[2f4b430]	846
[f32d144]	847	# Recover _disp_obj_dict from xml file
	848	self._disp_obj_dict = {}
[b1e609c]	849	for item in DISPERSION_LIST:
[2296316]	850	# Get node
	851	node = get_content("ns:%s" % item[0], entry)
	852	for attr in node:
[b1e609c]	853	name = str(attr.get('name'))
[f32d144]	854	val = attr.get('value')
[2296316]	855	value = val.split(" instance")[0]
	856	disp_name = value.split("<")[1]
[11a7e11]	857	try:
[2296316]	858	# Try to recover disp_model object from strings
[79492222]	859	com = "from sas.models.dispersion_models "
[2c44cf8]	860	com += "import %s as disp"
[2296316]	861	com_name = disp_name.split(".")[3]
	862	exec com % com_name
[2c44cf8]	863	disp_model = disp()
[b1e609c]	864	attribute = getattr(self, item[1])
	865	attribute[name] = com_name
[7673ecd]	866	except Exception:
	867	logging.error(traceback.format_exc())
[2f4b430]	868
[f32d144]	869	# get self.values and self.weights dic. if exists
[b1e609c]	870	for item in LIST_OF_MODEL_ATTRIBUTES:
[2296316]	871	node = get_content("ns:%s" % item[0], entry)
	872	dic = {}
[b1e609c]	873	value_list = []
[2296316]	874	for par in node:
	875	name = par.get('name')
	876	values = par.text.split('\n')
	877	# Get lines only with numbers
	878	for line in values:
	879	try:
[f32d144]	880	val = float(line)
[b1e609c]	881	value_list.append(val)
[7673ecd]	882	except Exception:
[2296316]	883	# pass if line is empty (it happens)
[7673ecd]	884	logging.error(traceback.format_exc())
[0e33a8d]	885	dic[name] = numpy.array(value_list)
[b1e609c]	886	setattr(self, item[1], dic)
[2f4b430]	887
[2296316]	888	def set_plot_state(self, figs, canvases):
	889	"""
	890	Build image state that wx.html understand
	891	by plotting, putting it into wx.FileSystem image object
	892
	893	"""
	894	images = []
	895	# some imports
	896	import wx
	897
	898	# Reset memory
	899	self.imgRAM = None
	900	wx.MemoryFSHandler()
[2f4b430]	901
[2296316]	902	# For no figures in the list, prepare empty plot
	903	if figs == None or len(figs) == 0:
	904	figs = [None]
[2f4b430]	905
[f32d144]	906	# Loop over the list of figures
[2296316]	907	# use wx.MemoryFSHandler
[f32d144]	908	self.imgRAM = wx.MemoryFSHandler()
[2296316]	909	for fig in figs:
	910	if figs != None:
	911	ind = figs.index(fig)
	912	canvas = canvases[ind]
[2f4b430]	913
[b1e609c]	914	#store the image in wx.FileSystem Object
[2296316]	915	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
[2f4b430]	916
[2296316]	917	# index of the fig
	918	ind = figs.index(fig)
[2f4b430]	919
[2296316]	920	#AddFile, image can be retrieved with 'memory:filename'
[f32d144]	921	self.imgRAM.AddFile('img_fit%s.png' % ind,
[2296316]	922	canvas.bitmap, wx.BITMAP_TYPE_PNG)
[2f4b430]	923
[2296316]	924	#append figs
	925	images.append(fig)
[2f4b430]	926
[c0ff8cc]	927	return images
[61cada5]	928
[f32d144]	929
[61cada5]	930	class Reader(CansasReader):
	931	"""
[5062bbf]	932	Class to load a .fitv fitting file
[61cada5]	933	"""
	934	## File type
	935	type_name = "Fitting"
[2f4b430]	936
[61cada5]	937	## Wildcards
[b35d3d1]	938	type = ["Fitting files (.fitv)\|.fitv"
[b9a5f0e]	939	"SASView file (.svs)\|.svs"]
[61cada5]	940	## List of allowed extensions
[f32d144]	941	ext = ['.fitv', '.FITV', '.svs', 'SVS']
[2f4b430]	942
[61cada5]	943	def __init__(self, call_back=None, cansas=True):
[df7ed14]	944	CansasReader.__init__(self)
[61cada5]	945	"""
[5062bbf]	946	Initialize the call-back method to be called
	947	after we load a file
[2f4b430]	948
[5062bbf]	949	:param call_back: call-back method
	950	:param cansas: True = files will be written/read in CanSAS format
	951	False = write CanSAS format
[2f4b430]	952
[61cada5]	953	"""
	954	## Call back method to be executed after a file is read
	955	self.call_back = call_back
	956	## CanSAS format flag
	957	self.cansas = cansas
[75fbd17]	958	self.state = None
[2f4b430]	959
[75fbd17]	960	def get_state(self):
	961	return self.state
[2f4b430]	962
[61cada5]	963	def read(self, path):
[f32d144]	964	"""
[5062bbf]	965	Load a new P(r) inversion state from file
[2f4b430]	966
[5062bbf]	967	:param path: file path
[2f4b430]	968
[61cada5]	969	"""
[e9b12eaf]	970	if self.cansas == True:
[61cada5]	971	return self._read_cansas(path)
[2f4b430]	972
[e9b12eaf]	973	def _data2d_to_xml_doc(self, datainfo):
[61cada5]	974	"""
[5062bbf]	975	Create an XML document to contain the content of a Data2D
[2f4b430]	976
[5062bbf]	977	:param datainfo: Data2D object
[2f4b430]	978
[61cada5]	979	"""
	980	if not issubclass(datainfo.__class__, Data2D):
	981	raise RuntimeError, "The cansas writer expects a Data2D instance"
[2f4b430]	982
[61cada5]	983	doc = xml.dom.minidom.Document()
	984	main_node = doc.createElement("SASroot")
	985	main_node.setAttribute("version", self.version)
[df7ed14]	986	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
	987	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
[b1e609c]	988	main_node.setAttribute("xsi:schemaLocation",
	989	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
[2f4b430]	990
[61cada5]	991	doc.appendChild(main_node)
[2f4b430]	992
[61cada5]	993	entry_node = doc.createElement("SASentry")
	994	main_node.appendChild(entry_node)
[2f4b430]	995
[61cada5]	996	write_node(doc, entry_node, "Title", datainfo.title)
[df7ed14]	997	if datainfo is not None:
	998	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
[61cada5]	999	for item in datainfo.run:
	1000	runname = {}
[2f4b430]	1001	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item])) > 1:
[b1e609c]	1002	runname = {'name': datainfo.run_name[item]}
[61cada5]	1003	write_node(doc, entry_node, "Run", item, runname)
	1004	# Data info
[df7ed14]	1005	new_node = doc.createElement("SASdata")
	1006	entry_node.appendChild(new_node)
[b1e609c]	1007	for item in LIST_OF_DATA_2D_ATTR:
[e9b12eaf]	1008	element = doc.createElement(item[0])
[b1e609c]	1009	element.setAttribute(item[0], str(getattr(datainfo, item[1])))
[df7ed14]	1010	new_node.appendChild(element)
[2f4b430]	1011
[b1e609c]	1012	for item in LIST_OF_DATA_2D_VALUES:
[df7ed14]	1013	root_node = doc.createElement(item[0])
	1014	new_node.appendChild(root_node)
[38226d26]	1015	temp_list = None
[b1e609c]	1016	temp_list = getattr(datainfo, item[1])
[df7ed14]	1017
[2f4b430]	1018	if temp_list is None or len(temp_list) == 0:
[df7ed14]	1019	element = doc.createElement(item[0])
[b1e609c]	1020	element.appendChild(doc.createTextNode(str(temp_list)))
[df7ed14]	1021	root_node.appendChild(element)
[35b556d]	1022	else:
	1023	for value in temp_list:
[df7ed14]	1024	element = doc.createElement(item[0])
[b1e609c]	1025	element.setAttribute(item[0], str(value))
[df7ed14]	1026	root_node.appendChild(element)
[2f4b430]	1027
[61cada5]	1028	# Sample info
	1029	sample = doc.createElement("SASsample")
	1030	if datainfo.sample.name is not None:
	1031	sample.setAttribute("name", str(datainfo.sample.name))
	1032	entry_node.appendChild(sample)
	1033	write_node(doc, sample, "ID", str(datainfo.sample.ID))
[f32d144]	1034	write_node(doc, sample, "thickness", datainfo.sample.thickness,
	1035	{"unit": datainfo.sample.thickness_unit})
[61cada5]	1036	write_node(doc, sample, "transmission", datainfo.sample.transmission)
[f32d144]	1037	write_node(doc, sample, "temperature", datainfo.sample.temperature,
	1038	{"unit": datainfo.sample.temperature_unit})
[2f4b430]	1039
[61cada5]	1040	for item in datainfo.sample.details:
	1041	write_node(doc, sample, "details", item)
[2f4b430]	1042
[61cada5]	1043	pos = doc.createElement("position")
[f32d144]	1044	written = write_node(doc, pos, "x", datainfo.sample.position.x,
	1045	{"unit": datainfo.sample.position_unit})
	1046	written = written \| write_node(doc, pos, "y",
	1047	datainfo.sample.position.y,
	1048	{"unit": datainfo.sample.position_unit})
	1049	written = written \| write_node(doc, pos, "z",
	1050	datainfo.sample.position.z,
	1051	{"unit": datainfo.sample.position_unit})
[61cada5]	1052	if written == True:
	1053	sample.appendChild(pos)
[2f4b430]	1054
[61cada5]	1055	ori = doc.createElement("orientation")
[f32d144]	1056	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
	1057	{"unit": datainfo.sample.orientation_unit})
	1058	written = written \| write_node(doc, ori, "pitch",
	1059	datainfo.sample.orientation.y,
	1060	{"unit": datainfo.sample.orientation_unit})
	1061	written = written \| write_node(doc, ori, "yaw",
	1062	datainfo.sample.orientation.z,
	1063	{"unit": datainfo.sample.orientation_unit})
[61cada5]	1064	if written == True:
	1065	sample.appendChild(ori)
[2f4b430]	1066
[61cada5]	1067	# Instrument info
	1068	instr = doc.createElement("SASinstrument")
	1069	entry_node.appendChild(instr)
[2f4b430]	1070
[61cada5]	1071	write_node(doc, instr, "name", datainfo.instrument)
[2f4b430]	1072
[61cada5]	1073	# Source
	1074	source = doc.createElement("SASsource")
	1075	if datainfo.source.name is not None:
	1076	source.setAttribute("name", str(datainfo.source.name))
	1077	instr.appendChild(source)
[2f4b430]	1078
[61cada5]	1079	write_node(doc, source, "radiation", datainfo.source.radiation)
	1080	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
	1081	size = doc.createElement("beam_size")
	1082	if datainfo.source.beam_size_name is not None:
	1083	size.setAttribute("name", str(datainfo.source.beam_size_name))
[f32d144]	1084	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
	1085	{"unit": datainfo.source.beam_size_unit})
	1086	written = written \| write_node(doc, size, "y",
	1087	datainfo.source.beam_size.y,
	1088	{"unit": datainfo.source.beam_size_unit})
	1089	written = written \| write_node(doc, size, "z",
	1090	datainfo.source.beam_size.z,
	1091	{"unit": datainfo.source.beam_size_unit})
[61cada5]	1092	if written == True:
	1093	source.appendChild(size)
[2f4b430]	1094
[f32d144]	1095	write_node(doc, source, "wavelength", datainfo.source.wavelength,
	1096	{"unit": datainfo.source.wavelength_unit})
	1097	write_node(doc, source, "wavelength_min",
	1098	datainfo.source.wavelength_min,
	1099	{"unit": datainfo.source.wavelength_min_unit})
	1100	write_node(doc, source, "wavelength_max",
	1101	datainfo.source.wavelength_max,
	1102	{"unit": datainfo.source.wavelength_max_unit})
	1103	write_node(doc, source, "wavelength_spread",
	1104	datainfo.source.wavelength_spread,
	1105	{"unit": datainfo.source.wavelength_spread_unit})
[2f4b430]	1106
[61cada5]	1107	# Collimation
	1108	for item in datainfo.collimation:
	1109	coll = doc.createElement("SAScollimation")
	1110	if item.name is not None:
	1111	coll.setAttribute("name", str(item.name))
	1112	instr.appendChild(coll)
[2f4b430]	1113
[f32d144]	1114	write_node(doc, coll, "length", item.length,
	1115	{"unit": item.length_unit})
[2f4b430]	1116
[61cada5]	1117	for apert in item.aperture:
	1118	ap = doc.createElement("aperture")
	1119	if apert.name is not None:
	1120	ap.setAttribute("name", str(apert.name))
	1121	if apert.type is not None:
	1122	ap.setAttribute("type", str(apert.type))
	1123	coll.appendChild(ap)
[2f4b430]	1124
[f32d144]	1125	write_node(doc, ap, "distance", apert.distance,
	1126	{"unit": apert.distance_unit})
[2f4b430]	1127
[61cada5]	1128	size = doc.createElement("size")
	1129	if apert.size_name is not None:
	1130	size.setAttribute("name", str(apert.size_name))
[f32d144]	1131	written = write_node(doc, size, "x", apert.size.x,
	1132	{"unit": apert.size_unit})
	1133	written = written \| write_node(doc, size, "y", apert.size.y,
	1134	{"unit": apert.size_unit})
	1135	written = written \| write_node(doc, size, "z", apert.size.z,
	1136	{"unit": apert.size_unit})
[61cada5]	1137	if written == True:
	1138	ap.appendChild(size)
	1139
	1140	# Detectors
	1141	for item in datainfo.detector:
	1142	det = doc.createElement("SASdetector")
	1143	written = write_node(doc, det, "name", item.name)
[f32d144]	1144	written = written \| write_node(doc, det, "SDD", item.distance,
	1145	{"unit": item.distance_unit})
	1146	written = written \| write_node(doc, det, "slit_length",
	1147	item.slit_length,
	1148	{"unit": item.slit_length_unit})
[61cada5]	1149	if written == True:
	1150	instr.appendChild(det)
[2f4b430]	1151
[61cada5]	1152	off = doc.createElement("offset")
[f32d144]	1153	written = write_node(doc, off, "x", item.offset.x,
	1154	{"unit": item.offset_unit})
	1155	written = written \| write_node(doc, off, "y", item.offset.y,
	1156	{"unit": item.offset_unit})
	1157	written = written \| write_node(doc, off, "z", item.offset.z,
	1158	{"unit": item.offset_unit})
[61cada5]	1159	if written == True:
	1160	det.appendChild(off)
[2f4b430]	1161
[61cada5]	1162	center = doc.createElement("beam_center")
[f32d144]	1163	written = write_node(doc, center, "x", item.beam_center.x,
	1164	{"unit": item.beam_center_unit})
	1165	written = written \| write_node(doc, center, "y",
	1166	item.beam_center.y,
	1167	{"unit": item.beam_center_unit})
	1168	written = written \| write_node(doc, center, "z",
	1169	item.beam_center.z,
	1170	{"unit": item.beam_center_unit})
[61cada5]	1171	if written == True:
	1172	det.appendChild(center)
[2f4b430]	1173
[61cada5]	1174	pix = doc.createElement("pixel_size")
[f32d144]	1175	written = write_node(doc, pix, "x", item.pixel_size.x,
	1176	{"unit": item.pixel_size_unit})
	1177	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
	1178	{"unit": item.pixel_size_unit})
	1179	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
	1180	{"unit": item.pixel_size_unit})
[61cada5]	1181	if written == True:
	1182	det.appendChild(pix)
[2f4b430]	1183
[61cada5]	1184	ori = doc.createElement("orientation")
[f32d144]	1185	written = write_node(doc, ori, "roll", item.orientation.x,
	1186	{"unit": item.orientation_unit})
	1187	written = written \| write_node(doc, ori, "pitch",
	1188	item.orientation.y,
	1189	{"unit": item.orientation_unit})
	1190	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
	1191	{"unit": item.orientation_unit})
[61cada5]	1192	if written == True:
	1193	det.appendChild(ori)
[2f4b430]	1194
[61cada5]	1195	# Processes info
	1196	for item in datainfo.process:
	1197	node = doc.createElement("SASprocess")
	1198	entry_node.appendChild(node)
	1199
	1200	write_node(doc, node, "name", item.name)
	1201	write_node(doc, node, "date", item.date)
	1202	write_node(doc, node, "description", item.description)
	1203	for term in item.term:
	1204	value = term['value']
	1205	del term['value']
	1206	write_node(doc, node, "term", value, term)
	1207	for note in item.notes:
	1208	write_node(doc, node, "SASprocessnote", note)
	1209	# Return the document, and the SASentry node associated with
	1210	# the data we just wrote
	1211	return doc, entry_node
[2f4b430]	1212
[61cada5]	1213	def _parse_state(self, entry):
	1214	"""
[5062bbf]	1215	Read a fit result from an XML node
[2f4b430]	1216
[f32d144]	1217	:param entry: XML node to read from
[2f4b430]	1218
[5062bbf]	1219	:return: PageState object
[61cada5]	1220	"""
	1221	# Create an empty state
[2f4b430]	1222	state = None
[61cada5]	1223	# Locate the P(r) node
	1224	try:
[f32d144]	1225	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
	1226	namespaces={'ns': CANSAS_NS})
	1227	if nodes != []:
[b35d3d1]	1228	# Create an empty state
[f32d144]	1229	state = PageState()
[b35d3d1]	1230	state.fromXML(node=nodes[0])
[2f4b430]	1231
[61cada5]	1232	except:
	1233	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
[2f4b430]	1234
[61cada5]	1235	return state
[2f4b430]	1236
[ac5b69d]	1237	def _parse_save_state_entry(self, dom):
[e9b12eaf]	1238	"""
[5062bbf]	1239	Parse a SASentry
[2f4b430]	1240
[5062bbf]	1241	:param node: SASentry node
[2f4b430]	1242
[df7ed14]	1243	:return: Data1D/Data2D object
[2f4b430]	1244
[e9b12eaf]	1245	"""
[df7ed14]	1246	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
	1247	if not node or node[0].text.lstrip().rstrip() != "Data2D":
[ac5b69d]	1248	return_value, _ = self._parse_entry(dom)
	1249	numpy.trim_zeros(return_value.x)
	1250	numpy.trim_zeros(return_value.y)
	1251	numpy.trim_zeros(return_value.dy)
	1252	size_dx = return_value.dx.size
	1253	size_dxl = return_value.dxl.size
	1254	size_dxw = return_value.dxw.size
	1255	if size_dxl == 0 and size_dxw == 0:
	1256	return_value.dxl = None
	1257	return_value.dxw = None
	1258	numpy.trim_zeros(return_value.dx)
	1259	elif size_dx == 0:
	1260	return_value.dx = None
	1261	size_dx = size_dxl
	1262	numpy.trim_zeros(return_value.dxl)
	1263	numpy.trim_zeros(return_value.dxw)
[2f4b430]	1264
[ac5b69d]	1265	return return_value, _
[2f4b430]	1266
[df7ed14]	1267	#Parse 2D
[e9b12eaf]	1268	data_info = Data2D()
[2f4b430]	1269
[f32d144]	1270	# Look up title
[e9b12eaf]	1271	self._store_content('ns:Title', dom, 'title', data_info)
[2f4b430]	1272
[f32d144]	1273	# Look up run number
[e9b12eaf]	1274	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
[f32d144]	1275	for item in nodes:
[e9b12eaf]	1276	if item.text is not None:
	1277	value = item.text.strip()
	1278	if len(value) > 0:
	1279	data_info.run.append(value)
	1280	if item.get('name') is not None:
	1281	data_info.run_name[value] = item.get('name')
[2f4b430]	1282
[f32d144]	1283	# Look up instrument name
	1284	self._store_content('ns:SASinstrument/ns:name', dom,
	1285	'instrument', data_info)
[e9b12eaf]	1286
	1287	# Notes
	1288	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
	1289	for note in note_list:
	1290	try:
	1291	if note.text is not None:
	1292	note_value = note.text.strip()
	1293	if len(note_value) > 0:
	1294	data_info.notes.append(note_value)
[7673ecd]	1295	except Exception:
[e9b12eaf]	1296	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
	1297	self.errors.append(err_mess)
	1298	logging.error(err_mess)
[2f4b430]	1299
[e9b12eaf]	1300	# Sample info ###################
	1301	entry = get_content('ns:SASsample', dom)
	1302	if entry is not None:
	1303	data_info.sample.name = entry.get('name')
[2f4b430]	1304
[b1e609c]	1305	self._store_content('ns:SASsample/ns:ID', dom, 'ID', data_info.sample)
	1306	self._store_float('ns:SASsample/ns:thickness', dom, 'thickness', data_info.sample)
	1307	self._store_float('ns:SASsample/ns:transmission', dom, 'transmission', data_info.sample)
	1308	self._store_float('ns:SASsample/ns:temperature', dom, 'temperature', data_info.sample)
[2f4b430]	1309
[b1e609c]	1310	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1311	for item in nodes:
	1312	try:
	1313	if item.text is not None:
	1314	detail_value = item.text.strip()
	1315	if len(detail_value) > 0:
	1316	data_info.sample.details.append(detail_value)
[7673ecd]	1317	except Exception:
[e9b12eaf]	1318	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
	1319	self.errors.append(err_mess)
	1320	logging.error(err_mess)
[2f4b430]	1321
[e9b12eaf]	1322	# Position (as a vector)
[b1e609c]	1323	self._store_float('ns:SASsample/ns:position/ns:x', dom, 'position.x', data_info.sample)
	1324	self._store_float('ns:SASsample/ns:position/ns:y', dom, 'position.y', data_info.sample)
	1325	self._store_float('ns:SASsample/ns:position/ns:z', dom, 'position.z', data_info.sample)
[2f4b430]	1326
[e9b12eaf]	1327	# Orientation (as a vector)
[f32d144]	1328	self._store_float('ns:SASsample/ns:orientation/ns:roll',
[b1e609c]	1329	dom, 'orientation.x', data_info.sample)
[f32d144]	1330	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
[b1e609c]	1331	dom, 'orientation.y', data_info.sample)
[f32d144]	1332	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
[b1e609c]	1333	dom, 'orientation.z', data_info.sample)
[2f4b430]	1334
[e9b12eaf]	1335	# Source info ###################
	1336	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
	1337	if entry is not None:
	1338	data_info.source.name = entry.get('name')
[2f4b430]	1339
[f32d144]	1340	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
[b1e609c]	1341	dom, 'radiation', data_info.source)
[f32d144]	1342	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
[b1e609c]	1343	dom, 'beam_shape', data_info.source)
[f32d144]	1344	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
[b1e609c]	1345	dom, 'wavelength', data_info.source)
[f32d144]	1346	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
[b1e609c]	1347	dom, 'wavelength_min', data_info.source)
[f32d144]	1348	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
[b1e609c]	1349	dom, 'wavelength_max', data_info.source)
[f32d144]	1350	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
[b1e609c]	1351	dom, 'wavelength_spread', data_info.source)
[2f4b430]	1352
[f32d144]	1353	# Beam size (as a vector)
[e9b12eaf]	1354	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
	1355	if entry is not None:
	1356	data_info.source.beam_size_name = entry.get('name')
[2f4b430]	1357
[f32d144]	1358	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
[b1e609c]	1359	dom, 'beam_size.x', data_info.source)
[f32d144]	1360	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
[b1e609c]	1361	dom, 'beam_size.y', data_info.source)
[f32d144]	1362	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
[b1e609c]	1363	dom, 'beam_size.z', data_info.source)
[2f4b430]	1364
[e9b12eaf]	1365	# Collimation info ###################
[f32d144]	1366	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
	1367	namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1368	for item in nodes:
	1369	collim = Collimation()
	1370	if item.get('name') is not None:
	1371	collim.name = item.get('name')
[f32d144]	1372	self._store_float('ns:length', item, 'length', collim)
[2f4b430]	1373
[e9b12eaf]	1374	# Look for apertures
[f32d144]	1375	apert_list = item.xpath('ns:aperture',
	1376	namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1377	for apert in apert_list:
[f32d144]	1378	aperture = Aperture()
[2f4b430]	1379
[e9b12eaf]	1380	# Get the name and type of the aperture
	1381	aperture.name = apert.get('name')
	1382	aperture.type = apert.get('type')
[2f4b430]	1383
[f32d144]	1384	self._store_float('ns:distance', apert, 'distance', aperture)
[2f4b430]	1385
[e9b12eaf]	1386	entry = get_content('ns:size', apert)
	1387	if entry is not None:
	1388	aperture.size_name = entry.get('name')
[2f4b430]	1389
[f32d144]	1390	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
	1391	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
[e9b12eaf]	1392	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
[2f4b430]	1393
[e9b12eaf]	1394	collim.aperture.append(aperture)
[2f4b430]	1395
[e9b12eaf]	1396	data_info.collimation.append(collim)
[2f4b430]	1397
[e9b12eaf]	1398	# Detector info ######################
[f32d144]	1399	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
	1400	namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1401	for item in nodes:
[2f4b430]	1402
[e9b12eaf]	1403	detector = Detector()
[2f4b430]	1404
[e9b12eaf]	1405	self._store_content('ns:name', item, 'name', detector)
[f32d144]	1406	self._store_float('ns:SDD', item, 'distance', detector)
[2f4b430]	1407
[e9b12eaf]	1408	# Detector offset (as a vector)
[f32d144]	1409	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
	1410	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
	1411	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
[2f4b430]	1412
[e9b12eaf]	1413	# Detector orientation (as a vector)
[f32d144]	1414	self._store_float('ns:orientation/ns:roll', item,
	1415	'orientation.x', detector)
	1416	self._store_float('ns:orientation/ns:pitch', item,
	1417	'orientation.y', detector)
	1418	self._store_float('ns:orientation/ns:yaw', item,
	1419	'orientation.z', detector)
[2f4b430]	1420
[e9b12eaf]	1421	# Beam center (as a vector)
[f32d144]	1422	self._store_float('ns:beam_center/ns:x', item,
	1423	'beam_center.x', detector)
	1424	self._store_float('ns:beam_center/ns:y', item,
	1425	'beam_center.y', detector)
	1426	self._store_float('ns:beam_center/ns:z', item,
	1427	'beam_center.z', detector)
[2f4b430]	1428
[e9b12eaf]	1429	# Pixel size (as a vector)
[f32d144]	1430	self._store_float('ns:pixel_size/ns:x', item,
	1431	'pixel_size.x', detector)
	1432	self._store_float('ns:pixel_size/ns:y', item,
	1433	'pixel_size.y', detector)
	1434	self._store_float('ns:pixel_size/ns:z', item,
	1435	'pixel_size.z', detector)
[2f4b430]	1436
[e9b12eaf]	1437	self._store_float('ns:slit_length', item, 'slit_length', detector)
[2f4b430]	1438
[f32d144]	1439	data_info.detector.append(detector)
[e9b12eaf]	1440
	1441	# Processes info ######################
	1442	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
	1443	for item in nodes:
	1444	process = Process()
	1445	self._store_content('ns:name', item, 'name', process)
	1446	self._store_content('ns:date', item, 'date', process)
	1447	self._store_content('ns:description', item, 'description', process)
[2f4b430]	1448
[e9b12eaf]	1449	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
	1450	for term in term_list:
	1451	try:
	1452	term_attr = {}
	1453	for attr in term.keys():
	1454	term_attr[attr] = term.get(attr).strip()
	1455	if term.text is not None:
	1456	term_attr['value'] = term.text.strip()
	1457	process.term.append(term_attr)
	1458	except:
	1459	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
	1460	self.errors.append(err_mess)
	1461	logging.error(err_mess)
[2f4b430]	1462
[f32d144]	1463	note_list = item.xpath('ns:SASprocessnote',
	1464	namespaces={'ns': CANSAS_NS})
[e9b12eaf]	1465	for note in note_list:
	1466	if note.text is not None:
	1467	process.notes.append(note.text.strip())
[2f4b430]	1468
[e9b12eaf]	1469	data_info.process.append(process)
[2f4b430]	1470
[e9b12eaf]	1471	# Data info ######################
	1472	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
[f32d144]	1473	if len(nodes) > 1:
[e9b12eaf]	1474	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
[2f4b430]	1475
[df7ed14]	1476	for entry in nodes:
[b1e609c]	1477	for item in LIST_OF_DATA_2D_ATTR:
[df7ed14]	1478	#get node
[f32d144]	1479	node = get_content('ns:%s' % item[0], entry)
[b1e609c]	1480	setattr(data_info, item[1], parse_entry_helper(node, item))
[2f4b430]	1481
[b1e609c]	1482	for item in LIST_OF_DATA_2D_VALUES:
[f32d144]	1483	field = get_content('ns:%s' % item[0], entry)
[b1e609c]	1484	value_list = []
[df7ed14]	1485	if field is not None:
[b1e609c]	1486	value_list = [parse_entry_helper(node, item) for node in field]
	1487	if len(value_list) < 2:
	1488	setattr(data_info, item[0], None)
[44f7c1b]	1489	else:
[b1e609c]	1490	setattr(data_info, item[0], numpy.array(value_list))
[2f4b430]	1491
[e9b12eaf]	1492	return data_info
	1493
[61cada5]	1494	def _read_cansas(self, path):
[f32d144]	1495	"""
[5062bbf]	1496	Load data and P(r) information from a CanSAS XML file.
[2f4b430]	1497
[5062bbf]	1498	:param path: file path
[2f4b430]	1499
[f32d144]	1500	:return: Data1D object if a single SASentry was found,
[5062bbf]	1501	or a list of Data1D objects if multiple entries were found,
	1502	or None of nothing was found
[2f4b430]	1503
[5062bbf]	1504	:raise RuntimeError: when the file can't be opened
	1505	:raise ValueError: when the length of the data vectors are inconsistent
[2f4b430]	1506
[61cada5]	1507	"""
	1508	output = []
[f32d144]	1509	basename = os.path.basename(path)
[b63dc6e]	1510	root, extension = os.path.splitext(basename)
	1511	ext = extension.lower()
[61cada5]	1512	try:
	1513	if os.path.isfile(path):
[2f4b430]	1514
[61cada5]	1515	#TODO: eventually remove the check for .xml once
	1516	# the P(r) writer/reader is truly complete.
[b63dc6e]	1517	if ext in self.ext or \
	1518	ext == '.xml':
[2f4b430]	1519
[61cada5]	1520	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
	1521	# Check the format version number
[f32d144]	1522	# Specifying the namespace will take care of the file format version
[61cada5]	1523	root = tree.getroot()
[f32d144]	1524	entry_list = root.xpath('ns:SASentry',
	1525	namespaces={'ns': CANSAS_NS})
	1526	for entry in entry_list:
[e9b12eaf]	1527	try:
[ac5b69d]	1528	sas_entry, _ = self._parse_save_state_entry(entry)
[e9b12eaf]	1529	except:
[df7ed14]	1530	raise
[61cada5]	1531	fitstate = self._parse_state(entry)
[2f4b430]	1532
[b35d3d1]	1533	#state could be None when .svs file is loaded
	1534	#in this case, skip appending to output
	1535	if fitstate != None:
	1536	sas_entry.meta_data['fitstate'] = fitstate
	1537	sas_entry.filename = fitstate.file
	1538	output.append(sas_entry)
[61cada5]	1539	else:
[b63dc6e]	1540	self.call_back(format=ext)
[61cada5]	1541	raise RuntimeError, "%s is not a file" % path
[b35d3d1]	1542
[61cada5]	1543	# Return output consistent with the loader's api
[f32d144]	1544	if len(output) == 0:
	1545	self.call_back(state=None, datainfo=None, format=ext)
[61cada5]	1546	return None
	1547	else:
[b35d3d1]	1548	for ind in range(len(output)):
	1549	# Call back to post the new state
	1550	state = output[ind].meta_data['fitstate']
	1551	t = time.localtime(state.timestamp)
	1552	time_str = time.strftime("%b %d %H:%M", t)
	1553	# Check that no time stamp is already appended
	1554	max_char = state.file.find("[")
	1555	if max_char < 0:
	1556	max_char = len(state.file)
[ef16f59]	1557	original_fname = state.file[0:max_char]
[f32d144]	1558	state.file = original_fname + ' [' + time_str + ']'
[2f4b430]	1559
[b35d3d1]	1560	if state is not None and state.is_data is not None:
[b1e609c]	1561	output[ind].is_data = state.is_data
[2f4b430]	1562
[b35d3d1]	1563	output[ind].filename = state.file
	1564	state.data = output[ind]
[f32d144]	1565	state.data.name = output[ind].filename # state.data_name
[b35d3d1]	1566	state.data.id = state.data_id
	1567	if state.is_data is not None:
	1568	state.data.is_data = state.is_data
[f32d144]	1569	if output[ind].run_name is not None\
	1570	and len(output[ind].run_name) != 0:
[654e8e0]	1571	if isinstance(output[ind].run_name, dict):
	1572	name = output[ind].run_name.keys()[0]
	1573	else:
	1574	name = output[ind].run_name
[f32d144]	1575	else:
	1576	name = original_fname
[ef16f59]	1577	state.data.group_id = name
	1578	#store state in fitting
[f32d144]	1579	self.call_back(state=state,
	1580	datainfo=output[ind], format=ext)
	1581	self.state = state
[ef16f59]	1582	return output
[61cada5]	1583	except:
[4bee68d]	1584	self.call_back(format=ext)
[61cada5]	1585	raise
[2f4b430]	1586
[61cada5]	1587	def write(self, filename, datainfo=None, fitstate=None):
	1588	"""
[b35d3d1]	1589	Write the content of a Data1D as a CanSAS XML file only for standalone
[2f4b430]	1590
[5062bbf]	1591	:param filename: name of the file to write
	1592	:param datainfo: Data1D object
	1593	:param fitstate: PageState object
[2f4b430]	1594
[61cada5]	1595	"""
	1596	# Sanity check
	1597	if self.cansas == True:
	1598	# Add fitting information to the XML document
[ef16f59]	1599	doc = self.write_toXML(datainfo, fitstate)
[61cada5]	1600	# Write the XML document
	1601	else:
[ac5b69d]	1602	doc = fitstate.toXML(file=filename)
[2f4b430]	1603
[ac5b69d]	1604	# Save the document no matter the type
	1605	fd = open(filename, 'w')
	1606	fd.write(doc.toprettyxml())
	1607	fd.close()
[2f4b430]	1608
[b35d3d1]	1609	def write_toXML(self, datainfo=None, state=None):
	1610	"""
[f32d144]	1611	Write toXML, a helper for write(),
	1612	could be used by guimanager._on_save()
[2f4b430]	1613
[b35d3d1]	1614	: return: xml doc
	1615	"""
[3c44c66]	1616
[b35d3d1]	1617	if state.data is None:
[c10d9d6c]	1618	data = sas.sascalc.dataloader.data_info.Data1D(x=[], y=[])
[a805118]	1619	return None
[3b148c3]	1620	elif not state.data.is_data:
	1621	return None
[f32d144]	1622	else:
[b35d3d1]	1623	#make sure title and data run is filled up.
[f32d144]	1624	if state.data.title == None or state.data.title == '':
	1625	state.data.title = state.data.name
	1626	if state.data.run_name == None or state.data.run_name == {}:
[028a0e8]	1627	state.data.run = [str(state.data.name)]
	1628	state.data.run_name[0] = state.data.name
[2f4b430]	1629
[f32d144]	1630	if issubclass(state.data.__class__,
[c10d9d6c]	1631	sas.sascalc.dataloader.data_info.Data1D):
[b35d3d1]	1632	data = state.data
	1633	doc, sasentry = self._to_xml_doc(data)
	1634	else:
	1635	data = state.data
	1636	doc, sasentry = self._data2d_to_xml_doc(data)
[2f4b430]	1637
[b35d3d1]	1638	if state is not None:
[ac5b69d]	1639	doc = state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
[2f4b430]	1640
[f32d144]	1641	return doc
[2f4b430]	1642
[f32d144]	1643	# Simple html report templet
[2296316]	1644	HEADER = "<html>\n"
	1645	HEADER += "<head>\n"
	1646	HEADER += "<meta http-equiv=Content-Type content='text/html; "
	1647	HEADER += "charset=windows-1252'> \n"
	1648	HEADER += "<meta name=Generator >\n"
	1649	HEADER += "</head>\n"
	1650	HEADER += "<body lang=EN-US>\n"
	1651	HEADER += "<div class=WordSection1>\n"
[14d2daa]	1652	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
	1653	HEADER += "%s</font></center></span></center></b></p>"
[2296316]	1654	HEADER += "<p class=MsoNormal> </p>"
[14d2daa]	1655	PARA = "<p class=MsoNormal><font size='4' > %s \n"
	1656	PARA += "</font></p>"
	1657	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
	1658	CENTRE += "</font></center></p>"
[2296316]	1659	FEET_1 = \
	1660	"""
[3a3dd9c]	1661	<p class=MsoNormal> </p>
[14d2daa]	1662	<br>
	1663	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
[f32d144]	1664	</font></span></center></b></p>
	1665	<p class=MsoNormal> </p>
	1666	<center>
[14d2daa]	1667	<br><font size='4' >Model Computation</font>
[f32d144]	1668	<br><font size='4' >Data: "%s"</font><br>
[2296316]	1669	"""
	1670	FEET_2 = \
	1671	"""
[f32d144]	1672	<img src="%s" >
[2296316]	1673	</img>
	1674	"""
	1675	FEET_3 = \
	1676	"""
[f32d144]	1677	</center>
[2296316]	1678	</div>
	1679	</body>
	1680	</html>
	1681	"""
	1682	ELINE = "<p class=MsoNormal> </p>"
	1683
[3c44c66]	1684	if __name__ == "__main__":
	1685	state = PageState(parent=None)
	1686	#state.toXML()
	1687	"""
[2f4b430]	1688
[3c44c66]	1689	file = open("test_state", "w")
	1690	pickle.dump(state, file)
	1691	print pickle.dumps(state)
	1692	state.data_name = "hello---->"
	1693	pickle.dump(state, file)
	1694	file = open("test_state", "r")
	1695	new_state= pickle.load(file)
	1696	print "new state", new_state
	1697	new_state= pickle.load(file)
	1698	print "new state", new_state
	1699	#print "state", state
	1700	"""
	1701	import bsddb
	1702	import pickle
[f32d144]	1703	db = bsddb.btopen('file_state.db', 'c')
[3c44c66]	1704	val = (pickle.dumps(state), "hello", "hi")
[f32d144]	1705	db['state1'] = pickle.dumps(val)
[3c44c66]	1706	print pickle.loads(db['state1'])
	1707	state.data_name = "hello---->22"
[f32d144]	1708	db['state2'] = pickle.dumps(state)
[3c44c66]	1709	state.data_name = "hello---->2"
[f32d144]	1710	db['state3'] = pickle.dumps(state)
[3c44c66]	1711	del db['state3']
	1712	state.data_name = "hello---->3"
[f32d144]	1713	db['state4'] = pickle.dumps(state)
[3c44c66]	1714	new_state = pickle.loads(db['state1'])
	1715	#print db.last()
	1716	db.set_location('state2')
	1717	state.data_name = "hello---->5"
[f32d144]	1718	db['aastate5'] = pickle.dumps(state)
[3c44c66]	1719	db.keys().sort()
	1720	print pickle.loads(db['state2'])
[2f4b430]	1721
[f32d144]	1722	db.close()

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SasView

source: sasview/src/sas/sasgui/perspectives/fitting/pagestate.py @ ce94504

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