"""
Class that holds a fit page state
"""
################################################################################
#This software was developed by the University of Tennessee as part of the
#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
#project funded by the US National Science Foundation.
#
#See the license text in license.txt
#
#copyright 2009, University of Tennessee
################################################################################
import time
import os
import sys
import copy
import logging
import numpy
import string
import xml.dom.minidom
from xml.dom.minidom import parseString
from lxml import etree
import sans.dataloader
from sans.dataloader.readers.cansas_reader import Reader as CansasReader
from sans.dataloader.readers.cansas_reader import get_content, write_node
from sans.dataloader.data_info import Data2D
from sans.dataloader.data_info import Collimation
from sans.dataloader.data_info import Detector
from sans.dataloader.data_info import Process
from sans.dataloader.data_info import Aperture
#Information to read/write state as xml
FITTING_NODE_NAME = 'fitting_plug_in'
CANSAS_NS = "cansas1d/1.0"
list_of_data_attributes = [["is_data", "is_data", "bool"],
["group_id", "data_group_id", "string"],
["data_name", "data_name", "string"],
["data_id", "data_id", "string"],
["name", "name", "string"],
["data_name", "data_name", "string"]]
list_of_state_attributes = [["engine_type", "engine_type", "string"],
["qmin", "qmin", "float"],
["qmax", "qmax", "float"],
["npts", "npts", "float"],
#["shape_rbutton", "shape_rbutton", "bool"],
#["shape_indep_rbutton", "shape_indep_rbutton", "bool"],
#["plugin_rbutton", "plugin_rbutton", "bool"],
#["struct_rbutton", "struct_rbutton", "bool"],
["categorycombobox", "categorycombobox", "string"],
["formfactorcombobox", "formfactorcombobox", "string"],
["structurecombobox", "structurecombobox", "string"],
["multi_factor","multi_factor","float"],
["magnetic_on","magnetic_on", "bool"],
["enable_smearer","enable_smearer","bool"],
["disable_smearer","disable_smearer","bool"],
["pinhole_smearer","pinhole_smearer","bool"],
["slit_smearer","slit_smearer","bool"],
["enable_disp","enable_disp","bool"],
["disable_disp","disable_disp","bool"],
["dI_noweight","dI_noweight","bool"],
["dI_didata","dI_didata","bool"],
["dI_sqrdata","dI_sqrdata","bool"],
["dI_idata","dI_idata","bool"],
["enable2D","enable2D","bool"],
["cb1","cb1","bool"],
["tcChi","tcChi","float"],
["smearer", "smearer", "float"],
["smear_type","smear_type", "string"],
["dq_l", "dq_l", "string"],
["dq_r","dq_r", "string"],
["dx_max", "dx_max", "float"],
["dx_min","dx_min", "float"],
["dxl", "dxl", "float"],
["dxw","dxw", "float"]]
list_of_model_attributes = [["values", "values"],
["weights", "weights"]]
list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]]
list_of_state_parameters = [["parameters", "parameters"],
["str_parameters", "str_parameters"],
["orientation_parameters", "orientation_params"],
["dispersity_parameters", "orientation_params_disp"],
["fixed_param", "fixed_param"],
["fittable_param", "fittable_param"]]
list_of_data_2d_attr = [["xmin", "xmin", "float"],
["xmax", "xmax", "float"],
["ymin", "ymin", "float"],
["ymax", "ymax", "float"],
["_xaxis", "_xaxis", "string"],
["_xunit", "_xunit", "string"],
["_yaxis", "_yaxis", "string"],
["_yunit", "_yunit", "string"],
["_zaxis", "_zaxis", "string"],
["_zunit", "_zunit", "string"]]
list_of_data2d_values = [["qx_data", "qx_data", "float"],
["qy_data", "qy_data", "float"],
["dqx_data", "dqx_data", "float"],
["dqy_data", "dqy_data", "float"],
["data", "data", "float"],
["q_data", "q_data", "float"],
["err_data", "err_data", "float"],
["mask", "mask", "bool"]]
def parse_entry_helper(node, item):
"""
Create a numpy list from value extrated from the node
:param node: node from each the value is stored
:param item: list name of three strings.the two first are name of data
attribute and the third one is the type of the value of that
attribute. type can be string, float, bool, etc.
: return: numpy array
"""
if node is not None:
if item[2] == "string":
return str(node.get(item[0]).strip())
elif item[2] == "bool":
try:
return node.get(item[0]).strip() == "True"
except:
return None
else:
try:
return float(node.get(item[0]))
except:
return None
class PageState(object):
"""
Contains information to reconstruct a page of the fitpanel.
"""
def __init__(self, parent=None, model=None, data=None):
"""
Initialize the current state
:param model: a selected model within a page
:param data:
"""
self.file = None
#Time of state creation
self.timestamp = time.time()
## Data member to store the dispersion object created
self._disp_obj_dict = {}
#------------------------
#Data used for fitting
self.data = data
# model data
self.theory_data = None
#Is 2D
self.is_2D = False
self.images = None
#save additional information on data that dataloader.reader does not read
self.is_data = None
self.data_name = ""
if self.data is not None:
self.data_name = self.data.name
self.data_id = None
if self.data is not None and hasattr(self.data, "id"):
self.data_id = self.data.id
self.data_group_id = None
if self.data is not None and hasattr(self.data, "group_id"):
self.data_group_id = self.data.group_id
## reset True change the state of exsiting button
self.reset = False
#engine type
self.engine_type = None
# flag to allow data2D plot
self.enable2D = False
# model on which the fit would be performed
self.model = model
self.m_name = None
#list of process done to model
self.process = []
#fit page manager
self.manager = None
#Store the parent of this panel parent
# For this application fitpanel is the parent
self.parent = parent
# Event_owner is the owner of model event
self.event_owner = None
##page name
self.page_name = ""
# Contains link between model, all its parameters, and panel organization
self.parameters = []
# String parameter list that can not be fitted
self.str_parameters = []
# Contains list of parameters that cannot be fitted and reference to
#panel objects
self.fixed_param = []
# Contains list of parameters with dispersity and reference to
#panel objects
self.fittable_param = []
## orientation parameters
self.orientation_params = []
## orientation parameters for gaussian dispersity
self.orientation_params_disp = []
## smearer info
self.smearer = None
self.smear_type = None
self.dq_l = None
self.dq_r = None
self.dx_max = None
self.dx_min = None
self.dxl = None
self.dxw = None
#list of dispersion parameters
self.disp_list = []
if self.model is not None:
self.disp_list = self.model.getDispParamList()
self.disp_cb_dict = {}
self.values = {}
self.weights = {}
#contains link between a model and selected parameters to fit
self.param_toFit = []
##dictionary of model type and model class
self.model_list_box = None
## save the state of the context menu
self.saved_states = {}
## save selection of combobox
self.formfactorcombobox = None
self.categorycombobox = None
self.structurecombobox = None
## radio box to select type of model
#self.shape_rbutton = False
#self.shape_indep_rbutton = False
#self.struct_rbutton = False
#self.plugin_rbutton = False
## the indice of the current selection
self.disp_box = 0
## Qrange
## Q range
self.qmin = 0.001
self.qmax = 0.1
#reset data range
self.qmax_x = None
self.qmin_x = None
self.npts = None
self.name = ""
self.multi_factor = None
self.magnetic_on = False
## enable smearering state
self.enable_smearer = False
self.disable_smearer = True
self.pinhole_smearer = False
self.slit_smearer = False
# weighting options
self.dI_noweight = False
self.dI_didata = True
self.dI_sqrdata = False
self.dI_idata = False
## disperity selection
self.enable_disp = False
self.disable_disp = True
## state of selected all check button
self.cb1 = False
## store value of chisqr
self.tcChi = None
def clone(self):
"""
Create a new copy of the current object
"""
model = None
if self.model is not None:
model = self.model.clone()
model.name = self.model.name
obj = PageState(self.parent, model=model)
obj.file = copy.deepcopy(self.file)
obj.data = copy.deepcopy(self.data)
if self.data is not None:
self.data_name = self.data.name
obj.data_name = self.data_name
obj.is_data = self.is_data
obj.model_list_box = copy.deepcopy(self.model_list_box)
obj.engine_type = copy.deepcopy(self.engine_type)
obj.categorycombobox = self.categorycombobox
obj.formfactorcombobox = self.formfactorcombobox
obj.structurecombobox = self.structurecombobox
#obj.shape_rbutton = self.shape_rbutton
#obj.shape_indep_rbutton = self.shape_indep_rbutton
#obj.struct_rbutton = self.struct_rbutton
#obj.plugin_rbutton = self.plugin_rbutton
obj.manager = self.manager
obj.event_owner = self.event_owner
obj.disp_list = copy.deepcopy(self.disp_list)
obj.enable2D = copy.deepcopy(self.enable2D)
obj.parameters = copy.deepcopy(self.parameters)
obj.str_parameters = copy.deepcopy(self.str_parameters)
obj.fixed_param = copy.deepcopy(self.fixed_param)
obj.fittable_param = copy.deepcopy(self.fittable_param)
obj.orientation_params = copy.deepcopy(self.orientation_params)
obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
obj.enable_disp = copy.deepcopy(self.enable_disp)
obj.disable_disp = copy.deepcopy(self.disable_disp)
obj.tcChi = self.tcChi
if len(self._disp_obj_dict) > 0:
for k, v in self._disp_obj_dict.iteritems():
obj._disp_obj_dict[k] = v
if len(self.disp_cb_dict) > 0:
for k, v in self.disp_cb_dict.iteritems():
obj.disp_cb_dict[k] = v
if len(self.values) > 0:
for k, v in self.values.iteritems():
obj.values[k] = v
if len(self.weights) > 0:
for k, v in self.weights.iteritems():
obj.weights[k] = v
obj.enable_smearer = copy.deepcopy(self.enable_smearer)
obj.disable_smearer = copy.deepcopy(self.disable_smearer)
obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
obj.slit_smearer = copy.deepcopy(self.slit_smearer)
obj.smear_type = copy.deepcopy(self.smear_type)
obj.dI_noweight = copy.deepcopy(self.dI_noweight)
obj.dI_didata = copy.deepcopy(self.dI_didata)
obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
obj.dI_idata = copy.deepcopy(self.dI_idata)
obj.dq_l = copy.deepcopy(self.dq_l)
obj.dq_r = copy.deepcopy(self.dq_r)
obj.dx_max = copy.deepcopy(self.dx_max)
obj.dx_min = copy.deepcopy(self.dx_min)
obj.dxl = copy.deepcopy(self.dxl)
obj.dxw = copy.deepcopy(self.dxw)
obj.disp_box = copy.deepcopy(self.disp_box)
obj.qmin = copy.deepcopy(self.qmin)
obj.qmax = copy.deepcopy(self.qmax)
obj.multi_factor = self.multi_factor
obj.magnetic_on = self.magnetic_on
obj.npts = copy.deepcopy(self.npts)
obj.cb1 = copy.deepcopy(self.cb1)
obj.smearer = copy.deepcopy(self.smearer)
for name, state in self.saved_states.iteritems():
copy_name = copy.deepcopy(name)
copy_state = state.clone()
obj.saved_states[copy_name] = copy_state
return obj
def _repr_helper(self, list, rep):
"""
Helper method to print a state
"""
for item in list:
rep += "parameter name: %s \n" % str(item[1])
rep += "value: %s\n" % str(item[2])
rep += "selected: %s\n" % str(item[0])
rep += "error displayed : %s \n" % str(item[4][0])
rep += "error value:%s \n" % str(item[4][1])
rep += "minimum displayed : %s \n" % str(item[5][0])
rep += "minimum value : %s \n" % str(item[5][1])
rep += "maximum displayed : %s \n" % str(item[6][0])
rep += "maximum value : %s \n" % str(item[6][1])
rep += "parameter unit: %s\n\n" % str(item[7])
return rep
def __repr__(self):
"""
output string for printing
"""
rep = "\nState name: %s\n" % self.file
t = time.localtime(self.timestamp)
time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
rep += "State created: %s\n" % time_str
rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
rep += "is data : %s\n" % self.is_data
rep += "data's name : %s\n" % self.data_name
rep += "data's id : %s\n" % self.data_id
if self.model != None:
m_name = self.model.__class__.__name__
if m_name == 'Model':
m_name = self.m_name
rep += "model name : %s\n" % m_name
else:
rep += "model name : None\n"
#rep += "model type (form factor) selected: %s\n" % self.shape_rbutton
rep += "multi_factor : %s\n" % str(self.multi_factor)
rep += "magnetic_on : %s\n"% str(self.magnetic_on)
rep += "model type (Category) selected: %s\n" % self.categorycombobox
#rep += "model type (shape independent) selected: %s\n" % self.shape_indep_rbutton
#rep += "model type (structure factor) selected: %s\n" % self.struct_rbutton
#rep += "model type (plug-in ) selected: %s\n" % self.plugin_rbutton
rep += "data : %s\n" % str(self.data)
rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
str(self.qmax), str(self.npts))
rep += "Dispersion selection : %s\n" % str(self.disp_box)
rep += "Smearing enable : %s\n" % str(self.enable_smearer)
rep += "Smearing disable : %s\n" % str(self.disable_smearer)
rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
rep += "Dispersity enable : %s\n" % str(self.enable_disp)
rep += "Dispersity disable : %s\n" % str(self.disable_disp)
rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
rep += "dI_noweight : %s\n" % str(self.dI_noweight)
rep += "dI_didata : %s\n" % str(self.dI_didata)
rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
rep += "dI_idata : %s\n" % str(self.dI_idata)
rep += "2D enable : %s\n" % str(self.enable2D)
rep += "All parameters checkbox selected: %s\n" % (self.cb1)
rep += "Value of Chisqr : %s\n" % str(self.tcChi)
rep += "Smear object : %s\n" % str(self.smearer)
rep += "Smear type : %s\n" % (self.smear_type)
rep += "dq_l : %s\n" % self.dq_l
rep += "dq_r : %s\n" % self.dq_r
rep += "dx_max : %s\n" % str(self.dx_max)
rep += "dx_min : %s\n" % str(self.dx_min)
rep += "dxl : %s\n" % str(self.dxl)
rep += "dxw : %s\n" % str(self.dxw)
rep += "model : %s\n\n" % str(self.model)
temp_parameters = []
temp_fittable_param = []
if self.data.__class__.__name__ == "Data2D":
self.is_2D = True
else:
self.is_2D = False
if self.data is not None:
if not self.is_2D:
for item in self.parameters:
if not item in self.orientation_params:
temp_parameters.append(item)
for item in self.fittable_param:
if not item in self.orientation_params_disp:
temp_fittable_param.append(item)
else:
temp_parameters = self.parameters
temp_fittable_param = self.fittable_param
rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
rep = self._repr_helper(list=temp_parameters, rep=rep)
rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
rep = self._repr_helper(list=self.str_parameters, rep=rep)
rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
rep = self._repr_helper(list=temp_fittable_param, rep=rep)
"""
if is_2D:
rep += "number orientation parameters"
rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
rep = self._repr_helper( list=self.orientation_params, rep=rep)
rep += "number dispersity parameters"
rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
"""
return rep
def set_report_string(self):
"""
Get the values (strings) from __str__ for report
"""
# Dictionary of teh report strings
repo_time = ""
model_name = ""
title = ""
title_name = ""
file_name = ""
param_string = ""
paramval_string = ""
chi2_string = ""
multi_factor_string = ""
q_range = ""
strings = self.__repr__()
lines = strings.split('\n')
# get all string values from __str__()
for line in lines:
value = ""
content = line.split(":")
name = content[0]
try:
value = content[1]
except:
pass
if name.count("State created"):
repo_time = "" + value
if name.count("parameter name"):
val_name = value.split(".")
if len(val_name) > 1:
if val_name[1].count("width"):
param_string += value + ','
else:
continue
else:
param_string += value + ','
if name == "value":
param_string += value + ','
if name == "error value":
param_string += value + ','
if name == "parameter unit":
param_string += value + ':'
if name == "Value of Chisqr ":
chi2 = ("Chi2/Npts = " + value)
chi2_string = CENTRE % chi2
if name == "multi_factor ":
muti_factor = ("muti_factor = " + value)
muti_factor_string = CENTRE % muti_factor
if name == "magentic_on ":
magentic_on = ("magentic_on = " + value)
if string(value) == 'True':
magentic_on_string = CENTRE % magentic_on
if name == "Title":
if len(value.strip()) == 0:
continue
title = value + " [" + repo_time + "]"
title_name = HEADER % title
if name == "data ":
try:
file = ("File name:" + content[2])
file_name = CENTRE % file
if len(title) == 0:
title = content[2] + " [" + repo_time + "]"
title_name = HEADER % title
except:
pass
if name == "model name ":
try:
modelname = "Model name:" + content[1]
except:
modelname = "Model name:" + " NAN"
model_name = CENTRE % modelname
if name == "Plotting Range":
try:
q_range = content[1] + " = " + content[2] \
+ " = " + content[3].split(",")[0]
q_name = ("Q Range: " + q_range)
q_range = CENTRE % q_name
except:
pass
paramval = ""
for lines in param_string.split(":"):
line = lines.split(",")
if len(lines) > 0:
param = line[0]
param += " = " + line[1]
if len(line[2].split()) > 0 and not line[2].count("None"):
param += " +- " + line[2]
if len(line[3].split()) > 0 and not line[3].count("None"):
param += " " + line[3]
if not paramval.count(param):
paramval += param + "\n"
paramval_string += CENTRE % param + "\n"
text_string = "\n\n\n" + title + "\n\n" + file + \
"\n" + q_name + \
"\n" + chi2 + \
"\n\n" + paramval
title_name = self._check_html_format(title_name)
file_name = self._check_html_format(file_name)
title = self._check_html_format(title)
html_string = title_name + "\n" + file_name + \
"\n" + model_name + \
"\n" + q_range + \
"\n" + chi2_string + \
"\n" + ELINE + \
"\n" + paramval_string + \
"\n" + ELINE + \
"\n" + FEET_1 % title + \
"\n" + FEET_2
return html_string, text_string, title
def _check_html_format(self, name):
"""
Check string '%' for html format
"""
if name.count('%'):
name = name.replace('%', '%')
return name
def report(self, figs=None, canvases=None):
"""
Invoke report dialog panel
: param figs: list of pylab figures [list]
"""
from sans.perspectives.fitting.report_dialog import ReportDialog
# get the strings for report
html_str, text_str, title = self.set_report_string()
# Allow 2 figures to append
if len(figs) == 1:
add_str = FEET_3
elif len(figs) == 2:
add_str = ELINE
add_str += FEET_2 % ("%s")
add_str += ELINE
add_str += FEET_3
elif len(figs) > 2:
add_str = ELINE
add_str += FEET_2 % ("%s")
add_str += ELINE
add_str += FEET_2 % ("%s")
add_str += ELINE
add_str += FEET_3
else:
add_str = ""
# final report html strings
report_str = html_str % ("%s") + add_str
# make plot image
images = self.set_plot_state(figs, canvases)
report_list = [report_str, text_str, images]
dialog = ReportDialog(report_list, None, -1, "")
dialog.ShowModal()
def _toXML_helper(self, thelist, element, newdoc):
"""
Helper method to create xml file for saving state
"""
for item in thelist:
sub_element = newdoc.createElement('parameter')
sub_element.setAttribute('name', str(item[1]))
sub_element.setAttribute('value', str(item[2]))
sub_element.setAttribute('selected_to_fit', str(item[0]))
sub_element.setAttribute('error_displayed', str(item[4][0]))
sub_element.setAttribute('error_value', str(item[4][1]))
sub_element.setAttribute('minimum_displayed', str(item[5][0]))
sub_element.setAttribute('minimum_value', str(item[5][1]))
sub_element.setAttribute('maximum_displayed', str(item[6][0]))
sub_element.setAttribute('maximum_value', str(item[6][1]))
sub_element.setAttribute('unit', str(item[7]))
element.appendChild(sub_element)
def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
"""
Writes the state of the InversionControl panel to file, as XML.
Compatible with standalone writing, or appending to an
already existing XML document. In that case, the XML document
is required. An optional entry node in the XML document may also be given.
:param file: file to write to
:param doc: XML document object [optional]
:param entry_node: XML node within the XML document at which we will append the data [optional]
"""
from xml.dom.minidom import getDOMImplementation
# Check whether we have to write a standalone XML file
if doc is None:
impl = getDOMImplementation()
doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
top_element = newdoc.documentElement
else:
# We are appending to an existing document
newdoc = doc
try:
top_element = newdoc.createElement(FITTING_NODE_NAME)
except:
string = etree.tostring(doc, pretty_print=True)
newdoc = parseString(string)
top_element = newdoc.createElement(FITTING_NODE_NAME)
if entry_node is None:
newdoc.documentElement.appendChild(top_element)
else:
try:
entry_node.appendChild(top_element)
except:
node_name = entry_node.tag
node_list = newdoc.getElementsByTagName(node_name)
entry_node = node_list.item(0)
entry_node.appendChild(top_element)
attr = newdoc.createAttribute("version")
attr.nodeValue = '1.0'
top_element.setAttributeNode(attr)
# File name
element = newdoc.createElement("filename")
if self.file is not None:
element.appendChild(newdoc.createTextNode(str(self.file)))
else:
element.appendChild(newdoc.createTextNode(str(file)))
top_element.appendChild(element)
element = newdoc.createElement("timestamp")
element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
attr = newdoc.createAttribute("epoch")
attr.nodeValue = str(self.timestamp)
element.setAttributeNode(attr)
top_element.appendChild(element)
# Inputs
inputs = newdoc.createElement("Attributes")
top_element.appendChild(inputs)
if self.data is not None and hasattr(self.data, "group_id"):
self.data_group_id = self.data.group_id
if self.data is not None and hasattr(self.data, "is_data"):
self.is_data = self.data.is_data
if self.data is not None:
self.data_name = self.data.name
if self.data is not None and hasattr(self.data, "id"):
self.data_id = self.data.id
for item in list_of_data_attributes:
element = newdoc.createElement(item[0])
exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
inputs.appendChild(element)
for item in list_of_state_attributes:
element = newdoc.createElement(item[0])
exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
inputs.appendChild(element)
# For self.values ={ disp_param_name: [vals,...],...}
# and for self.weights ={ disp_param_name: [weights,...],...}
list = {}
for item in list_of_model_attributes:
element = newdoc.createElement(item[0])
exec "list = self.%s" % item[1]
for key, value in list.iteritems():
sub_element = newdoc.createElement(key)
sub_element.setAttribute('name', str(key))
for val in value:
com = "sub_element.appendChild"
com += "(newdoc.createTextNode(str(%s)))"
exec com % val
element.appendChild(sub_element)
inputs.appendChild(element)
# Create doc for the dictionary of self._disp_obj_dic
for item in list_of_obj_dic:
element = newdoc.createElement(item[0])
exec "list = self.%s" % item[1]
for key, val in list.iteritems():
value = repr(val)
sub_element = newdoc.createElement(key)
sub_element.setAttribute('name', str(key))
sub_element.setAttribute('value', str(value))
element.appendChild(sub_element)
inputs.appendChild(element)
for item in list_of_state_parameters:
element = newdoc.createElement(item[0])
com = "self._toXML_helper(thelist=self.%s,"
com += " element=element, newdoc=newdoc)"
exec com % item[1]
inputs.appendChild(element)
# Save the file
if doc is None:
fd = open(file, 'w')
fd.write(newdoc.toprettyxml())
fd.close()
return None
else:
return newdoc
def _fromXML_helper(self, node, list):
"""
Helper function to write state to xml
"""
for item in node:
try:
name = item.get('name')
except:
name = None
try:
value = item.get('value')
except:
value = None
try:
selected_to_fit = (item.get('selected_to_fit') == "True")
except:
selected_to_fit = None
try:
error_displayed = (item.get('error_displayed') == "True")
except:
error_displayed = None
try:
error_value = item.get('error_value')
except:
error_value = None
try:
minimum_displayed = (item.get('minimum_displayed') == "True")
except:
minimum_displayed = None
try:
minimum_value = item.get('minimum_value')
except:
minimum_value = None
try:
maximum_displayed = (item.get('maximum_displayed') == "True")
except:
maximum_displayed = None
try:
maximum_value = item.get('maximum_value')
except:
maximum_value = None
try:
unit = item.get('unit')
except:
unit = None
list.append([selected_to_fit, name, value, "+/-",
[error_displayed, error_value],
[minimum_displayed, minimum_value],
[maximum_displayed, maximum_value], unit])
def fromXML(self, file=None, node=None):
"""
Load fitting state from a file
:param file: .fitv file
:param node: node of a XML document to read from
"""
if file is not None:
msg = "PageState no longer supports non-CanSAS"
msg += " format for fitting files"
raise RuntimeError, msg
if node.get('version')and node.get('version') == '1.0':
# Get file name
entry = get_content('ns:filename', node)
if entry is not None:
self.file = entry.text.strip()
# Get time stamp
entry = get_content('ns:timestamp', node)
if entry is not None and entry.get('epoch'):
try:
self.timestamp = float(entry.get('epoch'))
except:
msg = "PageState.fromXML: Could not"
msg += " read timestamp\n %s" % sys.exc_value
logging.error(msg)
# Parse fitting attributes
entry = get_content('ns:Attributes', node)
for item in list_of_data_attributes:
node = get_content('ns:%s' % item[0], entry)
try:
exec "self.%s = parse_entry_helper(node, item)" % item[0]
except:
raise
if entry is not None:
for item in list_of_state_attributes:
node = get_content('ns:%s' % item[0], entry)
try:
exec "self.%s = parse_entry_helper(node, item)" % \
str(item[0])
except:
raise
for item in list_of_state_parameters:
node = get_content("ns:%s" % item[0], entry)
exec "self._fromXML_helper(node=node, list=self.%s)" % \
item[1]
# Recover _disp_obj_dict from xml file
self._disp_obj_dict = {}
disp_model = None
for item in list_of_obj_dic:
# Get node
node = get_content("ns:%s" % item[0], entry)
for attr in node:
name = attr.get('name')
val = attr.get('value')
value = val.split(" instance")[0]
disp_name = value.split("<")[1]
try:
# Try to recover disp_model object from strings
com = "from sans.models.dispersion_models "
com += "import %s as disp"
com_name = disp_name.split(".")[3]
exec com % com_name
disp_model = disp()
exec "self.%s['%s'] = com_name" % (item[1], name)
except:
pass
# get self.values and self.weights dic. if exists
for item in list_of_model_attributes:
node = get_content("ns:%s" % item[0], entry)
dic = {}
list = []
for par in node:
name = par.get('name')
values = par.text.split('\n')
# Get lines only with numbers
for line in values:
try:
val = float(line)
list.append(val)
except:
# pass if line is empty (it happens)
pass
dic[name] = numpy.array(list)
exec "self.%s = dic" % item[1]
def set_plot_state(self, figs, canvases):
"""
Build image state that wx.html understand
by plotting, putting it into wx.FileSystem image object
"""
images = []
# some imports
import wx
# Reset memory
self.imgRAM = None
wx.MemoryFSHandler()
# For no figures in the list, prepare empty plot
if figs == None or len(figs) == 0:
figs = [None]
# Loop over the list of figures
# use wx.MemoryFSHandler
self.imgRAM = wx.MemoryFSHandler()
for fig in figs:
if figs != None:
ind = figs.index(fig)
canvas = canvases[ind]
#store the image in wx.FileSystem Object
wx.FileSystem.AddHandler(wx.MemoryFSHandler())
# index of the fig
ind = figs.index(fig)
#AddFile, image can be retrieved with 'memory:filename'
self.imgRAM.AddFile('img_fit%s.png' % ind,
canvas.bitmap, wx.BITMAP_TYPE_PNG)
#append figs
images.append(fig)
return images
class Reader(CansasReader):
"""
Class to load a .fitv fitting file
"""
## File type
type_name = "Fitting"
## Wildcards
type = ["Fitting files (*.fitv)|*.fitv"
"SANSView file (*.svs)|*.svs"]
## List of allowed extensions
ext = ['.fitv', '.FITV', '.svs', 'SVS']
def __init__(self, call_back=None, cansas=True):
CansasReader.__init__(self)
"""
Initialize the call-back method to be called
after we load a file
:param call_back: call-back method
:param cansas: True = files will be written/read in CanSAS format
False = write CanSAS format
"""
## Call back method to be executed after a file is read
self.call_back = call_back
## CanSAS format flag
self.cansas = cansas
self.state = None
def get_state(self):
return self.state
def read(self, path):
"""
Load a new P(r) inversion state from file
:param path: file path
"""
if self.cansas == True:
return self._read_cansas(path)
def _data2d_to_xml_doc(self, datainfo):
"""
Create an XML document to contain the content of a Data2D
:param datainfo: Data2D object
"""
if not issubclass(datainfo.__class__, Data2D):
raise RuntimeError, "The cansas writer expects a Data2D instance"
doc = xml.dom.minidom.Document()
main_node = doc.createElement("SASroot")
main_node.setAttribute("version", self.version)
main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
doc.appendChild(main_node)
entry_node = doc.createElement("SASentry")
main_node.appendChild(entry_node)
write_node(doc, entry_node, "Title", datainfo.title)
if datainfo is not None:
write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
for item in datainfo.run:
runname = {}
if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
runname = {'name': datainfo.run_name[item] }
write_node(doc, entry_node, "Run", item, runname)
# Data info
new_node = doc.createElement("SASdata")
entry_node.appendChild(new_node)
for item in list_of_data_2d_attr:
element = doc.createElement(item[0])
exec "element.setAttribute(item[0], str(datainfo.%s))" % (item[1])
new_node.appendChild(element)
for item in list_of_data2d_values:
root_node = doc.createElement(item[0])
new_node.appendChild(root_node)
temp_list = None
exec "temp_list = datainfo.%s" % item[1]
if temp_list is None or len(temp_list)== 0:
element = doc.createElement(item[0])
exec "element.appendChild(doc.createTextNode(str(%s)))" % temp_list
root_node.appendChild(element)
else:
for value in temp_list:
element = doc.createElement(item[0])
exec "element.setAttribute(item[0], str(%s))" % value
root_node.appendChild(element)
# Sample info
sample = doc.createElement("SASsample")
if datainfo.sample.name is not None:
sample.setAttribute("name", str(datainfo.sample.name))
entry_node.appendChild(sample)
write_node(doc, sample, "ID", str(datainfo.sample.ID))
write_node(doc, sample, "thickness", datainfo.sample.thickness,
{"unit": datainfo.sample.thickness_unit})
write_node(doc, sample, "transmission", datainfo.sample.transmission)
write_node(doc, sample, "temperature", datainfo.sample.temperature,
{"unit": datainfo.sample.temperature_unit})
for item in datainfo.sample.details:
write_node(doc, sample, "details", item)
pos = doc.createElement("position")
written = write_node(doc, pos, "x", datainfo.sample.position.x,
{"unit": datainfo.sample.position_unit})
written = written | write_node(doc, pos, "y",
datainfo.sample.position.y,
{"unit": datainfo.sample.position_unit})
written = written | write_node(doc, pos, "z",
datainfo.sample.position.z,
{"unit": datainfo.sample.position_unit})
if written == True:
sample.appendChild(pos)
ori = doc.createElement("orientation")
written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
{"unit": datainfo.sample.orientation_unit})
written = written | write_node(doc, ori, "pitch",
datainfo.sample.orientation.y,
{"unit": datainfo.sample.orientation_unit})
written = written | write_node(doc, ori, "yaw",
datainfo.sample.orientation.z,
{"unit": datainfo.sample.orientation_unit})
if written == True:
sample.appendChild(ori)
# Instrument info
instr = doc.createElement("SASinstrument")
entry_node.appendChild(instr)
write_node(doc, instr, "name", datainfo.instrument)
# Source
source = doc.createElement("SASsource")
if datainfo.source.name is not None:
source.setAttribute("name", str(datainfo.source.name))
instr.appendChild(source)
write_node(doc, source, "radiation", datainfo.source.radiation)
write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
size = doc.createElement("beam_size")
if datainfo.source.beam_size_name is not None:
size.setAttribute("name", str(datainfo.source.beam_size_name))
written = write_node(doc, size, "x", datainfo.source.beam_size.x,
{"unit": datainfo.source.beam_size_unit})
written = written | write_node(doc, size, "y",
datainfo.source.beam_size.y,
{"unit": datainfo.source.beam_size_unit})
written = written | write_node(doc, size, "z",
datainfo.source.beam_size.z,
{"unit": datainfo.source.beam_size_unit})
if written == True:
source.appendChild(size)
write_node(doc, source, "wavelength", datainfo.source.wavelength,
{"unit": datainfo.source.wavelength_unit})
write_node(doc, source, "wavelength_min",
datainfo.source.wavelength_min,
{"unit": datainfo.source.wavelength_min_unit})
write_node(doc, source, "wavelength_max",
datainfo.source.wavelength_max,
{"unit": datainfo.source.wavelength_max_unit})
write_node(doc, source, "wavelength_spread",
datainfo.source.wavelength_spread,
{"unit": datainfo.source.wavelength_spread_unit})
# Collimation
for item in datainfo.collimation:
coll = doc.createElement("SAScollimation")
if item.name is not None:
coll.setAttribute("name", str(item.name))
instr.appendChild(coll)
write_node(doc, coll, "length", item.length,
{"unit": item.length_unit})
for apert in item.aperture:
ap = doc.createElement("aperture")
if apert.name is not None:
ap.setAttribute("name", str(apert.name))
if apert.type is not None:
ap.setAttribute("type", str(apert.type))
coll.appendChild(ap)
write_node(doc, ap, "distance", apert.distance,
{"unit": apert.distance_unit})
size = doc.createElement("size")
if apert.size_name is not None:
size.setAttribute("name", str(apert.size_name))
written = write_node(doc, size, "x", apert.size.x,
{"unit": apert.size_unit})
written = written | write_node(doc, size, "y", apert.size.y,
{"unit": apert.size_unit})
written = written | write_node(doc, size, "z", apert.size.z,
{"unit": apert.size_unit})
if written == True:
ap.appendChild(size)
# Detectors
for item in datainfo.detector:
det = doc.createElement("SASdetector")
written = write_node(doc, det, "name", item.name)
written = written | write_node(doc, det, "SDD", item.distance,
{"unit": item.distance_unit})
written = written | write_node(doc, det, "slit_length",
item.slit_length,
{"unit": item.slit_length_unit})
if written == True:
instr.appendChild(det)
off = doc.createElement("offset")
written = write_node(doc, off, "x", item.offset.x,
{"unit": item.offset_unit})
written = written | write_node(doc, off, "y", item.offset.y,
{"unit": item.offset_unit})
written = written | write_node(doc, off, "z", item.offset.z,
{"unit": item.offset_unit})
if written == True:
det.appendChild(off)
center = doc.createElement("beam_center")
written = write_node(doc, center, "x", item.beam_center.x,
{"unit": item.beam_center_unit})
written = written | write_node(doc, center, "y",
item.beam_center.y,
{"unit": item.beam_center_unit})
written = written | write_node(doc, center, "z",
item.beam_center.z,
{"unit": item.beam_center_unit})
if written == True:
det.appendChild(center)
pix = doc.createElement("pixel_size")
written = write_node(doc, pix, "x", item.pixel_size.x,
{"unit": item.pixel_size_unit})
written = written | write_node(doc, pix, "y", item.pixel_size.y,
{"unit": item.pixel_size_unit})
written = written | write_node(doc, pix, "z", item.pixel_size.z,
{"unit": item.pixel_size_unit})
if written == True:
det.appendChild(pix)
ori = doc.createElement("orientation")
written = write_node(doc, ori, "roll", item.orientation.x,
{"unit": item.orientation_unit})
written = written | write_node(doc, ori, "pitch",
item.orientation.y,
{"unit": item.orientation_unit})
written = written | write_node(doc, ori, "yaw", item.orientation.z,
{"unit": item.orientation_unit})
if written == True:
det.appendChild(ori)
# Processes info
for item in datainfo.process:
node = doc.createElement("SASprocess")
entry_node.appendChild(node)
write_node(doc, node, "name", item.name)
write_node(doc, node, "date", item.date)
write_node(doc, node, "description", item.description)
for term in item.term:
value = term['value']
del term['value']
write_node(doc, node, "term", value, term)
for note in item.notes:
write_node(doc, node, "SASprocessnote", note)
# Return the document, and the SASentry node associated with
# the data we just wrote
return doc, entry_node
def _parse_state(self, entry):
"""
Read a fit result from an XML node
:param entry: XML node to read from
:return: PageState object
"""
# Create an empty state
state = None
# Locate the P(r) node
try:
nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
namespaces={'ns': CANSAS_NS})
if nodes != []:
# Create an empty state
state = PageState()
state.fromXML(node=nodes[0])
except:
logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
return state
def _parse_save_state_entry(self, dom):
"""
Parse a SASentry
:param node: SASentry node
:return: Data1D/Data2D object
"""
node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
if not node or node[0].text.lstrip().rstrip() != "Data2D":
return_value, _ = self._parse_entry(dom)
numpy.trim_zeros(return_value.x)
numpy.trim_zeros(return_value.y)
numpy.trim_zeros(return_value.dy)
size_dx = return_value.dx.size
size_dxl = return_value.dxl.size
size_dxw = return_value.dxw.size
if size_dxl == 0 and size_dxw == 0:
return_value.dxl = None
return_value.dxw = None
numpy.trim_zeros(return_value.dx)
elif size_dx == 0:
return_value.dx = None
size_dx = size_dxl
numpy.trim_zeros(return_value.dxl)
numpy.trim_zeros(return_value.dxw)
return return_value, _
#Parse 2D
data_info = Data2D()
# Look up title
self._store_content('ns:Title', dom, 'title', data_info)
# Look up run number
nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
for item in nodes:
if item.text is not None:
value = item.text.strip()
if len(value) > 0:
data_info.run.append(value)
if item.get('name') is not None:
data_info.run_name[value] = item.get('name')
# Look up instrument name
self._store_content('ns:SASinstrument/ns:name', dom,
'instrument', data_info)
# Notes
note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
for note in note_list:
try:
if note.text is not None:
note_value = note.text.strip()
if len(note_value) > 0:
data_info.notes.append(note_value)
except:
err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
self.errors.append(err_mess)
logging.error(err_mess)
# Sample info ###################
entry = get_content('ns:SASsample', dom)
if entry is not None:
data_info.sample.name = entry.get('name')
self._store_content('ns:SASsample/ns:ID',
dom, 'ID', data_info.sample)
self._store_float('ns:SASsample/ns:thickness',
dom, 'thickness', data_info.sample)
self._store_float('ns:SASsample/ns:transmission',
dom, 'transmission', data_info.sample)
self._store_float('ns:SASsample/ns:temperature',
dom, 'temperature', data_info.sample)
nodes = dom.xpath('ns:SASsample/ns:details',
namespaces={'ns': CANSAS_NS})
for item in nodes:
try:
if item.text is not None:
detail_value = item.text.strip()
if len(detail_value) > 0:
data_info.sample.details.append(detail_value)
except:
err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
self.errors.append(err_mess)
logging.error(err_mess)
# Position (as a vector)
self._store_float('ns:SASsample/ns:position/ns:x',
dom, 'position.x', data_info.sample)
self._store_float('ns:SASsample/ns:position/ns:y',
dom, 'position.y', data_info.sample)
self._store_float('ns:SASsample/ns:position/ns:z',
dom, 'position.z', data_info.sample)
# Orientation (as a vector)
self._store_float('ns:SASsample/ns:orientation/ns:roll',
dom, 'orientation.x', data_info.sample)
self._store_float('ns:SASsample/ns:orientation/ns:pitch',
dom, 'orientation.y', data_info.sample)
self._store_float('ns:SASsample/ns:orientation/ns:yaw',
dom, 'orientation.z', data_info.sample)
# Source info ###################
entry = get_content('ns:SASinstrument/ns:SASsource', dom)
if entry is not None:
data_info.source.name = entry.get('name')
self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
dom, 'radiation', data_info.source)
self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
dom, 'beam_shape', data_info.source)
self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
dom, 'wavelength', data_info.source)
self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
dom, 'wavelength_min', data_info.source)
self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
dom, 'wavelength_max', data_info.source)
self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
dom, 'wavelength_spread', data_info.source)
# Beam size (as a vector)
entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
if entry is not None:
data_info.source.beam_size_name = entry.get('name')
self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
dom, 'beam_size.x', data_info.source)
self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
dom, 'beam_size.y', data_info.source)
self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
dom, 'beam_size.z', data_info.source)
# Collimation info ###################
nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
namespaces={'ns': CANSAS_NS})
for item in nodes:
collim = Collimation()
if item.get('name') is not None:
collim.name = item.get('name')
self._store_float('ns:length', item, 'length', collim)
# Look for apertures
apert_list = item.xpath('ns:aperture',
namespaces={'ns': CANSAS_NS})
for apert in apert_list:
aperture = Aperture()
# Get the name and type of the aperture
aperture.name = apert.get('name')
aperture.type = apert.get('type')
self._store_float('ns:distance', apert, 'distance', aperture)
entry = get_content('ns:size', apert)
if entry is not None:
aperture.size_name = entry.get('name')
self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
collim.aperture.append(aperture)
data_info.collimation.append(collim)
# Detector info ######################
nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
namespaces={'ns': CANSAS_NS})
for item in nodes:
detector = Detector()
self._store_content('ns:name', item, 'name', detector)
self._store_float('ns:SDD', item, 'distance', detector)
# Detector offset (as a vector)
self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
# Detector orientation (as a vector)
self._store_float('ns:orientation/ns:roll', item,
'orientation.x', detector)
self._store_float('ns:orientation/ns:pitch', item,
'orientation.y', detector)
self._store_float('ns:orientation/ns:yaw', item,
'orientation.z', detector)
# Beam center (as a vector)
self._store_float('ns:beam_center/ns:x', item,
'beam_center.x', detector)
self._store_float('ns:beam_center/ns:y', item,
'beam_center.y', detector)
self._store_float('ns:beam_center/ns:z', item,
'beam_center.z', detector)
# Pixel size (as a vector)
self._store_float('ns:pixel_size/ns:x', item,
'pixel_size.x', detector)
self._store_float('ns:pixel_size/ns:y', item,
'pixel_size.y', detector)
self._store_float('ns:pixel_size/ns:z', item,
'pixel_size.z', detector)
self._store_float('ns:slit_length', item, 'slit_length', detector)
data_info.detector.append(detector)
# Processes info ######################
nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
for item in nodes:
process = Process()
self._store_content('ns:name', item, 'name', process)
self._store_content('ns:date', item, 'date', process)
self._store_content('ns:description', item, 'description', process)
term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
for term in term_list:
try:
term_attr = {}
for attr in term.keys():
term_attr[attr] = term.get(attr).strip()
if term.text is not None:
term_attr['value'] = term.text.strip()
process.term.append(term_attr)
except:
err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
self.errors.append(err_mess)
logging.error(err_mess)
note_list = item.xpath('ns:SASprocessnote',
namespaces={'ns': CANSAS_NS})
for note in note_list:
if note.text is not None:
process.notes.append(note.text.strip())
data_info.process.append(process)
# Data info ######################
nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
if len(nodes) > 1:
raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
for entry in nodes:
for item in list_of_data_2d_attr:
#get node
node = get_content('ns:%s' % item[0], entry)
exec "data_info.%s = parse_entry_helper(node, item)" % item[1]
for item in list_of_data2d_values:
field = get_content('ns:%s' % item[0], entry)
list = []
if field is not None:
list = [parse_entry_helper(node, item) for node in field]
if len(list) < 2:
exec "data_info.%s = None" % item[0]
else:
exec "data_info.%s = numpy.array(list)" % item[0]
return data_info
def _read_cansas(self, path):
"""
Load data and P(r) information from a CanSAS XML file.
:param path: file path
:return: Data1D object if a single SASentry was found,
or a list of Data1D objects if multiple entries were found,
or None of nothing was found
:raise RuntimeError: when the file can't be opened
:raise ValueError: when the length of the data vectors are inconsistent
"""
output = []
basename = os.path.basename(path)
root, extension = os.path.splitext(basename)
ext = extension.lower()
try:
if os.path.isfile(path):
#TODO: eventually remove the check for .xml once
# the P(r) writer/reader is truly complete.
if ext in self.ext or \
ext == '.xml':
tree = etree.parse(path, parser=etree.ETCompatXMLParser())
# Check the format version number
# Specifying the namespace will take care of the file format version
root = tree.getroot()
entry_list = root.xpath('ns:SASentry',
namespaces={'ns': CANSAS_NS})
for entry in entry_list:
try:
sas_entry, _ = self._parse_save_state_entry(entry)
except:
raise
fitstate = self._parse_state(entry)
#state could be None when .svs file is loaded
#in this case, skip appending to output
if fitstate != None:
sas_entry.meta_data['fitstate'] = fitstate
sas_entry.filename = fitstate.file
output.append(sas_entry)
else:
self.call_back(format=ext)
raise RuntimeError, "%s is not a file" % path
# Return output consistent with the loader's api
if len(output) == 0:
self.call_back(state=None, datainfo=None, format=ext)
return None
else:
for ind in range(len(output)):
# Call back to post the new state
state = output[ind].meta_data['fitstate']
t = time.localtime(state.timestamp)
time_str = time.strftime("%b %d %H:%M", t)
# Check that no time stamp is already appended
max_char = state.file.find("[")
if max_char < 0:
max_char = len(state.file)
original_fname = state.file[0:max_char]
state.file = original_fname + ' [' + time_str + ']'
if state is not None and state.is_data is not None:
exec 'output[%d].is_data = state.is_data' % ind
output[ind].filename = state.file
state.data = output[ind]
state.data.name = output[ind].filename # state.data_name
state.data.id = state.data_id
if state.is_data is not None:
state.data.is_data = state.is_data
if output[ind].run_name is not None\
and len(output[ind].run_name) != 0:
name = output[ind].run_name
else:
name = original_fname
state.data.group_id = name
#store state in fitting
self.call_back(state=state,
datainfo=output[ind], format=ext)
self.state = state
return output
except:
self.call_back(format=ext)
#self.state= state
raise
def write(self, filename, datainfo=None, fitstate=None):
"""
Write the content of a Data1D as a CanSAS XML file only for standalone
:param filename: name of the file to write
:param datainfo: Data1D object
:param fitstate: PageState object
"""
# Sanity check
if self.cansas == True:
# Add fitting information to the XML document
doc = self.write_toXML(datainfo, fitstate)
# Write the XML document
else:
doc = fitstate.toXML(file=filename)
# Save the document no matter the type
fd = open(filename, 'w')
fd.write(doc.toprettyxml())
fd.close()
def write_toXML(self, datainfo=None, state=None):
"""
Write toXML, a helper for write(),
could be used by guimanager._on_save()
: return: xml doc
"""
if state.data is None:
data = sans.dataloader.data_info.Data1D(x=[], y=[])
return None
elif not state.data.is_data:
return None
else:
#make sure title and data run is filled up.
if state.data.title == None or state.data.title == '':
state.data.title = state.data.name
if state.data.run_name == None or state.data.run_name == {}:
state.data.run = [str(state.data.name)]
state.data.run_name[0] = state.data.name
if issubclass(state.data.__class__,
sans.dataloader.data_info.Data1D):
data = state.data
doc, sasentry = self._to_xml_doc(data)
else:
data = state.data
doc, sasentry = self._data2d_to_xml_doc(data)
if state is not None:
doc = state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
return doc
# Simple html report templet
HEADER = "\n"
HEADER += "\n"
HEADER += " \n"
HEADER += "\n"
HEADER += "\n"
HEADER += "\n"
HEADER += "\n"
HEADER += "
"
HEADER += "%s
"
HEADER += "
"
PARA = "
%s \n"
PARA += "
"
CENTRE = "
%s \n"
CENTRE += ""
FEET_1 = \
"""
Graph
Model Computation
Data: "%s"
"""
FEET_2 = \
"""
"""
FEET_3 = \
"""
"
if __name__ == "__main__":
state = PageState(parent=None)
#state.toXML()
"""
file = open("test_state", "w")
pickle.dump(state, file)
print pickle.dumps(state)
state.data_name = "hello---->"
pickle.dump(state, file)
file = open("test_state", "r")
new_state= pickle.load(file)
print "new state", new_state
new_state= pickle.load(file)
print "new state", new_state
#print "state", state
"""
import bsddb
import pickle
db = bsddb.btopen('file_state.db', 'c')
val = (pickle.dumps(state), "hello", "hi")
db['state1'] = pickle.dumps(val)
print pickle.loads(db['state1'])
state.data_name = "hello---->22"
db['state2'] = pickle.dumps(state)
state.data_name = "hello---->2"
db['state3'] = pickle.dumps(state)
del db['state3']
state.data_name = "hello---->3"
db['state4'] = pickle.dumps(state)
new_state = pickle.loads(db['state1'])
#print db.last()
db.set_location('state2')
state.data_name = "hello---->5"
db['aastate5'] = pickle.dumps(state)
db.keys().sort()
print pickle.loads(db['state2'])
db.close()