1 | |
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2 | |
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3 | ################################################################################ |
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4 | #This software was developed by the University of Tennessee as part of the |
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5 | #Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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6 | #project funded by the US National Science Foundation. |
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7 | # |
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8 | #See the license text in license.txt |
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9 | # |
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10 | #copyright 2009, University of Tennessee |
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11 | ################################################################################ |
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12 | |
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13 | import time |
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14 | import os |
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15 | import sys |
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16 | import copy |
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17 | import logging |
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18 | import numpy |
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19 | |
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20 | import xml.dom.minidom |
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21 | from xml.dom.minidom import parse |
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22 | from lxml import etree |
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23 | |
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24 | import DataLoader |
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25 | from DataLoader.readers.cansas_reader import Reader as CansasReader |
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26 | from DataLoader.readers.cansas_reader import get_content, write_node |
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27 | from DataLoader.data_info import Data2D, Detector |
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28 | |
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29 | #Information to read/write state as xml |
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30 | FITTING_NODE_NAME = 'fitting_plug_in' |
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31 | CANSAS_NS = "cansas1d/1.0" |
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32 | |
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33 | list_of_data_attributes = [["is_data", "is_data", "bool"], |
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34 | ["group_id", "data_group_id", "string"], |
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35 | ["data_name", "data_name", "string"], |
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36 | ["data_id", "data_id", "string"], |
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37 | ["name", "name", "string"], |
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38 | ["data_name", "data_name", "string"]] |
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39 | list_of_state_attributes = [["engine_type", "engine_type", "string"], |
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40 | ["qmin", "qmin", "float"], |
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41 | ["qmax", "qmax", "float"], |
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42 | ["npts", "npts", "float"], |
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43 | ["shape_rbutton", "shape_rbutton", "bool"], |
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44 | ["shape_indep_rbutton", "shape_indep_rbutton", "bool"], |
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45 | ["plugin_rbutton", "plugin_rbutton","bool"], |
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46 | ["struct_rbutton", "struct_rbutton", "bool"], |
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47 | ["formfactorcombobox", "formfactorcombobox", "float"], |
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48 | ["structurecombobox", "structurecombobox", "float"], |
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49 | ["disp_box", "disp_box", "float"], |
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50 | ["enable_smearer","enable_smearer","bool"], |
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51 | ["disable_smearer","disable_smearer","bool"], |
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52 | ["pinhole_smearer","pinhole_smearer","bool"], |
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53 | ["slit_smearer","slit_smearer","bool"], |
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54 | ["enable_disp","enable_disp","bool"], |
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55 | ["disable_disp","disable_disp","bool"], |
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56 | ["slit_smearer","slit_smearer","bool"], |
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57 | ["enable2D","enable2D","bool"], |
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58 | ["cb1","cb1","bool"], |
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59 | ["tcChi","tcChi","float"], |
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60 | ["smearer", "smearer", "float"], |
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61 | ["smear_type","smear_type", "string"], |
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62 | ["dq_l", "dq_l", "string"], |
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63 | ["dq_r","dq_r", "string"]] |
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64 | |
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65 | list_of_model_attributes = [["values", "values"], |
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66 | ["weights", "weights"]] |
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67 | |
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68 | list_of_state_parameters = [["parameters", "parameters"] , |
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69 | ["str_parameters", "str_parameters"] , |
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70 | ["orientation_parameters", "orientation_params"], |
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71 | ["dispersity_parameters", "orientation_params_disp"], |
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72 | ["fixed_param", "fixed_param"], |
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73 | ["fittable_param","fittable_param"]] |
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74 | list_of_data_2d_attr = [["xmin", "xmin","float"], |
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75 | ["xmax","xmax","float"], |
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76 | ["ymin","ymin","float"], |
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77 | ["ymax","ymax","float"], |
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78 | ["_xaxis","_xaxis", "string"], |
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79 | ["_xunit", "_xunit", "string"], |
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80 | ["_yaxis","_yaxis","string"], |
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81 | ["_yunit","_yunit","string"], |
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82 | ["_zaxis","_zaxis","string"], |
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83 | ["_zunit","_zunit","string"]] |
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84 | list_of_data2d_values = [["qx_data","qx_data","float"], |
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85 | ["qy_data","qy_data","float"], |
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86 | ["dqx_data","dqx_data","float"], |
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87 | ["dqy_data","dqy_data","float"], |
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88 | ["data","data","float"], |
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89 | ["q_data","q_data","float"], |
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90 | ["err_data","err_data","float"], |
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91 | ["mask","mask","bool"]] |
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92 | |
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93 | def parse_entry_helper( node, item): |
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94 | """ |
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95 | Create a numpy list from value extrated from the node |
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96 | |
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97 | :param node: node from each the value is stored |
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98 | :param item: list name of three strings.the two first are name of data |
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99 | attribute and the third one is the type of the value of that |
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100 | attribute. type can be string, float, bool, etc. |
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101 | |
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102 | : return: numpy array |
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103 | """ |
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104 | if node is not None: |
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105 | if item[2] == "string": |
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106 | return str(node.get(item[0]).strip()) |
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107 | elif item[2] == "bool": |
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108 | try: |
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109 | return node.get(item[0]).strip() == "True" |
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110 | |
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111 | except: |
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112 | return None |
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113 | else: |
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114 | try: |
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115 | return float(node.get(item[0])) |
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116 | except: |
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117 | return None |
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118 | |
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119 | |
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120 | class PageState(object): |
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121 | """ |
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122 | Contains information to reconstruct a page of the fitpanel. |
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123 | """ |
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124 | def __init__(self, parent=None, model=None, data=None): |
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125 | |
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126 | """ |
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127 | Initialize the current state |
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128 | |
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129 | :param model: a selected model within a page |
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130 | :param data: |
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131 | |
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132 | """ |
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133 | self.file = None |
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134 | #Time of state creation |
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135 | self.timestamp = time.time() |
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136 | ## Data member to store the dispersion object created |
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137 | self._disp_obj_dict = {} |
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138 | #------------------------ |
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139 | #Data used for fitting |
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140 | self.data = data |
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141 | #save additional information on data that dataloader.reader does not read |
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142 | self.is_data = None |
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143 | self.data_name = "" |
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144 | |
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145 | if self.data is not None: |
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146 | self.data_name = self.data.name |
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147 | self.data_id = None |
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148 | if self.data is not None and hasattr(self.data, "id"): |
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149 | self.data_id = self.data.id |
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150 | self.data_group_id = None |
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151 | if self.data is not None and hasattr(self.data, "group_id"): |
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152 | self.data_group_id = self.data.group_id |
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153 | |
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154 | ## reset True change the state of exsiting button |
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155 | self.reset = False |
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156 | |
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157 | #engine type |
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158 | self.engine_type = None |
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159 | # flag to allow data2D plot |
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160 | self.enable2D = False |
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161 | # model on which the fit would be performed |
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162 | self.model = model |
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163 | |
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164 | #fit page manager |
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165 | self.manager = None |
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166 | #Store the parent of this panel parent |
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167 | # For this application fitpanel is the parent |
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168 | self.parent = parent |
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169 | # Event_owner is the owner of model event |
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170 | self.event_owner = None |
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171 | ##page name |
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172 | self.page_name = "" |
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173 | # Contains link between model ,all its parameters, and panel organization |
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174 | self.parameters = [] |
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175 | # String parameter list that can not be fitted |
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176 | self.str_parameters = [] |
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177 | # Contains list of parameters that cannot be fitted and reference to |
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178 | #panel objects |
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179 | self.fixed_param = [] |
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180 | # Contains list of parameters with dispersity and reference to |
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181 | #panel objects |
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182 | self.fittable_param = [] |
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183 | ## orientation parameters |
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184 | self.orientation_params = [] |
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185 | ## orientation parmaters for gaussian dispersity |
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186 | self.orientation_params_disp = [] |
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187 | ## smearer info |
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188 | self.smearer = None |
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189 | self.smear_type = None |
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190 | self.dq_l = None |
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191 | self.dq_r = None |
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192 | |
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193 | #list of dispersion paramaters |
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194 | self.disp_list =[] |
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195 | if self.model is not None: |
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196 | self.disp_list = self.model.getDispParamList() |
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197 | self._disp_obj_dict = {} |
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198 | self.disp_cb_dict = {} |
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199 | self.values = [] |
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200 | self.weights = [] |
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201 | |
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202 | #contains link between a model and selected parameters to fit |
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203 | self.param_toFit = [] |
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204 | ##dictionary of model type and model class |
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205 | self.model_list_box = None |
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206 | ## save the state of the context menu |
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207 | self.saved_states = {} |
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208 | ## save selection of combobox |
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209 | self.formfactorcombobox = None |
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210 | self.structurecombobox = None |
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211 | ## radio box to select type of model |
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212 | self.shape_rbutton = False |
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213 | self.shape_indep_rbutton = False |
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214 | self.struct_rbutton = False |
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215 | self.plugin_rbutton = False |
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216 | ## the indice of the current selection |
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217 | self.disp_box = 0 |
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218 | ## Qrange |
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219 | ## Q range |
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220 | self.qmin = 0.001 |
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221 | self.qmax = 0.1 |
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222 | #reset data range |
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223 | self.qmax_x = None |
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224 | self.qmin_x = None |
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225 | |
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226 | self.npts = None |
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227 | self.name = "" |
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228 | self.multi_factor = None |
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229 | ## enable smearering state |
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230 | self.enable_smearer = False |
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231 | self.disable_smearer = True |
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232 | self.pinhole_smearer = False |
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233 | self.slit_smearer = False |
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234 | ## disperity selection |
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235 | self.enable_disp = False |
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236 | self.disable_disp = True |
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237 | |
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238 | ## state of selected all check button |
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239 | self.cb1 = False |
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240 | ## store value of chisqr |
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241 | self.tcChi = None |
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242 | |
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243 | def clone(self): |
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244 | """ |
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245 | Create a new copy of the current object |
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246 | """ |
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247 | model = None |
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248 | if self.model is not None: |
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249 | model = self.model.clone() |
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250 | model.name = self.model.name |
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251 | obj = PageState(self.parent, model=model) |
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252 | obj.file = copy.deepcopy(self.file) |
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253 | obj.data = copy.deepcopy(self.data) |
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254 | if self.data is not None: |
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255 | self.data_name = self.data.name |
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256 | obj.data_name = self.data_name |
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257 | obj.is_data = self.is_data |
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258 | obj.model_list_box = copy.deepcopy(self.model_list_box) |
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259 | obj.engine_type = copy.deepcopy(self.engine_type) |
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260 | |
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261 | obj.formfactorcombobox = self.formfactorcombobox |
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262 | obj.structurecombobox = self.structurecombobox |
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263 | |
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264 | obj.shape_rbutton = self.shape_rbutton |
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265 | obj.shape_indep_rbutton = self.shape_indep_rbutton |
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266 | obj.struct_rbutton = self.struct_rbutton |
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267 | obj.plugin_rbutton = self.plugin_rbutton |
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268 | |
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269 | obj.manager = self.manager |
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270 | obj.event_owner = self.event_owner |
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271 | obj.disp_list = copy.deepcopy(self.disp_list) |
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272 | |
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273 | obj.enable2D = copy.deepcopy(self.enable2D) |
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274 | obj.parameters = copy.deepcopy(self.parameters) |
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275 | obj.str_parameters = copy.deepcopy(self.str_parameters) |
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276 | obj.fixed_param = copy.deepcopy(self.fixed_param) |
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277 | obj.fittable_param = copy.deepcopy(self.fittable_param) |
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278 | obj.orientation_params = copy.deepcopy(self.orientation_params) |
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279 | obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp) |
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280 | obj.enable_disp = copy.deepcopy(self.enable_disp) |
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281 | obj.disable_disp = copy.deepcopy(self.disable_disp) |
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282 | obj.tcChi = self.tcChi |
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283 | |
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284 | if len(self._disp_obj_dict)>0: |
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285 | for k , v in self._disp_obj_dict.iteritems(): |
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286 | obj._disp_obj_dict[k]= v |
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287 | if len(self.disp_cb_dict)>0: |
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288 | for k , v in self.disp_cb_dict.iteritems(): |
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289 | obj.disp_cb_dict[k]= v |
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290 | |
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291 | obj.values = copy.deepcopy(self.values) |
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292 | obj.weights = copy.deepcopy(self.weights) |
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293 | obj.enable_smearer = copy.deepcopy(self.enable_smearer) |
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294 | obj.disable_smearer = copy.deepcopy(self.disable_smearer) |
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295 | obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer) |
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296 | obj.slit_smearer = copy.deepcopy(self.slit_smearer) |
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297 | obj.smear_type = copy.deepcopy(self.smear_type) |
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298 | obj.dq_l = copy.deepcopy(self.dq_l) |
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299 | obj.dq_r = copy.deepcopy(self.dq_r) |
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300 | |
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301 | obj.disp_box = copy.deepcopy(self.disp_box) |
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302 | obj.qmin = copy.deepcopy(self.qmin) |
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303 | obj.qmax = copy.deepcopy(self.qmax) |
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304 | obj.multi_factor = copy.deepcopy(self.multi_factor) |
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305 | obj.npts = copy.deepcopy(self.npts ) |
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306 | obj.cb1 = copy.deepcopy(self.cb1) |
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307 | obj.smearer = copy.deepcopy(self.smearer) |
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308 | |
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309 | for name, state in self.saved_states.iteritems(): |
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310 | copy_name = copy.deepcopy(name) |
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311 | copy_state = state.clone() |
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312 | obj.saved_states[copy_name]= copy_state |
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313 | return obj |
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314 | |
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315 | def _repr_helper(self, list, rep): |
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316 | """ |
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317 | Helper method to print a state |
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318 | """ |
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319 | for item in list: |
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320 | rep += "parameter name: %s \n"%str(item[1]) |
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321 | rep += "value: %s\n"%str(item[2]) |
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322 | rep += "selected: %s\n"%str(item[0]) |
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323 | rep += "error displayed : %s \n"%str(item[4][0]) |
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324 | rep += "error value:%s \n"%str(item[4][1]) |
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325 | rep += "minimum displayed : %s \n"%str(item[5][0]) |
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326 | rep += "minimum value : %s \n"%str(item[5][1]) |
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327 | rep += "maximum displayed : %s \n"%str(item[6][0]) |
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328 | rep += "maximum value : %s \n"%str(item[6][1]) |
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329 | rep += "parameter unit: %s\n\n"%str(item[7]) |
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330 | return rep |
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331 | |
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332 | def __repr__(self): |
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333 | """ |
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334 | output string for printing |
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335 | """ |
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336 | rep = "\nState name: %s\n"%self.file |
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337 | t = time.localtime(self.timestamp) |
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338 | time_str = time.strftime("%b %d %H:%M", t) |
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339 | rep += "State created on : %s\n"%time_str |
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340 | rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox |
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341 | rep += "State structure factor combobox selection: %s\n"%self.structurecombobox |
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342 | rep += "is data : %s\n"%self.is_data |
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343 | rep += "data's name : %s\n"%self.data_name |
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344 | rep += "data's id : %s\n"%self.data_id |
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345 | rep += "model type (form factor) selected: %s\n"%self.shape_rbutton |
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346 | rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton |
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347 | rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton |
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348 | rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton |
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349 | rep += "data : %s\n"% str(self.data) |
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350 | rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin), |
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351 | str(self.qmax),str(self.npts)) |
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352 | rep += "Dispersion selection : %s\n"%str(self.disp_box) |
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353 | rep += "Smearing enable : %s\n"%str(self.enable_smearer) |
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354 | rep += "Smearing disable : %s\n"%str(self.disable_smearer) |
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355 | rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer) |
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356 | rep += "Slit smearer enable : %s\n"%str(self.slit_smearer) |
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357 | rep += "Dispersity enable : %s\n"%str(self.enable_disp) |
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358 | rep += "Dispersity disable : %s\n"%str(self.disable_disp) |
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359 | rep += "Slit smearer enable: %s\n"%str(self.slit_smearer) |
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360 | rep += "2D enable : %s\n"%str(self.enable2D) |
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361 | rep += "All parameters checkbox selected: %s\n"%(self.cb1) |
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362 | rep += "Value of Chisqr : %s\n"%str(self.tcChi) |
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363 | rep += "Smear object : %s\n"%str(self.smearer) |
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364 | rep += "Smear type : %s\n"%(self.smear_type) |
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365 | rep += "dq_l : %s\n"%self.dq_l |
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366 | rep += "dq_r : %s\n"%self.dq_r |
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367 | |
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368 | rep += "model : %s\n\n"% str(self.model) |
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369 | rep += "number parameters(self.parameters): %s\n"%len(self.parameters) |
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370 | rep = self._repr_helper( list=self.parameters, rep=rep) |
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371 | rep += "number str_parameters(self.str_parameters): %s\n"%len(self.str_parameters) |
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372 | rep = self._repr_helper( list=self.str_parameters, rep=rep) |
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373 | rep += "number orientation parameters" |
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374 | rep += "(self.orientation_params): %s\n"%len(self.orientation_params) |
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375 | rep = self._repr_helper( list=self.orientation_params, rep=rep) |
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376 | rep += "number dispersity parameters" |
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377 | rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp) |
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378 | rep = self._repr_helper( list=self.orientation_params_disp, rep=rep) |
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379 | |
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380 | return rep |
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381 | |
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382 | def _toXML_helper(self, list, element, newdoc): |
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383 | """ |
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384 | Helper method to create xml file for saving state |
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385 | """ |
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386 | for item in list: |
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387 | sub_element = newdoc.createElement('parameter') |
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388 | sub_element.setAttribute('name', str(item[1])) |
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389 | sub_element.setAttribute('value', str(item[2])) |
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390 | sub_element.setAttribute('selected_to_fit', str(item[0])) |
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391 | sub_element.setAttribute('error_displayed', str(item[4][0])) |
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392 | sub_element.setAttribute('error_value', str(item[4][1])) |
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393 | sub_element.setAttribute('minimum_displayed', str(item[5][0])) |
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394 | sub_element.setAttribute('minimum_value', str(item[5][1])) |
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395 | sub_element.setAttribute('maximum_displayed', str(item[6][0])) |
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396 | sub_element.setAttribute('maximum_value', str(item[6][1])) |
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397 | sub_element.setAttribute('unit', str(item[7])) |
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398 | element.appendChild(sub_element) |
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399 | |
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400 | def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None): |
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401 | """ |
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402 | Writes the state of the InversionControl panel to file, as XML. |
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403 | |
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404 | Compatible with standalone writing, or appending to an |
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405 | already existing XML document. In that case, the XML document |
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406 | is required. An optional entry node in the XML document may also be given. |
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407 | |
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408 | :param file: file to write to |
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409 | :param doc: XML document object [optional] |
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410 | :param entry_node: XML node within the XML document at which we will append the data [optional] |
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411 | |
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412 | """ |
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413 | from xml.dom.minidom import getDOMImplementation |
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414 | |
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415 | # Check whether we have to write a standalone XML file |
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416 | if doc is None: |
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417 | impl = getDOMImplementation() |
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418 | doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0") |
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419 | newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type) |
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420 | top_element = newdoc.documentElement |
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421 | else: |
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422 | # We are appending to an existing document |
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423 | newdoc = doc |
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424 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
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425 | if entry_node is None: |
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426 | newdoc.documentElement.appendChild(top_element) |
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427 | else: |
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428 | entry_node.appendChild(top_element) |
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429 | |
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430 | attr = newdoc.createAttribute("version") |
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431 | attr.nodeValue = '1.0' |
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432 | top_element.setAttributeNode(attr) |
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433 | |
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434 | # File name |
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435 | element = newdoc.createElement("filename") |
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436 | if self.file is not None: |
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437 | element.appendChild(newdoc.createTextNode(str(self.file))) |
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438 | else: |
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439 | element.appendChild(newdoc.createTextNode(str(file))) |
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440 | top_element.appendChild(element) |
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441 | |
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442 | element = newdoc.createElement("timestamp") |
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443 | element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp))) |
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444 | attr = newdoc.createAttribute("epoch") |
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445 | attr.nodeValue = str(self.timestamp) |
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446 | element.setAttributeNode(attr) |
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447 | top_element.appendChild(element) |
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448 | # Inputs |
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449 | inputs = newdoc.createElement("Attributes") |
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450 | top_element.appendChild(inputs) |
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451 | |
---|
452 | |
---|
453 | if self.data is not None and hasattr(self.data, "group_id"): |
---|
454 | self.data_group_id = self.data.group_id |
---|
455 | if self.data is not None and hasattr(self.data, "is_data"): |
---|
456 | self.is_data = self.data.is_data |
---|
457 | if self.data is not None: |
---|
458 | self.data_name = self.data.name |
---|
459 | if self.data is not None and hasattr(self.data, "id"): |
---|
460 | self.data_id = self.data.id |
---|
461 | |
---|
462 | for item in list_of_data_attributes: |
---|
463 | element = newdoc.createElement(item[0]) |
---|
464 | exec "element.setAttribute(item[0], str(self.%s))"%(item[1]) |
---|
465 | inputs.appendChild(element) |
---|
466 | |
---|
467 | for item in list_of_state_attributes: |
---|
468 | element = newdoc.createElement(item[0]) |
---|
469 | exec "element.setAttribute(item[0], str(self.%s))"%(item[1]) |
---|
470 | inputs.appendChild(element) |
---|
471 | |
---|
472 | for item in list_of_model_attributes: |
---|
473 | element = newdoc.createElement(item[0]) |
---|
474 | exec "list = self.%s"%item[1] |
---|
475 | for value in list: |
---|
476 | exec "element.appendChild(newdoc.createTextNode(str(%s)))"%value |
---|
477 | inputs.appendChild(element) |
---|
478 | |
---|
479 | for item in list_of_state_parameters: |
---|
480 | element = newdoc.createElement(item[0]) |
---|
481 | exec "self._toXML_helper(list=self.%s, element=element, newdoc=newdoc)"%item[1] |
---|
482 | inputs.appendChild(element) |
---|
483 | |
---|
484 | # Save the file |
---|
485 | if doc is None: |
---|
486 | fd = open(file, 'w') |
---|
487 | fd.write(newdoc.toprettyxml()) |
---|
488 | fd.close() |
---|
489 | return None |
---|
490 | else: |
---|
491 | return newdoc.toprettyxml() |
---|
492 | |
---|
493 | def _fromXML_helper(self, node, list): |
---|
494 | """ |
---|
495 | Helper function to write state to xml |
---|
496 | """ |
---|
497 | for item in node: |
---|
498 | try: |
---|
499 | name = item.get('name') |
---|
500 | except: |
---|
501 | name = None |
---|
502 | try: |
---|
503 | value = item.get('value') |
---|
504 | except: |
---|
505 | value = None |
---|
506 | try: |
---|
507 | selected_to_fit = (item.get('selected_to_fit') == "True") |
---|
508 | except: |
---|
509 | selected_to_fit = None |
---|
510 | try: |
---|
511 | error_displayed = (item.get('error_displayed') == "True") |
---|
512 | except: |
---|
513 | error_displayed = None |
---|
514 | try: |
---|
515 | error_value = item.get('error_value') |
---|
516 | except: |
---|
517 | error_value = None |
---|
518 | try: |
---|
519 | minimum_displayed = (item.get('minimum_displayed')== "True") |
---|
520 | except: |
---|
521 | minimum_displayed = None |
---|
522 | try: |
---|
523 | minimum_value = item.get('minimum_value') |
---|
524 | except: |
---|
525 | minimum_value = None |
---|
526 | try: |
---|
527 | maximum_displayed = (item.get('maximum_displayed') == "True") |
---|
528 | except: |
---|
529 | maximum_displayed = None |
---|
530 | try: |
---|
531 | maximum_value = item.get('maximum_value') |
---|
532 | except: |
---|
533 | maximum_value = None |
---|
534 | try: |
---|
535 | unit = item.get('unit') |
---|
536 | except: |
---|
537 | unit = None |
---|
538 | list.append([selected_to_fit, name, value, "+/-",[error_displayed, error_value], |
---|
539 | [minimum_displayed,minimum_value],[maximum_displayed,maximum_value], unit]) |
---|
540 | |
---|
541 | def fromXML(self, file=None, node=None): |
---|
542 | """ |
---|
543 | Load fitting state from a file |
---|
544 | |
---|
545 | :param file: .fitv file |
---|
546 | :param node: node of a XML document to read from |
---|
547 | |
---|
548 | """ |
---|
549 | if file is not None: |
---|
550 | msg = "PageState no longer supports non-CanSAS" |
---|
551 | msg += " format for fitting files" |
---|
552 | raise RuntimeError, msg |
---|
553 | |
---|
554 | if node.get('version')and node.get('version') == '1.0': |
---|
555 | |
---|
556 | # Get file name |
---|
557 | entry = get_content('ns:filename', node) |
---|
558 | if entry is not None: |
---|
559 | self.file = entry.text.strip() |
---|
560 | |
---|
561 | # Get time stamp |
---|
562 | entry = get_content('ns:timestamp', node) |
---|
563 | if entry is not None and entry.get('epoch'): |
---|
564 | try: |
---|
565 | self.timestamp = float(entry.get('epoch')) |
---|
566 | except: |
---|
567 | msg = "PageState.fromXML: Could not" |
---|
568 | msg += " read timestamp\n %s" % sys.exc_value |
---|
569 | logging.error(msg) |
---|
570 | |
---|
571 | # Parse fitting attributes |
---|
572 | entry = get_content('ns:Attributes', node) |
---|
573 | for item in list_of_data_attributes: |
---|
574 | node = get_content('ns:%s'%item[0], entry) |
---|
575 | try: |
---|
576 | exec "self.%s = parse_entry_helper(node, item)"%item[0] |
---|
577 | |
---|
578 | except: |
---|
579 | raise |
---|
580 | |
---|
581 | if entry is not None: |
---|
582 | |
---|
583 | for item in list_of_state_attributes: |
---|
584 | node = get_content('ns:%s'%item[0], entry) |
---|
585 | try: |
---|
586 | exec "self.%s = parse_entry_helper(node, item)"%str(item[0]) |
---|
587 | except: |
---|
588 | raise |
---|
589 | |
---|
590 | for item in list_of_model_attributes: |
---|
591 | node = get_content("ns:%s"%item[0], entry) |
---|
592 | list = [] |
---|
593 | for value in node: |
---|
594 | try: |
---|
595 | list.append(float(value)) |
---|
596 | except: |
---|
597 | list.append(None) |
---|
598 | exec "self.%s = list"%item[1] |
---|
599 | |
---|
600 | for item in list_of_state_parameters: |
---|
601 | node = get_content("ns:%s"%item[0], entry) |
---|
602 | exec "self._fromXML_helper(node=node, list=self.%s)"%item[1] |
---|
603 | |
---|
604 | |
---|
605 | class Reader(CansasReader): |
---|
606 | """ |
---|
607 | Class to load a .fitv fitting file |
---|
608 | """ |
---|
609 | ## File type |
---|
610 | type_name = "Fitting" |
---|
611 | |
---|
612 | ## Wildcards |
---|
613 | type = ["Fitting files (*.fitv)|*.fitv" |
---|
614 | "SANSView file (*.svs)|*.svs"] |
---|
615 | ## List of allowed extensions |
---|
616 | ext=['.fitv', '.FITV', '.svs', 'SVS'] |
---|
617 | |
---|
618 | def __init__(self, call_back=None, cansas=True): |
---|
619 | CansasReader.__init__(self) |
---|
620 | """ |
---|
621 | Initialize the call-back method to be called |
---|
622 | after we load a file |
---|
623 | |
---|
624 | :param call_back: call-back method |
---|
625 | :param cansas: True = files will be written/read in CanSAS format |
---|
626 | False = write CanSAS format |
---|
627 | |
---|
628 | """ |
---|
629 | ## Call back method to be executed after a file is read |
---|
630 | self.call_back = call_back |
---|
631 | ## CanSAS format flag |
---|
632 | self.cansas = cansas |
---|
633 | self.state = None |
---|
634 | def get_state(self): |
---|
635 | return self.state |
---|
636 | |
---|
637 | def read(self, path): |
---|
638 | """ |
---|
639 | Load a new P(r) inversion state from file |
---|
640 | |
---|
641 | :param path: file path |
---|
642 | |
---|
643 | """ |
---|
644 | if self.cansas == True: |
---|
645 | return self._read_cansas(path) |
---|
646 | |
---|
647 | def _data2d_to_xml_doc(self, datainfo): |
---|
648 | """ |
---|
649 | Create an XML document to contain the content of a Data2D |
---|
650 | |
---|
651 | :param datainfo: Data2D object |
---|
652 | |
---|
653 | """ |
---|
654 | if not issubclass(datainfo.__class__, Data2D): |
---|
655 | raise RuntimeError, "The cansas writer expects a Data2D instance" |
---|
656 | |
---|
657 | doc = xml.dom.minidom.Document() |
---|
658 | main_node = doc.createElement("SASroot") |
---|
659 | main_node.setAttribute("version", self.version) |
---|
660 | main_node.setAttribute("xmlns", "cansas1d/%s" % self.version) |
---|
661 | main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance") |
---|
662 | main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version) |
---|
663 | |
---|
664 | doc.appendChild(main_node) |
---|
665 | |
---|
666 | entry_node = doc.createElement("SASentry") |
---|
667 | main_node.appendChild(entry_node) |
---|
668 | |
---|
669 | write_node(doc, entry_node, "Title", datainfo.title) |
---|
670 | if datainfo is not None: |
---|
671 | write_node(doc, entry_node, "data_class", datainfo.__class__.__name__) |
---|
672 | for item in datainfo.run: |
---|
673 | runname = {} |
---|
674 | if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1: |
---|
675 | runname = {'name': datainfo.run_name[item] } |
---|
676 | write_node(doc, entry_node, "Run", item, runname) |
---|
677 | # Data info |
---|
678 | new_node = doc.createElement("SASdata") |
---|
679 | entry_node.appendChild(new_node) |
---|
680 | for item in list_of_data_2d_attr: |
---|
681 | element = doc.createElement(item[0]) |
---|
682 | exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1]) |
---|
683 | new_node.appendChild(element) |
---|
684 | |
---|
685 | for item in list_of_data2d_values: |
---|
686 | root_node = doc.createElement(item[0]) |
---|
687 | new_node.appendChild(root_node) |
---|
688 | |
---|
689 | exec "temp_list = datainfo.%s"%item[1] |
---|
690 | |
---|
691 | if temp_list is None or len(temp_list)== 0: |
---|
692 | element = doc.createElement(item[0]) |
---|
693 | exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list |
---|
694 | root_node.appendChild(element) |
---|
695 | else: |
---|
696 | for value in temp_list: |
---|
697 | element = doc.createElement(item[0]) |
---|
698 | exec "element.setAttribute(item[0], str(%s))"%value |
---|
699 | root_node.appendChild(element) |
---|
700 | |
---|
701 | # Sample info |
---|
702 | sample = doc.createElement("SASsample") |
---|
703 | if datainfo.sample.name is not None: |
---|
704 | sample.setAttribute("name", str(datainfo.sample.name)) |
---|
705 | entry_node.appendChild(sample) |
---|
706 | write_node(doc, sample, "ID", str(datainfo.sample.ID)) |
---|
707 | write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit}) |
---|
708 | write_node(doc, sample, "transmission", datainfo.sample.transmission) |
---|
709 | write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit}) |
---|
710 | |
---|
711 | for item in datainfo.sample.details: |
---|
712 | write_node(doc, sample, "details", item) |
---|
713 | |
---|
714 | pos = doc.createElement("position") |
---|
715 | written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit}) |
---|
716 | written = written | write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit}) |
---|
717 | written = written | write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit}) |
---|
718 | if written == True: |
---|
719 | sample.appendChild(pos) |
---|
720 | |
---|
721 | ori = doc.createElement("orientation") |
---|
722 | written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit}) |
---|
723 | written = written | write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit}) |
---|
724 | written = written | write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit}) |
---|
725 | if written == True: |
---|
726 | sample.appendChild(ori) |
---|
727 | |
---|
728 | # Instrument info |
---|
729 | instr = doc.createElement("SASinstrument") |
---|
730 | entry_node.appendChild(instr) |
---|
731 | |
---|
732 | write_node(doc, instr, "name", datainfo.instrument) |
---|
733 | |
---|
734 | # Source |
---|
735 | source = doc.createElement("SASsource") |
---|
736 | if datainfo.source.name is not None: |
---|
737 | source.setAttribute("name", str(datainfo.source.name)) |
---|
738 | instr.appendChild(source) |
---|
739 | |
---|
740 | write_node(doc, source, "radiation", datainfo.source.radiation) |
---|
741 | write_node(doc, source, "beam_shape", datainfo.source.beam_shape) |
---|
742 | size = doc.createElement("beam_size") |
---|
743 | if datainfo.source.beam_size_name is not None: |
---|
744 | size.setAttribute("name", str(datainfo.source.beam_size_name)) |
---|
745 | written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit}) |
---|
746 | written = written | write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit}) |
---|
747 | written = written | write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit}) |
---|
748 | if written == True: |
---|
749 | source.appendChild(size) |
---|
750 | |
---|
751 | write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit}) |
---|
752 | write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit}) |
---|
753 | write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit}) |
---|
754 | write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit}) |
---|
755 | |
---|
756 | # Collimation |
---|
757 | for item in datainfo.collimation: |
---|
758 | coll = doc.createElement("SAScollimation") |
---|
759 | if item.name is not None: |
---|
760 | coll.setAttribute("name", str(item.name)) |
---|
761 | instr.appendChild(coll) |
---|
762 | |
---|
763 | write_node(doc, coll, "length", item.length, {"unit":item.length_unit}) |
---|
764 | |
---|
765 | for apert in item.aperture: |
---|
766 | ap = doc.createElement("aperture") |
---|
767 | if apert.name is not None: |
---|
768 | ap.setAttribute("name", str(apert.name)) |
---|
769 | if apert.type is not None: |
---|
770 | ap.setAttribute("type", str(apert.type)) |
---|
771 | coll.appendChild(ap) |
---|
772 | |
---|
773 | write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit}) |
---|
774 | |
---|
775 | size = doc.createElement("size") |
---|
776 | if apert.size_name is not None: |
---|
777 | size.setAttribute("name", str(apert.size_name)) |
---|
778 | written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit}) |
---|
779 | written = written | write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit}) |
---|
780 | written = written | write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit}) |
---|
781 | if written == True: |
---|
782 | ap.appendChild(size) |
---|
783 | |
---|
784 | # Detectors |
---|
785 | for item in datainfo.detector: |
---|
786 | det = doc.createElement("SASdetector") |
---|
787 | written = write_node(doc, det, "name", item.name) |
---|
788 | written = written | write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit}) |
---|
789 | written = written | write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit}) |
---|
790 | if written == True: |
---|
791 | instr.appendChild(det) |
---|
792 | |
---|
793 | off = doc.createElement("offset") |
---|
794 | written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit}) |
---|
795 | written = written | write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit}) |
---|
796 | written = written | write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit}) |
---|
797 | if written == True: |
---|
798 | det.appendChild(off) |
---|
799 | |
---|
800 | center = doc.createElement("beam_center") |
---|
801 | written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit}) |
---|
802 | written = written | write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit}) |
---|
803 | written = written | write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit}) |
---|
804 | if written == True: |
---|
805 | det.appendChild(center) |
---|
806 | |
---|
807 | pix = doc.createElement("pixel_size") |
---|
808 | written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit}) |
---|
809 | written = written | write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit}) |
---|
810 | written = written | write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit}) |
---|
811 | if written == True: |
---|
812 | det.appendChild(pix) |
---|
813 | |
---|
814 | ori = doc.createElement("orientation") |
---|
815 | written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit}) |
---|
816 | written = written | write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit}) |
---|
817 | written = written | write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit}) |
---|
818 | if written == True: |
---|
819 | det.appendChild(ori) |
---|
820 | |
---|
821 | # Processes info |
---|
822 | for item in datainfo.process: |
---|
823 | node = doc.createElement("SASprocess") |
---|
824 | entry_node.appendChild(node) |
---|
825 | |
---|
826 | write_node(doc, node, "name", item.name) |
---|
827 | write_node(doc, node, "date", item.date) |
---|
828 | write_node(doc, node, "description", item.description) |
---|
829 | for term in item.term: |
---|
830 | value = term['value'] |
---|
831 | del term['value'] |
---|
832 | write_node(doc, node, "term", value, term) |
---|
833 | for note in item.notes: |
---|
834 | write_node(doc, node, "SASprocessnote", note) |
---|
835 | # Return the document, and the SASentry node associated with |
---|
836 | # the data we just wrote |
---|
837 | return doc, entry_node |
---|
838 | |
---|
839 | def _parse_state(self, entry): |
---|
840 | """ |
---|
841 | Read a fit result from an XML node |
---|
842 | |
---|
843 | :param entry: XML node to read from |
---|
844 | |
---|
845 | :return: PageState object |
---|
846 | """ |
---|
847 | # Create an empty state |
---|
848 | state = None |
---|
849 | # Locate the P(r) node |
---|
850 | try: |
---|
851 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS}) |
---|
852 | if nodes !=[]: |
---|
853 | # Create an empty state |
---|
854 | state = PageState() |
---|
855 | state.fromXML(node=nodes[0]) |
---|
856 | except: |
---|
857 | logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value) |
---|
858 | |
---|
859 | return state |
---|
860 | |
---|
861 | |
---|
862 | |
---|
863 | def _parse_entry(self, dom): |
---|
864 | """ |
---|
865 | Parse a SASentry |
---|
866 | |
---|
867 | :param node: SASentry node |
---|
868 | |
---|
869 | :return: Data1D/Data2D object |
---|
870 | |
---|
871 | """ |
---|
872 | node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS}) |
---|
873 | if not node or node[0].text.lstrip().rstrip() != "Data2D": |
---|
874 | return CansasReader._parse_entry(self, dom) |
---|
875 | |
---|
876 | #Parse 2D |
---|
877 | data_info = Data2D() |
---|
878 | |
---|
879 | # Look up title |
---|
880 | self._store_content('ns:Title', dom, 'title', data_info) |
---|
881 | |
---|
882 | # Look up run number |
---|
883 | nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS}) |
---|
884 | for item in nodes: |
---|
885 | if item.text is not None: |
---|
886 | value = item.text.strip() |
---|
887 | if len(value) > 0: |
---|
888 | data_info.run.append(value) |
---|
889 | if item.get('name') is not None: |
---|
890 | data_info.run_name[value] = item.get('name') |
---|
891 | |
---|
892 | # Look up instrument name |
---|
893 | self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info) |
---|
894 | |
---|
895 | # Notes |
---|
896 | note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS}) |
---|
897 | for note in note_list: |
---|
898 | try: |
---|
899 | if note.text is not None: |
---|
900 | note_value = note.text.strip() |
---|
901 | if len(note_value) > 0: |
---|
902 | data_info.notes.append(note_value) |
---|
903 | except: |
---|
904 | err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value |
---|
905 | self.errors.append(err_mess) |
---|
906 | logging.error(err_mess) |
---|
907 | |
---|
908 | # Sample info ################### |
---|
909 | entry = get_content('ns:SASsample', dom) |
---|
910 | if entry is not None: |
---|
911 | data_info.sample.name = entry.get('name') |
---|
912 | |
---|
913 | self._store_content('ns:SASsample/ns:ID', |
---|
914 | dom, 'ID', data_info.sample) |
---|
915 | self._store_float('ns:SASsample/ns:thickness', |
---|
916 | dom, 'thickness', data_info.sample) |
---|
917 | self._store_float('ns:SASsample/ns:transmission', |
---|
918 | dom, 'transmission', data_info.sample) |
---|
919 | self._store_float('ns:SASsample/ns:temperature', |
---|
920 | dom, 'temperature', data_info.sample) |
---|
921 | |
---|
922 | nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS}) |
---|
923 | for item in nodes: |
---|
924 | try: |
---|
925 | if item.text is not None: |
---|
926 | detail_value = item.text.strip() |
---|
927 | if len(detail_value) > 0: |
---|
928 | data_info.sample.details.append(detail_value) |
---|
929 | except: |
---|
930 | err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value |
---|
931 | self.errors.append(err_mess) |
---|
932 | logging.error(err_mess) |
---|
933 | |
---|
934 | # Position (as a vector) |
---|
935 | self._store_float('ns:SASsample/ns:position/ns:x', |
---|
936 | dom, 'position.x', data_info.sample) |
---|
937 | self._store_float('ns:SASsample/ns:position/ns:y', |
---|
938 | dom, 'position.y', data_info.sample) |
---|
939 | self._store_float('ns:SASsample/ns:position/ns:z', |
---|
940 | dom, 'position.z', data_info.sample) |
---|
941 | |
---|
942 | # Orientation (as a vector) |
---|
943 | self._store_float('ns:SASsample/ns:orientation/ns:roll', |
---|
944 | dom, 'orientation.x', data_info.sample) |
---|
945 | self._store_float('ns:SASsample/ns:orientation/ns:pitch', |
---|
946 | dom, 'orientation.y', data_info.sample) |
---|
947 | self._store_float('ns:SASsample/ns:orientation/ns:yaw', |
---|
948 | dom, 'orientation.z', data_info.sample) |
---|
949 | |
---|
950 | # Source info ################### |
---|
951 | entry = get_content('ns:SASinstrument/ns:SASsource', dom) |
---|
952 | if entry is not None: |
---|
953 | data_info.source.name = entry.get('name') |
---|
954 | |
---|
955 | self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation', |
---|
956 | dom, 'radiation', data_info.source) |
---|
957 | self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape', |
---|
958 | dom, 'beam_shape', data_info.source) |
---|
959 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength', |
---|
960 | dom, 'wavelength', data_info.source) |
---|
961 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min', |
---|
962 | dom, 'wavelength_min', data_info.source) |
---|
963 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max', |
---|
964 | dom, 'wavelength_max', data_info.source) |
---|
965 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread', |
---|
966 | dom, 'wavelength_spread', data_info.source) |
---|
967 | |
---|
968 | # Beam size (as a vector) |
---|
969 | entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom) |
---|
970 | if entry is not None: |
---|
971 | data_info.source.beam_size_name = entry.get('name') |
---|
972 | |
---|
973 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x', |
---|
974 | dom, 'beam_size.x', data_info.source) |
---|
975 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y', |
---|
976 | dom, 'beam_size.y', data_info.source) |
---|
977 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z', |
---|
978 | dom, 'beam_size.z', data_info.source) |
---|
979 | |
---|
980 | # Collimation info ################### |
---|
981 | nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS}) |
---|
982 | for item in nodes: |
---|
983 | collim = Collimation() |
---|
984 | if item.get('name') is not None: |
---|
985 | collim.name = item.get('name') |
---|
986 | self._store_float('ns:length', item, 'length', collim) |
---|
987 | |
---|
988 | # Look for apertures |
---|
989 | apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS}) |
---|
990 | for apert in apert_list: |
---|
991 | aperture = Aperture() |
---|
992 | |
---|
993 | # Get the name and type of the aperture |
---|
994 | aperture.name = apert.get('name') |
---|
995 | aperture.type = apert.get('type') |
---|
996 | |
---|
997 | self._store_float('ns:distance', apert, 'distance', aperture) |
---|
998 | |
---|
999 | entry = get_content('ns:size', apert) |
---|
1000 | if entry is not None: |
---|
1001 | aperture.size_name = entry.get('name') |
---|
1002 | |
---|
1003 | self._store_float('ns:size/ns:x', apert, 'size.x', aperture) |
---|
1004 | self._store_float('ns:size/ns:y', apert, 'size.y', aperture) |
---|
1005 | self._store_float('ns:size/ns:z', apert, 'size.z', aperture) |
---|
1006 | |
---|
1007 | collim.aperture.append(aperture) |
---|
1008 | |
---|
1009 | data_info.collimation.append(collim) |
---|
1010 | |
---|
1011 | # Detector info ###################### |
---|
1012 | nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS}) |
---|
1013 | for item in nodes: |
---|
1014 | |
---|
1015 | detector = Detector() |
---|
1016 | |
---|
1017 | self._store_content('ns:name', item, 'name', detector) |
---|
1018 | self._store_float('ns:SDD', item, 'distance', detector) |
---|
1019 | |
---|
1020 | # Detector offset (as a vector) |
---|
1021 | self._store_float('ns:offset/ns:x', item, 'offset.x', detector) |
---|
1022 | self._store_float('ns:offset/ns:y', item, 'offset.y', detector) |
---|
1023 | self._store_float('ns:offset/ns:z', item, 'offset.z', detector) |
---|
1024 | |
---|
1025 | # Detector orientation (as a vector) |
---|
1026 | self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector) |
---|
1027 | self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector) |
---|
1028 | self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector) |
---|
1029 | |
---|
1030 | # Beam center (as a vector) |
---|
1031 | self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector) |
---|
1032 | self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector) |
---|
1033 | self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector) |
---|
1034 | |
---|
1035 | # Pixel size (as a vector) |
---|
1036 | self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector) |
---|
1037 | self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector) |
---|
1038 | self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector) |
---|
1039 | |
---|
1040 | self._store_float('ns:slit_length', item, 'slit_length', detector) |
---|
1041 | |
---|
1042 | data_info.detector.append(detector) |
---|
1043 | |
---|
1044 | # Processes info ###################### |
---|
1045 | nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS}) |
---|
1046 | for item in nodes: |
---|
1047 | process = Process() |
---|
1048 | self._store_content('ns:name', item, 'name', process) |
---|
1049 | self._store_content('ns:date', item, 'date', process) |
---|
1050 | self._store_content('ns:description', item, 'description', process) |
---|
1051 | |
---|
1052 | term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS}) |
---|
1053 | for term in term_list: |
---|
1054 | try: |
---|
1055 | term_attr = {} |
---|
1056 | for attr in term.keys(): |
---|
1057 | term_attr[attr] = term.get(attr).strip() |
---|
1058 | if term.text is not None: |
---|
1059 | term_attr['value'] = term.text.strip() |
---|
1060 | process.term.append(term_attr) |
---|
1061 | except: |
---|
1062 | err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value |
---|
1063 | self.errors.append(err_mess) |
---|
1064 | logging.error(err_mess) |
---|
1065 | |
---|
1066 | note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS}) |
---|
1067 | for note in note_list: |
---|
1068 | if note.text is not None: |
---|
1069 | process.notes.append(note.text.strip()) |
---|
1070 | |
---|
1071 | data_info.process.append(process) |
---|
1072 | |
---|
1073 | |
---|
1074 | # Data info ###################### |
---|
1075 | nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS}) |
---|
1076 | if len(nodes)>1: |
---|
1077 | raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries" |
---|
1078 | |
---|
1079 | for entry in nodes: |
---|
1080 | for item in list_of_data_2d_attr: |
---|
1081 | #get node |
---|
1082 | node = get_content('ns:%s'%item[0], entry) |
---|
1083 | exec "data_info.%s = parse_entry_helper(node, item)"%(item[1]) |
---|
1084 | |
---|
1085 | for item in list_of_data2d_values: |
---|
1086 | field = get_content('ns:%s'%item[0], entry) |
---|
1087 | list = [] |
---|
1088 | if field is not None: |
---|
1089 | list = [parse_entry_helper(node, item) for node in field] |
---|
1090 | exec "data_info.%s = numpy.array(list)"%item[0] |
---|
1091 | |
---|
1092 | return data_info |
---|
1093 | |
---|
1094 | def _read_cansas(self, path): |
---|
1095 | """ |
---|
1096 | Load data and P(r) information from a CanSAS XML file. |
---|
1097 | |
---|
1098 | :param path: file path |
---|
1099 | |
---|
1100 | :return: Data1D object if a single SASentry was found, |
---|
1101 | or a list of Data1D objects if multiple entries were found, |
---|
1102 | or None of nothing was found |
---|
1103 | |
---|
1104 | :raise RuntimeError: when the file can't be opened |
---|
1105 | :raise ValueError: when the length of the data vectors are inconsistent |
---|
1106 | |
---|
1107 | """ |
---|
1108 | output = [] |
---|
1109 | basename = os.path.basename(path) |
---|
1110 | root, extension = os.path.splitext(basename) |
---|
1111 | ext = extension.lower() |
---|
1112 | try: |
---|
1113 | if os.path.isfile(path): |
---|
1114 | |
---|
1115 | #TODO: eventually remove the check for .xml once |
---|
1116 | # the P(r) writer/reader is truly complete. |
---|
1117 | if ext in self.ext or \ |
---|
1118 | ext == '.xml': |
---|
1119 | |
---|
1120 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
---|
1121 | # Check the format version number |
---|
1122 | # Specifying the namespace will take care of the file format version |
---|
1123 | root = tree.getroot() |
---|
1124 | entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS}) |
---|
1125 | for entry in entry_list: |
---|
1126 | try: |
---|
1127 | sas_entry = self._parse_entry(entry) |
---|
1128 | except: |
---|
1129 | raise |
---|
1130 | fitstate = self._parse_state(entry) |
---|
1131 | |
---|
1132 | #state could be None when .svs file is loaded |
---|
1133 | #in this case, skip appending to output |
---|
1134 | if fitstate != None: |
---|
1135 | sas_entry.meta_data['fitstate'] = fitstate |
---|
1136 | sas_entry.filename = fitstate.file |
---|
1137 | output.append(sas_entry) |
---|
1138 | else: |
---|
1139 | self.call_back(format=ext) |
---|
1140 | raise RuntimeError, "%s is not a file" % path |
---|
1141 | |
---|
1142 | # Return output consistent with the loader's api |
---|
1143 | if len(output)==0: |
---|
1144 | self.call_back(state=None, datainfo=None,format=ext) |
---|
1145 | return None |
---|
1146 | else: |
---|
1147 | for ind in range(len(output)): |
---|
1148 | # Call back to post the new state |
---|
1149 | state = output[ind].meta_data['fitstate'] |
---|
1150 | t = time.localtime(state.timestamp) |
---|
1151 | time_str = time.strftime("%b %d %H:%M", t) |
---|
1152 | # Check that no time stamp is already appended |
---|
1153 | max_char = state.file.find("[") |
---|
1154 | if max_char < 0: |
---|
1155 | max_char = len(state.file) |
---|
1156 | original_fname = state.file[0:max_char] |
---|
1157 | state.file = original_fname +' [' + time_str + ']' |
---|
1158 | |
---|
1159 | |
---|
1160 | if state is not None and state.is_data is not None: |
---|
1161 | exec 'output[%d].is_data = state.is_data'% ind |
---|
1162 | |
---|
1163 | output[ind].filename = state.file |
---|
1164 | state.data = output[ind] |
---|
1165 | state.data.name = output[ind].filename #state.data_name |
---|
1166 | state.data.id = state.data_id |
---|
1167 | if state.is_data is not None: |
---|
1168 | state.data.is_data = state.is_data |
---|
1169 | if output[ind].run_name is not None and len(output[ind].run_name) != 0 : |
---|
1170 | name = output[ind].run_name |
---|
1171 | else: |
---|
1172 | name=original_fname |
---|
1173 | state.data.group_id = name |
---|
1174 | #store state in fitting |
---|
1175 | #self.call_back(state=state, datainfo=output[ind],format=ext) |
---|
1176 | self.state= state |
---|
1177 | return output |
---|
1178 | |
---|
1179 | except: |
---|
1180 | #self.call_back(format=ext) |
---|
1181 | self.state= state |
---|
1182 | raise |
---|
1183 | |
---|
1184 | def write(self, filename, datainfo=None, fitstate=None): |
---|
1185 | """ |
---|
1186 | Write the content of a Data1D as a CanSAS XML file only for standalone |
---|
1187 | |
---|
1188 | :param filename: name of the file to write |
---|
1189 | :param datainfo: Data1D object |
---|
1190 | :param fitstate: PageState object |
---|
1191 | |
---|
1192 | """ |
---|
1193 | # Sanity check |
---|
1194 | if self.cansas == True: |
---|
1195 | |
---|
1196 | # Add fitting information to the XML document |
---|
1197 | doc = self.write_toXML(datainfo, fitstate) |
---|
1198 | # Write the XML document |
---|
1199 | fd = open(filename, 'w') |
---|
1200 | fd.write(doc.toprettyxml()) |
---|
1201 | fd.close() |
---|
1202 | else: |
---|
1203 | fitstate.toXML(file=filename) |
---|
1204 | |
---|
1205 | def write_toXML(self, datainfo=None, state=None): |
---|
1206 | """ |
---|
1207 | Write toXML, a helper for write() , could be used by guimanager._on_save() |
---|
1208 | |
---|
1209 | : return: xml doc |
---|
1210 | """ |
---|
1211 | |
---|
1212 | if state.data is None: |
---|
1213 | data = DataLoader.data_info.Data1D(x=[], y=[]) |
---|
1214 | else: |
---|
1215 | #make sure title and data run is filled up. |
---|
1216 | if state.data.title == None or state.data.title=='': state.data.title = state.data.name |
---|
1217 | if state.data.run_name == None or state.data.run_name=={}: |
---|
1218 | state.data.run = [str(state.data.name)] |
---|
1219 | state.data.run_name[0] = state.data.name |
---|
1220 | |
---|
1221 | if issubclass(state.data.__class__, DataLoader.data_info.Data1D): |
---|
1222 | |
---|
1223 | data = state.data |
---|
1224 | doc, sasentry = self._to_xml_doc(data) |
---|
1225 | else: |
---|
1226 | data = state.data |
---|
1227 | doc, sasentry = self._data2d_to_xml_doc(data) |
---|
1228 | |
---|
1229 | |
---|
1230 | if state is not None: |
---|
1231 | state.toXML(doc=doc, file=data.name, entry_node=sasentry) |
---|
1232 | |
---|
1233 | return doc |
---|
1234 | |
---|
1235 | if __name__ == "__main__": |
---|
1236 | state = PageState(parent=None) |
---|
1237 | #state.toXML() |
---|
1238 | """ |
---|
1239 | |
---|
1240 | file = open("test_state", "w") |
---|
1241 | pickle.dump(state, file) |
---|
1242 | print pickle.dumps(state) |
---|
1243 | state.data_name = "hello---->" |
---|
1244 | pickle.dump(state, file) |
---|
1245 | file = open("test_state", "r") |
---|
1246 | new_state= pickle.load(file) |
---|
1247 | print "new state", new_state |
---|
1248 | new_state= pickle.load(file) |
---|
1249 | print "new state", new_state |
---|
1250 | #print "state", state |
---|
1251 | """ |
---|
1252 | import bsddb |
---|
1253 | import pickle |
---|
1254 | db= bsddb.btopen('file_state.db', 'c') |
---|
1255 | val = (pickle.dumps(state), "hello", "hi") |
---|
1256 | db['state1']= pickle.dumps(val) |
---|
1257 | print pickle.loads(db['state1']) |
---|
1258 | state.data_name = "hello---->22" |
---|
1259 | db['state2']= pickle.dumps(state) |
---|
1260 | state.data_name = "hello---->2" |
---|
1261 | db['state3']= pickle.dumps(state) |
---|
1262 | del db['state3'] |
---|
1263 | state.data_name = "hello---->3" |
---|
1264 | db['state4']= pickle.dumps(state) |
---|
1265 | new_state = pickle.loads(db['state1']) |
---|
1266 | #print db.last() |
---|
1267 | db.set_location('state2') |
---|
1268 | state.data_name = "hello---->5" |
---|
1269 | db['aastate5']= pickle.dumps(state) |
---|
1270 | db.keys().sort() |
---|
1271 | print pickle.loads(db['state2']) |
---|
1272 | |
---|
1273 | db.close() |
---|