1 | import os,os.path, re |
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2 | import sys, wx, logging |
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3 | import string, numpy, pylab, math |
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4 | |
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5 | from sans.guitools.plottables import Data1D, Theory1D |
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6 | from sans.guitools.PlotPanel import PlotPanel |
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7 | from sans.guicomm.events import NewPlotEvent, StatusEvent |
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8 | from copy import deepcopy |
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9 | from sans.fit.AbstractFitEngine import Model |
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10 | from sans.fit.AbstractFitEngine import Data |
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11 | from fitproblem import FitProblem |
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12 | from fitpanel import FitPanel |
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13 | |
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14 | import models |
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15 | import fitpage |
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16 | class PlottableData(Data,Data1D): |
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17 | """ class plottable data""" |
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18 | def __init__(self,data,data1d): |
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19 | self.x = data1d.x |
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20 | self.y = data1d.y |
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21 | self.dx= data1d.dx |
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22 | self.dy= data1d.dy |
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23 | |
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24 | self.group_id= data1d.group_id |
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25 | x_name, x_units = data1d.get_xaxis() |
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26 | y_name, y_units = data1d.get_yaxis() |
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27 | self.xaxis( x_name, x_units) |
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28 | self.yaxis( y_name, y_units ) |
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29 | self.qmin=data.qmin |
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30 | self.qmax=data.qmax |
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31 | class Plugin: |
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32 | """ |
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33 | """ |
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34 | |
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35 | def __init__(self): |
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36 | ## Plug-in name |
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37 | self.sub_menu = "Fitting" |
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38 | |
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39 | ## Reference to the parent window |
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40 | self.parent = None |
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41 | self.menu_mng = models.ModelManager() |
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42 | ## List of panels for the simulation perspective (names) |
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43 | self.perspective = [] |
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44 | # Start with a good default |
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45 | self.elapsed = 0.022 |
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46 | self.fitter = None |
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47 | |
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48 | #Flag to let the plug-in know that it is running standalone |
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49 | self.standalone=True |
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50 | ## Fit engine |
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51 | self._fit_engine = 'scipy' |
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52 | # Log startup |
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53 | logging.info("Fitting plug-in started") |
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54 | |
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55 | def populate_menu(self, id, owner): |
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56 | """ |
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57 | Create a menu for the Fitting plug-in |
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58 | @param id: id to create a menu |
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59 | @param owner: owner of menu |
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60 | @ return : list of information to populate the main menu |
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61 | """ |
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62 | #Menu for fitting |
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63 | self.menu1 = wx.Menu() |
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64 | id1 = wx.NewId() |
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65 | self.menu1.Append(id1, '&Show fit panel') |
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66 | wx.EVT_MENU(owner, id1, self.on_perspective) |
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67 | |
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68 | #menu for model |
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69 | menu2 = wx.Menu() |
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70 | self.menu_mng.populate_menu(menu2, owner) |
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71 | id2 = wx.NewId() |
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72 | owner.Bind(models.EVT_MODEL,self._on_model_menu) |
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73 | self.fit_panel.set_owner(owner) |
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74 | self.fit_panel.set_model_list(self.menu_mng.get_model_list()) |
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75 | owner.Bind(fitpage.EVT_MODEL_BOX,self._on_model_panel) |
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76 | #owner.Bind(modelpage.EVT_MODEL_DRAW,self.draw_model) |
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77 | |
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78 | return [(id, self.menu1, "Fitting"),(id2, menu2, "Model")] |
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79 | |
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80 | |
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81 | def help(self, evt): |
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82 | """ |
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83 | Show a general help dialog. |
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84 | TODO: replace the text with a nice image |
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85 | """ |
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86 | pass |
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87 | |
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88 | def get_context_menu(self, graph=None): |
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89 | """ |
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90 | Get the context menu items available for P(r) |
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91 | @param graph: the Graph object to which we attach the context menu |
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92 | @return: a list of menu items with call-back function |
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93 | """ |
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94 | |
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95 | self.graph=graph |
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96 | for item in graph.plottables: |
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97 | if item.name==graph.selected_plottable and item.__class__.__name__ is not "Theory1D": |
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98 | return [["Select Data", "Dialog with fitting parameters ", self._onSelect]] |
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99 | return [] |
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100 | |
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101 | |
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102 | def get_panels(self, parent): |
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103 | """ |
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104 | Create and return a list of panel objects |
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105 | """ |
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106 | self.parent = parent |
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107 | # Creation of the fit panel |
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108 | self.fit_panel = FitPanel(self.parent, -1) |
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109 | #Set the manager forthe main panel |
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110 | self.fit_panel.set_manager(self) |
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111 | # List of windows used for the perspective |
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112 | self.perspective = [] |
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113 | self.perspective.append(self.fit_panel.window_name) |
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114 | # take care of saving data, model and page associated with each other |
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115 | self.page_finder={} |
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116 | self.index_model=0 |
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117 | return [self.fit_panel] |
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118 | |
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119 | |
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120 | def get_perspective(self): |
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121 | """ |
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122 | Get the list of panel names for this perspective |
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123 | """ |
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124 | return self.perspective |
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125 | |
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126 | |
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127 | def on_perspective(self, event): |
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128 | """ |
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129 | Call back function for the perspective menu item. |
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130 | We notify the parent window that the perspective |
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131 | has changed. |
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132 | """ |
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133 | self.parent.set_perspective(self.perspective) |
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134 | |
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135 | |
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136 | def post_init(self): |
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137 | """ |
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138 | Post initialization call back to close the loose ends |
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139 | [Somehow openGL needs this call] |
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140 | """ |
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141 | self.parent.set_perspective(self.perspective) |
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142 | |
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143 | |
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144 | def _onSelect(self,event): |
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145 | """ |
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146 | when Select data to fit a new page is created .Its reference is |
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147 | added to self.page_finder |
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148 | """ |
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149 | self.panel = event.GetEventObject() |
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150 | for item in self.panel.graph.plottables: |
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151 | if item.name == self.panel.graph.selected_plottable: |
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152 | try: |
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153 | name = item.group_id # item in Data1D |
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154 | except: |
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155 | name = 'Fit' |
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156 | try: |
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157 | page = self.fit_panel.add_fit_page(name) |
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158 | page.set_data_name(item) |
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159 | self.page_finder[page]= FitProblem() |
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160 | #creating Data type |
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161 | data1= Data(sans_data=item) |
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162 | datas=PlottableData(data=data1,data1d=item) |
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163 | self.page_finder[page].add_data(datas) |
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164 | except: |
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165 | raise |
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166 | wx.PostEvent(self.parent, StatusEvent(status="Fitting error: \ |
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167 | data already Selected ")) |
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168 | |
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169 | |
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170 | def get_page_finder(self): |
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171 | """ @return self.page_finder used also by simfitpage.py""" |
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172 | return self.page_finder |
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173 | |
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174 | |
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175 | def set_page_finder(self,modelname,param,values): |
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176 | """ |
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177 | Used by simfitpage.py to reset a parameter given the string constrainst. |
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178 | @param modelname: the name ot the model for with the parameter has to reset |
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179 | @param value: can be a string in this case. |
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180 | @note: expecting park used for fit. |
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181 | """ |
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182 | sim_page=self.fit_panel.get_page(0) |
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183 | for page, value in self.page_finder.iteritems(): |
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184 | if page != sim_page: |
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185 | list=value.get_model() |
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186 | model=list[0] |
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187 | if model.name== modelname: |
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188 | value.set_model_param(param,values) |
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189 | break |
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190 | |
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191 | |
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192 | |
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193 | def split_string(self,item): |
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194 | """ |
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195 | recieve a word containing "" |
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196 | """ |
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197 | #print "fitting: split :went here" |
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198 | |
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199 | if string.find(item,".")!=-1: |
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200 | param_names= re.split("\.",item) |
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201 | model_name=param_names[0] |
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202 | param_name=param_names[1] |
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203 | return model_name,param_name |
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204 | |
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205 | |
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206 | def _single_fit_completed(self,result,pars,current_pg,qmin,qmax): |
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207 | """ |
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208 | |
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209 | """ |
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210 | try: |
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211 | for page, value in self.page_finder.iteritems(): |
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212 | if page== current_pg: |
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213 | data = value.get_data() |
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214 | list = value.get_model() |
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215 | model= list[0] |
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216 | break |
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217 | #print "fitting : result",result,result.pvec,result.cov,result.fitness |
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218 | i = 0 |
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219 | for name in pars: |
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220 | if result.pvec.__class__==numpy.float64: |
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221 | model.setParam(name,result.pvec) |
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222 | else: |
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223 | model.setParam(name,result.pvec[i]) |
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224 | #print "fitting: i name out[i]", i,name,float(result.pvec[i]) |
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225 | i += 1 |
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226 | new_cov=[] |
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227 | if result.cov !=None: |
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228 | for j in range(len(result.cov)): |
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229 | new_cov.append(result.cov[j][j]) |
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230 | else: |
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231 | new_cov=None |
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232 | current_pg.onsetValues(result.fitness, result.pvec,new_cov) |
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233 | self.plot_helper(currpage=current_pg,qmin=qmin,qmax=qmax) |
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234 | except: |
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235 | raise |
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236 | wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value)) |
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237 | |
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238 | |
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239 | def _simul_fit_completed(self,result,qmin,qmax): |
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240 | """ |
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241 | Parameter estimation completed, |
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242 | display the results to the user |
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243 | @param alpha: estimated best alpha |
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244 | @param elapsed: computation time |
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245 | """ |
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246 | try: |
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247 | for page, value in self.page_finder.iteritems(): |
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248 | data = value.get_data() |
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249 | list = value.get_model() |
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250 | model= list[0] |
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251 | |
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252 | small_out = [] |
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253 | small_cov = [] |
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254 | i = 0 |
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255 | for p in result.parameters: |
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256 | print "fitting: fit in park fitting", p.name, p.value,p.stderr |
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257 | model_name,param_name = self.split_string(p.name) |
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258 | print "fitting: simultfit",model.name,model_name,param_name ,p.name,param_name,p.value |
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259 | if model.name == model_name: |
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260 | print "fitting: hello",p.name,param_name,p.value |
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261 | small_out.append(p.value ) |
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262 | small_cov.append(p.stderr) |
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263 | model.setParam(param_name,p.value) |
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264 | #print "fitting: out of each page",page,small_out,small_cov,data.group_id |
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265 | page.onsetValues(result.fitness, small_out,small_cov) |
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266 | self.plot_helper(currpage= page,qmin= qmin,qmax= qmax) |
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267 | except: |
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268 | wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value)) |
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269 | |
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270 | |
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271 | def _completed(self,result,pars,current_pg, elapsed): |
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272 | """ |
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273 | Method called with the results when the inversion |
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274 | is done |
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275 | |
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276 | @param out: output coefficient for the base functions |
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277 | @param cov: covariance matrix |
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278 | @param pr: Invertor instance |
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279 | @param elapsed: time spent computing |
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280 | """ |
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281 | |
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282 | # Save useful info |
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283 | self.elapsed = elapsed |
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284 | # Keep a copy of the last result |
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285 | self._last_out = result.pvec |
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286 | self._last_cov = result.cov |
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287 | self._last_chisqr=result.fitness |
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288 | #print "fitting: initial parameter ",pars |
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289 | #result=self.fitter.fit(qmin,qmax) |
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290 | |
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291 | #print "fitting : result",result,result.pvec,result.cov,result.fitness |
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292 | i = 0 |
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293 | for name in pars: |
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294 | if result.pvec.__class__==numpy.float64: |
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295 | model.model.setParam(name,result.pvec) |
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296 | else: |
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297 | model.model.setParam(name,result.pvec[i]) |
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298 | #print "fitting: i name out[i]", i,name,float(result.pvec[i]) |
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299 | i += 1 |
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300 | new_cov=[] |
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301 | if result.cov !=None: |
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302 | for j in range(len(result.cov)): |
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303 | new_cov.append(result.cov[j][j]) |
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304 | else: |
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305 | new_cov=None |
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306 | current_pg.onsetValues(result.fitness, result.pvec,new_cov) |
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307 | self.plot_helper(currpage=current_pg,qmin=qmin,qmax=qmax) |
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308 | |
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309 | |
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310 | def _on_single_fit(self,id=None,qmin=None,qmax=None): |
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311 | """ |
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312 | perform fit for the current page and return chisqr,out and cov |
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313 | @param engineName: type of fit to be performed |
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314 | @param id: unique id corresponding to a fit problem(model, set of data) |
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315 | @param model: model to fit |
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316 | |
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317 | """ |
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318 | #set an engine to perform fit |
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319 | from sans.fit.Fitting import Fit |
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320 | self.fitter= Fit(self._fit_engine) |
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321 | #Setting an id to store model and data |
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322 | if id==None: |
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323 | id=0 |
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324 | self.id=id |
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325 | current_pg=self.fit_panel.get_current_page() |
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326 | for page, value in self.page_finder.iteritems(): |
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327 | if page ==current_pg : |
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328 | #print "fitting: self.page_finder",self.page_finder |
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329 | data = value.get_data() |
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330 | list=value.get_model() |
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331 | model=list[0] |
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332 | |
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333 | #Create dictionary of parameters for fitting used |
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334 | pars=[] |
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335 | templist=[] |
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336 | try: |
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337 | templist=current_pg.get_param_list() |
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338 | except: |
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339 | raise |
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340 | wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value)) |
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341 | return |
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342 | #for element in templist: |
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343 | # print "fitting: templist",str(element[0].GetLabelText()) |
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344 | #print "fitting: model list",model.getParamList() |
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345 | for element in templist: |
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346 | try: |
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347 | pars.append(str(element[0].GetLabelText())) |
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348 | except: |
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349 | raise |
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350 | wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value)) |
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351 | return |
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352 | #print "fitting: pars",pars |
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353 | pars.sort() |
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354 | print "fitting: model ",model.__class__.__name__ |
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355 | self.fitter.set_model(Model(model),model.name, self.id, pars) |
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356 | self.fitter.set_data(data,self.id,qmin,qmax) |
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357 | #Do the fit SCIPY |
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358 | try: |
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359 | result=self.fitter.fit() |
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360 | self._single_fit_completed(result,pars,current_pg,qmin,qmax) |
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361 | |
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362 | except: |
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363 | wx.PostEvent(self.parent, StatusEvent(status="Single Fit error: %s" % sys.exc_value)) |
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364 | return |
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365 | |
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366 | def _on_simul_fit(self, id=None,qmin=None,qmax=None): |
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367 | """ |
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368 | perform fit for all the pages selected on simpage and return chisqr,out and cov |
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369 | @param engineName: type of fit to be performed |
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370 | @param id: unique id corresponding to a fit problem(model, set of data) |
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371 | in park_integration |
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372 | @param model: model to fit |
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373 | |
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374 | """ |
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375 | #print "fitting: probabily breaking on fit call" |
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376 | #set an engine to perform fit |
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377 | from sans.fit.Fitting import Fit |
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378 | self.fitter= Fit(self._fit_engine) |
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379 | #Setting an id to store model and data |
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380 | if id==None: |
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381 | id = 0 |
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382 | self.id = id |
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383 | for page, value in self.page_finder.iteritems(): |
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384 | try: |
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385 | #print "fitting: self.page_finder",value |
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386 | data = value.get_data() |
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387 | #print "fitting: data",data |
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388 | list = value.get_model() |
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389 | model= list[0] |
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390 | if data != None : |
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391 | #Create dictionary of parameters for fitting used |
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392 | pars = [] |
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393 | templist = [] |
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394 | try: |
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395 | templist = page.get_param_list() |
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396 | except: |
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397 | wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value)) |
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398 | return |
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399 | |
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400 | for element in templist: |
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401 | try: |
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402 | name = str(element[0].GetLabelText()) |
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403 | pars.append(name) |
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404 | except: |
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405 | wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value)) |
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406 | return |
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407 | |
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408 | print "fitting: pars",pars,model.name |
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409 | #print "fitter",self.fitter |
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410 | #print "fitting: model name",model.name |
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411 | self.fitter.set_model(Model(model),model.name, self.id, pars) |
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412 | self.fitter.set_data(data,self.id,qmin,qmax) |
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413 | else: |
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414 | raise ValueError," Fitting: cannot set model with empty parameter" |
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415 | self.id += 1 |
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416 | except: |
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417 | raise |
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418 | wx.PostEvent(self.parent, StatusEvent(status="Fitting error: %s" % sys.exc_value)) |
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419 | return |
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420 | #Do the fit SCIPY |
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421 | try: |
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422 | result=self.fitter.fit() |
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423 | self._simul_fit_completed(result,qmin,qmax) |
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424 | except: |
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425 | raise |
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426 | wx.PostEvent(self.parent, StatusEvent(status="Simultaneous Fitting error: %s" % sys.exc_value)) |
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427 | return |
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428 | |
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429 | def _on_change_engine(self, engine='park'): |
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430 | """ |
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431 | Allow to select the type of engine to perform fit |
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432 | @param engine: the key work of the engine |
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433 | """ |
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434 | self._fit_engine = engine |
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435 | |
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436 | |
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437 | def _on_model_panel(self, evt): |
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438 | """ |
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439 | react to model selection on any combo box or model menu.plot the model |
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440 | """ |
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441 | model = evt.model |
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442 | name = evt.name |
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443 | sim_page=self.fit_panel.get_page(0) |
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444 | current_pg = self.fit_panel.get_current_page() |
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445 | if current_pg != sim_page: |
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446 | current_pg.set_model_name(name) |
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447 | current_pg.set_panel(model) |
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448 | try: |
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449 | data=self.page_finder[current_pg].get_data() |
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450 | M_name="M"+str(self.index_model)+"= "+name+"("+data.group_id+")" |
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451 | except: |
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452 | raise |
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453 | M_name="M"+str(self.index_model)+"= "+name |
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454 | model.name="M"+str(self.index_model) |
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455 | self.index_model += 1 |
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456 | self.page_finder[current_pg].set_theory("Fitness") |
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457 | #print "on model",model.name |
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458 | self.page_finder[current_pg].set_model(model,M_name) |
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459 | self.plot_helper(currpage= current_pg,qmin= None,qmax= None) |
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460 | sim_page.add_model(self.page_finder) |
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461 | |
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462 | |
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463 | def redraw_model(self,qmin= None,qmax= None): |
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464 | """ |
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465 | Draw a theory according to model changes or data range. |
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466 | @param qmin: the minimum value plotted for theory |
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467 | @param qmax: the maximum value plotted for theory |
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468 | """ |
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469 | current_pg=self.fit_panel.get_current_page() |
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470 | for page, value in self.page_finder.iteritems(): |
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471 | if page ==current_pg : |
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472 | break |
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473 | self.plot_helper(currpage=page,qmin= qmin,qmax= qmax) |
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474 | |
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475 | def plot_helper(self,currpage,qmin=None,qmax=None): |
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476 | """ |
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477 | Plot a theory given a model and data |
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478 | @param model: the model from where the theory is derived |
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479 | @param currpage: page in a dictionary referring to some data |
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480 | """ |
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481 | #print "fitting: plot helper" |
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482 | if self.fit_panel.get_page_count() >1: |
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483 | for page in self.page_finder.iterkeys(): |
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484 | if page==currpage : |
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485 | break |
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486 | |
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487 | data=self.page_finder[page].get_data() |
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488 | list=self.page_finder[page].get_model() |
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489 | model=list[0] |
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490 | if data!=None: |
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491 | theory = Theory1D(x=[], y=[]) |
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492 | theory.name = self.page_finder[page].get_theory() |
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493 | theory.group_id = data.group_id |
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494 | |
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495 | x_name, x_units = data.get_xaxis() |
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496 | y_name, y_units = data.get_yaxis() |
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497 | theory.xaxis(x_name, x_units) |
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498 | theory.yaxis(y_name, y_units) |
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499 | |
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500 | if qmin == None : |
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501 | qmin = min(data.x) |
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502 | if qmax == None : |
---|
503 | qmax = max(data.x) |
---|
504 | try: |
---|
505 | tempx = qmin |
---|
506 | tempy = model.run(qmin) |
---|
507 | theory.x.append(tempx) |
---|
508 | theory.y.append(tempy) |
---|
509 | except : |
---|
510 | wx.PostEvent(self.parent, StatusEvent(status="fitting \ |
---|
511 | skipping point x %g %s" %(qmin, sys.exc_value))) |
---|
512 | |
---|
513 | for i in range(len(data.x)): |
---|
514 | try: |
---|
515 | if data.x[i]> qmin and data.x[i]< qmax: |
---|
516 | tempx = data.x[i] |
---|
517 | tempy = model.run(tempx) |
---|
518 | |
---|
519 | theory.x.append(tempx) |
---|
520 | theory.y.append(tempy) |
---|
521 | except: |
---|
522 | wx.PostEvent(self.parent, StatusEvent(status="fitting \ |
---|
523 | skipping point x %g %s" %(data.x[i], sys.exc_value))) |
---|
524 | try: |
---|
525 | tempx = qmax |
---|
526 | tempy = model.run(qmax) |
---|
527 | theory.x.append(tempx) |
---|
528 | theory.y.append(tempy) |
---|
529 | except: |
---|
530 | wx.PostEvent(self.parent, StatusEvent(status="fitting \ |
---|
531 | skipping point x %g %s" %(qmax, sys.exc_value))) |
---|
532 | try: |
---|
533 | from sans.guicomm.events import NewPlotEvent |
---|
534 | #print"fitting: theory",theory |
---|
535 | wx.PostEvent(self.parent, NewPlotEvent(plot=theory, title="Analytical model")) |
---|
536 | except: |
---|
537 | raise |
---|
538 | print "SimView.complete1D: could not import sans.guicomm.events" |
---|
539 | |
---|
540 | |
---|
541 | def _on_model_menu(self, evt): |
---|
542 | """ |
---|
543 | Plot a theory from a model selected from the menu |
---|
544 | """ |
---|
545 | print "_on_model_menu done" |
---|
546 | #name = evt.model.__class__.__name__ |
---|
547 | name="Model View" |
---|
548 | model=evt.modelinfo.model() |
---|
549 | description=evt.modelinfo.description |
---|
550 | self.fit_panel.add_model_page(model,description,name) |
---|
551 | self.draw_model(model) |
---|
552 | |
---|
553 | def draw_model(self,model): |
---|
554 | x = pylab.arange(0.001, 0.1, 0.001) |
---|
555 | xlen = len(x) |
---|
556 | dy = numpy.zeros(xlen) |
---|
557 | y = numpy.zeros(xlen) |
---|
558 | |
---|
559 | for i in range(xlen): |
---|
560 | y[i] = model.run(x[i]) |
---|
561 | dy[i] = math.sqrt(math.fabs(y[i])) |
---|
562 | try: |
---|
563 | |
---|
564 | new_plot = Theory1D(x, y) |
---|
565 | #new_plot.name = evt.model.__class__.__name__ |
---|
566 | new_plot.name ="Fitness" |
---|
567 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
568 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
569 | |
---|
570 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Analytical model")) |
---|
571 | except: |
---|
572 | print "SimView.complete1D: could not import sans.guicomm.events" |
---|
573 | |
---|
574 | if __name__ == "__main__": |
---|
575 | i = Plugin() |
---|
576 | |
---|
577 | |
---|
578 | |
---|
579 | |
---|