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50 | <h1>Source code for sas.perspectives.pr.inversion_state</h1><div class="highlight"><pre> |
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51 | <span class="sd">"""</span> |
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52 | <span class="sd"> Handling of P(r) inversion states</span> |
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53 | <span class="sd">"""</span> |
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54 | <span class="c">################################################################################</span> |
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55 | <span class="c">#This software was developed by the University of Tennessee as part of the</span> |
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56 | <span class="c">#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)</span> |
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57 | <span class="c">#project funded by the US National Science Foundation. </span> |
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58 | <span class="c">#</span> |
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59 | <span class="c">#See the license text in license.txt</span> |
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60 | <span class="c">#</span> |
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61 | <span class="c">#copyright 2009, University of Tennessee</span> |
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62 | <span class="c">################################################################################</span> |
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63 | |
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64 | |
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65 | <span class="kn">import</span> <span class="nn">time</span> |
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66 | <span class="kn">import</span> <span class="nn">os</span> |
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67 | <span class="kn">import</span> <span class="nn">sys</span> |
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68 | <span class="kn">import</span> <span class="nn">logging</span> |
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69 | <span class="kn">from</span> <span class="nn">lxml</span> <span class="kn">import</span> <span class="n">etree</span> |
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70 | <span class="kn">from</span> <span class="nn">sas.guiframe.dataFitting</span> <span class="kn">import</span> <span class="n">Data1D</span> |
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71 | <span class="kn">from</span> <span class="nn">sas.dataloader.readers.cansas_reader</span> <span class="kn">import</span> <span class="n">Reader</span> <span class="k">as</span> <span class="n">CansasReader</span> |
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72 | <span class="kn">from</span> <span class="nn">sas.dataloader.readers.cansas_reader</span> <span class="kn">import</span> <span class="n">get_content</span> |
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73 | |
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74 | <span class="n">PRNODE_NAME</span> <span class="o">=</span> <span class="s">'pr_inversion'</span> |
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75 | <span class="n">CANSAS_NS</span> <span class="o">=</span> <span class="s">"cansas1d/1.0"</span> |
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76 | |
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77 | <span class="c"># Translation of names between stored and object data</span> |
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78 | <span class="c">## List of P(r) inversion inputs </span> |
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79 | <span class="n">in_list</span> <span class="o">=</span> <span class="p">[[</span><span class="s">"nterms"</span><span class="p">,</span> <span class="s">"nfunc"</span><span class="p">],</span> |
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80 | <span class="p">[</span><span class="s">"d_max"</span><span class="p">,</span> <span class="s">"d_max"</span><span class="p">],</span> |
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81 | <span class="p">[</span><span class="s">"alpha"</span><span class="p">,</span> <span class="s">"alpha"</span><span class="p">],</span> |
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82 | <span class="p">[</span><span class="s">"slit_width"</span><span class="p">,</span> <span class="s">"width"</span><span class="p">],</span> |
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83 | <span class="p">[</span><span class="s">"slit_height"</span><span class="p">,</span> <span class="s">"height"</span><span class="p">],</span> |
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84 | <span class="p">[</span><span class="s">"qmin"</span><span class="p">,</span> <span class="s">"qmin"</span><span class="p">],</span> |
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85 | <span class="p">[</span><span class="s">"qmax"</span><span class="p">,</span> <span class="s">"qmax"</span><span class="p">],</span> |
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86 | <span class="p">[</span><span class="s">"estimate_bck"</span><span class="p">,</span> <span class="s">"estimate_bck"</span><span class="p">]]</span> |
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87 | |
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88 | <span class="c">## List of P(r) inversion outputs</span> |
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89 | <span class="n">out_list</span> <span class="o">=</span> <span class="p">[[</span><span class="s">"elapsed"</span><span class="p">,</span> <span class="s">"elapsed"</span><span class="p">],</span> |
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90 | <span class="p">[</span><span class="s">"rg"</span><span class="p">,</span> <span class="s">"rg"</span><span class="p">],</span> |
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91 | <span class="p">[</span><span class="s">"iq0"</span><span class="p">,</span> <span class="s">"iq0"</span><span class="p">],</span> |
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92 | <span class="p">[</span><span class="s">"bck"</span><span class="p">,</span> <span class="s">"bck"</span><span class="p">],</span> |
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93 | <span class="p">[</span><span class="s">"chi2"</span><span class="p">,</span> <span class="s">"chi2"</span><span class="p">],</span> |
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94 | <span class="p">[</span><span class="s">"osc"</span><span class="p">,</span> <span class="s">"osc"</span><span class="p">],</span> |
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95 | <span class="p">[</span><span class="s">"pos"</span><span class="p">,</span> <span class="s">"pos"</span><span class="p">],</span> |
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96 | <span class="p">[</span><span class="s">"pos_err"</span><span class="p">,</span> <span class="s">"pos_err"</span><span class="p">],</span> |
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97 | <span class="p">[</span><span class="s">"alpha_estimate"</span><span class="p">,</span> <span class="s">"alpha_estimate"</span><span class="p">],</span> |
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98 | <span class="p">[</span><span class="s">"nterms_estimate"</span><span class="p">,</span> <span class="s">"nterms_estimate"</span><span class="p">]]</span> |
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99 | |
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100 | <div class="viewcode-block" id="InversionState"><a class="viewcode-back" href="../../../../dev/api/sas.perspectives.pr.html#sas.perspectives.pr.inversion_state.InversionState">[docs]</a><span class="k">class</span> <span class="nc">InversionState</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
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101 | <span class="sd">"""</span> |
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102 | <span class="sd"> Class to hold the state information of the InversionControl panel.</span> |
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103 | <span class="sd"> """</span> |
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104 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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105 | <span class="sd">"""</span> |
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106 | <span class="sd"> Default values</span> |
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107 | <span class="sd"> """</span> |
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108 | <span class="c"># Input </span> |
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109 | <span class="bp">self</span><span class="o">.</span><span class="n">file</span> <span class="o">=</span> <span class="bp">None</span> |
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110 | <span class="bp">self</span><span class="o">.</span><span class="n">estimate_bck</span> <span class="o">=</span> <span class="bp">False</span> |
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111 | <span class="bp">self</span><span class="o">.</span><span class="n">timestamp</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span> |
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112 | |
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113 | <span class="c"># Inversion parameters</span> |
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114 | <span class="bp">self</span><span class="o">.</span><span class="n">nfunc</span> <span class="o">=</span> <span class="bp">None</span> |
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115 | <span class="bp">self</span><span class="o">.</span><span class="n">d_max</span> <span class="o">=</span> <span class="bp">None</span> |
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116 | <span class="bp">self</span><span class="o">.</span><span class="n">alpha</span> <span class="o">=</span> <span class="bp">None</span> |
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117 | |
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118 | <span class="c"># Slit parameters</span> |
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119 | <span class="bp">self</span><span class="o">.</span><span class="n">height</span> <span class="o">=</span> <span class="bp">None</span> |
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120 | <span class="bp">self</span><span class="o">.</span><span class="n">width</span> <span class="o">=</span> <span class="bp">None</span> |
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121 | |
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122 | <span class="c"># Q range</span> |
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123 | <span class="bp">self</span><span class="o">.</span><span class="n">qmin</span> <span class="o">=</span> <span class="bp">None</span> |
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124 | <span class="bp">self</span><span class="o">.</span><span class="n">qmax</span> <span class="o">=</span> <span class="bp">None</span> |
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125 | |
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126 | <span class="c"># Outputs</span> |
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127 | <span class="bp">self</span><span class="o">.</span><span class="n">elapsed</span> <span class="o">=</span> <span class="bp">None</span> |
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128 | <span class="bp">self</span><span class="o">.</span><span class="n">rg</span> <span class="o">=</span> <span class="bp">None</span> |
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129 | <span class="bp">self</span><span class="o">.</span><span class="n">iq0</span> <span class="o">=</span> <span class="bp">None</span> |
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130 | <span class="bp">self</span><span class="o">.</span><span class="n">bck</span> <span class="o">=</span> <span class="bp">None</span> |
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131 | <span class="bp">self</span><span class="o">.</span><span class="n">chi2</span> <span class="o">=</span> <span class="bp">None</span> |
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132 | <span class="bp">self</span><span class="o">.</span><span class="n">osc</span> <span class="o">=</span> <span class="bp">None</span> |
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133 | <span class="bp">self</span><span class="o">.</span><span class="n">pos</span> <span class="o">=</span> <span class="bp">None</span> |
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134 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_err</span> <span class="o">=</span> <span class="bp">None</span> |
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135 | |
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136 | <span class="c"># Estimates</span> |
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137 | <span class="bp">self</span><span class="o">.</span><span class="n">alpha_estimate</span> <span class="o">=</span> <span class="bp">None</span> |
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138 | <span class="bp">self</span><span class="o">.</span><span class="n">nterms_estimate</span> <span class="o">=</span> <span class="bp">None</span> |
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139 | |
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140 | <span class="c"># Data</span> |
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141 | <span class="bp">self</span><span class="o">.</span><span class="n">q</span> <span class="o">=</span> <span class="bp">None</span> |
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142 | <span class="bp">self</span><span class="o">.</span><span class="n">iq_obs</span> <span class="o">=</span> <span class="bp">None</span> |
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143 | <span class="bp">self</span><span class="o">.</span><span class="n">iq_calc</span> <span class="o">=</span> <span class="bp">None</span> |
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144 | |
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145 | <span class="c"># Coefficients</span> |
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146 | <span class="bp">self</span><span class="o">.</span><span class="n">coefficients</span> <span class="o">=</span> <span class="bp">None</span> |
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147 | <span class="bp">self</span><span class="o">.</span><span class="n">covariance</span> <span class="o">=</span> <span class="bp">None</span> |
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148 | |
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149 | <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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150 | <span class="sd">"""</span> |
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151 | <span class="sd"> Pretty print</span> |
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152 | <span class="sd"> </span> |
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153 | <span class="sd"> :return: string representing the state</span> |
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154 | <span class="sd"> </span> |
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155 | <span class="sd"> """</span> |
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156 | <span class="n">state</span> <span class="o">=</span> <span class="s">"File: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">file</span> |
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157 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"Timestamp: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">timestamp</span> |
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158 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"Estimate bck: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">estimate_bck</span><span class="p">)</span> |
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159 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"No. terms: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nfunc</span><span class="p">)</span> |
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160 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"D_max: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">d_max</span><span class="p">)</span> |
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161 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"Alpha: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">alpha</span><span class="p">)</span> |
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162 | |
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163 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"Slit height: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">height</span><span class="p">)</span> |
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164 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"Slit width: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">width</span><span class="p">)</span> |
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165 | |
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166 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"Qmin: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">qmin</span><span class="p">)</span> |
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167 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"Qmax: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">qmax</span><span class="p">)</span> |
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168 | |
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169 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"</span><span class="se">\n</span><span class="s">Estimates:</span><span class="se">\n</span><span class="s">"</span> |
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170 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" Alpha: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">alpha_estimate</span><span class="p">)</span> |
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171 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" Nterms: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nterms_estimate</span><span class="p">)</span> |
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172 | |
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173 | <span class="n">state</span> <span class="o">+=</span> <span class="s">"</span><span class="se">\n</span><span class="s">Outputs:</span><span class="se">\n</span><span class="s">"</span> |
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174 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" Elapsed: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">elapsed</span><span class="p">)</span> |
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175 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" Rg: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rg</span><span class="p">)</span> |
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176 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" I(q=0): </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">iq0</span><span class="p">)</span> |
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177 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" Bck: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bck</span><span class="p">)</span> |
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178 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" Chi^2: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">chi2</span><span class="p">)</span> |
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179 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" Oscillation:</span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">osc</span><span class="p">)</span> |
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180 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" Positive: </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos</span><span class="p">)</span> |
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181 | <span class="n">state</span> <span class="o">+=</span> <span class="s">" 1-sigma pos:</span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_err</span><span class="p">)</span> |
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182 | |
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183 | <span class="k">return</span> <span class="n">state</span> |
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184 | |
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185 | <div class="viewcode-block" id="InversionState.toXML"><a class="viewcode-back" href="../../../../dev/api/sas.perspectives.pr.html#sas.perspectives.pr.inversion_state.InversionState.toXML">[docs]</a> <span class="k">def</span> <span class="nf">toXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="s">"pr_state.prv"</span><span class="p">,</span> <span class="n">doc</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">entry_node</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
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186 | <span class="sd">"""</span> |
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187 | <span class="sd"> Writes the state of the InversionControl panel to file, as XML.</span> |
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188 | <span class="sd"> </span> |
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189 | <span class="sd"> Compatible with standalone writing, or appending to an</span> |
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190 | <span class="sd"> already existing XML document. In that case, the XML document</span> |
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191 | <span class="sd"> is required. An optional entry node in the XML document </span> |
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192 | <span class="sd"> may also be given.</span> |
---|
193 | <span class="sd"> </span> |
---|
194 | <span class="sd"> :param file: file to write to</span> |
---|
195 | <span class="sd"> :param doc: XML document object [optional]</span> |
---|
196 | <span class="sd"> :param entry_node: XML node within the XML document at which </span> |
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197 | <span class="sd"> we will append the data [optional]</span> |
---|
198 | <span class="sd"> </span> |
---|
199 | <span class="sd"> """</span> |
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200 | <span class="c">#TODO: Get this to work</span> |
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201 | <span class="kn">from</span> <span class="nn">xml.dom.minidom</span> <span class="kn">import</span> <span class="n">getDOMImplementation</span> |
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202 | |
---|
203 | <span class="c"># Check whether we have to write a standalone XML file</span> |
---|
204 | <span class="k">if</span> <span class="n">doc</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> |
---|
205 | <span class="n">impl</span> <span class="o">=</span> <span class="n">getDOMImplementation</span><span class="p">()</span> |
---|
206 | |
---|
207 | <span class="n">doc_type</span> <span class="o">=</span> <span class="n">impl</span><span class="o">.</span><span class="n">createDocumentType</span><span class="p">(</span><span class="n">PRNODE_NAME</span><span class="p">,</span> <span class="s">"1.0"</span><span class="p">,</span> <span class="s">"1.0"</span><span class="p">)</span> |
---|
208 | |
---|
209 | <span class="n">newdoc</span> <span class="o">=</span> <span class="n">impl</span><span class="o">.</span><span class="n">createDocument</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="n">PRNODE_NAME</span><span class="p">,</span> <span class="n">doc_type</span><span class="p">)</span> |
---|
210 | <span class="n">top_element</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">documentElement</span> |
---|
211 | <span class="k">else</span><span class="p">:</span> |
---|
212 | <span class="c"># We are appending to an existing document</span> |
---|
213 | <span class="n">newdoc</span> <span class="o">=</span> <span class="n">doc</span> |
---|
214 | <span class="n">top_element</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createElement</span><span class="p">(</span><span class="n">PRNODE_NAME</span><span class="p">)</span> |
---|
215 | <span class="k">if</span> <span class="n">entry_node</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> |
---|
216 | <span class="n">newdoc</span><span class="o">.</span><span class="n">documentElement</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">top_element</span><span class="p">)</span> |
---|
217 | <span class="k">else</span><span class="p">:</span> |
---|
218 | <span class="n">entry_node</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">top_element</span><span class="p">)</span> |
---|
219 | |
---|
220 | <span class="n">attr</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createAttribute</span><span class="p">(</span><span class="s">"version"</span><span class="p">)</span> |
---|
221 | <span class="n">attr</span><span class="o">.</span><span class="n">nodeValue</span> <span class="o">=</span> <span class="s">'1.0'</span> |
---|
222 | <span class="n">top_element</span><span class="o">.</span><span class="n">setAttributeNode</span><span class="p">(</span><span class="n">attr</span><span class="p">)</span> |
---|
223 | |
---|
224 | <span class="c"># File name</span> |
---|
225 | <span class="n">element</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createElement</span><span class="p">(</span><span class="s">"filename"</span><span class="p">)</span> |
---|
226 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">file</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
227 | <span class="n">element</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">newdoc</span><span class="o">.</span><span class="n">createTextNode</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="p">)))</span> |
---|
228 | <span class="k">else</span><span class="p">:</span> |
---|
229 | <span class="n">element</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">newdoc</span><span class="o">.</span><span class="n">createTextNode</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="nb">file</span><span class="p">)))</span> |
---|
230 | <span class="n">top_element</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">element</span><span class="p">)</span> |
---|
231 | |
---|
232 | <span class="n">element</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createElement</span><span class="p">(</span><span class="s">"timestamp"</span><span class="p">)</span> |
---|
233 | <span class="n">element</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">newdoc</span><span class="o">.</span><span class="n">createTextNode</span><span class="p">(</span><span class="n">time</span><span class="o">.</span><span class="n">ctime</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">timestamp</span><span class="p">)))</span> |
---|
234 | <span class="n">attr</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createAttribute</span><span class="p">(</span><span class="s">"epoch"</span><span class="p">)</span> |
---|
235 | <span class="n">attr</span><span class="o">.</span><span class="n">nodeValue</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">timestamp</span><span class="p">)</span> |
---|
236 | <span class="n">element</span><span class="o">.</span><span class="n">setAttributeNode</span><span class="p">(</span><span class="n">attr</span><span class="p">)</span> |
---|
237 | <span class="n">top_element</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">element</span><span class="p">)</span> |
---|
238 | |
---|
239 | <span class="c"># Inputs</span> |
---|
240 | <span class="n">inputs</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createElement</span><span class="p">(</span><span class="s">"inputs"</span><span class="p">)</span> |
---|
241 | <span class="n">top_element</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">inputs</span><span class="p">)</span> |
---|
242 | |
---|
243 | <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">in_list</span><span class="p">:</span> |
---|
244 | <span class="n">element</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createElement</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> |
---|
245 | <span class="n">cmd</span> <span class="o">=</span> <span class="s">"element.appendChild(newdoc.createTextNode(str(self.</span><span class="si">%s</span><span class="s">)))"</span> |
---|
246 | <span class="k">exec</span> <span class="n">cmd</span> <span class="o">%</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> |
---|
247 | <span class="n">inputs</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">element</span><span class="p">)</span> |
---|
248 | |
---|
249 | <span class="c"># Outputs</span> |
---|
250 | <span class="n">outputs</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createElement</span><span class="p">(</span><span class="s">"outputs"</span><span class="p">)</span> |
---|
251 | <span class="n">top_element</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">outputs</span><span class="p">)</span> |
---|
252 | |
---|
253 | <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">out_list</span><span class="p">:</span> |
---|
254 | <span class="n">element</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createElement</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> |
---|
255 | <span class="n">cmd</span> <span class="o">=</span> <span class="s">"element.appendChild(newdoc.createTextNode(str(self.</span><span class="si">%s</span><span class="s">)))"</span> |
---|
256 | <span class="k">exec</span> <span class="n">cmd</span> <span class="o">%</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> |
---|
257 | <span class="n">outputs</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">element</span><span class="p">)</span> |
---|
258 | |
---|
259 | <span class="c"># Save output coefficients and its covariance matrix</span> |
---|
260 | <span class="n">element</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createElement</span><span class="p">(</span><span class="s">"coefficients"</span><span class="p">)</span> |
---|
261 | <span class="n">element</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">newdoc</span><span class="o">.</span><span class="n">createTextNode</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">coefficients</span><span class="p">)))</span> |
---|
262 | <span class="n">outputs</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">element</span><span class="p">)</span> |
---|
263 | <span class="n">element</span> <span class="o">=</span> <span class="n">newdoc</span><span class="o">.</span><span class="n">createElement</span><span class="p">(</span><span class="s">"covariance"</span><span class="p">)</span> |
---|
264 | <span class="n">element</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">newdoc</span><span class="o">.</span><span class="n">createTextNode</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">covariance</span><span class="p">)))</span> |
---|
265 | <span class="n">outputs</span><span class="o">.</span><span class="n">appendChild</span><span class="p">(</span><span class="n">element</span><span class="p">)</span> |
---|
266 | |
---|
267 | <span class="c"># Save the file</span> |
---|
268 | <span class="k">if</span> <span class="n">doc</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> |
---|
269 | <span class="n">fd</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span> |
---|
270 | <span class="n">fd</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">newdoc</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">())</span> |
---|
271 | <span class="n">fd</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> |
---|
272 | <span class="k">return</span> <span class="bp">None</span> |
---|
273 | <span class="k">else</span><span class="p">:</span> |
---|
274 | <span class="k">return</span> <span class="n">newdoc</span> |
---|
275 | </div> |
---|
276 | <div class="viewcode-block" id="InversionState.fromXML"><a class="viewcode-back" href="../../../../dev/api/sas.perspectives.pr.html#sas.perspectives.pr.inversion_state.InversionState.fromXML">[docs]</a> <span class="k">def</span> <span class="nf">fromXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">node</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
---|
277 | <span class="sd">"""</span> |
---|
278 | <span class="sd"> Load a P(r) inversion state from a file</span> |
---|
279 | <span class="sd"> </span> |
---|
280 | <span class="sd"> :param file: .prv file</span> |
---|
281 | <span class="sd"> :param node: node of a XML document to read from</span> |
---|
282 | <span class="sd"> </span> |
---|
283 | <span class="sd"> """</span> |
---|
284 | <span class="k">if</span> <span class="nb">file</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
285 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"InversionState no longer supports non-CanSAS"</span> |
---|
286 | <span class="n">msg</span> <span class="o">+=</span> <span class="s">" format for P(r) files"</span> |
---|
287 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">msg</span> |
---|
288 | |
---|
289 | <span class="k">if</span> <span class="n">node</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'version'</span><span class="p">)</span> <span class="ow">and</span> <span class="n">node</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'version'</span><span class="p">)</span> <span class="o">==</span> <span class="s">'1.0'</span><span class="p">:</span> |
---|
290 | |
---|
291 | <span class="c"># Get file name</span> |
---|
292 | <span class="n">entry</span> <span class="o">=</span> <span class="n">get_content</span><span class="p">(</span><span class="s">'ns:filename'</span><span class="p">,</span> <span class="n">node</span><span class="p">)</span> |
---|
293 | <span class="k">if</span> <span class="n">entry</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
294 | <span class="bp">self</span><span class="o">.</span><span class="n">file</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> |
---|
295 | |
---|
296 | <span class="c"># Get time stamp</span> |
---|
297 | <span class="n">entry</span> <span class="o">=</span> <span class="n">get_content</span><span class="p">(</span><span class="s">'ns:timestamp'</span><span class="p">,</span> <span class="n">node</span><span class="p">)</span> |
---|
298 | <span class="k">if</span> <span class="n">entry</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">entry</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'epoch'</span><span class="p">):</span> |
---|
299 | <span class="k">try</span><span class="p">:</span> |
---|
300 | <span class="bp">self</span><span class="o">.</span><span class="n">timestamp</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">entry</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'epoch'</span><span class="p">))</span> |
---|
301 | <span class="k">except</span><span class="p">:</span> |
---|
302 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"InversionState.fromXML: Could not read "</span> |
---|
303 | <span class="n">msg</span> <span class="o">+=</span> <span class="s">"timestamp</span><span class="se">\n</span><span class="s"> </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_value</span> |
---|
304 | <span class="n">logging</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span> |
---|
305 | |
---|
306 | <span class="c"># Parse inversion inputs</span> |
---|
307 | <span class="n">entry</span> <span class="o">=</span> <span class="n">get_content</span><span class="p">(</span><span class="s">'ns:inputs'</span><span class="p">,</span> <span class="n">node</span><span class="p">)</span> |
---|
308 | <span class="k">if</span> <span class="n">entry</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
309 | <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">in_list</span><span class="p">:</span> |
---|
310 | <span class="n">input_field</span> <span class="o">=</span> <span class="n">get_content</span><span class="p">(</span><span class="s">'ns:</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">entry</span><span class="p">)</span> |
---|
311 | <span class="k">if</span> <span class="n">input_field</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
312 | <span class="k">try</span><span class="p">:</span> |
---|
313 | <span class="n">cmd</span> <span class="o">=</span> <span class="s">'self.</span><span class="si">%s</span><span class="s"> = float(input_field.text.strip())'</span> |
---|
314 | <span class="k">exec</span> <span class="n">cmd</span> <span class="o">%</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> |
---|
315 | <span class="k">except</span><span class="p">:</span> |
---|
316 | <span class="k">exec</span> <span class="s">'self.</span><span class="si">%s</span><span class="s"> = None'</span> <span class="o">%</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> |
---|
317 | <span class="n">input_field</span> <span class="o">=</span> <span class="n">get_content</span><span class="p">(</span><span class="s">'ns:estimate_bck'</span><span class="p">,</span> <span class="n">entry</span><span class="p">)</span> |
---|
318 | <span class="k">if</span> <span class="n">input_field</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
319 | <span class="k">try</span><span class="p">:</span> |
---|
320 | <span class="bp">self</span><span class="o">.</span><span class="n">estimate_bck</span> <span class="o">=</span> <span class="n">input_field</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">==</span><span class="s">'True'</span> |
---|
321 | <span class="k">except</span><span class="p">:</span> |
---|
322 | <span class="bp">self</span><span class="o">.</span><span class="n">estimate_bck</span> <span class="o">=</span> <span class="bp">False</span> |
---|
323 | |
---|
324 | <span class="c"># Parse inversion outputs</span> |
---|
325 | <span class="n">entry</span> <span class="o">=</span> <span class="n">get_content</span><span class="p">(</span><span class="s">'ns:outputs'</span><span class="p">,</span> <span class="n">node</span><span class="p">)</span> |
---|
326 | <span class="k">if</span> <span class="n">entry</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
327 | <span class="c"># Output parameters (scalars)</span> |
---|
328 | <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">out_list</span><span class="p">:</span> |
---|
329 | <span class="n">input_field</span> <span class="o">=</span> <span class="n">get_content</span><span class="p">(</span><span class="s">'ns:</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">entry</span><span class="p">)</span> |
---|
330 | <span class="k">if</span> <span class="n">input_field</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
331 | <span class="k">try</span><span class="p">:</span> |
---|
332 | <span class="n">cmd</span> <span class="o">=</span> <span class="s">'self.</span><span class="si">%s</span><span class="s"> = float(input_field.text.strip())'</span> |
---|
333 | <span class="k">exec</span> <span class="n">cmd</span> <span class="o">%</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> |
---|
334 | <span class="k">except</span><span class="p">:</span> |
---|
335 | <span class="k">exec</span> <span class="s">'self.</span><span class="si">%s</span><span class="s"> = None'</span> <span class="o">%</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> |
---|
336 | |
---|
337 | <span class="c"># Look for coefficients</span> |
---|
338 | <span class="c"># Format is [value, value, value, value]</span> |
---|
339 | <span class="n">coeff</span> <span class="o">=</span> <span class="n">get_content</span><span class="p">(</span><span class="s">'ns:coefficients'</span><span class="p">,</span> <span class="n">entry</span><span class="p">)</span> |
---|
340 | <span class="k">if</span> <span class="n">coeff</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
341 | <span class="c"># Remove brackets</span> |
---|
342 | <span class="n">c_values</span> <span class="o">=</span> <span class="n">coeff</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">'['</span><span class="p">,</span><span class="s">''</span><span class="p">)</span> |
---|
343 | <span class="n">c_values</span> <span class="o">=</span> <span class="n">c_values</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">']'</span><span class="p">,</span><span class="s">''</span><span class="p">)</span> |
---|
344 | <span class="n">toks</span> <span class="o">=</span> <span class="n">c_values</span><span class="o">.</span><span class="n">split</span><span class="p">()</span> |
---|
345 | <span class="bp">self</span><span class="o">.</span><span class="n">coefficients</span> <span class="o">=</span> <span class="p">[]</span> |
---|
346 | <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">toks</span><span class="p">:</span> |
---|
347 | <span class="k">try</span><span class="p">:</span> |
---|
348 | <span class="bp">self</span><span class="o">.</span><span class="n">coefficients</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">c</span><span class="p">))</span> |
---|
349 | <span class="k">except</span><span class="p">:</span> |
---|
350 | <span class="c"># Bad data, skip. We will count the number of </span> |
---|
351 | <span class="c"># coefficients at the very end and deal with </span> |
---|
352 | <span class="c"># inconsistencies then.</span> |
---|
353 | <span class="k">pass</span> |
---|
354 | <span class="c"># Sanity check</span> |
---|
355 | <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">coefficients</span><span class="p">)</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">nfunc</span><span class="p">:</span> |
---|
356 | <span class="c"># Inconsistent number of coefficients.</span> |
---|
357 | <span class="c"># Don't keep the data.</span> |
---|
358 | <span class="n">err_msg</span> <span class="o">=</span> <span class="s">"InversionState.fromXML: inconsistant "</span> |
---|
359 | <span class="n">err_msg</span> <span class="o">+=</span> <span class="s">"number of coefficients: "</span> |
---|
360 | <span class="n">err_msg</span> <span class="o">+=</span> <span class="s">"</span><span class="si">%d</span><span class="s"> </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">coefficients</span><span class="p">),</span> |
---|
361 | <span class="bp">self</span><span class="o">.</span><span class="n">nfunc</span><span class="p">)</span> |
---|
362 | <span class="n">logging</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">err_msg</span><span class="p">)</span> |
---|
363 | <span class="bp">self</span><span class="o">.</span><span class="n">coefficients</span> <span class="o">=</span> <span class="bp">None</span> |
---|
364 | |
---|
365 | <span class="c"># Look for covariance matrix</span> |
---|
366 | <span class="c"># Format is [ [value, value], [value, value] ]</span> |
---|
367 | <span class="n">coeff</span> <span class="o">=</span> <span class="n">get_content</span><span class="p">(</span><span class="s">'ns:covariance'</span><span class="p">,</span> <span class="n">entry</span><span class="p">)</span> |
---|
368 | <span class="k">if</span> <span class="n">coeff</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
369 | <span class="c"># Parse rows</span> |
---|
370 | <span class="n">rows</span> <span class="o">=</span> <span class="n">coeff</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'['</span><span class="p">)</span> |
---|
371 | <span class="bp">self</span><span class="o">.</span><span class="n">covariance</span> <span class="o">=</span> <span class="p">[]</span> |
---|
372 | <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">rows</span><span class="p">:</span> |
---|
373 | <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> |
---|
374 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span> |
---|
375 | <span class="c"># Remove end bracket</span> |
---|
376 | <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">']'</span><span class="p">,</span><span class="s">''</span><span class="p">)</span> |
---|
377 | <span class="n">c_values</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">split</span><span class="p">()</span> |
---|
378 | <span class="n">cov_row</span> <span class="o">=</span> <span class="p">[]</span> |
---|
379 | <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">c_values</span><span class="p">:</span> |
---|
380 | <span class="k">try</span><span class="p">:</span> |
---|
381 | <span class="n">cov_row</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">c</span><span class="p">))</span> |
---|
382 | <span class="k">except</span><span class="p">:</span> |
---|
383 | <span class="c"># Bad data, skip. We will count the number of </span> |
---|
384 | <span class="c"># coefficients at the very end and deal with </span> |
---|
385 | <span class="c"># inconsistencies then.</span> |
---|
386 | <span class="k">pass</span> |
---|
387 | <span class="c"># Sanity check: check the number of entries in the row</span> |
---|
388 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">cov_row</span><span class="p">)</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">nfunc</span><span class="p">:</span> |
---|
389 | <span class="bp">self</span><span class="o">.</span><span class="n">covariance</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cov_row</span><span class="p">)</span> |
---|
390 | <span class="c"># Sanity check: check the number of rows in the covariance</span> |
---|
391 | <span class="c"># matrix</span> |
---|
392 | <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">covariance</span><span class="p">)</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">nfunc</span><span class="p">:</span> |
---|
393 | <span class="c"># Inconsistent dimensions of the covariance matrix.</span> |
---|
394 | <span class="c"># Don't keep the data.</span> |
---|
395 | <span class="n">err_msg</span> <span class="o">=</span> <span class="s">"InversionState.fromXML: "</span> |
---|
396 | <span class="n">err_msg</span> <span class="o">+=</span> <span class="s">"inconsistant dimensions of the "</span> |
---|
397 | <span class="n">err_msg</span> <span class="o">+=</span> <span class="s">" covariance matrix: "</span> |
---|
398 | <span class="n">err_msg</span> <span class="o">+=</span> <span class="s">"</span><span class="si">%d</span><span class="s"> </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">covariance</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">nfunc</span><span class="p">)</span> |
---|
399 | <span class="n">logging</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">err_msg</span><span class="p">)</span> |
---|
400 | <span class="bp">self</span><span class="o">.</span><span class="n">covariance</span> <span class="o">=</span> <span class="bp">None</span> |
---|
401 | </div></div> |
---|
402 | <div class="viewcode-block" id="Reader"><a class="viewcode-back" href="../../../../dev/api/sas.perspectives.pr.html#sas.perspectives.pr.inversion_state.Reader">[docs]</a><span class="k">class</span> <span class="nc">Reader</span><span class="p">(</span><span class="n">CansasReader</span><span class="p">):</span> |
---|
403 | <span class="sd">"""</span> |
---|
404 | <span class="sd"> Class to load a .prv P(r) inversion file</span> |
---|
405 | <span class="sd"> """</span> |
---|
406 | <span class="c">## File type</span> |
---|
407 | <span class="n">type_name</span> <span class="o">=</span> <span class="s">"P(r)"</span> |
---|
408 | |
---|
409 | <span class="c">## Wildcards</span> |
---|
410 | <span class="nb">type</span> <span class="o">=</span> <span class="p">[</span><span class="s">"P(r) files (*.prv)|*.prv"</span><span class="p">,</span> |
---|
411 | <span class="s">"SASView files (*.svs)|*.svs"</span><span class="p">]</span> |
---|
412 | <span class="c">## List of allowed extensions</span> |
---|
413 | <span class="n">ext</span> <span class="o">=</span> <span class="p">[</span><span class="s">'.prv'</span><span class="p">,</span> <span class="s">'.PRV'</span><span class="p">,</span> <span class="s">'.svs'</span><span class="p">,</span> <span class="s">'.SVS'</span><span class="p">]</span> |
---|
414 | |
---|
415 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">call_back</span><span class="p">,</span> <span class="n">cansas</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span> |
---|
416 | <span class="sd">"""</span> |
---|
417 | <span class="sd"> Initialize the call-back method to be called</span> |
---|
418 | <span class="sd"> after we load a file</span> |
---|
419 | <span class="sd"> </span> |
---|
420 | <span class="sd"> :param call_back: call-back method</span> |
---|
421 | <span class="sd"> :param cansas: True = files will be written/read in CanSAS format</span> |
---|
422 | <span class="sd"> False = write CanSAS format</span> |
---|
423 | <span class="sd"> </span> |
---|
424 | <span class="sd"> """</span> |
---|
425 | <span class="c">## Call back method to be executed after a file is read</span> |
---|
426 | <span class="bp">self</span><span class="o">.</span><span class="n">call_back</span> <span class="o">=</span> <span class="n">call_back</span> |
---|
427 | <span class="c">## CanSAS format flag</span> |
---|
428 | <span class="bp">self</span><span class="o">.</span><span class="n">cansas</span> <span class="o">=</span> <span class="n">cansas</span> |
---|
429 | <span class="bp">self</span><span class="o">.</span><span class="n">state</span> <span class="o">=</span> <span class="bp">None</span> |
---|
430 | |
---|
431 | <div class="viewcode-block" id="Reader.read"><a class="viewcode-back" href="../../../../dev/api/sas.perspectives.pr.html#sas.perspectives.pr.inversion_state.Reader.read">[docs]</a> <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span> |
---|
432 | <span class="sd">""" </span> |
---|
433 | <span class="sd"> Load a new P(r) inversion state from file</span> |
---|
434 | <span class="sd"> </span> |
---|
435 | <span class="sd"> :param path: file path</span> |
---|
436 | <span class="sd"> </span> |
---|
437 | <span class="sd"> :return: None</span> |
---|
438 | <span class="sd"> </span> |
---|
439 | <span class="sd"> """</span> |
---|
440 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">cansas</span><span class="o">==</span><span class="bp">True</span><span class="p">:</span> |
---|
441 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_read_cansas</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> |
---|
442 | <span class="k">else</span><span class="p">:</span> |
---|
443 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_read_standalone</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> |
---|
444 | </div> |
---|
445 | <span class="k">def</span> <span class="nf">_read_standalone</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span> |
---|
446 | <span class="sd">""" </span> |
---|
447 | <span class="sd"> Load a new P(r) inversion state from file.</span> |
---|
448 | <span class="sd"> The P(r) node is assumed to be the top element.</span> |
---|
449 | <span class="sd"> </span> |
---|
450 | <span class="sd"> :param path: file path</span> |
---|
451 | <span class="sd"> </span> |
---|
452 | <span class="sd"> :return: None</span> |
---|
453 | <span class="sd"> </span> |
---|
454 | <span class="sd"> """</span> |
---|
455 | <span class="c"># Read the new state from file</span> |
---|
456 | <span class="n">state</span> <span class="o">=</span> <span class="n">InversionState</span><span class="p">()</span> |
---|
457 | <span class="n">state</span><span class="o">.</span><span class="n">fromXML</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">path</span><span class="p">)</span> |
---|
458 | |
---|
459 | <span class="c"># Call back to post the new state</span> |
---|
460 | <span class="bp">self</span><span class="o">.</span><span class="n">state</span> <span class="o">=</span> <span class="n">state</span> |
---|
461 | <span class="c">#self.call_back(state)</span> |
---|
462 | <span class="k">return</span> <span class="bp">None</span> |
---|
463 | |
---|
464 | <span class="k">def</span> <span class="nf">_parse_prstate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entry</span><span class="p">):</span> |
---|
465 | <span class="sd">"""</span> |
---|
466 | <span class="sd"> Read a p(r) inversion result from an XML node</span> |
---|
467 | <span class="sd"> </span> |
---|
468 | <span class="sd"> :param entry: XML node to read from </span> |
---|
469 | <span class="sd"> </span> |
---|
470 | <span class="sd"> :return: InversionState object</span> |
---|
471 | <span class="sd"> </span> |
---|
472 | <span class="sd"> """</span> |
---|
473 | <span class="n">state</span> <span class="o">=</span> <span class="bp">None</span> |
---|
474 | |
---|
475 | <span class="c"># Locate the P(r) node</span> |
---|
476 | <span class="k">try</span><span class="p">:</span> |
---|
477 | <span class="n">nodes</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">xpath</span><span class="p">(</span><span class="s">'ns:</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="n">PRNODE_NAME</span><span class="p">,</span> |
---|
478 | <span class="n">namespaces</span><span class="o">=</span><span class="p">{</span><span class="s">'ns'</span><span class="p">:</span> <span class="n">CANSAS_NS</span><span class="p">})</span> |
---|
479 | <span class="k">if</span> <span class="n">nodes</span> <span class="o">!=</span><span class="p">[]:</span> |
---|
480 | <span class="c"># Create an empty state</span> |
---|
481 | <span class="n">state</span> <span class="o">=</span> <span class="n">InversionState</span><span class="p">()</span> |
---|
482 | <span class="n">state</span><span class="o">.</span><span class="n">fromXML</span><span class="p">(</span><span class="n">node</span><span class="o">=</span><span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> |
---|
483 | <span class="k">except</span><span class="p">:</span> |
---|
484 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"XML document does not contain P(r) "</span> |
---|
485 | <span class="n">msg</span> <span class="o">+=</span> <span class="s">"information.</span><span class="se">\n</span><span class="s"> </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_value</span> |
---|
486 | <span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span> |
---|
487 | |
---|
488 | <span class="k">return</span> <span class="n">state</span> |
---|
489 | |
---|
490 | <span class="k">def</span> <span class="nf">_read_cansas</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span> |
---|
491 | <span class="sd">""" </span> |
---|
492 | <span class="sd"> Load data and P(r) information from a CanSAS XML file.</span> |
---|
493 | <span class="sd"> </span> |
---|
494 | <span class="sd"> :param path: file path</span> |
---|
495 | <span class="sd"> </span> |
---|
496 | <span class="sd"> :return: Data1D object if a single SASentry was found, </span> |
---|
497 | <span class="sd"> or a list of Data1D objects if multiple entries were found,</span> |
---|
498 | <span class="sd"> or None of nothing was found</span> |
---|
499 | <span class="sd"> </span> |
---|
500 | <span class="sd"> :raise RuntimeError: when the file can't be opened</span> |
---|
501 | <span class="sd"> :raise ValueError: when the length of the data vectors are inconsistent</span> |
---|
502 | <span class="sd"> </span> |
---|
503 | <span class="sd"> """</span> |
---|
504 | <span class="n">output</span> <span class="o">=</span> <span class="p">[]</span> |
---|
505 | |
---|
506 | <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">path</span><span class="p">):</span> |
---|
507 | <span class="n">basename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> |
---|
508 | <span class="n">root</span><span class="p">,</span> <span class="n">extension</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">basename</span><span class="p">)</span> |
---|
509 | <span class="c">#TODO: eventually remove the check for .xml once</span> |
---|
510 | <span class="c"># the P(r) writer/reader is truly complete.</span> |
---|
511 | <span class="k">if</span> <span class="n">extension</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ext</span> <span class="ow">or</span> <span class="n">extension</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">'.xml'</span><span class="p">:</span> |
---|
512 | |
---|
513 | <span class="n">tree</span> <span class="o">=</span> <span class="n">etree</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">parser</span><span class="o">=</span><span class="n">etree</span><span class="o">.</span><span class="n">ETCompatXMLParser</span><span class="p">())</span> |
---|
514 | <span class="c"># Check the format version number</span> |
---|
515 | <span class="c"># Specifying the namespace will take care of the file </span> |
---|
516 | <span class="c">#format version </span> |
---|
517 | <span class="n">root</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">getroot</span><span class="p">()</span> |
---|
518 | |
---|
519 | <span class="n">entry_list</span> <span class="o">=</span> <span class="n">root</span><span class="o">.</span><span class="n">xpath</span><span class="p">(</span><span class="s">'/ns:SASroot/ns:SASentry'</span><span class="p">,</span> |
---|
520 | <span class="n">namespaces</span><span class="o">=</span><span class="p">{</span><span class="s">'ns'</span><span class="p">:</span> <span class="n">CANSAS_NS</span><span class="p">})</span> |
---|
521 | |
---|
522 | <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">entry_list</span><span class="p">:</span> |
---|
523 | <span class="n">sas_entry</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parse_entry</span><span class="p">(</span><span class="n">entry</span><span class="p">)</span> |
---|
524 | <span class="n">prstate</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parse_prstate</span><span class="p">(</span><span class="n">entry</span><span class="p">)</span> |
---|
525 | <span class="c">#prstate could be None when .svs file is loaded</span> |
---|
526 | <span class="c">#in this case, skip appending to output</span> |
---|
527 | <span class="k">if</span> <span class="n">prstate</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span> |
---|
528 | <span class="n">sas_entry</span><span class="o">.</span><span class="n">meta_data</span><span class="p">[</span><span class="s">'prstate'</span><span class="p">]</span> <span class="o">=</span> <span class="n">prstate</span> |
---|
529 | <span class="n">sas_entry</span><span class="o">.</span><span class="n">filename</span> <span class="o">=</span> <span class="n">prstate</span><span class="o">.</span><span class="n">file</span> |
---|
530 | <span class="n">output</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sas_entry</span><span class="p">)</span> |
---|
531 | <span class="k">else</span><span class="p">:</span> |
---|
532 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="s">"</span><span class="si">%s</span><span class="s"> is not a file"</span> <span class="o">%</span> <span class="n">path</span> |
---|
533 | |
---|
534 | <span class="c"># Return output consistent with the loader's api</span> |
---|
535 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">output</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> |
---|
536 | <span class="k">return</span> <span class="bp">None</span> |
---|
537 | <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">output</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> |
---|
538 | <span class="c"># Call back to post the new state</span> |
---|
539 | <span class="bp">self</span><span class="o">.</span><span class="n">call_back</span><span class="p">(</span><span class="n">output</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">meta_data</span><span class="p">[</span><span class="s">'prstate'</span><span class="p">],</span> <span class="n">datainfo</span> <span class="o">=</span> <span class="n">output</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> |
---|
540 | <span class="c">#self.state = output[0].meta_data['prstate']</span> |
---|
541 | <span class="k">return</span> <span class="n">output</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> |
---|
542 | <span class="k">else</span><span class="p">:</span> |
---|
543 | <span class="k">return</span> <span class="n">output</span> |
---|
544 | |
---|
545 | |
---|
546 | <div class="viewcode-block" id="Reader.write"><a class="viewcode-back" href="../../../../dev/api/sas.perspectives.pr.html#sas.perspectives.pr.inversion_state.Reader.write">[docs]</a> <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">datainfo</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">prstate</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
---|
547 | <span class="sd">"""</span> |
---|
548 | <span class="sd"> Write the content of a Data1D as a CanSAS XML file</span> |
---|
549 | <span class="sd"> </span> |
---|
550 | <span class="sd"> :param filename: name of the file to write</span> |
---|
551 | <span class="sd"> :param datainfo: Data1D object</span> |
---|
552 | <span class="sd"> :param prstate: InversionState object</span> |
---|
553 | <span class="sd"> </span> |
---|
554 | <span class="sd"> """</span> |
---|
555 | <span class="c"># Sanity check</span> |
---|
556 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">cansas</span> <span class="o">==</span> <span class="bp">True</span><span class="p">:</span> |
---|
557 | <span class="n">doc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">write_toXML</span><span class="p">(</span><span class="n">datainfo</span><span class="p">,</span> <span class="n">prstate</span><span class="p">)</span> |
---|
558 | <span class="c"># Write the XML document</span> |
---|
559 | <span class="n">fd</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span> |
---|
560 | <span class="n">fd</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">doc</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">())</span> |
---|
561 | <span class="n">fd</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> |
---|
562 | <span class="k">else</span><span class="p">:</span> |
---|
563 | <span class="n">prstate</span><span class="o">.</span><span class="n">toXML</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">filename</span><span class="p">)</span> |
---|
564 | </div> |
---|
565 | <div class="viewcode-block" id="Reader.write_toXML"><a class="viewcode-back" href="../../../../dev/api/sas.perspectives.pr.html#sas.perspectives.pr.inversion_state.Reader.write_toXML">[docs]</a> <span class="k">def</span> <span class="nf">write_toXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">datainfo</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">state</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
---|
566 | <span class="sd">"""</span> |
---|
567 | <span class="sd"> Write toXML, a helper for write()</span> |
---|
568 | <span class="sd"> </span> |
---|
569 | <span class="sd"> : return: xml doc</span> |
---|
570 | <span class="sd"> """</span> |
---|
571 | <span class="k">if</span> <span class="n">datainfo</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> |
---|
572 | <span class="n">datainfo</span> <span class="o">=</span> <span class="n">Data1D</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="p">[],</span> <span class="n">y</span><span class="o">=</span><span class="p">[])</span> |
---|
573 | <span class="k">elif</span> <span class="ow">not</span> <span class="nb">issubclass</span><span class="p">(</span><span class="n">datainfo</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span> <span class="n">Data1D</span><span class="p">):</span> |
---|
574 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"The cansas writer expects a Data1D "</span> |
---|
575 | <span class="n">msg</span> <span class="o">+=</span> <span class="s">"instance: </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">datainfo</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span><span class="p">)</span> |
---|
576 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">msg</span> |
---|
577 | |
---|
578 | <span class="c"># Create basic XML document</span> |
---|
579 | <span class="n">doc</span><span class="p">,</span> <span class="n">sasentry</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_to_xml_doc</span><span class="p">(</span><span class="n">datainfo</span><span class="p">)</span> |
---|
580 | |
---|
581 | <span class="c"># Add the invariant information to the XML document</span> |
---|
582 | <span class="k">if</span> <span class="n">state</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
583 | <span class="n">doc</span> <span class="o">=</span> <span class="n">state</span><span class="o">.</span><span class="n">toXML</span><span class="p">(</span><span class="n">doc</span><span class="o">=</span><span class="n">doc</span><span class="p">,</span> <span class="n">entry_node</span><span class="o">=</span><span class="n">sasentry</span><span class="p">)</span> |
---|
584 | |
---|
585 | <span class="k">return</span> <span class="n">doc</span> |
---|
586 | </div></div> |
---|
587 | </pre></div> |
---|
588 | |
---|
589 | </div> |
---|
590 | </div> |
---|
591 | </div> |
---|
592 | <div class="sphinxsidebar"> |
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593 | <div class="sphinxsidebarwrapper"> |
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594 | <div id="searchbox" style="display: none"> |
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595 | <h3>Quick search</h3> |
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596 | <form class="search" action="../../../../search.html" method="get"> |
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597 | <input type="text" name="q" /> |
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598 | <input type="submit" value="Go" /> |
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599 | <input type="hidden" name="check_keywords" value="yes" /> |
---|
600 | <input type="hidden" name="area" value="default" /> |
---|
601 | </form> |
---|
602 | <p class="searchtip" style="font-size: 90%"> |
---|
603 | Enter search terms or a module, class or function name. |
---|
604 | </p> |
---|
605 | </div> |
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606 | <script type="text/javascript">$('#searchbox').show(0);</script> |
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607 | </div> |
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608 | </div> |
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609 | <div class="clearer"></div> |
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610 | </div> |
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611 | <div class="related"> |
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612 | <h3>Navigation</h3> |
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613 | <ul> |
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614 | <li class="right" style="margin-right: 10px"> |
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615 | <a href="../../../../genindex.html" title="General Index" |
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616 | >index</a></li> |
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617 | <li class="right" > |
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618 | <a href="../../../../py-modindex.html" title="Python Module Index" |
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619 | >modules</a> |</li> |
---|
620 | <li><a href="../../../../index.html">SasView 3.0.0 documentation</a> »</li> |
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621 | <li><a href="../../../index.html" >Module code</a> »</li> |
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622 | </ul> |
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623 | </div> |
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624 | <div class="footer"> |
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625 | © Copyright 2013, The SasView Project. |
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626 | Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. |
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627 | </div> |
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628 | </body> |
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629 | </html> |
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