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50 | <h1>Source code for sas.calculator.sas_gen</h1><div class="highlight"><pre> |
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51 | <span class="sd">"""</span> |
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52 | <span class="sd">SAS generic computation and sld file readers</span> |
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53 | <span class="sd">"""</span> |
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54 | <span class="kn">from</span> <span class="nn">sas.models.BaseComponent</span> <span class="kn">import</span> <span class="n">BaseComponent</span> |
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55 | <span class="kn">import</span> <span class="nn">sas.models.sas_extension.sld2i</span> <span class="kn">as</span> <span class="nn">mod</span> |
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56 | <span class="kn">from</span> <span class="nn">periodictable</span> <span class="kn">import</span> <span class="n">formula</span> |
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57 | <span class="kn">from</span> <span class="nn">periodictable</span> <span class="kn">import</span> <span class="n">nsf</span> |
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58 | <span class="kn">import</span> <span class="nn">numpy</span> |
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59 | <span class="kn">import</span> <span class="nn">os</span> |
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60 | <span class="kn">import</span> <span class="nn">copy</span> |
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61 | |
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62 | <span class="n">MFactor_AM</span> <span class="o">=</span> <span class="mf">2.853E-12</span> |
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63 | <span class="n">MFactor_mT</span> <span class="o">=</span> <span class="mf">2.3164E-9</span> |
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64 | <span class="n">METER2ANG</span> <span class="o">=</span> <span class="mf">1.0E+10</span> |
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65 | <span class="c">#Avogadro constant [1/mol]</span> |
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66 | <span class="n">NA</span> <span class="o">=</span> <span class="mf">6.02214129e+23</span> |
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67 | |
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68 | <div class="viewcode-block" id="mag2sld"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.mag2sld">[docs]</a><span class="k">def</span> <span class="nf">mag2sld</span><span class="p">(</span><span class="n">mag</span><span class="p">,</span> <span class="n">v_unit</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
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69 | <span class="sd">"""</span> |
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70 | <span class="sd"> Convert magnetization to magnatic SLD</span> |
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71 | <span class="sd"> sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton)</span> |
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72 | <span class="sd"> Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]???</span> |
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73 | <span class="sd"> """</span> |
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74 | <span class="k">if</span> <span class="n">v_unit</span> <span class="o">==</span> <span class="s">"A/m"</span><span class="p">:</span> |
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75 | <span class="n">factor</span> <span class="o">=</span> <span class="n">MFactor_AM</span> |
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76 | <span class="k">elif</span> <span class="n">v_unit</span> <span class="o">==</span> <span class="s">"mT"</span><span class="p">:</span> |
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77 | <span class="n">factor</span> <span class="o">=</span> <span class="n">MFactor_mT</span> |
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78 | <span class="k">else</span><span class="p">:</span> |
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79 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">"Invalid valueunit"</span> |
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80 | <span class="n">sld_m</span> <span class="o">=</span> <span class="n">factor</span> <span class="o">*</span> <span class="n">mag</span> |
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81 | <span class="k">return</span> <span class="n">sld_m</span> |
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82 | </div> |
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83 | <div class="viewcode-block" id="transform_center"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.transform_center">[docs]</a><span class="k">def</span> <span class="nf">transform_center</span><span class="p">(</span><span class="n">pos_x</span><span class="p">,</span> <span class="n">pos_y</span><span class="p">,</span> <span class="n">pos_z</span><span class="p">):</span> |
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84 | <span class="sd">"""</span> |
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85 | <span class="sd"> re-center </span> |
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86 | <span class="sd"> </span> |
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87 | <span class="sd"> :return: posx, posy, posz [arrays]</span> |
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88 | <span class="sd"> """</span> |
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89 | <span class="n">posx</span> <span class="o">=</span> <span class="n">pos_x</span> <span class="o">-</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">pos_x</span><span class="p">)</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="n">pos_x</span><span class="p">))</span> <span class="o">/</span> <span class="mf">2.0</span> |
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90 | <span class="n">posy</span> <span class="o">=</span> <span class="n">pos_y</span> <span class="o">-</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">pos_y</span><span class="p">)</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="n">pos_y</span><span class="p">))</span> <span class="o">/</span> <span class="mf">2.0</span> |
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91 | <span class="n">posz</span> <span class="o">=</span> <span class="n">pos_z</span> <span class="o">-</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">pos_z</span><span class="p">)</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="n">pos_z</span><span class="p">))</span> <span class="o">/</span> <span class="mf">2.0</span> |
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92 | <span class="k">return</span> <span class="n">posx</span><span class="p">,</span> <span class="n">posy</span><span class="p">,</span> <span class="n">posz</span> |
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93 | </div> |
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94 | <div class="viewcode-block" id="GenSAS"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.GenSAS">[docs]</a><span class="k">class</span> <span class="nc">GenSAS</span><span class="p">(</span><span class="n">BaseComponent</span><span class="p">):</span> |
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95 | <span class="sd">"""</span> |
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96 | <span class="sd"> Generic SAS computation Model based on sld (n & m) arrays</span> |
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97 | <span class="sd"> """</span> |
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98 | <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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99 | <span class="sd">"""</span> |
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100 | <span class="sd"> Init</span> |
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101 | <span class="sd"> </span> |
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102 | <span class="sd"> :Params sld_data: MagSLD object</span> |
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103 | <span class="sd"> """</span> |
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104 | <span class="c"># Initialize BaseComponent</span> |
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105 | <span class="n">BaseComponent</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> |
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106 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_data</span> <span class="o">=</span> <span class="bp">None</span> |
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107 | <span class="bp">self</span><span class="o">.</span><span class="n">data_pos_unit</span> <span class="o">=</span> <span class="bp">None</span> |
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108 | <span class="bp">self</span><span class="o">.</span><span class="n">data_x</span> <span class="o">=</span> <span class="bp">None</span> |
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109 | <span class="bp">self</span><span class="o">.</span><span class="n">data_y</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">data_z</span> <span class="o">=</span> <span class="bp">None</span> |
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111 | <span class="bp">self</span><span class="o">.</span><span class="n">data_sldn</span> <span class="o">=</span> <span class="bp">None</span> |
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112 | <span class="bp">self</span><span class="o">.</span><span class="n">data_mx</span> <span class="o">=</span> <span class="bp">None</span> |
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113 | <span class="bp">self</span><span class="o">.</span><span class="n">data_my</span> <span class="o">=</span> <span class="bp">None</span> |
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114 | <span class="bp">self</span><span class="o">.</span><span class="n">data_mz</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">data_vol</span> <span class="o">=</span> <span class="bp">None</span> <span class="c">#[A^3]</span> |
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116 | <span class="bp">self</span><span class="o">.</span><span class="n">is_avg</span> <span class="o">=</span> <span class="bp">False</span> |
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117 | <span class="c">## Name of the model</span> |
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118 | <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">"GenSAS"</span> |
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119 | <span class="c">## Define parameters</span> |
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120 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="p">{}</span> |
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121 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'scale'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> |
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122 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'background'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span> |
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123 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'solvent_SLD'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span> |
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124 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'total_volume'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> |
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125 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'Up_frac_in'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> |
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126 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'Up_frac_out'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> |
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127 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'Up_theta'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span> |
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128 | <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="s">'GenSAS'</span> |
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129 | <span class="c">## Parameter details [units, min, max]</span> |
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130 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="p">{}</span> |
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131 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">'scale'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">''</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span> |
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132 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">'background'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">'[1/cm]'</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span> |
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133 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">'solvent_SLD'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">'1/A^(2)'</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span> |
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134 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">'total_volume'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">'A^(3)'</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span> |
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135 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">'Up_frac_in'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">'[u/(u+d)]'</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span> |
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136 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">'Up_frac_out'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">'[u/(u+d)]'</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span> |
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137 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">'Up_theta'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">'[deg]'</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span> |
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138 | <span class="c"># fixed parameters</span> |
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139 | <span class="bp">self</span><span class="o">.</span><span class="n">fixed</span> <span class="o">=</span> <span class="p">[]</span> |
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140 | |
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141 | <div class="viewcode-block" id="GenSAS.set_pixel_volumes"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.GenSAS.set_pixel_volumes">[docs]</a> <span class="k">def</span> <span class="nf">set_pixel_volumes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">volume</span><span class="p">):</span> |
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142 | <span class="sd">"""</span> |
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143 | <span class="sd"> Set the volume of a pixel in (A^3) unit</span> |
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144 | <span class="sd"> :Param volume: pixel volume [float]</span> |
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145 | <span class="sd"> """</span> |
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146 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_vol</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
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147 | <span class="k">raise</span> |
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148 | <span class="bp">self</span><span class="o">.</span><span class="n">data_vol</span> <span class="o">=</span> <span class="n">volume</span> |
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149 | </div> |
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150 | <div class="viewcode-block" id="GenSAS.set_is_avg"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.GenSAS.set_is_avg">[docs]</a> <span class="k">def</span> <span class="nf">set_is_avg</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">is_avg</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span> |
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151 | <span class="sd">"""</span> |
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152 | <span class="sd"> Sets is_avg: [bool]</span> |
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153 | <span class="sd"> """</span> |
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154 | <span class="bp">self</span><span class="o">.</span><span class="n">is_avg</span> <span class="o">=</span> <span class="n">is_avg</span> |
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155 | </div> |
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156 | <span class="k">def</span> <span class="nf">_gen</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span> |
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157 | <span class="sd">"""</span> |
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158 | <span class="sd"> Evaluate the function</span> |
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159 | <span class="sd"> :Param x: array of x-values</span> |
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160 | <span class="sd"> :Param y: array of y-values</span> |
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161 | <span class="sd"> :Param i: array of initial i-value </span> |
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162 | <span class="sd"> :return: function value</span> |
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163 | <span class="sd"> """</span> |
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164 | <span class="n">pos_x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_x</span> |
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165 | <span class="n">pos_y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_y</span> |
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166 | <span class="n">pos_z</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_z</span> |
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167 | <span class="n">len_x</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">pos_x</span><span class="p">)</span> |
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168 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_avg</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
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169 | <span class="n">len_x</span> <span class="o">*=</span> <span class="o">-</span><span class="mi">1</span> |
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170 | <span class="n">pos_x</span><span class="p">,</span> <span class="n">pos_y</span><span class="p">,</span> <span class="n">pos_z</span> <span class="o">=</span> <span class="n">transform_center</span><span class="p">(</span><span class="n">pos_x</span><span class="p">,</span> <span class="n">pos_y</span><span class="p">,</span> <span class="n">pos_z</span><span class="p">)</span> |
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171 | <span class="n">len_q</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> |
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172 | <span class="n">sldn</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data_sldn</span><span class="p">)</span> |
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173 | <span class="n">sldn</span> <span class="o">-=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'solvent_SLD'</span><span class="p">]</span> |
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174 | <span class="n">model</span> <span class="o">=</span> <span class="n">mod</span><span class="o">.</span><span class="n">new_GenI</span><span class="p">(</span><span class="n">len_x</span><span class="p">,</span> <span class="n">pos_x</span><span class="p">,</span> <span class="n">pos_y</span><span class="p">,</span> <span class="n">pos_z</span><span class="p">,</span> |
---|
175 | <span class="n">sldn</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_mx</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_my</span><span class="p">,</span> |
---|
176 | <span class="bp">self</span><span class="o">.</span><span class="n">data_mz</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_vol</span><span class="p">,</span> |
---|
177 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'Up_frac_in'</span><span class="p">],</span> |
---|
178 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'Up_frac_out'</span><span class="p">],</span> |
---|
179 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'Up_theta'</span><span class="p">])</span> |
---|
180 | <span class="k">if</span> <span class="n">y</span> <span class="o">==</span> <span class="p">[]:</span> |
---|
181 | <span class="n">mod</span><span class="o">.</span><span class="n">genicom</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">len_q</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> |
---|
182 | <span class="k">else</span><span class="p">:</span> |
---|
183 | <span class="n">mod</span><span class="o">.</span><span class="n">genicomXY</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">len_q</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> |
---|
184 | <span class="n">vol_correction</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_total_volume</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'total_volume'</span><span class="p">]</span> |
---|
185 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'scale'</span><span class="p">]</span> <span class="o">*</span> <span class="n">vol_correction</span> <span class="o">*</span> <span class="n">i</span> <span class="o">+</span> \ |
---|
186 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'background'</span><span class="p">]</span> |
---|
187 | |
---|
188 | <div class="viewcode-block" id="GenSAS.set_sld_data"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.GenSAS.set_sld_data">[docs]</a> <span class="k">def</span> <span class="nf">set_sld_data</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sld_data</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
---|
189 | <span class="sd">"""</span> |
---|
190 | <span class="sd"> Sets sld_data</span> |
---|
191 | <span class="sd"> """</span> |
---|
192 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_data</span> <span class="o">=</span> <span class="n">sld_data</span> |
---|
193 | <span class="bp">self</span><span class="o">.</span><span class="n">data_pos_unit</span> <span class="o">=</span> <span class="n">sld_data</span><span class="o">.</span><span class="n">pos_unit</span> |
---|
194 | <span class="bp">self</span><span class="o">.</span><span class="n">data_x</span> <span class="o">=</span> <span class="n">sld_data</span><span class="o">.</span><span class="n">pos_x</span> |
---|
195 | <span class="bp">self</span><span class="o">.</span><span class="n">data_y</span> <span class="o">=</span> <span class="n">sld_data</span><span class="o">.</span><span class="n">pos_y</span> |
---|
196 | <span class="bp">self</span><span class="o">.</span><span class="n">data_z</span> <span class="o">=</span> <span class="n">sld_data</span><span class="o">.</span><span class="n">pos_z</span> |
---|
197 | <span class="bp">self</span><span class="o">.</span><span class="n">data_sldn</span> <span class="o">=</span> <span class="n">sld_data</span><span class="o">.</span><span class="n">sld_n</span> |
---|
198 | <span class="bp">self</span><span class="o">.</span><span class="n">data_mx</span> <span class="o">=</span> <span class="n">sld_data</span><span class="o">.</span><span class="n">sld_mx</span> |
---|
199 | <span class="bp">self</span><span class="o">.</span><span class="n">data_my</span> <span class="o">=</span> <span class="n">sld_data</span><span class="o">.</span><span class="n">sld_my</span> |
---|
200 | <span class="bp">self</span><span class="o">.</span><span class="n">data_mz</span> <span class="o">=</span> <span class="n">sld_data</span><span class="o">.</span><span class="n">sld_mz</span> |
---|
201 | <span class="bp">self</span><span class="o">.</span><span class="n">data_vol</span> <span class="o">=</span> <span class="n">sld_data</span><span class="o">.</span><span class="n">vol_pix</span> |
---|
202 | <span class="bp">self</span><span class="o">.</span><span class="n">data_total_volume</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="n">sld_data</span><span class="o">.</span><span class="n">vol_pix</span><span class="p">)</span> |
---|
203 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'total_volume'</span><span class="p">]</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="n">sld_data</span><span class="o">.</span><span class="n">vol_pix</span><span class="p">)</span> |
---|
204 | </div> |
---|
205 | <div class="viewcode-block" id="GenSAS.getProfile"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.GenSAS.getProfile">[docs]</a> <span class="k">def</span> <span class="nf">getProfile</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
206 | <span class="sd">"""</span> |
---|
207 | <span class="sd"> Get SLD profile </span> |
---|
208 | <span class="sd"> </span> |
---|
209 | <span class="sd"> : return: sld_data</span> |
---|
210 | <span class="sd"> """</span> |
---|
211 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">sld_data</span> |
---|
212 | </div> |
---|
213 | <div class="viewcode-block" id="GenSAS.run"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.GenSAS.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">):</span> |
---|
214 | <span class="sd">""" </span> |
---|
215 | <span class="sd"> Evaluate the model</span> |
---|
216 | <span class="sd"> :param x: simple value</span> |
---|
217 | <span class="sd"> :return: (I value)</span> |
---|
218 | <span class="sd"> """</span> |
---|
219 | <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">'list'</span><span class="p">:</span> |
---|
220 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
221 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"Not a 1D."</span> |
---|
222 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
223 | <span class="n">i_out</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> |
---|
224 | <span class="c"># 1D I is found at y =0 in the 2D pattern</span> |
---|
225 | <span class="n">out</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_gen</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="p">[],</span> <span class="n">i_out</span> <span class="p">)</span> |
---|
226 | <span class="k">return</span> <span class="n">out</span> |
---|
227 | <span class="k">else</span><span class="p">:</span> |
---|
228 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"Q must be given as list of qx's and qy's"</span> |
---|
229 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
230 | </div> |
---|
231 | <div class="viewcode-block" id="GenSAS.runXY"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.GenSAS.runXY">[docs]</a> <span class="k">def</span> <span class="nf">runXY</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">):</span> |
---|
232 | <span class="sd">""" </span> |
---|
233 | <span class="sd"> Evaluate the model</span> |
---|
234 | <span class="sd"> :param x: simple value</span> |
---|
235 | <span class="sd"> :return: I value</span> |
---|
236 | <span class="sd"> :Use this runXY() for the computation</span> |
---|
237 | <span class="sd"> """</span> |
---|
238 | <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">'list'</span><span class="p">:</span> |
---|
239 | <span class="n">i_out</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> |
---|
240 | <span class="n">out</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_gen</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">i_out</span><span class="p">)</span> |
---|
241 | <span class="k">return</span> <span class="n">out</span> |
---|
242 | <span class="k">else</span><span class="p">:</span> |
---|
243 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"Q must be given as list of qx's and qy's"</span> |
---|
244 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
245 | </div> |
---|
246 | <div class="viewcode-block" id="GenSAS.evalDistribution"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.GenSAS.evalDistribution">[docs]</a> <span class="k">def</span> <span class="nf">evalDistribution</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">qdist</span><span class="p">):</span> |
---|
247 | <span class="sd">"""</span> |
---|
248 | <span class="sd"> Evaluate a distribution of q-values.</span> |
---|
249 | <span class="sd"> * For 1D, a numpy array is expected as input: evalDistribution(q) where q is a numpy array.</span> |
---|
250 | <span class="sd"> * For 2D, a list of numpy arrays are expected: [qx_prime,qy_prime], where 1D arrays.</span> |
---|
251 | <span class="sd"> :param qdist: ndarray of scalar q-values or list [qx,qy] where qx,qy are 1D ndarrays </span> |
---|
252 | <span class="sd"> """</span> |
---|
253 | <span class="k">if</span> <span class="n">qdist</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">'list'</span><span class="p">:</span> |
---|
254 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">qdist</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span> |
---|
255 | <span class="n">out</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">qdist</span><span class="p">)</span> |
---|
256 | <span class="k">else</span><span class="p">:</span> |
---|
257 | <span class="n">out</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">runXY</span><span class="p">(</span><span class="n">qdist</span><span class="p">)</span> |
---|
258 | <span class="k">return</span> <span class="n">out</span> |
---|
259 | <span class="k">else</span><span class="p">:</span> |
---|
260 | <span class="n">mesg</span> <span class="o">=</span> <span class="s">"evalDistribution is expecting an ndarray of "</span> |
---|
261 | <span class="n">mesg</span> <span class="o">+=</span> <span class="s">"a list [qx,qy] where qx,qy are arrays."</span> |
---|
262 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">mesg</span> |
---|
263 | </div></div> |
---|
264 | <div class="viewcode-block" id="OMF2SLD"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMF2SLD">[docs]</a><span class="k">class</span> <span class="nc">OMF2SLD</span><span class="p">:</span> |
---|
265 | <span class="sd">"""</span> |
---|
266 | <span class="sd"> Convert OMFData to MAgData</span> |
---|
267 | <span class="sd"> """</span> |
---|
268 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
269 | <span class="sd">"""</span> |
---|
270 | <span class="sd"> Init</span> |
---|
271 | <span class="sd"> """</span> |
---|
272 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span> <span class="o">=</span> <span class="bp">None</span> |
---|
273 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span> <span class="o">=</span> <span class="bp">None</span> |
---|
274 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span> <span class="o">=</span> <span class="bp">None</span> |
---|
275 | <span class="bp">self</span><span class="o">.</span><span class="n">mx</span> <span class="o">=</span> <span class="bp">None</span> |
---|
276 | <span class="bp">self</span><span class="o">.</span><span class="n">my</span> <span class="o">=</span> <span class="bp">None</span> |
---|
277 | <span class="bp">self</span><span class="o">.</span><span class="n">mz</span> <span class="o">=</span> <span class="bp">None</span> |
---|
278 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> <span class="o">=</span> <span class="bp">None</span> |
---|
279 | <span class="bp">self</span><span class="o">.</span><span class="n">vol_pix</span> <span class="o">=</span> <span class="bp">None</span> |
---|
280 | <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">=</span> <span class="bp">None</span> |
---|
281 | <span class="bp">self</span><span class="o">.</span><span class="n">omfdata</span> <span class="o">=</span> <span class="bp">None</span> |
---|
282 | |
---|
283 | <div class="viewcode-block" id="OMF2SLD.set_data"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMF2SLD.set_data">[docs]</a> <span class="k">def</span> <span class="nf">set_data</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">omfdata</span><span class="p">,</span> <span class="n">shape</span><span class="o">=</span><span class="s">'rectangular'</span><span class="p">):</span> |
---|
284 | <span class="sd">"""</span> |
---|
285 | <span class="sd"> Set all data</span> |
---|
286 | <span class="sd"> """</span> |
---|
287 | <span class="bp">self</span><span class="o">.</span><span class="n">omfdata</span> <span class="o">=</span> <span class="n">omfdata</span> |
---|
288 | <span class="n">length</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">omfdata</span><span class="o">.</span><span class="n">xnodes</span> <span class="o">*</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">ynodes</span> <span class="o">*</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">znodes</span><span class="p">)</span> |
---|
289 | <span class="n">pos_x</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="n">omfdata</span><span class="o">.</span><span class="n">xmin</span><span class="p">,</span> |
---|
290 | <span class="n">omfdata</span><span class="o">.</span><span class="n">xnodes</span><span class="o">*</span><span class="n">omfdata</span><span class="o">.</span><span class="n">xstepsize</span> <span class="o">+</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">xmin</span><span class="p">,</span> |
---|
291 | <span class="n">omfdata</span><span class="o">.</span><span class="n">xstepsize</span><span class="p">)</span> |
---|
292 | <span class="n">pos_y</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="n">omfdata</span><span class="o">.</span><span class="n">ymin</span><span class="p">,</span> |
---|
293 | <span class="n">omfdata</span><span class="o">.</span><span class="n">ynodes</span><span class="o">*</span><span class="n">omfdata</span><span class="o">.</span><span class="n">ystepsize</span> <span class="o">+</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">ymin</span><span class="p">,</span> |
---|
294 | <span class="n">omfdata</span><span class="o">.</span><span class="n">ystepsize</span><span class="p">)</span> |
---|
295 | <span class="n">pos_z</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="n">omfdata</span><span class="o">.</span><span class="n">zmin</span><span class="p">,</span> |
---|
296 | <span class="n">omfdata</span><span class="o">.</span><span class="n">znodes</span><span class="o">*</span><span class="n">omfdata</span><span class="o">.</span><span class="n">zstepsize</span> <span class="o">+</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">zmin</span><span class="p">,</span> |
---|
297 | <span class="n">omfdata</span><span class="o">.</span><span class="n">zstepsize</span><span class="p">)</span> |
---|
298 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">tile</span><span class="p">(</span><span class="n">pos_x</span><span class="p">,</span> <span class="nb">int</span><span class="p">(</span><span class="n">omfdata</span><span class="o">.</span><span class="n">ynodes</span> <span class="o">*</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">znodes</span><span class="p">))</span> |
---|
299 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span> <span class="o">=</span> <span class="n">pos_y</span><span class="o">.</span><span class="n">repeat</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">omfdata</span><span class="o">.</span><span class="n">xnodes</span><span class="p">))</span> |
---|
300 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">tile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">,</span> <span class="nb">int</span><span class="p">(</span><span class="n">omfdata</span><span class="o">.</span><span class="n">znodes</span><span class="p">))</span> |
---|
301 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span> <span class="o">=</span> <span class="n">pos_z</span><span class="o">.</span><span class="n">repeat</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">omfdata</span><span class="o">.</span><span class="n">xnodes</span> <span class="o">*</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">ynodes</span><span class="p">))</span> |
---|
302 | <span class="bp">self</span><span class="o">.</span><span class="n">mx</span> <span class="o">=</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">mx</span> |
---|
303 | <span class="bp">self</span><span class="o">.</span><span class="n">my</span> <span class="o">=</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">my</span> |
---|
304 | <span class="bp">self</span><span class="o">.</span><span class="n">mz</span> <span class="o">=</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">mz</span> |
---|
305 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">length</span><span class="p">)</span> |
---|
306 | |
---|
307 | <span class="k">if</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">mx</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
308 | <span class="bp">self</span><span class="o">.</span><span class="n">mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">length</span><span class="p">)</span> |
---|
309 | <span class="k">if</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">my</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
310 | <span class="bp">self</span><span class="o">.</span><span class="n">my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">length</span><span class="p">)</span> |
---|
311 | <span class="k">if</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">mz</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
312 | <span class="bp">self</span><span class="o">.</span><span class="n">mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">length</span><span class="p">)</span> |
---|
313 | |
---|
314 | <span class="bp">self</span><span class="o">.</span><span class="n">_check_data_length</span><span class="p">(</span><span class="n">length</span><span class="p">)</span> |
---|
315 | <span class="bp">self</span><span class="o">.</span><span class="n">remove_null_points</span><span class="p">(</span><span class="bp">False</span><span class="p">,</span> <span class="bp">False</span><span class="p">)</span> |
---|
316 | <span class="n">mask</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">ones</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">sld_n</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">bool</span><span class="p">)</span> |
---|
317 | <span class="k">if</span> <span class="n">shape</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">'ellipsoid'</span><span class="p">:</span> |
---|
318 | <span class="k">try</span><span class="p">:</span> |
---|
319 | <span class="c"># Pixel (step) size included</span> |
---|
320 | <span class="n">x_c</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">)</span> <span class="o">+</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">)</span> |
---|
321 | <span class="n">y_c</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">)</span> <span class="o">+</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">)</span> |
---|
322 | <span class="n">z_c</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">)</span> <span class="o">+</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">)</span> |
---|
323 | <span class="n">x_d</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">)</span> <span class="o">-</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">)</span> |
---|
324 | <span class="n">y_d</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">)</span> <span class="o">-</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">)</span> |
---|
325 | <span class="n">z_d</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">)</span> <span class="o">-</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">)</span> |
---|
326 | <span class="n">x_r</span> <span class="o">=</span> <span class="p">(</span><span class="n">x_d</span> <span class="o">+</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">xstepsize</span><span class="p">)</span> <span class="o">/</span> <span class="mf">2.0</span> |
---|
327 | <span class="n">y_r</span> <span class="o">=</span> <span class="p">(</span><span class="n">y_d</span> <span class="o">+</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">ystepsize</span><span class="p">)</span> <span class="o">/</span> <span class="mf">2.0</span> |
---|
328 | <span class="n">z_r</span> <span class="o">=</span> <span class="p">(</span><span class="n">z_d</span> <span class="o">+</span> <span class="n">omfdata</span><span class="o">.</span><span class="n">zstepsize</span><span class="p">)</span> <span class="o">/</span> <span class="mf">2.0</span> |
---|
329 | <span class="n">x_dir2</span> <span class="o">=</span> <span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span> <span class="o">-</span> <span class="n">x_c</span> <span class="o">/</span> <span class="mf">2.0</span><span class="p">)</span> <span class="o">/</span> <span class="n">x_r</span><span class="p">)</span> |
---|
330 | <span class="n">x_dir2</span> <span class="o">*=</span> <span class="n">x_dir2</span> |
---|
331 | <span class="n">y_dir2</span> <span class="o">=</span> <span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span> <span class="o">-</span> <span class="n">y_c</span> <span class="o">/</span> <span class="mf">2.0</span><span class="p">)</span> <span class="o">/</span> <span class="n">y_r</span><span class="p">)</span> |
---|
332 | <span class="n">y_dir2</span> <span class="o">*=</span> <span class="n">y_dir2</span> |
---|
333 | <span class="n">z_dir2</span> <span class="o">=</span> <span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span> <span class="o">-</span> <span class="n">z_c</span> <span class="o">/</span> <span class="mf">2.0</span><span class="p">)</span> <span class="o">/</span> <span class="n">z_r</span><span class="p">)</span> |
---|
334 | <span class="n">z_dir2</span> <span class="o">*=</span> <span class="n">z_dir2</span> |
---|
335 | <span class="n">mask</span> <span class="o">=</span> <span class="p">(</span><span class="n">x_dir2</span> <span class="o">+</span> <span class="n">y_dir2</span> <span class="o">+</span> <span class="n">z_dir2</span><span class="p">)</span> <span class="o"><=</span> <span class="mf">1.0</span> |
---|
336 | <span class="k">except</span><span class="p">:</span> |
---|
337 | <span class="k">pass</span> |
---|
338 | <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">=</span> <span class="n">MagSLD</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">[</span><span class="n">mask</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">[</span><span class="n">mask</span><span class="p">],</span> |
---|
339 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">[</span><span class="n">mask</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span><span class="p">[</span><span class="n">mask</span><span class="p">],</span> |
---|
340 | <span class="bp">self</span><span class="o">.</span><span class="n">mx</span><span class="p">[</span><span class="n">mask</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">my</span><span class="p">[</span><span class="n">mask</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">mz</span><span class="p">[</span><span class="n">mask</span><span class="p">])</span> |
---|
341 | <span class="bp">self</span><span class="o">.</span><span class="n">output</span><span class="o">.</span><span class="n">set_pix_type</span><span class="p">(</span><span class="s">'pixel'</span><span class="p">)</span> |
---|
342 | <span class="bp">self</span><span class="o">.</span><span class="n">output</span><span class="o">.</span><span class="n">set_pixel_symbols</span><span class="p">(</span><span class="s">'pixel'</span><span class="p">)</span> |
---|
343 | </div> |
---|
344 | <div class="viewcode-block" id="OMF2SLD.get_omfdata"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMF2SLD.get_omfdata">[docs]</a> <span class="k">def</span> <span class="nf">get_omfdata</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
345 | <span class="sd">"""</span> |
---|
346 | <span class="sd"> Return all data</span> |
---|
347 | <span class="sd"> """</span> |
---|
348 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">omfdata</span> |
---|
349 | </div> |
---|
350 | <div class="viewcode-block" id="OMF2SLD.get_output"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMF2SLD.get_output">[docs]</a> <span class="k">def</span> <span class="nf">get_output</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
351 | <span class="sd">"""</span> |
---|
352 | <span class="sd"> Return output</span> |
---|
353 | <span class="sd"> """</span> |
---|
354 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span> |
---|
355 | </div> |
---|
356 | <span class="k">def</span> <span class="nf">_check_data_length</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">length</span><span class="p">):</span> |
---|
357 | <span class="sd">"""</span> |
---|
358 | <span class="sd"> Check if the data lengths are consistent</span> |
---|
359 | <span class="sd"> :Params length: data length</span> |
---|
360 | <span class="sd"> """</span> |
---|
361 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"Error: Inconsistent data length."</span> |
---|
362 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">)</span> <span class="o">!=</span> <span class="n">length</span><span class="p">:</span> |
---|
363 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
364 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">)</span> <span class="o">!=</span> <span class="n">length</span><span class="p">:</span> |
---|
365 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
366 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">)</span> <span class="o">!=</span> <span class="n">length</span><span class="p">:</span> |
---|
367 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
368 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mx</span><span class="p">)</span> <span class="o">!=</span> <span class="n">length</span><span class="p">:</span> |
---|
369 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
370 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">my</span><span class="p">)</span> <span class="o">!=</span> <span class="n">length</span><span class="p">:</span> |
---|
371 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
372 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mz</span><span class="p">)</span> <span class="o">!=</span> <span class="n">length</span><span class="p">:</span> |
---|
373 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
374 | |
---|
375 | <div class="viewcode-block" id="OMF2SLD.remove_null_points"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMF2SLD.remove_null_points">[docs]</a> <span class="k">def</span> <span class="nf">remove_null_points</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">remove</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">recenter</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span> |
---|
376 | <span class="sd">"""</span> |
---|
377 | <span class="sd"> Removes any mx, my, and mz = 0 points</span> |
---|
378 | <span class="sd"> """</span> |
---|
379 | <span class="k">if</span> <span class="n">remove</span><span class="p">:</span> |
---|
380 | <span class="n">is_nonzero</span> <span class="o">=</span> <span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mx</span><span class="p">)</span> <span class="o">+</span> <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">my</span><span class="p">)</span> <span class="o">+</span> |
---|
381 | <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mz</span><span class="p">))</span><span class="o">.</span><span class="n">nonzero</span><span class="p">()</span> |
---|
382 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">is_nonzero</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
383 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">[</span><span class="n">is_nonzero</span><span class="p">]</span> |
---|
384 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">[</span><span class="n">is_nonzero</span><span class="p">]</span> |
---|
385 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">[</span><span class="n">is_nonzero</span><span class="p">]</span> |
---|
386 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span><span class="p">[</span><span class="n">is_nonzero</span><span class="p">]</span> |
---|
387 | <span class="bp">self</span><span class="o">.</span><span class="n">mx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">mx</span><span class="p">[</span><span class="n">is_nonzero</span><span class="p">]</span> |
---|
388 | <span class="bp">self</span><span class="o">.</span><span class="n">my</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">my</span><span class="p">[</span><span class="n">is_nonzero</span><span class="p">]</span> |
---|
389 | <span class="bp">self</span><span class="o">.</span><span class="n">mz</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">mz</span><span class="p">[</span><span class="n">is_nonzero</span><span class="p">]</span> |
---|
390 | <span class="k">if</span> <span class="n">recenter</span><span class="p">:</span> |
---|
391 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span> <span class="o">-=</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">)</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">))</span> <span class="o">/</span> <span class="mf">2.0</span> |
---|
392 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span> <span class="o">-=</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">)</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">))</span> <span class="o">/</span> <span class="mf">2.0</span> |
---|
393 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span> <span class="o">-=</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">)</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">))</span> <span class="o">/</span> <span class="mf">2.0</span> |
---|
394 | </div> |
---|
395 | <div class="viewcode-block" id="OMF2SLD.get_magsld"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMF2SLD.get_magsld">[docs]</a> <span class="k">def</span> <span class="nf">get_magsld</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
396 | <span class="sd">"""</span> |
---|
397 | <span class="sd"> return MagSLD</span> |
---|
398 | <span class="sd"> """</span> |
---|
399 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span> |
---|
400 | |
---|
401 | </div></div> |
---|
402 | <div class="viewcode-block" id="OMFReader"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMFReader">[docs]</a><span class="k">class</span> <span class="nc">OMFReader</span><span class="p">:</span> |
---|
403 | <span class="sd">"""</span> |
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404 | <span class="sd"> Class to load omf/ascii files (3 columns w/header).</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">"OMF ASCII"</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">"OMF files (*.OMF, *.omf)|*.omf"</span><span class="p">]</span> |
---|
411 | <span class="c">## List of allowed extensions</span> |
---|
412 | <span class="n">ext</span> <span class="o">=</span> <span class="p">[</span><span class="s">'.omf'</span><span class="p">,</span> <span class="s">'.OMF'</span><span class="p">]</span> |
---|
413 | |
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414 | <div class="viewcode-block" id="OMFReader.read"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMFReader.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> |
---|
415 | <span class="sd">"""</span> |
---|
416 | <span class="sd"> Load data file</span> |
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417 | <span class="sd"> :param path: file path</span> |
---|
418 | <span class="sd"> :return: x, y, z, sld_n, sld_mx, sld_my, sld_mz</span> |
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419 | <span class="sd"> """</span> |
---|
420 | <span class="c">#data_conv_m = None</span> |
---|
421 | <span class="n">desc</span> <span class="o">=</span> <span class="s">""</span> |
---|
422 | <span class="n">mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
423 | <span class="n">my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
424 | <span class="n">mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
425 | <span class="k">try</span><span class="p">:</span> |
---|
426 | <span class="n">data_conv_val</span> <span class="o">=</span> <span class="bp">None</span> |
---|
427 | <span class="n">data_conv_mesh</span> <span class="o">=</span> <span class="bp">None</span> |
---|
428 | <span class="n">input_f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s">'rb'</span><span class="p">)</span> |
---|
429 | <span class="n">buff</span> <span class="o">=</span> <span class="n">input_f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> |
---|
430 | <span class="n">lines</span> <span class="o">=</span> <span class="n">buff</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span> |
---|
431 | <span class="n">input_f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> |
---|
432 | <span class="n">output</span> <span class="o">=</span> <span class="n">OMFData</span><span class="p">()</span> |
---|
433 | <span class="n">valueunit</span> <span class="o">=</span> <span class="bp">None</span> |
---|
434 | <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span> |
---|
435 | <span class="n">toks</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()</span> |
---|
436 | <span class="c"># Read data</span> |
---|
437 | <span class="k">try</span><span class="p">:</span> |
---|
438 | <span class="n">_mx</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> |
---|
439 | <span class="n">_my</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> |
---|
440 | <span class="n">_mz</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> |
---|
441 | <span class="n">_mx</span> <span class="o">=</span> <span class="n">mag2sld</span><span class="p">(</span><span class="n">_mx</span><span class="p">,</span> <span class="n">valueunit</span><span class="p">)</span> |
---|
442 | <span class="n">_my</span> <span class="o">=</span> <span class="n">mag2sld</span><span class="p">(</span><span class="n">_my</span><span class="p">,</span> <span class="n">valueunit</span><span class="p">)</span> |
---|
443 | <span class="n">_mz</span> <span class="o">=</span> <span class="n">mag2sld</span><span class="p">(</span><span class="n">_mz</span><span class="p">,</span> <span class="n">valueunit</span><span class="p">)</span> |
---|
444 | <span class="n">mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mx</span><span class="p">,</span> <span class="n">_mx</span><span class="p">)</span> |
---|
445 | <span class="n">my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">my</span><span class="p">,</span> <span class="n">_my</span><span class="p">)</span> |
---|
446 | <span class="n">mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mz</span><span class="p">,</span> <span class="n">_mz</span><span class="p">)</span> |
---|
447 | <span class="k">except</span><span class="p">:</span> |
---|
448 | <span class="c"># Skip non-data lines</span> |
---|
449 | <span class="k">pass</span> |
---|
450 | <span class="c">#Reading Header; Segment count ignored</span> |
---|
451 | <span class="n">s_line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">":"</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span> |
---|
452 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"oommf"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
453 | <span class="n">oommf</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
454 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"title"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
455 | <span class="n">title</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
456 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"desc"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
457 | <span class="n">desc</span> <span class="o">+=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
458 | <span class="n">desc</span> <span class="o">+=</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span> |
---|
459 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"meshtype"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
460 | <span class="n">meshtype</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
461 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"meshunit"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
462 | <span class="n">meshunit</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
463 | <span class="k">if</span> <span class="n">meshunit</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"m"</span><span class="p">)</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span> |
---|
464 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"Error: </span><span class="se">\n</span><span class="s">"</span> |
---|
465 | <span class="n">msg</span> <span class="o">+=</span> <span class="s">"We accept only m as meshunit"</span> |
---|
466 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">msg</span> |
---|
467 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"xbase"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
468 | <span class="n">xbase</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
469 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"ybase"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
470 | <span class="n">ybase</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
471 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"zbase"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
472 | <span class="n">zbase</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
473 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"xstepsize"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
474 | <span class="n">xstepsize</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
475 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"ystepsize"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
476 | <span class="n">ystepsize</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
477 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"zstepsize"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
478 | <span class="n">zstepsize</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
479 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"xnodes"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
480 | <span class="n">xnodes</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
481 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"ynodes"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
482 | <span class="n">ynodes</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
483 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"znodes"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
484 | <span class="n">znodes</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
485 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"xmin"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
486 | <span class="n">xmin</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
487 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"ymin"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
488 | <span class="n">ymin</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
489 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"zmin"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
490 | <span class="n">zmin</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
491 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"xmax"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
492 | <span class="n">xmax</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
493 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"ymax"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
494 | <span class="n">ymax</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
495 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"zmax"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
496 | <span class="n">zmax</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
497 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"valueunit"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
498 | <span class="n">valueunit</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span> |
---|
499 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"valuemultiplier"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
500 | <span class="n">valuemultiplier</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
501 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"valuerangeminmag"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
502 | <span class="n">valuerangeminmag</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
503 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"valuerangemaxmag"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
504 | <span class="n">valuerangemaxmag</span> <span class="o">=</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">()</span> |
---|
505 | <span class="k">if</span> <span class="n">s_line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"end"</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
506 | <span class="c">#output.set_sldms(mx, my, mz) </span> |
---|
507 | <span class="n">output</span><span class="o">.</span><span class="n">filename</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">output</span><span class="o">.</span><span class="n">oommf</span> <span class="o">=</span> <span class="n">oommf</span> |
---|
509 | <span class="n">output</span><span class="o">.</span><span class="n">title</span> <span class="o">=</span> <span class="n">title</span> |
---|
510 | <span class="n">output</span><span class="o">.</span><span class="n">desc</span> <span class="o">=</span> <span class="n">desc</span> |
---|
511 | <span class="n">output</span><span class="o">.</span><span class="n">meshtype</span> <span class="o">=</span> <span class="n">meshtype</span> |
---|
512 | <span class="n">output</span><span class="o">.</span><span class="n">xbase</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">xbase</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
513 | <span class="n">output</span><span class="o">.</span><span class="n">ybase</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">ybase</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
514 | <span class="n">output</span><span class="o">.</span><span class="n">zbase</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">zbase</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
515 | <span class="n">output</span><span class="o">.</span><span class="n">xstepsize</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">xstepsize</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
516 | <span class="n">output</span><span class="o">.</span><span class="n">ystepsize</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">ystepsize</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
517 | <span class="n">output</span><span class="o">.</span><span class="n">zstepsize</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">zstepsize</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
518 | <span class="n">output</span><span class="o">.</span><span class="n">xnodes</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">xnodes</span><span class="p">)</span> |
---|
519 | <span class="n">output</span><span class="o">.</span><span class="n">ynodes</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">ynodes</span><span class="p">)</span> |
---|
520 | <span class="n">output</span><span class="o">.</span><span class="n">znodes</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">znodes</span><span class="p">)</span> |
---|
521 | <span class="n">output</span><span class="o">.</span><span class="n">xmin</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">xmin</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
522 | <span class="n">output</span><span class="o">.</span><span class="n">ymin</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">ymin</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
523 | <span class="n">output</span><span class="o">.</span><span class="n">zmin</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">zmin</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
524 | <span class="n">output</span><span class="o">.</span><span class="n">xmax</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">xmax</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
525 | <span class="n">output</span><span class="o">.</span><span class="n">ymax</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">ymax</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
526 | <span class="n">output</span><span class="o">.</span><span class="n">zmax</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">zmax</span><span class="p">)</span> <span class="o">*</span> <span class="n">METER2ANG</span> |
---|
527 | <span class="n">output</span><span class="o">.</span><span class="n">valuemultiplier</span> <span class="o">=</span> <span class="n">valuemultiplier</span> |
---|
528 | <span class="n">output</span><span class="o">.</span><span class="n">valuerangeminmag</span> <span class="o">=</span> <span class="n">mag2sld</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">valuerangeminmag</span><span class="p">),</span> \ |
---|
529 | <span class="n">valueunit</span><span class="p">)</span> |
---|
530 | <span class="n">output</span><span class="o">.</span><span class="n">valuerangemaxmag</span> <span class="o">=</span> <span class="n">mag2sld</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">valuerangemaxmag</span><span class="p">),</span> \ |
---|
531 | <span class="n">valueunit</span><span class="p">)</span> |
---|
532 | <span class="n">output</span><span class="o">.</span><span class="n">set_m</span><span class="p">(</span><span class="n">mx</span><span class="p">,</span> <span class="n">my</span><span class="p">,</span> <span class="n">mz</span><span class="p">)</span> |
---|
533 | <span class="k">return</span> <span class="n">output</span> |
---|
534 | <span class="k">except</span><span class="p">:</span> |
---|
535 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"</span><span class="si">%s</span><span class="s"> is not supported: </span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="n">path</span> |
---|
536 | <span class="n">msg</span> <span class="o">+=</span> <span class="s">"We accept only Text format OMF file."</span> |
---|
537 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">msg</span> |
---|
538 | </div></div> |
---|
539 | <div class="viewcode-block" id="PDBReader"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.PDBReader">[docs]</a><span class="k">class</span> <span class="nc">PDBReader</span><span class="p">:</span> |
---|
540 | <span class="sd">"""</span> |
---|
541 | <span class="sd"> PDB reader class: limited for reading the lines starting with 'ATOM'</span> |
---|
542 | <span class="sd"> """</span> |
---|
543 | <span class="n">type_name</span> <span class="o">=</span> <span class="s">"PDB"</span> |
---|
544 | <span class="c">## Wildcards</span> |
---|
545 | <span class="nb">type</span> <span class="o">=</span> <span class="p">[</span><span class="s">"pdb files (*.PDB, *.pdb)|*.pdb"</span><span class="p">]</span> |
---|
546 | <span class="c">## List of allowed extensions</span> |
---|
547 | <span class="n">ext</span> <span class="o">=</span> <span class="p">[</span><span class="s">'.pdb'</span><span class="p">,</span> <span class="s">'.PDB'</span><span class="p">]</span> |
---|
548 | |
---|
549 | <div class="viewcode-block" id="PDBReader.read"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.PDBReader.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> |
---|
550 | <span class="sd">"""</span> |
---|
551 | <span class="sd"> Load data file</span> |
---|
552 | <span class="sd"> </span> |
---|
553 | <span class="sd"> :param path: file path</span> |
---|
554 | <span class="sd"> </span> |
---|
555 | <span class="sd"> :return: MagSLD</span> |
---|
556 | <span class="sd"> </span> |
---|
557 | <span class="sd"> :raise RuntimeError: when the file can't be opened</span> |
---|
558 | <span class="sd"> """</span> |
---|
559 | <span class="n">pos_x</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
560 | <span class="n">pos_y</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
561 | <span class="n">pos_z</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
562 | <span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
563 | <span class="n">sld_mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
564 | <span class="n">sld_my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
565 | <span class="n">sld_mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
566 | <span class="n">vol_pix</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
567 | <span class="n">pix_symbol</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
568 | <span class="n">x_line</span> <span class="o">=</span> <span class="p">[]</span> |
---|
569 | <span class="n">y_line</span> <span class="o">=</span> <span class="p">[]</span> |
---|
570 | <span class="n">z_line</span> <span class="o">=</span> <span class="p">[]</span> |
---|
571 | <span class="n">x_lines</span> <span class="o">=</span> <span class="p">[]</span> |
---|
572 | <span class="n">y_lines</span> <span class="o">=</span> <span class="p">[]</span> |
---|
573 | <span class="n">z_lines</span> <span class="o">=</span> <span class="p">[]</span> |
---|
574 | <span class="k">try</span><span class="p">:</span> |
---|
575 | <span class="n">input_f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s">'rb'</span><span class="p">)</span> |
---|
576 | <span class="n">buff</span> <span class="o">=</span> <span class="n">input_f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> |
---|
577 | <span class="n">lines</span> <span class="o">=</span> <span class="n">buff</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span> |
---|
578 | <span class="n">input_f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> |
---|
579 | <span class="n">pre_num</span> <span class="o">=</span> <span class="mi">0</span> |
---|
580 | <span class="n">num</span> <span class="o">=</span> <span class="mi">0</span> |
---|
581 | <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span> |
---|
582 | <span class="k">try</span><span class="p">:</span> |
---|
583 | <span class="c"># check if line starts with "ATOM"</span> |
---|
584 | <span class="k">if</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">'ATM'</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">or</span> \ |
---|
585 | <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s">'ATOM'</span><span class="p">:</span> |
---|
586 | <span class="c"># define fields of interest</span> |
---|
587 | <span class="n">atom_id</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">6</span><span class="p">:</span><span class="mi">11</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> |
---|
588 | <span class="n">atom_name</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="mi">16</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> |
---|
589 | <span class="k">try</span><span class="p">:</span> |
---|
590 | <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">12</span><span class="p">])</span> |
---|
591 | <span class="n">atom_name</span> <span class="o">=</span> <span class="n">atom_name</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> |
---|
592 | <span class="k">except</span><span class="p">:</span> |
---|
593 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">atom_name</span><span class="p">)</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span> |
---|
594 | <span class="n">atom_name</span> <span class="o">=</span> <span class="n">atom_name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> |
---|
595 | <span class="k">elif</span> <span class="n">line</span><span class="p">[</span><span class="mi">12</span><span class="p">]</span> <span class="o">!=</span> <span class="s">' '</span><span class="p">:</span> |
---|
596 | <span class="n">atom_name</span> <span class="o">=</span> <span class="n">atom_name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="o">+</span> \ |
---|
597 | <span class="n">atom_name</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> |
---|
598 | <span class="k">else</span><span class="p">:</span> |
---|
599 | <span class="n">atom_name</span> <span class="o">=</span> <span class="n">atom_name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> |
---|
600 | <span class="c">#res_name = line[17:20].strip()</span> |
---|
601 | <span class="c">#chain_name = line[21:22].strip()</span> |
---|
602 | <span class="n">_pos_x</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">30</span><span class="p">:</span><span class="mi">38</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> |
---|
603 | <span class="n">_pos_y</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">38</span><span class="p">:</span><span class="mi">46</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> |
---|
604 | <span class="n">_pos_z</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">46</span><span class="p">:</span><span class="mi">54</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> |
---|
605 | |
---|
606 | <span class="n">pos_x</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pos_x</span><span class="p">,</span> <span class="n">_pos_x</span><span class="p">)</span> |
---|
607 | <span class="n">pos_y</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pos_y</span><span class="p">,</span> <span class="n">_pos_y</span><span class="p">)</span> |
---|
608 | <span class="n">pos_z</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pos_z</span><span class="p">,</span> <span class="n">_pos_z</span><span class="p">)</span> |
---|
609 | <span class="k">try</span><span class="p">:</span> |
---|
610 | <span class="c"># sld in Ang unit (from fm)</span> |
---|
611 | <span class="c">#val = formula(atom_name).atoms.keys()[0].neutron.b_c</span> |
---|
612 | <span class="c">#val *= 1.0e-5</span> |
---|
613 | <span class="n">val</span> <span class="o">=</span> <span class="n">nsf</span><span class="o">.</span><span class="n">neutron_sld</span><span class="p">(</span><span class="n">atom_name</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> |
---|
614 | <span class="c"># sld in Ang^-2 unit</span> |
---|
615 | <span class="n">val</span> <span class="o">*=</span> <span class="mf">1.0e-6</span> |
---|
616 | <span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_n</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span> |
---|
617 | <span class="n">atom</span> <span class="o">=</span> <span class="n">formula</span><span class="p">(</span><span class="n">atom_name</span><span class="p">)</span> |
---|
618 | <span class="c"># cm to A units</span> |
---|
619 | <span class="n">vol</span> <span class="o">=</span> <span class="mf">1.0e+24</span> <span class="o">*</span> <span class="n">atom</span><span class="o">.</span><span class="n">mass</span> <span class="o">/</span> <span class="n">atom</span><span class="o">.</span><span class="n">density</span> <span class="o">/</span> <span class="n">NA</span> |
---|
620 | <span class="n">vol_pix</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">vol_pix</span><span class="p">,</span> <span class="n">vol</span><span class="p">)</span> |
---|
621 | <span class="k">except</span><span class="p">:</span> |
---|
622 | <span class="k">print</span> <span class="s">"Error: set the sld of </span><span class="si">%s</span><span class="s"> to zero"</span><span class="o">%</span> <span class="n">atom_name</span> |
---|
623 | <span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_n</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">)</span> |
---|
624 | <span class="n">sld_mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_mx</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> |
---|
625 | <span class="n">sld_my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_my</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> |
---|
626 | <span class="n">sld_mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_mz</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> |
---|
627 | <span class="n">pix_symbol</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pix_symbol</span><span class="p">,</span> <span class="n">atom_name</span><span class="p">)</span> |
---|
628 | <span class="k">elif</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">'CONECT'</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span> <span class="p">:</span> |
---|
629 | <span class="n">toks</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()</span> |
---|
630 | <span class="n">num</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span> |
---|
631 | <span class="n">val_list</span> <span class="o">=</span> <span class="p">[]</span> |
---|
632 | <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">toks</span><span class="p">[</span><span class="mi">2</span><span class="p">:]:</span> |
---|
633 | <span class="k">try</span><span class="p">:</span> |
---|
634 | <span class="n">int_val</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">val</span><span class="p">)</span> |
---|
635 | <span class="k">except</span><span class="p">:</span> |
---|
636 | <span class="k">break</span> |
---|
637 | <span class="k">if</span> <span class="n">int_val</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> |
---|
638 | <span class="k">break</span> |
---|
639 | <span class="n">val_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">int_val</span><span class="p">)</span> |
---|
640 | <span class="c">#need val_list ordered </span> |
---|
641 | <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">val_list</span><span class="p">:</span> |
---|
642 | <span class="n">index</span> <span class="o">=</span> <span class="n">val</span> <span class="o">-</span> <span class="mi">1</span> |
---|
643 | <span class="k">if</span> <span class="p">(</span><span class="n">pos_x</span><span class="p">[</span><span class="n">index</span><span class="p">],</span> <span class="n">pos_x</span><span class="p">[</span><span class="n">num</span><span class="p">])</span> <span class="ow">in</span> <span class="n">x_line</span> <span class="ow">and</span> \ |
---|
644 | <span class="p">(</span><span class="n">pos_y</span><span class="p">[</span><span class="n">index</span><span class="p">],</span> <span class="n">pos_y</span><span class="p">[</span><span class="n">num</span><span class="p">])</span> <span class="ow">in</span> <span class="n">y_line</span> <span class="ow">and</span> \ |
---|
645 | <span class="p">(</span><span class="n">pos_z</span><span class="p">[</span><span class="n">index</span><span class="p">],</span> <span class="n">pos_z</span><span class="p">[</span><span class="n">num</span><span class="p">])</span> <span class="ow">in</span> <span class="n">z_line</span><span class="p">:</span> |
---|
646 | <span class="k">continue</span> |
---|
647 | <span class="n">x_line</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">pos_x</span><span class="p">[</span><span class="n">num</span><span class="p">],</span> <span class="n">pos_x</span><span class="p">[</span><span class="n">index</span><span class="p">]))</span> |
---|
648 | <span class="n">y_line</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">pos_y</span><span class="p">[</span><span class="n">num</span><span class="p">],</span> <span class="n">pos_y</span><span class="p">[</span><span class="n">index</span><span class="p">]))</span> |
---|
649 | <span class="n">z_line</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">pos_z</span><span class="p">[</span><span class="n">num</span><span class="p">],</span> <span class="n">pos_z</span><span class="p">[</span><span class="n">index</span><span class="p">]))</span> |
---|
650 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x_line</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
651 | <span class="n">x_lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">x_line</span><span class="p">)</span> |
---|
652 | <span class="n">y_lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">y_line</span><span class="p">)</span> |
---|
653 | <span class="n">z_lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z_line</span><span class="p">)</span> |
---|
654 | <span class="k">except</span><span class="p">:</span> |
---|
655 | <span class="k">pass</span> |
---|
656 | <span class="c">#re-centering</span> |
---|
657 | <span class="c">#pos_x -= (min(pos_x) + max(pos_x)) / 2.0</span> |
---|
658 | <span class="c">#pos_y -= (min(pos_y) + max(pos_y)) / 2.0</span> |
---|
659 | <span class="c">#pos_z -= (min(pos_z) + max(pos_z)) / 2.0</span> |
---|
660 | |
---|
661 | <span class="n">output</span> <span class="o">=</span> <span class="n">MagSLD</span><span class="p">(</span><span class="n">pos_x</span><span class="p">,</span> <span class="n">pos_y</span><span class="p">,</span> <span class="n">pos_z</span><span class="p">,</span> <span class="n">sld_n</span><span class="p">,</span> <span class="n">sld_mx</span><span class="p">,</span> <span class="n">sld_my</span><span class="p">,</span> <span class="n">sld_mz</span><span class="p">)</span> |
---|
662 | <span class="n">output</span><span class="o">.</span><span class="n">set_conect_lines</span><span class="p">(</span><span class="n">x_line</span><span class="p">,</span> <span class="n">y_line</span><span class="p">,</span> <span class="n">z_line</span><span class="p">)</span> |
---|
663 | <span class="n">output</span><span class="o">.</span><span class="n">filename</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> |
---|
664 | <span class="n">output</span><span class="o">.</span><span class="n">set_pix_type</span><span class="p">(</span><span class="s">'atom'</span><span class="p">)</span> |
---|
665 | <span class="n">output</span><span class="o">.</span><span class="n">set_pixel_symbols</span><span class="p">(</span><span class="n">pix_symbol</span><span class="p">)</span> |
---|
666 | <span class="n">output</span><span class="o">.</span><span class="n">set_nodes</span><span class="p">()</span> |
---|
667 | <span class="n">output</span><span class="o">.</span><span class="n">set_pixel_volumes</span><span class="p">(</span><span class="n">vol_pix</span><span class="p">)</span> |
---|
668 | <span class="n">output</span><span class="o">.</span><span class="n">sld_unit</span> <span class="o">=</span> <span class="s">'1/A^(2)'</span> |
---|
669 | <span class="k">return</span> <span class="n">output</span> |
---|
670 | <span class="k">except</span><span class="p">:</span> |
---|
671 | <span class="ne">RuntimeError</span><span class="p">,</span> <span class="s">"</span><span class="si">%s</span><span class="s"> is not a sld file"</span> <span class="o">%</span> <span class="n">path</span> |
---|
672 | </div> |
---|
673 | <div class="viewcode-block" id="PDBReader.write"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.PDBReader.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">path</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> |
---|
674 | <span class="sd">"""</span> |
---|
675 | <span class="sd"> Write</span> |
---|
676 | <span class="sd"> """</span> |
---|
677 | <span class="c">#Not implemented </span> |
---|
678 | <span class="k">print</span> <span class="s">"Not implemented... "</span> |
---|
679 | </div></div> |
---|
680 | <div class="viewcode-block" id="SLDReader"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.SLDReader">[docs]</a><span class="k">class</span> <span class="nc">SLDReader</span><span class="p">:</span> |
---|
681 | <span class="sd">"""</span> |
---|
682 | <span class="sd"> Class to load ascii files (7 columns).</span> |
---|
683 | <span class="sd"> """</span> |
---|
684 | <span class="c">## File type</span> |
---|
685 | <span class="n">type_name</span> <span class="o">=</span> <span class="s">"SLD ASCII"</span> |
---|
686 | |
---|
687 | <span class="c">## Wildcards</span> |
---|
688 | <span class="nb">type</span> <span class="o">=</span> <span class="p">[</span><span class="s">"sld files (*.SLD, *.sld)|*.sld"</span><span class="p">,</span> |
---|
689 | <span class="s">"txt files (*.TXT, *.txt)|*.txt"</span><span class="p">,</span> |
---|
690 | <span class="s">"all files (*.*)|*.*"</span><span class="p">]</span> |
---|
691 | <span class="c">## List of allowed extensions</span> |
---|
692 | <span class="n">ext</span> <span class="o">=</span> <span class="p">[</span><span class="s">'.sld'</span><span class="p">,</span> <span class="s">'.SLD'</span><span class="p">,</span> <span class="s">'.txt'</span><span class="p">,</span> <span class="s">'.TXT'</span><span class="p">,</span> <span class="s">'.*'</span><span class="p">]</span> |
---|
693 | |
---|
694 | <div class="viewcode-block" id="SLDReader.read"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.SLDReader.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> |
---|
695 | <span class="sd">"""</span> |
---|
696 | <span class="sd"> Load data file</span> |
---|
697 | <span class="sd"> </span> |
---|
698 | <span class="sd"> :param path: file path</span> |
---|
699 | <span class="sd"> </span> |
---|
700 | <span class="sd"> :return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz</span> |
---|
701 | <span class="sd"> </span> |
---|
702 | <span class="sd"> :raise RuntimeError: when the file can't be opened</span> |
---|
703 | <span class="sd"> :raise ValueError: when the length of the data vectors are inconsistent</span> |
---|
704 | <span class="sd"> """</span> |
---|
705 | <span class="k">try</span><span class="p">:</span> |
---|
706 | <span class="n">pos_x</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
707 | <span class="n">pos_y</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
708 | <span class="n">pos_z</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
709 | <span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
710 | <span class="n">sld_mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
711 | <span class="n">sld_my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
712 | <span class="n">sld_mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
713 | <span class="k">try</span><span class="p">:</span> |
---|
714 | <span class="c"># Use numpy to speed up loading</span> |
---|
715 | <span class="n">input_f</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="s">'float'</span><span class="p">,</span> <span class="n">skiprows</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> |
---|
716 | <span class="n">ndmin</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">unpack</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span> |
---|
717 | <span class="n">pos_x</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">input_f</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> |
---|
718 | <span class="n">pos_y</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">input_f</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> |
---|
719 | <span class="n">pos_z</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">input_f</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> |
---|
720 | <span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">input_f</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span> |
---|
721 | <span class="n">sld_mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">input_f</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span> |
---|
722 | <span class="n">sld_my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">input_f</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span> |
---|
723 | <span class="n">sld_mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">input_f</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span> |
---|
724 | <span class="n">ncols</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">input_f</span><span class="p">)</span> |
---|
725 | <span class="k">if</span> <span class="n">ncols</span> <span class="o">==</span> <span class="mi">8</span><span class="p">:</span> |
---|
726 | <span class="n">vol_pix</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">input_f</span><span class="p">[</span><span class="mi">7</span><span class="p">])</span> |
---|
727 | <span class="k">elif</span> <span class="n">ncols</span> <span class="o">==</span> <span class="mi">7</span><span class="p">:</span> |
---|
728 | <span class="n">vol_pix</span> <span class="o">=</span> <span class="bp">None</span> |
---|
729 | <span class="k">except</span><span class="p">:</span> |
---|
730 | <span class="c"># For older version of numpy</span> |
---|
731 | <span class="n">input_f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s">'rb'</span><span class="p">)</span> |
---|
732 | <span class="n">buff</span> <span class="o">=</span> <span class="n">input_f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> |
---|
733 | <span class="n">lines</span> <span class="o">=</span> <span class="n">buff</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span> |
---|
734 | <span class="n">input_f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> |
---|
735 | <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span> |
---|
736 | <span class="n">toks</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()</span> |
---|
737 | <span class="k">try</span><span class="p">:</span> |
---|
738 | <span class="n">_pos_x</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> |
---|
739 | <span class="n">_pos_y</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> |
---|
740 | <span class="n">_pos_z</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> |
---|
741 | <span class="n">_sld_n</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span> |
---|
742 | <span class="n">_sld_mx</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span> |
---|
743 | <span class="n">_sld_my</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span> |
---|
744 | <span class="n">_sld_mz</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span> |
---|
745 | |
---|
746 | <span class="n">pos_x</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pos_x</span><span class="p">,</span> <span class="n">_pos_x</span><span class="p">)</span> |
---|
747 | <span class="n">pos_y</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pos_y</span><span class="p">,</span> <span class="n">_pos_y</span><span class="p">)</span> |
---|
748 | <span class="n">pos_z</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pos_z</span><span class="p">,</span> <span class="n">_pos_z</span><span class="p">)</span> |
---|
749 | <span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_n</span><span class="p">,</span> <span class="n">_sld_n</span><span class="p">)</span> |
---|
750 | <span class="n">sld_mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_mx</span><span class="p">,</span> <span class="n">_sld_mx</span><span class="p">)</span> |
---|
751 | <span class="n">sld_my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_my</span><span class="p">,</span> <span class="n">_sld_my</span><span class="p">)</span> |
---|
752 | <span class="n">sld_mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_mz</span><span class="p">,</span> <span class="n">_sld_mz</span><span class="p">)</span> |
---|
753 | <span class="k">try</span><span class="p">:</span> |
---|
754 | <span class="n">_vol_pix</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">toks</span><span class="p">[</span><span class="mi">7</span><span class="p">])</span> |
---|
755 | <span class="n">vol_pix</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">vol_pix</span><span class="p">,</span> <span class="n">_vol_pix</span><span class="p">)</span> |
---|
756 | <span class="k">except</span><span class="p">:</span> |
---|
757 | <span class="n">vol_pix</span> <span class="o">=</span> <span class="bp">None</span> |
---|
758 | <span class="k">except</span><span class="p">:</span> |
---|
759 | <span class="c"># Skip non-data lines</span> |
---|
760 | <span class="k">pass</span> |
---|
761 | |
---|
762 | <span class="c"># re-center </span> |
---|
763 | <span class="c">#pos_x -= (min(pos_x) + max(pos_x)) / 2.0</span> |
---|
764 | <span class="c">#pos_y -= (min(pos_y) + max(pos_y)) / 2.0</span> |
---|
765 | <span class="c">#pos_z -= (min(pos_z) + max(pos_z)) / 2.0</span> |
---|
766 | |
---|
767 | <span class="n">output</span> <span class="o">=</span> <span class="n">MagSLD</span><span class="p">(</span><span class="n">pos_x</span><span class="p">,</span> <span class="n">pos_y</span><span class="p">,</span> <span class="n">pos_z</span><span class="p">,</span> <span class="n">sld_n</span><span class="p">,</span> |
---|
768 | <span class="n">sld_mx</span><span class="p">,</span> <span class="n">sld_my</span><span class="p">,</span> <span class="n">sld_mz</span><span class="p">)</span> |
---|
769 | |
---|
770 | <span class="n">output</span><span class="o">.</span><span class="n">filename</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> |
---|
771 | <span class="n">output</span><span class="o">.</span><span class="n">set_pix_type</span><span class="p">(</span><span class="s">'pixel'</span><span class="p">)</span> |
---|
772 | <span class="n">output</span><span class="o">.</span><span class="n">set_pixel_symbols</span><span class="p">(</span><span class="s">'pixel'</span><span class="p">)</span> |
---|
773 | <span class="k">if</span> <span class="n">vol_pix</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span> |
---|
774 | <span class="n">output</span><span class="o">.</span><span class="n">set_pixel_volumes</span><span class="p">(</span><span class="n">vol_pix</span><span class="p">)</span> |
---|
775 | <span class="k">return</span> <span class="n">output</span> |
---|
776 | <span class="k">except</span><span class="p">:</span> |
---|
777 | <span class="ne">RuntimeError</span><span class="p">,</span> <span class="s">"</span><span class="si">%s</span><span class="s"> is not a sld file"</span> <span class="o">%</span> <span class="n">path</span> |
---|
778 | </div> |
---|
779 | <div class="viewcode-block" id="SLDReader.write"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.SLDReader.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">path</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> |
---|
780 | <span class="sd">"""</span> |
---|
781 | <span class="sd"> Write sld file</span> |
---|
782 | <span class="sd"> </span> |
---|
783 | <span class="sd"> :Param path: file path </span> |
---|
784 | <span class="sd"> :Param data: MagSLD data object</span> |
---|
785 | <span class="sd"> """</span> |
---|
786 | <span class="k">if</span> <span class="n">path</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
787 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">"Missing the file path."</span> |
---|
788 | <span class="k">if</span> <span class="n">data</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
789 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">"Missing the data to save."</span> |
---|
790 | |
---|
791 | <span class="n">x_val</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">pos_x</span> |
---|
792 | <span class="n">y_val</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">pos_y</span> |
---|
793 | <span class="n">z_val</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">pos_z</span> |
---|
794 | <span class="n">vol_pix</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">vol_pix</span> |
---|
795 | |
---|
796 | <span class="n">length</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">x_val</span><span class="p">)</span> |
---|
797 | |
---|
798 | <span class="n">sld_n</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sld_n</span> |
---|
799 | <span class="k">if</span> <span class="n">sld_n</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
800 | <span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zerros</span><span class="p">(</span><span class="n">length</span><span class="p">)</span> |
---|
801 | |
---|
802 | <span class="n">sld_mx</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sld_mx</span> |
---|
803 | <span class="k">if</span> <span class="n">sld_mx</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
804 | <span class="n">sld_mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zerros</span><span class="p">(</span><span class="n">length</span><span class="p">)</span> |
---|
805 | <span class="n">sld_my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zerros</span><span class="p">(</span><span class="n">length</span><span class="p">)</span> |
---|
806 | <span class="n">sld_mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zerros</span><span class="p">(</span><span class="n">length</span><span class="p">)</span> |
---|
807 | <span class="k">else</span><span class="p">:</span> |
---|
808 | <span class="n">sld_my</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sld_my</span> |
---|
809 | <span class="n">sld_mz</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sld_mz</span> |
---|
810 | |
---|
811 | <span class="n">out</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span> |
---|
812 | <span class="c"># First Line: Column names</span> |
---|
813 | <span class="n">out</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix"</span><span class="p">)</span> |
---|
814 | <span class="k">for</span> <span class="n">ind</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">length</span><span class="p">):</span> |
---|
815 | <span class="n">out</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="si">%g</span><span class="s"> </span><span class="si">%g</span><span class="s"> </span><span class="si">%g</span><span class="s"> </span><span class="si">%g</span><span class="s"> </span><span class="si">%g</span><span class="s"> </span><span class="si">%g</span><span class="s"> </span><span class="si">%g</span><span class="s"> </span><span class="si">%g</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">x_val</span><span class="p">[</span><span class="n">ind</span><span class="p">],</span> <span class="n">y_val</span><span class="p">[</span><span class="n">ind</span><span class="p">],</span> |
---|
816 | <span class="n">z_val</span><span class="p">[</span><span class="n">ind</span><span class="p">],</span> <span class="n">sld_n</span><span class="p">[</span><span class="n">ind</span><span class="p">],</span> |
---|
817 | <span class="n">sld_mx</span><span class="p">[</span><span class="n">ind</span><span class="p">],</span> <span class="n">sld_my</span><span class="p">[</span><span class="n">ind</span><span class="p">],</span> |
---|
818 | <span class="n">sld_mz</span><span class="p">[</span><span class="n">ind</span><span class="p">],</span> <span class="n">vol_pix</span><span class="p">[</span><span class="n">ind</span><span class="p">]))</span> |
---|
819 | <span class="n">out</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> |
---|
820 | |
---|
821 | </div></div> |
---|
822 | <div class="viewcode-block" id="OMFData"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMFData">[docs]</a><span class="k">class</span> <span class="nc">OMFData</span><span class="p">:</span> |
---|
823 | <span class="sd">"""</span> |
---|
824 | <span class="sd"> OMF Data.</span> |
---|
825 | <span class="sd"> """</span> |
---|
826 | <span class="n">_meshunit</span> <span class="o">=</span> <span class="s">"A"</span> |
---|
827 | <span class="n">_valueunit</span> <span class="o">=</span> <span class="s">"A^(-2)"</span> |
---|
828 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
829 | <span class="sd">"""</span> |
---|
830 | <span class="sd"> Init for mag SLD</span> |
---|
831 | <span class="sd"> """</span> |
---|
832 | <span class="bp">self</span><span class="o">.</span><span class="n">filename</span> <span class="o">=</span> <span class="s">'default'</span> |
---|
833 | <span class="bp">self</span><span class="o">.</span><span class="n">oommf</span> <span class="o">=</span> <span class="s">''</span> |
---|
834 | <span class="bp">self</span><span class="o">.</span><span class="n">title</span> <span class="o">=</span> <span class="s">''</span> |
---|
835 | <span class="bp">self</span><span class="o">.</span><span class="n">desc</span> <span class="o">=</span> <span class="s">''</span> |
---|
836 | <span class="bp">self</span><span class="o">.</span><span class="n">meshtype</span> <span class="o">=</span> <span class="s">''</span> |
---|
837 | <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_meshunit</span> |
---|
838 | <span class="bp">self</span><span class="o">.</span><span class="n">valueunit</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_valueunit</span> |
---|
839 | <span class="bp">self</span><span class="o">.</span><span class="n">xbase</span> <span class="o">=</span> <span class="mf">0.0</span> |
---|
840 | <span class="bp">self</span><span class="o">.</span><span class="n">ybase</span> <span class="o">=</span> <span class="mf">0.0</span> |
---|
841 | <span class="bp">self</span><span class="o">.</span><span class="n">zbase</span> <span class="o">=</span> <span class="mf">0.0</span> |
---|
842 | <span class="bp">self</span><span class="o">.</span><span class="n">xstepsize</span> <span class="o">=</span> <span class="mf">6.0</span> |
---|
843 | <span class="bp">self</span><span class="o">.</span><span class="n">ystepsize</span> <span class="o">=</span> <span class="mf">6.0</span> |
---|
844 | <span class="bp">self</span><span class="o">.</span><span class="n">zstepsize</span> <span class="o">=</span> <span class="mf">6.0</span> |
---|
845 | <span class="bp">self</span><span class="o">.</span><span class="n">xnodes</span> <span class="o">=</span> <span class="mf">10.0</span> |
---|
846 | <span class="bp">self</span><span class="o">.</span><span class="n">ynodes</span> <span class="o">=</span> <span class="mf">10.0</span> |
---|
847 | <span class="bp">self</span><span class="o">.</span><span class="n">znodes</span> <span class="o">=</span> <span class="mf">10.0</span> |
---|
848 | <span class="bp">self</span><span class="o">.</span><span class="n">xmin</span> <span class="o">=</span> <span class="mf">0.0</span> |
---|
849 | <span class="bp">self</span><span class="o">.</span><span class="n">ymin</span> <span class="o">=</span> <span class="mf">0.0</span> |
---|
850 | <span class="bp">self</span><span class="o">.</span><span class="n">zmin</span> <span class="o">=</span> <span class="mf">0.0</span> |
---|
851 | <span class="bp">self</span><span class="o">.</span><span class="n">xmax</span> <span class="o">=</span> <span class="mf">60.0</span> |
---|
852 | <span class="bp">self</span><span class="o">.</span><span class="n">ymax</span> <span class="o">=</span> <span class="mf">60.0</span> |
---|
853 | <span class="bp">self</span><span class="o">.</span><span class="n">zmax</span> <span class="o">=</span> <span class="mf">60.0</span> |
---|
854 | <span class="bp">self</span><span class="o">.</span><span class="n">mx</span> <span class="o">=</span> <span class="bp">None</span> |
---|
855 | <span class="bp">self</span><span class="o">.</span><span class="n">my</span> <span class="o">=</span> <span class="bp">None</span> |
---|
856 | <span class="bp">self</span><span class="o">.</span><span class="n">mz</span> <span class="o">=</span> <span class="bp">None</span> |
---|
857 | <span class="bp">self</span><span class="o">.</span><span class="n">valuemultiplier</span> <span class="o">=</span> <span class="mf">1.</span> |
---|
858 | <span class="bp">self</span><span class="o">.</span><span class="n">valuerangeminmag</span> <span class="o">=</span> <span class="mi">0</span> |
---|
859 | <span class="bp">self</span><span class="o">.</span><span class="n">valuerangemaxmag</span> <span class="o">=</span> <span class="mi">0</span> |
---|
860 | |
---|
861 | <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
862 | <span class="sd">"""</span> |
---|
863 | <span class="sd"> doc strings</span> |
---|
864 | <span class="sd"> """</span> |
---|
865 | <span class="n">_str</span> <span class="o">=</span> <span class="s">"Type: </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">__class__</span><span class="o">.</span><span class="n">__name__</span> |
---|
866 | <span class="n">_str</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">filename</span> |
---|
867 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"OOMMF: </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">oommf</span> |
---|
868 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"Title: </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">title</span> |
---|
869 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"Desc: </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">desc</span> |
---|
870 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"meshtype: </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">meshtype</span> |
---|
871 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"meshunit: </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">meshunit</span><span class="p">)</span> |
---|
872 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"xbase: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">xbase</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
873 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"ybase: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">ybase</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
874 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"zbase: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">zbase</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
875 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"xstepsize: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">xstepsize</span><span class="p">),</span> |
---|
876 | <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
877 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"ystepsize: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">ystepsize</span><span class="p">),</span> |
---|
878 | <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
879 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"zstepsize: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">zstepsize</span><span class="p">),</span> |
---|
880 | <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
881 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"xnodes: </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">xnodes</span><span class="p">)</span> |
---|
882 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"ynodes: </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">ynodes</span><span class="p">)</span> |
---|
883 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"znodes: </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">znodes</span><span class="p">)</span> |
---|
884 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"xmin: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">xmin</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
885 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"ymin: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">ymin</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
886 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"zmin: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">zmin</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
887 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"xmax: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">xmax</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
888 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"ymax: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">ymax</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
889 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"zmax: </span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">zmax</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">meshunit</span><span class="p">)</span> |
---|
890 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"valueunit: </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">valueunit</span> |
---|
891 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"valuemultiplier: </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">valuemultiplier</span><span class="p">)</span> |
---|
892 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"ValueRangeMinMag:</span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">valuerangeminmag</span><span class="p">),</span> |
---|
893 | <span class="bp">self</span><span class="o">.</span><span class="n">valueunit</span><span class="p">)</span> |
---|
894 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"ValueRangeMaxMag:</span><span class="si">%s</span><span class="s"> [</span><span class="si">%s</span><span class="s">]</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</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">valuerangemaxmag</span><span class="p">),</span> |
---|
895 | <span class="bp">self</span><span class="o">.</span><span class="n">valueunit</span><span class="p">)</span> |
---|
896 | <span class="k">return</span> <span class="n">_str</span> |
---|
897 | |
---|
898 | <div class="viewcode-block" id="OMFData.set_m"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.OMFData.set_m">[docs]</a> <span class="k">def</span> <span class="nf">set_m</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mx</span><span class="p">,</span> <span class="n">my</span><span class="p">,</span> <span class="n">mz</span><span class="p">):</span> |
---|
899 | <span class="sd">"""</span> |
---|
900 | <span class="sd"> Set the Mx, My, Mz values</span> |
---|
901 | <span class="sd"> """</span> |
---|
902 | <span class="bp">self</span><span class="o">.</span><span class="n">mx</span> <span class="o">=</span> <span class="n">mx</span> |
---|
903 | <span class="bp">self</span><span class="o">.</span><span class="n">my</span> <span class="o">=</span> <span class="n">my</span> |
---|
904 | <span class="bp">self</span><span class="o">.</span><span class="n">mz</span> <span class="o">=</span> <span class="n">mz</span> |
---|
905 | </div></div> |
---|
906 | <div class="viewcode-block" id="MagSLD"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD">[docs]</a><span class="k">class</span> <span class="nc">MagSLD</span><span class="p">:</span> |
---|
907 | <span class="sd">"""</span> |
---|
908 | <span class="sd"> Magnetic SLD.</span> |
---|
909 | <span class="sd"> """</span> |
---|
910 | <span class="n">pos_x</span> <span class="o">=</span> <span class="bp">None</span> |
---|
911 | <span class="n">pos_y</span> <span class="o">=</span> <span class="bp">None</span> |
---|
912 | <span class="n">pos_z</span> <span class="o">=</span> <span class="bp">None</span> |
---|
913 | <span class="n">sld_n</span> <span class="o">=</span> <span class="bp">None</span> |
---|
914 | <span class="n">sld_mx</span> <span class="o">=</span> <span class="bp">None</span> |
---|
915 | <span class="n">sld_my</span> <span class="o">=</span> <span class="bp">None</span> |
---|
916 | <span class="n">sld_mz</span> <span class="o">=</span> <span class="bp">None</span> |
---|
917 | <span class="c"># Units</span> |
---|
918 | <span class="n">_pos_unit</span> <span class="o">=</span> <span class="s">'A'</span> |
---|
919 | <span class="n">_sld_unit</span> <span class="o">=</span> <span class="s">'1/A^(2)'</span> |
---|
920 | <span class="n">_pix_type</span> <span class="o">=</span> <span class="s">'pixel'</span> |
---|
921 | |
---|
922 | <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">pos_x</span><span class="p">,</span> <span class="n">pos_y</span><span class="p">,</span> <span class="n">pos_z</span><span class="p">,</span> <span class="n">sld_n</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> |
---|
923 | <span class="n">sld_mx</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">sld_my</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">sld_mz</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">vol_pix</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
---|
924 | <span class="sd">"""</span> |
---|
925 | <span class="sd"> Init for mag SLD</span> |
---|
926 | <span class="sd"> :params : All should be numpy 1D array</span> |
---|
927 | <span class="sd"> """</span> |
---|
928 | <span class="bp">self</span><span class="o">.</span><span class="n">is_data</span> <span class="o">=</span> <span class="bp">True</span> |
---|
929 | <span class="bp">self</span><span class="o">.</span><span class="n">filename</span> <span class="o">=</span> <span class="s">''</span> |
---|
930 | <span class="bp">self</span><span class="o">.</span><span class="n">xstepsize</span> <span class="o">=</span> <span class="mf">6.0</span> |
---|
931 | <span class="bp">self</span><span class="o">.</span><span class="n">ystepsize</span> <span class="o">=</span> <span class="mf">6.0</span> |
---|
932 | <span class="bp">self</span><span class="o">.</span><span class="n">zstepsize</span> <span class="o">=</span> <span class="mf">6.0</span> |
---|
933 | <span class="bp">self</span><span class="o">.</span><span class="n">xnodes</span> <span class="o">=</span> <span class="mf">10.0</span> |
---|
934 | <span class="bp">self</span><span class="o">.</span><span class="n">ynodes</span> <span class="o">=</span> <span class="mf">10.0</span> |
---|
935 | <span class="bp">self</span><span class="o">.</span><span class="n">znodes</span> <span class="o">=</span> <span class="mf">10.0</span> |
---|
936 | <span class="bp">self</span><span class="o">.</span><span class="n">has_stepsize</span> <span class="o">=</span> <span class="bp">False</span> |
---|
937 | <span class="bp">self</span><span class="o">.</span><span class="n">has_conect</span> <span class="o">=</span> <span class="bp">False</span> |
---|
938 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_unit</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pos_unit</span> |
---|
939 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_unit</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sld_unit</span> |
---|
940 | <span class="bp">self</span><span class="o">.</span><span class="n">pix_type</span> <span class="o">=</span> <span class="s">'pixel'</span> |
---|
941 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span> <span class="o">=</span> <span class="n">pos_x</span> |
---|
942 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span> <span class="o">=</span> <span class="n">pos_y</span> |
---|
943 | <span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span> <span class="o">=</span> <span class="n">pos_z</span> |
---|
944 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> <span class="o">=</span> <span class="n">sld_n</span> |
---|
945 | <span class="bp">self</span><span class="o">.</span><span class="n">line_x</span> <span class="o">=</span> <span class="bp">None</span> |
---|
946 | <span class="bp">self</span><span class="o">.</span><span class="n">line_y</span> <span class="o">=</span> <span class="bp">None</span> |
---|
947 | <span class="bp">self</span><span class="o">.</span><span class="n">line_z</span> <span class="o">=</span> <span class="bp">None</span> |
---|
948 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_mx</span> <span class="o">=</span> <span class="n">sld_mx</span> |
---|
949 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_my</span> <span class="o">=</span> <span class="n">sld_my</span> |
---|
950 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_mz</span> <span class="o">=</span> <span class="n">sld_mz</span> |
---|
951 | <span class="bp">self</span><span class="o">.</span><span class="n">vol_pix</span> <span class="o">=</span> <span class="n">vol_pix</span> |
---|
952 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_m</span> <span class="o">=</span> <span class="bp">None</span> |
---|
953 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_phi</span> <span class="o">=</span> <span class="bp">None</span> |
---|
954 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_theta</span> <span class="o">=</span> <span class="bp">None</span> |
---|
955 | <span class="bp">self</span><span class="o">.</span><span class="n">pix_symbol</span> <span class="o">=</span> <span class="bp">None</span> |
---|
956 | <span class="k">if</span> <span class="n">sld_mx</span> <span class="o">!=</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">sld_my</span> <span class="o">!=</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">sld_mz</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span> |
---|
957 | <span class="bp">self</span><span class="o">.</span><span class="n">set_sldms</span><span class="p">(</span><span class="n">sld_mx</span><span class="p">,</span> <span class="n">sld_my</span><span class="p">,</span> <span class="n">sld_mz</span><span class="p">)</span> |
---|
958 | <span class="bp">self</span><span class="o">.</span><span class="n">set_nodes</span><span class="p">()</span> |
---|
959 | |
---|
960 | <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
961 | <span class="sd">"""</span> |
---|
962 | <span class="sd"> doc strings</span> |
---|
963 | <span class="sd"> """</span> |
---|
964 | <span class="n">_str</span> <span class="o">=</span> <span class="s">"Type: </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">__class__</span><span class="o">.</span><span class="n">__name__</span> |
---|
965 | <span class="n">_str</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">filename</span> |
---|
966 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"Axis_unit: </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">pos_unit</span> |
---|
967 | <span class="n">_str</span> <span class="o">+=</span> <span class="s">"SLD_unit: </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">sld_unit</span> |
---|
968 | <span class="k">return</span> <span class="n">_str</span> |
---|
969 | |
---|
970 | <div class="viewcode-block" id="MagSLD.set_pix_type"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.set_pix_type">[docs]</a> <span class="k">def</span> <span class="nf">set_pix_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pix_type</span><span class="p">):</span> |
---|
971 | <span class="sd">"""</span> |
---|
972 | <span class="sd"> Set pixel type</span> |
---|
973 | <span class="sd"> :Param pix_type: string, 'pixel' or 'atom'</span> |
---|
974 | <span class="sd"> """</span> |
---|
975 | <span class="bp">self</span><span class="o">.</span><span class="n">pix_type</span> <span class="o">=</span> <span class="n">pix_type</span> |
---|
976 | </div> |
---|
977 | <div class="viewcode-block" id="MagSLD.set_sldn"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.set_sldn">[docs]</a> <span class="k">def</span> <span class="nf">set_sldn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sld_n</span><span class="p">):</span> |
---|
978 | <span class="sd">"""</span> |
---|
979 | <span class="sd"> Sets neutron SLD</span> |
---|
980 | <span class="sd"> """</span> |
---|
981 | <span class="k">if</span> <span class="n">sld_n</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">'float'</span><span class="p">:</span> |
---|
982 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_data</span><span class="p">:</span> |
---|
983 | <span class="c"># For data, put the value to only the pixels w non-zero M </span> |
---|
984 | <span class="n">is_nonzero</span> <span class="o">=</span> <span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sld_mx</span><span class="p">)</span> <span class="o">+</span> |
---|
985 | <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sld_my</span><span class="p">)</span> <span class="o">+</span> |
---|
986 | <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sld_mz</span><span class="p">))</span><span class="o">.</span><span class="n">nonzero</span><span class="p">()</span> |
---|
987 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</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">pos_x</span><span class="p">))</span> |
---|
988 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span><span class="p">[</span><span class="n">is_nonzero</span><span class="p">])</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
989 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span><span class="p">[</span><span class="n">is_nonzero</span><span class="p">]</span> <span class="o">=</span> <span class="n">sld_n</span> |
---|
990 | <span class="k">else</span><span class="p">:</span> |
---|
991 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span><span class="o">.</span><span class="n">fill</span><span class="p">(</span><span class="n">sld_n</span><span class="p">)</span> |
---|
992 | <span class="k">else</span><span class="p">:</span> |
---|
993 | <span class="c"># For non-data, put the value to all the pixels</span> |
---|
994 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">ones</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">pos_x</span><span class="p">))</span> <span class="o">*</span> <span class="n">sld_n</span> |
---|
995 | <span class="k">else</span><span class="p">:</span> |
---|
996 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> <span class="o">=</span> <span class="n">sld_n</span> |
---|
997 | </div> |
---|
998 | <div class="viewcode-block" id="MagSLD.set_sldms"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.set_sldms">[docs]</a> <span class="k">def</span> <span class="nf">set_sldms</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sld_mx</span><span class="p">,</span> <span class="n">sld_my</span><span class="p">,</span> <span class="n">sld_mz</span><span class="p">):</span> |
---|
999 | <span class="sd">"""</span> |
---|
1000 | <span class="sd"> Sets (\|m\|, m_theta, m_phi)</span> |
---|
1001 | <span class="sd"> """</span> |
---|
1002 | <span class="k">if</span> <span class="n">sld_mx</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">'float'</span><span class="p">:</span> |
---|
1003 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_mx</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">ones</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">pos_x</span><span class="p">))</span> <span class="o">*</span> <span class="n">sld_mx</span> |
---|
1004 | <span class="k">else</span><span class="p">:</span> |
---|
1005 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_mx</span> <span class="o">=</span> <span class="n">sld_mx</span> |
---|
1006 | <span class="k">if</span> <span class="n">sld_my</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">'float'</span><span class="p">:</span> |
---|
1007 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_my</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">ones</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">pos_x</span><span class="p">))</span> <span class="o">*</span> <span class="n">sld_my</span> |
---|
1008 | <span class="k">else</span><span class="p">:</span> |
---|
1009 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_my</span> <span class="o">=</span> <span class="n">sld_my</span> |
---|
1010 | <span class="k">if</span> <span class="n">sld_mz</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">'float'</span><span class="p">:</span> |
---|
1011 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_mz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">ones</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">pos_x</span><span class="p">))</span> <span class="o">*</span> <span class="n">sld_mz</span> |
---|
1012 | <span class="k">else</span><span class="p">:</span> |
---|
1013 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_mz</span> <span class="o">=</span> <span class="n">sld_mz</span> |
---|
1014 | |
---|
1015 | <span class="n">sld_m</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">sld_mx</span> <span class="o">*</span> <span class="n">sld_mx</span> <span class="o">+</span> <span class="n">sld_my</span> <span class="o">*</span> <span class="n">sld_my</span> <span class="o">+</span> \ |
---|
1016 | <span class="n">sld_mz</span> <span class="o">*</span> <span class="n">sld_mz</span><span class="p">)</span> |
---|
1017 | <span class="bp">self</span><span class="o">.</span><span class="n">sld_m</span> <span class="o">=</span> <span class="n">sld_m</span> |
---|
1018 | </div> |
---|
1019 | <div class="viewcode-block" id="MagSLD.set_pixel_symbols"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.set_pixel_symbols">[docs]</a> <span class="k">def</span> <span class="nf">set_pixel_symbols</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">symbol</span><span class="o">=</span><span class="s">'pixel'</span><span class="p">):</span> |
---|
1020 | <span class="sd">"""</span> |
---|
1021 | <span class="sd"> Set pixel</span> |
---|
1022 | <span class="sd"> :Params pixel: str; pixel or atomic symbol, or array of strings</span> |
---|
1023 | <span class="sd"> """</span> |
---|
1024 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
1025 | <span class="k">return</span> |
---|
1026 | <span class="k">if</span> <span class="n">symbol</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">'str'</span><span class="p">:</span> |
---|
1027 | <span class="bp">self</span><span class="o">.</span><span class="n">pix_symbol</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">repeat</span><span class="p">(</span><span class="n">symbol</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">sld_n</span><span class="p">))</span> |
---|
1028 | <span class="k">else</span><span class="p">:</span> |
---|
1029 | <span class="bp">self</span><span class="o">.</span><span class="n">pix_symbol</span> <span class="o">=</span> <span class="n">symbol</span> |
---|
1030 | </div> |
---|
1031 | <div class="viewcode-block" id="MagSLD.set_pixel_volumes"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.set_pixel_volumes">[docs]</a> <span class="k">def</span> <span class="nf">set_pixel_volumes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vol</span><span class="p">):</span> |
---|
1032 | <span class="sd">"""</span> |
---|
1033 | <span class="sd"> Set pixel volumes</span> |
---|
1034 | <span class="sd"> :Params pixel: str; pixel or atomic symbol, or array of strings</span> |
---|
1035 | <span class="sd"> """</span> |
---|
1036 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
1037 | <span class="k">return</span> |
---|
1038 | <span class="k">if</span> <span class="n">vol</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">'ndarray'</span><span class="p">:</span> |
---|
1039 | <span class="bp">self</span><span class="o">.</span><span class="n">vol_pix</span> <span class="o">=</span> <span class="n">vol</span> |
---|
1040 | <span class="k">elif</span> <span class="n">vol</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">'float'</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span> |
---|
1041 | <span class="bp">self</span><span class="o">.</span><span class="n">vol_pix</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">repeat</span><span class="p">(</span><span class="n">vol</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">sld_n</span><span class="p">))</span> |
---|
1042 | <span class="k">else</span><span class="p">:</span> |
---|
1043 | <span class="bp">self</span><span class="o">.</span><span class="n">vol_pix</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1044 | </div> |
---|
1045 | <div class="viewcode-block" id="MagSLD.get_sldn"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.get_sldn">[docs]</a> <span class="k">def</span> <span class="nf">get_sldn</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
1046 | <span class="sd">"""</span> |
---|
1047 | <span class="sd"> Returns nuclear sld</span> |
---|
1048 | <span class="sd"> """</span> |
---|
1049 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">sld_n</span> |
---|
1050 | </div> |
---|
1051 | <div class="viewcode-block" id="MagSLD.get_sld_mxyz"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.get_sld_mxyz">[docs]</a> <span class="k">def</span> <span class="nf">get_sld_mxyz</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
1052 | <span class="sd">"""</span> |
---|
1053 | <span class="sd"> Returns (sld_mx, sldmy, sld_mz)</span> |
---|
1054 | <span class="sd"> """</span> |
---|
1055 | <span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sld_mx</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sldmy</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sld_mz</span><span class="p">)</span> |
---|
1056 | </div> |
---|
1057 | <div class="viewcode-block" id="MagSLD.get_sld_m"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.get_sld_m">[docs]</a> <span class="k">def</span> <span class="nf">get_sld_m</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
1058 | <span class="sd">"""</span> |
---|
1059 | <span class="sd"> Returns (sldm, sld_theta, sld_phi)</span> |
---|
1060 | <span class="sd"> """</span> |
---|
1061 | <span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sldm</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sld_theta</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sld_phi</span><span class="p">)</span> |
---|
1062 | </div> |
---|
1063 | <div class="viewcode-block" id="MagSLD.set_nodes"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.set_nodes">[docs]</a> <span class="k">def</span> <span class="nf">set_nodes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
1064 | <span class="sd">"""</span> |
---|
1065 | <span class="sd"> Set xnodes, ynodes, and znodes</span> |
---|
1066 | <span class="sd"> """</span> |
---|
1067 | <span class="bp">self</span><span class="o">.</span><span class="n">set_stepsize</span><span class="p">()</span> |
---|
1068 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pix_type</span> <span class="o">==</span> <span class="s">'pixel'</span><span class="p">:</span> |
---|
1069 | <span class="k">try</span><span class="p">:</span> |
---|
1070 | <span class="n">xdist</span> <span class="o">=</span> <span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">)</span> <span class="o">-</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">))</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">xstepsize</span> |
---|
1071 | <span class="n">ydist</span> <span class="o">=</span> <span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">)</span> <span class="o">-</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">))</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">ystepsize</span> |
---|
1072 | <span class="n">zdist</span> <span class="o">=</span> <span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">)</span> <span class="o">-</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">))</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">zstepsize</span> |
---|
1073 | <span class="bp">self</span><span class="o">.</span><span class="n">xnodes</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">xdist</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span> |
---|
1074 | <span class="bp">self</span><span class="o">.</span><span class="n">ynodes</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">ydist</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span> |
---|
1075 | <span class="bp">self</span><span class="o">.</span><span class="n">znodes</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">zdist</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span> |
---|
1076 | <span class="k">except</span><span class="p">:</span> |
---|
1077 | <span class="bp">self</span><span class="o">.</span><span class="n">xnodes</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1078 | <span class="bp">self</span><span class="o">.</span><span class="n">ynodes</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1079 | <span class="bp">self</span><span class="o">.</span><span class="n">znodes</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1080 | <span class="k">else</span><span class="p">:</span> |
---|
1081 | <span class="bp">self</span><span class="o">.</span><span class="n">xnodes</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1082 | <span class="bp">self</span><span class="o">.</span><span class="n">ynodes</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1083 | <span class="bp">self</span><span class="o">.</span><span class="n">znodes</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1084 | </div> |
---|
1085 | <div class="viewcode-block" id="MagSLD.set_stepsize"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.set_stepsize">[docs]</a> <span class="k">def</span> <span class="nf">set_stepsize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
1086 | <span class="sd">"""</span> |
---|
1087 | <span class="sd"> Set xtepsize, ystepsize, and zstepsize</span> |
---|
1088 | <span class="sd"> """</span> |
---|
1089 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pix_type</span> <span class="o">==</span> <span class="s">'pixel'</span><span class="p">:</span> |
---|
1090 | <span class="k">try</span><span class="p">:</span> |
---|
1091 | <span class="n">xpos_pre</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> |
---|
1092 | <span class="n">ypos_pre</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> |
---|
1093 | <span class="n">zpos_pre</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> |
---|
1094 | <span class="k">for</span> <span class="n">x_pos</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_x</span><span class="p">:</span> |
---|
1095 | <span class="k">if</span> <span class="n">xpos_pre</span> <span class="o">!=</span> <span class="n">x_pos</span><span class="p">:</span> |
---|
1096 | <span class="bp">self</span><span class="o">.</span><span class="n">xstepsize</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="n">x_pos</span> <span class="o">-</span> <span class="n">xpos_pre</span><span class="p">)</span> |
---|
1097 | <span class="k">break</span> |
---|
1098 | <span class="k">for</span> <span class="n">y_pos</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_y</span><span class="p">:</span> |
---|
1099 | <span class="k">if</span> <span class="n">ypos_pre</span> <span class="o">!=</span> <span class="n">y_pos</span><span class="p">:</span> |
---|
1100 | <span class="bp">self</span><span class="o">.</span><span class="n">ystepsize</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="n">y_pos</span> <span class="o">-</span> <span class="n">ypos_pre</span><span class="p">)</span> |
---|
1101 | <span class="k">break</span> |
---|
1102 | <span class="k">for</span> <span class="n">z_pos</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_z</span><span class="p">:</span> |
---|
1103 | <span class="k">if</span> <span class="n">zpos_pre</span> <span class="o">!=</span> <span class="n">z_pos</span><span class="p">:</span> |
---|
1104 | <span class="bp">self</span><span class="o">.</span><span class="n">zstepsize</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="n">z_pos</span> <span class="o">-</span> <span class="n">zpos_pre</span><span class="p">)</span> |
---|
1105 | <span class="k">break</span> |
---|
1106 | <span class="c">#default pix volume</span> |
---|
1107 | <span class="bp">self</span><span class="o">.</span><span class="n">vol_pix</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">ones</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">pos_x</span><span class="p">))</span> |
---|
1108 | <span class="n">vol</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">xstepsize</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">ystepsize</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">zstepsize</span> |
---|
1109 | <span class="bp">self</span><span class="o">.</span><span class="n">set_pixel_volumes</span><span class="p">(</span><span class="n">vol</span><span class="p">)</span> |
---|
1110 | <span class="bp">self</span><span class="o">.</span><span class="n">has_stepsize</span> <span class="o">=</span> <span class="bp">True</span> |
---|
1111 | <span class="k">except</span><span class="p">:</span> |
---|
1112 | <span class="bp">self</span><span class="o">.</span><span class="n">xstepsize</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1113 | <span class="bp">self</span><span class="o">.</span><span class="n">ystepsize</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1114 | <span class="bp">self</span><span class="o">.</span><span class="n">zstepsize</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1115 | <span class="bp">self</span><span class="o">.</span><span class="n">vol_pix</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1116 | <span class="bp">self</span><span class="o">.</span><span class="n">has_stepsize</span> <span class="o">=</span> <span class="bp">False</span> |
---|
1117 | <span class="k">else</span><span class="p">:</span> |
---|
1118 | <span class="bp">self</span><span class="o">.</span><span class="n">xstepsize</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1119 | <span class="bp">self</span><span class="o">.</span><span class="n">ystepsize</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1120 | <span class="bp">self</span><span class="o">.</span><span class="n">zstepsize</span> <span class="o">=</span> <span class="bp">None</span> |
---|
1121 | <span class="bp">self</span><span class="o">.</span><span class="n">has_stepsize</span> <span class="o">=</span> <span class="bp">True</span> |
---|
1122 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">xstepsize</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">ystepsize</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">zstepsize</span> |
---|
1123 | </div> |
---|
1124 | <div class="viewcode-block" id="MagSLD.set_conect_lines"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.MagSLD.set_conect_lines">[docs]</a> <span class="k">def</span> <span class="nf">set_conect_lines</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">line_x</span><span class="p">,</span> <span class="n">line_y</span><span class="p">,</span> <span class="n">line_z</span><span class="p">):</span> |
---|
1125 | <span class="sd">"""</span> |
---|
1126 | <span class="sd"> Set bonding line data if taken from pdb</span> |
---|
1127 | <span class="sd"> """</span> |
---|
1128 | <span class="k">if</span> <span class="n">line_x</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">!=</span> <span class="s">'list'</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">line_x</span><span class="p">)</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span> |
---|
1129 | <span class="k">return</span> |
---|
1130 | <span class="k">if</span> <span class="n">line_y</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">!=</span> <span class="s">'list'</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">line_y</span><span class="p">)</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span> |
---|
1131 | <span class="k">return</span> |
---|
1132 | <span class="k">if</span> <span class="n">line_z</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">!=</span> <span class="s">'list'</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">line_z</span><span class="p">)</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span> |
---|
1133 | <span class="k">return</span> |
---|
1134 | <span class="bp">self</span><span class="o">.</span><span class="n">has_conect</span> <span class="o">=</span> <span class="bp">True</span> |
---|
1135 | <span class="bp">self</span><span class="o">.</span><span class="n">line_x</span> <span class="o">=</span> <span class="n">line_x</span> |
---|
1136 | <span class="bp">self</span><span class="o">.</span><span class="n">line_y</span> <span class="o">=</span> <span class="n">line_y</span> |
---|
1137 | <span class="bp">self</span><span class="o">.</span><span class="n">line_z</span> <span class="o">=</span> <span class="n">line_z</span> |
---|
1138 | |
---|
1139 | </div></div> |
---|
1140 | <div class="viewcode-block" id="test_load"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.test_load">[docs]</a><span class="k">def</span> <span class="nf">test_load</span><span class="p">():</span> |
---|
1141 | <span class="kn">from</span> <span class="nn">sas.plottools.arrow3d</span> <span class="kn">import</span> <span class="n">Arrow3D</span> |
---|
1142 | <span class="kn">import</span> <span class="nn">os</span> |
---|
1143 | <span class="nb">dir</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">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">curdir</span><span class="p">)</span> |
---|
1144 | <span class="k">print</span> <span class="nb">dir</span> |
---|
1145 | <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">6</span><span class="p">):</span> |
---|
1146 | <span class="nb">dir</span><span class="p">,</span> <span class="n">_</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">split</span><span class="p">(</span><span class="nb">dir</span><span class="p">)</span> |
---|
1147 | <span class="n">tfile</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">join</span><span class="p">(</span><span class="nb">dir</span><span class="p">,</span> <span class="s">"test"</span><span class="p">,</span> <span class="s">"CoreXY_ShellZ.txt"</span><span class="p">)</span> |
---|
1148 | <span class="n">ofile</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">join</span><span class="p">(</span><span class="nb">dir</span><span class="p">,</span> <span class="s">"test"</span><span class="p">,</span> <span class="s">"A_Raw_Example-1.omf"</span><span class="p">)</span> |
---|
1149 | <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">tfile</span><span class="p">):</span> |
---|
1150 | <span class="n">tfpath</span> <span class="o">=</span> <span class="n">tfile</span> |
---|
1151 | <span class="n">ofpath</span> <span class="o">=</span> <span class="n">ofile</span> |
---|
1152 | <span class="k">break</span> |
---|
1153 | <span class="n">reader</span> <span class="o">=</span> <span class="n">SLDReader</span><span class="p">()</span> |
---|
1154 | <span class="n">oreader</span> <span class="o">=</span> <span class="n">OMFReader</span><span class="p">()</span> |
---|
1155 | <span class="n">output</span> <span class="o">=</span> <span class="n">reader</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">tfpath</span><span class="p">)</span> |
---|
1156 | <span class="n">ooutput</span> <span class="o">=</span> <span class="n">oreader</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">ofpath</span><span class="p">)</span> |
---|
1157 | <span class="n">foutput</span> <span class="o">=</span> <span class="n">OMF2SLD</span><span class="p">()</span> |
---|
1158 | <span class="n">foutput</span><span class="o">.</span><span class="n">set_data</span><span class="p">(</span><span class="n">ooutput</span><span class="p">)</span> |
---|
1159 | |
---|
1160 | <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="kn">as</span> <span class="nn">plt</span> |
---|
1161 | <span class="kn">from</span> <span class="nn">mpl_toolkits.mplot3d</span> <span class="kn">import</span> <span class="n">Axes3D</span> |
---|
1162 | <span class="n">fig</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span> |
---|
1163 | <span class="n">ax</span> <span class="o">=</span> <span class="n">fig</span><span class="o">.</span><span class="n">gca</span><span class="p">(</span><span class="n">projection</span><span class="o">=</span><span class="s">'3d'</span><span class="p">)</span> |
---|
1164 | <span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">output</span><span class="o">.</span><span class="n">pos_x</span><span class="p">,</span> <span class="n">output</span><span class="o">.</span><span class="n">pos_y</span><span class="p">,</span> <span class="n">output</span><span class="o">.</span><span class="n">pos_z</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="s">"g"</span><span class="p">,</span> |
---|
1165 | <span class="n">alpha</span> <span class="o">=</span> <span class="mf">0.7</span><span class="p">,</span> <span class="n">markeredgecolor</span><span class="o">=</span><span class="s">'gray'</span><span class="p">,</span><span class="n">rasterized</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span> |
---|
1166 | <span class="n">gap</span> <span class="o">=</span> <span class="mi">7</span> |
---|
1167 | <span class="n">max_mx</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">output</span><span class="o">.</span><span class="n">sld_mx</span><span class="p">)</span> |
---|
1168 | <span class="n">max_my</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">output</span><span class="o">.</span><span class="n">sld_my</span><span class="p">)</span> |
---|
1169 | <span class="n">max_mz</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">output</span><span class="o">.</span><span class="n">sld_mz</span><span class="p">)</span> |
---|
1170 | <span class="n">max_m</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">max_mx</span><span class="p">,</span><span class="n">max_my</span><span class="p">,</span><span class="n">max_mz</span><span class="p">)</span> |
---|
1171 | <span class="n">x2</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">pos_x</span><span class="o">+</span><span class="n">output</span><span class="o">.</span><span class="n">sld_mx</span><span class="o">/</span><span class="n">max_m</span> <span class="o">*</span> <span class="n">gap</span> |
---|
1172 | <span class="n">y2</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">pos_y</span><span class="o">+</span><span class="n">output</span><span class="o">.</span><span class="n">sld_my</span><span class="o">/</span><span class="n">max_m</span> <span class="o">*</span> <span class="n">gap</span> |
---|
1173 | <span class="n">z2</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">pos_z</span><span class="o">+</span><span class="n">output</span><span class="o">.</span><span class="n">sld_mz</span><span class="o">/</span><span class="n">max_m</span> <span class="o">*</span> <span class="n">gap</span> |
---|
1174 | <span class="n">x_arrow</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">column_stack</span><span class="p">((</span><span class="n">output</span><span class="o">.</span><span class="n">pos_x</span><span class="p">,</span><span class="n">x2</span><span class="p">))</span> |
---|
1175 | <span class="n">y_arrow</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">column_stack</span><span class="p">((</span><span class="n">output</span><span class="o">.</span><span class="n">pos_y</span><span class="p">,</span><span class="n">y2</span><span class="p">))</span> |
---|
1176 | <span class="n">z_arrow</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">column_stack</span><span class="p">((</span><span class="n">output</span><span class="o">.</span><span class="n">pos_z</span><span class="p">,</span><span class="n">z2</span><span class="p">))</span> |
---|
1177 | <span class="n">unit_x2</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">sld_mx</span> <span class="o">/</span> <span class="n">max_m</span> |
---|
1178 | <span class="n">unit_y2</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">sld_my</span> <span class="o">/</span> <span class="n">max_m</span> |
---|
1179 | <span class="n">unit_z2</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">sld_mz</span> <span class="o">/</span> <span class="n">max_m</span> |
---|
1180 | <span class="n">color_x</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="n">unit_x2</span> <span class="o">*</span> <span class="mf">0.8</span><span class="p">)</span> |
---|
1181 | <span class="n">color_y</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="n">unit_y2</span> <span class="o">*</span> <span class="mf">0.8</span><span class="p">)</span> |
---|
1182 | <span class="n">color_z</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">fabs</span><span class="p">(</span><span class="n">unit_z2</span> <span class="o">*</span> <span class="mf">0.8</span><span class="p">)</span> |
---|
1183 | <span class="n">colors</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">column_stack</span><span class="p">((</span><span class="n">color_x</span><span class="p">,</span> <span class="n">color_y</span><span class="p">,</span> <span class="n">color_z</span><span class="p">))</span> |
---|
1184 | <span class="n">a</span> <span class="o">=</span> <span class="n">Arrow3D</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="n">x_arrow</span><span class="p">,</span><span class="n">y_arrow</span><span class="p">,</span><span class="n">z_arrow</span><span class="p">,</span> <span class="n">colors</span><span class="p">,</span> <span class="n">mutation_scale</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> |
---|
1185 | <span class="n">arrowstyle</span><span class="o">=</span><span class="s">"->"</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s">"y"</span><span class="p">,</span> <span class="n">alpha</span> <span class="o">=</span> <span class="mf">0.5</span><span class="p">)</span> |
---|
1186 | |
---|
1187 | <span class="n">ax</span><span class="o">.</span><span class="n">add_artist</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> |
---|
1188 | <span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> |
---|
1189 | </div> |
---|
1190 | <div class="viewcode-block" id="test"><a class="viewcode-back" href="../../../dev/api/sas.calculator.html#sas.calculator.sas_gen.test">[docs]</a><span class="k">def</span> <span class="nf">test</span><span class="p">():</span> |
---|
1191 | <span class="kn">import</span> <span class="nn">os</span> |
---|
1192 | <span class="nb">dir</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">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">curdir</span><span class="p">)</span> |
---|
1193 | <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span> |
---|
1194 | <span class="nb">dir</span><span class="p">,</span> <span class="n">_</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">split</span><span class="p">(</span><span class="nb">dir</span><span class="p">)</span> |
---|
1195 | <span class="c">#tfile = os.path.join(dir, "test", "C_Example_Converted.txt")</span> |
---|
1196 | <span class="n">ofile</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">join</span><span class="p">(</span><span class="nb">dir</span><span class="p">,</span> <span class="s">"test"</span><span class="p">,</span> <span class="s">"A_Raw_Example-1.omf"</span><span class="p">)</span> |
---|
1197 | <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">ofile</span><span class="p">):</span> |
---|
1198 | <span class="c">#tfpath = tfile</span> |
---|
1199 | <span class="n">ofpath</span> <span class="o">=</span> <span class="n">ofile</span> |
---|
1200 | <span class="k">break</span> |
---|
1201 | <span class="c">#reader = SLDReader()</span> |
---|
1202 | <span class="n">oreader</span> <span class="o">=</span> <span class="n">OMFReader</span><span class="p">()</span> |
---|
1203 | <span class="c">#output = reader.read(tfpath)</span> |
---|
1204 | <span class="n">ooutput</span> <span class="o">=</span> <span class="n">oreader</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">ofpath</span><span class="p">)</span> |
---|
1205 | <span class="n">foutput</span> <span class="o">=</span> <span class="n">OMF2SLD</span><span class="p">()</span> |
---|
1206 | <span class="n">foutput</span><span class="o">.</span><span class="n">set_data</span><span class="p">(</span><span class="n">ooutput</span><span class="p">)</span> |
---|
1207 | <span class="n">writer</span> <span class="o">=</span> <span class="n">SLDReader</span><span class="p">()</span> |
---|
1208 | <span class="n">writer</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">ofpath</span><span class="p">),</span> <span class="s">"out.txt"</span><span class="p">),</span> |
---|
1209 | <span class="n">foutput</span><span class="o">.</span><span class="n">output</span><span class="p">)</span> |
---|
1210 | <span class="n">model</span> <span class="o">=</span> <span class="n">GenSAS</span><span class="p">()</span> |
---|
1211 | <span class="n">model</span><span class="o">.</span><span class="n">set_sld_data</span><span class="p">(</span><span class="n">foutput</span><span class="o">.</span><span class="n">output</span><span class="p">)</span> |
---|
1212 | <span class="n">x</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">1000</span><span class="p">)</span><span class="o">/</span><span class="mf">10000.</span> <span class="o">+</span> <span class="mf">1e-5</span> |
---|
1213 | <span class="n">y</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">1000</span><span class="p">)</span><span class="o">/</span><span class="mf">10000.</span> <span class="o">+</span> <span class="mf">1e-5</span> |
---|
1214 | <span class="c">#z = numpy.arange(1000)/10000. + 1e-5</span> |
---|
1215 | <span class="n">i</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">1000</span><span class="p">)</span> |
---|
1216 | <span class="n">out</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">runXY</span><span class="p">([</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">i</span><span class="p">])</span> |
---|
1217 | </div> |
---|
1218 | <span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span> |
---|
1219 | <span class="n">test</span><span class="p">()</span> |
---|
1220 | <span class="n">test_load</span><span class="p">()</span> |
---|
1221 | </pre></div> |
---|
1222 | |
---|
1223 | </div> |
---|
1224 | </div> |
---|
1225 | </div> |
---|
1226 | <div class="sphinxsidebar"> |
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1227 | <div class="sphinxsidebarwrapper"> |
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1228 | <div id="searchbox" style="display: none"> |
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1229 | <h3>Quick search</h3> |
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1230 | <form class="search" action="../../../search.html" method="get"> |
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1231 | <input type="text" name="q" /> |
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1232 | <input type="submit" value="Go" /> |
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1233 | <input type="hidden" name="check_keywords" value="yes" /> |
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1234 | <input type="hidden" name="area" value="default" /> |
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1235 | </form> |
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1236 | <p class="searchtip" style="font-size: 90%"> |
---|
1237 | Enter search terms or a module, class or function name. |
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1238 | </p> |
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1239 | </div> |
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1240 | <script type="text/javascript">$('#searchbox').show(0);</script> |
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1241 | </div> |
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1242 | </div> |
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1243 | <div class="clearer"></div> |
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1244 | </div> |
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1245 | <div class="related"> |
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1246 | <h3>Navigation</h3> |
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1247 | <ul> |
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1248 | <li class="right" style="margin-right: 10px"> |
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1249 | <a href="../../../genindex.html" title="General Index" |
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1250 | >index</a></li> |
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1251 | <li class="right" > |
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1252 | <a href="../../../py-modindex.html" title="Python Module Index" |
---|
1253 | >modules</a> |</li> |
---|
1254 | <li><a href="../../../index.html">SasView 3.0.0 documentation</a> »</li> |
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1255 | <li><a href="../../index.html" >Module code</a> »</li> |
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1256 | </ul> |
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1257 | </div> |
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1258 | <div class="footer"> |
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1259 | © Copyright 2013, The SasView Project. |
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1260 | Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. |
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1261 | </div> |
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1262 | </body> |
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1263 | </html> |
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