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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> |
---|
| 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> |
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| 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 | |
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| 401 | </div></div> |
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| 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> |
---|
| 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 | |
---|
| 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> |
---|
| 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> |
---|
| 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"> |
---|
| 1227 | <div class="sphinxsidebarwrapper"> |
---|
| 1228 | <div id="searchbox" style="display: none"> |
---|
| 1229 | <h3>Quick search</h3> |
---|
| 1230 | <form class="search" action="../../../search.html" method="get"> |
---|
| 1231 | <input type="text" name="q" /> |
---|
| 1232 | <input type="submit" value="Go" /> |
---|
| 1233 | <input type="hidden" name="check_keywords" value="yes" /> |
---|
| 1234 | <input type="hidden" name="area" value="default" /> |
---|
| 1235 | </form> |
---|
| 1236 | <p class="searchtip" style="font-size: 90%"> |
---|
| 1237 | Enter search terms or a module, class or function name. |
---|
| 1238 | </p> |
---|
| 1239 | </div> |
---|
| 1240 | <script type="text/javascript">$('#searchbox').show(0);</script> |
---|
| 1241 | </div> |
---|
| 1242 | </div> |
---|
| 1243 | <div class="clearer"></div> |
---|
| 1244 | </div> |
---|
| 1245 | <div class="related"> |
---|
| 1246 | <h3>Navigation</h3> |
---|
| 1247 | <ul> |
---|
| 1248 | <li class="right" style="margin-right: 10px"> |
---|
| 1249 | <a href="../../../genindex.html" title="General Index" |
---|
| 1250 | >index</a></li> |
---|
| 1251 | <li class="right" > |
---|
| 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> |
---|
| 1255 | <li><a href="../../index.html" >Module code</a> »</li> |
---|
| 1256 | </ul> |
---|
| 1257 | </div> |
---|
| 1258 | <div class="footer"> |
---|
| 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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