htdocs update (master)

Author: DiamondLightSource-build-server

documentation/programs/xia2_multiplex.html

@@ -153,17 +153,6 @@ <h2>Basic parameters<a class="headerlink" href="#basic-parameters" title="Link t
   <span class="n">emax</span> <span class="o">=</span> <span class="mi">4</span>
 <span class="p">}</span>
 <span class="n">rescale_after_resolution_cutoff</span> <span class="o">=</span> <span class="kc">False</span>
-<span class="n">filtering</span> <span class="p">{</span>
-  <span class="n">method</span> <span class="o">=</span> <span class="kc">None</span> <span class="n">deltacchalf</span>
-  <span class="n">deltacchalf</span> <span class="p">{</span>
-    <span class="n">max_cycles</span> <span class="o">=</span> <span class="kc">None</span>
-    <span class="n">max_percent_removed</span> <span class="o">=</span> <span class="kc">None</span>
-    <span class="n">min_completeness</span> <span class="o">=</span> <span class="kc">None</span>
-    <span class="n">mode</span> <span class="o">=</span> <span class="n">dataset</span> <span class="n">image_group</span>
-    <span class="n">group_size</span> <span class="o">=</span> <span class="kc">None</span>
-    <span class="n">stdcutoff</span> <span class="o">=</span> <span class="kc">None</span>
-  <span class="p">}</span>
-<span class="p">}</span>
 <span class="n">multi_crystal_analysis</span> <span class="p">{</span>
   <span class="n">unit_cell</span> <span class="o">=</span> <span class="kc">None</span>
   <span class="n">n_bins</span> <span class="o">=</span> <span class="mi">20</span>
@@ -194,6 +183,17 @@ <h2>Basic parameters<a class="headerlink" href="#basic-parameters" title="Link t
     <span class="n">distinct_clusters</span> <span class="o">=</span> <span class="kc">False</span>
   <span class="p">}</span>
 <span class="p">}</span>
+<span class="n">filtering</span> <span class="p">{</span>
+  <span class="n">method</span> <span class="o">=</span> <span class="kc">None</span> <span class="n">deltacchalf</span>
+  <span class="n">deltacchalf</span> <span class="p">{</span>
+    <span class="n">max_cycles</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">max_percent_removed</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">min_completeness</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">mode</span> <span class="o">=</span> <span class="n">dataset</span> <span class="n">image_group</span>
+    <span class="n">group_size</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">stdcutoff</span> <span class="o">=</span> <span class="kc">None</span>
+  <span class="p">}</span>
+<span class="p">}</span>
 <span class="n">identifiers</span> <span class="o">=</span> <span class="kc">None</span>
 <span class="n">dose</span> <span class="o">=</span> <span class="kc">None</span>
 <span class="n">nproc</span> <span class="o">=</span> <span class="n">Auto</span>
@@ -522,39 +522,6 @@ <h2>Full parameter definitions<a class="headerlink" href="#full-parameter-defini
   <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Re-scale the data after application of a resolution cutoff&quot;</span>
   <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Rescale after resolution cutoff&quot;</span>
   <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">bool</span>
-<span class="n">filtering</span>
-  <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="n">Filtering</span>
-<span class="p">{</span>
-  <span class="n">method</span> <span class="o">=</span> <span class="kc">None</span> <span class="n">deltacchalf</span>
-    <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Choice of whether to do any filtering cycles, default None.&quot;</span>
-    <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="n">choice</span>
-  <span class="n">deltacchalf</span>
-    <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;ΔCC½&quot;</span>
-  <span class="p">{</span>
-    <span class="n">max_cycles</span> <span class="o">=</span> <span class="kc">None</span>
-      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Maximum number of cycles&quot;</span>
-      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">value_min</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-    <span class="n">max_percent_removed</span> <span class="o">=</span> <span class="kc">None</span>
-      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Maximum percentage removed&quot;</span>
-      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-    <span class="n">min_completeness</span> <span class="o">=</span> <span class="kc">None</span>
-      <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Desired minimum completeness, as a percentage (0 - 100).&quot;</span>
-      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Minimum completeness&quot;</span>
-      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">value_min</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">value_max</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span> <span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-    <span class="n">mode</span> <span class="o">=</span> <span class="n">dataset</span> <span class="n">image_group</span>
-      <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Perform analysis on whole datasets or batch groups&quot;</span>
-      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="n">choice</span>
-    <span class="n">group_size</span> <span class="o">=</span> <span class="kc">None</span>
-      <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;The number of images to group together when calculating delta&quot;</span>
-              <span class="s2">&quot;cchalf in image_group mode&quot;</span>
-      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Group size&quot;</span>
-      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">value_min</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-    <span class="n">stdcutoff</span> <span class="o">=</span> <span class="kc">None</span>
-      <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Datasets with a ΔCC½ below (mean - stdcutoff*std) are removed&quot;</span>
-      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Standard deviation cutoff&quot;</span>
-      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-  <span class="p">}</span>
-<span class="p">}</span>
 <span class="n">multi_crystal_analysis</span> <span class="p">{</span>
   <span class="n">unit_cell</span> <span class="o">=</span> <span class="kc">None</span>
     <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Unit cell&quot;</span>
@@ -637,6 +604,39 @@ <h2>Full parameter definitions<a class="headerlink" href="#full-parameter-defini
       <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">bool</span>
   <span class="p">}</span>
 <span class="p">}</span>
+<span class="n">filtering</span>
+  <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="n">Filtering</span>
+<span class="p">{</span>
+  <span class="n">method</span> <span class="o">=</span> <span class="kc">None</span> <span class="n">deltacchalf</span>
+    <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Choice of whether to do any filtering cycles, default None.&quot;</span>
+    <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="n">choice</span>
+  <span class="n">deltacchalf</span>
+    <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;ΔCC½&quot;</span>
+  <span class="p">{</span>
+    <span class="n">max_cycles</span> <span class="o">=</span> <span class="kc">None</span>
+      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Maximum number of cycles&quot;</span>
+      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">value_min</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="n">max_percent_removed</span> <span class="o">=</span> <span class="kc">None</span>
+      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Maximum percentage removed&quot;</span>
+      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="n">min_completeness</span> <span class="o">=</span> <span class="kc">None</span>
+      <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Desired minimum completeness, as a percentage (0 - 100).&quot;</span>
+      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Minimum completeness&quot;</span>
+      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">value_min</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">value_max</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span> <span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="n">mode</span> <span class="o">=</span> <span class="n">dataset</span> <span class="n">image_group</span>
+      <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Perform analysis on whole datasets or batch groups&quot;</span>
+      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="n">choice</span>
+    <span class="n">group_size</span> <span class="o">=</span> <span class="kc">None</span>
+      <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;The number of images to group together when calculating delta&quot;</span>
+              <span class="s2">&quot;cchalf in image_group mode&quot;</span>
+      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Group size&quot;</span>
+      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">value_min</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="n">stdcutoff</span> <span class="o">=</span> <span class="kc">None</span>
+      <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Datasets with a ΔCC½ below (mean - stdcutoff*std) are removed&quot;</span>
+      <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="s2">&quot;Standard deviation cutoff&quot;</span>
+      <span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">allow_none</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+  <span class="p">}</span>
+<span class="p">}</span>
 <span class="n">identifiers</span> <span class="o">=</span> <span class="kc">None</span>
   <span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Unique DIALS identifiers of experiments to be merged&quot;</span>
   <span class="o">.</span><span class="n">short_caption</span> <span class="o">=</span> <span class="n">Identifiers</span>