htdocs update (master)

_modules/dials/algorithms/indexing/lattice_search/pinkindexer.html

@@ -414,7 +414,7 @@ <h1>Source code for dials.algorithms.indexing.lattice_search.pinkindexer</h1><di
 
         <span class="k">if</span> <span class="n">target_symmetry_primitive</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">raise</span> <span class="n">DialsIndexError</span><span class="p">(</span>
-                <span class="s2">&quot;Target unit cell and space group must be provided for small_cell&quot;</span>
+                <span class="s2">&quot;Target unit cell and space group must be provided for pink_indexer&quot;</span>
             <span class="p">)</span>
 
         <span class="n">target_cell</span> <span class="o">=</span> <span class="n">target_symmetry_primitive</span><span class="o">.</span><span class="n">unit_cell</span><span class="p">()</span>

_modules/index.html

@@ -72,6 +72,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="dials/algorithms/indexing/basis_vector_search/strategy.html">dials.algorithms.indexing.basis_vector_search.strategy</a></li>
 <li><a href="dials/algorithms/indexing/compare_orientation_matrices.html">dials.algorithms.indexing.compare_orientation_matrices</a></li>
 <li><a href="dials/algorithms/indexing/indexer.html">dials.algorithms.indexing.indexer</a></li>
+<li><a href="dials/algorithms/indexing/lattice_search/ffb_indexer.html">dials.algorithms.indexing.lattice_search.ffb_indexer</a></li>
 <li><a href="dials/algorithms/indexing/lattice_search/low_res_spot_match.html">dials.algorithms.indexing.lattice_search.low_res_spot_match</a></li>
 <li><a href="dials/algorithms/indexing/lattice_search/pinkindexer.html">dials.algorithms.indexing.lattice_search.pinkindexer</a></li>
 <li><a href="dials/algorithms/indexing/lattice_search/strategy.html">dials.algorithms.indexing.lattice_search.strategy</a></li>

about.html

@@ -122,6 +122,7 @@ <h2>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Link t
 Derek Mendez
 Graeme Winter
 Huw Jenkins
+Hans-Christian Stadler
 Ian Rees
 Iris Young
 James Beilsten-Edmands

documentation/library_reference/algorithms/dials.algorithms.indexing.html

@@ -573,6 +573,61 @@
 </section>
 <section id="module-dials.algorithms.indexing.lattice_search">
 <span id="dials-algorithms-indexing-lattice-search"></span><h2>dials.algorithms.indexing.lattice_search<a class="headerlink" href="#module-dials.algorithms.indexing.lattice_search" title="Link to this heading">¶</a></h2>
+<dl class="py class">
+<dt class="sig sig-object py" id="dials.algorithms.indexing.lattice_search.FfbIndexer">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dials.algorithms.indexing.lattice_search.</span></span><span class="sig-name descname"><span class="pre">FfbIndexer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target_symmetry_primitive</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_lattices</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/dials/algorithms/indexing/lattice_search/ffb_indexer.html#FfbIndexer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dials.algorithms.indexing.lattice_search.FfbIndexer" title="Link to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#dials.algorithms.indexing.lattice_search.Strategy" title="dials.algorithms.indexing.lattice_search.strategy.Strategy"><code class="xref py py-class docutils literal notranslate"><span class="pre">Strategy</span></code></a></p>
+<p>A lattice search strategy using a Cuda-accelerated implementation of the TORO algorithm.
+For more info, see:
+[Gasparotto P, et al. TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial crystallography. J. Appl. Cryst. 2024 57(4)](<a class="reference external" href="https://doi.org/10.1107/S1600576724003182">https://doi.org/10.1107/S1600576724003182</a>)</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="dials.algorithms.indexing.lattice_search.FfbIndexer.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target_symmetry_primitive</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_lattices</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/dials/algorithms/indexing/lattice_search/ffb_indexer.html#FfbIndexer.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dials.algorithms.indexing.lattice_search.FfbIndexer.__init__" title="Link to this definition">¶</a></dt>
+<dd><p>Construct FfbIndexer object.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>target_symmetry_primitive</strong> (<a class="reference external" href="https://cctbx.github.io/cctbx/cctbx.crystal.html#cctbx.crystal.symmetry" title="(in CCTBX vNone)"><em>cctbx.crystal.symmetry</em></a>) – The target
+crystal symmetry and unit cell</p></li>
+<li><p><strong>max_lattices</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a>) – The maximum number of lattice models to find</p></li>
+<li><p><strong>params</strong> (<em>phil</em><em>,</em><em>optional</em>) – Phil params</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>None</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="dials.algorithms.indexing.lattice_search.FfbIndexer.find_crystal_models">
+<span class="sig-name descname"><span class="pre">find_crystal_models</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reflections</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">experiments</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/dials/algorithms/indexing/lattice_search/ffb_indexer.html#FfbIndexer.find_crystal_models"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dials.algorithms.indexing.lattice_search.FfbIndexer.find_crystal_models" title="Link to this definition">¶</a></dt>
+<dd><p>Find a list of candidate crystal models.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>reflections</strong> (<em>dials.array_family.flex.reflection_table</em>) – The found spots centroids and associated data</p></li>
+<li><p><strong>experiments</strong> (<em>dxtbx.model.experiment_list.ExperimentList</em>) – The experimental geometry models</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A list of candidate crystal models.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="dials.algorithms.indexing.lattice_search.FfbIndexer.phil_help">
+<span class="sig-name descname"><span class="pre">phil_help</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'A</span> <span class="pre">lattice</span> <span class="pre">search</span> <span class="pre">strategy</span> <span class="pre">for</span> <span class="pre">very</span> <span class="pre">fast</span> <span class="pre">indexing</span> <span class="pre">using</span> <span class="pre">Cuda</span> <span class="pre">acceleration'</span></em><a class="headerlink" href="#dials.algorithms.indexing.lattice_search.FfbIndexer.phil_help" title="Link to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="dials.algorithms.indexing.lattice_search.FfbIndexer.phil_scope">
+<span class="sig-name descname"><span class="pre">phil_scope</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">&lt;libtbx.phil.scope</span> <span class="pre">object&gt;</span></em><a class="headerlink" href="#dials.algorithms.indexing.lattice_search.FfbIndexer.phil_scope" title="Link to this definition">¶</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
 <dl class="py class">
 <dt class="sig sig-object py" id="dials.algorithms.indexing.lattice_search.LowResSpotMatch">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dials.algorithms.indexing.lattice_search.</span></span><span class="sig-name descname"><span class="pre">LowResSpotMatch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target_symmetry_primitive</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_lattices</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/dials/algorithms/indexing/lattice_search/low_res_spot_match.html#LowResSpotMatch"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dials.algorithms.indexing.lattice_search.LowResSpotMatch" title="Link to this definition">¶</a></dt>