Deploying to gh-pages from @ f8d88b8 🚀

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 13f414d23c87e7ab6845f74255c984e6
+config: 38e647a1ad5b910b669ed012bb05995f
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/graphnet/data/constants.html

@@ -367,6 +367,7 @@ <h1 id="modules-graphnet-data-constants--page-root">Source code for graphnet.dat
     <span class="n">ICECUBE86</span> <span class="o">=</span> <span class="p">[</span>
         <span class="s2">"energy"</span><span class="p">,</span>
         <span class="s2">"energy_track"</span><span class="p">,</span>
+        <span class="s2">"energy_cascade"</span><span class="p">,</span>
         <span class="s2">"position_x"</span><span class="p">,</span>
         <span class="s2">"position_y"</span><span class="p">,</span>
         <span class="s2">"position_z"</span><span class="p">,</span>
@@ -432,7 +433,7 @@ <h1 id="modules-graphnet-data-constants--page-root">Source code for graphnet.dat
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/dataconverter.html

@@ -536,15 +536,22 @@ <h1 id="modules-graphnet-data-dataconverter--page-root">Source code for graphnet
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">class_name</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
 
     <span class="nd">@final</span>
-    <span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">directories</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]])</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+    <span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">directories</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]],</span>
+        <span class="n">recursive</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">bool</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">"""Convert I3-files in `directories.</span>
 
 <span class="sd">        Args:</span>
 <span class="sd">            directories: One or more directories, the I3 files within which</span>
 <span class="sd">                should be converted to an intermediate file format.</span>
+<span class="sd">            recursive: Whether or not to search the directories recursively.</span>
 <span class="sd">        """</span>
         <span class="c1"># Find all I3 and GCD files in the specified directories.</span>
-        <span class="n">i3_files</span><span class="p">,</span> <span class="n">gcd_files</span> <span class="o">=</span> <span class="n">find_i3_files</span><span class="p">(</span><span class="n">directories</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_gcd_rescue</span><span class="p">)</span>
+        <span class="n">i3_files</span><span class="p">,</span> <span class="n">gcd_files</span> <span class="o">=</span> <span class="n">find_i3_files</span><span class="p">(</span>
+            <span class="n">directories</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_gcd_rescue</span><span class="p">,</span> <span class="n">recursive</span>
+        <span class="p">)</span>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">i3_files</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No files found in </span><span class="si">{</span><span class="n">directories</span><span class="si">}</span><span class="s2">."</span><span class="p">)</span>
             <span class="k">return</span>
@@ -946,7 +953,7 @@ <h1 id="modules-graphnet-data-dataconverter--page-root">Source code for graphnet
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/dataloader.html

@@ -439,7 +439,7 @@ <h1 id="modules-graphnet-data-dataloader--page-root">Source code for graphnet.da
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/dataset/dataset.html

@@ -1071,7 +1071,7 @@ <h1 id="modules-graphnet-data-dataset-dataset--page-root">Source code for graphn
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/dataset/parquet/parquet_dataset.html

@@ -482,7 +482,7 @@ <h1 id="modules-graphnet-data-dataset-parquet-parquet-dataset--page-root">Source
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/dataset/sqlite/sqlite_dataset.html

@@ -497,7 +497,7 @@ <h1 id="modules-graphnet-data-dataset-sqlite-sqlite-dataset--page-root">Source c
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3extractor.html

@@ -460,7 +460,7 @@ <h1 id="modules-graphnet-data-extractors-i3extractor--page-root">Source code for
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3featureextractor.html

@@ -391,7 +391,6 @@ <h1 id="modules-graphnet-data-extractors-i3featureextractor--page-root">Source c
             <span class="s2">"event_time"</span><span class="p">:</span> <span class="p">[],</span>
             <span class="s2">"hlc"</span><span class="p">:</span> <span class="p">[],</span>
             <span class="s2">"awtd"</span><span class="p">:</span> <span class="p">[],</span>
-            <span class="s2">"fadc"</span><span class="p">:</span> <span class="p">[],</span>
             <span class="s2">"string"</span><span class="p">:</span> <span class="p">[],</span>
             <span class="s2">"pmt_number"</span><span class="p">:</span> <span class="p">[],</span>
             <span class="s2">"dom_number"</span><span class="p">:</span> <span class="p">[],</span>
@@ -489,16 +488,15 @@ <h1 id="modules-graphnet-data-extractors-i3featureextractor--page-root">Source c
                 <span class="n">output</span><span class="p">[</span><span class="s2">"is_saturated_dom"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">is_saturated_dom</span><span class="p">)</span>
                 <span class="n">output</span><span class="p">[</span><span class="s2">"is_errata_dom"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">is_errata_dom</span><span class="p">)</span>
                 <span class="n">output</span><span class="p">[</span><span class="s2">"event_time"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">event_time</span><span class="p">)</span>
+
                 <span class="c1"># Pulse flags</span>
                 <span class="n">flags</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">pulse</span><span class="p">,</span> <span class="s2">"flags"</span><span class="p">,</span> <span class="n">padding_value</span><span class="p">)</span>
                 <span class="k">if</span> <span class="n">flags</span> <span class="o">==</span> <span class="n">padding_value</span><span class="p">:</span>
-                    <span class="n">output</span><span class="p">[</span><span class="s2">"hlc"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">padding_value</span><span class="p">)</span>  <span class="c1"># bit 0</span>
-                    <span class="n">output</span><span class="p">[</span><span class="s2">"awtd"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">padding_value</span><span class="p">)</span>  <span class="c1"># bit 1</span>
-                    <span class="n">output</span><span class="p">[</span><span class="s2">"fadc"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">padding_value</span><span class="p">)</span>  <span class="c1"># bit 2</span>
+                    <span class="n">output</span><span class="p">[</span><span class="s2">"hlc"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">padding_value</span><span class="p">)</span>
+                    <span class="n">output</span><span class="p">[</span><span class="s2">"awtd"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">padding_value</span><span class="p">)</span>
                 <span class="k">else</span><span class="p">:</span>
                     <span class="n">output</span><span class="p">[</span><span class="s2">"hlc"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">pulse</span><span class="o">.</span><span class="n">flags</span> <span class="o">&gt;&gt;</span> <span class="mi">0</span><span class="p">)</span> <span class="o">&amp;</span> <span class="mh">0x1</span><span class="p">)</span>  <span class="c1"># bit 0</span>
-                    <span class="n">output</span><span class="p">[</span><span class="s2">"awtd"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">pulse</span><span class="o">.</span><span class="n">flags</span> <span class="o">&gt;&gt;</span> <span class="mi">1</span><span class="p">)</span> <span class="o">&amp;</span> <span class="mh">0x1</span><span class="p">)</span>  <span class="c1"># bit 1</span>
-                    <span class="n">output</span><span class="p">[</span><span class="s2">"fadc"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">pulse</span><span class="o">.</span><span class="n">flags</span> <span class="o">&gt;&gt;</span> <span class="mi">2</span><span class="p">)</span> <span class="o">&amp;</span> <span class="mh">0x1</span><span class="p">)</span>  <span class="c1"># bit 2</span>
+                    <span class="n">output</span><span class="p">[</span><span class="s2">"awtd"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_parse_awtd_flag</span><span class="p">(</span><span class="n">pulse</span><span class="p">))</span>
 
         <span class="k">return</span> <span class="n">output</span>
 
@@ -515,7 +513,28 @@ <h1 id="modules-graphnet-data-extractors-i3featureextractor--page-root">Source c
                 <span class="n">rde</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_calibration</span><span class="o">.</span><span class="n">dom_cal</span><span class="p">[</span><span class="n">om_key</span><span class="p">]</span><span class="o">.</span><span class="n">relative_dom_eff</span>
             <span class="k">except</span><span class="p">:</span>  <span class="c1"># noqa: E722</span>
                 <span class="n">rde</span> <span class="o">=</span> <span class="n">padding_value</span>
-        <span class="k">return</span> <span class="n">rde</span></div>
+        <span class="k">return</span> <span class="n">rde</span>
+
+    <span class="k">def</span> <span class="nf">_parse_awtd_flag</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span> <span class="n">pulse</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span> <span class="n">fadc_min_width_ns</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">6.0</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">"""Parse awtd flag from pulse width.</span>
+
+<span class="sd">        Returns True if the pulse was readout using the awtd digitizer.</span>
+
+<span class="sd">        Method by Tom Stuttard.</span>
+
+<span class="sd">        Notes from Tom:</span>
+<span class="sd">        Function to read the bits of the pulse flags and unpack them into</span>
+<span class="sd">        meaningful info Using pulse width rather than flags to separate FADC vs</span>
+<span class="sd">        ATWD pulses, due to a known issue.</span>
+<span class="sd">        https://github.com/icecube/icetray/issues/2721 Note that the issue</span>
+<span class="sd">        states to use 8ns, but I have found that actually 6ns is correct.</span>
+<span class="sd">        """</span>
+        <span class="c1"># Use pulse width to check whether a pulse is</span>
+        <span class="c1"># (a) FADC-only, or</span>
+        <span class="c1"># includes ATWD (and probably also FADC)</span>
+        <span class="k">return</span> <span class="n">pulse</span><span class="o">.</span><span class="n">width</span> <span class="o">&lt;</span> <span class="p">(</span><span class="n">fadc_min_width_ns</span> <span class="o">*</span> <span class="n">icetray</span><span class="o">.</span><span class="n">I3Units</span><span class="o">.</span><span class="n">ns</span><span class="p">)</span></div>
 
 
 
@@ -643,7 +662,7 @@ <h1 id="modules-graphnet-data-extractors-i3featureextractor--page-root">Source c
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3genericextractor.html

@@ -632,7 +632,7 @@ <h1 id="modules-graphnet-data-extractors-i3genericextractor--page-root">Source c
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3hybridrecoextractor.html

@@ -396,7 +396,7 @@ <h1 id="modules-graphnet-data-extractors-i3hybridrecoextractor--page-root">Sourc
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3ntmuonlabelsextractor.html

@@ -403,7 +403,7 @@ <h1 id="modules-graphnet-data-extractors-i3ntmuonlabelsextractor--page-root">Sou
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3particleextractor.html

@@ -388,7 +388,7 @@ <h1 id="modules-graphnet-data-extractors-i3particleextractor--page-root">Source
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3pisaextractor.html

@@ -381,7 +381,7 @@ <h1 id="modules-graphnet-data-extractors-i3pisaextractor--page-root">Source code
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3quesoextractor.html

@@ -391,7 +391,7 @@ <h1 id="modules-graphnet-data-extractors-i3quesoextractor--page-root">Source cod
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3retroextractor.html

@@ -463,7 +463,7 @@ <h1 id="modules-graphnet-data-extractors-i3retroextractor--page-root">Source cod
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using

_modules/graphnet/data/extractors/i3splinempeextractor.html

@@ -375,7 +375,7 @@ <h1 id="modules-graphnet-data-extractors-i3splinempeextractor--page-root">Source
       <div class="md-footer-meta__inner md-grid">
         <div class="md-footer-copyright">
           <div class="md-footer-copyright__highlight">
-              &#169; Copyright 2021-2023, GraphNeT team.
+              &#169; Copyright 2021-2024, GraphNeT team.
 
           </div>
             Created using