Update documentations

_modules/hippynn/databases/database.html

@@ -139,9 +139,11 @@ <h1>Source code for hippynn.databases.database</h1><div class="highlight"><pre>
             <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;All arrays:&quot;</span><span class="p">)</span>
             <span class="n">prettyprint_arrays</span><span class="p">(</span><span class="n">arr_dict</span><span class="p">)</span>
 
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">allow_unfound</span><span class="p">:</span>
-            <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">var_list</span><span class="p">:</span>
-                <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">arr_dict</span> <span class="ow">and</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">&quot;indices&quot;</span><span class="p">,</span> <span class="s2">&quot;split_indices&quot;</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">var_list</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">arr_dict</span> <span class="ow">and</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">&quot;indices&quot;</span><span class="p">,</span> <span class="s2">&quot;split_indices&quot;</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">allow_unfound</span><span class="p">:</span>
+                    <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Required database quantity &#39;</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s2">&#39; not present.&quot;</span><span class="p">)</span>
+                <span class="k">else</span><span class="p">:</span>
                     <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span>
                         <span class="sa">f</span><span class="s2">&quot;Array dictionary missing required variable:&#39;</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s2">&#39;.&quot;</span>
                         <span class="s2">&quot;Pass allow_unfound=True to avoid checking of inputs targets.&quot;</span>

_modules/hippynn/databases/ondisk.html

@@ -111,11 +111,11 @@ <h1>Source code for hippynn.databases.ondisk</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="DirectoryDatabase.__init__">
 <a class="viewcode-back" href="../../../api_documentation/hippynn.databases.ondisk.html#hippynn.databases.DirectoryDatabase.__init__">[docs]</a>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">directory</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">targets</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="n">quiet</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">allow_unfound</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">if</span> <span class="n">allow_unfound</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;DirectoryDatabase class does not support allow_unfound argument.&quot;</span><span class="p">)</span>
+        <span class="c1">#if allow_unfound:</span>
+        <span class="c1">#    raise ValueError(&quot;DirectoryDatabase class does not support allow_unfound argument.&quot;)</span>
 
         <span class="n">arr_dict</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_arrays</span><span class="p">(</span><span class="n">directory</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">targets</span><span class="p">,</span> <span class="n">quiet</span><span class="o">=</span><span class="n">quiet</span><span class="p">)</span>
-        <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">arr_dict</span><span class="p">,</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">targets</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span> <span class="n">quiet</span><span class="o">=</span><span class="n">quiet</span><span class="p">)</span>
+        <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">arr_dict</span><span class="p">,</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">targets</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span> <span class="n">quiet</span><span class="o">=</span><span class="n">quiet</span><span class="p">,</span> <span class="n">allow_unfound</span><span class="o">=</span><span class="n">allow_unfound</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">restarter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">make_restarter</span><span class="p">(</span>
             <span class="n">directory</span><span class="p">,</span>
@@ -125,6 +125,7 @@ <h1>Source code for hippynn.databases.ondisk</h1><div class="highlight"><pre>
             <span class="o">*</span><span class="n">args</span><span class="p">,</span>
             <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
             <span class="n">quiet</span><span class="o">=</span><span class="n">quiet</span><span class="p">,</span>
+            <span class="n">allow_unfound</span><span class="o">=</span><span class="n">allow_unfound</span><span class="p">,</span>
         <span class="p">)</span></div>
 
 

_modules/hippynn/graphs/nodes/base/base.html

@@ -109,7 +109,17 @@ <h1>Source code for hippynn.graphs.nodes.base.base</h1><div class="highlight"><p
 
 <div class="viewcode-block" id="InputNode.__init__">
 <a class="viewcode-back" href="../../../../../api_documentation/hippynn.graphs.nodes.base.base.html#hippynn.graphs.nodes.base.base.InputNode.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">db_name</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">db_name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">index_state</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="s2">&quot;_index_state&quot;</span><span class="p">)</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_index_state</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">index_state</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">index_state</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_index_state</span><span class="p">:</span>
+                    <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Cannot override IdxType </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_index_state</span><span class="si">}</span><span class="s2"> of node type </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="n">__name___</span><span class="si">}</span><span class="s2"> &quot;</span>
+                                     <span class="sa">f</span><span class="s2">&quot;with user-specified type </span><span class="si">{</span><span class="n">index_state</span><span class="si">}</span><span class="s2">.&quot;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">index_state</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_index_state</span> <span class="o">=</span> <span class="n">index_state</span>
+
         <span class="k">if</span> <span class="n">db_name</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s2">&quot;Input node requires name or db_name arguments.&quot;</span><span class="p">)</span>
         <span class="k">if</span> <span class="n">name</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">db_name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>

_modules/hippynn/graphs/nodes/loss.html

@@ -85,8 +85,7 @@ <h1>Source code for hippynn.graphs.nodes.loss</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">...</span> <span class="kn">import</span> <span class="n">settings</span>
 <span class="kn">from</span> <span class="nn">..indextypes</span> <span class="kn">import</span> <span class="n">IdxType</span><span class="p">,</span> <span class="n">elementwise_compare_reduce</span>
 <span class="kn">from</span> <span class="nn">.base</span> <span class="kn">import</span> <span class="n">SingleNode</span>
-<span class="kn">from</span> <span class="nn">...layers.algebra</span> <span class="kn">import</span> <span class="n">LambdaModule</span>
-
+<span class="kn">from</span> <span class="nn">...layers</span> <span class="kn">import</span> <span class="n">algebra</span> <span class="k">as</span> <span class="n">algebra_modules</span>
 <span class="kn">from</span> <span class="nn">...layers</span> <span class="kn">import</span> <span class="n">regularization</span> <span class="k">as</span> <span class="n">reg_modules</span>
 
 
@@ -130,7 +129,7 @@ <h1>Source code for hippynn.graphs.nodes.loss</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="nf">__init_subclass__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">op</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="k">if</span> <span class="n">op</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="bp">cls</span><span class="o">.</span><span class="n">_classname</span> <span class="o">=</span> <span class="n">op</span><span class="o">.</span><span class="vm">__name__</span>
-            <span class="bp">cls</span><span class="o">.</span><span class="n">torch_module</span> <span class="o">=</span> <span class="n">LambdaModule</span><span class="p">(</span><span class="n">op</span><span class="p">)</span></div>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">torch_module</span> <span class="o">=</span> <span class="n">algebra_modules</span><span class="o">.</span><span class="n">LambdaModule</span><span class="p">(</span><span class="n">op</span><span class="p">)</span></div>
 
 
 
@@ -191,7 +190,34 @@ <h1>Source code for hippynn.graphs.nodes.loss</h1><div class="highlight"><pre>
                 <span class="c1"># Note: as of now, we need to wrap raw operations as a loss module because</span>
                 <span class="c1"># the graph module&#39;s ModuleList can&#39;t take non-torch operations.</span>
                 <span class="c1"># Add the lambda to the graph module instead to put the problem nearer to the solution?</span>
-                <span class="bp">cls</span><span class="o">.</span><span class="n">torch_module</span> <span class="o">=</span> <span class="n">LambdaModule</span><span class="p">(</span><span class="n">op</span><span class="p">)</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">torch_module</span> <span class="o">=</span> <span class="n">algebra_modules</span><span class="o">.</span><span class="n">LambdaModule</span><span class="p">(</span><span class="n">op</span><span class="p">)</span>
+
+<span class="k">class</span> <span class="nc">_WeightedCompareLoss</span><span class="p">(</span><span class="n">SingleNode</span><span class="p">):</span>
+    <span class="n">_index_state</span> <span class="o">=</span> <span class="n">IdxType</span><span class="o">.</span><span class="n">Scalar</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">predicted</span><span class="p">,</span><span class="n">true</span><span class="p">,</span> <span class="n">weight</span><span class="p">):</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">{}</span><span class="s2">(</span><span class="si">{}</span><span class="s2">,</span><span class="si">{}</span><span class="s2">,</span><span class="si">{}</span><span class="s2">)&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_classname</span><span class="p">,</span> <span class="n">predicted</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">true</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">weight</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+        <span class="n">predicted</span><span class="p">,</span> <span class="n">true</span><span class="p">,</span> <span class="n">weight</span> <span class="o">=</span> <span class="n">elementwise_compare_reduce</span><span class="p">(</span><span class="n">predicted</span><span class="p">,</span> <span class="n">true</span><span class="p">,</span> <span class="n">weight</span><span class="p">)</span>
+        <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="p">,</span> <span class="p">(</span><span class="n">predicted</span><span class="p">,</span> <span class="n">true</span><span class="p">,</span> <span class="n">weight</span><span class="p">),</span> <span class="n">module</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">of_node</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">node</span><span class="p">,</span> <span class="n">weight</span><span class="p">):</span>
+        <span class="n">node</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">main_output</span>
+        <span class="n">true</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">true</span>
+        <span class="n">predicted</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">pred</span>
+        <span class="n">weight</span> <span class="o">=</span> <span class="n">weight</span><span class="o">.</span><span class="n">true</span>
+        <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">predicted</span><span class="p">,</span> <span class="n">true</span><span class="p">,</span> <span class="n">weight</span><span class="p">)</span>
+
+<div class="viewcode-block" id="WeightedMSELoss">
+<a class="viewcode-back" href="../../../../api_documentation/hippynn.graphs.nodes.loss.html#hippynn.graphs.nodes.loss.WeightedMSELoss">[docs]</a>
+<span class="k">class</span> <span class="nc">WeightedMSELoss</span><span class="p">(</span><span class="n">_WeightedCompareLoss</span><span class="p">):</span>
+    <span class="n">_classname</span> <span class="o">=</span> <span class="s2">&quot;WeightedMSE&quot;</span>
+    <span class="n">torch_module</span> <span class="o">=</span> <span class="n">algebra_modules</span><span class="o">.</span><span class="n">WeightedMSELoss</span><span class="p">()</span></div>
+
+
+<div class="viewcode-block" id="WeightedMAELoss">
+<a class="viewcode-back" href="../../../../api_documentation/hippynn.graphs.nodes.loss.html#hippynn.graphs.nodes.loss.WeightedMAELoss">[docs]</a>
+<span class="k">class</span> <span class="nc">WeightedMAELoss</span><span class="p">(</span><span class="n">_WeightedCompareLoss</span><span class="p">):</span>
+    <span class="n">_classname</span> <span class="o">=</span> <span class="s2">&quot;WeightedMAE&quot;</span>
+    <span class="n">torch_module</span> <span class="o">=</span> <span class="n">algebra_modules</span><span class="o">.</span><span class="n">WeightedMAELoss</span><span class="p">()</span></div>
 
 
 <div class="viewcode-block" id="RsqMod">