Update documentation

Author: mantid-builder

_modules/mantidimaging/core/io/instrument_log_implmentations.html

@@ -605,15 +605,15 @@ <h1>Source code for mantidimaging.core.io.instrument_log_implmentations</h1><div
 
 
     <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">_has_imat_header</span><span class="p">(</span><span class="n">line</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">_has_imat_header</span><span class="p">(</span><span class="n">line</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
         <span class="n">HEADERS</span> <span class="o">=</span> <span class="p">[</span>
             <span class="s2">&quot;TIME STAMP,IMAGE TYPE,IMAGE COUNTER,COUNTS BM3 before image,COUNTS BM3 after image&quot;</span><span class="p">,</span>
             <span class="s2">&quot;TIME STAMP  IMAGE TYPE   IMAGE COUNTER   COUNTS BM3 before image   COUNTS BM3 after image&quot;</span><span class="p">,</span>
         <span class="p">]</span>
         <span class="k">return</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">in</span> <span class="n">HEADERS</span>
 
     <span class="nd">@classmethod</span>
-    <span class="k">def</span> <span class="nf">_has_imat_data_line</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">line</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">_has_imat_data_line</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">line</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="n">_</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">read_imat_date</span><span class="p">(</span><span class="n">line</span><span class="p">[:</span><span class="mi">24</span><span class="p">])</span>
         <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>

_modules/mantidimaging/core/io/saver.html

@@ -487,7 +487,7 @@ <h1>Source code for mantidimaging.core.net.help_pages</h1><div class="highlight"
 
 <div class="viewcode-block" id="open_user_operation_docs">
 <a class="viewcode-back" href="../../../../api/mantidimaging.core.net.help_pages.html#mantidimaging.core.net.help_pages.open_user_operation_docs">[docs]</a>
-<span class="k">def</span> <span class="nf">open_user_operation_docs</span><span class="p">(</span><span class="n">operation_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">open_user_operation_docs</span><span class="p">(</span><span class="n">operation_name</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="n">page_url</span> <span class="o">=</span> <span class="s2">&quot;operations/index&quot;</span>
     <span class="n">section</span> <span class="o">=</span> <span class="n">operation_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">,</span> <span class="s2">&quot;-&quot;</span><span class="p">)</span>
     <span class="n">open_help_webpage</span><span class="p">(</span><span class="n">SECTION_USER_GUIDE</span><span class="p">,</span> <span class="n">page_url</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span></div>
@@ -496,7 +496,7 @@ <h1>Source code for mantidimaging.core.net.help_pages</h1><div class="highlight"
 
 <div class="viewcode-block" id="open_help_webpage">
 <a class="viewcode-back" href="../../../../api/mantidimaging.core.net.help_pages.html#mantidimaging.core.net.help_pages.open_help_webpage">[docs]</a>
-<span class="k">def</span> <span class="nf">open_help_webpage</span><span class="p">(</span><span class="n">section_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">page_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">section</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">open_help_webpage</span><span class="p">(</span><span class="n">section_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">page_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">section</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
     <span class="k">if</span> <span class="n">section</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
         <span class="n">url</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">section_url</span><span class="si">}{</span><span class="n">page_url</span><span class="si">}</span><span class="s2">.html#</span><span class="si">{</span><span class="n">section</span><span class="si">}</span><span class="s2">&quot;</span>
     <span class="k">else</span><span class="p">:</span>

_modules/mantidimaging/core/net/help_pages.html

@@ -511,7 +511,7 @@ <h1>Source code for mantidimaging.core.parallel.shared</h1><div class="highlight
                      <span class="n">num_operations</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
                      <span class="n">arrays</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">pu</span><span class="o">.</span><span class="n">SharedArray</span><span class="p">]</span> <span class="o">|</span> <span class="n">pu</span><span class="o">.</span><span class="n">SharedArray</span><span class="p">,</span>
                      <span class="n">params</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">],</span>
-                     <span class="n">progress</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+                     <span class="n">progress</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
     <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arrays</span><span class="p">,</span> <span class="n">pu</span><span class="o">.</span><span class="n">SharedArray</span><span class="p">):</span>
         <span class="n">arrays</span> <span class="o">=</span> <span class="p">[</span><span class="n">arrays</span><span class="p">]</span>
     <span class="n">all_data_in_shared_memory</span><span class="p">,</span> <span class="n">data</span> <span class="o">=</span> <span class="n">_check_shared_mem_and_get_data</span><span class="p">(</span><span class="n">arrays</span><span class="p">)</span>

_modules/mantidimaging/core/parallel/shared.html

@@ -501,7 +501,7 @@ <h1>Source code for mantidimaging.core.parallel.utility</h1><div class="highligh
 
 <div class="viewcode-block" id="enough_memory">
 <a class="viewcode-back" href="../../../../api/mantidimaging.core.parallel.utility.html#mantidimaging.core.parallel.utility.enough_memory">[docs]</a>
-<span class="k">def</span> <span class="nf">enough_memory</span><span class="p">(</span><span class="n">shape</span><span class="p">,</span> <span class="n">dtype</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">enough_memory</span><span class="p">(</span><span class="n">shape</span><span class="p">,</span> <span class="n">dtype</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
     <span class="k">return</span> <span class="n">full_size_KB</span><span class="p">(</span><span class="n">shape</span><span class="o">=</span><span class="n">shape</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">dtype</span><span class="p">)</span> <span class="o">&lt;</span> <span class="n">system_free_memory</span><span class="p">()</span><span class="o">.</span><span class="n">kb</span><span class="p">()</span></div>
 
 
@@ -596,7 +596,7 @@ <h1>Source code for mantidimaging.core.parallel.utility</h1><div class="highligh
 
 <div class="viewcode-block" id="execute_impl">
 <a class="viewcode-back" href="../../../../api/mantidimaging.core.parallel.utility.html#mantidimaging.core.parallel.utility.execute_impl">[docs]</a>
-<span class="k">def</span> <span class="nf">execute_impl</span><span class="p">(</span><span class="n">img_num</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">partial_func</span><span class="p">:</span> <span class="n">partial</span><span class="p">,</span> <span class="n">is_shared_data</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span> <span class="n">progress</span><span class="p">:</span> <span class="n">Progress</span><span class="p">,</span> <span class="n">msg</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">execute_impl</span><span class="p">(</span><span class="n">img_num</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">partial_func</span><span class="p">:</span> <span class="n">partial</span><span class="p">,</span> <span class="n">is_shared_data</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span> <span class="n">progress</span><span class="p">:</span> <span class="n">Progress</span><span class="p">,</span> <span class="n">msg</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="n">task_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2">&quot;</span>
     <span class="n">progress</span> <span class="o">=</span> <span class="n">Progress</span><span class="o">.</span><span class="n">ensure_instance</span><span class="p">(</span><span class="n">progress</span><span class="p">,</span> <span class="n">num_steps</span><span class="o">=</span><span class="n">img_num</span><span class="p">,</span> <span class="n">task_name</span><span class="o">=</span><span class="n">task_name</span><span class="p">)</span>
     <span class="n">indices_list</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="n">img_num</span><span class="p">)</span>
@@ -624,7 +624,7 @@ <h1>Source code for mantidimaging.core.parallel.utility</h1><div class="highligh
                           <span class="n">num_operations</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
                           <span class="n">is_shared_data</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span>
                           <span class="n">progress</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-                          <span class="n">msg</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">):</span>
+                          <span class="n">msg</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
     <span class="n">task_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2">&quot;</span>
     <span class="n">progress</span> <span class="o">=</span> <span class="n">Progress</span><span class="o">.</span><span class="n">ensure_instance</span><span class="p">(</span><span class="n">progress</span><span class="p">,</span> <span class="n">num_steps</span><span class="o">=</span><span class="n">num_operations</span><span class="p">,</span> <span class="n">task_name</span><span class="o">=</span><span class="n">task_name</span><span class="p">)</span>
     <span class="n">indices_list</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="n">num_operations</span><span class="p">)</span>

_modules/mantidimaging/core/parallel/utility.html

@@ -505,14 +505,14 @@ <h1>Source code for mantidimaging.core.reconstruct.astra_recon</h1><div class="h
 <span class="c1"># https://github.com/dkazanc/ToMoBAR/blob/5990aaa264e2f08bd9b0069c8847e5021fbf2ee2/src/Python/tomobar/supp/astraOP.py#L20-L70</span>
 <div class="viewcode-block" id="rotation_matrix2d">
 <a class="viewcode-back" href="../../../../api/mantidimaging.core.reconstruct.astra_recon.html#mantidimaging.core.reconstruct.astra_recon.rotation_matrix2d">[docs]</a>
-<span class="k">def</span> <span class="nf">rotation_matrix2d</span><span class="p">(</span><span class="n">theta</span><span class="p">:</span> <span class="nb">float</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">rotation_matrix2d</span><span class="p">(</span><span class="n">theta</span><span class="p">:</span> <span class="nb">float</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
     <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">theta</span><span class="p">),</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">theta</span><span class="p">)],</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">theta</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">theta</span><span class="p">)]])</span></div>
 
 
 
 <div class="viewcode-block" id="vec_geom_init2d">
 <a class="viewcode-back" href="../../../../api/mantidimaging.core.reconstruct.astra_recon.html#mantidimaging.core.reconstruct.astra_recon.vec_geom_init2d">[docs]</a>
-<span class="k">def</span> <span class="nf">vec_geom_init2d</span><span class="p">(</span><span class="n">angles_rad</span><span class="p">:</span> <span class="n">ProjectionAngles</span><span class="p">,</span> <span class="n">detector_spacing_x</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="n">center_rot_offset</span><span class="p">:</span> <span class="nb">float</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">vec_geom_init2d</span><span class="p">(</span><span class="n">angles_rad</span><span class="p">:</span> <span class="n">ProjectionAngles</span><span class="p">,</span> <span class="n">detector_spacing_x</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="n">center_rot_offset</span><span class="p">:</span> <span class="nb">float</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
     <span class="n">angles_value</span> <span class="o">=</span> <span class="n">angles_rad</span><span class="o">.</span><span class="n">value</span>
     <span class="n">s0</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.0</span><span class="p">]</span>  <span class="c1"># source</span>
     <span class="n">u0</span> <span class="o">=</span> <span class="p">[</span><span class="n">detector_spacing_x</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">]</span>  <span class="c1"># detector coordinates</span>

_modules/mantidimaging/core/reconstruct/astra_recon.html

@@ -506,7 +506,7 @@ <h1>Source code for mantidimaging.core.reconstruct.base_recon</h1><div class="hi
 <div class="viewcode-block" id="BaseRecon.prepare_sinogram">
 <a class="viewcode-back" href="../../../../api/mantidimaging.core.reconstruct.base_recon.html#mantidimaging.core.reconstruct.base_recon.BaseRecon.prepare_sinogram">[docs]</a>
     <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">prepare_sinogram</span><span class="p">(</span><span class="n">data</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">recon_params</span><span class="p">:</span> <span class="n">ReconstructionParameters</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">prepare_sinogram</span><span class="p">(</span><span class="n">data</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">recon_params</span><span class="p">:</span> <span class="n">ReconstructionParameters</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
         <span class="n">logged_data</span> <span class="o">=</span> <span class="n">BaseRecon</span><span class="o">.</span><span class="n">negative_log</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
         <span class="k">if</span> <span class="n">recon_params</span><span class="o">.</span><span class="n">beam_hardening_coefs</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="n">coefs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">]</span> <span class="o">+</span> <span class="n">recon_params</span><span class="o">.</span><span class="n">beam_hardening_coefs</span><span class="p">)</span>