docs(master): Update docs of development line

master/_modules/sdcflows/utils/wrangler.html

@@ -661,6 +661,7 @@ <h1>Source code for sdcflows.utils.wrangler</h1><div class="highlight"><pre>
             <span class="s2">&quot;Dataset includes `B0FieldIdentifier` metadata.&quot;</span>
             <span class="s2">&quot;Any data missing this metadata will be ignored.&quot;</span>
         <span class="p">)</span>
+
         <span class="k">for</span> <span class="n">b0_id</span> <span class="ow">in</span> <span class="n">b0_ids</span><span class="p">:</span>
             <span class="c1"># Found B0FieldIdentifier metadata entries</span>
             <span class="n">b0_entities</span> <span class="o">=</span> <span class="n">base_entities</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>

master/_modules/sdcflows/workflows/fit/fieldmap.html

@@ -408,9 +408,7 @@ <h1>Source code for sdcflows.workflows.fit.fieldmap</h1><div class="highlight"><
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="kn">from</span> <span class="nn">...interfaces.bspline</span> <span class="kn">import</span> <span class="p">(</span>
         <span class="n">BSplineApprox</span><span class="p">,</span>
-        <span class="n">DEFAULT_LF_ZOOMS_MM</span><span class="p">,</span>
         <span class="n">DEFAULT_HF_ZOOMS_MM</span><span class="p">,</span>
-        <span class="n">DEFAULT_ZOOMS_MM</span><span class="p">,</span>
     <span class="p">)</span>
     <span class="kn">from</span> <span class="nn">...interfaces.fmap</span> <span class="kn">import</span> <span class="n">CheckRegister</span>
 
@@ -436,9 +434,11 @@ <h1>Source code for sdcflows.workflows.fit.fieldmap</h1><div class="highlight"><
     <span class="n">magnitude_wf</span> <span class="o">=</span> <span class="n">init_magnitude_wf</span><span class="p">(</span><span class="n">omp_nthreads</span><span class="o">=</span><span class="n">omp_nthreads</span><span class="p">)</span>
     <span class="n">bs_filter</span> <span class="o">=</span> <span class="n">pe</span><span class="o">.</span><span class="n">Node</span><span class="p">(</span><span class="n">BSplineApprox</span><span class="p">(),</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;bs_filter&quot;</span><span class="p">)</span>
     <span class="n">bs_filter</span><span class="o">.</span><span class="n">interface</span><span class="o">.</span><span class="n">_always_run</span> <span class="o">=</span> <span class="n">debug</span>
-    <span class="n">bs_filter</span><span class="o">.</span><span class="n">inputs</span><span class="o">.</span><span class="n">bs_spacing</span> <span class="o">=</span> <span class="p">(</span>
-        <span class="p">[</span><span class="n">DEFAULT_LF_ZOOMS_MM</span><span class="p">,</span> <span class="n">DEFAULT_HF_ZOOMS_MM</span><span class="p">]</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">sloppy</span> <span class="k">else</span> <span class="p">[</span><span class="n">DEFAULT_ZOOMS_MM</span><span class="p">]</span>
-    <span class="p">)</span>
+    <span class="n">bs_filter</span><span class="o">.</span><span class="n">inputs</span><span class="o">.</span><span class="n">bs_spacing</span> <span class="o">=</span> <span class="p">[</span><span class="n">DEFAULT_HF_ZOOMS_MM</span><span class="p">]</span>
+
+    <span class="k">if</span> <span class="n">sloppy</span><span class="p">:</span>
+        <span class="n">bs_filter</span><span class="o">.</span><span class="n">inputs</span><span class="o">.</span><span class="n">zooms_min</span> <span class="o">=</span> <span class="mf">4.0</span>
+
     <span class="n">bs_filter</span><span class="o">.</span><span class="n">inputs</span><span class="o">.</span><span class="n">extrapolate</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">debug</span>
 
     <span class="c1"># fmt: off</span>

master/api/sdcflows.config.html

@@ -508,7 +508,7 @@ <h2>Other responsibilities<a class="headerlink" href="#other-responsibilities" t
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="sdcflows.config.environment.free_mem">
-<span class="sig-name descname"><span class="pre">free_mem</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">11.1</span></em><a class="headerlink" href="#sdcflows.config.environment.free_mem" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">free_mem</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">11.2</span></em><a class="headerlink" href="#sdcflows.config.environment.free_mem" title="Link to this definition">¶</a></dt>
 <dd><p>Free memory at start.</p>
 </dd></dl>
 
@@ -659,7 +659,7 @@ <h2>Other responsibilities<a class="headerlink" href="#other-responsibilities" t
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="sdcflows.config.execution.run_uuid">
-<span class="sig-name descname"><span class="pre">run_uuid</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'20240620-063625_aa656dcc-508e-4b57-9fae-367422e68a70'</span></em><a class="headerlink" href="#sdcflows.config.execution.run_uuid" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">run_uuid</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'20240704-112639_22b7f099-188e-4b8f-b542-9daa4f09a6a6'</span></em><a class="headerlink" href="#sdcflows.config.execution.run_uuid" title="Link to this definition">¶</a></dt>
 <dd><p>Unique identifier of this particular run.</p>
 </dd></dl>
 

master/api/sdcflows.interfaces.bspline.html

@@ -424,18 +424,18 @@
 <dt class="field-even">Optional Inputs<span class="colon">:</span></dt>
 <dd class="field-even"><ul class="simple">
 <li><p><strong>bs_spacing</strong> (<em>a list of items which are a tuple of the form: (a float, a float, a float)</em>) – Spacing between B-Spline control points.
-(Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">[(40.0,</span> <span class="pre">40.0,</span> <span class="pre">20.0)]</span></code>)</p></li>
+(Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">[(16.0,</span> <span class="pre">16.0,</span> <span class="pre">10.0)]</span></code>)</p></li>
 <li><p><strong>debug</strong> (<em>a boolean</em>) – Generate extra assets for debugging.
 (Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">False</span></code>)</p></li>
 <li><p><strong>extrapolate</strong> (<em>a boolean</em>) – Generate a field, extrapolated outside the brain mask.
 (Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">True</span></code>)</p></li>
 <li><p><strong>in_mask</strong> (<em>a pathlike object or string representing an existing file</em>) – Path to a brain mask.</p></li>
-<li><p><strong>recenter</strong> (<em>‘mode’ or ‘median’ or ‘mean’ or False</em>) – Strategy to recenter the distribution of the input fieldmap.
-(Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">mode</span></code>)</p></li>
+<li><p><strong>recenter</strong> (<em>‘median’ or ‘mode’ or ‘mean’ or False</em>) – Strategy to recenter the distribution of the input fieldmap.
+(Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">median</span></code>)</p></li>
 <li><p><strong>ridge_alpha</strong> (<em>a float</em>) – Controls the regularization.
-(Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">0.01</span></code>)</p></li>
+(Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">0.0001</span></code>)</p></li>
 <li><p><strong>zooms_min</strong> (<em>a float or a legal value</em>) – Limit minimum image zooms, set 0.0 to use the original image.
-(Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">4.0</span></code>)</p></li>
+(Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">1.0</span></code>)</p></li>
 </ul>
 </dd>
 <dt class="field-odd">Outputs<span class="colon">:</span></dt>
@@ -444,6 +444,7 @@
 <li><p><strong>out_error</strong> (<em>a pathlike object or string representing an existing file</em>)</p></li>
 <li><p><strong>out_extrapolated</strong> (<em>a pathlike object or string representing a file</em>)</p></li>
 <li><p><strong>out_field</strong> (<em>a pathlike object or string representing an existing file</em>)</p></li>
+<li><p><strong>out_intercept</strong> (<em>a float</em>)</p></li>
 </ul>
 </dd>
 </dl>