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update rest of the notebooks from gh-pages - 2017-07-19 19:41:48
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‎notebooks/basic_iteration.html

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‎notebooks/basic_joinnodes.html

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@@ -11799,7 +11799,7 @@ <h1 id="JoinNode">JoinNode<a class="anchor-link" href="#JoinNode">&#182;</a></h1
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</div>
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<div class="inner_cell">
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<div class="text_cell_render border-box-sizing rendered_html">
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<h2 id="Simple-example">Simple example<a class="anchor-link" href="#Simple-example">&#182;</a></h2><p>Let's consider the very simple example depicted at the top of this page:</p>
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<h2 id="Simple-example">Simple example<a class="anchor-link" href="#Simple-example">&#182;</a></h2><p>Let's consider the very simple example depicted at the top of this page (since <code>A</code> is not defined, the cell will crash if you try to run):</p>
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@@ -11809,7 +11809,7 @@ <h2 id="Simple-example">Simple example<a class="anchor-link" href="#Simple-examp
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<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
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<div class=" highlight hl-ipython2"><pre><span></span><span class="kn">from</span> <span class="nn">nipype</span> <span class="kn">import</span> <span class="n">Node</span><span class="p">,</span> <span class="n">JoinNode</span><span class="p">,</span> <span class="n">Workflow</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">nipype</span> <span class="k">import</span> <span class="n">Node</span><span class="p">,</span> <span class="n">JoinNode</span><span class="p">,</span> <span class="n">Workflow</span>
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<span class="c1"># Specify fake input node A</span>
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<span class="n">a</span> <span class="o">=</span> <span class="n">Node</span><span class="p">(</span><span class="n">interface</span><span class="o">=</span><span class="n">A</span><span class="p">(),</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;a&quot;</span><span class="p">)</span>
@@ -11865,8 +11865,8 @@ <h2 id="More-realistic-example">More realistic example<a class="anchor-link" hre
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<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
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<div class="inner_cell">
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<div class="input_area">
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<div class=" highlight hl-ipython2"><pre><span></span><span class="kn">from</span> <span class="nn">nipype</span> <span class="kn">import</span> <span class="n">JoinNode</span><span class="p">,</span> <span class="n">Node</span><span class="p">,</span> <span class="n">Workflow</span>
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<span class="kn">from</span> <span class="nn">nipype.interfaces.utility</span> <span class="kn">import</span> <span class="n">Function</span><span class="p">,</span> <span class="n">IdentityInterface</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">nipype</span> <span class="k">import</span> <span class="n">JoinNode</span><span class="p">,</span> <span class="n">Node</span><span class="p">,</span> <span class="n">Workflow</span>
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<span class="kn">from</span> <span class="nn">nipype.interfaces.utility</span> <span class="k">import</span> <span class="n">Function</span><span class="p">,</span> <span class="n">IdentityInterface</span>
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</pre></div>
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</div>
@@ -11879,8 +11879,8 @@ <h2 id="More-realistic-example">More realistic example<a class="anchor-link" hre
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<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
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<div class="inner_cell">
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<div class="input_area">
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<div class=" highlight hl-ipython2"><pre><span></span><span class="c1"># Create iteration node</span>
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<span class="kn">from</span> <span class="nn">nipype</span> <span class="kn">import</span> <span class="n">IdentityInterface</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Create iteration node</span>
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<span class="kn">from</span> <span class="nn">nipype</span> <span class="k">import</span> <span class="n">IdentityInterface</span>
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<span class="n">iternode</span> <span class="o">=</span> <span class="n">Node</span><span class="p">(</span><span class="n">IdentityInterface</span><span class="p">(</span><span class="n">fields</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;number_id&#39;</span><span class="p">]),</span>
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<span class="n">name</span><span class="o">=</span><span class="s2">&quot;iternode&quot;</span><span class="p">)</span>
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<span class="n">iternode</span><span class="o">.</span><span class="n">iterables</span> <span class="o">=</span> <span class="p">[(</span><span class="s1">&#39;number_id&#39;</span><span class="p">,</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">9</span><span class="p">])]</span>
@@ -11896,9 +11896,9 @@ <h2 id="More-realistic-example">More realistic example<a class="anchor-link" hre
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<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
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<div class="inner_cell">
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<div class=" highlight hl-ipython2"><pre><span></span><span class="c1"># Create join node - compute square root for each element in the joined list</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Create join node - compute square root for each element in the joined list</span>
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<span class="k">def</span> <span class="nf">compute_sqrt</span><span class="p">(</span><span class="n">numbers</span><span class="p">):</span>
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<span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">sqrt</span>
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<span class="kn">from</span> <span class="nn">math</span> <span class="k">import</span> <span class="n">sqrt</span>
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<span class="k">return</span> <span class="p">[</span><span class="n">sqrt</span><span class="p">(</span><span class="n">e</span><span class="p">)</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">numbers</span><span class="p">]</span>
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<span class="n">joinnode</span> <span class="o">=</span> <span class="n">JoinNode</span><span class="p">(</span><span class="n">Function</span><span class="p">(</span><span class="n">input_names</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;numbers&#39;</span><span class="p">],</span>
@@ -11919,7 +11919,7 @@ <h2 id="More-realistic-example">More realistic example<a class="anchor-link" hre
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<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
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<div class="inner_cell">
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<div class=" highlight hl-ipython2"><pre><span></span><span class="c1"># Create the workflow and run it</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Create the workflow and run it</span>
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<span class="n">joinflow</span> <span class="o">=</span> <span class="n">Workflow</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;joinflow&#39;</span><span class="p">)</span>
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<span class="n">joinflow</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">iternode</span><span class="p">,</span> <span class="s1">&#39;number_id&#39;</span><span class="p">,</span> <span class="n">joinnode</span><span class="p">,</span> <span class="s1">&#39;numbers&#39;</span><span class="p">)</span>
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<span class="n">res</span> <span class="o">=</span> <span class="n">joinflow</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
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<div class="prompt"></div>
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<div class="output_subarea output_stream output_stdout output_text">
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<pre>170306-22:38:22,861 workflow INFO:
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<pre>170715-22:55:10,963 workflow INFO:
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Workflow joinflow settings: [&#39;check&#39;, &#39;execution&#39;, &#39;logging&#39;]
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170306-22:38:22,871 workflow INFO:
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170715-22:55:10,997 workflow INFO:
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Running serially.
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Executing node joinnode in dir: /tmp/tmpm8NCMb/joinflow/joinnode
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170715-22:55:10,999 workflow INFO:
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Executing node joinnode in dir: /tmp/tmp0mqxl90s/joinflow/joinnode
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</pre>
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<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
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<div class=" highlight hl-ipython2"><pre><span></span><span class="n">res</span><span class="o">.</span><span class="n">nodes</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">outputs</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">res</span><span class="o">.</span><span class="n">nodes</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">outputs</span>
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</pre></div>
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<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
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<div class=" highlight hl-ipython2"><pre><span></span><span class="n">res</span><span class="o">.</span><span class="n">nodes</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">inputs</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">res</span><span class="o">.</span><span class="n">nodes</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">inputs</span>
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