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<div class="section" id="code-for-example-experiment">
<span id="cheat-sheet"></span><h1>Code for Example Experiment<a class="headerlink" href="#code-for-example-experiment" title="Permalink to this headline">¶</a></h1>
<p>Here is a sample code covering the entire process from defining <code class="docutils literal"><span class="pre">Sample</span></code> and
<code class="docutils literal"><span class="pre">ScanPlan</span></code> objects to running different kinds of runs.</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="c1"># bt list method to see all objects we have available for data collection</span>
<span class="n">bt</span><span class="o">.</span><span class="n">list</span><span class="p">()</span>
<span class="c1"># Ideally, Sample information should be filled before you come.</span>
<span class="c1"># you can fill out the spreadsheet and then use ``import_sample`` function.</span>
<span class="c1"># Let's still have an example here of how to do it explicitly</span>
<span class="n">Sample</span><span class="p">(</span><span class="n">bt</span><span class="p">,</span> <span class="s1">'sammple_name'</span><span class="p">:</span><span class="s1">'NaCl'</span><span class="p">,</span>
<span class="p">{</span><span class="s1">'sample_composition'</span><span class="p">:</span> <span class="p">{</span><span class="s1">'Na'</span><span class="p">:</span><span class="mf">0.5</span><span class="p">,</span> <span class="s1">'Cl'</span><span class="p">:</span><span class="mf">0.5</span><span class="p">},</span>
<span class="s1">'sample_phase'</span><span class="p">:</span> <span class="p">{</span><span class="s1">'NaCl'</span><span class="p">:</span><span class="mi">1</span><span class="p">},</span>
<span class="s1">'composition_string'</span><span class="p">:</span> <span class="s1">'Na0.09Cl0.09H1.82O0.91'</span><span class="p">,</span>
<span class="s1">'holder'</span><span class="p">:{</span><span class="s1">'shape'</span><span class="p">:</span><span class="s1">'capillary'</span><span class="p">,</span><span class="s1">'ID'</span><span class="p">:</span><span class="s1">'1 mm'</span><span class="p">,</span><span class="s1">'madeOf'</span><span class="p">:</span><span class="s1">'kapton'</span><span class="p">},</span>
<span class="s1">'tags'</span><span class="p">:[</span><span class="s1">'looked kinda green'</span><span class="p">,</span><span class="s1">'dropped on the floor during loading'</span><span class="p">],</span>
<span class="s1">'<anythingElseIwant>'</span><span class="p">:</span><span class="s1">'<description>'</span><span class="p">,</span>
<span class="s1">'<andSoOn>'</span><span class="p">:</span><span class="s1">'<etc>'</span>
<span class="p">}</span> <span class="c1"># rich metadata will save a lot of time later!</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="c1"># define "ct" scanplan with exp = 0.5</span>
<span class="n">ScanPlan</span><span class="p">(</span><span class="n">bt</span><span class="p">,</span> <span class="n">ct</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span>
<span class="c1"># define "Tramp" scanplan with exp = 0.5, startingT = 300, endingT = 310, Tstep = 2</span>
<span class="n">ScanPlan</span><span class="p">(</span><span class="n">bt</span><span class="p">,</span> <span class="n">Tramp</span> <span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mi">300</span><span class="p">,</span> <span class="mi">310</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="c1"># define "Tramp" scanplan with exp = 0.5, startingT = 310, endingT = 250, Tstep = 5</span>
<span class="n">ScanPlan</span><span class="p">(</span><span class="n">bt</span><span class="p">,</span> <span class="n">Tramp</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mi">310</span><span class="p">,</span> <span class="mi">250</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
<span class="c1"># define a "time series" scanplan with exp = 0.5, num=10, delay = 2</span>
<span class="n">ScanPlan</span><span class="p">(</span><span class="n">bt</span><span class="p">,</span> <span class="n">tseries</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
<span class="c1"># Then let's do a calibration run with Ni, exposure time = 60s, and perform calibration in calibration software</span>
<span class="n">run_calibration</span><span class="p">()</span>
<span class="n">bt</span><span class="o">.</span><span class="n">list</span><span class="p">()</span> <span class="c1"># returns the 'NaCl' sample object at position 17 and the 'ct_0.5' ScanPlan object at position 20</span>
<span class="n">xrun</span><span class="p">(</span><span class="mi">17</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
<span class="c1"># the data are saved into the NSLS-II database (don't worry) but we want to get the image so</span>
<span class="c1"># type:</span>
<span class="n">save_last_tiff</span><span class="p">()</span> <span class="c1"># save tiffs from last scan</span>
<span class="c1"># now we have everything set up, it is super-easy to sequence lots of interesting scans</span>
<span class="c1"># this does a series of different scans on the same sample</span>
<span class="n">xrun</span><span class="p">(</span><span class="mi">17</span><span class="p">,</span><span class="mi">21</span><span class="p">)</span> <span class="c1"># assume 'Tramp_0.5_300_310_2' ScanPlan object at position 21</span>
<span class="n">xrun</span><span class="p">(</span><span class="mi">17</span><span class="p">,</span><span class="mi">22</span><span class="p">)</span> <span class="c1"># assume 'Tramp_0.5_310_250_5' ScanPlan object at position 23</span>
<span class="n">save_tiff</span><span class="p">(</span><span class="n">db</span><span class="p">[</span><span class="o">-</span><span class="mi">3</span><span class="p">:])</span> <span class="c1"># save tiffs from last three scans</span>
<span class="c1"># this does the same scan on a series of samples</span>
<span class="n">xrun</span><span class="p">(</span><span class="mi">17</span><span class="p">,</span><span class="mi">21</span><span class="p">)</span> <span class="c1"># running sample at index 17 with 'Tramp_0.5_300_310_2' ScanPlan</span>
<span class="n">xrun</span><span class="p">(</span><span class="mi">18</span><span class="p">,</span><span class="mi">21</span><span class="p">)</span> <span class="c1"># running sample at index 18 with 'Tramp_0.5_300_310_2' ScanPlan</span>
<span class="n">xrun</span><span class="p">(</span><span class="mi">19</span><span class="p">,</span><span class="mi">21</span><span class="p">)</span> <span class="c1"># running sample at index 19 with 'Tramp_0.5_300_310_2' ScanPlan</span>
<span class="n">save_tiff</span><span class="p">(</span><span class="n">db</span><span class="p">[</span><span class="o">-</span><span class="mi">3</span><span class="p">:])</span> <span class="c1"># save tiffs from last three scans</span>
</pre></div>
</div>
<p>FIXME: if we have a <code class="docutils literal"><span class="pre">view_last_image()</span></code> function, document this one too.</p>
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