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<div class="section" id="beamline-configuration">
<h1>Beamline Configuration<a class="headerlink" href="#beamline-configuration" title="Permalink to this headline">¶</a></h1>
<div class="section" id="ipython-profiles">
<h2>IPython profiles<a class="headerlink" href="#ipython-profiles" title="Permalink to this headline">¶</a></h2>
<p>Configuration can be done interactively or in a Python script.
At NSLS-II, configuration is done by startup scripts that are part of an
<a class="reference external" href="https://ipython.org/ipython-doc/dev/config/intro.html#profiles">IPython profile</a>
. But note that it is not essential to use IPython or IPython profile in
general – this is just a convenience.</p>
<p>Profiles are stored in (or soft-linked) from <code class="docutils literal"><span class="pre">~/.ipython</span></code> in the user profile
of individual users or shared beamline accounts.</p>
<p>The standard profile is called “collection,” and the startup scripts are
located in <code class="docutils literal"><span class="pre">~/.ipython/profile_collection/startup/</span></code>. As stated in the
quick start page, they can be invoked by typing:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>ipython --profile<span class="o">=</span>collection
</pre></div>
</div>
<p>To refresh a script that has been edited, restart IPython or re-execute the
script using <code class="docutils literal"><span class="pre">%run</span> <span class="pre">-i</span> <span class="pre">~/.ipython/profile_collection/startup/<FILENAME></span></code>.
Do this for any file(s) that have been updated. (There is no way to run
all files at once.)</p>
</div>
<div class="section" id="example-configuration-file">
<h2>Example Configuration File<a class="headerlink" href="#example-configuration-file" title="Permalink to this headline">¶</a></h2>
<p>This is a example IPython profile startup file.:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="c1"># Make ophyd listen to pyepics.</span>
from ophyd import setup_ophyd
setup_ophyd<span class="o">()</span>
<span class="c1"># Subscribe metadatastore to documents.</span>
<span class="c1"># If this is removed, data is not saved to metadatastore.</span>
import metadatastore.commands
from bluesky.global_state import gs
gs.RE.subscribe_lossless<span class="o">(</span><span class="s1">'all'</span>, metadatastore.commands.insert<span class="o">)</span>
<span class="c1"># At the end of every run, verify that files were saved and</span>
<span class="c1"># print a confirmation message.</span>
from bluesky.callbacks.broker import verify_files_saved
gs.RE.subscribe<span class="o">(</span><span class="s1">'stop'</span>, post_run<span class="o">(</span>verify_files_saved<span class="o">))</span>
<span class="c1"># Import matplotlib and put it in interactive mode.</span>
import matplotlib.pyplot as plt
plt.ion<span class="o">()</span>
<span class="c1"># Make plots update live while scans run.</span>
from bluesky.utils import install_qt_kicker
install_qt_kicker<span class="o">()</span>
<span class="c1"># Optional: set any metadata that rarely changes.</span>
<span class="c1"># RE.md['beamline_id'] = 'YOUR_BEAMLINE_HERE'</span>
<span class="c1"># convenience imports</span>
from ophyd.commands import *
from bluesky.callbacks import *
from bluesky.spec_api import *
from bluesky.global_state import gs, abort, stop, resume
from databroker import <span class="o">(</span>DataBroker as db, get_events, get_images,
get_table, get_fields, restream, process<span class="o">)</span>
from <span class="nb">time</span> import sleep
import numpy as np
<span class="nv">RE</span> <span class="o">=</span> gs.RE <span class="c1"># convenience alias</span>
<span class="c1"># Uncomment the following lines to turn on verbose messages for debugging.</span>
<span class="c1"># import logging</span>
<span class="c1"># ophyd.logger.setLevel(logging.DEBUG)</span>
<span class="c1"># logging.basicConfig(level=logging.DEBUG)</span>
</pre></div>
</div>
</div>
<div class="section" id="configuring-the-olog">
<h2>Configuring the Olog<a class="headerlink" href="#configuring-the-olog" title="Permalink to this headline">¶</a></h2>
<div class="section" id="essential-configuration">
<h3>Essential Configuration<a class="headerlink" href="#essential-configuration" title="Permalink to this headline">¶</a></h3>
<p>pyOlog requires a configuration file to specify the connection
settings. As root, create a file at <code class="docutils literal"><span class="pre">/etc/pyOlog.conf</span></code> with the following
contents.:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="o">[</span>DEFAULT<span class="o">]</span>
<span class="nv">url</span> <span class="o">=</span> https://<beamline>-log.cs.nsls2.local:8181/Olog
<span class="nv">logbooks</span> <span class="o">=</span> Commissioning <span class="c1"># use the name of an existing logbook</span>
<span class="nv">username</span> <span class="o">=</span> <username>
<span class="nv">password</span> <span class="o">=</span> <password>
</pre></div>
</div>
<p>where <code class="docutils literal"><span class="pre"><beamline></span></code> is the designation formatted like <code class="docutils literal"><span class="pre">xf23id1</span></code>.</p>
</div>
<div class="section" id="integration-with-bluesky">
<h3>Integration with Bluesky<a class="headerlink" href="#integration-with-bluesky" title="Permalink to this headline">¶</a></h3>
<p>Bluesky automatically logs basic scan information at the start of a
scan. (All of this information is strictly a subset of what is
also stored in metadatastore – this is just a convenience.)</p>
<p>Back in an IPython profile startup file, add:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>from functools import partial
from pyOlog import SimpleOlogClient
from bluesky.callbacks.olog import logbook_cb_factory
<span class="c1"># Set up the logbook. This configures bluesky's summaries of</span>
<span class="c1"># data acquisition (scan type, ID, etc.).</span>
<span class="nv">LOGBOOKS</span> <span class="o">=</span> <span class="o">[</span><span class="s1">'Data Acquisition'</span><span class="o">]</span> <span class="c1"># list of logbook names to publish to</span>
<span class="nv">simple_olog_client</span> <span class="o">=</span> SimpleOlogClient<span class="o">()</span>
<span class="nv">generic_logbook_func</span> <span class="o">=</span> simple_olog_client.log
<span class="nv">configured_logbook_func</span> <span class="o">=</span> partial<span class="o">(</span>generic_logbook_func, <span class="nv">logbooks</span><span class="o">=</span>LOGBOOKS<span class="o">)</span>
<span class="nv">cb</span> <span class="o">=</span> logbook_cb_factory<span class="o">(</span>configured_logbook_func<span class="o">)</span>
RE.subscribe<span class="o">(</span><span class="s1">'start'</span>, cb<span class="o">)</span>
</pre></div>
</div>
</div>
<div class="section" id="integration-with-ophyd">
<h3>Integration with Ophyd<a class="headerlink" href="#integration-with-ophyd" title="Permalink to this headline">¶</a></h3>
<p>Ophyd has as <code class="docutils literal"><span class="pre">log_pos</span></code> method that writes the current position of all
positioners into the log. To enable this, add the following to an IPython
profile startup file, add:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="c1"># This is for ophyd.commands.get_logbook, which simply looks for</span>
<span class="c1"># a variable called 'logbook' in the global IPython namespace.</span>
<span class="nv">logbook</span> <span class="o">=</span> simple_olog_client
</pre></div>
</div>
<p>The log entires will be written into the logbook specified in
<code class="docutils literal"><span class="pre">.pyOlog.conf</span></code> (in our example, “Commissioning”), not the logbook
used by bluesky (in our example, “Data Acquisition”).</p>
</div>
<div class="section" id="olog-ipython-magics">
<h3>Olog IPython “Magics”<a class="headerlink" href="#olog-ipython-magics" title="Permalink to this headline">¶</a></h3>
<p>“Magics” are special IPython commands (not part of Python itself). They
begin with %. There are two IPython magics for conveniently writing to
the Olog.</p>
<ul class="simple">
<li>Type <code class="docutils literal"><span class="pre">%logit</span></code> to quickly type a text log entry.</li>
<li>Type <code class="docutils literal"><span class="pre">%grabit</span></code>, select an area of the screen to capture, and type in a
text caption.</li>
</ul>
<p>These require their own special configuration. In the profile directory, such
as <code class="docutils literal"><span class="pre">~/.ipython/profile_collection</span></code>, edit the file <code class="docutils literal"><span class="pre">ipython_config.py</span></code>.</p>
<p>Add the line:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>c.InteractiveShellApp.extensions <span class="o">=</span> <span class="o">[</span><span class="s1">'pyOlog.cli.ipy'</span><span class="o">]</span>
</pre></div>
</div>
<p>The log entires will be written into the logbook specified in
<code class="docutils literal"><span class="pre">.pyOlog.conf</span></code> (in our example, “Commissioning”), not the logbook
used by bluesky (in our example, “Data Acquisition”).</p>
</div>
</div>
<div class="section" id="defining-hardware-objects">
<h2>Defining Hardware Objects<a class="headerlink" href="#defining-hardware-objects" title="Permalink to this headline">¶</a></h2>
<p>For example:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>from ophyd import EpicsMotor
<span class="c1"># the two-theta motor</span>
<span class="nv">tth</span> <span class="o">=</span> EpicsMotor<span class="o">(</span><span class="s1">'XF:28IDC-ES:1{Dif:1-Ax:2ThI}Mtr'</span>, <span class="nv">name</span><span class="o">=</span><span class="s1">'tth'</span><span class="o">)</span>
</pre></div>
</div>
<p>See the <a class="reference external" href="http://nsls-ii.github.io/ophyd">ophyd documentation</a> for more.</p>
</div>
<div class="section" id="set-up-default-global-state">
<h2>Set up Default (“Global State”)<a class="headerlink" href="#set-up-default-global-state" title="Permalink to this headline">¶</a></h2>
<p>Set attributes of <code class="docutils literal"><span class="pre">gs</span></code>. This can be done interactively or in a startup file.:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>gs.DETS <span class="o">=</span> <span class="o">[</span>det1, det2<span class="o">]</span>
gs.TABLE_COLS <span class="o">=</span> <span class="o">[</span><span class="s1">'det1'</span><span class="o">]</span>
gs.PLOT_Y <span class="o">=</span> <span class="s1">'det1'</span>
</pre></div>
</div>
</div>
<div class="section" id="customizing-ipython">
<h2>Customizing IPython<a class="headerlink" href="#customizing-ipython" title="Permalink to this headline">¶</a></h2>
<p>Running the following</p>
<div class="highlight-ipython"><div class="highlight"><pre><span></span><span class="gp">In [1]: </span><span class="o">%</span><span class="k">config</span> PromptManager.in_template = '\T In [\\#]: '
<span class="gp">In [2]: </span><span class="o">%</span><span class="k">config</span> PromptManager.out_template = '\T Out[\\#]: '
</pre></div>
</div>
<p>will make your terminal look like this:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>10:01:40 In <span class="o">[</span>49<span class="o">]</span>: 1
10:01:42 Out<span class="o">[</span>49<span class="o">]</span>: 1
10:01:42 In <span class="o">[</span>50<span class="o">]</span>:
10:02:21 In <span class="o">[</span>50<span class="o">]</span>: <span class="nv">a</span> <span class="o">=</span> 2
10:02:28 In <span class="o">[</span>51<span class="o">]</span>:
</pre></div>
</div>
<p>It is not much more work to customize that timestamp to be truncated, include
date / day of week etc. See <a class="reference external" href="https://ipython.org/ipython-doc/3/config/details.html#prompts">this section of the IPython documentation</a> for details.</p>
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