-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathusb_Beamtime.html
More file actions
325 lines (218 loc) · 13.8 KB
/
Copy pathusb_Beamtime.html
File metadata and controls
325 lines (218 loc) · 13.8 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Setting up your Beamtime — xpdAcq 0.5 documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="top" title="xpdAcq 0.5 documentation" href="index.html"/>
<link rel="up" title="For XPD Users" href="xpdusers.html"/>
<link rel="next" title="Setting up your XPD acuisition objects" href="usb_Experiment.html"/>
<link rel="prev" title="Overview of the bsui+xpdAcq environment" href="sb_icollection.html"/>
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search">
<a href="index.html" class="icon icon-home"> xpdAcq
</a>
<div class="version">
0.5
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="quickstart.html">Quick Start</a></li>
</ul>
<ul class="current">
<li class="toctree-l1 current"><a class="reference internal" href="xpdusers.html">For XPD Users</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="sb_overview.html">Overview of xpd acquisition environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="sb_icollection.html">Overview of the bsui+xpdAcq environment</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Setting up your Beamtime</a></li>
<li class="toctree-l2"><a class="reference internal" href="usb_Experiment.html">Setting up your XPD acuisition objects</a></li>
<li class="toctree-l2"><a class="reference internal" href="usb_Scan.html">ScanPlan objects</a></li>
<li class="toctree-l2"><a class="reference internal" href="usb_Where.html">Where did all my Sample and Scan objects go?????</a></li>
<li class="toctree-l2"><a class="reference internal" href="usb_Where.html#bt-list-is-your-friends">bt.list() is your friends</a></li>
<li class="toctree-l2"><a class="reference internal" href="usb_Where.html#bt-list-gotchas">bt.list() Gotchas</a></li>
<li class="toctree-l2"><a class="reference internal" href="usb_Running.html">Running scans</a></li>
<li class="toctree-l2"><a class="reference internal" href="usb_QuickAssess.html">Initial assessment of your data</a></li>
<li class="toctree-l2"><a class="reference internal" href="usb_GlobalOptions.html">xpdAcq Configuration</a></li>
</ul>
</li>
</ul>
<ul>
<li class="toctree-l1"><a class="reference internal" href="beamlinestaff.html">For Beamline Staff</a></li>
</ul>
<ul>
<li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">Troubleshooting</a></li>
</ul>
<ul>
<li class="toctree-l1"><a class="reference internal" href="release_note.html">Release Notes</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">xpdAcq</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html">Docs</a> »</li>
<li><a href="xpdusers.html">For XPD Users</a> »</li>
<li>Setting up your Beamtime</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/usb_Beamtime.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="setting-up-your-beamtime">
<span id="usb-beamtime"></span><h1>Setting up your Beamtime<a class="headerlink" href="#setting-up-your-beamtime" title="Permalink to this headline">¶</a></h1>
<p>This will usually be carried out by the beamline scientist. To check if all is well,
carry out the following steps:</p>
<blockquote>
<div><ol class="arabic simple">
<li>Check if you are in the collection environment</li>
<li>Type <code class="docutils literal"><span class="pre">bt</span></code>. It should return similar output as the following:</li>
</ol>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">bt</span>
<span class="go">{'bt_experimenters': ['Tim', 'Liu'],</span>
<span class="go"> 'bt_piLast': 'Billinge',</span>
<span class="go"> 'bt_safN': '300564',</span>
<span class="go"> 'bt_uid': 'c76a6fe1',</span>
<span class="go"> 'bt_wavelength': 0.1832}</span>
</pre></div>
</div>
<p>If not, please contact your beamline scientist.</p>
</div></blockquote>
<p>This object is a container that contains critical information about
your beamtime. You can investigate what is inside.</p>
<p>To see the kinds of information is contained, place a dot after bt and hit <cite>tab</cite>. The information (but not their values) will be listed.</p>
<a class="reference internal image-reference" href="_images/usb_beamtime_bt_0.png"><img alt="_images/usb_beamtime_bt_0.png" class="align-center" src="_images/usb_beamtime_bt_0.png" style="width: 400px; height: 200px;" /></a>
<p>To see what is contained in a specific field, type <code class="docutils literal"><span class="pre">bt.<thing></span></code> and hit return. For example, in our case:</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">bt</span><span class="o">.</span><span class="n">wavelength</span>
<span class="go">0.1832</span>
</pre></div>
</div>
<p>this is a beamtime (<cite>‘bt’</cite>) type of object with name <cite>‘bt’</cite>. More interesting
is the metadata it contains:</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">bt</span><span class="o">.</span><span class="n">md</span>
<span class="go">{'bt_experimenters': ['Tim', 'Liu'],</span>
<span class="go"> 'bt_piLast': 'Billinge',</span>
<span class="go"> 'bt_safN': '300564',</span>
<span class="go"> 'bt_uid': 'c76a6fe1',</span>
<span class="go"> 'bt_wavelength': 0.1832}</span>
</pre></div>
</div>
<p>The instrument responsible, created an initial version of <code class="docutils literal"><span class="pre">bt</span></code> with information
from the Safety Approval Form (SAF) form: PI’s last name, SAF number
and the experimenters.</p>
<p>When the beamtime object is created, it is given its own unique-ID, the <code class="docutils literal"><span class="pre">bt_uid</span></code>.
As long as you use the XPD acquisition software, every scan you make during your beamtime,
along with the other Beamtime level metadata,
will contain this <code class="docutils literal"><span class="pre">'bt_uid'</span></code> metadata field with the same uid value.
This can be searched for later in the scan headers, and used to find all the data
collected during your beamtime.</p>
<p>Some of the other things in the container are not quantities, or attributes, but
functions, or <cite>methods</cite>.</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">bt</span><span class="o">.</span><span class="n">list</span>
<span class="go"><bound method XPD.list of <class 'xpdacq.beamtime.Beamtime'>></span>
</pre></div>
</div>
<p>This means that <code class="docutils literal"><span class="pre">bt</span></code> not only contains beamtime information, but it can do things. In this
case, <code class="docutils literal"><span class="pre">bt.list</span></code> will list all the xpd-acquire-objects that have been created at
the time. To execute a method, add a parentheses to the end of <code class="docutils literal"><span class="pre">bt.list()</span></code>
and hit return. So far, there is only 1 object, the <cite>bt</cite> object with name <cite>bt</cite>.</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">bt</span><span class="o">.</span><span class="n">list</span><span class="p">()</span>
<span class="go"> ScanPlans:</span>
<span class="go"> 0: 'ct_5'</span>
<span class="go"> 1: 'ct_0.1'</span>
<span class="go"> 2: 'ct_1'</span>
<span class="go"> 3: 'ct_10'</span>
<span class="go"> 4: 'ct_30'</span>
<span class="go"> 5: 'ct_60'</span>
<span class="go"> Samples:</span>
<span class="go"> 0: Setup</span>
<span class="go"> 1: Ni_calibrant</span>
<span class="go"> 2: bkgd_kapton_0.9mmOD</span>
<span class="go"> 3: bkgd_kapton_1mmOD</span>
<span class="go"> 4: bkgd_kapton_0.5mmOD</span>
<span class="go"> 5: activated_carbon_1</span>
<span class="go"> 6: activated_carbon_2</span>
<span class="go"> 7: activated_carbon_3</span>
<span class="go"> ...</span>
</pre></div>
</div>
<p>As we mentioned before, if <code class="docutils literal"><span class="pre">bt</span></code> doesn’t exist,</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">bt</span>
<span class="go">---------------------------------------------------------------------------</span>
<span class="go">NameError Traceback (most recent call last)</span>
<span class="go"><ipython-input-1-d0d7ab093f8d> in <module>()</span>
<span class="go">----> 1 bt</span>
<span class="go">NameError: name 'bt' is not defined</span>
</pre></div>
</div>
<p>speak to your beamline scientist as there may be other aspects of the
environment setup that need to be fixed. If you ever do have to create
(we call it <cite>instantiate</cite>) a new <code class="docutils literal"><span class="pre">bt</span></code> object, it is done like this:</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">bt</span> <span class="o">=</span> <span class="n">Beamtime</span><span class="p">(</span><span class="s1">'Billinge'</span><span class="p">,</span><span class="mi">300256</span><span class="p">,</span> <span class="p">[</span><span class="s1">'Simon'</span><span class="p">,</span><span class="s1">'Billinge'</span><span class="p">,</span> <span class="s1">'Chia-Hao'</span><span class="p">,</span><span class="s1">'Liu'</span><span class="p">],</span> <span class="mf">0.18326</span><span class="p">)</span>
</pre></div>
</div>
<p>We will assume that <code class="docutils literal"><span class="pre">bt</span></code> exists. Now, we move on to the next step, <a class="reference internal" href="usb_Experiment.html#usb-experiment"><span class="std std-ref">Setting up your XPD acuisition objects</span></a> within our beamtime.</p>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="usb_Experiment.html" class="btn btn-neutral float-right" title="Setting up your XPD acuisition objects" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="sb_icollection.html" class="btn btn-neutral" title="Overview of the bsui+xpdAcq environment" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
<div role="contentinfo">
<p>
© Copyright (c) 2016 trustees of Columbia University in the City of New York.
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'0.5',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
</script>
</body>
</html>