-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathfeatures.html
More file actions
321 lines (223 loc) · 13.1 KB
/
Copy pathfeatures.html
File metadata and controls
321 lines (223 loc) · 13.1 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
<!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>xpdAcq features — 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"/>
<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>
<li class="toctree-l1"><a class="reference internal" href="xpdusers.html">For XPD Users</a></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><code class="docutils literal"><span class="pre">xpdAcq</span></code> features</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/features.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="xpdacq-features">
<span id="feature"></span><h1><code class="docutils literal"><span class="pre">xpdAcq</span></code> features<a class="headerlink" href="#xpdacq-features" title="Permalink to this headline">¶</a></h1>
<div class="section" id="automated-dark-collection">
<span id="auto-dark"></span><h2>Automated dark collection<a class="headerlink" href="#automated-dark-collection" title="Permalink to this headline">¶</a></h2>
<p>you might have found something weird when you running a <code class="docutils literal"><span class="pre">xrun</span></code> command:</p>
<p><em>I only requested one ``xrun`` but program runs two scans</em></p>
<p>So what happen?</p>
<p>That is actually a feature called auto-dark subtraction of <code class="docutils literal"><span class="pre">xpdAcq</span></code>.
When you are running your experiment, <code class="docutils literal"><span class="pre">xpdAcq</span></code> actually checks if you have
collected a <strong>fresh and appropriate</strong> dark frame every time it collects a scan.
The definition of <strong>fresh and appropriate</strong> is:</p>
<div class="section" id="nice-and-fresh">
<h3><strong>Nice and fresh</strong><a class="headerlink" href="#nice-and-fresh" title="Permalink to this headline">¶</a></h3>
<div class="highlight-none"><div class="highlight"><pre><span></span>Given a certain period T (``dark window``), there exists a dark frame
with the same **total exposure time** and exactly the same **acquisition time**
as the light frame we are about collect.
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p>At <strong>XPD</strong>, area detector is running in <code class="docutils literal"><span class="pre">continuous</span> <span class="pre">acquisition</span></code> mode,
which means detector keeps <strong>reading</strong> but only <strong>saves</strong> image when <code class="docutils literal"><span class="pre">xpdAcq</span></code>
tells it to with desired exposure time. In short,</p>
<ul class="last simple">
<li>acquisition time defines how fast is detector reading time,
ranged from 0.1s to 5s.</li>
<li>exposure time means total exposure time, which user defined.</li>
</ul>
</div>
<p>Automated dark collection is enabled by default and it can be turned off by:</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="n">glbl</span><span class="o">.</span><span class="n">auto_dark</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">glbl</span><span class="o">.</span><span class="n">shutter_control</span> <span class="o">=</span> <span class="bp">False</span>
</pre></div>
</div>
<p>And period of dark window can be modified by:</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="n">glbl</span><span class="o">.</span><span class="n">dk_window</span> <span class="o">=</span> <span class="mi">200</span> <span class="c1"># in minutes. default is 3000 minutes</span>
</pre></div>
</div>
<p>Having <code class="docutils literal"><span class="pre">auto_dark</span></code> set to <code class="docutils literal"><span class="pre">True</span></code> is strongly recommended as this enables
<code class="docutils literal"><span class="pre">xpdAcq</span></code> to do automated dark frame subtraction when you pull out data from
centralized <strong>NSLSL-II</strong> server.</p>
</div>
</div>
<div class="section" id="automated-calibration-capture">
<span id="auto-calib"></span><h2>Automated calibration capture<a class="headerlink" href="#automated-calibration-capture" title="Permalink to this headline">¶</a></h2>
<p>Often times, keeping track with which calibration file is associated with
certain scan is very tiring. <code class="docutils literal"><span class="pre">xpdAcq</span></code> makes this easier for you. Before every
scan is being collected, program goes to grab the most recent calibration
parameters in <code class="docutils literal"><span class="pre">/home/xf28id1/xpdUser/config_base</span></code> and load them as part of
metadata so that you can reference them whenever you want and make in-situ data
reduction possible!</p>
<div class="section" id="quick-guide-of-calibration-steps-with-pyfai">
<span id="calib-manual"></span><h3>Quick guide of calibration steps with pyFAI<a class="headerlink" href="#quick-guide-of-calibration-steps-with-pyfai" title="Permalink to this headline">¶</a></h3>
<ol class="arabic simple">
<li>First you will see an image window like this:</li>
</ol>
<blockquote>
<div><a class="reference internal image-reference" href="_images/calib_05.png"><img alt="_images/calib_05.png" class="align-center" src="_images/calib_05.png" style="width: 400px; height: 300px;" /></a>
<p>That is the image we want to perform azimuthal calibration with. Use magnify
tool at the tool bar to zoom in and <strong>right click</strong> rings. Starting from
the first, inner ring and to outer rings. Usually a few rings (~5) should be
enough.</p>
<a class="reference internal image-reference" href="_images/calib_07.png"><img alt="_images/calib_07.png" class="align-center" src="_images/calib_07.png" style="width: 400px; height: 300px;" /></a>
</div></blockquote>
<p>2. After selecting rings, click on the <em>original</em> terminal and hit <code class="docutils literal"><span class="pre"><enter></span></code>.
Then you will be requested to supply indices of rings you just selected.
Remember index <strong>starts from 0</strong> as we are using <code class="docutils literal"><span class="pre">python</span></code>.
After supplying all indices, you should have a window to show your calibration:</p>
<blockquote>
<div><a class="reference internal image-reference" href="_images/calib_08.png"><img alt="_images/calib_08.png" class="align-center" src="_images/calib_08.png" style="width: 400px; height: 300px;" /></a>
<p>Program will ask you if you want to modify parameters, in most of case, you
don’t have to. So just hit <code class="docutils literal"><span class="pre"><enter></span></code> in the terminal and integration will be
done.</p>
</div></blockquote>
<ol class="arabic simple" start="3">
<li>Finally 1D integration and 2D regrouping results will pop out:</li>
</ol>
<blockquote>
<div><a class="reference internal image-reference" href="_images/calib_09.png"><img alt="_images/calib_09.png" class="align-center" src="_images/calib_09.png" style="width: 400px; height: 300px;" /></a>
<p>You can qualitatively interrogate your calibration by looking if lines in
2D regrouping are straight or not.</p>
<p>After this step, a calibration file with name <code class="docutils literal"><span class="pre">pyFAI_calib.yml</span></code> will be
saved under <code class="docutils literal"><span class="pre">/home/xf28id1/xpdUser/config_base</span></code></p>
</div></blockquote>
<p>Alright, you are done then! With <code class="docutils literal"><span class="pre">`automated</span> <span class="pre">calibration</span> <span class="pre">capture</span></code> feature, <code class="docutils literal"><span class="pre">xpdAcq</span></code>
will load calibration parameters from the most recent config file.</p>
</div>
</div>
<div class="section" id="metadata-imported-from-spreadsheet">
<span id="import-sample"></span><h2>metadata imported from spreadsheet<a class="headerlink" href="#metadata-imported-from-spreadsheet" title="Permalink to this headline">¶</a></h2>
<p>In order to facilitate , we suggest you to enter
as much information as you can and that is the main philosophy behind <code class="docutils literal"><span class="pre">xpdAcq</span></code>.</p>
<p>Typing in sample metadata during beamtime is always less efficient and it wastes
your time so a pre-populated excel sheet with all metadata entered beforehand
turns out to be the solution.</p>
<div class="section" id="parsing-rules">
<h3>parsing rules<a class="headerlink" href="#parsing-rules" title="Permalink to this headline">¶</a></h3>
<ul>
<li><p class="first"><strong>comma separated fields</strong>: information entities are separated by a comma.</p>
<blockquote>
<div><ul class="simple">
<li><code class="docutils literal"><span class="pre">cif</span> <span class="pre">name</span></code>: pointer of potential structures for your sampel, if any.</li>
<li><code class="docutils literal"><span class="pre">Tags</span></code>: any comment you want to put on for this measurement.</li>
</ul>
</div></blockquote>
</li>
<li><p class="first"><strong>name fields</strong>:</p>
</li>
<li><p class="first"><strong>phase string</strong>:</p>
</li>
</ul>
</div>
</div>
<div class="section" id="auto-masking">
<span id="auto-mask"></span><h2>Auto-masking<a class="headerlink" href="#auto-masking" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>auto-masking with user defined beamstop mask</li>
</ul>
</div>
</div>
</div>
</div>
<footer>
<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>