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  • fact/tools/pyscripts/doc/_build/html/getting_started.html

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    4449          <div class="body">
    4550           
    46   <div class="section" id="classes">
     51  <div class="section" id="getting-started">
     52<h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
     53<ol class="arabic simple">
     54<li>Get an account at the FACT data center at ISDC</li>
     55<li>Setup your environment variables</li>
     56<li>Checkout the pyfact software repository</li>
     57<li>Try a few examples</li>
     58</ol>
     59<div class="section" id="important-links">
     60<h2>1. Important links<a class="headerlink" href="#important-links" title="Permalink to this headline">¶</a></h2>
     61<dl class="docutils">
     62<dt><strong>FACT data center at ISDC</strong> &lt;<a class="reference external" href="http://www.isdc.unige.ch/fact/datacenter">http://www.isdc.unige.ch/fact/datacenter</a>&gt;**</dt>
     63<dd>here you find instructions how to get an account, how to set it up and how to use it</dd>
     64<dt><strong>SVN repository</strong> &lt;<a class="reference external" href="https://fact.isdc.unige.ch/svn/fact/">https://fact.isdc.unige.ch/svn/fact/</a>&gt;</dt>
     65<dd>hosts all FACT software (including pyfact)</dd>
     66<dt><strong>FACT run database</strong> &lt;<a class="reference external" href="https://www.fact-project.org/run_db/db/fact_runinfo.php">https://www.fact-project.org/run_db/db/fact_runinfo.php</a>&gt;</dt>
     67<dd>here you find information about all available runs</dd>
     68<dt><strong>eLogbook</strong> &lt;<a class="reference external" href="https://www.fact-project.org/logbook/">https://www.fact-project.org/logbook/</a>&gt;</dt>
     69<dd>telescope logbook used since Dec. 1, 2012; for logbook information before this date have a look here: &lt;<a class="reference external" href="http://fact.ethz.ch/FACTelog/index.jsp">http://fact.ethz.ch/FACTelog/index.jsp</a>&gt;</dd>
     70<dt><strong>FACT La Palma pages</strong> &lt;<a class="reference external" href="https://www.fact-project.org/">https://www.fact-project.org/</a>&gt;</dt>
     71<dd>plenty of information concerning the telescope in La Palma</dd>
     72</dl>
     73</div>
     74<div class="section" id="environment-variables">
     75<h2>2. Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline">¶</a></h2>
     76<p>set the following env variables depending on the SHELL you are using, for instance in .bashrc or .tcshrc</p>
     77<ul>
     78<li><p class="first"><strong>ROOTSYS</strong>: /swdev_nfs/root_v5.28.00</p>
     79</li>
     80<li><p class="first"><strong>PATH</strong>: add $ROOTSYS/bin</p>
     81</li>
     82<li><p class="first"><strong>PATH</strong>: add /swdev_nfs/FACT++</p>
     83</li>
     84<li><p class="first"><strong>LD_LIBRARY_PATH</strong>: $ROOTSYS/lib:/swdev_nfs/FACT++/.libs</p>
     85</li>
     86<li><p class="first"><strong>PYTHONPATH</strong>: $ROOTSYS/lib</p>
     87</li>
     88<li><dl class="first docutils">
     89<dt><strong>PYTHONPATH</strong>: add all directories where python should search for modules. At least:</dt>
     90<dd><ul class="first last simple">
     91<li>pyscripts/pyfact</li>
     92<li>pyscript/tools</li>
     93<li>pyscripts/ecamples</li>
     94<li>py</li>
     95</ul>
     96</dd>
     97</dl>
     98</li>
     99</ul>
     100<p>the absolute path depends on where you have checked (or will check) out the pyscripts repository</p>
     101</div>
     102<div class="section" id="check-out-the-repository">
     103<h2>3. Check out the repository<a class="headerlink" href="#check-out-the-repository" title="Permalink to this headline">¶</a></h2>
     104<p>svn co <a class="reference external" href="https://fact.isdc.unige.ch/svn/fact/tools/pyscripts/">https://fact.isdc.unige.ch/svn/fact/tools/pyscripts/</a></p>
     105</div>
     106<div class="section" id="create-pyfits-library">
     107<h2>4. Create pyfits library<a class="headerlink" href="#create-pyfits-library" title="Permalink to this headline">¶</a></h2>
     108<p>FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the default tool:</p>
     109<p><cite>pyfits &lt;http://www.stsci.edu/institute/software_hardware/pyfits&gt;</cite>.</p>
     110<p>To mitigate this problem a C++ class defined in <cite>fits.h</cite> is used. A simple possibility to create an interface of this C++ class and python is to use the</p>
     111<p><cite>pyroot http://root.cern.ch/drupal/category/package-context/pyroot&gt;</cite> module.</p>
     112<p>simple:</p>
     113<div class="highlight-python"><pre>[pceth118] /home/luster/py &gt; root
     114ROOT 5.28/00h (branches/v5-28-00-patches@42209, Feb 13 2012, 23:52:00 on linux)
     115CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
     116Type ? for help. Commands must be C++ statements.
     117Enclose multiple statements between { }.
     118root [0] .L fits.h++
     119Info in &lt;TUnixSystem::ACLiC&gt;: creating shared library /home/luster/py/./fits_h.so
     120root [1]</pre>
     121</div>
     122</div>
     123<div class="section" id="run-examples">
     124<h2>5. Run examples<a class="headerlink" href="#run-examples" title="Permalink to this headline">¶</a></h2>
     125</div>
     126</div>
     127<div class="section" id="classes">
    47128<h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h1>
    48129<div class="section" id="pyfact-py">
    … …  
    50131<div class="section" id="rawdata-access">
    51132<h3>rawdata access<a class="headerlink" href="#rawdata-access" title="Permalink to this headline">¶</a></h3>
     133<dl class="class">
     134<dt id="pyfact.RawData">
     135<em class="property">class </em><tt class="descclassname">pyfact.</tt><tt class="descname">RawData</tt><big>(</big><em>data_file_name</em>, <em>calib_file_name</em>, <em>user_action_calib=&lt;function &lt;lambda&gt; at 0xa818844&gt;</em>, <em>baseline_file_name=''</em>, <em>return_dict=None</em><big>)</big><a class="headerlink" href="#pyfact.RawData" title="Permalink to this definition">¶</a></dt>
     136<dd><p>raw data access and calibration</p>
     137<ul class="simple">
     138<li>open raw data file and drs calibration file</li>
     139<li>performs amplitude calibration</li>
     140<li>performs baseline substraction if wanted</li>
     141<li>provides all data in an array:
     142row = number of pixel
     143col = length of region of interest</li>
     144</ul>
     145<p>initialize object</p>
     146<p>open data file and calibration data file
     147get basic information about the data in data_file_name
     148allocate buffers for data access</p>
     149<p>data_file_name   : fits or fits.gz file of the data including the path
     150calib_file_name : fits or fits.gz file containing DRS calibration data
     151baseline_file_name : npy file containing the baseline values</p>
     152<dl class="method">
     153<dt id="pyfact.RawData.baseline_correct">
     154<tt class="descname">baseline_correct</tt><big>(</big><big>)</big><a class="headerlink" href="#pyfact.RawData.baseline_correct" title="Permalink to this definition">¶</a></dt>
     155<dd><p>subtract baseline from the data</p>
     156</dd></dl>
     157
     158<dl class="method">
     159<dt id="pyfact.RawData.baseline_read_values">
     160<tt class="descname">baseline_read_values</tt><big>(</big><em>file</em>, <em>bsl_hist='bsl_sum/hplt_mean'</em><big>)</big><a class="headerlink" href="#pyfact.RawData.baseline_read_values" title="Permalink to this definition">¶</a></dt>
     161<dd><p>open ROOT file with baseline histogram and read baseline values
     162file       name of the root file
     163bsl_hist   path to the histogram containing the basline values</p>
     164</dd></dl>
     165
     166<dl class="attribute">
     167<dt id="pyfact.RawData.board_times">
     168<tt class="descname">board_times</tt><a class="headerlink" href="#pyfact.RawData.board_times" title="Permalink to this definition">¶</a></dt>
     169<dd><p>time when the FAD was triggered, in some strange units...</p>
     170</dd></dl>
     171
     172<dl class="attribute">
     173<dt id="pyfact.RawData.calib_file">
     174<tt class="descname">calib_file</tt><a class="headerlink" href="#pyfact.RawData.calib_file" title="Permalink to this definition">¶</a></dt>
     175<dd><p>drs calibration file</p>
     176</dd></dl>
     177
     178<dl class="method">
     179<dt id="pyfact.RawData.calibrate_drs_amplitude">
     180<tt class="descname">calibrate_drs_amplitude</tt><big>(</big><big>)</big><a class="headerlink" href="#pyfact.RawData.calibrate_drs_amplitude" title="Permalink to this definition">¶</a></dt>
     181<dd><p>perform the drs amplitude calibration of the event data</p>
     182</dd></dl>
     183
     184<dl class="attribute">
     185<dt id="pyfact.RawData.data">
     186<tt class="descname">data</tt><a class="headerlink" href="#pyfact.RawData.data" title="Permalink to this definition">¶</a></dt>
     187<dd><p>1D array with raw data</p>
     188</dd></dl>
     189
     190<dl class="attribute">
     191<dt id="pyfact.RawData.data_file">
     192<tt class="descname">data_file</tt><a class="headerlink" href="#pyfact.RawData.data_file" title="Permalink to this definition">¶</a></dt>
     193<dd><p>data file (fits object)</p>
     194</dd></dl>
     195
     196<dl class="method">
     197<dt id="pyfact.RawData.info">
     198<tt class="descname">info</tt><big>(</big><big>)</big><a class="headerlink" href="#pyfact.RawData.info" title="Permalink to this definition">¶</a></dt>
     199<dd><p>print run information</p>
     200</dd></dl>
     201
     202<dl class="attribute">
     203<dt id="pyfact.RawData.nevents">
     204<tt class="descname">nevents</tt><a class="headerlink" href="#pyfact.RawData.nevents" title="Permalink to this definition">¶</a></dt>
     205<dd><p>number of events in the data run</p>
     206</dd></dl>
     207
     208<dl class="method">
     209<dt id="pyfact.RawData.next">
     210<tt class="descname">next</tt><big>(</big><big>)</big><a class="headerlink" href="#pyfact.RawData.next" title="Permalink to this definition">¶</a></dt>
     211<dd><p>used by __iter__</p>
     212</dd></dl>
     213
     214<dl class="method">
     215<dt id="pyfact.RawData.next_event">
     216<tt class="descname">next_event</tt><big>(</big><big>)</big><a class="headerlink" href="#pyfact.RawData.next_event" title="Permalink to this definition">¶</a></dt>
     217<dd><p>load the next event from disk and calibrate it</p>
     218</dd></dl>
     219
     220<dl class="attribute">
     221<dt id="pyfact.RawData.npix">
     222<tt class="descname">npix</tt><a class="headerlink" href="#pyfact.RawData.npix" title="Permalink to this definition">¶</a></dt>
     223<dd><p>number of pixels (should be 1440)</p>
     224</dd></dl>
     225
     226<dl class="attribute">
     227<dt id="pyfact.RawData.nroi">
     228<tt class="descname">nroi</tt><a class="headerlink" href="#pyfact.RawData.nroi" title="Permalink to this definition">¶</a></dt>
     229<dd><p>region of interest (number of DRS slices read)</p>
     230</dd></dl>
     231
     232<dl class="attribute">
     233<dt id="pyfact.RawData.start_cells">
     234<tt class="descname">start_cells</tt><a class="headerlink" href="#pyfact.RawData.start_cells" title="Permalink to this definition">¶</a></dt>
     235<dd><p>slice where drs readout started</p>
     236</dd></dl>
     237
     238</dd></dl>
     239
    52240</div>
    53241<div class="section" id="fnames-of-a-data-run">
    54242<h3>fnames of a data run<a class="headerlink" href="#fnames-of-a-data-run" title="Permalink to this headline">¶</a></h3>
     243<dl class="class">
     244<dt id="pyfact.fnames">
     245<em class="property">class </em><tt class="descclassname">pyfact.</tt><tt class="descname">fnames</tt><big>(</big><em>specifier=['012', '023', '2011', '11', '24'], rpath='/scratch_nfs/res/bsl/', zipped=True</em><big>)</big><a class="headerlink" href="#pyfact.fnames" title="Permalink to this definition">¶</a></dt>
     246<dd><p>organize file names of a FACT data run</p>
     247<dl class="docutils">
     248<dt>specifier <span class="classifier-delimiter">:</span> <span class="classifier">list of strings defined as:</span></dt>
     249<dd>[ &#8216;DRS calibration file&#8217;, &#8216;Data file&#8217;, &#8216;YYYY&#8217;, &#8216;MM&#8217;, &#8216;DD&#8217;]</dd>
     250</dl>
     251<p>rpath     : directory path for the results; YYYYMMDD will be appended to rpath
     252zipped    : use zipped (True) or unzipped (Data)</p>
     253<dl class="method">
     254<dt id="pyfact.fnames.info">
     255<tt class="descname">info</tt><big>(</big><big>)</big><a class="headerlink" href="#pyfact.fnames.info" title="Permalink to this definition">¶</a></dt>
     256<dd><p>print complete filenames</p>
     257</dd></dl>
     258
     259<dl class="method">
     260<dt id="pyfact.fnames.make">
     261<tt class="descname">make</tt><big>(</big><em>specifier</em>, <em>rpath</em>, <em>zipped</em><big>)</big><a class="headerlink" href="#pyfact.fnames.make" title="Permalink to this definition">¶</a></dt>
     262<dd><p>create (make) the filenames</p>
     263<p>names   : dictionary of filenames, tags { &#8216;data&#8217;, &#8216;drscal&#8217;, &#8216;results&#8217; }
     264data    : name of the data file
     265drscal  : name of the drs calibration file
     266results : radikal of file name(s) for results (to be completed  by suffixes)</p>
     267</dd></dl>
     268
     269</dd></dl>
     270
    55271</div>
    56272</div>
    … …  
    65281  <h3><a href="index.html">Table Of Contents</a></h3>
    66282  <ul>
    67 <li><a class="reference internal" href="#">Classes</a><ul>
     283<li><a class="reference internal" href="#">Getting Started</a><ul>
     284<li><a class="reference internal" href="#important-links">1. Important links</a></li>
     285<li><a class="reference internal" href="#environment-variables">2. Environment variables</a></li>
     286<li><a class="reference internal" href="#check-out-the-repository">3. Check out the repository</a></li>
     287<li><a class="reference internal" href="#create-pyfits-library">4. Create pyfits library</a></li>
     288<li><a class="reference internal" href="#run-examples">5. Run examples</a></li>
     289</ul>
     290</li>
     291<li><a class="reference internal" href="#classes">Classes</a><ul>
    68292<li><a class="reference internal" href="#pyfact-py">pyfact.py</a><ul>
    69293<li><a class="reference internal" href="#rawdata-access">rawdata access</a></li>
    … …  
    75299</ul>
    76300
     301  <h4>Previous topic</h4>
     302  <p class="topless"><a href="introduction.html"
     303                        title="previous chapter">Introduction</a></p>
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