Changeset 13316


Ignore:
Timestamp:
04/05/12 14:10:40 (13 years ago)
Author:
lusterma
Message:
worked on doc
Location:
fact/tools/pyscripts
Files:
32 edited

Legend:

Unmodified
Added
Removed

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

    r13151 r13316  
    11# Sphinx build info version 1
    22# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
    3 config: 4ccce79467c3c1e26dd2c30bdca24749
     3config: ba772b99f74f3e46a3c0f95d44c9931e
    44tags: fbb0d17656682115ca4d033fb2f83ba1

  • fact/tools/pyscripts/doc/_build/html/_sources/classes.txt

    r13151 r13316  
    1818
    1919FIR filter functions
    20 --------------------
     20=====================
    2121.. autoclass:: fir_filter
    2222        :members:

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

    r13151 r13316  
     1===============
     2Getting Started
     3===============
     4
     51) Get an account at the FACT data center at ISDC
     62) Setup your environment variables
     73) Checkout the pyfact software repository
     84) Try a few examples
     9
     101. Important links
     11=================================
     12
     13**FACT data center at ISDC** <http://www.isdc.unige.ch/fact/datacenter>**
     14    here you find instructions how to get an account, how to set it up and how to use it
     15
     16**SVN repository** <https://fact.isdc.unige.ch/svn/fact/>
     17    hosts all FACT software (including pyfact)
     18
     19**FACT run database** <https://www.fact-project.org/run_db/db/fact_runinfo.php>
     20    here you find information about all available runs
     21
     22**eLogbook** <https://www.fact-project.org/logbook/>
     23  telescope logbook used since Dec. 1, 2012; for logbook information before this date have a look here: <http://fact.ethz.ch/FACTelog/index.jsp>
     24
     25**FACT La Palma pages** <https://www.fact-project.org/>
     26  plenty of information concerning the telescope in La Palma
     27
     282. Environment variables
     29=====================
     30set the following env variables depending on the SHELL you are using, for instance in .bashrc or .tcshrc
     31
     32* **ROOTSYS**: /swdev_nfs/root_v5.28.00
     33* **PATH**: add $ROOTSYS/bin
     34* **PATH**: add /swdev_nfs/FACT++
     35* **LD_LIBRARY_PATH**: $ROOTSYS/lib:/swdev_nfs/FACT++/.libs
     36* **PYTHONPATH**: $ROOTSYS/lib
     37* **PYTHONPATH**: add all directories where python should search for modules. At least:
     38    * pyscripts/pyfact
     39    * pyscript/tools
     40    * pyscripts/ecamples
     41    * py
     42
     43the absolute path depends on where you have checked (or will check) out the pyscripts repository
     44
     453. Check out the repository
     46========================
     47svn co https://fact.isdc.unige.ch/svn/fact/tools/pyscripts/
     48
     494. Create pyfits library
     50========================
     51FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the default tool:
     52
     53`pyfits <http://www.stsci.edu/institute/software_hardware/pyfits>`.
     54
     55To mitigate this problem a C++ class defined in `fits.h` is used. A simple possibility to create an interface of this C++ class and python is to use the
     56
     57`pyroot http://root.cern.ch/drupal/category/package-context/pyroot>` module.
     58
     59simple::
     60
     61  [pceth118] /home/luster/py > root
     62  ROOT 5.28/00h (branches/v5-28-00-patches@42209, Feb 13 2012, 23:52:00 on linux)
     63  CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
     64  Type ? for help. Commands must be C++ statements.
     65  Enclose multiple statements between { }.
     66  root [0] .L fits.h++
     67  Info in <TUnixSystem::ACLiC>: creating shared library /home/luster/py/./fits_h.so
     68  root [1]
     69
     70
     71
     725. Run examples
     73============
     74
     75
    176=======
    277Classes
    … …  
    883rawdata access
    984-------
    10 .. autoclass:: pyfact.rawdata
     85.. autoclass:: pyfact.RawData
    1186    :members:
    1287

  • fact/tools/pyscripts/doc/_build/html/_sources/index.txt

    r13151 r13316  
    1313
    1414   introduction
     15   getting_started
    1516   classes
    1617   examples

  • fact/tools/pyscripts/doc/_build/html/_sources/introduction.txt

    r13151 r13316  
    99* examples
    1010
    11 The code of pyfact follows the `Style Guide for python code <http://www.python.org/dev/peps/pep-0008/>_.
     11If you are new to python you need to learn the basics. In any case it would be wise to study the following book:
     12
     13*A Primer on Scientific Programming with Python - Hans Petter Langtangen*
     14
     15pyfact is supposed to follow closely the programming style thought in this book.
     16
     17`python documentation pages <http://docs.python.org/>`_
     18
     19`astropython.org <http://www.astropython.org/resources>`_
     20
     21Python version and modules used
     22-------------------------------
     23As long as you work on the ISDC FACT cluster most things should be just fine.
     24|python version: 2.6.6
     25|--- add later: list of modules
     26
     27Style guide and coding conventions
     28----------------------------------
     29The code of pyfact follows the `Style Guide for python code <http://www.python.org/dev/peps/pep-0008/>.

  • fact/tools/pyscripts/doc/_build/html/_static/basic.css

    r13151 r13316  
    55 * Sphinx stylesheet -- basic theme.
    66 *
    7  * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
     7 * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
    88 * :license: BSD, see LICENSE for details.
    99 *
    … …  
    7878    font-family: sans-serif;
    7979    font-size: 1em;
    80 }
    81 
    82 div.sphinxsidebar input[type="text"] {
    83     width: 170px;
    84 }
    85 
    86 div.sphinxsidebar input[type="submit"] {
    87     width: 30px;
    8880}
    8981
    … …  
    222214}
    223215
    224 img.align-left, .figure.align-left, object.align-left {
    225     clear: left;
    226     float: left;
    227     margin-right: 1em;
    228 }
    229 
    230 img.align-right, .figure.align-right, object.align-right {
    231     clear: right;
    232     float: right;
    233     margin-left: 1em;
    234 }
    235 
    236 img.align-center, .figure.align-center, object.align-center {
    237   display: block;
    238   margin-left: auto;
    239   margin-right: auto;
    240 }
    241 
    242216.align-left {
    243217    text-align: left;
    … …  
    245219
    246220.align-center {
     221    clear: both;
    247222    text-align: center;
    248223}
    … …  
    421396
    422397.footnote:target  {
    423     background-color: #ffa;
     398    background-color: #ffa
    424399}
    425400
    … …  
    448423}
    449424
    450 abbr, acronym {
    451     border-bottom: dotted 1px;
    452     cursor: help;
    453 }
    454 
    455425/* -- code displays --------------------------------------------------------- */
    456426
    457427pre {
    458428    overflow: auto;
    459     overflow-y: hidden;  /* fixes display issues on Chrome browsers */
    460429}
    461430

  • fact/tools/pyscripts/doc/_build/html/_static/default.css

    r13151 r13316  
    55 * Sphinx stylesheet -- default theme.
    66 *
    7  * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
     7 * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
    88 * :license: BSD, see LICENSE for details.
    99 *

  • fact/tools/pyscripts/doc/_build/html/_static/doctools.js

    r13151 r13316  
    33 * ~~~~~~~~~~~
    44 *
    5  * Sphinx JavaScript utilities for all documentation.
     5 * Sphinx JavaScript utilties for all documentation.
    66 *
    7  * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
     7 * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
    88 * :license: BSD, see LICENSE for details.
    99 *
    … …  
    186186        });
    187187      }, 10);
    188       $('<p class="highlight-link"><a href="javascript:Documentation.' +
    189         'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
    190           .appendTo($('#searchbox'));
     188      $('<li class="highlight-link"><a href="javascript:Documentation.' +
     189        'hideSearchWords()">' + _('Hide Search Matches') + '</a></li>')
     190          .appendTo($('.sidebar .this-page-menu'));
    191191    }
    192192  },
    … …  
    214214   */
    215215  hideSearchWords : function() {
    216     $('#searchbox .highlight-link').fadeOut(300);
     216    $('.sidebar .this-page-menu li.highlight-link').fadeOut(300);
    217217    $('span.highlighted').removeClass('highlighted');
    218218  },

  • fact/tools/pyscripts/doc/_build/html/_static/searchtools.js

    r13151 r13316  
    11/*
    2  * searchtools.js_t
    3  * ~~~~~~~~~~~~~~~~
     2 * searchtools.js
     3 * ~~~~~~~~~~~~~~
    44 *
    55 * Sphinx JavaScript utilties for the full-text search.
    66 *
    7  * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
     7 * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
    88 * :license: BSD, see LICENSE for details.
    99 *
    … …  
    3737}
    3838
    39 
    4039/**
    4140 * Porter Stemmer
    4241 */
    43 var Stemmer = function() {
     42var PorterStemmer = function() {
    4443
    4544  var step2list = {
    … …  
    302301
    303302  query : function(query) {
    304     var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
    305 
    306     // Stem the searchterms and add them to the correct list
    307     var stemmer = new Stemmer();
     303    var stopwords = ['and', 'then', 'into', 'it', 'as', 'are', 'in',
     304                     'if', 'for', 'no', 'there', 'their', 'was', 'is',
     305                     'be', 'to', 'that', 'but', 'they', 'not', 'such',
     306                     'with', 'by', 'a', 'on', 'these', 'of', 'will',
     307                     'this', 'near', 'the', 'or', 'at'];
     308
     309    // stem the searchterms and add them to the correct list
     310    var stemmer = new PorterStemmer();
    308311    var searchterms = [];
    309312    var excluded = [];
    310313    var hlterms = [];
    311314    var tmp = query.split(/\s+/);
    312     var objectterms = [];
     315    var object = (tmp.length == 1) ? tmp[0].toLowerCase() : null;
    313316    for (var i = 0; i < tmp.length; i++) {
    314       if (tmp[i] != "") {
    315           objectterms.push(tmp[i].toLowerCase());
    316       }
    317 
    318317      if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
    319318          tmp[i] == "") {
    … …  
    346345    var titles = this._index.titles;
    347346    var terms = this._index.terms;
     347    var objects = this._index.objects;
     348    var objtypes = this._index.objtypes;
     349    var objnames = this._index.objnames;
    348350    var fileMap = {};
    349351    var files = null;
    … …  
    356358
    357359    // lookup as object
    358     for (var i = 0; i < objectterms.length; i++) {
    359       var others = [].concat(objectterms.slice(0,i),
    360                              objectterms.slice(i+1, objectterms.length))
    361       var results = this.performObjectSearch(objectterms[i], others);
    362       // Assume first word is most likely to be the object,
    363       // other words more likely to be in description.
    364       // Therefore put matches for earlier words first.
    365       // (Results are eventually used in reverse order).
    366       objectResults = results[0].concat(objectResults);
    367       importantResults = results[1].concat(importantResults);
    368       unimportantResults = results[2].concat(unimportantResults);
    369     }
     360    if (object != null) {
     361      for (var prefix in objects) {
     362        for (var name in objects[prefix]) {
     363          var fullname = (prefix ? prefix + '.' : '') + name;
     364          if (fullname.toLowerCase().indexOf(object) > -1) {
     365            match = objects[prefix][name];
     366            descr = objnames[match[1]] + _(', in ') + titles[match[0]];
     367            // XXX the generated anchors are not generally correct
     368            // XXX there may be custom prefixes
     369            result = [filenames[match[0]], fullname, '#'+fullname, descr];
     370            switch (match[2]) {
     371            case 1: objectResults.push(result); break;
     372            case 0: importantResults.push(result); break;
     373            case 2: unimportantResults.push(result); break;
     374            }
     375          }
     376        }
     377      }
     378    }
     379
     380    // sort results descending
     381    objectResults.sort(function(a, b) {
     382      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
     383    });
     384
     385    importantResults.sort(function(a, b) {
     386      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
     387    });
     388
     389    unimportantResults.sort(function(a, b) {
     390      return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
     391    });
     392
    370393
    371394    // perform the search on the required terms
    … …  
    467490              displayNextItem();
    468491            });
    469           }, "text");
     492          });
    470493        } else {
    471494          // no source available, just display title
    … …  
    488511    }
    489512    displayNextItem();
    490   },
    491 
    492   performObjectSearch : function(object, otherterms) {
    493     var filenames = this._index.filenames;
    494     var objects = this._index.objects;
    495     var objnames = this._index.objnames;
    496     var titles = this._index.titles;
    497 
    498     var importantResults = [];
    499     var objectResults = [];
    500     var unimportantResults = [];
    501 
    502     for (var prefix in objects) {
    503       for (var name in objects[prefix]) {
    504         var fullname = (prefix ? prefix + '.' : '') + name;
    505         if (fullname.toLowerCase().indexOf(object) > -1) {
    506           var match = objects[prefix][name];
    507           var objname = objnames[match[1]][2];
    508           var title = titles[match[0]];
    509           // If more than one term searched for, we require other words to be
    510           // found in the name/title/description
    511           if (otherterms.length > 0) {
    512             var haystack = (prefix + ' ' + name + ' ' +
    513                             objname + ' ' + title).toLowerCase();
    514             var allfound = true;
    515             for (var i = 0; i < otherterms.length; i++) {
    516               if (haystack.indexOf(otherterms[i]) == -1) {
    517                 allfound = false;
    518                 break;
    519               }
    520             }
    521             if (!allfound) {
    522               continue;
    523             }
    524           }
    525           var descr = objname + _(', in ') + title;
    526           anchor = match[3];
    527           if (anchor == '')
    528             anchor = fullname;
    529           else if (anchor == '-')
    530             anchor = objnames[match[1]][1] + '-' + fullname;
    531           result = [filenames[match[0]], fullname, '#'+anchor, descr];
    532           switch (match[2]) {
    533           case 1: objectResults.push(result); break;
    534           case 0: importantResults.push(result); break;
    535           case 2: unimportantResults.push(result); break;
    536           }
    537         }
    538       }
    539     }
    540 
    541     // sort results descending
    542     objectResults.sort(function(a, b) {
    543       return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
    544     });
    545 
    546     importantResults.sort(function(a, b) {
    547       return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
    548     });
    549 
    550     unimportantResults.sort(function(a, b) {
    551       return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
    552     });
    553 
    554     return [importantResults, objectResults, unimportantResults]
    555513  }
    556514}

  • fact/tools/pyscripts/doc/_build/html/_static/sidebar.js

    r13151 r13316  
    1717 * reset to the default (expanded).
    1818 *
    19  * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
     19 * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
    2020 * :license: BSD, see LICENSE for details.
    2121 *
    … …  
    2929  var sidebar = $('.sphinxsidebar');
    3030  var sidebarwrapper = $('.sphinxsidebarwrapper');
    31 
    32   // for some reason, the document has no sidebar; do not run into errors
    33   if (!sidebar.length) return;
    3431
    3532  // original margin-left of the bodywrapper and width of the sidebar

  • fact/tools/pyscripts/doc/_build/html/_static/underscore.js

    r13151 r13316  
    1 // Underscore.js 0.5.5
    2 // (c) 2009 Jeremy Ashkenas, DocumentCloud Inc.
    3 // Underscore is freely distributable under the terms of the MIT license.
    4 // Portions of Underscore are inspired by or borrowed from Prototype.js,
    5 // Oliver Steele's Functional, and John Resig's Micro-Templating.
    6 // For all details and documentation:
    7 // http://documentcloud.github.com/underscore/
    81(function(){var j=this,n=j._,i=function(a){this._wrapped=a},m=typeof StopIteration!=="undefined"?StopIteration:"__break__",b=j._=function(a){return new i(a)};if(typeof exports!=="undefined")exports._=b;var k=Array.prototype.slice,o=Array.prototype.unshift,p=Object.prototype.toString,q=Object.prototype.hasOwnProperty,r=Object.prototype.propertyIsEnumerable;b.VERSION="0.5.5";b.each=function(a,c,d){try{if(a.forEach)a.forEach(c,d);else if(b.isArray(a)||b.isArguments(a))for(var e=0,f=a.length;e<f;e++)c.call(d,
    92a[e],e,a);else{var g=b.keys(a);f=g.length;for(e=0;e<f;e++)c.call(d,a[g[e]],g[e],a)}}catch(h){if(h!=m)throw h;}return a};b.map=function(a,c,d){if(a&&b.isFunction(a.map))return a.map(c,d);var e=[];b.each(a,function(f,g,h){e.push(c.call(d,f,g,h))});return e};b.reduce=function(a,c,d,e){if(a&&b.isFunction(a.reduce))return a.reduce(b.bind(d,e),c);b.each(a,function(f,g,h){c=d.call(e,c,f,g,h)});return c};b.reduceRight=function(a,c,d,e){if(a&&b.isFunction(a.reduceRight))return a.reduceRight(b.bind(d,e),c);

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

    r13151 r13316  
    44  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
    55
    6 
    76<html xmlns="http://www.w3.org/1999/xhtml">
    87  <head>
    98    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
    109   
    11     <title>Classes &mdash; pyfact 0.1 documentation</title>
    12    
     10    <title>Classes &mdash; pyfact v0.1 documentation</title>
    1311    <link rel="stylesheet" href="_static/default.css" type="text/css" />
    1412    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
    15    
    1613    <script type="text/javascript">
    1714      var DOCUMENTATION_OPTIONS = {
    … …  
    2623    <script type="text/javascript" src="_static/underscore.js"></script>
    2724    <script type="text/javascript" src="_static/doctools.js"></script>
    28     <link rel="top" title="pyfact 0.1 documentation" href="index.html" />
     25    <link rel="top" title="pyfact v0.1 documentation" href="index.html" />
    2926    <link rel="next" title="Examples" href="examples.html" />
    3027    <link rel="prev" title="Introduction" href="introduction.html" />
    … …  
    4340          <a href="introduction.html" title="Introduction"
    4441             accesskey="P">previous</a> |</li>
    45         <li><a href="index.html">pyfact 0.1 documentation</a> &raquo;</li>
     42        <li><a href="index.html">pyfact v0.1 documentation</a> &raquo;</li>
    4643      </ul>
    4744    </div> 
    … …  
    6158<div class="section" id="fnames-of-a-data-run">
    6259<h3>fnames of a data run<a class="headerlink" href="#fnames-of-a-data-run" title="Permalink to this headline">¶</a></h3>
     60<dl class="class">
     61<dt id="pyfact.fnames">
     62<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>
     63<dd><p>organize file names of a FACT data run</p>
     64<dl class="docutils">
     65<dt>specifier <span class="classifier-delimiter">:</span> <span class="classifier">list of strings defined as:</span></dt>
     66<dd>[ &#8216;DRS calibration file&#8217;, &#8216;Data file&#8217;, &#8216;YYYY&#8217;, &#8216;MM&#8217;, &#8216;DD&#8217;]</dd>
     67</dl>
     68<p>rpath     : directory path for the results; YYYYMMDD will be appended to rpath
     69zipped    : use zipped (True) or unzipped (Data)</p>
     70<dl class="method">
     71<dt id="pyfact.fnames.info">
     72<tt class="descname">info</tt><big>(</big><big>)</big><a class="headerlink" href="#pyfact.fnames.info" title="Permalink to this definition">¶</a></dt>
     73<dd><p>print complete filenames</p>
     74</dd></dl>
     75
     76<dl class="method">
     77<dt id="pyfact.fnames.make">
     78<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>
     79<dd><p>create (make) the filenames</p>
     80<p>names   : dictionary of filenames, tags { &#8216;data&#8217;, &#8216;drscal&#8217;, &#8216;results&#8217; }
     81data    : name of the data file
     82drscal  : name of the drs calibration file
     83results : radikal of file name(s) for results (to be completed  by suffixes)</p>
     84</dd></dl>
     85
     86</dd></dl>
     87
     88</div>
    6389</div>
    6490<div class="section" id="fir-filter-functions">
    65 <h3>FIR filter functions<a class="headerlink" href="#fir-filter-functions" title="Permalink to this headline">¶</a></h3>
    66 </div>
     91<h2>FIR filter functions<a class="headerlink" href="#fir-filter-functions" title="Permalink to this headline">¶</a></h2>
    6792</div>
    6893</div>
    … …  
    80105<li><a class="reference internal" href="#rawdata-access">rawdata access</a></li>
    81106<li><a class="reference internal" href="#fnames-of-a-data-run">fnames of a data run</a></li>
    82 <li><a class="reference internal" href="#fir-filter-functions">FIR filter functions</a></li>
    83107</ul>
    84108</li>
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  • fact/tools/pyscripts/doc/_build/html/examples.html

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

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    … …  
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    49 <h1 id="index">Index</h1>
     44   <h1 id="index">Index</h1>
    5045
    51 <div class="genindex-jumpbox">
    52  
    53 </div>
     46   <div class="genindex-jumpbox">
     47   <a href="#B"><strong>B</strong></a> | <a href="#C"><strong>C</strong></a> | <a href="#D"><strong>D</strong></a> | <a href="#F"><strong>F</strong></a> | <a href="#I"><strong>I</strong></a> | <a href="#M"><strong>M</strong></a> | <a href="#N"><strong>N</strong></a> | <a href="#R"><strong>R</strong></a> | <a href="#S"><strong>S</strong></a>
     48   </div>
     49<h2 id="B">B</h2>
     50<table width="100%" class="indextable genindextable"><tr>
     51  <td width="33%" valign="top"><dl>
     52    <dt><a href="getting_started.html#pyfact.RawData.baseline_correct">baseline_correct() (pyfact.RawData method)</a></dt>
     53    <dt><a href="getting_started.html#pyfact.RawData.baseline_read_values">baseline_read_values() (pyfact.RawData method)</a></dt>
     54</dl></td>
     55  <td width="33%" valign="top"><dl>
     56    <dt><a href="getting_started.html#pyfact.RawData.board_times">board_times (pyfact.RawData attribute)</a></dt>
     57</dl></td>
     58</tr></table>
     59
     60<h2 id="C">C</h2>
     61<table width="100%" class="indextable genindextable"><tr>
     62  <td width="33%" valign="top"><dl>
     63    <dt><a href="getting_started.html#pyfact.RawData.calib_file">calib_file (pyfact.RawData attribute)</a></dt>
     64</dl></td>
     65  <td width="33%" valign="top"><dl>
     66    <dt><a href="getting_started.html#pyfact.RawData.calibrate_drs_amplitude">calibrate_drs_amplitude() (pyfact.RawData method)</a></dt>
     67</dl></td>
     68</tr></table>
     69
     70<h2 id="D">D</h2>
     71<table width="100%" class="indextable genindextable"><tr>
     72  <td width="33%" valign="top"><dl>
     73    <dt><a href="getting_started.html#pyfact.RawData.data">data (pyfact.RawData attribute)</a></dt>
     74</dl></td>
     75  <td width="33%" valign="top"><dl>
     76    <dt><a href="getting_started.html#pyfact.RawData.data_file">data_file (pyfact.RawData attribute)</a></dt>
     77</dl></td>
     78</tr></table>
     79
     80<h2 id="F">F</h2>
     81<table width="100%" class="indextable genindextable"><tr>
     82  <td width="33%" valign="top"><dl>
     83    <dt><a href="classes.html#pyfact.fnames">fnames (class in pyfact)</a>, <a href="getting_started.html#pyfact.fnames">[1]</a></dt>
     84</dl></td>
     85</tr></table>
     86
     87<h2 id="I">I</h2>
     88<table width="100%" class="indextable genindextable"><tr>
     89  <td width="33%" valign="top"><dl>
     90    <dt><a href="classes.html#pyfact.fnames.info">info() (pyfact.fnames method)</a>, <a href="getting_started.html#pyfact.fnames.info">[1]</a></dt>
     91    <dd><dl>
     92      <dt><a href="getting_started.html#pyfact.RawData.info">(pyfact.RawData method)</a></dt>
     93  </dl></dd>
     94</dl></td>
     95</tr></table>
     96
     97<h2 id="M">M</h2>
     98<table width="100%" class="indextable genindextable"><tr>
     99  <td width="33%" valign="top"><dl>
     100    <dt><a href="classes.html#pyfact.fnames.make">make() (pyfact.fnames method)</a>, <a href="getting_started.html#pyfact.fnames.make">[1]</a></dt>
     101</dl></td>
     102</tr></table>
     103
     104<h2 id="N">N</h2>
     105<table width="100%" class="indextable genindextable"><tr>
     106  <td width="33%" valign="top"><dl>
     107    <dt><a href="getting_started.html#pyfact.RawData.nevents">nevents (pyfact.RawData attribute)</a></dt>
     108    <dt><a href="getting_started.html#pyfact.RawData.next">next() (pyfact.RawData method)</a></dt>
     109    <dt><a href="getting_started.html#pyfact.RawData.next_event">next_event() (pyfact.RawData method)</a></dt>
     110</dl></td>
     111  <td width="33%" valign="top"><dl>
     112    <dt><a href="getting_started.html#pyfact.RawData.npix">npix (pyfact.RawData attribute)</a></dt>
     113    <dt><a href="getting_started.html#pyfact.RawData.nroi">nroi (pyfact.RawData attribute)</a></dt>
     114</dl></td>
     115</tr></table>
     116
     117<h2 id="R">R</h2>
     118<table width="100%" class="indextable genindextable"><tr>
     119  <td width="33%" valign="top"><dl>
     120    <dt><a href="getting_started.html#pyfact.RawData">RawData (class in pyfact)</a></dt>
     121</dl></td>
     122</tr></table>
     123
     124<h2 id="S">S</h2>
     125<table width="100%" class="indextable genindextable"><tr>
     126  <td width="33%" valign="top"><dl>
     127    <dt><a href="getting_started.html#pyfact.RawData.start_cells">start_cells (pyfact.RawData attribute)</a></dt>
     128</dl></td>
     129</tr></table>
     130
    54131
    55132
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  • fact/tools/pyscripts/doc/_build/html/getting_started.html

    r13151 r13316  
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    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>
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    6158<li>examples</li>
    6259</ul>
    63 <p>The code of pyfact follows the <a href="#id1"><span class="problematic" id="id2">`</span></a>Style Guide for python code &lt;<a class="reference external" href="http://www.python.org/dev/peps/pep-0008/">http://www.python.org/dev/peps/pep-0008/</a>&gt;_.</p>
     60<p>If you are new to python you need to learn the basics. In any case it would be wise to study the following book:</p>
     61<p><em>A Primer on Scientific Programming with Python - Hans Petter Langtangen</em></p>
     62<p>pyfact is supposed to follow closely the programming style thought in this book.</p>
     63<p><a class="reference external" href="http://docs.python.org/">python documentation pages</a></p>
     64<p><a class="reference external" href="http://www.astropython.org/resources">astropython.org</a></p>
     65<div class="section" id="python-version-and-modules-used">
     66<h2>Python version and modules used<a class="headerlink" href="#python-version-and-modules-used" title="Permalink to this headline">¶</a></h2>
     67<p>As long as you work on the ISDC FACT cluster most things should be just fine.
     68<a href="#id1"><span class="problematic" id="id2">|</span></a>python version: 2.6.6
     69<a href="#id3"><span class="problematic" id="id4">|</span></a>&#8212; add later: list of modules</p>
     70</div>
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     72<h2>Style guide and coding conventions<a class="headerlink" href="#style-guide-and-coding-conventions" title="Permalink to this headline">¶</a></h2>
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     74</div>
    6475</div>
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    r13151 r13316  
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  • fact/tools/pyscripts/doc/_build/html/search.html

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  • fact/tools/pyscripts/doc/_build/html/searchindex.js

    r13151 r13316  
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  • fact/tools/pyscripts/doc/getting_started.rst

    r13151 r13316  
     1===============
     2Getting Started
     3===============
     4
     51) Get an account at the FACT data center at ISDC
     62) Setup your environment variables
     73) Checkout the pyfact software repository
     84) Try a few examples
     9
     101. Important links
     11=================================
     12
     13**FACT data center at ISDC** <http://www.isdc.unige.ch/fact/datacenter>**
     14    here you find instructions how to get an account, how to set it up and how to use it
     15
     16**SVN repository** <https://fact.isdc.unige.ch/svn/fact/>
     17    hosts all FACT software (including pyfact)
     18
     19**FACT run database** <https://www.fact-project.org/run_db/db/fact_runinfo.php>
     20    here you find information about all available runs
     21
     22**eLogbook** <https://www.fact-project.org/logbook/>
     23  telescope logbook used since Dec. 1, 2012; for logbook information before this date have a look here: <http://fact.ethz.ch/FACTelog/index.jsp>
     24
     25**FACT La Palma pages** <https://www.fact-project.org/>
     26  plenty of information concerning the telescope in La Palma
     27
     282. Environment variables
     29=====================
     30set the following env variables depending on the SHELL you are using, for instance in .bashrc or .tcshrc
     31
     32* **ROOTSYS**: /swdev_nfs/root_v5.28.00
     33* **PATH**: add $ROOTSYS/bin
     34* **PATH**: add /swdev_nfs/FACT++
     35* **LD_LIBRARY_PATH**: $ROOTSYS/lib:/swdev_nfs/FACT++/.libs
     36* **PYTHONPATH**: $ROOTSYS/lib
     37* **PYTHONPATH**: add all directories where python should search for modules. At least:
     38    * pyscripts/pyfact
     39    * pyscript/tools
     40    * pyscripts/ecamples
     41    * py
     42
     43the absolute path depends on where you have checked (or will check) out the pyscripts repository
     44
     453. Check out the repository
     46========================
     47svn co https://fact.isdc.unige.ch/svn/fact/tools/pyscripts/
     48
     494. Create pyfits library
     50========================
     51FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the default tool:
     52
     53`pyfits <http://www.stsci.edu/institute/software_hardware/pyfits>`.
     54
     55To mitigate this problem a C++ class defined in `fits.h` is used. A simple possibility to create an interface of this C++ class and python is to use the
     56
     57`pyroot http://root.cern.ch/drupal/category/package-context/pyroot>` module.
     58
     59simple::
     60
     61  [pceth118] /home/luster/py > root
     62  ROOT 5.28/00h (branches/v5-28-00-patches@42209, Feb 13 2012, 23:52:00 on linux)
     63  CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
     64  Type ? for help. Commands must be C++ statements.
     65  Enclose multiple statements between { }.
     66  root [0] .L fits.h++
     67  Info in <TUnixSystem::ACLiC>: creating shared library /home/luster/py/./fits_h.so
     68  root [1]
     69
     70
     71
     725. Run examples
     73============
     74
     75
    176=======
    277Classes
    … …  
    883rawdata access
    984-------
    10 .. autoclass:: pyfact.rawdata
     85.. autoclass:: pyfact.RawData
    1186    :members:
    1287

  • fact/tools/pyscripts/doc/index.rst

    r13151 r13316  
    1313
    1414   introduction
     15   getting_started
    1516   classes
    1617   examples

  • fact/tools/pyscripts/doc/introduction.rst

    r13151 r13316  
    99* examples
    1010
    11 The code of pyfact follows the `Style Guide for python code <http://www.python.org/dev/peps/pep-0008/>_.
     11If you are new to python you need to learn the basics. In any case it would be wise to study the following book:
     12
     13*A Primer on Scientific Programming with Python - Hans Petter Langtangen*
     14
     15pyfact is supposed to follow closely the programming style thought in this book.
     16
     17`python documentation pages <http://docs.python.org/>`_
     18
     19`astropython.org <http://www.astropython.org/resources>`_
     20
     21Python version and modules used
     22-------------------------------
     23As long as you work on the ISDC FACT cluster most things should be just fine.
     24|python version: 2.6.6
     25|--- add later: list of modules
     26
     27Style guide and coding conventions
     28----------------------------------
     29The code of pyfact follows the `Style Guide for python code <http://www.python.org/dev/peps/pep-0008/>.

  • fact/tools/pyscripts/tools/spike_ana.py

    r13144 r13316  
    6969    #print singles[0], a, b, data[a,b-1], data[a,b], data[1,b+1]
    7070
    71 data_file_name = '/data00/fact-construction/raw/2011/11/24/20111124_117.fits.gz'
    72 calib_file_name = '/data00/fact-construction/raw/2011/11/24/20111124_111.drs.fits.gz'
     71data_file_name = '/home/luster/win7/FACT/data/raw/20111124/20111124_117.fits.gz'
     72calib_file_name = '/home/luster/win7/FACT/data/raw/20111124/20111124_114.drs.fits.gz'
    7373run = RawData( data_file_name, calib_file_name )
    7474
    … …  
    8080    print 'event ', ev
    8181    ev += 1
    82     if ev == 10:
     82    if ev == 100:
    8383        break
    8484    remove_spikes(data)
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