Ignore:
Timestamp:
04/05/12 17:32:54 (13 years ago)
Author:
lusterma
Message:
updated
Location:
fact/tools/pyscripts/doc
Files:
18 edited

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

    r13316 r13324  
    3939    * pyscript/tools
    4040    * pyscripts/ecamples
    41     * py
    4241
    4342the absolute path depends on where you have checked (or will check) out the pyscripts repository
    … …  
    4746svn co https://fact.isdc.unige.ch/svn/fact/tools/pyscripts/
    4847
    49 4. Create pyfits library
     484. Create pyfits_h.so library
    5049========================
    51 FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the default tool:
     50FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the existing tools:
    5251
    53 `pyfits <http://www.stsci.edu/institute/software_hardware/pyfits>`.
     52`pyfits <http://www.stsci.edu/institute/software_hardware/pyfits>` which uses `cfitsio <http://heasarc.gsfc.nasa.gov/fitsio/>`_.
    5453
    55 To 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
     54To mitigate this problem a C++ class defined in fits.h [#f1]_ is used. A simple possibility to create an interface of this C++ class is to use ROOT and later to import it using the
     55`pyroot <http://root.cern.ch/drupal/category/package-context/pyroot>`_ module.
    5656
    57 `pyroot http://root.cern.ch/drupal/category/package-context/pyroot>` module.
     57got to the directory: pyscripts/pyfact
    5858
    5959simple::
    6060
    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)
     61  [lusterma@isdc-cn02 pyfact]$ root
     62  ROOT 5.28/00 (trunk@37585, Dec 14 2010, 15:20:27 on linuxx8664gcc)
    6363  CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
    6464  Type ? for help. Commands must be C++ statements.
    6565  Enclose multiple statements between { }.
     66
    6667  root [0] .L fits.h++
    67   Info in <TUnixSystem::ACLiC>: creating shared library /home/luster/py/./fits_h.so
     68  Info in <TUnixSystem::ACLiC>: creating shared library /home_nfs/isdc/lusterma/pyscripts/pyfact/./fits_h.so
    6869  root [1]
    6970
     71This might not work for whatenver reason then it should be done like this::
    7072
     73  $rootcint -f my_dict.C -c fits.h izstream.h
     74  $g++ -fPIC -c -I$ROOTSYS/include my_dict.C -o my_dict.o
     75  $g++ -o fits_h.so -shared my_dict.o
     76
     77Now you can check if the reading rawdata is working:
     78
     79$ pyfact.py
     80
     81this should print some data from a few events
    7182
    72835. Run examples
    … …  
    93104
    94105
     106.. rubric:: Footnotes
     107.. [#f1] fits.h (here named pyfits.h) is part of MARS and was written by T.Bretz, it was added to this repository for convienience

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

    r13316 r13324  
    2525    <link rel="top" title="pyfact v0.1 documentation" href="index.html" />
    2626    <link rel="next" title="Examples" href="examples.html" />
    27     <link rel="prev" title="Introduction" href="introduction.html" />
     27    <link rel="prev" title="Getting Started" href="getting_started.html" />
    2828  </head>
    2929  <body>
    … …  
    3838             accesskey="N">next</a> |</li>
    3939        <li class="right" >
    40           <a href="introduction.html" title="Introduction"
     40          <a href="getting_started.html" title="Getting Started"
    4141             accesskey="P">previous</a> |</li>
    4242        <li><a href="index.html">pyfact v0.1 documentation</a> &raquo;</li>
    … …  
    113113
    114114  <h4>Previous topic</h4>
    115   <p class="topless"><a href="introduction.html"
    116                         title="previous chapter">Introduction</a></p>
     115  <p class="topless"><a href="getting_started.html"
     116                        title="previous chapter">Getting Started</a></p>
    117117  <h4>Next topic</h4>
    118118  <p class="topless"><a href="examples.html"
    … …  
    150150             >next</a> |</li>
    151151        <li class="right" >
    152           <a href="introduction.html" title="Introduction"
     152          <a href="getting_started.html" title="Getting Started"
    153153             >previous</a> |</li>
    154154        <li><a href="index.html">pyfact v0.1 documentation</a> &raquo;</li>

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

    r13316 r13324  
    9292<li>pyscript/tools</li>
    9393<li>pyscripts/ecamples</li>
    94 <li>py</li>
    9594</ul>
    9695</dd>
    … …  
    104103<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>
    105104</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>
     105<div class="section" id="create-pyfits-h-so-library">
     106<h2>4. Create pyfits_h.so library<a class="headerlink" href="#create-pyfits-h-so-library" title="Permalink to this headline">¶</a></h2>
     107<p>FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the existing tools:</p>
     108<p><cite>pyfits &lt;http://www.stsci.edu/institute/software_hardware/pyfits&gt;</cite> which uses <a class="reference external" href="http://heasarc.gsfc.nasa.gov/fitsio/">cfitsio</a>.</p>
     109<p>To mitigate this problem a C++ class defined in fits.h <a class="footnote-reference" href="#f1" id="id1">[1]</a> is used. A simple possibility to create an interface of this C++ class is to use ROOT and later to import it using the
     110<a class="reference external" href="http://root.cern.ch/drupal/category/package-context/pyroot">pyroot</a> module.</p>
     111<p>got to the directory: pyscripts/pyfact</p>
    112112<p>simple:</p>
    113 <div class="highlight-python"><pre>[pceth118] /home/luster/py &gt; root
    114 ROOT 5.28/00h (branches/v5-28-00-patches@42209, Feb 13 2012, 23:52:00 on linux)
     113<div class="highlight-python"><pre>[lusterma@isdc-cn02 pyfact]$ root
     114ROOT 5.28/00 (trunk@37585, Dec 14 2010, 15:20:27 on linuxx8664gcc)
    115115CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
    116116Type ? for help. Commands must be C++ statements.
    117117Enclose multiple statements between { }.
     118
    118119root [0] .L fits.h++
    119 Info in &lt;TUnixSystem::ACLiC&gt;: creating shared library /home/luster/py/./fits_h.so
     120Info in &lt;TUnixSystem::ACLiC&gt;: creating shared library /home_nfs/isdc/lusterma/pyscripts/pyfact/./fits_h.so
    120121root [1]</pre>
    121122</div>
     123<p>This might not work for whatenver reason then it should be done like this:</p>
     124<div class="highlight-python"><pre>$rootcint -f my_dict.C -c fits.h izstream.h
     125$g++ -fPIC -c -I$ROOTSYS/include my_dict.C -o my_dict.o
     126$g++ -o fits_h.so -shared my_dict.o</pre>
     127</div>
     128<p>Now you can check if the reading rawdata is working:</p>
     129<p>$ pyfact.py</p>
     130<p>this should print some data from a few events</p>
    122131</div>
    123132<div class="section" id="run-examples">
    … …  
    133142<dl class="class">
    134143<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>
     144<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 0xab028b4&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>
    136145<dd><p>raw data access and calibration</p>
    137146<ul class="simple">
    … …  
    269278</dd></dl>
    270279
     280<p class="rubric">Footnotes</p>
     281<table class="docutils footnote" frame="void" id="f1" rules="none">
     282<colgroup><col class="label" /><col /></colgroup>
     283<tbody valign="top">
     284<tr><td class="label"><a class="fn-backref" href="#id1">[1]</a></td><td>fits.h (here named pyfits.h) is part of MARS and was written by T.Bretz, it was added to this repository for convienience</td></tr>
     285</tbody>
     286</table>
    271287</div>
    272288</div>
    … …  
    285301<li><a class="reference internal" href="#environment-variables">2. Environment variables</a></li>
    286302<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>
     303<li><a class="reference internal" href="#create-pyfits-h-so-library">4. Create pyfits_h.so library</a></li>
    288304<li><a class="reference internal" href="#run-examples">5. Run examples</a></li>
    289305</ul>

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

    r13316 r13324  
    5959<li class="toctree-l2"><a class="reference internal" href="getting_started.html#environment-variables">2. Environment variables</a></li>
    6060<li class="toctree-l2"><a class="reference internal" href="getting_started.html#check-out-the-repository">3. Check out the repository</a></li>
    61 <li class="toctree-l2"><a class="reference internal" href="getting_started.html#create-pyfits-library">4. Create pyfits library</a></li>
     61<li class="toctree-l2"><a class="reference internal" href="getting_started.html#create-pyfits-h-so-library">4. Create pyfits_h.so library</a></li>
    6262<li class="toctree-l2"><a class="reference internal" href="getting_started.html#run-examples">5. Run examples</a></li>
    6363</ul>

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

    r13316 r13324  
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     85\newlabel{classes:pyfact.fnames.make}{{4.1.2}{9}{fnames of a data run\relax }{section*.23}{}}
     86\@writefile{toc}{\contentsline {section}{\numberline {4.2}FIR filter functions}{9}{section.4.2}}
     87\newlabel{classes:fir-filter-functions}{{4.2}{9}{FIR filter functions\relax }{section.4.2}{}}
     88\@writefile{toc}{\contentsline {chapter}{\numberline {5}Examples}{11}{chapter.5}}
    4989\@writefile{lof}{\addvspace {10\p@ }}
    5090\@writefile{lot}{\addvspace {10\p@ }}
    51 \newlabel{index:indices-and-tables}{{5}{11}{Indices and tables\relax }{chapter.5}{}}
     91\newlabel{examples::doc}{{5}{11}{Examples\relax }{chapter.5}{}}
     92\newlabel{examples:examples}{{5}{11}{Examples\relax }{chapter.5}{}}
     93\@writefile{toc}{\contentsline {section}{\numberline {5.1}calling a system command}{11}{section.5.1}}
     94\newlabel{examples:calling-a-system-command}{{5.1}{11}{calling a system command\relax }{section.5.1}{}}
     95\@writefile{toc}{\contentsline {chapter}{\numberline {6}phyton in FACT}{13}{chapter.6}}
     96\@writefile{lof}{\addvspace {10\p@ }}
     97\@writefile{lot}{\addvspace {10\p@ }}
     98\newlabel{python:phyton-in-fact}{{6}{13}{phyton in FACT\relax }{chapter.6}{}}
     99\newlabel{python::doc}{{6}{13}{phyton in FACT\relax }{chapter.6}{}}
     100\@writefile{toc}{\contentsline {chapter}{\numberline {7}Indices and tables}{15}{chapter.7}}
     101\@writefile{lof}{\addvspace {10\p@ }}
     102\@writefile{lot}{\addvspace {10\p@ }}
     103\newlabel{index:indices-and-tables}{{7}{15}{Indices and tables\relax }{chapter.7}{}}
     104\@writefile{toc}{\contentsline {chapter}{Index}{17}{section*.24}}

  • fact/tools/pyscripts/doc/_build/latex/pyfact.idx

    r13151 r13324  
     1\indexentry{RawData (class in pyfact)|hyperpage}{7}
     2\indexentry{baseline\_correct() (pyfact.RawData method)|hyperpage}{7}
     3\indexentry{baseline\_read\_values() (pyfact.RawData method)|hyperpage}{7}
     4\indexentry{board\_times (pyfact.RawData attribute)|hyperpage}{7}
     5\indexentry{calib\_file (pyfact.RawData attribute)|hyperpage}{7}
     6\indexentry{calibrate\_drs\_amplitude() (pyfact.RawData method)|hyperpage}{7}
     7\indexentry{data (pyfact.RawData attribute)|hyperpage}{7}
     8\indexentry{data\_file (pyfact.RawData attribute)|hyperpage}{7}
     9\indexentry{info() (pyfact.RawData method)|hyperpage}{7}
     10\indexentry{nevents (pyfact.RawData attribute)|hyperpage}{8}
     11\indexentry{next() (pyfact.RawData method)|hyperpage}{8}
     12\indexentry{next\_event() (pyfact.RawData method)|hyperpage}{8}
     13\indexentry{npix (pyfact.RawData attribute)|hyperpage}{8}
     14\indexentry{nroi (pyfact.RawData attribute)|hyperpage}{8}
     15\indexentry{start\_cells (pyfact.RawData attribute)|hyperpage}{8}
     16\indexentry{fnames (class in pyfact)|hyperpage}{8}
     17\indexentry{info() (pyfact.fnames method)|hyperpage}{8}
     18\indexentry{make() (pyfact.fnames method)|hyperpage}{8}
     19\indexentry{fnames (class in pyfact)|hyperpage}{9}
     20\indexentry{info() (pyfact.fnames method)|hyperpage}{9}
     21\indexentry{make() (pyfact.fnames method)|hyperpage}{9}

  • fact/tools/pyscripts/doc/_build/latex/pyfact.ilg

    r13151 r13324  
    11This is makeindex, version 2.14 [02-Oct-2002] (kpathsea + Thai support).
    22Scanning style file ./python.ist......done (6 attributes redefined, 0 ignored).
    3 Scanning input file pyfact.idx...done (0 entries accepted, 0 rejected).
    4 Nothing written in pyfact.ind.
     3Scanning input file pyfact.idx....done (21 entries accepted, 0 rejected).
     4Sorting entries....done (91 comparisons).
     5Generating output file pyfact.ind....done (48 lines written, 0 warnings).
     6Output written in pyfact.ind.
    57Transcript written in pyfact.ilg.

  • fact/tools/pyscripts/doc/_build/latex/pyfact.ind

    r13151 r13324  
     1\begin{theindex}
     2\def\bigletter#1{{\Large\sffamily#1}\nopagebreak\vspace{1mm}}
     3
     4  \bigletter B
     5  \item baseline\_correct() (pyfact.RawData method), \hyperpage{7}
     6  \item baseline\_read\_values() (pyfact.RawData method), \hyperpage{7}
     7  \item board\_times (pyfact.RawData attribute), \hyperpage{7}
     8
     9  \indexspace
     10  \bigletter C
     11  \item calib\_file (pyfact.RawData attribute), \hyperpage{7}
     12  \item calibrate\_drs\_amplitude() (pyfact.RawData method), \hyperpage{7}
     13
     14  \indexspace
     15  \bigletter D
     16  \item data (pyfact.RawData attribute), \hyperpage{7}
     17  \item data\_file (pyfact.RawData attribute), \hyperpage{7}
     18
     19  \indexspace
     20  \bigletter F
     21  \item fnames (class in pyfact), \hyperpage{8, 9}
     22
     23  \indexspace
     24  \bigletter I
     25  \item info() (pyfact.fnames method), \hyperpage{8, 9}
     26  \item info() (pyfact.RawData method), \hyperpage{7}
     27
     28  \indexspace
     29  \bigletter M
     30  \item make() (pyfact.fnames method), \hyperpage{8, 9}
     31
     32  \indexspace
     33  \bigletter N
     34  \item nevents (pyfact.RawData attribute), \hyperpage{8}
     35  \item next() (pyfact.RawData method), \hyperpage{8}
     36  \item next\_event() (pyfact.RawData method), \hyperpage{8}
     37  \item npix (pyfact.RawData attribute), \hyperpage{8}
     38  \item nroi (pyfact.RawData attribute), \hyperpage{8}
     39
     40  \indexspace
     41  \bigletter R
     42  \item RawData (class in pyfact), \hyperpage{7}
     43
     44  \indexspace
     45  \bigletter S
     46  \item start\_cells (pyfact.RawData attribute), \hyperpage{8}
     47
     48\end{theindex}

  • fact/tools/pyscripts/doc/_build/latex/pyfact.log

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     1This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4) (format=pdflatex 2012.3.14)  5 APR 2012 18:22
    22entering extended mode
    33**pyfact.tex
    … …  
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    854854Chapter 2.
     855
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     875_nfs/res/bsl/',
     876 []
     877
     878[8]
    870879Chapter 4.
    871 [9] [10
     880
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     884 []
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     897Chapter 6.
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     900]
     901Chapter 7.
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     927Output written on pyfact.pdf (21 pages, 154318 bytes).

  • fact/tools/pyscripts/doc/_build/latex/pyfact.out

    r13151 r13324  
    11\BOOKMARK [0][-]{chapter.1}{Introduction}{}
    2 \BOOKMARK [0][-]{chapter.2}{Classes}{}
    3 \BOOKMARK [1][-]{section.2.1}{pyfact.py}{chapter.2}
    4 \BOOKMARK [0][-]{chapter.3}{Examples}{}
    5 \BOOKMARK [1][-]{section.3.1}{calling a system command}{chapter.3}
    6 \BOOKMARK [0][-]{chapter.4}{phyton in FACT}{}
    7 \BOOKMARK [0][-]{chapter.5}{Indices and tables}{}
     2\BOOKMARK [1][-]{section.1.1}{Python version and modules used}{chapter.1}
     3\BOOKMARK [1][-]{section.1.2}{Style guide and coding conventions}{chapter.1}
     4\BOOKMARK [0][-]{chapter.2}{Getting Started}{}
     5\BOOKMARK [1][-]{section.2.1}{1. Important links}{chapter.2}
     6\BOOKMARK [1][-]{section.2.2}{2. Environment variables}{chapter.2}
     7\BOOKMARK [1][-]{section.2.3}{3. Check out the repository}{chapter.2}
     8\BOOKMARK [1][-]{section.2.4}{4. Create pyfits\137h.so library}{chapter.2}
     9\BOOKMARK [1][-]{section.2.5}{5. Run examples}{chapter.2}
     10\BOOKMARK [0][-]{chapter.3}{Classes}{}
     11\BOOKMARK [1][-]{section.3.1}{pyfact.py}{chapter.3}
     12\BOOKMARK [0][-]{chapter.4}{Classes}{}
     13\BOOKMARK [1][-]{section.4.1}{pyfact.py}{chapter.4}
     14\BOOKMARK [1][-]{section.4.2}{FIR filter functions}{chapter.4}
     15\BOOKMARK [0][-]{chapter.5}{Examples}{}
     16\BOOKMARK [1][-]{section.5.1}{calling a system command}{chapter.5}
     17\BOOKMARK [0][-]{chapter.6}{phyton in FACT}{}
     18\BOOKMARK [0][-]{chapter.7}{Indices and tables}{}
     19\BOOKMARK [0][-]{section*.24}{Index}{}

  • fact/tools/pyscripts/doc/_build/latex/pyfact.tex

    r13151 r13324  
    1313
    1414\title{pyfact Documentation}
    15 \date{February 09, 2012}
     15\date{April 05, 2012}
    1616\release{0.1}
    1717\author{Werner Lustermann}
    … …  
    135135\end{itemize}
    136136
     137If you are new to python you need to learn the basics. In any case it would be wise to study the following book:
     138
     139\emph{A Primer on Scientific Programming with Python - Hans Petter Langtangen}
     140
     141pyfact is supposed to follow closely the programming style thought in this book.
     142
     143\href{http://docs.python.org/}{python documentation pages}
     144
     145\href{http://www.astropython.org/resources}{astropython.org}
     146
     147
     148\section{Python version and modules used}
     149\label{introduction:python-version-and-modules-used}
     150As long as you work on the ISDC FACT cluster most things should be just fine.
     151{\color{red}\bfseries{}\textbar{}}python version: 2.6.6
     152{\color{red}\bfseries{}\textbar{}}--- add later: list of modules
     153
     154
     155\section{Style guide and coding conventions}
     156\label{introduction:style-guide-and-coding-conventions}
     157The code of pyfact follows the {\color{red}\bfseries{}{}`}Style Guide for python code \textless{}\href{http://www.python.org/dev/peps/pep-0008/}{http://www.python.org/dev/peps/pep-0008/}\textgreater{}.
     158
     159
     160\chapter{Getting Started}
     161\label{getting_started:getting-started}\label{getting_started::doc}\begin{enumerate}
     162\item {}
     163Get an account at the FACT data center at ISDC
     164
     165\item {}
     166Setup your environment variables
     167
     168\item {}
     169Checkout the pyfact software repository
     170
     171\item {}
     172Try a few examples
     173
     174\end{enumerate}
     175
     176
     177\section{1. Important links}
     178\label{getting_started:important-links}\begin{description}
     179\item[{\textbf{FACT data center at ISDC} \textless{}\href{http://www.isdc.unige.ch/fact/datacenter}{http://www.isdc.unige.ch/fact/datacenter}\textgreater{}**}] \leavevmode
     180here you find instructions how to get an account, how to set it up and how to use it
     181
     182\item[{\textbf{SVN repository} \textless{}\href{https://fact.isdc.unige.ch/svn/fact/}{https://fact.isdc.unige.ch/svn/fact/}\textgreater{}}] \leavevmode
     183hosts all FACT software (including pyfact)
     184
     185\item[{\textbf{FACT run database} \textless{}\href{https://www.fact-project.org/run\_db/db/fact\_runinfo.php}{https://www.fact-project.org/run\_db/db/fact\_runinfo.php}\textgreater{}}] \leavevmode
     186here you find information about all available runs
     187
     188\item[{\textbf{eLogbook} \textless{}\href{https://www.fact-project.org/logbook/}{https://www.fact-project.org/logbook/}\textgreater{}}] \leavevmode
     189telescope logbook used since Dec. 1, 2012; for logbook information before this date have a look here: \textless{}\href{http://fact.ethz.ch/FACTelog/index.jsp}{http://fact.ethz.ch/FACTelog/index.jsp}\textgreater{}
     190
     191\item[{\textbf{FACT La Palma pages} \textless{}\href{https://www.fact-project.org/}{https://www.fact-project.org/}\textgreater{}}] \leavevmode
     192plenty of information concerning the telescope in La Palma
     193
     194\end{description}
     195
     196
     197\section{2. Environment variables}
     198\label{getting_started:environment-variables}
     199set the following env variables depending on the SHELL you are using, for instance in .bashrc or .tcshrc
     200\begin{itemize}
     201\item {}
     202\textbf{ROOTSYS}: /swdev\_nfs/root\_v5.28.00
     203
     204\item {}
     205\textbf{PATH}: add \$ROOTSYS/bin
     206
     207\item {}
     208\textbf{PATH}: add /swdev\_nfs/FACT++
     209
     210\item {}
     211\textbf{LD\_LIBRARY\_PATH}: \$ROOTSYS/lib:/swdev\_nfs/FACT++/.libs
     212
     213\item {}
     214\textbf{PYTHONPATH}: \$ROOTSYS/lib
     215
     216\item {} \begin{description}
     217\item[{\textbf{PYTHONPATH}: add all directories where python should search for modules. At least:}] \leavevmode\begin{itemize}
     218\item {}
     219pyscripts/pyfact
     220
     221\item {}
     222pyscript/tools
     223
     224\item {}
     225pyscripts/ecamples
     226
     227\end{itemize}
     228
     229\end{description}
     230
     231\end{itemize}
     232
     233the absolute path depends on where you have checked (or will check) out the pyscripts repository
     234
     235
     236\section{3. Check out the repository}
     237\label{getting_started:check-out-the-repository}
     238svn co \href{https://fact.isdc.unige.ch/svn/fact/tools/pyscripts/}{https://fact.isdc.unige.ch/svn/fact/tools/pyscripts/}
     239
     240
     241\section{4. Create pyfits\_h.so library}
     242\label{getting_started:create-pyfits-h-so-library}
     243FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the existing tools:
     244
     245\emph{pyfits \textless{}http://www.stsci.edu/institute/software\_hardware/pyfits\textgreater{}} which uses \href{http://heasarc.gsfc.nasa.gov/fitsio/}{cfitsio}.
     246
     247To mitigate this problem a C++ class defined in fits.h \footnote{
     248fits.h (here named pyfits.h) is part of MARS and was written by T.Bretz, it was added to this repository for convienience
     249} is used. A simple possibility to create an interface of this C++ class is to use ROOT and later to import it using the
     250\href{http://root.cern.ch/drupal/category/package-context/pyroot}{pyroot} module.
     251
     252got to the directory: pyscripts/pyfact
     253
     254simple:
     255
     256\begin{Verbatim}[commandchars=@\[\]]
     257@PYGZlb[]lusterma@PYGZat[]isdc-cn02 pyfact@PYGZrb[]@$ root
     258ROOT 5.28/00 (trunk@PYGZat[]37585, Dec 14 2010, 15:20:27 on linuxx8664gcc)
     259CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
     260Type ? for help. Commands must be C++ statements.
     261Enclose multiple statements between { }.
     262
     263root @PYGZlb[]0@PYGZrb[] .L fits.h++
     264Info in @textless[]TUnixSystem::ACLiC@textgreater[]: creating shared library /home@_nfs/isdc/lusterma/pyscripts/pyfact/./fits@_h.so
     265root @PYGZlb[]1@PYGZrb[]
     266\end{Verbatim}
     267
     268This might not work for whatenver reason then it should be done like this:
     269
     270\begin{Verbatim}[commandchars=@\[\]]
     271@$rootcint -f my@_dict.C -c fits.h izstream.h
     272@$g++ -fPIC -c -I@$ROOTSYS/include my@_dict.C -o my@_dict.o
     273@$g++ -o fits@_h.so -shared my@_dict.o
     274\end{Verbatim}
     275
     276Now you can check if the reading rawdata is working:
     277
     278\$ pyfact.py
     279
     280this should print some data from a few events
     281
     282
     283\section{5. Run examples}
     284\label{getting_started:run-examples}
     285
     286\chapter{Classes}
     287\label{getting_started:classes}
     288
     289\section{pyfact.py}
     290\label{getting_started:pyfact-py}
     291
     292\subsection{rawdata access}
     293\label{getting_started:rawdata-access}\index{RawData (class in pyfact)}
     294
     295\begin{fulllineitems}
     296\phantomsection\label{getting_started:pyfact.RawData}\pysiglinewithargsret{\strong{class }\code{pyfact.}\bfcode{RawData}}{\emph{data\_file\_name}, \emph{calib\_file\_name}, \emph{user\_action\_calib=\textless{}function \textless{}lambda\textgreater{} at 0xab028b4\textgreater{}}, \emph{baseline\_file\_name='`}, \emph{return\_dict=None}}{}
     297raw data access and calibration
     298\begin{itemize}
     299\item {}
     300open raw data file and drs calibration file
     301
     302\item {}
     303performs amplitude calibration
     304
     305\item {}
     306performs baseline substraction if wanted
     307
     308\item {}
     309provides all data in an array:
     310row = number of pixel
     311col = length of region of interest
     312
     313\end{itemize}
     314
     315initialize object
     316
     317open data file and calibration data file
     318get basic information about the data in data\_file\_name
     319allocate buffers for data access
     320
     321data\_file\_name   : fits or fits.gz file of the data including the path
     322calib\_file\_name : fits or fits.gz file containing DRS calibration data
     323baseline\_file\_name : npy file containing the baseline values
     324\index{baseline\_correct() (pyfact.RawData method)}
     325
     326\begin{fulllineitems}
     327\phantomsection\label{getting_started:pyfact.RawData.baseline_correct}\pysiglinewithargsret{\bfcode{baseline\_correct}}{}{}
     328subtract baseline from the data
     329
     330\end{fulllineitems}
     331
     332\index{baseline\_read\_values() (pyfact.RawData method)}
     333
     334\begin{fulllineitems}
     335\phantomsection\label{getting_started:pyfact.RawData.baseline_read_values}\pysiglinewithargsret{\bfcode{baseline\_read\_values}}{\emph{file}, \emph{bsl\_hist='bsl\_sum/hplt\_mean'}}{}
     336open ROOT file with baseline histogram and read baseline values
     337file       name of the root file
     338bsl\_hist   path to the histogram containing the basline values
     339
     340\end{fulllineitems}
     341
     342\index{board\_times (pyfact.RawData attribute)}
     343
     344\begin{fulllineitems}
     345\phantomsection\label{getting_started:pyfact.RawData.board_times}\pysigline{\bfcode{board\_times}}{}
     346time when the FAD was triggered, in some strange units...
     347
     348\end{fulllineitems}
     349
     350\index{calib\_file (pyfact.RawData attribute)}
     351
     352\begin{fulllineitems}
     353\phantomsection\label{getting_started:pyfact.RawData.calib_file}\pysigline{\bfcode{calib\_file}}{}
     354drs calibration file
     355
     356\end{fulllineitems}
     357
     358\index{calibrate\_drs\_amplitude() (pyfact.RawData method)}
     359
     360\begin{fulllineitems}
     361\phantomsection\label{getting_started:pyfact.RawData.calibrate_drs_amplitude}\pysiglinewithargsret{\bfcode{calibrate\_drs\_amplitude}}{}{}
     362perform the drs amplitude calibration of the event data
     363
     364\end{fulllineitems}
     365
     366\index{data (pyfact.RawData attribute)}
     367
     368\begin{fulllineitems}
     369\phantomsection\label{getting_started:pyfact.RawData.data}\pysigline{\bfcode{data}}{}
     3701D array with raw data
     371
     372\end{fulllineitems}
     373
     374\index{data\_file (pyfact.RawData attribute)}
     375
     376\begin{fulllineitems}
     377\phantomsection\label{getting_started:pyfact.RawData.data_file}\pysigline{\bfcode{data\_file}}{}
     378data file (fits object)
     379
     380\end{fulllineitems}
     381
     382\index{info() (pyfact.RawData method)}
     383
     384\begin{fulllineitems}
     385\phantomsection\label{getting_started:pyfact.RawData.info}\pysiglinewithargsret{\bfcode{info}}{}{}
     386print run information
     387
     388\end{fulllineitems}
     389
     390\index{nevents (pyfact.RawData attribute)}
     391
     392\begin{fulllineitems}
     393\phantomsection\label{getting_started:pyfact.RawData.nevents}\pysigline{\bfcode{nevents}}{}
     394number of events in the data run
     395
     396\end{fulllineitems}
     397
     398\index{next() (pyfact.RawData method)}
     399
     400\begin{fulllineitems}
     401\phantomsection\label{getting_started:pyfact.RawData.next}\pysiglinewithargsret{\bfcode{next}}{}{}
     402used by \_\_iter\_\_
     403
     404\end{fulllineitems}
     405
     406\index{next\_event() (pyfact.RawData method)}
     407
     408\begin{fulllineitems}
     409\phantomsection\label{getting_started:pyfact.RawData.next_event}\pysiglinewithargsret{\bfcode{next\_event}}{}{}
     410load the next event from disk and calibrate it
     411
     412\end{fulllineitems}
     413
     414\index{npix (pyfact.RawData attribute)}
     415
     416\begin{fulllineitems}
     417\phantomsection\label{getting_started:pyfact.RawData.npix}\pysigline{\bfcode{npix}}{}
     418number of pixels (should be 1440)
     419
     420\end{fulllineitems}
     421
     422\index{nroi (pyfact.RawData attribute)}
     423
     424\begin{fulllineitems}
     425\phantomsection\label{getting_started:pyfact.RawData.nroi}\pysigline{\bfcode{nroi}}{}
     426region of interest (number of DRS slices read)
     427
     428\end{fulllineitems}
     429
     430\index{start\_cells (pyfact.RawData attribute)}
     431
     432\begin{fulllineitems}
     433\phantomsection\label{getting_started:pyfact.RawData.start_cells}\pysigline{\bfcode{start\_cells}}{}
     434slice where drs readout started
     435
     436\end{fulllineitems}
     437
     438
     439\end{fulllineitems}
     440
     441
     442
     443\subsection{fnames of a data run}
     444\label{getting_started:fnames-of-a-data-run}\index{fnames (class in pyfact)}
     445
     446\begin{fulllineitems}
     447\phantomsection\label{getting_started:pyfact.fnames}\pysiglinewithargsret{\strong{class }\code{pyfact.}\bfcode{fnames}}{\emph{specifier={[}`012', `023', `2011', `11', `24'{]}, rpath='/scratch\_nfs/res/bsl/', zipped=True}}{}
     448organize file names of a FACT data run
     449\begin{description}
     450\item[{specifier}] \leavevmode{[}list of strings defined as:{]}
     451{[} `DRS calibration file', `Data file', `YYYY', `MM', `DD'{]}
     452
     453\end{description}
     454
     455rpath     : directory path for the results; YYYYMMDD will be appended to rpath
     456zipped    : use zipped (True) or unzipped (Data)
     457\index{info() (pyfact.fnames method)}
     458
     459\begin{fulllineitems}
     460\phantomsection\label{getting_started:pyfact.fnames.info}\pysiglinewithargsret{\bfcode{info}}{}{}
     461print complete filenames
     462
     463\end{fulllineitems}
     464
     465\index{make() (pyfact.fnames method)}
     466
     467\begin{fulllineitems}
     468\phantomsection\label{getting_started:pyfact.fnames.make}\pysiglinewithargsret{\bfcode{make}}{\emph{specifier}, \emph{rpath}, \emph{zipped}}{}
     469create (make) the filenames
     470
     471names   : dictionary of filenames, tags \{ `data', `drscal', `results' \}
     472data    : name of the data file
     473drscal  : name of the drs calibration file
     474results : radikal of file name(s) for results (to be completed  by suffixes)
     475
     476\end{fulllineitems}
     477
     478
     479\end{fulllineitems}
     480
     481
    137482
    138483\chapter{Classes}
    … …  
    146491
    147492\subsection{fnames of a data run}
    148 \label{classes:fnames-of-a-data-run}
     493\label{classes:fnames-of-a-data-run}\index{fnames (class in pyfact)}
     494
     495\begin{fulllineitems}
     496\phantomsection\label{classes:pyfact.fnames}\pysiglinewithargsret{\strong{class }\code{pyfact.}\bfcode{fnames}}{\emph{specifier={[}`012', `023', `2011', `11', `24'{]}, rpath='/scratch\_nfs/res/bsl/', zipped=True}}{}
     497organize file names of a FACT data run
     498\begin{description}
     499\item[{specifier}] \leavevmode{[}list of strings defined as:{]}
     500{[} `DRS calibration file', `Data file', `YYYY', `MM', `DD'{]}
     501
     502\end{description}
     503
     504rpath     : directory path for the results; YYYYMMDD will be appended to rpath
     505zipped    : use zipped (True) or unzipped (Data)
     506\index{info() (pyfact.fnames method)}
     507
     508\begin{fulllineitems}
     509\phantomsection\label{classes:pyfact.fnames.info}\pysiglinewithargsret{\bfcode{info}}{}{}
     510print complete filenames
     511
     512\end{fulllineitems}
     513
     514\index{make() (pyfact.fnames method)}
     515
     516\begin{fulllineitems}
     517\phantomsection\label{classes:pyfact.fnames.make}\pysiglinewithargsret{\bfcode{make}}{\emph{specifier}, \emph{rpath}, \emph{zipped}}{}
     518create (make) the filenames
     519
     520names   : dictionary of filenames, tags \{ `data', `drscal', `results' \}
     521data    : name of the data file
     522drscal  : name of the drs calibration file
     523results : radikal of file name(s) for results (to be completed  by suffixes)
     524
     525\end{fulllineitems}
     526
     527
     528\end{fulllineitems}
     529
     530
     531
     532\section{FIR filter functions}
     533\label{classes:fir-filter-functions}
    149534
    150535\chapter{Examples}

  • fact/tools/pyscripts/doc/_build/latex/pyfact.toc

    r13151 r13324  
    11\select@language {english}
    22\contentsline {chapter}{\numberline {1}Introduction}{3}{chapter.1}
    3 \contentsline {chapter}{\numberline {2}Classes}{5}{chapter.2}
    4 \contentsline {section}{\numberline {2.1}pyfact.py}{5}{section.2.1}
    5 \contentsline {subsection}{\numberline {2.1.1}rawdata access}{5}{subsection.2.1.1}
    6 \contentsline {subsection}{\numberline {2.1.2}fnames of a data run}{5}{subsection.2.1.2}
    7 \contentsline {chapter}{\numberline {3}Examples}{7}{chapter.3}
    8 \contentsline {section}{\numberline {3.1}calling a system command}{7}{section.3.1}
    9 \contentsline {chapter}{\numberline {4}phyton in FACT}{9}{chapter.4}
    10 \contentsline {chapter}{\numberline {5}Indices and tables}{11}{chapter.5}
     3\contentsline {section}{\numberline {1.1}Python version and modules used}{3}{section.1.1}
     4\contentsline {section}{\numberline {1.2}Style guide and coding conventions}{3}{section.1.2}
     5\contentsline {chapter}{\numberline {2}Getting Started}{5}{chapter.2}
     6\contentsline {section}{\numberline {2.1}1. Important links}{5}{section.2.1}
     7\contentsline {section}{\numberline {2.2}2. Environment variables}{5}{section.2.2}
     8\contentsline {section}{\numberline {2.3}3. Check out the repository}{6}{section.2.3}
     9\contentsline {section}{\numberline {2.4}4. Create pyfits\_h.so library}{6}{section.2.4}
     10\contentsline {section}{\numberline {2.5}5. Run examples}{6}{section.2.5}
     11\contentsline {chapter}{\numberline {3}Classes}{7}{chapter.3}
     12\contentsline {section}{\numberline {3.1}pyfact.py}{7}{section.3.1}
     13\contentsline {subsection}{\numberline {3.1.1}rawdata access}{7}{subsection.3.1.1}
     14\contentsline {subsection}{\numberline {3.1.2}fnames of a data run}{8}{subsection.3.1.2}
     15\contentsline {chapter}{\numberline {4}Classes}{9}{chapter.4}
     16\contentsline {section}{\numberline {4.1}pyfact.py}{9}{section.4.1}
     17\contentsline {subsection}{\numberline {4.1.1}rawdata access}{9}{subsection.4.1.1}
     18\contentsline {subsection}{\numberline {4.1.2}fnames of a data run}{9}{subsection.4.1.2}
     19\contentsline {section}{\numberline {4.2}FIR filter functions}{9}{section.4.2}
     20\contentsline {chapter}{\numberline {5}Examples}{11}{chapter.5}
     21\contentsline {section}{\numberline {5.1}calling a system command}{11}{section.5.1}
     22\contentsline {chapter}{\numberline {6}phyton in FACT}{13}{chapter.6}
     23\contentsline {chapter}{\numberline {7}Indices and tables}{15}{chapter.7}
     24\contentsline {chapter}{Index}{17}{section*.24}

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

    r13316 r13324  
    3939    * pyscript/tools
    4040    * pyscripts/ecamples
    41     * py
    4241
    4342the absolute path depends on where you have checked (or will check) out the pyscripts repository
    … …  
    4746svn co https://fact.isdc.unige.ch/svn/fact/tools/pyscripts/
    4847
    49 4. Create pyfits library
     484. Create pyfits_h.so library
    5049========================
    51 FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the default tool:
     50FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the existing tools:
    5251
    53 `pyfits <http://www.stsci.edu/institute/software_hardware/pyfits>`.
     52`pyfits <http://www.stsci.edu/institute/software_hardware/pyfits>` which uses `cfitsio <http://heasarc.gsfc.nasa.gov/fitsio/>`_.
    5453
    55 To 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
     54To mitigate this problem a C++ class defined in fits.h [#f1]_ is used. A simple possibility to create an interface of this C++ class is to use ROOT and later to import it using the
     55`pyroot <http://root.cern.ch/drupal/category/package-context/pyroot>`_ module.
    5656
    57 `pyroot http://root.cern.ch/drupal/category/package-context/pyroot>` module.
     57got to the directory: pyscripts/pyfact
    5858
    5959simple::
    6060
    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)
     61  [lusterma@isdc-cn02 pyfact]$ root
     62  ROOT 5.28/00 (trunk@37585, Dec 14 2010, 15:20:27 on linuxx8664gcc)
    6363  CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
    6464  Type ? for help. Commands must be C++ statements.
    6565  Enclose multiple statements between { }.
     66
    6667  root [0] .L fits.h++
    67   Info in <TUnixSystem::ACLiC>: creating shared library /home/luster/py/./fits_h.so
     68  Info in <TUnixSystem::ACLiC>: creating shared library /home_nfs/isdc/lusterma/pyscripts/pyfact/./fits_h.so
    6869  root [1]
    6970
     71This might not work for whatenver reason then it should be done like this::
    7072
     73  $rootcint -f my_dict.C -c fits.h izstream.h
     74  $g++ -fPIC -c -I$ROOTSYS/include my_dict.C -o my_dict.o
     75  $g++ -o fits_h.so -shared my_dict.o
     76
     77Now you can check if the reading rawdata is working:
     78
     79$ ./pyfact.py
     80
     81this should print some data from a few events
    7182
    72835. Run examples
    … …  
    93104
    94105
     106.. rubric:: Footnotes
     107.. [#f1] fits.h (here named pyfits.h) is part of MARS and was written by T.Bretz, it was added to this repository for convienience
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