| 1 | ===============
|
|---|
| 2 | Getting Started
|
|---|
| 3 | ===============
|
|---|
| 4 |
|
|---|
| 5 | 1) Get an account at the FACT data center at ISDC
|
|---|
| 6 | 2) Setup your environment variables
|
|---|
| 7 | 3) Checkout the pyfact software repository
|
|---|
| 8 | 4) Try a few examples
|
|---|
| 9 |
|
|---|
| 10 | 1. 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 |
|
|---|
| 28 | 2. Environment variables
|
|---|
| 29 | ========================
|
|---|
| 30 | set the following env variables depending on the SHELL you are using, for instance in .bashrc or .tcshrc
|
|---|
| 31 |
|
|---|
| 32 |
|
|---|
| 33 | * **ROOTSYS**: /swdev_nfs/root_v5.28.00
|
|---|
| 34 | * **PATH**: add $ROOTSYS/bin
|
|---|
| 35 | * **LD_LIBRARY_PATH**: add $ROOTSYS/lib
|
|---|
| 36 | * **PYTHONPATH**: $ROOTSYS/lib
|
|---|
| 37 | * **PYTHONPATH**: add all directories where python should search for modules. At least:
|
|---|
| 38 | * pyscripts/pyfact
|
|---|
| 39 | * **LD_LIBRARY_PATH**: add the path to pyfits_h.so
|
|---|
| 40 | * pyscripts/pyfact in many cases
|
|---|
| 41 |
|
|---|
| 42 | the absolute path depends on where you have checked (or will check) out the pyscripts repository
|
|---|
| 43 |
|
|---|
| 44 | example .bashrc::
|
|---|
| 45 |
|
|---|
| 46 | # this is just a convenient shortcut
|
|---|
| 47 | export MY_PYFACT=/home_nfs/isdc/neise/py/pyscripts/pyfact
|
|---|
| 48 |
|
|---|
| 49 | # this is needed for ROOT only
|
|---|
| 50 | export ROOTSYS=/swdev_nfs/root_v5.28.00
|
|---|
| 51 | export PATH=$ROOTSYS/bin:$PATH
|
|---|
| 52 | export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
|
|---|
| 53 |
|
|---|
| 54 | # this is needed for Python to find the pyfact classes and PyROOT
|
|---|
| 55 | export PYTHONPATH=$MY_PYFACT
|
|---|
| 56 | export PYTHONPATH=$ROOTSYS/lib:$PYTHONPATH
|
|---|
| 57 |
|
|---|
| 58 | #this is one of many possible ways, for ROOT to find pyfits_h.so
|
|---|
| 59 | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MY_PYFACT
|
|---|
| 60 |
|
|---|
| 61 |
|
|---|
| 62 | 3. Check out the repository
|
|---|
| 63 | ===========================
|
|---|
| 64 | svn co https://fact.isdc.unige.ch/svn/fact/tools/pyscripts py
|
|---|
| 65 |
|
|---|
| 66 |
|
|---|
| 67 | 4. Create the needed *.so libs @ ISDC
|
|---|
| 68 | ======================================
|
|---|
| 69 |
|
|---|
| 70 | FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the existing tools:
|
|---|
| 71 |
|
|---|
| 72 | `pyfits <http://www.stsci.edu/institute/software_hardware/pyfits>` which uses `cfitsio <http://heasarc.gsfc.nasa.gov/fitsio/>`_.
|
|---|
| 73 |
|
|---|
| 74 | To 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
|
|---|
| 75 | `pyroot <http://root.cern.ch/drupal/category/package-context/pyroot>`_ module.
|
|---|
| 76 |
|
|---|
| 77 | example::
|
|---|
| 78 |
|
|---|
| 79 | neise@isdc-viewer00:~/py/pyfact$ root -l -q makelibs.C
|
|---|
| 80 | root [0]
|
|---|
| 81 | Processing makelibs.C...
|
|---|
| 82 | Info in <TUnixSystem::ACLiC>: creating shared library /home_nfs/isdc/neise/test_py/pyfact/./izstream_h.so
|
|---|
| 83 | Info in <TUnixSystem::ACLiC>: creating shared library /home_nfs/isdc/neise/test_py/pyfact/./factfits_h.so
|
|---|
| 84 | [... quite some warnings ...]
|
|---|
| 85 |
|
|---|
| 86 | neise@isdc-viewer00:~/py/pyfact$ ls *.so
|
|---|
| 87 | calfactfits_h.so factfits_h.so izstream_h.so
|
|---|
| 88 |
|
|---|
| 89 | 5. Test if everything is running
|
|---|
| 90 | =================================
|
|---|
| 91 |
|
|---|
| 92 | each module in pyfact should have some test methods implemented.
|
|---|
| 93 | In case one would like to test the module *pyfact*, one can simple execute
|
|---|
| 94 | the module source file.
|
|---|
| 95 |
|
|---|
| 96 | Just test if everything is running like this::
|
|---|
| 97 |
|
|---|
| 98 | neise@isdc-viewer00:~/py/pyfact$ pyfact.py
|
|---|
| 99 | showing test of iterator of RawData class
|
|---|
| 100 | in order to test the SlowData classe please use: ./pyfact.py fits-file-name
|
|---|
| 101 | ev 1 data[0,0] = -7.68806196438 start_cell[0] = 426 trigger type = 416
|
|---|
| 102 | ev 2 data[0,0] = 0.792280672486 start_cell[0] = 437 trigger type = 416
|
|---|
| 103 | ev 3 data[0,0] = 54.9490855517 start_cell[0] = 449 trigger type = 416
|
|---|
| 104 | ev 4 data[0,0] = 3.9482592671 start_cell[0] = 461 trigger type = 416
|
|---|
| 105 | ev 5 data[0,0] = -66.4329317281 start_cell[0] = 474 trigger type = 416
|
|---|
| 106 | ev 6 data[0,0] = 8.2917625181 start_cell[0] = 485 trigger type = 416
|
|---|
| 107 | ev 7 data[0,0] = -41.6565116079 start_cell[0] = 498 trigger type = 416
|
|---|
| 108 | ev 8 data[0,0] = 33.4668984163 start_cell[0] = 509 trigger type = 416
|
|---|
| 109 | ev 9 data[0,0] = -28.520090549 start_cell[0] = 522 trigger type = 416
|
|---|
| 110 | ev 10 data[0,0] = -20.4925692795 start_cell[0] = 533 trigger type = 416
|
|---|
| 111 |
|
|---|
| 112 | This should work at ISDC only, but if it does not work, please ask somebody for help.
|
|---|
| 113 |
|
|---|
| 114 |
|
|---|
| 115 | 6. Old way of creating the so files
|
|---|
| 116 | ===================================
|
|---|
| 117 |
|
|---|
| 118 | -----------This is a depricated section---------------
|
|---|
| 119 |
|
|---|
| 120 | FACT data are stored in (gzipped) fits files, but the data files are too large to be read by the existing tools:
|
|---|
| 121 |
|
|---|
| 122 | `pyfits <http://www.stsci.edu/institute/software_hardware/pyfits>` which uses `cfitsio <http://heasarc.gsfc.nasa.gov/fitsio/>`_.
|
|---|
| 123 |
|
|---|
| 124 | To 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
|
|---|
| 125 | `pyroot <http://root.cern.ch/drupal/category/package-context/pyroot>`_ module.
|
|---|
| 126 |
|
|---|
| 127 | example::
|
|---|
| 128 |
|
|---|
| 129 | neise@isdc-viewer00:~/py/pyscripts/pyfact$ root
|
|---|
| 130 | ROOT 5.28/00 (trunk@37585, Dec 14 2010, 15:20:27 on linuxx8664gcc)
|
|---|
| 131 | CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
|
|---|
| 132 | Type ? for help. Commands must be C++ statements.
|
|---|
| 133 | Enclose multiple statements between { }.
|
|---|
| 134 | root [0] .L pyfits.h++
|
|---|
| 135 | Info in <TUnixSystem::ACLiC>: creating shared library /home_nfs/isdc/neise/py/pyscripts/pyfact/./pyfits_h.so
|
|---|
| 136 | In file included from /home_nfs/isdc/neise/py/pyscripts/pyfact/pyfits_h_ACLiC_dict.h:34,
|
|---|
| 137 | from /home_nfs/isdc/neise/py/pyscripts/pyfact/pyfits_h_ACLiC_dict.cxx:17:
|
|---|
| 138 | /home_nfs/isdc/neise/py/pyscripts/pyfact/./pyfits.h: In member function »size_t std::fits::Table::GetN(const std::string&) const«:
|
|---|
| 139 | /home_nfs/isdc/neise/py/pyscripts/pyfact/./pyfits.h:442: Warnung: Deklaration von »it« überdeckt einen vorhergehenden lokalen Bezeichner
|
|---|
| 140 | /home_nfs/isdc/neise/py/pyscripts/pyfact/./pyfits.h:437: Warnung: Verdeckte Deklaration ist hier
|
|---|
| 141 | root [1] .q
|
|---|
| 142 |
|
|---|
| 143 | check if it worked::
|
|---|
| 144 |
|
|---|
| 145 | neise@isdc-viewer00:~/py/pyscripts/pyfact$ ls pyfits*
|
|---|
| 146 | pyfits.h pyfits_h.d pyfits_h.so
|
|---|
| 147 |
|
|---|
| 148 |
|
|---|
| 149 | This might not work for whatenver reason then you can try this::
|
|---|
| 150 |
|
|---|
| 151 | $rootcint -f my_dict.C -c pyfits.h izstream.h
|
|---|
| 152 | $g++ -fPIC -c -I$ROOTSYS/include my_dict.C -o my_dict.o
|
|---|
| 153 | $g++ -o pyfits_h.so -shared my_dict.o
|
|---|
| 154 |
|
|---|
| 155 |
|
|---|
| 156 | In case one uses root 5.32 instead of root 5.28, one should do::
|
|---|
| 157 |
|
|---|
| 158 | neise@isdc-viewer00:~/py/pyscripts/pyfact$ root -b
|
|---|
| 159 | *******************************************
|
|---|
| 160 | * *
|
|---|
| 161 | * W E L C O M E to R O O T *
|
|---|
| 162 | * *
|
|---|
| 163 | * Version 5.32/00 2 December 2011 *
|
|---|
| 164 | * *
|
|---|
| 165 | * You are welcome to visit our Web site *
|
|---|
| 166 | * http://root.cern.ch *
|
|---|
| 167 | * *
|
|---|
| 168 | *******************************************
|
|---|
| 169 |
|
|---|
| 170 | ROOT 5.32/00 (tags/v5-32-00@42375, Dec 02 2011, 12:42:25 on linuxx8664gcc)
|
|---|
| 171 |
|
|---|
| 172 | CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
|
|---|
| 173 | Type ? for help. Commands must be C++ statements.
|
|---|
| 174 | Enclose multiple statements between { }.
|
|---|
| 175 | root [0] gSystem->Load("/usr/lib64/libz.so")
|
|---|
| 176 | (int)0
|
|---|
| 177 | root [1] .L pyfits.h++
|
|---|
| 178 | Info in <TUnixSystem::ACLiC>: creating shared library /home_nfs/isdc/neise/py/pyscripts/pyfact/./pyfits_h.so
|
|---|
| 179 | In file included from /home_nfs/isdc/neise/py/pyscripts/pyfact/pyfits_h_ACLiC_dict.h:34,
|
|---|
| 180 | from /home_nfs/isdc/neise/py/pyscripts/pyfact/pyfits_h_ACLiC_dict.cxx:17:
|
|---|
| 181 | /home_nfs/isdc/neise/py/pyscripts/pyfact/./pyfits.h: In member function »size_t std::fits::Table::GetN(const std::string&) const«:
|
|---|
| 182 | /home_nfs/isdc/neise/py/pyscripts/pyfact/./pyfits.h:442: Warnung: Deklaration von »it« überdeckt einen vorhergehenden lokalen Bezeichner
|
|---|
| 183 | /home_nfs/isdc/neise/py/pyscripts/pyfact/./pyfits.h:437: Warnung: Verdeckte Deklaration ist hier
|
|---|
| 184 | root [2] .q
|
|---|
| 185 | neise@isdc-viewer00:~/py/pyscripts/pyfact$ ls pyfits*
|
|---|
| 186 | pyfits.h pyfits_h.d pyfits_h.so
|
|---|
| 187 |
|
|---|
| 188 |
|
|---|
| 189 | .. rubric:: Footnotes
|
|---|
| 190 | .. [#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
|
|---|
