[[TOC]]
This page is far from being complete. While I give an introduction to my students, I try to write down a few notes, hoping that it can serve as a small introduction and help future students. 

== Analysis Steps ==

To analyse data, you should be familiar with the following steps: 

=== technical information ===
 set ROOT environment::
   ''source /path_to_ROOT/bin/thisroot.sh'' (you can put this into your .bashrc file)
 how to start a macro::
   go to Mars directory[[BR]]
   start ''root''[[BR]]
   execute ''.x path/macro.C("with maybe some variable", 2)'' [[BR]]
   example ''.x fact/analysis/star.C("/path/sequencefile.txt",5.3,3.2,"inpath","outpath")'' [[BR]]
   or directly ''root -b -q fact/analysis/star.C\(\"/path/sequencefile.txt\"\,5.3\,3.2\,\"inpath\"\,\"outpath\"\)'' (-b for without display)
 rawdata in wü:: /fact/raw/YYYY/MM/DD/YYYYMMDD_FFF.fits.fz
 callisto in Wü:: /scratch/local/dorner/data.2013.05.11/callisto/YYYY/MM/DD/ (temporary path, will be changed)
 star in Wü:: /scratch/local/dorner/data.2013.05.11/star/YYYY/MM/DD/ (temporary path, will be changed)
 sequences in Wü:: /scratch/local/dorner/sequences/YYYY/MM/DD/ (temporary path, will be changed)

=== callisto === 
 what is done?:: 
   calculation of calibration constants, extraction of signal, calibration of data
 macro::
   Mars/fact/analysis/callisto.C
 input:: 
  sequence file, rawdata (files found with information in sequence file
 output:: 
  YYYYMMDD_SSS-calibration.root (plots), YYYYMMDD_FFF_C.root (one per run)

=== star ===
 what is done?::
  image cleaning, calculation of image parameter
 macro::
  Mars/fact/analysis/star.C
 input::
  sequence file, callisto output
 output:: 
  YYYYMMDD_SSS-images.root (plots), YYYYMMDD_FFF_I.root (one per run)

=== merpp ===
 what is done?::
  merge auxiliary information to data 
 macro::
  Mars/fact/analysis/merpp.C
 input::
  sequence file, YYYYMMDD_FFF_I.root
 output:: 
  YYYYMMDD_FFF_I.root (one per run)

=== ganymed === 
 what is done?::
   background suppression, calculation of excess(, energy reconstruction)
 macro::
   Mars/fact/analysis/ganymed.C
 input::
  dataset file, star output (_I.root files)
 output::
  name-analysis.root (result, eventlist after cuts, plots), name-summary.root (event list before cuts)

=== lightcurve === 
 what is done?::
   calculation of excess rate 
 macro::
   Mars/fact/analysis/lightcurve.C
 input::
   several datasets or information from DB


=== additional information ===

 sequence::
  a sequence of runs, consisting of: pedestal run, light pulser run, one or more data runs
 dataset::
  a collection of data runs
 YYYYMMDD:: night (date of sunset is used)
 FFF:: file number (starts with 0 every night
 SSS:: sequence number (number of first run in sequence)

=== dataset file ===
a dataset file is a simple text file containing one or more lines as e.g. 

/path_to_imageparameter_file YYYYMMDD_FFF_I.root

be aware that there is a space between the path and the file name

in the filename wildcards can be used

=== exercises A ===

1. run callisto for a sequence (check the macro to find out how to call the macro)
2. run star for the same sequence
3. run merpp for the same sequence
4. write a dataset file
5. run ganymed for this dataset file

== Data Check == 

Understanding the data and selecting only data with good quality is very important.

=== Available Information === 

what information does exist to check the data quality? 

* information from the rawdata
* information from the auxiliary data
* callisto output
* star output
* ganymed output

=== List of Tools ===  

* FACT++/viewer 
* topcat
* FACT++/fitsdump
* https://www.fact-project.org/viewer/
* http://www.astro.uni-wuerzburg.de/wikineu/index.php/How_to_plot_image_parameters
* Mars/showplot
* https://www.fact-project.org/run_db/db/fact_runinfo.php
* https://www.fact-project.org/run_db/db/run_comment.php
* https://www.fact-project.org/datacheck/dch.php (needs login)
* https://www.fact-project.org/logbook/
* https://www.fact-project.org/dch/scheduling.php

=== exercises B === 

1. search for some runs affected by lidar
1. compare star output plots for data affected by lidar with data not affected by lidar
1. plot image parameters for data affected and data not affected by lidar, as e.g. in https://www.fact-project.org/logbook/showthread.php?tid=1291
2. redo exercise A5 after selecting only runs with good quality

== Understanding the Data == 

=== exercise C1 ===

rate scan plot

plot of rates vs time (give time range) 

a) explain how the trigger threshold is determined
b) explain the structure in the plot rate-vs-time: where do the humps come from? where does the general decline come from? 

hints: use visibility tool, 2D threshold plot