KOSMA GILDAS DLC

This repository contains a number of functions using the gildas-python library. This includes

• spline fitting of spectra
• despike spectra and storing result in an associated array
• storing the index and quality measured in python/pandas table
• plotting this python/pandas table with various groupings/histogram
• interactive plotting of data (show spectra on click)
• filter spectra using complex data base like queries
• add assocated line windows to spectra using a map as an input
• return FFT power at a given frequency
• plot FFT using numpy libraries

The test folder contains example of the commands.

Installation

Install with

sudo -E make  install

The script will add links to the class build directory, if this is installed by root you may have persmission problems and load it in class with

@kosma-init

after that the command type: help KOSMA
And you should see the newly availble commands. Type help to get the class help, or alternatively /help to get the python help.

Examples

More examples are in the tests folder

Generte spline catalog

@kosma-init

sic mkdir spline_output
! kalibrate -d /data/sofia/data/fits/science_data/cycle_07/20190607_CLARENCE_HFA_LFA/ -s 31064 -F *HFAV_PX04* -m curfit=simplex -m tau=1 -m feff=0.97 -m skyhotobs=1 -m skyhotfit=1  -m hotcoldcal=1 -m write_tsys=1 -n 9999999 -m calfactors=1 -m common=1 -c spline_test_data.kosma -m skydiff=20

define structure kosma
file in data/spline_test_data.kosma
find
set unit v
set win -300 -180 20 40
! 
! generate spline archive
!
set source *diff*
find
for i 1 to found
    get n
    ! smooth level is important
    ! baseline features can be below the noise and 
    ! 40 is a good value for the typical HFAV/LFAV baseline structure
    smooth box 40
    spline /fit_spline /store_spline_in_archive -
           /spline_archive_filename spline_output/spline_archive_'telescope'.pkl-
           /logging_level info -
           /output_plots_path spline_output/
next

! apply spline and write spectr
! write spectra
file out spline_output/spline_test_output.kosma single /overwrite
set source SGRB2_CMZ
set mode y -100 100
find
for i 1 to found
    get n
    write
    get
    despike
    KOSMA\SPLINE /scale_spline_from_archive /spline_archive_filename spline_output/spline_archive_'telescope'.pkl -
                 /logging_level info  /search_scan_range 25 -
                 /spline_fit_type scale_spline_and_offset -
                 /smoothness_of_fit_data 50 /plot save_best_with_pickle -
                 /output_plots_path spline_output/
    let ry kosma%spline_corrected
    mod source 'source[:8]'_SPL
    write
next

exit

generate index table from class and plotting values

    @kosma-init
    file in "tests/data/multiline.kosma"
    find
    set unit v
    set win 0 1
    get_index /get_rms /fft_focus_freq 170 /fft_focus_freq 20 /parameter tau_signal /reload
    ! plot rms and group by telescope
    plot_index /xaxis number /yaxis rms /group_by telescope
    ! plot rms and group by telescope
    plot_index /xaxis number /yaxis rms /group_by telescope /histogram 100
    ! for more options
    plot_index /help
    ! click on point to show spectra

python-gildas Background

see instructions here:

https://www.iram.fr/IRAMFR/GILDAS/doc/pdf/gildas-python.pdf

Anaconda problems

excrept

     - Conflict with Anaconda: when installed from the downloadable
       installer, Anaconda comes with a lot of development tools and
       libraries which override the default system ones, but not in a
       consistent way. This is proved to break software compilation and/or
       execution (Gildas and others). For example:
         astro: /home/user/anaconda/lib/libstdc++.so.6: version
                GLIBCXX_3.4.21 not found (required by /home/user/
                gildas-exe-jan17a/x86_64-ubuntu16.04-gfortran/lib/libatm.so)
       This happens because Anaconda gives precedence to its own libraries
       (duplicate but different versions of system ones) in the user's
       environment. There are several ways out of this issue:
         a) Install Anaconda from your OS repositories (instead of custom
            installation in the user account). This way, there should be
            a correct integration of Anaconda within the OS.
         b) Keep Anaconda in the user account, but "hide" it during Gildas
            installation and execution. In other words, you have to ensure
            that there is no reference to Anaconda installation paths in
            the environment variables $PATH and $LD_LIBRARY_PATH. Once this
            is done recompile, install, and try executing Gildas. If it
            runs fine, a permanent solution could be to use a shell
            function which loads Anaconda environment only when needed,
            e.g.
              function anaconda() {
                  export PATH=...
                  export LD_LIBRARY_PATH=...
                  anaconda
              }