This version is no longer being maintained - please use ACTIN2 instead.
Reads fits files from HARPS, HARPS-N and ESPRESSO spectrographs, rdb tables, and outputs user defined spectral activity indices (along with other relevant data).
- numpy
- matplotlib
- astropy
Clone the github repository to a directory of your choice and install via python setup.py install.
The config_lines.txt file is the line configuration file (instructions inside). This file is used to add line parameters to calculate any index as long as the line cores and bandpasses are inside the spectral range and spectral orders range (for 2d spectra) of the spectrograph. ACTIN will check this at start and give an error message if line parameters don't match the spectra.
Example of a config_lines.txt file:
Any index ind_id is calculated using the formula:
where Li and Rj are the fluxes in the ind_var main and reference lines, as indicated in the config file. ci and kj are the ln_c constants multiplied to each main and reference lines, respectively.
The description of the flux calculation is available in the Appendix A of Gomes da Silva et al. 2021.
I_CaII is the classical S-index Duncan et al. 1991 (not calibrated to the Mt. Wilson scale).
I_Ha16 and I_Ha06 are Halpha indices with 1.6 and 0.6 ang central bandpasses, respectively.
I_CaI is an activity insensitive line.
The line parameters for I_NaI, I_Ha16, and I_HeI come from Gomes da Silva et al. 2011.
The config file is available from the directory each OS uses for storing user data (*)
To get your path to the config file call actin without any arguments.
The file can be copied to another directory, modified, and then used by adding -cf dir/filename when running actin.
Usage:
actin -h [help] -f [files_list] -i [indices_list] -rv [rv_list] -cf [config_file] -s [output_path] -lp [output_path/same/show] -obj [object_name] -tl [target_list] -del [True/False] -t [test_file_type] -frc [True/False] -sp [True/False]
Arguments:
-h : Gives a description of the arguments available.
-f : List of files (formats S1D, S2D, e2ds, s1d, s1d_*_rv, or ADP) or rdb table(s) with headers obj, date, bjd, wave, flux, error_pixel (optional) to be read.
-i : List of indices to calculate. Indices ids must match the ones in the config file config_lines.txt.
-rv : List of RV values to calibrate wavelength. If not used, RVs are used from CCF files if available.
-cf : Path to configuration file. If not given the configuration file is read from installation directory To know installation directory call actin without arguments.
-s : Save output to .rdb table in specified path.
-lp : Save plots of the lines used to calculate the indices in the specified path. If same uses the path as specified in -s If show shows the plots without saving, useful to analyse the lines in one spectra.
-tl : List of stars to select from files.
-del : If True deletes any output file (data and logs only; only files that match current ACTIN call will be deleted) before reading the file list and saving output.
-obj : Object name to override the one from fits files in case the star has multiple names in different files (ex. Proxima, ProximaCen, Gl551). BE CAREFUL WHEN READING FILES FROM MULTIPLE STARS.
-t : Tests the program using the test files. Options are S2D, S1D, e2ds, s1d, adp or rdb to test these type of files.
-frc : Use fractional pixels if True (default), use integral pixels if False. If using False and calculating the I_CaII index as given in the original config_lines.txt file ACTIN will simulate the values of 's_raw' from the HARPS pipeline. Note however that this option might induce artificial variations in the indices due to the use of integral pixels in the bandpasses.
-sp : If True saves time-series and multi-plots to same directory as -s.
When running ACTIN for a second time with the same data on the same output directory use -del True otherwise the program will detect the same dates, ignore the measurements and not give any output.
When arguments accept lists, they can be given in the command line, e.g. -tl Gl273 Gl581, or from an ASCII file by using, e.g. -tl $(cat target_list.txt) where target_list.txt is a file with one column with the rows Gl273 and Gl581.
The example below will test the code using the test files provided in the package.
actin -t e2ds
Can also use the options s1d, S1D, S2D, ADP, and rdb to test on other file types.
actin -f ../fits/*/*e2ds_A.fits -i I_CaII I_Ha -s ../output -del True -tl Gl273 Gl581
This will execute ACTIN for all the subdirectories inside ../fits/ with files ending with e2ds_A.fits, calculate the indices I_CaII and I_Ha, output the data to ../output/star_names, and, before running the code, delete any output file that was previously there, in this case Gl273_HARPS_e2ds_data.rdb and Gl581_HARPS_e2ds_data.rdb. Only fits files belonging to the stars chosen in -tl will be read, in this case Gl273 and Gl581. Since -frc is True by default, fractional pixels will be used to compute the indices.
To use ACTIN as a module use import actin.actin as actin and then call the function:
actin.actin(files, calc_index=None, rv_in=None, config_file=None, save_output=False, ln_plts=False, obj_name=None, targ_list=None, del_out=False, frac=True, test=False, save_plots=False)
The arguments are the same as the ones described above (with just a slight different name in some cases).
Note that some arguments need to be given as lists when they accept lists, e.g. calc_index should be calc_index=['I_CaII'] even when using only one index.
The output rdb file has headers with data from the fits headers of the files (data headers) and data calculated by ACTIN (index headers).
Some of these headers might not be available if CCF files are not provided.
obj : Object targeted
instr : Instrument used
obs_date : Observation date
bjd : Barycentric Julian Date [days]
rv : Radial Velocity [m/s]
rv_err : Error of rv [m/s]
fwhm : Fullwidth-at-Half-Maximum of CCF profile [m/s]
fwhm_err : Error of fwhm [m/s]
cont : Contrast of CCF profile [%]
cont_err : Error of cont [%]
bis : Bisector inverse span of the CCF profile [m/s]
bis_err : Error of bis [m/s]
ccf_noise : CCF noise [m/s]
median_snr : Median signal-to-noise of spectrum
data_flg : Flag indicating if spectrum was not deblazed as ´noDeblazed´
bv : B-V colour
airmass : Airmass
exptime : Exposure time
These headers depend on the choices of indices to calculate.
<ind_id> is the identification of the index as in the configuration file.
<ln_id> is the identification of the line as in the configuration file.
I_<ind_id> : Value of the index <index_id>
I_<ind_id>_err : Error of index
I_<ind_id>_snr : Median signal-to-noise ratio of the orders used to calculate the index
I_<ind_id>_flg : Flag with value negFlux if negative values of flux found in the bandpasses of the index
I_<ind_id>_mfracneg : Maximum fraction of pixels with negative flux found in the bandpasses of the index
<ln_id>_npixels : Number of pixels (fractionary) inside the bandpass associated with the line <ind_ln>.
(*)
For OSX: ~/Library/Application Support/<AppName>
For Windows: C:\Documents and Settings\<User>\Application Data\Local Settings\<AppAuthor>\<AppName> or possibly C:\Documents and Settings\<User>\Application Data\<AppAuthor>\<AppName>
For Linux: ~/.local/share/<AppName>
If you use ACTIN in your research, please cite
Gomes da Silva, J. et al. JOSS 3, 667G (2018) (DOI: 10.21105/joss.00667)
or use the ready-made BibTex entry
@ARTICLE{2018JOSS....3..667G,
author = {{Gomes da Silva}, Jo{\~a}o and {Figueira}, Pedro and {Santos}, Nuno and
{Faria}, Jo{\~a}o},
title = "{ACTIN: A tool to calculate stellar activity indices}",
journal = {The Journal of Open Source Software},
keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics},
year = "2018",
month = "Nov",
volume = {3},
number = {31},
pages = {667},
doi = {10.21105/joss.00667},
archivePrefix = {arXiv},
eprint = {1811.11172},
primaryClass = {astro-ph.IM},
adsurl = {https://ui.adsabs.harvard.edu/abs/2018JOSS....3..667G},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
https://ui.adsabs.harvard.edu/abs/2018JOSS....3..667G/citations
For issues, bugs or if you would like to contribute to the development of this code contact Joao.Silva(at)astro.up.pt