This is the source code repository for the python routines employed to automatically reduce and analyze the data from the MEGARA IFU instrument at GTC, including the method developed to estimate the random uncertainties associated to the emission line properties.
This software was created by C. Cabello as part of her thesis work, developed under the supervision of N. Cardiel and J. Gallego, at the Departamento de Física de la Tierra y Astrofísica of the Universidad Complutense de Madrid.
The program is first mentioned in Cabello, C. - PhD Thesis 2023, and Cabello et al. 2024 in prep.
Maintainer: Cristina Cabello, [email protected]
Webpage (source): https://github.com/criscabe/MEGARA
1_simulations_reduction.py: This file software has been employed to add Gaussian noise to the images taken with the MEGARA IFU instrument at GTC and automatically reduce the simulated data.
The help function will provide information about the required and optional arguments:
criscabe:~/MEGARA/N/ $ python 1_simulations_reduction.py -h
usage: 1_simulations_reduction.py [-h] [--stage0] [--stage1] [--stage2]
[--stage3] [--stage4] [--stage5] [--stage6]
[--stage7] [--stage8] [--all]
nsimul initializer VPH target OB
Run MEGARA DRP
positional arguments:
nsimul Number of simulations
initializer Initializer of simulations
VPH VPH used during the observations
target Name of the target
OB Observing Block
optional arguments:
-h, --help show this help message and exit
--stage0 Run step 0: BIAS
--stage1 Run step 1: TraceMap
--stage2 Run step 2: ModelMap
--stage3 Run step 3: Wavelength calibration
--stage4 Run step 4: FiberFlat
--stage5 Run step 5: TwilightFlat
--stage6 Run step 6: LCB adquisition
--stage7 Run step 7: Standard Star
--stage8 Run step 8: Reduce LCB
--all Run all the steps of MEGARA DRPThe following command will run all the steps of MEGARA DRP performing 100 simulations on data taken with the LRR VPH:
$ python 1_simulations_reduction.py 100 0 LRR target_name ob1 --allThe user must replace 'target_name' for the name of the target, and 'ob1' for the observing block ID that is being reduced in the MEGARA DRP step 8.
In case the user is interested in running a particular step of MEGARA DRP (e.g., step 3: wavelength calibration), it should be specified as:
$ python 1_simulations_reduction.py 100 0 LRR target_name ob1 --stage32_lines_analysis.py: This file software has been employed to analyze simulated reduced MEGARA data (RSS images) and generate the maps with the emission-line properties.
The help function will provide information about the required and optional arguments:
criscabe:~/MEGARA/ $ python 2_lines_analysis.py -h
usage: 2_lines_analysis.py [-h] [-LINE LINE] [--analyze] [--plots]
[-f {0,1,2}] [-S S] [-w W] [-z Z] [-LW1 LW1]
[-LW2 LW2] [-CW1 CW1] [-CW2 CW2] [-PW1 PW1]
[-PW2 PW2]
nsimul initializer VPH target
ANALYZE the RSS images
positional arguments:
nsimul Number of simulations
initializer Initializer of simulations
VPH VPH used during the observations
target Name of the target
optional arguments:
-h, --help show this help message and exit
-LINE LINE Name of the emission line
--analyze Analyze the corresponding line
--plots Create and save the figures
-f {0,1,2} Fitting function (0=gauss_hermite, 1=gauss, 2=double_gauss)
-S S Mininum Signal-to-noise ratio in each spaxel
-w W Central rest-frame wavelength of the emission line (AA)
-z Z Redshift of the target
-LW1 LW1 Lower rest-frame wavelength (AA) for the emission-line fitting
-LW2 LW2 Upper rest-frame wavelength (AA) for the emission-line fitting
-CW1 CW1 Lower rest-frame wavelength (AA) for the continuum fitting
-CW2 CW2 Upper rest-frame wavelength (AA) for the continuum fitting
-PW1 PW1 Lower (observed) wavelength (AA) for the plot
-PW2 PW2 Upper (observed) wavelength (AA) for the plot
The positional arguments remain the same as in 1_simulations_reduction.py. In addition, the user must specify the name and central wavelength of the emission line to be analyzed, the redshift of the target, as well as different parameters to control the wavelenght range of the fit.
The following command shows an example of the Hα emission-line analysis (100 simulated images, LRR VPH, target at z=0.003465):
$ python 2_lines_analysis.py 100 0 LRR target_name -LINE Halpha --analyze
-f 0 -S 10 -w 6563 -z 0.003465 -LW1 6553 -LW2 6573 -CW1 6495 -CW2 6540 -PW1 6500 -PW2 6650The parameter 'plots' allows the user to create and save the maps of the emission-line properties (S/N, Flux, EW, velocity, velocity dispersion). The scale of each figure will be setted in the terminal during the first iteration of the simulated images.
- Warning: to avoid the generation of multiple (and maybe unnecessary) images in this step, we recommend to reduce the number of simulations to 2-5.
$ python 2_lines_analysis.py 5 0 LRR target_name -LINE Halpha --plots3_uncertainties.py: This file software has been employed to compute the median of the simulations, the residuals (real data - median of the simulations), and the random uncertainties of different parameters derived from the MEGARA data.
The help function will provide information about the required and optional arguments:
criscabe:~/MEGARA/ $ python 3_uncertainties.py -h
usage: 3_uncertainties.py [-h] [-LINE LINE] [--median] [--residuals]
[--uncertainties] [--plots]
target
Compute the median, residuals, and uncertainties of different parameters
positional arguments:
target Name of the target
optional arguments:
-h, --help show this help message and exit
-LINE LINE Name of the emission line
--median Compute the median values of the simulations
--residuals Compute the residuals (real values - median of simulations)
--uncertainties Compute the random uncertainties
--plots Create and save the figuresTo run this script, the user must indicate the name of the target and the emission line of interest. Then, it offers several options: compute the median values of the simulations, the residuals, or the uncertainties (or any/all these options).
As an example, the following command will compute the random uncertainties of several parameters derived from the Hα emission line and save the 2D maps:
$ python 3_uncertainties.py target_name -LINE Halpha --uncertainties --plots