This is the SDSS-V Local Volume Mapper (LVM) Data Analysis Pipeline (DAP) official repository.
The main and only script, lvm-dap, implements the Resolved Stellar Population method (Mejia-Narvaez+, in prep.). Instructions on how to run this code below.
usage: lvm-dap [-h] [--input-fmt INPUT_FMT] [--error-file ERROR_FILE] [--config-file CONFIG_FILE]
[--emission-lines-file EMISSION_LINES_FILE] [--mask-file MASK_FILE] [--sigma-gas SIGMA_GAS] [--ignore-gas]
[--rsp-nl-file RSP_NL_FILE] [--plot PLOT] [--flux-scale min max] [--w-range wmin wmax] [--w-range-nl wmin2 wmax2]
[--redshift input_redshift delta_redshift min_redshift max_redshift]
[--sigma input_sigma delta_sigma min_sigma max_sigma] [--AV input_AV delta_AV min_AV max_AV]
[--ext-curve {CCM,CAL}] [--RV RV] [--single-rsp] [--n-mc N_MC] [-o path] [-c] [-v] [-d]
spectrum-file rsp-file sigma-inst label
Run the spectral fitting procedure for the LVM
positional arguments:
spectrum-file input spectrum to fit
rsp-file the resolved stellar population basis
sigma-inst the standard deviation in wavelength of the Gaussian kernel to downgrade the resolution of the models to
match the observed spectrum. This is: sigma_inst^2 = sigma_obs^2 - sigma_mod^2
label string to label the current run
optional arguments:
-h, --help show this help message and exit
--input-fmt INPUT_FMT
the format of the input file. It can be either 'single' or 'rss'. Defaults to 'single'
--error-file ERROR_FILE
the error file
--config-file CONFIG_FILE
the configuration file used to set the parameters for the emission line fitting
--emission-lines-file EMISSION_LINES_FILE
file containing emission lines list
--mask-file MASK_FILE
the file listing the wavelength ranges to exclude during the fitting
--sigma-gas SIGMA_GAS
the guess velocity dispersion of the gas
--ignore-gas whether to ignore gas during the fitting or not. Defaults to False
--rsp-nl-file RSP_NL_FILE
the resolved stellar population *reduced* basis, for non-linear fitting
--plot PLOT whether to plot (1) or not (0, default) the fitting procedure. If 2, a plot of the result is store in a
file without display on screen
--flux-scale min max scale of the flux in the input spectrum
--w-range wmin wmax the wavelength range for the fitting procedure
--w-range-nl wmin2 wmax2
the wavelength range for the *non-linear* fitting procedure
--redshift input_redshift delta_redshift min_redshift max_redshift
the guess, step, minimum and maximum value for the redshift during the fitting
--sigma input_sigma delta_sigma min_sigma max_sigma
same as the redshift, but for the line-of-sight velocity dispersion
--AV input_AV delta_AV min_AV max_AV
same as the redshift, but for the dust extinction in the V-band
--ext-curve {CCM,CAL}
the extinction model to choose for the dust effects modelling. Choices are: ['CCM', 'CAL']
--RV RV total to selective extinction defined as: A_V / E(B-V). Default to 3.1
--single-rsp whether to fit a single stellar template to the target spectrum or not. Default to False
--n-mc N_MC number of MC realisations for the spectral fitting
-o path, --output-path path
path to the outputs. Defaults to '/disk-a/mejia/Research/UNAM/lvm-dap'
-c, --clear-outputs whether to remove or not a previous run with the same label (if present). Defaults to false
-v, --verbose if given, shows information about the progress of the script. Defaults to false.
-d, --debug debugging mode. Defaults to false.
We recommend installing in a virtual environment to avoid dependencies crashing. Some popular options are miniconda, venv, pipenv. We recommend venv.
Once you have created a virtual environment (if you chose to do so), simply run the following commands:
git clone https://github.com/sdss/lvmdap cd lvmdap pip install .
Then you need to download the content of the following directory in your computer:
http://ifs.astroscu.unam.mx/LVM/lvmdap_fitting-data/
We recommend you to define three environmental variables:
LVM_DAP : The directory in which the DAP is installed
LVM_DAP_CFG : The directory in which the configuration files are stored nominally ${LVM_DAP}/_legacy
LVM_DAP_RSP : The directory in which the RSP (stellar templates) are stored that would be the directory were is stored the content of the "lvmdap_fitting-data" URL e.g., export LVM_DAP_RSP="_fitting_data";
We will assume hereafter that LVM_DAP_RSP corresponds to "_fitting_data" for simplicity.
Go to the _examples directory and run the script fit_6109_strong.sh. If everything runs ok, the you have the required files to run the DAP.
If you want to run the notebooks in the testing notebooks section, you will need also to download the required data stored in google drive into the lvm-dap directory. Ask for access to [email protected].
If the installation went successfully (and you downloaded the data) your tree directory should look like:
├── dist
├── lvmdap
├── _examples
├── _fitting_data
├── _legacy
├── notebooks
├── poetry.lock
├── pyproject.toml
├── README.md
├── README.rst
├── run-fsps
├── run-fsps-MaNGA
├── run-fsps-MaNGA-v2
└── setup.py
and you should be able to run the following example:
lvm-dap _fitting-data/simulations/ssps/fsps-ssp-mist-miles-1p00000_0p00100gyr.txt _fitting-data/_basis_mastar_v2/stellar-basis-spectra-100.fits.gz 0.33283937056926377 1p00000_0p00100gyr --mask-file _fitting-data/_configs/MaNGA/mask_elines.txt --emission-lines-file _fitting-data/_configs/MaNGA/emission_lines_long_list.MaNGA --w-range 3600 10000 --w-range-nl 3600 4700 --redshift 0 0 0 0 --sigma 0 0 0 0 --AV 0 0 0 0
lvm-dap _fitting-data/simulations/ssps/fsps-ssp-mist-miles-1p00000_0p00100gyr.txt _fitting-data/_basis_mastar_v2/stellar-basis-spectra-100.fits.gz 0.33283937056926377 1p00000_0p00100gyr --mask-file _fitting-data/_configs/MaNGA/mask_elines.txt --emission-lines-file _fitting-data/_configs/MaNGA/emission_lines_long_list.MaNGA --w-range 3600 10000 --w-range-nl 3600 4700 --redshift 0 0 0 0 --sigma 0 0 0 0 --AV 0 0 0 0
which will produce the following output files:
1p00000_0p00100gyr 1p00000_0p00100gyr.autodetect.8400_9999.conf coeffs_1p00000_0p00100gyr
1p00000_0p00100gyr.autodetect.3600_5199.conf 1p00000_0p00100gyr.autodetect.auto_ssp_several.config elines_1p00000_0p00100gyr
1p00000_0p00100gyr.autodetect.5200_6799.conf 1p00000_0p00100gyr.autodetect.emission_lines.txt output.1p00000_0p00100gyr.fits.gz
1p00000_0p00100gyr.autodetect.6800_8399.conf 1p00000_0p00100gyr.autodetect.mask_elines.txt
You can get familiar with the full spectral analysis implemented in lvm-dap either running the notebooks in the notebooks folder or running the following example in the console:
lvm-dap CS.LMC_043.RSS.fits.gz _fitting-data/_basis_mastar_v2/stellar-basis-spectra-100.fits.gz 2.31 test --input-fmt rss --error-file e_CS.LMC_043.RSS.fits.gz --rsp-nl-file _fitting-data/_basis_mastar_v2/stellar-basis-spectra-5.fits.gz --w-range 4800 8000 --w-range-nl 4800 6000 --redshift 0.000875 0 -0.5 0.5 --sigma 0 0 0 350 --AV 0 0.01 0 1.6 --sigma-gas 3.7 --emission-lines-file _fitting-data/_configs/MaNGA/emission_lines_long_list.txt -c
This will analyse the MUSE-LMC pointing 43 in RSS format and produce the outputs in the same format as pyFIT3D.