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Local Volume Mapper Data Analysis Pipeline (LVM-DAP)

Introduction

The LVM-DAP is the official data analysis pipeline for the SDSS-V Local Volume Mapper (LVM). It provides routines and scripts to analyze and fit spectral data from LVM observations.

Main Scripts:

  • lvm-dap-conf: Fits FITS files in LVM format using a predefined configuration file.
  • lvm-dap-gen-out-mod: Generates output models from spectral data.
  • lvm-dap-sim: Simulates spectral data based on predefined parameters.
  • lvm-dap: Runs spectral fitting for LVM data.

Installation

Recommended Setup

It is recommended to install LVM-DAP in a virtual environment to avoid dependency issues. Options include:

Prerequisites

LVM-DAP depends on pyPipe3D (pyPipe3D, Lacerda et al. 2022). Install pyPipe3D before proceeding.

Installation Steps

# Create and activate a Conda environment
conda create --name lvmdap python=3.11
conda activate lvmdap

# Install required dependencies
conda install numpy=1.23.5  # Avoid compatibility issues
# OR
pip install numpy==1.23.5

# Install pyPipe3D
git clone https://gitlab.com/pipe3d/pyPipe3D.git
cd pyPipe3D
pip install . --user
cd ..

# Install LVM-DAP
git clone https://github.com/sdss/lvmdap.git
cd lvmdap
pip install . --user

Additional Data

Download and store the required fitting data from: Download LVM fitting data

Environmental Variables

Define the following environment variables:

export LVM_DAP="/path/to/lvmdap"  # LVM-DAP installation directory
export LVM_DAP_CFG="$LVM_DAP/_legacy"  # Configuration files directory
export LVM_DAP_RSP="_fitting_data"  # Stellar templates directory

Directory Structure

After a successful installation, the directory should be structured as follows:

├── dist
├── lvmdap
├── _examples
├── _fitting_data
├── _legacy    
├── notebooks
├── poetry.lock
├── pyproject.toml
├── README.md
├── README.rst
└── setup.py

Running Tests

Test 1: Running Example Script (deprecated, just for testing)

cd _examples/
chmod +x fit_6109_strong.sh
./fit_6109_strong.sh

Test 2: Running DAP on a FITS File

  1. Download the example FITS file:
  2. Place it inside _examples/data/
  3. Run the following command:
lvm-dap-conf _examples/data/lvmSFrame-example.fits.gz dap-4-example _legacy/lvm-dap_fast.yaml

Usage

lvm-dap-conf Command

Example YAML Configuration

# output directory
 output_path: "/disk-a/sanchez/LVM/LVM/ver_231113/output_dap/"
# LVM-DAP software directory  
 lvmdap_dir: "/home/sanchez/sda2/code/python/lvmdap"
# rsp-file for the full stellar decomposition 
 rsp-file: "../_fitting-data/_basis-binned_mastar/stellar-basis-spectra-binned-4-mastar.fits.gz"
# rsp-file for the derivation of the non-linear (NL) parameters (vel, vel_disp, Av)
 rsp-nl-file: "../_fitting-data/_basis-binned_mastar/stellar-basis-spectra-binned-4-mastar.fits.gz"
# approximate instrumental resolution in AA
 sigma-inst: 1
# input format for fitting the data (deprecated)
input-fmt: rss
# redshift range (or velocity) to explore in the NL
 redshift:
  -  0.0      # guess
  -  0.0001   # delta
  -  -0.0003  # min
  -  0.0003   # max
# velocity dispersion in km/s range to explore in the NL
 sigma:
  - 1  # guess
  - 5  # delta
  - 1  # min
  - 15 # max
# Dust attenuation in the V-band
 AV:
  - 0    # guess
  - 0.3  # delta
  - 0.0  # min
  - 1.5  # max
# list of strong emission lines to analyze
 emission-lines-file: ../_legacy/emission_lines_strong.LVM 
# emission-lines-file-long: ../_legacy/emission_lines_long_list.LVM
# full list of emission lines to analyze using the non-parametric fitting procedure
emission-lines-file-long: ../_legacy/emission_lines_strong.LVM
# Wavelength range in which the full stellar decomposition is peformed
w-range:
  - 3700
  - 9500
# Wavelength range in which the kinematics parameters (vel,vel_disp) are fitted
w-range-nl:
  - 3800
  - 4200
# File comprising the wavelength bands to be masked (e.g., the bands between spectrographs)
 mask-file: ../_legacy/mask_bands_LVM.txt
# File with a set wavelengths to mask (narrow range around the designed wavelength)
 mask_file: none
# Configuration file defining the emission lines to fit during the RSP fitting.
 config-file: ../_legacy/auto_ssp_LVM.config
# Flag indicating if any previous file with the same label should be removed
 clear_outputs: True
# not used so far. Possible binning the wavelength range to speed-up the fitting procedure
 bin-nl: 3
# not used so far. Possible binning in the derivation of Av to speed-up the process
 bin-AV: 50
# Flag to ignore the emission line fitting during the RSP analysis
 ignore_gas: False
# Initial guess for the velocity dispersion for the emission lines analysis in AA
 sigma-gas: 0.8
# Flag to perform the emission line fitting one once during the RSP analysis
single-gas-fit: True
# Flag indicating if instead of a decomposition the code looks for the best RSP in the template that
# matchs with the observed spectra
single_rsp: False
# Flag indicating wether to generate plots or not along the fitting process
 do_plots: 1
# Flux range for plotting. When set ot [-1,1] it will automatically determine the required range
 flux-scale-org:
  - -1 # min
  - 1  # max
# Range of fibers to fit in case that you do not want to fit the full RSS
 ny_range:
  - 500
  - 503
# Not used so far: range of spectral pixels to perform the fitting
 nx_range:
  - 100
  - 3000
  out-plot-format: "pdf"
# Format of the output plot format : "png"
 only-integrated: True
# Fit only the integrated spectrum or not
 auto-redshift: True
# Find the central redshift automatically using the integrated spectrum
auto_z_min: -0.005
auto_z_max: 0.01
auto_z_del: 0.0001
# Parameters that define the range min,max and delta
auto_z_bg: True
# Subtract the background to detect Ha+NII in the integrated spectrum to find the central redshift
auto_z_sc: True
# Correct the residual background for the integrated spectrum
sky-hack: False
# Appply a correction of the sky spectrum (deprecated, useful for DRP<1.0.3)
SN_CUT: 20
# SN cut for the multi-RSP analysis
SN_CUT_INT: 0.1
# SN cut for the single-RSP analysis
lvm-dap-conf [-h] [-d] lvm_file label config_yaml
  • lvm_file: FITS file in LVM format
  • label: Label for the current run
  • config_yaml: Configuration file for fitting parameters

lvm-dap-gen-out-mod Command

lvm-dap-gen-out-mod [-h] [-d] [-output_path OUTPUT_PATH] [--plot PLOT] [--flux-scale min max] lvm_file DAP_table_in label config_yaml
  • lvm_file: Input LVM spectrum that was fitted
  • DAP_table_in: DAP file generated by the LVM-DAP fitting
  • label: Label for the output file (e.g., LABEL.output.fits.gz)
  • config_yaml: Configuration file with fitting parameters

Options:

  • -d, --debug : Enable debugging mode (default: False)
  • -output_path OUTPUT_PATH : Directory to store the results
  • --plot PLOT : Whether to plot (1) or not (0, default). If 2, saves a plot without displaying on screen
  • --flux-scale min max : Scale of the flux in the input spectrum

lvm-dap-sim Command

lvm-dap-sim [-h] [-n_sim n_sim] [-n_st n_st] [-f_st f_scale_st] [-f_el f_scale_el] [-dap_fwhm dap_fwhm] [-d] lvm_file label config_yaml
  • lvm_file: Input LVM spectrum for the simulation
  • label: Label for the current run
  • config_yaml: Configuration file with fitting parameters

Options:

  • -h, --help : Show help message and exit
  • -n_sim n_sim : Number of simulated spectra (default: 10)
  • -n_st n_st : Number of stars included in the model (default: 10)
  • -f_st f_scale_st : Scaling factor applied to stellar population spectra (~S/N level, default: 1.0)
  • -f_el f_scale_el : Scaling factor applied to emission lines relative to reference (default: 1.0)
  • -dap_fwhm dap_fwhm : Scaling factor applied to DAP non-parametric dispersion for emission lines (default: 2.354)
  • -d, --debug : Enable debugging mode (default: False)

lvm-dap Command (Deprecated)

lvm-dap is now deprecated. Users are encouraged to use lvm-dap-conf, lvm-dap-gen-out-mod, or lvm-dap-sim instead.

lvm-dap [-h] [--config-file CONFIG_FILE] spectrum-file rsp-file sigma-inst label
  • spectrum-file: Input spectrum to fit
  • rsp-file: The resolved stellar population basis
  • sigma-inst: The resolution downgrade parameter
  • label: Label for the run

Troubleshooting & Additional Notes

  • If you encounter installation issues, check numpy version compatibility.
  • Ensure pyPipe3D is installed before LVM-DAP.
  • For support, refer to the official repository.

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