PyFOSC is a pipeline toolbox for long-slit spectroscopy data reduction written in Python. It can be used for FOSC (Faint Object Spectrograph and Camera) data from Xinglong/Lijiang 2-meter telescopes.
BFOSC (Beijing-Faint Object Spectrograph and Camera) is an instrument of the 2.16-m Telescope in Xinglong Observatory, National Astronomical Observatories, Chinese Academy of Sciences (NAOC) (IAU code: 327, coordinates: 40°23′39″ N, 117°34′30″ E). For more information about BFOSC, please see http://www.xinglong-naoc.org/html/en/gcyq/216/detail-18.html.
YFOSC (Yunnan-Faint Object Spectrograph and Camera) is an instrument of the 2.4-m Telescope in Lijiang Observatory, Yunnan Observatories, Chinese Academy of Sciences (YNAO) (IAU code: O44, coordinates: 26°42′33.1″ N, 100°1′51.6″ E). For more information about YFOSC, please see http://wiki.gmg.org.cn/pages/viewpage.action?pageId=557106.
IRAF
PyRAF
pandas
This package depends on IRAF and PyRAF. Although these two softwares will no longer be supported by their developers, you can still download and install them from AstroConda using its 'Legacy Software Stack'.
1.2. Install IRAF and PyRAF from astroconda
For detailed description on how to install IRAF and PyRAF from astroconda, you can either go to the documentation of AstroConda's Legacy Software Stack with IRAF, or my blog post How to install and initiate IRAF in Ubuntu/Mac OS. The minimal installation can be done with:
conda config --add channels http://ssb.stsci.edu/astroconda
conda create -n iraf27 python=2.7 iraf-all pyraf-all stsci
conda install -n iraf27 pandas
Note that every time you want to use IRAF/PyRAF and PyFOSC, you need to activate the env 'iraf27' that you have created:
source activate iraf27
And to deactivate, run:
source deactivate
You can use git clone
to download this package.
git clone https://github.com/rudolffu/pyfosc.git
In order to run PyFOSC commands in the terminal, you need to add the path of PyFOSC and its sub-directory src
to $PATH, by editing ~/.bashrc
(Linux, e.g., Ubuntu) or ~/.bash_profile
(Mac OS). An example of this can be:
export PATH=/Your/Path/to/pyfosc:$PATH
export PATH=/Your/Path/to/pyfosc/src:$PATH
First go to the working directory which contains FOSC spectroscopic data, activate iraf27
env and mkiraf
.
source activate iraf27 (#or conda activate iraf27)
mkiraf
Select xgterm
when the terminal prompts. Then run pyfosc_init
from iraf27
env:
pyfosc_init
Activate iraf27
env and run addheaderinfo.py
.
source activate iraf27
addheaderinfo.py
As PyFOSC pipeline reduce data grouped by different types (bias, flat, object, etc), make sure you have lists of fits files as follows:
zero.list --------------- List of bias files (e.g. bias*.fits).
flat.list --------------- List of flat field files (e.g. flat*.fits).
objall.list ------------- List of 2d spectra images of all objects (science targets and standard stars).
lampall.list ------------ List of all 2d lamp spectra images.
flatnall.list ----------- List of 2d images that need zero correction (flat.list + lampall.list + objall.list).
specall.list ------------ List of all 2d spectra images (objall.list + lampall.list).
The pyfosc$iraf_scripts
directory contains template cl
scripts that can be executed in IRAF/PyRAF to generate these lists. Users can modify the scripts for specific cases.
You can run pyfosc_run.sh
from iraf27
env:
pyfosc_run.sh
Alternatively, you can run the scripts step by step, following the order as:
makezero2m.py # Combine zero(bias) frames.
ccdotz.py # Do zero(bias), overscan correction and trimming.
makeflat2m.py # Combine flat fields.
makereflat2m.py # Do (illumination) normalization and get perfect flat.
divideflat2m.py # Do flat correction.
removecr2m.py # Remove cosmic rays in two-d images. Please go to 3. Credits for more information.
doapall.py # Extract spectra.
reidentlamp2m.py # Reidentify lamp spectra with previously stored ones.
#Can use identlamp2m.py instead to identify lamp by oneself.
wavecal2m.py # Do wavelength calibration, flux calibration.
telluric_base2m.py # Telluric correction and one-d spectra extraction.
Plot all final 1d spectra with:
plotonedsp.py
Move some intermediate files into INTMD
directory:
mvintmd.sh
This software uses BSD 3-Clause License.
Copyright (c) 2019, Yuming Fu
All rights reserved.
This software contains sources from third-party softwares.
The pyfosc$iraf_data/onedstds
directory is from IRAF
, and it contains standard calibration data for extinction and sensitivity calibration.
The pyfosc$iraf_task/lacos_im.cl
script is the IRAF
version for Laplacian Cosmic Ray Identification by Pieter G. van Dokkum (Yale) from http://www.astro.yale.edu/dokkum/lacosmic/. L.A.Cosmic is an algorithm for robust cosmic ray identification. It detects cosmic rays of arbitrary shapes and sizes, and distinguishes between undersampled point sources and cosmic rays. If you use this program please refer to P. G. van Dokkum, 2001, PASP, 113, 1420.
Please see COPYRIGHT
file and pyfosc$doc/LICENSES
directory for detailed copyright information.
Yuming Fu. (2020, June 29). PyFOSC: a pipeline toolbox for BFOSC/YFOSC long-slit spectroscopy data reduction (Version v1.0.1). Zenodo. https://doi.org/10.5281/zenodo.3915021
Cite the current version (v1.0.1) with bibtex:
@software{yuming_fu_2020_3915021,
author = {Yuming Fu},
title = {{PyFOSC: a pipeline toolbox for BFOSC/YFOSC long-slit spectroscopy data reduction}},
month = jun,
year = 2020,
publisher = {Zenodo},
version = {v1.0.1},
doi = {10.5281/zenodo.3915021},
url = {https://doi.org/10.5281/zenodo.3915021}
}