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@arfon
Last active Apr 16, 2020
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How to make TESS FITS cubes using Astrocut and MAST
# Author: Arfon Smith, Space Telescope Science Institute
# This script assumes the `s3://stpubdata` bucket is mounted at `/home/ubuntu/data`
# using the goofys tool (https://github.com/kahing/goofys)
import astroquery
from astrocut import CubeFactory
from astropy.io import fits
import numpy as np
import boto3
import os
from astroquery.mast import Catalogs, Observations
# We (currently) have two sectors of data, there are four cameras, and four chips per-camera.
# We want to make files named e.g. tess-s0001-1-1-cube.fits
sectors = ['0001', '0002']
cameras = [1,2,3,4]
chips = [1,2,3,4]
for sector in sectors:
for camera in cameras:
for chip in chips:
output_file = f"tess-s{sector}-{camera}-{chip}-cube.fits"
print(f"Working with {output_file}")
# Grab the observations from MAST for this given sector/camera/chip
obsTable = Observations.query_criteria(obs_id=f"tess-s{sector}-{camera}-{chip}")
# Next grab the products and filter for only the calibrated FFIs (FFIC files)
products = Observations.get_product_list(obsTable)
filtered = Observations.filter_products(products,
productSubGroupDescription="FFIC",
mrp_only=False)
# Turn on the S3 URLs
Observations.enable_cloud_dataset()
print(f"Grabbing S3 URLs for {output_file}")
s3_urls = Observations.get_cloud_uris(filtered)
input_files = []
# Loop through each URL and replace the s3://stpubdata/ prefix with the local path to the directory
# mounted with goofys
for url in s3_urls:
local_file_path = url.replace("s3://stpubdata/", "/home/ubuntu/data/")
input_files.append(local_file_path)
# Initialize a CubeFactory and pass it the input files and the output filename
cuber = CubeFactory()
cube_file = cuber.make_cube(input_files, cube_file=output_file, sector=int(sector))
BSD 3-Clause License
Copyright (C) 2010-2018 Association of Universities for Research in Astronomy (AURA)
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# Launch a big instance (c5d.9xlarge)
# Give it ~2000GB of local storage.
# Start with Ubuntu 18.04 LTS (ami-0ac019f4fcb7cb7e6)
# Update and install software:
sudo apt update
sudo apt install python3-pip
sudo pip3 install scipy
sudo pip3 install numpy
sudo pip3 install astropy
sudo pip3 install boto3
sudo pip3 install https://github.com/astropy/astroquery/archive/master.zip
sudo pip3 install https://github.com/spacetelescope/astrocut/archive/master.zip
# Set up the credentials file (this is needed by goofys and astroquery)
touch nano .aws/credentials
# This one will be picked up by Astroquery
[default]
aws_access_key_id = XXXXX
aws_secret_access_key = XXXXX
# Use this one at the end to write to the S3 stpubdata bucket with permission
[tess]
aws_access_key_id = XXXXX
aws_secret_access_key = XXXXX
Install goofys: https://gist.github.com/arfon/d93c788b4dcfd12029c8fb0d2fdeeb4c
# Make the files (using cube_maker.py)
# Finally copy the files to s3://stpubdata/tess/public/mast/...
# Finally regenerate the top level manifest.txt with `find . -type f > manifest.txt`
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