This is a time-series photometry pipeline that reduces images to light curves. It is a port of a pipeline originally developed for the HATPI project.
This pipeline has been used for the Cluster Difference Imaging Photometric Survey (CDIPS) image-subtraction reductions. The CDIPS project has made and is making light curves for stars in open clusters, moving groups, etc. It has a stand-alone repo.
In theory, if one wished to reproduce the CDIPS reductions, this pipeline would be the place to start. More practically, the code-base should provide readers and users with an entry-point into a particular set of programs that can be used for photometric and time-series analyses.
We're releasing it for general reproducibility and method-sharing and improvement reasons. (Without the expectation of converting you into a user).
0. How is this structured?
The pipeline is a collection of python functions that can be called from a
single "driver script" to go through steps described in the
paper. For the
CDIPS-I reduction, the driver script is
The idea is that you run this one program (calling the correct options), and
you get light curves from images. This can be done from a shell
State-awareness (i.e., whether previous reduction attempts succeeded or failed)
is minimal, and based on the pre-existence of files and if-else logic. A few
similar driver scripts are also in /drivers/, for example to reduce the ETE6
images. Most of the intermediate files in the pipe-trex reduction (e.g.,
fistar, fiphot, ficonv, etc files) are stored on-disk. A few pieces of metadata
(e.g., image quality diagnostics) are collected to a PostgreSQL database and
used for the reference frame selection steps.
The most important collections of sub-scripts are in
imagesubphot.py, which wrap the
fitsh tools used to do the aperture
photometry and image subtraction.
autoimagesub.py rolls up many of these
functions to enable pipeline-like functionality.
1.1 Operating system
This installation is only tested on linux boxes (Debian/Ubuntu). Compiling the
fitsh binaries (see below) might be challenging, but if you do it on MacOS,
please submit a PR describing your experience.
1.2 Environment basics
First, clone this repo into a working directory, that we will call $TREX.
git clone https://github.com/waqasbhatti/cdips-pipeline
Have a working version of conda on your path (the 64-bit linux version, presumably). Then
cd $PIPE_TREX conda env create -f environment_trex_37.yml -n trex_37 source activate trex_37
This deals with most of the details listed below, and is the recommended way to use pipe-trex. (A variety of "new" features since the 2018 development effort depend on using a 3.X environment).
An extra step is that to make
pipe-trex accessible to the virtual
environment, you currently need to add a
.pth file to the approriate
site-packages directory. See "Making pipe-trex accessible within virtual
If you opt instead for a 2.7 environment, make a virtual environment in some
local directory, for instance
~/local. We will call the environment trex_27:
pip install virtualenv; virtualenv --python=/usr/bin/python2.7 trex_27
Make sure your $PATH and $PYTHON_PATH environmental variables do not have any python-related things that will break your venv.
Active the empty python 2.7 environment:
source trex_27/bin/activate (trex_27) cd $PIPE_TREX (trex_27) pip install -r requirements.txt
This latter step will take some time. Then, ensure pyeebls and bleeding-edge astrobase are installed (they are commented out by default because they require a number of dependencies):
(trex_27) pip install pyeebls (trex_27) cd $ASTROBASE_DIR (trex_27) python setup.py develop
where I have assumed you may want to make contributions to astrobase as you develop, which you should!
For transit-fitting, you will want
(trex_27) pip install batman-package (trex_27) pip install corner (trex_27) cd $SOME_DIR (trex_27) git clone https://github.com/dfm/emcee (trex_27) cd emcee (trex_27) python setup.py install
1.3 catalog reading dependencies
In order to perform photometry, we project known-star catalogs onto images in order to know where the stars are. (This is more reliable than source extraction.)
The best catalog in town is Gaia DR2. To access it quickly,
gaia2read is a
useful program. Jason Kim wrote it for his junior thesis, and his source is
Sam Yee added an important piece of functionality: cutting on different
magnitudes, his fork is available
gaia2read to the command line, do the following:
(trex_27) cd $SOME_DIRECTORY (trex_27) git clone https://github.com/samuelyeewl/gaia2read (trex_27) cd gaia2read/gaialib2 (trex_27) make (trex_27) mv gaia2read $BINARY_DIRECTORY_ON_YOUR_PATH (trex_27) echo "/nfs/phn15/ar0/H/CAT/GaiaDR2" > ~/.gaia2readrc
$BINARY_DIRECTORY_ON_YOUR_PATH$ is for example
~/bin/, or some other
directory from which your path can read binaries.
The assumption of the last line is that you are doing this on the
phtess NFS filesystem, where the "DataPreparation" steps have
already been performed to download and sort the Gaia DR2 catalog.
1.4 anet and astrometry.net dependencies
You must use either
astrometry.net. The latter is strongly
recommended, since it's free. To install, follow this
page. If you're doing wide-field
work, be sure to get both the 4100 and 4200 indexes.
1.5 fitsh and HATpipe dependencies
This code inherits from the
project, developed mostly by Andras Pal. Much of
fitsh was inherited by
HATpipe circa 2010, when it forked. Again, because they are free, we opt for
fitsh versions, rather than the closed
HATpipe fork versions.
The utilities we want working on our path include:
Most of these are
fitsh tasks. The
fitsh installation instructions are
here, and they are simple:
cd ~/local wget http://fitsh.net/download/fitsh/fitsh-0.9.2.tar.gz tar xvzf fitsh-0.9.2.tar.gz cd fitsh-0.9.2 ./configure make make install
Check to make sure this gives you
1.6 PostgreSQL installation
For bookkeeping, you will also need a PostgreSQL database.
(If you're installing on Mac OS X, it is a good idea to change your kernel state
by modifying your
/etc/sysctl.conf file to include things discussed in the
READMEs from the above links.)
Once you've done this:
$ psql -U postgres # login as master user postgres=# create user hpx with password 'pwgoeshere' createdb; $ createdb -U hpx hpx
and add the appropriate password and info to your
To access the database:
psql -U hpx hpx launches the PostgreSQL database
hpx run by user
psql -U hpx -h xphtess1 hpx does the same,
for a database run on xphtess1, rather than localhost.
To create the tables, run the following:
psql$ \i photometry.sql psql$ \i xtrnsconvsub.sql psql$ \i imagesub-refino.sql
Beware that these also remove any information you already had in them. The relations include:
List of relations Schema | Name | Type | Owner --------+--------------------------------+----------+------- public | ap_photometry | table | hpx public | arefshiftedframes | table | hpx public | arefshiftedframes_framekey_seq | sequence | hpx public | astromrefs | table | hpx public | calibratedframes | table | hpx public | calibratedframes_framekey_seq | sequence | hpx public | filters | table | hpx public | frameinfo | table | hpx public | frameinfo_framekey_seq | sequence | hpx public | iphotfiles | table | hpx public | iphotobjects | table | hpx public | ism_photometry | table | hpx public | lcinfo | table | hpx public | objectinfo | table | hpx public | photindex_iphots | table | hpx public | photometryinfo | table | hpx public | photrefs | table | hpx public | subtractedframes | table | hpx public | subtractedframes_framekey_seq | sequence | hpx
1.7 Making pipe-trex accessible within virtual environment
For the moment, go into the venv's
and create a
.pth file, e.g.
pipe-trex.pth with the location of the local
git cloned repository in it:
Then activate the virtualenv, and see if you can import a module:
py> import imagesubphot as ism
For a conda environment, do the same thing, but the site-packages directory
will instead be at a path like
2 Getting Started
Some usage examples are given in the
2.1 Concepts: Directory structure
Everything must be in its right place for your photometry to Just Work. During an initial installation, you will need to make a directory structure as follows, where "." refers to a base directory of your chosing. (The pipeline assumes this directory structure has been made).
. ├── CAL # You must download calibrated fits images from MAST into here ├── # e.g., ./CAL/sector-4/tess2018307055940-s0004-1-2-0124-s_ffic.fits ├── ENGINEERING # You must download engineering files from MAST into here ├── # e.g., ./ENGINEERING/tess2018344132117_sector04-eng.fits ├── # ├── # The following are automatically populated: ├── BASE # Reference frames will go here ├── RED # Trimmed and calibrated frames will go here ├── LC # Lightcurves will go here ├── PROJ # Files used to document different reductions will go here ├── MOVIES # Movies will get made and will be put here └── REDTEMP # Temporary space for reduced files
At the second level:
. ├── CAL │ ├── sector-3 # e.g., ./CAL/sector-4/tess2018307055940-s0004-1-2-0124-s_ffic.fits │ └── sector-4 # As above. ├── ENGINEERING # As in the level-1 example. ├── BASE │ ├── frameinfo-cache # Once created, these two subdirectories are... │ └── reference-frames # ...automatically populated ├── LC │ ├── FULL # For LCs from a full sector │ └── TUNE # For short LCs from a subset of a sector ├── BASE # These directories have subdirectories that get made automatically. ├── RED # These directories have subdirectories that get made automatically. ├── LC # These directories have subdirectories that get made automatically. ├── PROJ # These directories have subdirectories that get made automatically. ├── MOVIES # These directories have subdirectories that get made automatically. └── REDTEMP # These directories have subdirectories that get made automatically.
Maintaining this structure is essential. Commands can be run from anywhere, provided that this structure is maintained.
Waqas Bhatti, Luke Bouma, Samuel Yee
Appendix. Notes on mac installation
Aside: compiling the HATpipe source on a mac is not advised, because many of the libraries are linux-specific. The entire pipeline is untested on macs, and the following are some notes from a failed attempt at getting the pipeline to work on a mac.
cd /Users/luke/local/HATpipe_R3186/source/2mass cp /usr/include/malloc/malloc.h . # change 2massread.c's malloc include statement to be `#include "malloc.h"`. ./hatconf.sh make
you then need to put the appropriately formatted ~150Gb of 2MASS index files
somewhere accessible, and point to them in your
cd /Users/luke/local/HATpipe_R3186/source/odoncontrib/anet brew install gsl # this is not a default on macs
If on a mac, you then must edit all six makefiles,
/Users/luke/local/HATpipe_R3186/source/odoncontrib/anet/Makefile /Users/luke/local/HATpipe_R3186/source/odoncontrib/anet/libc*/Makefile /Users/luke/local/HATpipe_R3186/source/odoncontrib/anet/libc*/*/Makefile
to use GNU
cp, because mac
cp has different options. Even then
though, linking on my mac fails because of architecture problems that I don't
understand. This is perhaps a waste of time, and you should just develop on
linux, if you have a very good internet connection, or do not develop.