WARNING: Package under development
Python package wrapping up the ongoing cluster analysis of the LSST/DESC cluster group. For more info, see the two following github repositories:
- A collection of notebooks for LSST
- The ReprocessingTaskForce repository
See also the private Trello board that we use to share our work.
To install:
git clone https://github.com/nicolaschotard/Clusters.git pip install Clusters/
To install in a local directory mypath, use:
pip install --prefix='mypath' Clusters/
and do not forget to add it to your PYTHONPATH.
To upgrade to a new version (after a git pull or a local modification), use:
pip install --upgrade (--prefix='mypath') Clusters/
To install a release version (no release version available yet):
pip install http://github.com/nicolaschotard/Cluster/archive/v0.1.tar.gz
Also works with the master:
pip install (--upgrade) https://github.com/nicolaschotard/Clusters/archive/master.zip
In the future, release versions will be listed at this location.
Package developers will want to run:
python setup.py develop
Clusters has for now the following dependencies (see the quick
installs below):
- Python 2.7 and libraries listed in the requirements file
- The LSST DM stack.
Photometric redshift estimators:
To install the python dependencies, simply do:
pip install -r requirements.txt
This four-step procedure should allow you to install and configure a
light version of the DM stack, but complete enough to use the
Clusters package. It should take ~10 minutes.
Get and install miniconda, if you do not have it already:
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh bash miniconda.sh -b -p $HOME/miniconda export PATH="$HOME/miniconda/bin:$PATH" conda config --set always_yes yes --set changeps1 no conda update -q conda
Install the needed part of the DM stack (we do not need the entire stack):
conda config --add channels http://conda.lsst.codes/stack/0.12.0 conda create -q -n lsst python=2.7 source activate lsst conda install -q gcc lsst-daf-persistence lsst-log lsst-afw lsst-skypix lsst-meas-algorithms lsst-pipe-tasks
Install a compatible version of the
obs_cfhtpackage, which is not yet avalaible in the conda repository:setup daf_persistence git clone https://github.com/lsst/obs_cfht.git cd obs_cfht git checkout b7ab2c4 setup -k -r . scons opt=3 eups declare -r . -t yourname
To use this install of the DM stack, do not forget these following setups:
export PATH="$HOME/miniconda/bin:$PATH" source activate lsst source eups-setups.sh setup daf_persistence setup obs_cfht -t yourname
If these steps went well, you should be able to use
clusters_data.py on one of the outputs of the DM stack (see below
to get some data).
You can download and install a pre-configured version of LEPHARE as followed:
for linux system:
wget https://lapp-owncloud.in2p3.fr/index.php/s/MDaXObLSD9IVQ1B/download -O lephare.tar.gz tar zxf lephare.tar.gz
for mac:
wget https://lapp-owncloud.in2p3.fr/index.php/s/bMTLiwfGK1SpOqE/download -O lephare.tar.gz tar zxf lephare.tar.gz
When the download is complete, exctract the lephare directory where it
suits you (mypath in this example), and set the following
environment variables (use setenv if needed):
export LEPHAREWORK="mypath/lephare/lephare_work" export LEPHAREDIR="mypath/lephare/lephare_dev" export PATH="$PATH:mypath/lephare/lephare_dev/source"
You should now be able to run clusters_zphot.py (only tested on
linux systems).
The following steps can be copied/pasted in order to install and test
BPZ quickly. It supposes that LEPHARE has been installed following the
procedure shown in the previous section (you need
$LEPHAREDIR/filt/cfht/megacam/\*.pb). Here are the official
install instructions
for BPZ.
Get BPZ:
export MYDIR="an install dir" # change that line cd MYDIR wget http://www.stsci.edu/~dcoe/BPZ/bpz-1.99.3.tar.gz tar -xvf bpz-1.99.3.tar.gz
Create needed enironment vairables:
export BPZPATH="$MYDIR/bpz-1.99.3" export PYTHONPATH=$PYTHONPATH:$BPZPATH export NUMERIX=numpy
Create the filter files using the LEPHARE install:
cd $BPZPATH/FILTER/
cp $LEPHAREDIR/filt/cfht/megacam/*.pb .
for f in *.pb; do mv "$f" "CFHT_megacam_${f%.pb}.res"; done
Test the install and the megacam filter:
wget https://lapp-owncloud.in2p3.fr/index.php/s/FP1vSMB7emLxwwg/download -O megacam_bpz.columns wget https://lapp-owncloud.in2p3.fr/index.php/s/HZbzCFLoy8Lcmwx/download -O megacam_bpz.in python $BPZPATH/bpz.py megacam_bpz.in -INTERP 2
All the scripts will take the same input YAML file, which contains necessary informations for the analysis or simply for plotting purpose, such as the name of the studied cluster. Keys are listed below and are case-sensitive. Additional keys are simply ignored. You can find examples of these configuration files in the config directory, or clicking here for MACSJ2243.3-0935.
| General keys | Type | Description [units] |
|---|---|---|
"cluster" |
string | Name of the cluster |
"ra" |
float | RA coordinate of the cluster [deg] |
"dec" |
float | DEC coordinate of the cluster [deg] |
"redshift" |
float | Cluster redshift |
"butler" |
string | Absolute path to the intput data (butler) |
"filter" |
list | List of filters to be considered, e.g., 'ugriz' (Megacam filters) |
"patch" |
list | List of patches to study |
The following list of optional keys can also be added to the configuration file. They correspond to specific configurations of the different steps of the analysis. While the previous list will most likely stay unchanged, the following one will be completed with new keys as this analysis will progress.
| Optional keys | Type | Description [units] |
|---|---|---|
"keys" |
dict | Dictionnary containing list of keys for the catalogs (see below) |
"zpara" |
list | List of paths to zphota configuration files (see below) |
"zspectro_file" |
string | File containing spectroz sample for LePhare training |
keysis a dictionary having the name of the different catalogs like deepCoadd_meas, deepCoadd_forced_src and forced_src. The list of keys for a given catalog can include:- "the_full_name_of_a_key";
- "*_a_part_of_a_key_name" or "an_other_part_of_a_key_name*" preceded or followed by a *;
- a combination of all the above: ["key1", "ke*", "*ey"];
- or a "*" to get all keys available in a catalog, which is the default value for all catalogs.
Clusters consists in several command-line executables that you
have to run in the right order.
Get the input data and dump them in a hdf5 file containing astropy tables (see the data format section of the documentation for detail):
clusters_data.py config.yaml (--output data.hdf5)
The memory you will need to load the data from the butler will for now
depend on the number of catalogs (e.g. the forced_src catalog),
patch, visits and CCD you will be loading. For instance, if you try to
load ~10 patches for 5 filters, and want all the keys of several
catalogs including the forced_src one (CCD-based), you could need
up to 16GB of memory. The best practice would thus be to first
check the list of existing keys of the catalogs you want to load
(--show option), fill the configuration file with your selected
list of keys using the keys parameter for each catalog, and
finally run clusters_data.py using this configuration file. You
can find an example for such cofiguration file there
and some detail on how to use the keys in the previous section. This
will allow you to adapt the content of the output file and work with
lighter data files.
Data validation plots can for now be found in the several notebooks available in:
https://github.com/nicolaschotard/Clusters/tree/master/notebooks
Correct the data for Milky Way extinction:
clusters_extinction.py config.yaml data.hdf5 (--output extinction.hdf5)
Get the photometric redshift using LEPHARE:
clusters_zphot.py config.yaml data.hdf5 (--extinction extinction.hdf5) (--output zphot.hdf5)
The configuration file(s) used in LEPHARE can be given with the option
--zpara. The code will loop over the different files and run
LEPHARE for each of them. All results are saved in the same hdf5
file. This list of configuration files can also be given in the
CONFIG.yaml file (see above). --zpara will overwrite what is given
in the configuration file.
Identify galaxies to be removed from the whole sample: Red sequence galaxies identified from color-color diagrams, foreground galaxies identified using photometric redshifts:
clusters_getbackground.py config.yaml cat_data.hdf5 z_data.hdf5 (--zmin z_min) (--zmax z_max) (--thresh_prob threshold)cat_data.hdf5is the catalogue from which magnitudes are read to produce the red sequence cut. After the background galaxies are identified, the astropy table 'deepCoadd_meas' is supplemented 3 boolean 'flag' columns (RS_flag,z_flag_hard,z_flag_pdz), corresponding to the RS cut and the hard and pdz redshift cuts. If True the object passed the cut and is to be kept. If--outputis used, the table is also saved in a separate*_background.hdf5filez_data.hdf5is the output file of clusters_zphot.py containing the pdz information.z_min,z_maxare used for a 'hard' redshift cut: all galaxies in [z_min,z_max] are flagged.- threshold: if the probability of a galaxy to be located at z < z_cluster + 0.1 is larger than threshold [%], the galaxy is flagged to be removed.
Compute the shear:
clusters_shear config.yaml input.hdf5 output.hdf5
A pipeline script which run all the above step in a raw with standard options:
clusters_pipeline config.yaml
With any command, you can run with -h or --help to see all the
optional arguments, e.g., clusters_data.py -h.
If you have installed all the dependencies previoulsy mentionned, download the following test data set:
wget https://lapp-owncloud.in2p3.fr/index.php/s/xG2AoS2jggbmP0k/download -O testdata.tar.gz tar zxf testdata.tar.gz
The testdata directory contains a subset of the reprocessing data
available for MACSJ2243.3-0935. It can be used as a test set of the
code, but is not complete enough to run the full analysis. Here is the
full structure and content of the directory, which has the exact same
structure as a regulare DM stack output directory:
testdata/ ├── input │ ├── _mapper │ └── registry.sqlite3 ├── output │ ├── coadd_dir │ │ ├── deepCoadd │ │ │ ├── g │ │ │ │ └── 0 │ │ │ │ ├── 1,5 │ │ │ │ └── 1,5.fits │ │ │ └── skyMap.pickle │ │ ├── deepCoadd-results │ │ │ └── g │ │ │ └── 0 │ │ │ └── 1,5 │ │ │ ├── bkgd-g-0-1,5.fits │ │ │ ├── calexp-g-0-1,5.fits │ │ │ ├── detectMD-g-0-1,5.boost │ │ │ ├── det-g-0-1,5.fits │ │ │ ├── forced_src-g-0-1,5.fits │ │ │ ├── meas-g-0-1,5.fits │ │ │ ├── measMD-g-0-1,5.boost │ │ │ └── srcMatch-g-0-1,5.fits │ │ ├── forced │ │ │ └── 08BO01 │ │ │ └── SCL-2241_P1 │ │ │ └── 2008-09-03 │ │ │ └── g │ │ │ └── 0 │ │ │ ├── FORCEDSRC-1022175-00.fits │ │ │ ├── FORCEDSRC-1022175-09.fits │ │ │ ├── FORCEDSRC-1022176-00.fits │ │ │ ├── FORCEDSRC-1022176-09.fits │ │ │ ├── FORCEDSRC-1022177-00.fits │ │ │ ├── FORCEDSRC-1022177-09.fits │ │ │ ├── FORCEDSRC-1022178-00.fits │ │ │ ├── FORCEDSRC-1022178-09.fits │ │ │ ├── FORCEDSRC-1022179-00.fits │ │ │ ├── FORCEDSRC-1022179-09.fits │ │ │ ├── FORCEDSRC-1022180-00.fits │ │ │ └── FORCEDSRC-1022180-09.fits │ │ └── _parent -> ../ │ └── _parent -> ../input/ └── travis_test.yaml
With this data set, you should be able to test most of the
Clusters parts. You can start with the test suite available in the
tests directory. To do so, use:
python setup.py test
It will use the testdata that you have downloaded previoulsy and run the tests. This is also usefull if your goal is to add new tests.
If you have installed Clusters but do not have any data to run it
on, you can use one of our re-processing outputs for
MACSJ2243.3-0935. The corresponding configuration file is stored
under configs/. To use it, you either need
to be connected at CC-IN2P3, or change the path to the butler inside
the config file (if you already have a copy of this data). You could
also mount sps on your personal computer (see this how to).
The first step of the Clusters package is clusters_data.py,
which will get the data from the DM butler, convert them into
astropy tables and save them in a single hdf5 file. To do so,
you need the LSST DM stack to be installed. If you want to skip this
part and try the code whithout having to install the DM stack, you
could also use the outputs of this first step that you can download
from this repository, which
contains the following files:
|-- CL0016 | |-- [4.4G] CL0016_data.hdf5 # full data set | |-- [334M] CL0016_filtered_data.hdf5 # only quality-filtered galaxies | `-- [ 312] CL0016.yaml # configuration file |-- MACSJ224330935 | |-- [5.6G] MACSJ2243.3-0935_data.hdf5 # full data set | |-- [367M] MACSJ2243.3-0935_filtered_data.hdf5 # only quality-filtered galaxies | |-- [ 329] MACSJ2243.3-0935.yaml # configuration file
This short tutorial
explains how to use these hdf5 files to start an analysis.
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