Data walkthrough

Recommended code organization structure:

├── snndump        (to save the data)
│
├── SuperNNova
│   ├── supernnova
│   ├── env
│   ├── docs
│   ├── tests

To build the database:

  • Ensure you have raw data saved to {raw_dir}/raw

  • The default settings assume the raw data and fits are saved to snndump/raw

  • You can save the data in any folder, but you then have to specify the dump_dir with the --dump_dir XXX command.

  • You can specify a different place where the raw data is using --raw_dir XXX command.

  • You can specify a different place where the fits to data is using --fits_dir XXX command.

Activate the environment

Either use docker

cd env && python launch_docker.py (--use_cuda optional)

Or activate your conda environment

source activate <conda_env_name>

Creating a debugging database

Using command line: .. code:

python run.py --data --dump_dir tests/dump --raw_dir tests/raw --fits_dir tests/fits
  • This creates a database for a very small subset of all available data

  • This is intended for debugging purposes (training, validation can run very fast with this small database)

  • The database is saved to the specified tests/dump/processed

Using yaml: .. code:

python run_yaml.py <yaml_file_with_config> --mode data

an example <yaml_file_with_config> is at configs_yml.

Creating a database

Using command line: .. code:

python run.py --data --dump_dir <path/to/full/database/> --raw_dir <path/to/raw/data/> --fits_dir <path/to/fits/>

Using yaml: modify the configuration file .. code:

python run_yaml.py <yaml_file_with_config> --mode data
  • You DO NEED to download the raw data for this database or point where your data is.

  • This creates a database for all the available data with 80/10/10 train/validate/test splits.

  • Splits can be changed using --data_training or --data_testing commands. For yaml just add data_training: True or --data_testing: True.

  • The database is saved to the specified dump_dir, in the processed subfolder.

  • There is no need to specify salt2fits file to make the dataset. It can be used if available but it is not needed --fits_dir <empty/path/>.

  • Raw data can be in csv format with columns:

  • `` DES_PHOT.csv ``: SNID,MJD, FLUXCAL, FLUXCALERR, FLT

  • `` DES_HEAD.csv``: SNID, PEAKMJD, HOSTGAL_PHOTOZ, HOSTGAL_PHOTOZ_ERR, HOSTGAL_SPECZ, HOSTGAL_SPECZ_ERR, SIM_REDSHIFT_CMB, SIM_PEAKMAG_z, SIM_PEAKMAG_g, SIM_PEAKMAG_r, SIM_PEAKMAG_i, SNTYPE.

Creating a database for testing a trained model

This is how to create a database with only lightcurves to evaluate.

python run.py --dump_dir <path/to/save/database/> --data --data_testing  --raw_dir <path/to/raw/data/>

Note that: - using --data_testing option will generate a 100% testing set (see below for more details). Using command yaml: modify the configuration file with data_testing: True and use the --mode data.

Creating a database with photometry limited to a time window

Photometric measurements may span over a larger time range than the one desired for classification. For example, a year of photometry is much larger than the usual SN timespan. Therefore, it may be desirable to just use a subset of this photometry (observed epochs cuts). To do so:

python run.py --dump_dir <path/to/save/database/> --data --raw_dir <path/to/raw/data/>  --photo_window_files <path/to/csv/with/peakMJD> --photo_window_var <name/of/variable/in/csv/to/cut/on> --photo_window_min <negative/int/indicating/days/before/var> --photo_window_max <positive/int/indicating/days/after/var>

Creating a database with different survey

The default filter set is the one from the Dark Energy Survey Supernova g,r,i,z. If you want to use your own survey, you’ll need to specify your filters (Beware! as from 12/11/19 the input of possible combination of filters has been deprecated!).

python run.py --dump_dir <path/to/save/database/> --data --raw_dir <path/to/raw/data/>  --list_filters <your/filters>

e.g. ``–list_filters g r ``.

Using a different redshift label

The default redshift label is either HOSTGAL_SPECZ/HOSTGAL_PHOTOZ (with option zspe/zpho). If you want to use your own label, you’ll need to specify it. Beware, this will override also SIM_REDSHIFT_CMB used for the title of plotted light-curves.

python run.py --dump_dir <path/to/save/database/> --data --raw_dir <path/to/raw/data/>  --redshift_label <your/label>

e.g. --redshift_label REDSHIFT_FINAL.

Masking photometry

The default is to use all available photometry for classification. However, we support masking photometric epochs with a power of two mask. Any combination of these power of two integers, and with other numbers, will be eliminated from the database.

python run.py --dump_dir <path/to/save/database/> --data --raw_dir <path/to/raw/data/>  --phot_reject <your/label> --phot_reject_list <list/to/reject>

e.g. --phot_reject PHOTFLAG --phot_reject_list 8 16 32 64 128 256 512.

Under the hood

Preparing data splits

We first compute the data splits:

  • By default the HEAD FITS/csv files are analyzed to compute 80/10/10 train/test/val splits.

  • You can change if the database contains 99.5/0.5/0.5 train/test/val splits using --data_training command.

  • You can change if the database contains 0/0/100 train/test/val splits using --data_testing command. Beware, this option has other consequences.

  • The splits are different for the salt/photometry datasets

  • The splits are different depending on the classification target

  • We downsample the dataset so that for a given classification task, all classes have the same cardinality

  • The supernova/light-curve types supported can be changed using --sntypes. Default contains 7 classes. If a class is not given as input in --sntypes, it will be assigned to the last available tag. If a ‘Ia’ exists in provided --sntypes, this will be taken as tag 0 in data splits, else the first class will be used.

Preprocessing

We then pre-process each FITS/csv file

  • Join column from header files

  • Select columns that will be useful later on

  • Compute SNID to tag each light curve

  • Compute delta times between measures

  • Removal of delimiter rows

Pivot

We then pivot each preprocessed file: we will group time-wise close observations on the same row and each row in the dataframe will show a value for each of the flux and flux error column

  • All observations within 8 hours of each other are assigned the same MJD

  • Results are cached with pickle for faster loading

HDF5

The processed database is saved to dump_dir/processed in HDF5 format for convenient use in the ML pipeline

The HDF5 file is organized as follows:

├── data                            (variable length array to store time series)
│
│
├── dataset_photometry_2classes     (0: train set, 1: valid set, 2: test set, -1: not used)
├── dataset_photometry_7classes     (0: train set, 1: valid set, 2: test set, -1: not used)
│
├── target_photometry_2classes      (integer between 0 and 1, included)
├── target_photometry_7classes      (integer between 0 and 6, included)
│
│
├── features                        (array of str: feature names to be used)
├── normalizations
│   ├── FLUXCAL_g
│        ├── min
│        ├── mean                    Normalization coefficients for that feature
│        ├── std
│    ...
├── normalizations_global
│   ├── FLUXCAL
│       ├── min
│       ├── mean                    Normalization coefficients for that feature
│       ├── std                     In this scheme, the coefficients are shared between fluxes and flux errors
│   ...
│
├── SNID                            The ID of the lightcurve
├── PEAKMJD                         The MJD value at which a lightcurve reaches peak light
├── SNTYPE                          The type of the lightcurve (120, 121...)
│
...                                 (Other metadata / features about lightcurves)

The features used for classification are the following:

  • FLUXCAL_g (flux)

  • FLUXCAL_i (flux)

  • FLUXCAL_r (flux)

  • FLUXCAL_z (flux)

  • FLUXCALERR_g (flux error)

  • FLUXCALERR_i (flux error)

  • FLUXCALERR_r (flux error)

  • FLUXCALERR_z (flux error)

  • delta_time (time elapsed since previous observation in MJD)

  • HOSTGAL_PHOTOZ (photometric redshift)

  • HOSTGAL_PHOTOZ_ERR (photometric redshift error)

  • HOSTGAL_SPECZ (spectroscopic redshift)

  • HOSTGAL_SPECZ_ERR (spectroscopic redshift eror)

  • g (boolean flag indicating which band is present at a specific time step)

  • gi (boolean flag indicating which band is present at a specific time step)

  • gir (boolean flag indicating which band is present at a specific time step)

  • girz (boolean flag indicating which band is present at a specific time step)

  • giz (boolean flag indicating which band is present at a specific time step)

  • gr (boolean flag indicating which band is present at a specific time step)

  • grz (boolean flag indicating which band is present at a specific time step)

  • gz (boolean flag indicating which band is present at a specific time step)

  • i (boolean flag indicating which band is present at a specific time step)

  • ir (boolean flag indicating which band is present at a specific time step)

  • irz (boolean flag indicating which band is present at a specific time step)

  • iz (boolean flag indicating which band is present at a specific time step)

  • r (boolean flag indicating which band is present at a specific time step)

  • rz (boolean flag indicating which band is present at a specific time step)

  • z (boolean flag indicating which band is present at a specific time step)