gwdama 0.4.4

A GW data manager package and more

This package aims at providing a unified and easy to use interface to access Gravitational Wave (GW) data and output some well organised datasets, ready to be used for Machine Learning projects or Data Analys purposes (source properties, noise studies, etc.).

Data Preparation Workflow

The typical use case of this package concerns data preparation and can be viewed, in a pipeline, as the preliminary stage for Data Analysis. Although it is primarily meant for GW analyses, it is built to be sufficiently general to handle any data type. The basic workflow that can be implemented is the following:

1. Data acquisition: Data from GW detectors can be read from different locations, such as from local frame files (gwf), or from datasets previously saved with it, and especially from the Gravitational Wave Open Science Center (GWOSC).

2. Organisation into groups: Various acquisition channels, data epochs, or preliminary preprocessing operations, can be organised in a hierarchical way in various groups nad subgroups, each containing their own metadata;

3. Data preparation/preprocessing: Along with the original “raw” data, one can perform several pre-processing operations and data manipulations, included in this package, in order to make the dataset ready for the following Data Analysis stage of the pipeline. This processed data is conveniently organised into new groups, and the “raw” ones can be removed to save memory;

4. Reading and Writing: Once the dataset for a specific task has been created, this can be saved to disk into hdf5 format, preserving all the hierarchical group and sub-group structure and the metadata. This can be read back by GWdama for further data manipulation and preparation.

GW data manager package overview

GWdama currently comprises the main class GwDataManager, which behaves as a multi-purpose and multi-format container for data, which is based on h5py.File class with the addition of the methods and the attributes to import and manipulate GW data. Differently from the common application of h5py.File objects, a GwDataManager instance is, by default, set to occupy only a temporary file, which is authomatically deleted by python once closed, or some space in the RAM. Refer to the full documentation for further details.

Inside GwDataManager objects, data is stored into h5py.Dataset like objects organised into a hierarchical structure of h5py.Groups and sub-groups. These Datasets are created within an instance of GwDataManager() with the usual methods of h5py: create_dataset(name, shape, dtype). They contain data, typically of numeric type, and some attributes (or metadata). For example, for GW data, and in general all time series, it is important the information of when they have been recorded, and at which sampling frequency. A neme and a unit are also useful. These can be conveniently added and customised. Also a GwDatamanager object contains attributes for itself.

Installation

gwdama can be installed via pip:

$ pip install gwdama

and requires Python 3.6.0 or higher. The previous command automatically fulfils all the required dependencies (like on numpy, matplotlib), so you are ready to start generating datasets and making plots.

Further details can be found in the full documentation.

Creating a dataset

A dataset of, say, random numbers can be readily created as:

>>> from gwdama.io import GwDataManager
>>> import numpy as np

>>> dama = GwDataManager("my_dama")
>>> dama.create_dataset('random_n', data=np.random.normal(0, 1, (10,)))
>>> dama.create_dataset('a_list', data=[1, 2, 3, 4])
>>> dama.create_dataset('a_string', data="this is a string")

The string representation of the GwDataManager class provides a quick look at its structure and its attributes. You can call it with the method __str__() or simply by printing the object:

>>> print(dama)
my_dama:
  ├── a_list
  ├── a_string
  └── random_n

  Attributes:
     dama_name : my_dama
    time_stamp : 20-07-28_19h36m47s

Other attributes can be added to both the GwDataManager object and the Datasets therein:

>>> dama.attrs['owner'] = 'Francesco'  # The new attribute "owner" is added with value "Francesco"
>>> dama.show_attrs
my_dama:
  ├── a_list
  ├── a_string
  └── random_n

  Attributes:
     dama_name : my_dama
         owner : Francesco
    time_stamp : 20-07-28_19h36m47s

Datasets can be accessed from their keys, as reported in the structure shown above, with a syntax similar to that for dictionaries in Python:

>>> dset = dama['random_n']      # 'random_n' is the dataset key
>>> dset.attrs['t0'] = 0         # It is conveninet to use gps times
>>> dset.attrs['fsample'] = 10   # measured in Hz

>>> dset.show_attrs
fsample : 10
     t0 : 0

To get the data contained in this dataset, call its attribute data:

>>> dset.data
array([-0.73796689, -1.34206706, -0.97898291, -0.19846702,
       -0.85056961,  0.20206334,  0.84720009,  0.19527366,
       -0.9246727 , -0.04808732])

Writing and reading datasets

Now it is time to write your data to disc. Let’s say we want to store the information contained in our GwdataManager object into the hdf5 file out_dataset.h5:

>>> out_f = 'out_dataset.h5'
>>> write_gwdama_dataset(out_f)

Then remember to close your previous file before leaving the session:

>>> dama.close()
>>> del dama       # Redundant but usefull

Note

This operation is automatically performed every time the session is closed. However, it is good practice to do this manually every time there is no more need of a certain variable.

To read back your data:

>>> new_dama = GwDataManager(out_f)  # Same namse as the line above
Reading dama
>>> print(new_dama)
my_dama:
  ├── a_list
  ├── a_string
  └── random_n

  Attributes:
     dama_name : my_dama
         owner : Francesco
    time_stamp : 20-07-30_12h19m32s

Read open data

Open data can be accessed from both online and local virtual disks provided by CVMFS.

From online GWOSC

GW strain data can be read by means of the .read_gwdata() method. This basically takes as input an interval of time, which can be provided as a float in gps units or in UTC, in a human readible format (see next example), besides the label of the detector (H1, L1 or V1):

>>> event_gps = 1186746618                                      # GW170814
>>> dama = GwDataManager()                                      # Default name 'mydama' assigned
>>> dama.read_gwdata(event_gps - 50, event_gps +10, ifo='L1',   # Required params
                     m_data_source="gwosc-remote",              # data source
                     dts_key='online')                          # group key (optional, but useful)

From local CVMFS

CernVM-FS must be installed and configured on your computer. Refer to its description on the GWOSC website or to this Quick start guide.

Assuming your data are stored at the following path (you can always modify it by passing it as a parameter to read_gwdata()):

cvmfs_path = '/data2/cvmfs/gwosc.osgstorage.org/gwdata/'

data can be read with:

>>> start='2017-06-08 01:00:00'  # starting UTC time as a string
>>> end='2017-06-08 02:00:00'    # ending time as a string
>>> ifo='H1'                     # interfereometer tag

>>> rate='4k'                    # sample rate: 4k or 16k
>>> frmt='hdf5'                  # format of the data: gwf or hdf5

>>> dama.read_gwdata(start, end, m_data_source="gwosc-cvmfs", ifo=ifo, m_data_format=frmt)

Changelog

0.4.1

• Methods: hist, duration;

• Attributes: groups;

• Preprocessing functions: PSD, whiten, taper.

0.4.0

• Implemented support for data on Virgo Farm.

0.3.0

• Only open data can be imported either from online or via CVMFS;

• New methods to access data and attributes of datasets.