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Database

Data which are read from the database, as well as the output of various functions, are stored in :class:`~species.core.box.Box` objects. These can be used directly as input for the plotting functionalities of species (see examples in the :ref:`tutorials` section). Alternatively, users can easily extract the content of a :class:`~species.core.box.Box` and process or plot it to their own needs. The :func:`~species.core.box.Box.open_box` function can be used to see which attributes are inside a :class:`~species.core.box.Box`.

The following example will add available photometric data of PZ Tel B to the database, read the data and properties of the companion into an :class:`~species.core.box.ObjectBox`, and list its content.

import species

species.SpeciesInit()

database = species.Database()
database.add_companion(name='PZ Tel B')

objectbox = database.get_object(object_name='PZ Tel B')
objectbox.open_box()

As an example, a dictionary with the apparent magnitudes can be extracted from the :class:`~species.core.box.ObjectBox` in the following way:

app_mag = objectbox.magnitude

Databases can be conveniently reused since the data needs to be added only once. Want to know which data and attributes have been stored in the database? The :func:`~species.data.database.Database.list_content` method of :class:`~species.data.database.Database` can be used for listing the content of the HDF5 file:

database.list_content()

To delete a group or dataset from the HDF5 file, there is the :func:`~species.data.database.Database.delete_data` method which takes the path in the HDF5 structure as argument. For example, to remove all previously added photometric data of PZ Tel B:

database.delete_data("objects/PZ Tel B/photometry")

Important

Whenever data is added to the HDF5 database with a name tag that already exists, then the existing data is first deleted before the requested data is added to the database. For example, if the AMES-Cond spectra are present in the models/ames-cond group and add_model('ames-cond') is executed, then all spectra are first removed from that group before the requested spectra are added. Similarly, if the objects/beta Pic b/photometry/Paranal/NACO.Mp group contains NACO Mp data of beta Pic b then these data are first removed if that same filter is used by :func:`~species.data.database.Database.add_object`.