Database

The central component of a workflow is the Database. This object is used to store various types of data in the species_database.hdf5 file, which is located in the working folder or another location set in the species_config.ini file. Data needs to be added to a database only once, so databases can be conveniently reused by other workflows.

Want to know which data and attributes have been stored in the database? The list_content() method of Database is used for listing the content of the HDF5 file:

database.list_content()

Data which are read from the database, as well as the output of various functions, are stored in Box objects. These can be used as input for the plotting functionalities of species (see examples in the Tutorials section). Alternatively, users can extract the content of a Box and process it to their own needs.

The following example will add available photometric data of HR 8799 b to the database, and read the data of the companion into an ObjectBox. The open_box() method is used for listing the data in a Box.

import species

species.SpeciesInit()

database = species.Database()
database.add_companion(name='HR 8799 b')

objectbox = database.get_object(object_name='HR 8799 b')
objectbox.open_box()

Data are easily extracted as the attributes of a Box object. For example, in this example a dictionary with the apparent magnitudes is extracted from the ObjectBox:

app_mag = objectbox.magnitude

To delete a group or dataset from the HDF5 file, there is the delete_data() method which takes the path in the HDF5 structure as argument. For example, to remove all previously added photometric data of HR 8799 b:

database.delete_data("objects/HR 8799 b/photometry")

Important

When data is added to the HDF5 database by an existing name tag, then the existing data is first deleted before the requested data is added to the database. For example, when the AMES-Dusty spectra are present in the models/ames-dusty group and add_model('ames-dusty') 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 $M’$ data of beta Pic b then these data are first removed if that same filter is used by add_object().