agora.io.writer.Writer

class agora.io.writer.Writer(filename, compression=None)

Bases: BridgeH5

Class in charge of transforming data into compatible formats

Decoupling interface from implementation!

Parameters

filename: str Name of file to write into

flag: str, default=None

Flag to pass to the default file reader. If None the file remains closed.

compression: str, default=None

Compression method passed on to h5py writing functions (only used for

dataframes and other array-like data.)

Attributes

cell_tree

Methods

get_info_tree([fields])	Returns traps, time points and labels for this position in form of a tree in the hierarchy determined by the argument fields.
write(path[, data, meta, overwrite])	Parameters

close
find_ids
get_consecutives
get_existing_ids
get_npairs
get_npairs_over_time
write_arraylike
write_dset
write_index
write_meta
write_pd

__init__(filename, compression=None)

Methods

__init__(filename[, compression])
close()
find_ids(existing, new)
get_consecutives(tree, nstepsback)
get_existing_ids(f, paths)
get_info_tree([fields])	Returns traps, time points and labels for this position in form of a tree in the hierarchy determined by the argument fields.
get_npairs([nstepsback, tree])
get_npairs_over_time([nstepsback])
write(path[, data, meta, overwrite])	Parameters
write_arraylike(f, path, data, **kwargs)
write_dset(f, path, data)
write_index(f, path, pd_index, **kwargs)
write_meta(f, path, attr, data)
write_pd(f, path, df, **kwargs)

Attributes

cell_tree

get_info_tree(fields: Union[tuple, list] = ('trap', 'timepoint', 'cell_label'))

Returns traps, time points and labels for this position in form of a tree in the hierarchy determined by the argument fields. Note that it is compressed to non-empty elements and timepoints.

Default hierarchy is: - trap

• time point

• cell label

This function currently produces trees of depth 3, but it can easily be extended for deeper trees if needed (e.g. considering groups, chambers and/or positions).

input :fields: Fields to fetch from ‘cell_info’ inside the hdf5 storage

returns :tree: Nested dictionary where keys (or branches) are the upper levels

and the leaves are the last element of :fields:.

write(path: str, data: Optional[Iterable] = None, meta: Dict = {}, overwrite: Optional[str] = None)

Parameters

pathstr

Path inside h5 file to write into.

dataIterable, default = None

metaDict, default = {}