extraction.core.extractor.ExtractorParameters

class ExtractorParameters(tree, sub_bg={}, multichannel_ops={})

Bases: ParametersABC

Base class to define parameters for extraction.

Methods

from_yaml(source)	Returns instance from a yaml filename or stdin
guess_from_meta(store_name[, suffix])	Find the microscope used from the h5 metadata.
to_dict([iterable])	Recursive function to return a nested dictionary of the attributes of the class instance.
to_yaml([path])	Returns a yaml stream of the attributes of the class instance.
update(name, new_value)	Update values recursively if name is a dictionary, replace data where existing found or add if not.

default
from_dict
from_meta

Parameters

tree: dict

Nested dictionary indicating channels, reduction functions and metrics to be used. str channel -> U(function,None) reduction -> str metric If not of depth three, tree will be filled with None.

sub_bg: set

multichannel_ops: dict

Methods

from_yaml(source)	Returns instance from a yaml filename or stdin
guess_from_meta(store_name[, suffix])	Find the microscope used from the h5 metadata.
to_dict([iterable])	Recursive function to return a nested dictionary of the attributes of the class instance.
to_yaml([path])	Returns a yaml stream of the attributes of the class instance.
update(name, new_value)	Update values recursively if name is a dictionary, replace data where existing found or add if not.

default
from_dict
from_meta

__init__(tree, sub_bg={}, multichannel_ops={})

Parameters

tree: dict

Nested dictionary indicating channels, reduction functions and metrics to be used. str channel -> U(function,None) reduction -> str metric If not of depth three, tree will be filled with None.

sub_bg: set

multichannel_ops: dict

Methods

__init__(tree[, sub_bg, multichannel_ops])	Parameters
default()
from_dict(d)
from_meta(meta)
from_yaml(source)	Returns instance from a yaml filename or stdin
guess_from_meta(store_name[, suffix])	Find the microscope used from the h5 metadata.
to_dict([iterable])	Recursive function to return a nested dictionary of the attributes of the class instance.
to_yaml([path])	Returns a yaml stream of the attributes of the class instance.
update(name, new_value)	Update values recursively if name is a dictionary, replace data where existing found or add if not.

classmethod from_yaml(source)

Returns instance from a yaml filename or stdin

static guess_from_meta(store_name, suffix='fast')

Find the microscope used from the h5 metadata.

Parameters

store_namestr or Path

For a h5 file

suffixstr

Added at the end of the predicted parameter set

to_dict(iterable='null')

Recursive function to return a nested dictionary of the attributes of the class instance.

Return type

Dict

to_yaml(path=None)

Returns a yaml stream of the attributes of the class instance. If path is provided, the yaml stream is saved there.

Parameters

pathUnion[PosixPath, str]

Output path.

update(name, new_value)

Update values recursively if name is a dictionary, replace data where existing found or add if not. It warns against type changes.

If the existing structure under name is a dictionary, it looks for the first occurrence and modifies it accordingly.

If a leaf node that is to be changed is a collection, it adds the new elements.