Structure

class astrodendro.Structure(indices, values, children=[], idx=None, dendrogram=None)

Bases: object

A structure in the dendrogram, for example a leaf or a branch.

A structure that is part of a dendrogram knows which other structures it is related to. For example, it is possible to get the parent structure containing the present structure s by using the parent attribute:

>>> s.parent
<Structure type=branch idx=2152>

Likewise, the children attribute can be used to get a list of all sub-structures:

>>> s.children
[<Structure type=branch idx=1680>, <Structure type=branch idx=5771>]

A number of attributes and methods are available to explore the structure in more detail, such as the indices and values methods, which return the indices and values of the pixels that are part of the structure. These and other methods have a subtree= option, which if True (the default) returns the quantities related to structure and all sub-structures, and if False includes only the pixels that are part of the structure, but excluding any sub-structure.

Attributes Summary

ancestor	Find the ancestor of this leaf/branch non-recursively.
children	A list of all the sub-structures contained in the present structure.
descendants	Get a flattened list of all child leaves and branches.
height	This is defined as the minimum value in the children structures, or the peak value of the present structure if it has no children.
is_branch	Whether the present structure is a branch.
is_leaf	Whether the present structure is a leaf.
level	The level of the structure, i.e. how many structures need to be traversed to reach the present structure.
newick
parent	The parent structure containing the present structure.
smallest_index
vmax	The maximum value of pixels belonging to the branch (excluding sub-structure).
vmin	The minimum value of pixels belonging to the branch (excluding sub-structure).

Methods Summary

get_mask([shape, subtree])	Return a boolean mask outlining the structure.
get_npix([subtree])	Return the number of pixels in this structure.
get_peak([subtree])	Return (index, value) for the pixel with maximum value.
indices([subtree])	The indices of the pixels in this branch.
sorted_leaves([sort_key, reverse, subtree])	Return a list of sorted leaves.
values([subtree])	The values of the pixels in this branch.

Attributes Documentation

ancestor

Find the ancestor of this leaf/branch non-recursively.

This always returns an object (may return self if the object has no parent). Results are partially cached to reduce recursion depth. The caching assumes that once an object has been given a parent, that parent will never change.

This method should be equivalent to:

if self.parent == None:

return self

else:

return self.parent.ancestor

children

A list of all the sub-structures contained in the present structure.

descendants

Get a flattened list of all child leaves and branches.

height

This is defined as the minimum value in the children structures, or the peak value of the present structure if it has no children.

is_branch

Whether the present structure is a branch.

is_leaf

Whether the present structure is a leaf.

level

The level of the structure, i.e. how many structures need to be traversed to reach the present structure.

This is 0 for structures in the trunk, with values increasing in steps of 1 towards the leaves.

newick

parent

The parent structure containing the present structure.

smallest_index

vmax

The maximum value of pixels belonging to the branch (excluding sub-structure).

vmin

The minimum value of pixels belonging to the branch (excluding sub-structure).

Methods Documentation

get_mask(shape=None, subtree=True)

Return a boolean mask outlining the structure.

Parameters:

shapetuple, optional

The shape of the array upon which to compute the mask. This is only required if the structure is not attached to a dendrogram.

subtreebool, optional

Whether to recursively include all sub-structures in the mask.

Returns:

maskndarray

The mask outlining the structure (False values are used outside the structure, and True values inside).

get_npix(subtree=True)

Return the number of pixels in this structure.

Parameters:

subtreebool, optional

Whether to recursively include all sub-structures when counting the pixels.

Returns:

n_pixint

The number of pixels in this structure

get_peak(subtree=True)

Return (index, value) for the pixel with maximum value.

Parameters:

subtreebool, optional

Whether to recursively include all sub-structures when searching for the peak.

Returns:

indextuple

The n-dimensional index of the peak pixel

valuefloat

The value of the peak pixel

indices(subtree=True)

The indices of the pixels in this branch.

Parameters:

subtreebool, optional

Whether to recursively include all sub-structures

sorted_leaves(sort_key=<function Structure.<lambda>>, reverse=False, subtree=True)

Return a list of sorted leaves.

Parameters:

sort_keyfunction, optional

A function which given a structure will return a scalar that is then used for sorting. By default, this is set to a function that returns the peak value of a structure (including descendants).

reversebool, optional

Whether to reverse the sorting.

subtreebool, optional

Whether to recursively include all sub-structures in the list.

Returns:

leaveslist

A list of sorted leaves

values(subtree=True)

The values of the pixels in this branch.

Parameters:

subtreebool, optional

Whether to recursively include all sub-structures