Morphology

Functions related to analysing or manipulating neuron morpology.

`navis_fastcore.synapse_flow_centrality(node_ids, parent_ids, presynapses, postsynapses, mode='sum')`

Calculate synapse flow centrality for this neuron.

Please note that this implementation currently produces slightly different results than the implementation in navis. I'm not sure why that is but the differences seem to be negligible.

PARAMETER	DESCRIPTION
`node_ids`	`Array of int32 node IDs.` TYPE: `(N, ) array`
`parent_ids`	`Array of parent IDs for each node. Root nodes' parents must be -1.` TYPE: `(N, ) array`
`presynapses`	`Array of number of presynapses associated with each node.` TYPE: `(N, ) uint32 array`
`postsynapses`	`Array of number of postsynapses associated with each node.` TYPE: `(N, ) uint32 array`
`mode`	`The mode to calculate the flow centrality. "centrifugal" will calculate the flow from the root to the leaves, "centripetal" will calculate the flow from the leaves to the root, and "sum" will calculate the sum of both.` TYPE: `"centrifugal" \| "centripetal" \| "sum"` DEFAULT: `'sum'`

RETURNS	DESCRIPTION
`cc`	Synapse flow centrality for each node. TYPE: `(N, ) uint32 array`

`navis_fastcore.strahler_index(node_ids, parent_ids, method='standard', to_ignore=None, min_twig_size=None)`

Calculcate Strahler Index.

PARAMETER	DESCRIPTION
`node_ids`	`Array node IDs.` TYPE: `(N, ) array`
`parent_ids`	`Array of parent IDs for each node. Root nodes' parents must be -1.` TYPE: `(N, ) array`
`method`	`Method used to calculate Strahler indices: 'standard' will use the method described above; 'greedy' will always increase the index at converging branches whether these branches have the same index or not.` TYPE: `'standard' \| 'greedy'` DEFAULT: `'standard'`
`to_ignore`	`List of node IDs to ignore. Must be the FIRST node of the branch. Excluded branches will not contribute to Strahler index calculations and instead be assigned the SI of their parent branch.` TYPE: `iterable` DEFAULT: `None`
`min_twig_size`	`If provided, will ignore twigs with fewer nodes than this. Instead, they will be assigned the SI of their parent branch.` TYPE: `int` DEFAULT: `None`

RETURNS	DESCRIPTION
`strahler_index`	Strahler Index for each node. TYPE: `(N, ) int array`

Examples:

>>> import navis_fastcore as fastcore
>>> import numpy as np
>>> node_ids = np.arange(8)
>>> parent_ids = np.array([-1, 0, 1, 2, 1, 4, 5, 5])
>>> fastcore.strahler_index(node_ids, parent_ids)
array([2, 2, 1, 1, 2, 2, 1, 1], dtype=int32)

`navis_fastcore.prune_twigs(node_ids, parent_ids, threshold, weights=None, mask=None)`

Prune twigs shorter than a given threshold.

PARAMETER	DESCRIPTION
`node_ids`	`Array node IDs.` TYPE: `(N, ) array`
`parent_ids`	`Array of parent IDs for each node. Root nodes' parents must be -1.` TYPE: `(N, ) array`
`threshold`	`Twigs shorter than this threshold will be pruned.` TYPE: `float`
`weights`	Array of distances for each child -> parent connection. If ``None`` all node-to-node distances are set to 1. TYPE: `(N, ) float32 array` DEFAULT: `None`
`mask`	`Array of booleans to mask nodes that should not be pruned. Importantly, twigs with _any_ masked node will not be pruned.` TYPE: `(N, ) bool array` DEFAULT: `None`

RETURNS	DESCRIPTION
`keep`	Node IDs to keep. TYPE: `(M, ) integer array`

Examples:

>>> import navis_fastcore as fastcore
>>> import numpy as np
>>> node_ids = np.arange(7)
>>> parent_ids = np.array([-1, 0, 1, 2, 1, 4, 5])
>>> fastcore.prune_twigs(node_ids, parent_ids, 2)
array([0, 1, 4, 5, 6])
>>> mask = np.array([True, True, True, False, True, True, True])
>>> fastcore.prune_twigs(node_ids, parent_ids, 2, mask=mask)