motile_tracker.data_model.actions

This module contains all the low level actions used to control a Tracks object. Low level actions should control these aspects of Tracks:

adding/removing nodes and edges to/from the segmentation and graph

Updating the segmentation and graph attributes that are controlled by the segmentation.

Currently, position and area for nodes, and IOU for edges. - Keeping track of information needed to undo the given action. For removing a node, this means keeping track of the incident edges that were removed, along with their attributes.

The low level actions do not contain application logic, such as manipulating track ids, or validation of “allowed” actions. The actions should work on candidate graphs as well as solution graphs. Action groups can be constructed to represent application-level actions constructed from many low-level actions.

Classes

`TracksAction`
`ActionGroup`
`AddNodes`	Action for adding new nodes. If a segmentation should also be added, the
`DeleteNodes`	Action of deleting existing nodes
`UpdateNodeSegs`	Action for updating the segmentation associated with nodes. Cannot mix adding
`UpdateNodeAttrs`	Action for user updates to node attributes. Cannot update protected
`AddEdges`	Action for adding new edges
`DeleteEdges`	Action for deleting edges
`UpdateTrackID`

Module Contents

class motile_tracker.data_model.actions.TracksAction(tracks: motile_tracker.data_model.tracks.Tracks)

tracks

abstract inverse() → TracksAction

Get the inverse of this action. Calling this function does undo the action, since the change is applied in the action constructor.

Raises:

NotImplementedError: if the inverse is not implemented in the subclass

Returns:

TracksAction: An action that un-does this action, bringing the tracks: back to the exact state it had before applying this action.

class motile_tracker.data_model.actions.ActionGroup(tracks: motile_tracker.data_model.tracks.Tracks, actions: list[TracksAction])

Bases: TracksAction

actions

inverse() → ActionGroup

Get the inverse of this action. Calling this function does undo the action, since the change is applied in the action constructor.

Raises:

NotImplementedError: if the inverse is not implemented in the subclass

Returns:

TracksAction: An action that un-does this action, bringing the tracks: back to the exact state it had before applying this action.

class motile_tracker.data_model.actions.AddNodes(tracks: motile_tracker.data_model.tracks.Tracks, nodes: list[motile_tracker.data_model.tracks.Node], attributes: motile_tracker.data_model.tracks.Attrs, pixels: list[motile_tracker.data_model.tracks.SegMask] | None = None)

Bases: TracksAction

Action for adding new nodes. If a segmentation should also be added, the pixels for each node should be provided. The label to set the pixels will be taken from the node id. The existing pixel values are assumed to be zero - you must explicitly update any other segmentations that were overwritten using an UpdateNodes action if you want to be able to undo the action.

nodes

times

positions

pixels = None

attributes

inverse(): Invert the action to delete nodes instead

_apply(): Apply the action, and set segmentation if provided in self.pixels

class motile_tracker.data_model.actions.DeleteNodes(tracks: motile_tracker.data_model.tracks.Tracks, nodes: list[motile_tracker.data_model.tracks.Node], pixels: list[motile_tracker.data_model.tracks.SegMask] | None = None)

Bases: TracksAction

Action of deleting existing nodes If the tracks contain a segmentation, this action also constructs a reversible operation for setting involved pixels to zero

nodes

attributes

pixels

inverse(): Invert this action, and provide inverse segmentation operation if given

_apply()

ASSUMES THERE ARE NO INCIDENT EDGES - raises valueerror if an edge will be removed by this operation Steps: - For each node

set pixels to 0 if self.pixels is provided

Remove nodes from graph

class motile_tracker.data_model.actions.UpdateNodeSegs(tracks: motile_tracker.data_model.tracks.Tracks, nodes: list[motile_tracker.data_model.tracks.Node], pixels: list[motile_tracker.data_model.tracks.SegMask], added: bool = True)

Bases: TracksAction

Action for updating the segmentation associated with nodes. Cannot mix adding and removing pixels from segmentation: the added flag applies to all nodes

nodes

pixels

added = True

inverse(): Restore previous attributes

_apply(): Set new attributes

class motile_tracker.data_model.actions.UpdateNodeAttrs(tracks: motile_tracker.data_model.tracks.Tracks, nodes: list[motile_tracker.data_model.tracks.Node], attrs: motile_tracker.data_model.tracks.Attrs)

Bases: TracksAction

Action for user updates to node attributes. Cannot update protected attributes (time, area, track id), as these are controlled by internal application logic.

nodes

prev_attrs

new_attrs

inverse(): Restore previous attributes

_apply(): Set new attributes

class motile_tracker.data_model.actions.AddEdges(tracks: motile_tracker.data_model.tracks.Tracks, edges: list[motile_tracker.data_model.tracks.Edge])

Bases: TracksAction

Action for adding new edges

edges

inverse(): Delete edges

_apply(): Steps: - add each edge to the graph. Assumes all edges are valid (they should be checked at this point already)

class motile_tracker.data_model.actions.DeleteEdges(tracks: motile_tracker.data_model.tracks.Tracks, edges: list[motile_tracker.data_model.tracks.Edge])

Bases: TracksAction

Action for deleting edges

edges

inverse(): Restore edges and their attributes

_apply(): Steps: - Remove the edges from the graph

class motile_tracker.data_model.actions.UpdateTrackID(tracks: motile_tracker.data_model.solution_tracks.SolutionTracks, start_node: motile_tracker.data_model.tracks.Node, track_id: int)

Bases: TracksAction

start_node

old_track_id

new_track_id

inverse() → TracksAction: Restore the previous track_id

_apply(): Assign a new track id to the track starting with start_node.