motile_plugin.data_views

Submodules

• motile_plugin.data_views.views
• motile_plugin.data_views.views_coordinator

Classes

TreeWidget	pyqtgraph-based widget for lineage tree visualization and navigation
TrackGraph	Extended tracks layer that holds the track information and emits and responds
TrackLabels	Extended labels layer that holds the track information and emits
TrackPoints	Extended points layer that holds the track information and emits and
NodeSelectionList	Updates the current selection (0, 1, or 2) of nodes. Sends a signal on every update.
TracksViewer	Purposes of the TracksViewer:

Package Contents

class motile_plugin.data_views.TreeWidget(viewer: napari.Viewer)

Bases: qtpy.QtWidgets.QWidget

pyqtgraph-based widget for lineage tree visualization and navigation

track_df

lineage_df

graph = None

mode = 'all'

feature = 'tree'

view_direction = 'vertical'

tracks_viewer

selected_nodes

tree_widget: TreePlot

mode_widget

feature_widget

navigation_widget

keyPressEvent(event: qtpy.QtGui.QKeyEvent) → None

Handle key press events.

delete_node()

Delete a node.

create_edge()

Create an edge.

delete_edge()

Delete an edge.

undo()

Undo action.

redo()

Redo action.

toggle_display_mode()

Toggle display mode.

toggle_feature_mode()

Toggle feature mode.

set_mouse_enabled(x: bool, y: bool)

Enable or disable mouse zoom scrolling in X or Y direction.

keyReleaseEvent(ev)

Reset the mouse scrolling when releasing the X/Y key

_update_selected()

Called whenever the selection list is updated. Only re-computes the full graph information when the new selection is not in the lineage df (and in lineage mode)

_update_track_data(reset_view: bool | None = None) → None

Called when the TracksViewer emits the tracks_updated signal, indicating that a new set of tracks should be viewed.

_set_mode(mode: str) → None

Set the display mode to all or lineage view. Currently, linage view is always horizontal and all view is always vertical.

Args:

mode (str): The mode to set the view to. Options are “all” or “lineage”

_set_feature(feature: str) → None

Set the feature mode to ‘tree’ or ‘area’. For this the view is always horizontal.

Args:

feature (str): The feature to plot. Options are “tree” or “area”

_update_lineage_df() → None

Subset dataframe to include only nodes belonging to the current lineage

class motile_plugin.data_views.TrackGraph(name: str, tracks_viewer: motile_plugin.data_views.views_coordinator.tracks_viewer.TracksViewer)

Bases: napari.layers.Tracks

Extended tracks layer that holds the track information and emits and responds to dynamics visualization signals

tracks_viewer

tracks_layer_graph

colormap = 'turbo'

_refresh()

Refreshes the displayed tracks based on the graph in the current tracks_viewer.tracks

update_track_visibility(visible: list[int] | str) → None

Optionally show only the tracks of a current lineage

class motile_plugin.data_views.TrackLabels(viewer: napari.Viewer, data: numpy.array, name: str, opacity: float, scale: tuple, tracks_viewer: motile_plugin.data_views.views_coordinator.tracks_viewer.TracksViewer)

Bases: napari.layers.Labels

Extended labels layer that holds the track information and emits and responds to dynamics visualization signals

property _type_string: str

tracks_viewer

node_properties

viewer

_get_node_properties()

redo()

Overwrite the redo functionality of the labels layer and invoke redo action on the tracks_viewer.tracks_controller first

undo()

Overwrite undo function and invoke undo action on the tracks_viewer.tracks_controller

_parse_paint_event(event_val)

_summary_

Args:

event_val (list[tuple]): A list of paint “atoms” generated by the labels layer.

Each atom is a 3-tuple of arrays containing: - a numpy multi-index, pointing to the array elements that were changed (a tuple with len ndims) - the values corresponding to those elements before the change - the value after the change

Returns:

tuple(int, list[tuple]): The new value, and a list of node update actions

defined by the time point and node update item Each “action” is a 2-tuple containing: - a numpy multi-index, pointing to the array elements that were changed (a tuple with len ndims) - the value before the change

_on_paint(event)

Listen to the paint event and check which track_ids have changed

_refresh()

Refresh the data in the labels layer

update_label_colormap(visible: list[int] | str) → None

Updates the opacity of the label colormap to highlight the selected label and optionally hide cells not belonging to the current lineage

new_colormap()

Extended version of existing function, to emit refresh signal to also update colors in other layers/widgets

_check_selected_label()

Check whether the selected label is larger than the current max_track_id and if so add it to the colormap (otherwise it draws in transparent color until the refresh event)

class motile_plugin.data_views.TrackPoints(name: str, tracks_viewer: motile_plugin.data_views.views_coordinator.tracks_viewer.TracksViewer)

Bases: napari.layers.Points

Extended points layer that holds the track information and emits and responds to dynamics visualization signals

property _type_string: str

tracks_viewer

nodes

node_index_dict

_refresh()

Refresh the data in the points layer

_create_node_attrs(new_point: numpy.array) → tuple[numpy.array, dict]

Create attributes for a new node at given time point

_update_data(event)

Calls the tracks controller with to update the data in the Tracks object and dispatch the update

_update_selection()

Replaces the list of selected_nodes with the selection provided by the user

get_symbols(tracks: motile_plugin.data_model.Tracks, symbolmap: dict[motile_plugin.data_model.NodeType, str]) → list[str]

update_point_outline(visible: list[int] | str) → None

Update the outline color of the selected points and visibility according to display mode

Args:

visible (list[int] | str): A list of track ids, or “all”

class motile_plugin.data_views.NodeSelectionList

Bases: PyQt5.QtCore.QObject

Updates the current selection (0, 1, or 2) of nodes. Sends a signal on every update. Stores a list of node ids only.

list_updated

_list = []

add(item, append: bool | None = False)

Append or replace an item to the list, depending on the number of items present and the keyboard modifiers used. Emit update signal

add_list(items: list, append: bool | None = False)

Add nodes from a list and emit a single signal

flip()

Change the order of the items in the list

reset()

Empty list and emit update signal

__getitem__(index)

__len__()

class motile_plugin.data_views.TracksViewer(viewer: napari.viewer)

Purposes of the TracksViewer: - Emit signals that all widgets should use to update selection or update

the currently displayed Tracks object

• Storing the currently displayed tracks

• Store shared rendering information like colormaps (or symbol maps)

tracks_updated

classmethod get_instance(viewer=None)

viewer

colormap

symbolmap: dict[motile_plugin.data_model.NodeType, str]

mode = 'all'

tracks = None

visible = None

tracking_layers

selected_nodes

tracks_list

set_keybinds()

_refresh(node: str | None = None, refresh_view: bool = False) → None

Call refresh function on napari layers and the submit signal that tracks are updated Restore the selected_nodes, if possible

update_tracks(tracks: motile_plugin.data_model.Tracks, name: str) → None

Stop viewing a previous set of tracks and replace it with a new one. Will create new segmentation and tracks layers and add them to the viewer.

Args:

tracks (motile_plugin.core.Tracks): The tracks to visualize in napari. name (str): The name of the tracks to display in the layer names

toggle_display_mode(event=None) → None

Toggle the display mode between available options

set_display_mode(mode: str) → None

Update the display mode and call to update colormaps for points, labels, and tracks

filter_visible_nodes() → list[int]

Construct a list of track_ids that should be displayed

update_highlights() → None

If the time dimension is changed, update the highlighting in the seg layer

update_selection() → None

Sets the view and triggers visualization updates in other components

view_external_tracks(tracks: motile_plugin.data_model.SolutionTracks, name: str) → None

View tracks created externally. Assigns tracklet ids, adds a hypothesis dimension to the segmentation, and relabels the segmentation based on the assigned track ids. Then calls update_tracks.

Args:

tracks (Tracks): A tracks object to view, created externally from the plugin name (str): The name to display in napari layers

set_napari_view() → None

Adjust the current_step of the viewer to jump to the last item of the selected_nodes list

delete_node(event=None)

Calls the tracks controller to delete currently selected nodes

set_split_node(event=None)

set_endpoint_node(event=None)

set_linear_node(event=None)

delete_edge(event=None)

Calls the tracks controller to delete an edge between the two currently selected nodes

create_edge(event=None)

Calls the tracks controller to add an edge between the two currently selected nodes

undo(event=None)

redo(event=None)