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Update the logic for new nodes and track ids
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Pressing "m" now makes a new track as well as a new node. If you don't
press "m", it will always edit the previously selected track.

This mostly works the way I indended. Bugs include: erasing the node
throws a selection error. Probably other stuff I didn't get the chance
to test.
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@cmalinmayor
cmalinmayor committed Jan 13, 2025
1 parent df8437f commit 453d45f
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Showing 2 changed files with 112 additions and 80 deletions.
1 change: 1 addition & 0 deletions src/motile_tracker/data_model/solution_tracks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,7 @@ def _assign_tracklet_ids(self):
self.graph,
{node: {NodeAttr.TRACK_ID.value: track_id} for node in tracklet},
)
self.track_id_to_node[track_id] = list(tracklet)
track_id += 1
self.max_track_id = track_id - 1

Expand Down
191 changes: 111 additions & 80 deletions src/motile_tracker/data_views/views/layers/track_labels.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,45 @@
import napari
import numpy as np
from napari.utils import DirectLabelColormap
from napari.utils.action_manager import action_manager
from napari.utils.notifications import show_info
from napari.utils.translations import trans

if TYPE_CHECKING:
from motile_tracker.data_views.views_coordinator.tracks_viewer import TracksViewer
from motile_toolbox.candidate_graph.graph_attributes import NodeAttr


def new_label(layer: TrackLabels):
"""Set the currently selected label to the largest used label plus one."""
print("overriding new label")
_new_label(layer, new_track_id=True)


def _new_label(layer: TrackLabels, new_track_id=True):
if isinstance(layer.data, np.ndarray):
new_selected_label = np.max(layer.data) + 1
if layer.selected_label == new_selected_label:
show_info(
trans._(
"Current selected label is not being used. You will need to use it first "
"to be able to set the current select label to the next one available",
)
)
else:
layer.selected_label = new_selected_label
if new_track_id:
new_selected_track = layer.tracks_viewer.tracks.get_next_track_id()
layer.selected_track = new_selected_track
layer.colormap.color_dict[new_selected_label] = (
layer.tracks_viewer.colormap.map(layer.selected_track)
)
else:
show_info(
trans._("Calculating empty label on non-numpy array is not supported")
)


class TrackLabels(napari.layers.Labels):
"""Extended labels layer that holds the track information and emits
and responds to dynamics visualization signals"""
Expand All @@ -31,7 +64,7 @@ def __init__(
):
self.tracks_viewer = tracks_viewer
self.node_properties = self._get_node_properties()
self.current_track_id = None
self.selected_track = None

colormap = DirectLabelColormap(
color_dict={
Expand Down Expand Up @@ -200,7 +233,7 @@ def _on_paint(self, event):
if existing_node:
to_update_bigger.append((new_value, all_pixels))
else:
to_add.append((new_value, self.current_track_id, all_pixels))
to_add.append((new_value, self.selected_track, all_pixels))

self.tracks_viewer.tracks_controller.update_segmentations(
to_delete, to_update_smaller, to_update_bigger, to_add, current_timepoint
Expand Down Expand Up @@ -290,95 +323,93 @@ def update_selected_label(self):
self.selected_label = self.tracks_viewer.selected_nodes[0]

def _ensure_valid_label(self, event):
"""Make sure a valid label is selected, because it is not allowed to paint with a label that already exists at a different timepoint.
"""Make sure a valid label is selected, because it is not allowed to paint with a
label that already exists at a different timepoint.
Scenarios:
1. If a node with the selected label value (node id) exists at a different time point, check if there is any node with the same track_id at the current time point
1. If a node with the selected label value (node id) exists at a different time point,
check if there is any node with the same track_id at the current time point
1.a if there is a node with the same track id, select that one, so that it can be used to update an existing node
1.b if there is no node with the same track id, and the node_id value does not yet exist in the colormap dict, create a new node id and paint with the track_id of the selected label. Make sure to add it to the colormap dict. This can be used to add a new node with the same track id at a time point where it does not (yet) exist (anymore).
2. if there is no existing node with this value in the graph, but the node id is in the colormap dict, it means that the node was created but has not been used to paint with. Retrieve the track_id from self.current_track_id and use it to find if there are any nodes of this track id at current time point
3. If no node with this label exists yet, it is valid and can be used to start a new track id. Therefore, create a new node id and map a new color. Add it to the dictionary.
1.b if there is no node with the same track id, create a new node id and paint with the track_id of the selected label.
This can be used to add a new node with the same track id at a time point where it does not (yet) exist (anymore).
2. if there is no existing node with this value in the graph, it is assume that you want to add a node with the current track id
Retrieve the track_id from self.current_track_id and use it to find if there are any nodes of this track id
at current time point
3. If no node with this label exists yet, it is valid and can be used to start a new track id.
Therefore, create a new node id and map a new color. Add it to the dictionary.
4. If a node with the label exists at the current time point, it is valid and can be used to update the existing node in a paint event. No action is needed"""

self.events.selected_label.disconnect(self._ensure_valid_label)
if self.tracks_viewer.tracks is not None:
current_timepoint = self.viewer.dims.current_step[0]
t_values = np.array(self.node_properties["t"])
node_ids = np.array(self.node_properties["node_id"])

# check if a node with this node id exists anywhere
index = np.where(
(t_values == current_timepoint) & (node_ids == self.selected_label)
)[0]

if len(index) == 0:
if self.tracks_viewer.tracks.graph.has_node(
self.selected_label
): # selected label is not valid, select the nearest available one
self.current_track_id = self.tracks_viewer.tracks._get_node_attr(
self.selected_label, NodeAttr.TRACK_ID.value
# if a node with the given label is already in the graph
if self.tracks_viewer.tracks.graph.has_node(self.selected_label):
# Update the track id
self.selected_track = self.tracks_viewer.tracks._get_node_attr(
self.selected_label, NodeAttr.TRACK_ID.value
)
existing_time = self.tracks_viewer.tracks._get_node_attr(
self.selected_label, NodeAttr.TIME.value
)
if existing_time == current_timepoint:
# we are changing the existing node. This is fine
pass
else:
# if there is already a node in that track in this frame, edit that instead
edit = False
print(
self.tracks_viewer.tracks.track_id_to_node, self.selected_track
)

# is there any node with this track id at the current timepoint?
time_point_nodes = [
node
for node in self.tracks_viewer.tracks.graph.nodes()
if self.tracks_viewer.tracks.get_time(node) == current_timepoint
]
track_id_nodes = [
node
for node in time_point_nodes
if self.tracks_viewer.tracks._get_node_attr(
node, NodeAttr.TRACK_ID.value
)
== self.current_track_id
]

if len(track_id_nodes) > 0:
self.selected_label = track_id_nodes[
0
] # select the node with the same track id at the current time point
else:
color = self.colormap.color_dict[self.selected_label]
self.selected_label = (
np.max(self.data) + 1
) # pick an entirely new label, but use the same track id (color) by adding it to the colordict
self.colormap.color_dict[self.selected_label] = color
if (
self.selected_track
in self.tracks_viewer.tracks.track_id_to_node
):
for node in self.tracks_viewer.tracks.track_id_to_node[
self.selected_track
]:
if (
self.tracks_viewer.tracks._get_node_attr(
node, NodeAttr.TIME.value
)
== current_timepoint
):
# raise ValueError("Can't add new node with track id {self.selected_track} in time {current_timepoint}")

self.selected_label = node
edit = True
break

if not edit:
# use a new label, but the same track id
_new_label(self, new_track_id=False)
self.colormap = DirectLabelColormap(
color_dict=self.colormap.color_dict
)

# the current node does not exist in the graph. Find out if it should belong to a new track or if it belongs to an existing track id but has not been painted yet
elif self.selected_label in self.colormap.color_dict:
# is there a node with the associated track id at the current time point?
time_point_nodes = [
node
for node in self.tracks_viewer.tracks.graph.nodes()
if self.tracks_viewer.tracks.get_time(node) == current_timepoint
]
track_id_nodes = [
node
for node in time_point_nodes
if self.tracks_viewer.tracks._get_node_attr(
node, NodeAttr.TRACK_ID.value
)
== self.current_track_id
]
# the current node does not exist in the graph.
# Use the current selected_track as the track id (will be a new track if a new label was found with "m")
# Check that the track id is not already in this frame.
else:
# if there is already a node in that track in this frame, edit that instead
edit = False
if self.selected_track in self.tracks_viewer.tracks.track_id_to_node:
for node in self.tracks_viewer.tracks.track_id_to_node[
self.selected_track
]:
if (
self.tracks_viewer.tracks._get_node_attr(
node, NodeAttr.TIME.value
)
== current_timepoint
):
self.selected_label = node
edit = True
break
self.events.selected_label.connect(self._ensure_valid_label)

if len(track_id_nodes) > 0:
del self.colormap.color_dict[
self.selected_label
] # remove the unused label from the color_dict
self.selected_label = track_id_nodes[0]

# The currently selected_label does not exist in the graph nor in the colordict, it should be a new track
else:
# this node should belong to a new track, add it to the colormap
new_track_id = self.tracks_viewer.tracks.get_next_track_id()
self.colormap.color_dict[self.selected_label] = (
self.tracks_viewer.colormap.map(new_track_id)
)
self.colormap = DirectLabelColormap(
color_dict=self.colormap.color_dict
)
self.current_track_id = new_track_id
self.events.selected_label.connect(self._ensure_valid_label)
action_manager.register_action(
name="napari:new_label",
command=new_label,
keymapprovider=TrackLabels,
description="",
)

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