Add lineage tree view - Githubissues

cmalinmayor commented 2 months ago

Features of lineage tree view:

[x] See a lineage tree view of a result when tracking is done
[x] Colors in the tree view match the output segmentation/points/tracks
[x] Click on a node in the lineage tree view and navigate to the data (time and x/y/z) (keep the zoom)
[x] Click on point or label and select the point in the tree view (keep the zoom level of the tree view and pan)
[x] Add a highlight (colored outline and size) to the currently selected node in the tree view. Also highlight the point (colored outline, maybe size) in the data of the currently selected node
[x] Navigate with arrow keys along lineage (up/down). Decide what to do about divisions (do the side arrow keys do anything?)
[x] View just selected lineage(s) instead of all of them in the tree view
[x] Resetting the view/zoom of the tree widget when navigating with arrows (bug or feature?)
[x] Toggle didn't update in the UI when pressing L

Backend changes needed:

[x] Make a output track ID that is used to recolor the output segmentation or points and tracks
[x] Output a recolored points layer along with seg and track (even if you have an input segmentation)
[x] Save tracks_df in view controller only (not run)
[ ] Look at efficiency - it is kinda slow right now
[x] Refactor Layers into separate classes
[x] Revisit if the layers should hold onto the view controller or not (leaning yes)
[x] Revisit the lineage only mode changing (should we have a signal? Or just do the layers individually)
[x] Push motile toolbox track ids starting at 1 change

cmalinmayor commented 1 month ago

https://github.com/napari/napari/issues/6586 - This is related to the weird black ends of tracks on my computer, probably.

cmalinmayor commented 1 week ago

[x] Point size and/or outline size when selecting
[x] Tree widget check for tracks at initialization
[x] Scaling of layers when moving camera - store scale in Tracks object
[x] Make axis flipping generic, and call functions for navigation based on current axis orgientation
[x] Lineage selection separate from node selection for tree view
[x] Check coloring of tails in absence of segmentation
[x] Scaling/spacing - add keybinds to zoom only in x or y
[ ] Update README with all controls
[ ] Docstrings
[ ] Tests for non-UI functions
[x] Bug: Edges show up after clearing tree view for new run
[x] re-space out lineages in lineage view

funkelab / motile_napari_plugin