Taylla: deleting a division crashed TrackEdit

[TeunHuijben]

[raeesahhy]

Hi Teun, just a note that's maybe related to this, sometimes when I delete a node it also seems to crash TrackEdit - the napari window freezes for hours and the Terminal doesn't show the usual 'refreshed' line that appears after I delete other nodes/add new edges etc.

[TeunHuijben]

Thanks for flagging @raeesahhy! I am sorry that you encounter this... I remember seeing these problems when deleting a cell that was about to divide, but I think that problem is fixed now. Did you pull the latest version of TrackEdit?

If you have more specific information about when this bug happens, I am happy to have a look :)

[raeesahhy]

Hi @TeunHuijben thanks for your reply! I just re-attempted it after pulling the latest version of TrackEdit and got the same error.

Just to check, this is how I should be pulling the latest version, right?
git clone https://github.com/royerlab/trackedit.git --recurse-submodules

Hmm, it happens when I delete the nodes around the edges of the dataset (those came from errors in segmentations that are actually just background signal/stray cells wandering too far). I could work around this by cropping the dataset. I haven't experimented with deleting nodes within the main region of the tissue, though, so I'm not sure if the nodes being at the edge are the reason for the freezing.

Below is the code in the Terminal, the most recent activity at the bottom in bold being where TrackEdit freezes. The five lines in italics above that is what happens when I managed to successfully delete a node and TrackEdit didn't freeze. The difference between the two situations was that the italicised node was a solitary track at the edge of the background, but the emboldened one was a network of incorrect tracks at the edge of the background. I hope that clarifies?

(trackedit) (base) [rhayatud@m3a117 scripts]$ python script_kidney_validate.py
/fs04/scratch2/ra84/trackedit/scripts/script_kidney_validate.py:10: DeprecationWarning: numpy.core is deprecated and has been renamed to numpy._core. The numpy._core namespace contains private NumPy internals and its use is discouraged, as NumPy internals can change without warning in any release. In practice, most real-world usage of numpy.core is to access functionality in the public NumPy API. If that is the case, use the public NumPy API. If not, you are using NumPy internals. If you would still like to access an internal attribute, use numpy._core.numeric.
sys.modules["numpy._core.numeric"] = np.core.numeric
Database copied to: /home/rhayatud/ra84_scratch2/raeesah_cell_tracking/trained_solution_to_db_v1.db
old database: trained_solution_to_db.db
new database: trained_solution_to_db_v1.db
new logfile: data_v1_changelog.txt
metadata_loaded: {'shape': [10, 7, 1498, 2096]}
Added missing column to db: generic
Warning: Imaging zarr file or channel not specified. Imaging data not shown.

Red flag summary:
Total red flags: 303
added: 264
removed: 39
Making new tracking view controller
/fs04/scratch2/ra84/trackedit/.pixi/envs/default/lib/python3.11/site-packages/napari/_vispy/layers/scalar_field.py:197: UserWarning: data shape (7, 1498, 2096) exceeds GL_MAX_TEXTURE_SIZE 2048 in at least one axis and will be downsampled. Rendering is currently in 3D mode.
warnings.warn(
/fs04/scratch2/ra84/trackedit/trackedit/utils/utils.py:63: FutureWarning: The _dock_widgets property is private and should not be used in any plugin code. Please use the dock_widgets property instead.
viewer.window._dock_widgets["Layer List"] = new_dock
/fs04/scratch2/ra84/trackedit/.pixi/envs/default/lib/python3.11/site-packages/napari/_vispy/layers/scalar_field.py:197: UserWarning: data shape (7, 1498, 2096) exceeds GL_MAX_TEXTURE_SIZE 2048 in at least one axis and will be downsampled. Rendering is currently in 3D mode.
warnings.warn(
/fs04/scratch2/ra84/trackedit/.pixi/envs/default/lib/python3.11/site-packages/napari/_vispy/layers/scalar_field.py:197: UserWarning: data shape (7, 1498, 2096) exceeds GL_MAX_TEXTURE_SIZE 2048 in at least one axis and will be downsampled. Rendering is currently in 3D mode.!
0.02s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
/fs04/scratch2/ra84/trackedit/.pixi/envs/default/lib/python3.11/site-packages/napari/layers/labels/labels.py:908: UserWarning: Contours are not displayed during 3D rendering!
DeleteEdges: [[ 9011726 10013005]]
refreshed

WARNING: Edge is rejected because merges are currently not allowed.
AddEdges: [[ 9010529 10013005]]
clearing annotations for edges: [[ 9010529 10013005]]
refreshed

DeleteEdges: [(8010177, np.int64(9011687)), (np.int64(9011687), 10012975), (np.int64(9011687), 10012826)]
DeleteNodes: [np.int64(9011687)]
clearing annotations for nodes: [np.int64(9011687)]
orphaned_children []
refreshed

DeleteEdges: [(np.int64(9011684), 10013127), (np.int64(9011684), 10013128), (8010445, np.int64(9011684))]
DeleteNodes: [np.int64(9011684)]
clearing annotations for nodes: [np.int64(9011684)]
orphaned_children []