diff --git a/NOTES b/NOTES new file mode 100644 index 0000000..07702aa --- /dev/null +++ b/NOTES @@ -0,0 +1,35 @@ +# REFACTOR: + - merge multiple solver classes methods into constructor to make a single deeper function + +# TODO: + - IMPORTANT: free nodes after each hierarchy insertation to database and measure performance. + - IMPORTANT: refactor widget to use a tab per option (segment, link, track) + - add warning when DB already contains data. + - create homepage/docs. + - document config + - document database + - option to lock segmentations from hypothesis viz widget + +# NOTES: + - heuristic optimizer: + - add monte-carlo (probabilist) moves into local search function + - local search by removing a node and trying to add its overlapping nodes + + - slurm: + - segment: 1hr 30min, 790 jobs + - link: 30min, 789 jobs + - track 1st: 2hr 30min, 8 jobs of 100 time points + overlap + - track 2nd: 2hr, 8 jobs of 100 time points + overlap + - export: 20min + - total: about 7 hours + - NOTES: + - fix window overlap sql solution update by adding parents only when it already exists on solution + - segment step memory usage must be improved, with Daxi dataset it's using about 100GB per frame + - tracks should be divided into smaller chunks + - reduce tracking model build time with vector variables + +# ARTICLE: + - experiments comparing tracking results from essemble of connected components, watershed, cellpose, stardist vs their accuracy alone; + - experiments comparing results from binary contour (their own algorithm post processing) vs contour obtained from network output directly; + - cell-tracking challenge benchmark; + - qualitative results our dataset and jan funke datasets; diff --git a/pyproject.toml b/pyproject.toml index e96c68a..148f528 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,6 +40,11 @@ asv = "^0.5.1" "testing.postgresql" = "^1.3.0" pytrackmate = {git = "https://github.com/hadim/pytrackmate.git"} +[tool.poetry.extras] +flow = [ + "torch", +] + [tool.poetry.scripts] ultrack = "ultrack.cli.main:main"