vanvalenlab / deepcell-tracking / 71
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Refactor CellTracker with dynamic programming! (#12)

* Refactor class to camel case `CellTracker`.

* `create_track` no longer calls `get_features`, using cached `frame_features` via `get_frame_features` helper function instead.

* use coordinates='rc' to avoid a warning.

* Add resize utility and replace the resize calls in sub_area and get_features.

* add `get_frame`, `get_cells_in_frame`, `_build_cost_matrix`, and `get_input_pairs` as  helper functions.

* update `clean_up_annotations` with helper functions and fix uuid bug

* call `get_features` on specific frame and label (no lists) and remove `X` and `y` from function arguments.

* change `_track_cells` to `track_cells` as it is the main entrypoint.

* initialize track in init.  call `intialize_tracks` inside `track_cells`

* convert self.feature_shape from a dict to a function call with `get_feature_shape`

* `track_frame_features` is not the correct shape, index into first frame.

* refactor `_compute_feature` to `compute_distance`, and compute norm distance on axis=0 simultaneously.

* cache feature future_area in `self.tracks`

* move capped track check to get_input_pairs and do all pair assignments at once.

* use the index of the frame to update new tracks and parent tracks.

* when adding track data to an existing track, fetch it from frame_features instead of calling get_features

* update tests for fetch_track_feature, remove `absl` as a dependency.

1351 of 1992 relevant lines covered (67.82%)

2.72 hits per line

Jobs
ID Job ID Ran Files Coverage
1 71.1 3
68.07
 Travis Job 71.1
2 71.2 3
68.07
 Travis Job 71.2
3 71.3 3
68.07
 Travis Job 71.3
4 71.4 3
67.32
 Travis Job 71.4
Source Files on build 71