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Added the ability to set a custom stub cell value instead of np.nan #74

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merged 8 commits into from
Mar 28, 2022
Merged

Added the ability to set a custom stub cell value instead of np.nan #74

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f9699f9
Added the ability to set a custom stub cell value
freemansw1 Feb 18, 2022
49a160b
Switched names around as suggested, added metadata
freemansw1 Mar 7, 2022
c4ed4aa
Merge branch 'climate-processes:main' into non-tracked-cell-update
freemansw1 Mar 14, 2022
a7edce9
Reformatting from Black
freemansw1 Mar 14, 2022
59726ee
Revert "Reformatting from Black"
freemansw1 Mar 14, 2022
bdf65b6
Black formatting to tracking.py
freemansw1 Mar 14, 2022
7e7735b
Merge branch 'dev' into non-tracked-cell-update
freemansw1 Mar 14, 2022
44e863d
Merge branch 'dev' into non-tracked-cell-update
freemansw1 Mar 28, 2022
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24 changes: 18 additions & 6 deletions tobac/tracking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ def linking_trackpy(
adaptive_step=None,
adaptive_stop=None,
cell_number_start=1,
cell_number_unassigned=-1,
):
"""
Function to perform the linking of features in trajectories
Expand All @@ -42,6 +43,10 @@ def linking_trackpy(
flag choosing method used for feature detection
method_linking: str('predict' or 'random')
flag choosing method used for trajectory linking
cell_number_unassigned: int
Number to set the unassigned/non-tracked cells to. By default, this is -1.
Note that if you set this to `np.nan`, the data type of 'cell' will
change to float.
"""
# from trackpy import link_df
import trackpy as tp
Expand Down Expand Up @@ -139,12 +144,17 @@ def linking_trackpy(
# logging.debug("trajectories_cell.shape[0]: "+ str(trajectories_cell.shape[0]))

if trajectories_cell.shape[0] < stubs:
# logging.debug("cell" + str(cell)+ " is a stub ("+str(trajectories_cell.shape[0])+ "), setting cell number to Nan..")
stub_cell_nums.append(cell)

trajectories_unfiltered.loc[
trajectories_unfiltered["cell"].isin(stub_cell_nums), "cell"
] = np.nan
logging.debug(
"cell"
+ str(cell)
+ " is a stub ("
+ str(trajectories_cell.shape[0])
+ "), setting cell number to "
+ str(cell_number_unassigned)
)
trajectories_unfiltered.loc[
trajectories_unfiltered["cell"] == cell, "cell"
] = cell_number_unassigned

trajectories_filtered = trajectories_unfiltered

Expand All @@ -161,6 +171,8 @@ def linking_trackpy(
# logging.debug('start adding cell time to trajectories')
trajectories_filtered_filled = trajectories_filtered_unfilled
trajectories_final = add_cell_time(trajectories_filtered_filled)
# Add metadata
trajectories_final.attrs["cell_number_unassigned"] = cell_number_unassigned

# add coordinate to raw features identified:
logging.debug("start adding coordinates to detected features")
Expand Down