Skip to content

Fix #605: make background_array optional when skip_classification=True #607

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
KpradeepKumar25 wants to merge 2 commits into
base: main
Choose a base branch
from
Open

Fix #605: make background_array optional when skip_classification=True #607

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
00e1226
Fix: make background_array optional when skip_classification=True
KpradeepKumar25 Mar 21, 2026
317caa3
Fix argument order and add ValueError for missing background_array
KpradeepKumar25 Mar 21, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 9 additions & 3 deletions cellfinder/core/main.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,8 @@

def main(
signal_array: types.array,
background_array: types.array,
voxel_sizes: Tuple[float, float, float],
background_array: Optional[types.array] = None,
start_plane: int = 0,
end_plane: int = -1,
trained_model: Optional[os.PathLike] = None,
Expand Down Expand Up @@ -55,10 +55,11 @@ def main(
----------
signal_array : numpy.ndarray or dask array
3D array representing the signal data in z, y, x order.
background_array : numpy.ndarray or dask array
3D array representing the signal data in z, y, x order.
voxel_sizes : 3-tuple of floats
Size of your voxels in the z, y, and x dimensions (microns).
background_array : numpy.ndarray or dask array, optional
3D array representing the background data in z, y, x order.
Required when skip_classification=False. Defaults to None.
start_plane : int
First plane index to process (inclusive, to process a subset of the
data).
Expand Down Expand Up @@ -224,6 +225,11 @@ def main(
detect_finished_callback(points)

if not skip_classification:
if background_array is None:
raise ValueError(
"background_array is required when "
"skip_classification=False"
)
install_path = None
model_weights = prep.prep_model_weights(
model_weights, install_path, model
Expand Down
Loading