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Add GPU and batch size support to Cellpose #3

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Add GPU and batch size support to Cellpose #3

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2 changes: 2 additions & 0 deletions src/vpt_plugin_cellpose/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ class CellposeSegProperties:
model_dimensions: str
version: str
custom_weights: Optional[str] = None
use_gpu: bool = False


@dataclass(frozen=True)
Expand All @@ -18,3 +19,4 @@ class CellposeSegParameters:
flow_threshold: float
mask_threshold: float
minimum_mask_size: int
batch_size: Optional[int] = 8 # default in Cellpose v1*
5 changes: 3 additions & 2 deletions src/vpt_plugin_cellpose/predict.py
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Expand Up @@ -26,9 +26,9 @@ def run(images: ImageSet, properties: CellposeSegProperties, parameters: Cellpos
return np.zeros((image.shape[0],) + image.shape[1:-1])

if properties.custom_weights:
model = models.CellposeModel(gpu=False, pretrained_model=properties.custom_weights, net_avg=False)
model = models.CellposeModel(gpu=properties.use_gpu, pretrained_model=properties.custom_weights, net_avg=False)
else:
model = models.Cellpose(gpu=False, model_type=properties.model, net_avg=False)
model = models.Cellpose(gpu=properties.use_gpu, model_type=properties.model, net_avg=False)

to_segment_z = list(set(range(image.shape[0])).difference(empty_z_levels))
mask = model.eval(
Expand All @@ -42,6 +42,7 @@ def run(images: ImageSet, properties: CellposeSegProperties, parameters: Cellpos
min_size=parameters.minimum_mask_size,
tile=True,
do_3D=(properties.model_dimensions == "3D"),
batch_size=parameters.batch_size,
)[0]
mask = mask.reshape((len(to_segment_z),) + image.shape[1:-1])
for i in empty_z_levels:
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