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[bugfix] use resize_and_compute_masks in compute_masks #57

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merged 2 commits into from
Sep 23, 2024
Merged

[bugfix] use resize_and_compute_masks in compute_masks #57

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d0d197b
use esize_and_compute_masks in compute_masks
psobolewskiPhD Sep 22, 2024
0d23ad4
Merge branch 'main' into fix/recompute_masks
psobolewskiPhD Sep 23, 2024
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16 changes: 6 additions & 10 deletions cellpose_napari/_dock_widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,8 @@ def run_cellpose(image, model_type, custom_model, channels, channel_axis, diamet
CP = models.CellposeModel(pretrained_model=custom_model, gpu=True)
else:
CP = models.CellposeModel(model_type=model_type, gpu=True)

print(cellprob_threshold, flow_threshold)
masks, flows_orig, _ = CP.eval(image,
channels=channels,
channel_axis=channel_axis,
Expand Down Expand Up @@ -105,22 +107,16 @@ def compute_diameter(image, channels, model_type):

@thread_worker
def compute_masks(masks_orig, flows_orig, cellprob_threshold, flow_threshold):
import cv2
from cellpose.utils import fill_holes_and_remove_small_masks
from cellpose.dynamics import get_masks
from cellpose.transforms import resize_image
from cellpose.dynamics import resize_and_compute_masks

#print(flows_orig[3].shape, flows_orig[2].shape, masks_orig.shape)
flow_threshold = (31.0 - flow_threshold) / 10.
if flow_threshold==0.0:
flow_threshold = 0.0
logger.debug('flow_threshold=0 => no masks thrown out due to model mismatch')
logger.debug(f'computing masks with cellprob_threshold={cellprob_threshold}, flow_threshold={flow_threshold}')
maski = get_masks(flows_orig[3].copy(), iscell=(flows_orig[2] > cellprob_threshold),
flows=flows_orig[1], threshold=flow_threshold*(masks_orig.ndim<3))
maski = fill_holes_and_remove_small_masks(maski)
maski = resize_image(maski, masks_orig.shape[-2], masks_orig.shape[-1],
interpolation=cv2.INTER_NEAREST)
maski, _ = resize_and_compute_masks(flows_orig[1], cellprob=flows_orig[2], cellprob_threshold=cellprob_threshold,
flow_threshold=flow_threshold, resize=(masks_orig.shape[-2], masks_orig.shape[-1]))

return maski

@magicgui(
Expand Down
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