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Feature: Add basic progress indicator & activity info #33

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Feature: Add basic progress indicator & activity info #33

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a1854c9
Add basic progress indicator & activity info
psobolewskiPhD Aug 9, 2022
69db5db
Merge remote-tracking branch 'upstream/main' into feature/progress_bars
psobolewskiPhD Aug 26, 2022
4e1ba9e
Merge branch 'main' into feature/progress_bars
psobolewskiPhD Jun 19, 2023
a041396
Merge branch 'main' into feature/progress_bars
psobolewskiPhD Sep 13, 2024
5f95e78
Merge branch 'main' into feature/progress_bars
psobolewskiPhD Sep 23, 2024
e3c8921
Merge branch 'main' into feature/progress_bars
psobolewskiPhD Sep 25, 2024
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14 changes: 10 additions & 4 deletions cellpose_napari/_dock_widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@

from napari import Viewer
from napari.layers import Image, Shapes
from napari.utils.notifications import show_info

from magicgui import magicgui
import sys

Expand Down Expand Up @@ -58,7 +60,7 @@ def _deco(func):
return func
return _deco

@thread_worker
@thread_worker(progress=True)
@no_grad()
def run_cellpose(image, model_type, custom_model, channels, channel_axis, diameter,
resample, cellprob_threshold,
Expand All @@ -69,12 +71,16 @@ def run_cellpose(image, model_type, custom_model, channels, channel_axis, diamet
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}')

show_info('(Down)Loading models...')

if model_type=='custom':
CP = models.CellposeModel(pretrained_model=custom_model, gpu=True)
else:
CP = models.CellposeModel(model_type=model_type, gpu=True)

print(cellprob_threshold, flow_threshold)
show_info('Running Segmentation...')

masks, flows_orig, _ = CP.eval(image,
channels=channels,
channel_axis=channel_axis,
Expand All @@ -94,7 +100,7 @@ def run_cellpose(image, model_type, custom_model, channels, channel_axis, diamet
flows_orig = flows
return masks, flows_orig

@thread_worker
@thread_worker(progress=True)
def compute_diameter(image, channels, model_type):
from cellpose import models
model_type0 = model_type if model_type in CP_models[:4] else "cyto3"
Expand All @@ -105,7 +111,7 @@ def compute_diameter(image, channels, model_type):
del CP
return diam

@thread_worker
@thread_worker(progress=True)
def compute_masks(masks_orig, flows_orig, cellprob_threshold, flow_threshold):
from cellpose.dynamics import resize_and_compute_masks

Expand Down
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