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Update runcellpose.py (to fix the 'y_label unbound' error on MacOS using Cellpose 4 with MPS) #305

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Update runcellpose.py (to fix the 'y_label unbound' error on MacOS using Cellpose 4 with MPS) #305

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121 changes: 77 additions & 44 deletions active_plugins/runcellpose.py
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Original file line number Diff line number Diff line change
Expand Up @@ -895,57 +895,90 @@ def run(self, workspace):
"Failed to set GPU memory share. Please check your PyTorch installation. Not setting per-process memory share."
)

if self.specify_diameter.value:
MAX_RETRIES = 3
y_data = None
flows = None
last_exception = None

for attempt in range(MAX_RETRIES):
try:
y_data, flows, *_ = self.current_model.eval(
x_data,
z_axis=z_axis,
diameter=diam,
do_3D=self.do_3D.value,
anisotropy=anisotropy,
flow_threshold=self.flow_threshold.value,
cellprob_threshold=self.cellprob_threshold.value,
stitch_threshold=self.stitch_threshold.value, # is ignored if do_3D=True
min_size=self.min_size.value,
invert=self.invert.value,
LOGGER.info(
f"Cellpose Python v4 attempt {attempt + 1}/{MAX_RETRIES}"
)

except Exception as a:
print(f"Unable to create masks. Check your module settings. {a}")
finally:
if self.use_gpu.value and model.torch:
cleanup(self)
if not self.cache_model.value:
# Release the model's memory
self.current_model = None
self.current_model_params = None
else:
try:
y_data, flows, *_ = self.current_model.eval(
x_data,
# channel_axis=None,
# channels=channels,
z_axis=z_axis,
do_3D=self.do_3D.value,
anisotropy=anisotropy,
flow_threshold=self.flow_threshold.value,
cellprob_threshold=self.cellprob_threshold.value,
stitch_threshold=self.stitch_threshold.value, # is ignored if do_3D=True
min_size=self.min_size.value,
invert=self.invert.value,
if self.specify_diameter.value:
y_data, flows, *_ = self.current_model.eval(
x_data,
z_axis=z_axis,
diameter=diam,
do_3D=self.do_3D.value,
anisotropy=anisotropy,
flow_threshold=self.flow_threshold.value,
cellprob_threshold=self.cellprob_threshold.value,
stitch_threshold=self.stitch_threshold.value, # is ignored if do_3D=True
min_size=self.min_size.value,
invert=self.invert.value,
)
else:
y_data, flows, *_ = self.current_model.eval(
x_data,
# channel_axis=None,
# channels=channels,
z_axis=z_axis,
do_3D=self.do_3D.value,
anisotropy=anisotropy,
flow_threshold=self.flow_threshold.value,
cellprob_threshold=self.cellprob_threshold.value,
stitch_threshold=self.stitch_threshold.value, # is ignored if do_3D=True
min_size=self.min_size.value,
invert=self.invert.value,
)

LOGGER.info(
f"Cellpose Python v4 succeeded on attempt {attempt + 1}"
)
break

except Exception as a:
print(f"Unable to create masks. Check your module settings. {a}")
last_exception = a
LOGGER.error(
f"Unable to create masks on Cellpose Python v4 attempt "
f"{attempt + 1}/{MAX_RETRIES}. Check your module settings. {a}"
)

# Reset model between immediate retry attempts. This avoids reusing
# a partially failed Cellpose/MPS model state when multiple
# CellProfiler workers are loading cpsam concurrently.
if attempt < MAX_RETRIES - 1:
try:
if self.use_gpu.value:
cleanup(self)
except Exception:
pass

if self.mode.value == 'custom':
model_file, model_directory, model_path = get_custom_model_vars(self)
self.current_model = models.CellposeModel(
pretrained_model=model_path, gpu=self.use_gpu.value)
else:
self.current_model = models.CellposeModel(gpu=self.use_gpu.value)

finally:
if self.use_gpu.value:
cleanup(self)
if not self.cache_model.value:
# Release the model's memory
self.current_model = None
self.current_model_params = None

if self.remove_edge_masks:
if attempt == MAX_RETRIES - 1 or y_data is not None:
if self.use_gpu.value:
cleanup(self)
if not self.cache_model.value:
# Release the model's memory
self.current_model = None
self.current_model_params = None

if y_data is None:
raise RuntimeError(
f"Cellpose Python v4 failed after {MAX_RETRIES} attempts"
) from last_exception

# Empty masks are valid. Only remove edge masks after y_data exists.
if self.remove_edge_masks.value:
y_data = utils.remove_edge_masks(y_data)

else:
Expand Down