cellpose-napari
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`get_masks` interface changed from cellpose 1.x to 2.x
When clicking "recompute last masks with new cellprob + model match", I get the error:
File …/lib/python3.8/site-packages/cellpose_napari/_dock_widget.py:116, in widget_wrapper.<locals>.compute_masks(masks_orig=<class 'numpy.ndarray'> (1000, 1000) uint16, flows_orig=[<class 'numpy.ndarray'> (1560, 1560, 3) uint8, <class 'numpy.ndarray'> (2, 1560, 1560) float32, <class 'numpy.ndarray'> (1560, 1560) float32, <class 'numpy.ndarray'> (2, 1560, 1560) float32], cellprob_threshold=8.0, model_match_threshold=27.0)
114 logger.debug('flow_threshold=0 => no masks thrown out due to model mismatch')
115 logger.debug(f'computing masks with cellprob_threshold={cellprob_threshold}, flow_threshold={flow_threshold}')
--> 116 maski = get_masks(flows_orig[3].copy(), iscell=(flows_orig[2] > cellprob_threshold),
flows_orig[3] = <class 'numpy.ndarray'> (2, 1560, 1560) float32
flows_orig[2] = <class 'numpy.ndarray'> (1560, 1560) float32
cellprob_threshold = 8.0
flows_orig = [<class 'numpy.ndarray'> (1560, 1560, 3) uint8, <class 'numpy.ndarray'> (2, 1560, 1560) float32, <class 'numpy.ndarray'> (1560, 1560) float32, <class 'numpy.ndarray'> (2, 1560, 1560) float32]
flow_threshold = 0.4
flows_orig[1] = <class 'numpy.ndarray'> (2, 1560, 1560) float32
masks_orig = <class 'numpy.ndarray'> (1000, 1000) uint16
117 flows=flows_orig[1], threshold=flow_threshold*(masks_orig.ndim<3))
118 maski = fill_holes_and_remove_small_masks(maski)
119 maski = resize_image(maski, masks_orig.shape[-2], masks_orig.shape[-1],
120 interpolation=cv2.INTER_NEAREST)
TypeError: get_masks() got an unexpected keyword argument 'flows'
Environment: cellpose 1.0.2 cellpose-napari 0.1.5 napari 0.4.16 napari-plugin-engine 0.2.0
This is caused by the removal of the flows argument in the get_masks function in the transition from cellpose 1.x to 2.0. However, the requirements cellpose>=0.6.2 currently pull the latest package version. The current code would need to specify an upper limit cellpose>=0.6.2,<2, or be updated to the new interface.
Workaround:
Install cellpose==1.0.2
Hi,
I've encountered the same problem. Thanks for your workaround, I've forced the install of cellpose==1.0.2 as you suggested and it removed the get_mask TypeError. Unfortunately it still failed with the following error:
error: OpenCV(4.7.0) :-1: error: (-5:Bad argument) in function 'resize'
> Overload resolution failed:
> - src data type = 8 is not supported
> - Expected Ptr<cv::UMat> for argument 'src'
If it can be of use, I'm copying the full report
Full report
(base) PS C:> conda activate cellpose_napari (cellpose_napari) PS C:> napari -w cellpose-napari 100%|█████████████████████████████████████████████████████████████████████████████| 25.3M/25.3M [00:02<00:00, 11.2MB/s] 100%|█████████████████████████████████████████████████████████████████████████████| 25.3M/25.3M [00:01<00:00, 17.5MB/s] 100%|█████████████████████████████████████████████████████████████████████████████| 25.3M/25.3M [00:01<00:00, 14.3MB/s] 100%|█████████████████████████████████████████████████████████████████████████████| 25.3M/25.3M [00:02<00:00, 11.9MB/s] 11:49:07 WARNING cellprob_threshold and dist_threshold are being deprecated in a future release, use mask_threshold instead
error Traceback (most recent call last)
File C:\Program Files\Anaconda3\envs\cellpose_napari\lib\site-packages\superqt\utils_qthreading.py:617, in create_worker.
File C:\Program Files\Anaconda3\envs\cellpose_napari\lib\site-packages\superqt\utils_qthreading.py:178, in WorkerBase.run(self=<napari._qt.qthreading.FunctionWorker object>) 176 warnings.filterwarnings("always") 177 warnings.showwarning = lambda *w: self.warned.emit(w) --> 178 result = self.work() self = <napari._qt.qthreading.FunctionWorker object at 0x000001702A5F2430> 179 if isinstance(result, Exception): 180 if isinstance(result, RuntimeError): 181 # The Worker object has likely been deleted. 182 # A deleted wrapped C/C++ object may result in a runtime 183 # error that will cause segfault if we try to do much other 184 # than simply notify the user.
File C:\Program Files\Anaconda3\envs\cellpose_napari\lib\site-packages\superqt\utils_qthreading.py:357, in FunctionWorker.work(self=<napari._qt.qthreading.FunctionWorker object>)
356 def work(self) -> _R:
--> 357 return self._func(*self._args, **self._kwargs)
self._func = <function widget_wrapper.
File C:\Program Files\Anaconda3\envs\cellpose_napari\lib\site-packages\cellpose_napari_dock_widget.py:119, in widget_wrapper.
File C:\Program Files\Anaconda3\envs\cellpose_napari\lib\site-packages\cellpose\transforms.py:561, in resize_image(img0=<class 'numpy.ndarray'> (151, 658, 818) uint32, Ly=658, Lx=818, rsz=None, interpolation=0, no_channels=False) 559 imgs[i] = cv2.resize(img, (Lx, Ly), interpolation=interpolation) 560 else: --> 561 imgs = cv2.resize(img0, (Lx, Ly), interpolation=interpolation) Ly = 658 Lx = 818 img0 = <class 'numpy.ndarray'> (151, 658, 818) uint32 (Lx, Ly) = (818, 658) interpolation = 0 562 return imgs
error: OpenCV(4.7.0) :-1: error: (-5:Bad argument) in function 'resize'
Overload resolution failed:
- src data type = 8 is not supported
- Expected Ptrcv::UMat for argument 'src'
I can confirm this on cellpose 2.2.3 Traceback:
TypeError Traceback (most recent call last)
File ~/micromamba/envs/cellpose/lib/python3.10/site-packages/superqt/utils/_qthreading.py:617, in create_worker.<locals>.reraise(e=TypeError("get_masks() got an unexpected keyword argument 'flows'"))
616 def reraise(e):
--> 617 raise e
e = TypeError("get_masks() got an unexpected keyword argument 'flows'")
File ~/micromamba/envs/cellpose/lib/python3.10/site-packages/superqt/utils/_qthreading.py:178, in WorkerBase.run(self=<napari._qt.qthreading.FunctionWorker object>)
176 warnings.filterwarnings("always")
177 warnings.showwarning = lambda *w: self.warned.emit(w)
--> 178 result = self.work()
self = <napari._qt.qthreading.FunctionWorker object at 0x2b3635a20>
179 if isinstance(result, Exception):
180 if isinstance(result, RuntimeError):
181 # The Worker object has likely been deleted.
182 # A deleted wrapped C/C++ object may result in a runtime
183 # error that will cause segfault if we try to do much other
184 # than simply notify the user.
File ~/micromamba/envs/cellpose/lib/python3.10/site-packages/superqt/utils/_qthreading.py:358, in FunctionWorker.work(self=<napari._qt.qthreading.FunctionWorker object>)
357 def work(self) -> _R:
--> 358 return self._func(*self._args, **self._kwargs)
self._func = <function widget_wrapper.<locals>.compute_masks at 0x2b2f93250>
self = <napari._qt.qthreading.FunctionWorker object at 0x2b3635a20>
self._args = (<class 'numpy.ndarray'> (383, 512) uint16, [<class 'numpy.ndarray'> (383, 512, 3) uint8, <class 'numpy.ndarray'> (2, 383, 512) float32, <class 'numpy.ndarray'> (383, 512) float32, <class 'numpy.ndarray'> (2, 383, 512) float32], 0.0, 23.625)
self._kwargs = {}
File ~/micromamba/envs/cellpose/lib/python3.10/site-packages/cellpose_napari/_dock_widget.py:116, in widget_wrapper.<locals>.compute_masks(masks_orig=<class 'numpy.ndarray'> (383, 512) uint16, flows_orig=[<class 'numpy.ndarray'> (383, 512, 3) uint8, <class 'numpy.ndarray'> (2, 383, 512) float32, <class 'numpy.ndarray'> (383, 512) float32, <class 'numpy.ndarray'> (2, 383, 512) float32], cellprob_threshold=0.0, model_match_threshold=23.625)
114 logger.debug('flow_threshold=0 => no masks thrown out due to model mismatch')
115 logger.debug(f'computing masks with cellprob_threshold={cellprob_threshold}, flow_threshold={flow_threshold}')
--> 116 maski = get_masks(flows_orig[3].copy(), iscell=(flows_orig[2] > cellprob_threshold),
cellprob_threshold = 0.0
flows_orig[3] = <class 'numpy.ndarray'> (2, 383, 512) float32
flows_orig[2] = <class 'numpy.ndarray'> (383, 512) float32
flows_orig = [<class 'numpy.ndarray'> (383, 512, 3) uint8, <class 'numpy.ndarray'> (2, 383, 512) float32, <class 'numpy.ndarray'> (383, 512) float32, <class 'numpy.ndarray'> (2, 383, 512) float32]
flow_threshold = 0.7375
flows_orig[1] = <class 'numpy.ndarray'> (2, 383, 512) float32
masks_orig = <class 'numpy.ndarray'> (383, 512) uint16
117 flows=flows_orig[1], threshold=flow_threshold*(masks_orig.ndim<3))
118 maski = fill_holes_and_remove_small_masks(maski)
119 maski = resize_image(maski, masks_orig.shape[-2], masks_orig.shape[-1],
120 interpolation=cv2.INTER_NEAREST)
TypeError: get_masks() got an unexpected keyword argument 'flows'
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
File ~/micromamba/envs/cellpose/lib/python3.10/site-packages/superqt/utils/_qthreading.py:617, in create_worker.<locals>.reraise(e=TypeError("get_masks() got an unexpected keyword argument 'flows'"))
616 def reraise(e):
--> 617 raise e
e = TypeError("get_masks() got an unexpected keyword argument 'flows'")
File ~/micromamba/envs/cellpose/lib/python3.10/site-packages/superqt/utils/_qthreading.py:178, in WorkerBase.run(self=<napari._qt.qthreading.FunctionWorker object>)
176 warnings.filterwarnings("always")
177 warnings.showwarning = lambda *w: self.warned.emit(w)
--> 178 result = self.work()
self = <napari._qt.qthreading.FunctionWorker object at 0x2e7ff0af0>
179 if isinstance(result, Exception):
180 if isinstance(result, RuntimeError):
181 # The Worker object has likely been deleted.
182 # A deleted wrapped C/C++ object may result in a runtime
183 # error that will cause segfault if we try to do much other
184 # than simply notify the user.
File ~/micromamba/envs/cellpose/lib/python3.10/site-packages/superqt/utils/_qthreading.py:358, in FunctionWorker.work(self=<napari._qt.qthreading.FunctionWorker object>)
357 def work(self) -> _R:
--> 358 return self._func(*self._args, **self._kwargs)
self._func = <function widget_wrapper.<locals>.compute_masks at 0x2b2f93250>
self = <napari._qt.qthreading.FunctionWorker object at 0x2e7ff0af0>
self._args = (<class 'numpy.ndarray'> (383, 512) uint16, [<class 'numpy.ndarray'> (383, 512, 3) uint8, <class 'numpy.ndarray'> (2, 383, 512) float32, <class 'numpy.ndarray'> (383, 512) float32, <class 'numpy.ndarray'> (2, 383, 512) float32], 0.0, 23.625)
self._kwargs = {}
File ~/micromamba/envs/cellpose/lib/python3.10/site-packages/cellpose_napari/_dock_widget.py:116, in widget_wrapper.<locals>.compute_masks(masks_orig=<class 'numpy.ndarray'> (383, 512) uint16, flows_orig=[<class 'numpy.ndarray'> (383, 512, 3) uint8, <class 'numpy.ndarray'> (2, 383, 512) float32, <class 'numpy.ndarray'> (383, 512) float32, <class 'numpy.ndarray'> (2, 383, 512) float32], cellprob_threshold=0.0, model_match_threshold=23.625)
114 logger.debug('flow_threshold=0 => no masks thrown out due to model mismatch')
115 logger.debug(f'computing masks with cellprob_threshold={cellprob_threshold}, flow_threshold={flow_threshold}')
--> 116 maski = get_masks(flows_orig[3].copy(), iscell=(flows_orig[2] > cellprob_threshold),
cellprob_threshold = 0.0
flows_orig[3] = <class 'numpy.ndarray'> (2, 383, 512) float32
flows_orig[2] = <class 'numpy.ndarray'> (383, 512) float32
flows_orig = [<class 'numpy.ndarray'> (383, 512, 3) uint8, <class 'numpy.ndarray'> (2, 383, 512) float32, <class 'numpy.ndarray'> (383, 512) float32, <class 'numpy.ndarray'> (2, 383, 512) float32]
flow_threshold = 0.7375
flows_orig[1] = <class 'numpy.ndarray'> (2, 383, 512) float32
masks_orig = <class 'numpy.ndarray'> (383, 512) uint16
117 flows=flows_orig[1], threshold=flow_threshold*(masks_orig.ndim<3))
118 maski = fill_holes_and_remove_small_masks(maski)
119 maski = resize_image(maski, masks_orig.shape[-2], masks_orig.shape[-1],
120 interpolation=cv2.INTER_NEAREST)
TypeError: get_masks() got an unexpected keyword argument 'flows'
