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Numerical overflows while running surforama demo #22
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And another error: ValueError Traceback (most recent call last)
File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-sk/lib/python3.11/site-packages/surforama/app.py:218, in QtSurforama.update_colors_based_on_sampling(self=<surforama.app.QtSurforama object>, value=6)
215 all_samples.append(sample_value)
217 # Calculate min and max across all sampled values
--> 218 samples_min = np.min(all_samples)
all_samples = []
np.min = <function amin at 0x7f80eb9b1440>
np = <module 'numpy' from '/hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-sk/lib/python3.11/site-packages/numpy/__init__.py'>
219 samples_max = np.max(all_samples)
221 # Normalize and update colors based on the mean value
222 # of samples for each point
File <__array_function__ internals>:180, in amin(*args=([],), **kwargs={})
File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-sk/lib/python3.11/site-packages/numpy/core/fromnumeric.py:2918, in amin(a=[], axis=None, out=None, keepdims=<no value>, initial=<no value>, where=<no value>)
2802 @array_function_dispatch(_amin_dispatcher)
2803 def amin(a, axis=None, out=None, keepdims=np._NoValue, initial=np._NoValue,
2804 where=np._NoValue):
2805 """
2806 Return the minimum of an array or minimum along an axis.
2807
(...)
2916 6
2917 """
-> 2918 return _wrapreduction(a, np.minimum, 'min', axis, None, out,
np = <module 'numpy' from '/hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-sk/lib/python3.11/site-packages/numpy/__init__.py'>
a = []
np.minimum = <ufunc 'minimum'>
axis = None
out = None
keepdims = <no value>
initial = <no value>
where = <no value>
2919 keepdims=keepdims, initial=initial, where=where)
File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-sk/lib/python3.11/site-packages/numpy/core/fromnumeric.py:86, in _wrapreduction(obj=[], ufunc=<ufunc 'minimum'>, method='min', axis=None, dtype=None, out=None, **kwargs={'initial': <no value>, 'keepdims': <no value>, 'where': <no value>})
83 else:
84 return reduction(axis=axis, out=out, **passkwargs)
---> 86 return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
passkwargs = {}
obj = []
axis = None
dtype = None
out = None
ufunc = <ufunc 'minimum'>
ValueError: zero-size array to reduction operation minimum which has no identity |
Hey @saugatkandel , In which situation did you encounter your other issue? Was it also with the demo example? |
@LorenzLamm This was with the demo. I will try the fix later today, thanks! |
@saugatkandel the fix is merged (#23)! |
Hey, @saugatkandel ! Thanks for reporting this bug. I just cut a new release on pypi (0.0.3) that includes the fix by @LorenzLamm (#23). You can install the new version with Do you still see this issue with the new version? |
I think this is fixed by #23, so I will close this for now. If anybody encounters this issue, please feel free to comment and we re-open the issue! |
I am trying out surforama demo, and it looks quite interesting! However, I am running into frequent numerical overflow issues when I change the extend/contact surface and the surface thickness. There are ranges of values of both where I get the warning:
/hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-sk/lib/python3.11/site-packages/surforama/app.py:161: RuntimeWarning: overflow encountered in byte_scalars!
in the terminal. The surface looks completely black at these regions.
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