Numerical overflows while running surforama demo

[saugatkandel]

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.

[saugatkandel]

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

[LorenzLamm]

Hey @saugatkandel ,
I encountered the same issue with the overflow values and tried to fix it in #23.

In which situation did you encounter your other issue? Was it also with the demo example?

[saugatkandel]

@LorenzLamm This was with the demo. I will try the fix later today, thanks!

[kephale]

@saugatkandel the fix is merged (#23)!

[kevinyamauchi]

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 pip install --upgrade surforama.

Do you still see this issue with the new version?

[kevinyamauchi]

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!