RuntimeWarning: invalid value encountered in sqrt np.sqrt(1.0 - first_term - second_term))

[tomdertech]

This is my first attempt at using shampoo. I am getting the following error with the USAF_test.tif in the repo:

\Anaconda3\lib\site-packages\shampoo-0.1.dev156-py3.5.egg\shampoo\reconstruction.py:419: RuntimeWarning: invalid value encountered in sqrt
np.sqrt(1.0 - first_term - second_term))

The code I am using is here:

from shampoo import Hologram
import matplotlib.pyplot as plt

hologram_path = 'C:\\Users\\xxxxx\\Desktop\\usaf_sqt.tiff'
propagation_distance = 0.03685  # m
h = Hologram.from_tif(hologram_path, wavelength=470e-6, dx=3.5e-6, dy=3.5e-6)
wave = h.reconstruct(propagation_distance)
fig, ax = wave.plot()
fig.suptitle("USAF Target")
fig.tight_layout()
plt.show()

I have tried my own .tif and I get the same result. I have also tried modifying the propagation_distance, wavelength and dx,dy variables, but I get the same problem.

[bmorris3]

Hi @tomdertech! Just to clarify -- that's a warning and shouldn't prevent the code from being fully executed. Is the output figure being generated properly?

This particular warning is normal and occurs for all reconstructions.

[tomdertech]

Hi @bmorris3. That is correct. I am using pycharm, but no figure is produced.

[tomdertech]

Hi. I have tried running the example through Anaconda and it seems to "hang" after the warning.

This fits with my experience of not seeing the resulting figure when using pycharm.

[bmorris3]

I don't know what's wrong here, it should produce the figure after the reconstruction is completed. If you look at an activity monitor on your machine, can you tell if it's still computing the reconstruction while it appears to hang?