Save reconstructions to an HDF5 file, for opening with the Fiji HDF5 viewer.

hdf5_demo.py

from shampoo.reconstruction import Hologram
import numpy as np
import h5py

# Load the USAF test target hologram
h = Hologram.from_tif('data/USAF_test.tif')

# Make lists for holding the phase and intensity of each reconstruction
phases = []
intensities = []

# Reconstruct at three propagation distances
propagation_distances = [0.03585, 0.03685, 0.03785]

for d in propagation_distances:
    wave = h.reconstruct(d)

    phases.append(wave.phase)
    intensities.append(wave.intensity)

# Save the output to an HDF5 file, for this hologram, taken at the zeroth time, "t0"
hdf5_file_path = 'example.hdf5'
f = h5py.File(hdf5_file_path, 'w')
t0 = f.create_group("t0")

# Save the raw hologram, the intensities, and the phases, using LZF compression
phase_dataset = t0.create_dataset('phase', data=np.array(phases), compression='lzf')
intensity_dataset = t0.create_dataset('intensity', data=np.array(intensities), compression='lzf')
hologram_dataset = t0.create_dataset('hologram', data=np.array([h.hologram]), compression='lzf')

# Close the file stream
f.close()