Read theta array from encoder readout

• Angular information (theta array) is required for accurate tomographic reconstruction.

• If theta is not stored in the raw data, it is possible to simulate it as equally spaced between 0 and 180 degrees.

• Alternatively, we can read the rotation stage encoder readout during the scan (beta)

A. Load theta array stored in the HDF5 dataset

This is a calculated array of the ideal angles during the scan.

h5file = "/mnt/PETRA/SED/BEATS/IH/BEATS_first_scan-20230511T170626/BEATS_first_scan-20230511T170626.h5"
projs, _, _, theta = dxchange.read_aps_32id(h5file, exchange_rank=0, sino=(695, 705, 1))

print("Theta array size: ", theta.shape[:])

B. Simulate theta array

If theta is empty, we can retrieve it using the tomopy.angles method:

theta_tomopy = tomopy.angles(projs.shape[0])

C. Read theta_readout from encoder

Another option is to read the angle readout from the rotation stage:

theta_readout = dxchange.read_hdf5(h5file, '/exchange/theta_readout')

plt.plot(theta, label='theta')
plt.plot(theta_tomopy, label='theta tomopy')
# plt.plot(1.03*theta, label='1.03*theta')
plt.plot(theta_readout/180*np.pi, label='theta readout')
plt.legend()

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