def setup_reconstructed_data_small_npy(setup_gdrive_src_data_small):
"""
Loads AND Reconstructs SOURCE data.
SIZE: 512 x 512
TYPE: .npy
:param setup_gdrive_src_data_small:
:return: physical data object containing reconstructed data
"""
bg_dat, sm_dat = setup_gdrive_src_data_small
# compute initial reconstructor using background data
img_reconstructor = ImgReconstructor(bg_dat,
swing=0.03,
wavelength=532)
bg_stokes = img_reconstructor.compute_stokes(bg_dat)
bg_stokes_normalized = img_reconstructor.stokes_normalization(bg_stokes)
# compute sample stokes and correct with background data
sm_stokes = img_reconstructor.compute_stokes(sm_dat)
sm_stokes_normalized = img_reconstructor.stokes_normalization(sm_stokes)
sm_stokes_normalized = img_reconstructor.correct_background(sm_stokes_normalized, bg_stokes_normalized)
reconstructed_birefring = img_reconstructor.reconstruct_birefringence(sm_stokes_normalized)
yield reconstructed_birefring
def test_complete_reconstruction(setup_gdrive_src_data_small):
"""
tests compute sequence: background correction of birefringence from intensity data
one z, one t, one p
No config file parsing
No plotting
Parameters
----------
setup_gdrive_src_data_small : pytest fixture to load data from gdrive
Returns
-------
"""
bg_dat, sm_dat = setup_gdrive_src_data_small
# compute initial reconstructor using background data
img_reconstructor = ImgReconstructor(bg_dat, swing=0.03, wavelength=532)
bg_stokes = img_reconstructor.compute_stokes(bg_dat)
bg_stokes_normalized = img_reconstructor.stokes_normalization(bg_stokes)
# compute sample stokes and correct with background data
sm_stokes = img_reconstructor.compute_stokes(sm_dat)
sm_stokes_normalized = img_reconstructor.stokes_normalization(sm_stokes)
sm_stokes_normalized = img_reconstructor.correct_background(
sm_stokes_normalized, bg_stokes_normalized)
reconstructed_birefring = img_reconstructor.reconstruct_birefringence(
sm_stokes_normalized)
assert reconstructed_birefring.I_trans is not None
assert reconstructed_birefring.retard is not None
assert reconstructed_birefring.azimuth is not None
assert reconstructed_birefring.polarization is not None
def setup_reconstructed_data_small_tif(setup_gdrive_src_data_small):
"""
Loads AND Reconstructs SOURCE data.
SIZE: 512 x 512
TYPE: .tif
:param setup_gdrive_src_data_small:
:return: physical data object containing reconstructed data
"""
bg_dat, sm_dat = setup_gdrive_src_data_small
# compute initial reconstructor using background data
img_reconstructor = ImgReconstructor(bg_dat,
swing=0.03,
wavelength=532)
bg_stokes = img_reconstructor.compute_stokes(bg_dat)
bg_stokes_normalized = img_reconstructor.stokes_normalization(bg_stokes)
# compute sample stokes and correct with background data
sm_stokes = img_reconstructor.compute_stokes(sm_dat)
sm_stokes_normalized = img_reconstructor.stokes_normalization(sm_stokes)
sm_stokes_normalized = img_reconstructor.correct_background(sm_stokes_normalized, bg_stokes_normalized)
reconstructed_birefring = img_reconstructor.reconstruct_birefringence(sm_stokes_normalized)
# target data is scaled to uint16 (.tif)
spol = (65536*(reconstructed_birefring.polarization - reconstructed_birefring.polarization.min()) /
(reconstructed_birefring.polarization.ptp())).astype('uint16')
sazi = (65536*(reconstructed_birefring.azimuth - reconstructed_birefring.azimuth.min()) /
(reconstructed_birefring.azimuth.ptp())).astype('uint16')
stran = (65536*(reconstructed_birefring.I_trans - reconstructed_birefring.I_trans.min()) /
(reconstructed_birefring.I_trans.ptp())).astype('uint16')
sret = (65536*(reconstructed_birefring.retard - reconstructed_birefring.retard.min()) /
(reconstructed_birefring.retard.ptp())).astype('uint16')
reconstructed_birefring.I_trans = stran
reconstructed_birefring.retard = sret
reconstructed_birefring.polarization = spol
reconstructed_birefring.azimuth = sazi
yield reconstructed_birefring
reconstructor is initialized based on parameters from the experiment
usually these params are found in the config file parsed from metadata or config.yml
"""
img_reconstructor = ImgReconstructor(bg_int.data.shape,
bg_method="Local_fit",
n_slice_local_bg=1,
poly_fit_order=2,
swing=0.03,
wavelength=532,
azimuth_offset=0,
circularity='rcp')
#%%
print('computing background')
background_stokes = img_reconstructor.compute_stokes(bg_int)
background_normalized = img_reconstructor.stokes_normalization(
background_stokes)
#%%
print('computing stokes')
sample_stokes = img_reconstructor.compute_stokes(int_dat)
sample_normalized = img_reconstructor.stokes_normalization(sample_stokes)
#%%
print('correcting background')
# let's keep a few background correction outputs
sample_bg_corrected_local_fit = img_reconstructor.correct_background(
sample_normalized, background_normalized)
img_reconstructor.bg_method = "Local_filter"