def test_2d_autofocus_small_interval():
"""
Test for IndexError failure for brute method
(brute_step too small).
for k in range(N - 1, -1, -1):
> thisN = Nshape[k]
E IndexError: tuple index out of range
/scipy/optimize/optimize.py:3276: IndexError
"""
wavelength = 647e-9
rf = nrefocus.iface.RefocusNumpy(
field=load_cell("HL60_field.zip"),
wavelength=wavelength,
pixel_size=0.139e-6,
kernel="helmholtz",
)
# attempt to autofocus with interval smaller than brute_step
rf.autofocus(
metric="average gradient",
minimizer="lmfit",
interval=(0, 1.9 * wavelength),
)
def test_2d_autofocus_cell_helmholtz_average_gradient():
rf = nrefocus.iface.RefocusNumpy(
field=load_cell("HL60_field.zip"),
wavelength=647e-9,
pixel_size=0.139e-6,
kernel="helmholtz",
)
# attempt to autofocus with standard arguments
d = rf.autofocus(metric="average gradient",
minimizer="lmfit",
interval=(-5e-6, 5e-6))
assert np.allclose(d, -8.781356558557544e-07, atol=0)
nfield = rf.propagate(d)
assert np.allclose(nfield[10, 10],
1.0455603934920419 - 0.020475662236633177j,
atol=0)
def test_2d_autofocus_return_field():
rf = nrefocus.iface.RefocusNumpy(
field=load_cell("HL60_field.zip"),
wavelength=647e-9,
pixel_size=0.139e-6,
kernel="helmholtz",
)
# attempt to autofocus with standard arguments
d, nfield = rf.autofocus(
metric="average gradient",
minimizer="lmfit",
interval=(-5e-6, 5e-6),
ret_field=True,
)
nfield2 = rf.propagate(d)
assert np.all(nfield == nfield2)
def test_2d_autofocus_cell_helmholtz_average_gradient():
rf = nrefocus.iface.RefocusNumpy(
field=load_cell("HL60_field.zip"),
wavelength=647e-9,
pixel_size=0.139e-6,
kernel="helmholtz",
)
# attempt to autofocus with standard arguments
d = rf.autofocus(metric="average gradient",
minimizer="legacy",
interval=(-5e-6, 5e-6))
assert np.allclose(d, -8.69809203142537e-07, atol=0)
nfield = rf.propagate(d)
assert np.allclose(nfield[10, 10],
1.045874817165857 - 0.020467790949516538j,
atol=0)
def test_2d_autofocus_return_grid_field():
rf = nrefocus.iface.RefocusNumpy(
field=load_cell("HL60_field.zip"),
wavelength=647e-9,
pixel_size=0.139e-6,
kernel="helmholtz",
)
# attempt to autofocus with standard arguments
d, (dgrid, mgrid), nfield = rf.autofocus(
metric="average gradient",
minimizer="lmfit",
interval=(-5e-6, 5e-6),
ret_grid=True,
ret_field=True,
)
idx_metric_min = np.argmin(mgrid)
idx_distance = np.argmin(np.abs(dgrid - d))
assert idx_metric_min == idx_distance