def test__add_cti_serial_fast():
arr = np.array(([
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
]))
arr = ac.Array2D.manual(array=arr, pixel_scales=1.0).native
ccd = ac.CCDPhase(full_well_depth=1e3,
well_notch_depth=0.0,
well_fill_power=1.0)
trap_list = [
ac.TrapInstantCapture(density=10.0,
release_timescale=-1.0 / np.log(0.5))
]
clocker = ac.Clocker2D()
image_via_clocker = clocker.add_cti(data=arr,
serial_trap_list=trap_list,
serial_ccd=ccd)
clocker = ac.Clocker2D(serial_fast_pixels=(1, 3))
image_via_clocker_fast = clocker.add_cti(data=arr,
serial_trap_list=trap_list,
serial_ccd=ccd)
assert image_via_clocker == pytest.approx(image_via_clocker_fast, 1.0e-6)
def test__array_with_offset_through_arctic():
arr = ac.Array2D.manual(
array=[[1.0, 2.0], [3.0, 4.0]],
pixel_scales=1.0,
header=ac.Header(header_sci_obj=None,
header_hdu_obj=None,
readout_offsets=(3, 5)),
).native
roe = ac.ROE(
dwell_times=[1.0],
empty_traps_between_columns=True,
empty_traps_for_first_transfers=False,
force_release_away_from_readout=True,
use_integer_express_matrix=False,
)
ccd_phase = ac.CCDPhase(full_well_depth=1e3,
well_notch_depth=0.0,
well_fill_power=1.0)
ccd = ac.CCD(phases=[ccd_phase], fraction_of_traps_per_phase=[1.0])
traps = [ac.TrapInstantCapture(10.0, -1.0 / np.log(0.5))]
image_via_arctic = cti.add_cti(
image=arr,
parallel_traps=traps,
parallel_ccd=ccd,
parallel_roe=roe,
parallel_express=3,
parallel_offset=3,
)
clocker = ac.Clocker2D(parallel_express=3, parallel_roe=roe)
image_via_clocker = clocker.add_cti(data=arr,
parallel_trap_list=traps,
parallel_ccd=ccd_phase)
assert image_via_arctic == pytest.approx(image_via_clocker, 1.0e-4)
image_via_arctic = cti.add_cti(
image=arr,
serial_traps=traps,
serial_ccd=ccd,
serial_roe=roe,
serial_express=2,
serial_offset=5,
)
clocker = ac.Clocker2D(serial_express=2, serial_roe=roe)
image_via_clocker = clocker.add_cti(data=arr,
serial_trap_list=traps,
serial_ccd=ccd_phase)
assert image_via_arctic == pytest.approx(image_via_clocker, 1.0e-4)
def test__parallel_and_serial_checks_raise_exception(self, imaging_ci_7x7):
model = af.CollectionPriorModel(cti=af.Model(
ac.CTI2D,
parallel_traps=[
ac.TrapInstantCapture(density=1.1),
ac.TrapInstantCapture(density=1.1),
],
parallel_ccd=ac.CCDPhase(),
))
analysis = ac.AnalysisImagingCI(
dataset_ci=imaging_ci_7x7,
clocker=None,
settings_cti=ac.SettingsCTI2D(parallel_total_density_range=(1.0,
2.0)),
)
instance = model.instance_from_prior_medians()
with pytest.raises(exc.PriorException):
analysis.log_likelihood_function(instance=instance)
model = af.CollectionPriorModel(cti=af.Model(
ac.CTI2D,
serial_traps=[
ac.TrapInstantCapture(density=1.1),
ac.TrapInstantCapture(density=1.1),
],
serial_ccd=ac.CCDPhase(),
))
analysis = ac.AnalysisImagingCI(
dataset_ci=[imaging_ci_7x7],
clocker=None,
settings_cti=ac.SettingsCTI2D(serial_total_density_range=(1.0,
2.0)),
)
instance = model.instance_from_prior_medians()
with pytest.raises(exc.PriorException):
analysis.log_likelihood_function(instance=instance)
def test__add_cti_with_poisson_trap_densities():
arr = np.array(([
[1.0, 1.0, 1.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
]))
arr = ac.Array2D.manual(array=arr, pixel_scales=1.0).native
roe = ac.ROE(
dwell_times=[1.0],
empty_traps_between_columns=True,
empty_traps_for_first_transfers=False,
force_release_away_from_readout=True,
use_integer_express_matrix=False,
)
ccd = ac.CCDPhase(full_well_depth=1e3,
well_notch_depth=0.0,
well_fill_power=1.0)
trap_list = [
ac.TrapInstantCapture(density=10.0,
release_timescale=-1.0 / np.log(0.5))
]
clocker = ac.Clocker2D(
parallel_poisson_traps=True,
poisson_seed=1,
parallel_express=3,
parallel_roe=roe,
serial_express=3,
serial_roe=roe,
)
image_via_clocker = clocker.add_cti(
data=arr,
parallel_trap_list=trap_list,
parallel_ccd=ccd,
serial_trap_list=trap_list,
serial_ccd=ccd,
)
assert image_via_clocker[0, 0] == pytest.approx(0.980298, 1.0e-4)
assert image_via_clocker[0, 1] == pytest.approx(0.9901042, 1.0e-4)
assert image_via_clocker[0, 2] == pytest.approx(0.9901981, 1.0e-4)
assert (image_via_clocker[:, 3] > 0.0).all()
def test__add_cti_serial_fast__raises_exception_if_nonzero_outside_tuple():
ccd = ac.CCDPhase(full_well_depth=1e3,
well_notch_depth=0.0,
well_fill_power=1.0)
trap_list = [
ac.TrapInstantCapture(density=10.0,
release_timescale=-1.0 / np.log(0.5))
]
clocker = ac.Clocker2D(serial_fast_pixels=(1, 3))
arr = np.array(([
[0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
]))
arr = ac.Array2D.manual(array=arr, pixel_scales=1.0).native
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr, serial_trap_list=trap_list, serial_ccd=ccd)
arr = np.array(([
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
]))
arr = ac.Array2D.manual(array=arr, pixel_scales=1.0).native
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr, serial_trap_list=trap_list, serial_ccd=ccd)
arr = np.array(([
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 1.0, 1.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
]))
arr = ac.Array2D.manual(array=arr, pixel_scales=1.0).native
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr, serial_trap_list=trap_list, serial_ccd=ccd)
"""
clocker = ac.Clocker2D(serial_express=2)
"""
__CTI Model__
The CTI model used by arCTIc to add CTI to the input image in the serial direction, which contains:
- 3 trap species in the parallel direction.
- A simple CCD volume beta parametrization.
"""
serial_trap_0 = ac.TrapInstantCapture(density=0.0442, release_timescale=0.8)
serial_trap_1 = ac.TrapInstantCapture(density=0.1326, release_timescale=4.0)
serial_trap_2 = ac.TrapInstantCapture(density=3.9782, release_timescale=20.0)
serial_ccd = ac.CCDPhase(well_fill_power=0.8,
well_notch_depth=0.0,
full_well_depth=84700.0)
"""
__Simulate__
To simulate charge injection imaging, we pass the charge injection pattern to a `SimulatorImagingCI`, which adds CTI
via arCTIc and read-noise to the data.
This creates instances of the `ImagingCI` class, which include the images, noise-maps and pre_cti_data images.
"""
simulator = ac.ci.SimulatorImagingCI(read_noise=0.001, pixel_scales=0.1)
"""
We now pass each charge injection pattern to the simulator. This generate the charge injection image of each exposure
and before passing each image to arCTIc does the following:
- Uses an input read-out electronics corner to perform all rotations of the image before / after adding CTI.
def test__raises_exception_if_no_traps_or_ccd_passed():
arr = ac.Array2D.manual(
array=[[1.0, 2.0], [3.0, 4.0]],
pixel_scales=1.0,
header=ac.Header(header_sci_obj=None,
header_hdu_obj=None,
readout_offsets=(3, 5)),
).native
ccd_phase = ac.CCDPhase(full_well_depth=1e3,
well_notch_depth=0.0,
well_fill_power=1.0)
traps = [ac.TrapInstantCapture(10.0, -1.0 / np.log(0.5))]
clocker = ac.Clocker2D(parallel_express=3)
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr)
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr, parallel_trap_list=traps)
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr, serial_trap_list=traps)
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr,
parallel_trap_list=traps,
serial_trap_list=traps)
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr, parallel_ccd=ccd_phase)
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr, serial_ccd=ccd_phase)
with pytest.raises(exc.ClockerException):
clocker.add_cti(data=arr, parallel_ccd=ccd_phase, serial_ccd=ccd_phase)
with pytest.raises(exc.ClockerException):
clocker.remove_cti(data=arr)
with pytest.raises(exc.ClockerException):
clocker.remove_cti(data=arr, parallel_trap_list=traps)
with pytest.raises(exc.ClockerException):
clocker.remove_cti(data=arr, serial_trap_list=traps)
with pytest.raises(exc.ClockerException):
clocker.remove_cti(data=arr,
parallel_trap_list=traps,
serial_trap_list=traps)
with pytest.raises(exc.ClockerException):
clocker.remove_cti(data=arr, parallel_ccd=ccd_phase)
with pytest.raises(exc.ClockerException):
clocker.remove_cti(data=arr, serial_ccd=ccd_phase)
with pytest.raises(exc.ClockerException):
clocker.remove_cti(data=arr,
parallel_ccd=ccd_phase,
serial_ccd=ccd_phase)