def test__visualizer_with_preloaded_critical_curves_and_caustics_is_setup(
self,
masked_imaging_7x7,
tracer_x2_plane_7x7,
include_all,
plot_path,
plot_patch,
):
visualizer = vis.PhaseDatasetVisualizer(
masked_dataset=masked_imaging_7x7)
assert visualizer.include.preloaded_critical_curves == None
assert visualizer.include.preloaded_caustics == None
visualizer = visualizer.new_visualizer_with_preloaded_critical_curves_and_caustics(
preloaded_critical_curves=1, preloaded_caustics=2)
assert visualizer.include.preloaded_critical_curves == 1
assert visualizer.include.preloaded_caustics == 2
visualizer.include.critical_curves = False
visualizer.include.caustics = False
visualizer.visualize_ray_tracing(paths=af.Paths(),
tracer=tracer_x2_plane_7x7,
during_analysis=True)
assert (path.join(plot_path, "image", "ray_tracing",
"subplot_tracer.png") in plot_patch.paths)
def test__visualizes_hyper_images_using_config(
self,
masked_imaging_7x7,
hyper_model_image_7x7,
include_all,
hyper_galaxy_image_path_dict_7x7,
masked_imaging_fit_x2_plane_7x7,
plot_path,
plot_patch,
):
visualizer = vis.PhaseImagingVisualizer(
masked_dataset=masked_imaging_7x7)
visualizer = visualizer.new_visualizer_with_preloaded_critical_curves_and_caustics(
preloaded_critical_curves=include_all.preloaded_critical_curves,
preloaded_caustics=include_all.preloaded_caustics,
)
visualizer.visualize_hyper_images(
paths=af.Paths(),
hyper_galaxy_image_path_dict=hyper_galaxy_image_path_dict_7x7,
hyper_model_image=hyper_model_image_7x7,
contribution_maps_of_galaxies=masked_imaging_fit_x2_plane_7x7.
tracer.contribution_maps_of_planes,
)
assert (path.join(plot_path, "image", "hyper", "hyper_model_image.png")
in plot_patch.paths)
assert (path.join(plot_path, "image", "hyper",
"subplot_hyper_images_of_galaxies.png")
in plot_patch.paths)
assert (path.join(plot_path, "image", "hyper",
"subplot_contribution_maps_of_galaxies.png")
not in plot_patch.paths)
def test__visualizes_imaging_using_configs(self, masked_imaging_7x7,
include_all, plot_path,
plot_patch):
if os.path.exists(plot_path):
shutil.rmtree(plot_path)
visualizer = vis.PhaseImagingVisualizer(
masked_dataset=masked_imaging_7x7)
visualizer = visualizer.new_visualizer_with_preloaded_critical_curves_and_caustics(
preloaded_critical_curves=include_all.preloaded_critical_curves,
preloaded_caustics=include_all.preloaded_caustics,
)
visualizer.visualize_imaging(paths=af.Paths())
assert (path.join(plot_path, "image", "imaging", "subplot_imaging.png")
in plot_patch.paths)
assert path.join(plot_path, "image", "imaging",
"image.png") in plot_patch.paths
assert (path.join(plot_path, "image", "imaging", "noise_map.png")
not in plot_patch.paths)
assert path.join(plot_path, "image", "imaging",
"psf.png") in plot_patch.paths
assert (path.join(plot_path, "image", "imaging",
"inverse_noise_map.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "imaging",
"signal_to_noise_map.png") not in plot_patch.paths)
assert (path.join(plot_path, "image", "imaging",
"absolute_signal_to_noise_map.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "imaging",
"potential_chi_squared_map.png") in plot_patch.paths)
def test__visualize_stochastic_histogram(self, masked_imaging_7x7,
plot_path, plot_patch):
visualizer = vis.PhaseDatasetVisualizer(
masked_dataset=masked_imaging_7x7)
visualizer.visualize_stochastic_histogram(
paths=af.Paths(),
log_evidences=[1.0, 2.0, 1.0, 2.0, 3.0, 2.5],
max_log_evidence=3.0,
)
assert (path.join(plot_path, "image", "other",
"stochastic_histogram.png") in plot_patch.paths)
def test__visualizes_ray_tracing_using_configs(
self,
masked_imaging_7x7,
tracer_x2_plane_7x7,
include_all,
plot_path,
plot_patch,
):
if os.path.exists(plot_path):
shutil.rmtree(plot_path)
visualizer = vis.PhaseDatasetVisualizer(
masked_dataset=masked_imaging_7x7)
visualizer = visualizer.new_visualizer_with_preloaded_critical_curves_and_caustics(
preloaded_critical_curves=include_all.preloaded_critical_curves,
preloaded_caustics=include_all.preloaded_caustics,
)
visualizer.visualize_ray_tracing(paths=af.Paths(),
tracer=tracer_x2_plane_7x7,
during_analysis=False)
assert (path.join(plot_path, "image", "ray_tracing",
"subplot_tracer.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "ray_tracing", "image.png")
in plot_patch.paths)
assert (path.join(plot_path, "image", "ray_tracing",
"source_plane.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "ray_tracing", "convergence.png")
in plot_patch.paths)
assert (path.join(plot_path, "image", "ray_tracing", "potential.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "ray_tracing",
"deflections_y.png") not in plot_patch.paths)
assert (path.join(plot_path, "image", "ray_tracing",
"deflections_x.png") not in plot_patch.paths)
assert (path.join(plot_path, "image", "ray_tracing",
"magnification.png") in plot_patch.paths)
convergence = al.util.array.numpy_array_2d_from_fits(
file_path=path.join(plot_path, "image", "ray_tracing", "fits",
"convergence.fits"),
hdu=0,
)
assert convergence.shape == (5, 5)
def test__visualizes_interferometer_using_configs(self,
masked_interferometer_7,
include_all, plot_path,
plot_patch):
visualizer = vis.PhaseInterferometerVisualizer(
masked_dataset=masked_interferometer_7)
visualizer = visualizer.new_visualizer_with_preloaded_critical_curves_and_caustics(
preloaded_critical_curves=include_all.preloaded_critical_curves,
preloaded_caustics=include_all.preloaded_caustics,
)
visualizer.visualize_interferometer(paths=af.Paths())
assert (path.join(plot_path, "image", "interferometer",
"subplot_interferometer.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "interferometer",
"visibilities.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "interferometer",
"u_wavelengths.png") not in plot_patch.paths)
assert (path.join(plot_path, "image", "interferometer",
"v_wavelengths.png") not in plot_patch.paths)
n_live_points=60,
bound="multi",
sample="auto",
bootstrap=0,
enlarge=-1,
update_interval=-1.0,
vol_dec=0.5,
vol_check=2.0,
walks=25,
facc=0.5,
slices=5,
fmove=0.9,
max_move=100,
iterations_per_update=500,
number_of_cores=1,
paths=af.Paths(folders=["examples", "complex"]),
)
# %%
"""
To perform the fit with Dynesty, we pass it our model and analysis and we're good to go!
Checkout the folder 'autofit_workspace/output/dynestystatic', where the non-linear search results, visualizaion and
information can be found.
"""
# %%
result = dynesty.fit(model=model, analysis=analysis)
# %%
"""
n_live_points=100,
bound="multi",
sample="auto",
bootstrap=0,
enlarge=-1,
update_interval=-1.0,
vol_dec=0.5,
vol_check=2.0,
walks=25,
facc=0.5,
slices=5,
fmove=0.9,
max_move=100,
iterations_per_update=500,
number_of_cores=1,
paths=af.Paths(folders=["examples", "simple"]),
)
# %%
"""
To perform the fit with Dynesty, we pass it our model and analysis and we're good to go!
Checkout the folder 'autofit_workspace/output/dynestystatic', where the non-linear search results, visualizaion and
information can be found.
"""
# %%
result = dynesty.fit(model=model, analysis=analysis)
# %%
"""
for index in range(len(datas)):
"""The code below sets up the Analysis and creates the mask."""
analysis = a.Analysis(data=datas[index], noise_map=noise_maps[index])
"""
In all examples so far, our results have gone to the default path, which was the '/output/' folder and a folder
name after the non linear search. However, we can manually specify the path of the results in the 'output' folder.
We do this belo, using the Paths class and the input parameters 'folders' and 'non_linear_name'. These
define the names of folders that the phase goes in, in this case:
'/path/to/autofit_workspace/output/aggregator_example/gaussian_x1_0/emcee/'
"""
emcee = af.Emcee(
paths=af.Paths(folders=["aggregator_example", dataset_names[index]]),
nwalkers=30,
nsteps=1000,
initializer=af.InitializerBall(lower_limit=0.49, upper_limit=0.51),
auto_correlation_check_for_convergence=True,
auto_correlation_check_size=100,
auto_correlation_required_length=50,
auto_correlation_change_threshold=0.01,
number_of_cores=1,
)
print(
f"Emcee has begun running - checkout the autofit_workspace/output/{dataset_names[index]} folder for live "
f"output of the results. This Jupyter notebook cell with progress once Emcee has completed - this could take a "
f"few minutes!")
def test__source_and_lens__visualizes_fit_using_configs(
self,
masked_interferometer_7,
masked_interferometer_fit_x2_plane_inversion_7x7,
include_all,
plot_path,
plot_patch,
):
visualizer = vis.PhaseInterferometerVisualizer(
masked_dataset=masked_interferometer_7)
visualizer = visualizer.new_visualizer_with_preloaded_critical_curves_and_caustics(
preloaded_critical_curves=include_all.preloaded_critical_curves,
preloaded_caustics=include_all.preloaded_caustics,
)
visualizer.visualize_fit(
paths=af.Paths(),
fit=masked_interferometer_fit_x2_plane_inversion_7x7,
during_analysis=True,
)
assert (path.join(
plot_path,
"image",
"fit_interferometer",
"subplot_fit_interferometer.png",
) in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_interferometer",
"visibilities.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_interferometer",
"noise_map.png") not in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_interferometer",
"signal_to_noise_map.png") not in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_interferometer",
"model_visibilities.png") in plot_patch.paths)
assert (path.join(
plot_path,
"image",
"fit_interferometer",
"residual_map_vs_uv_distances_real.png",
) not in plot_patch.paths)
assert (path.join(
plot_path,
"image",
"fit_interferometer",
"normalized_residual_map_vs_uv_distances_real.png",
) in plot_patch.paths)
assert (path.join(
plot_path,
"image",
"fit_interferometer",
"chi_squared_map_vs_uv_distances_real.png",
) in plot_patch.paths)
# assert path.join(plot_path, "image","inversion","subplot_inversion.png") in plot_patch.paths
assert (path.join(plot_path, "image", "inversion",
"reconstructed_image.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"reconstruction.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion", "errors.png")
not in plot_patch.paths)
# assert path.join(plot_path, "image","inversion","residual_map.png") not in plot_patch.paths
# assert path.join(plot_path, "image","inversion","normalized_residual_map.png") not in plot_patch.paths
# assert path.join(plot_path, "image","inversion","chi_squared_map.png") in plot_patch.paths
assert (path.join(plot_path, "image", "inversion",
"regularization_weight_map.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"interpolated_reconstruction.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"interpolated_errors.png") in plot_patch.paths)
def test__source_and_lens__visualizes_fit_and_inversion_using_configs(
self,
masked_imaging_7x7,
masked_imaging_fit_x2_plane_inversion_7x7,
include_all,
plot_path,
plot_patch,
):
if os.path.exists(plot_path):
shutil.rmtree(plot_path)
visualizer = vis.PhaseImagingVisualizer(
masked_dataset=masked_imaging_7x7)
visualizer = visualizer.new_visualizer_with_preloaded_critical_curves_and_caustics(
preloaded_critical_curves=include_all.preloaded_critical_curves,
preloaded_caustics=include_all.preloaded_caustics,
)
visualizer.visualize_fit(
paths=af.Paths(),
fit=masked_imaging_fit_x2_plane_inversion_7x7,
during_analysis=False,
)
assert (path.join(plot_path, "image", "fit_imaging",
"subplot_fit_imaging.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging", "image.png")
in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging", "noise_map.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"signal_to_noise_map.png") not in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging", "model_image.png")
in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"residual_map.png") not in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"normalized_residual_map.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"chi_squared_map.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"subtracted_image_of_plane_0.png")
in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"subtracted_image_of_plane_1.png")
in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"model_image_of_plane_0.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"model_image_of_plane_1.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"plane_image_of_plane_0.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "fit_imaging",
"plane_image_of_plane_1.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"subplot_inversion.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"reconstructed_image.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"reconstruction.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion", "errors.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion", "residual_map.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"normalized_residual_map.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"chi_squared_map.png") in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"regularization_weight_map.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"interpolated_reconstruction.png")
not in plot_patch.paths)
assert (path.join(plot_path, "image", "inversion",
"interpolated_errors.png") in plot_patch.paths)
image = al.util.array.numpy_array_2d_from_fits(
file_path=path.join(plot_path, "image", "fit_imaging", "fits",
"image.fits"),
hdu=0,
)
assert image.shape == (5, 5)
image = al.util.array.numpy_array_2d_from_fits(
file_path=path.join(
plot_path,
"image",
"inversion",
"fits",
"interpolated_reconstruction.fits",
),
hdu=0,
)
assert image.shape == (7, 7)
def __init__(self, step_size=0.5):
self.step_size = step_size
self.paths = af.Paths()
