changes to configs

autocti/config/notation/label.ini

@@ -1,15 +1,15 @@
 [label]
-density = \rho
-release_timescale = \tau
-full_well_depth = h
-well_fill_alpha = \alpha
-well_fill_power = \beta
-well_fill_gamma = \gamma
-well_notch_depth = d
-scale_factor = \omega
+density=\rho
+release_timescale=\tau
+full_well_depth=h
+well_fill_alpha=\alpha
+well_fill_power=\beta
+well_fill_gamma=\gamma
+well_notch_depth=d
+scale_factor=\omega
 
 [subscript]
-TrapInstantCapture = s
-CIHyperNoiseScalar = H
-CCD = ccd
-CCDComplex = ccd
+TrapInstantCapture=s
+CIHyperNoiseScalar=H
+CCD=ccd
+CCDComplex=ccd

autocti/config/notation/label_format.ini

@@ -1,6 +1,6 @@
 [format]
-full_well_depth = {:.2f}
-well_fill_alpha = {:.2f}
-well_fill_power = {:.2f}
-well_fill_gamma = {:.2f}
-well_notch_depth = {:.2f}
+full_well_depth={:.2f}
+well_fill_alpha={:.2f}
+well_fill_power={:.2f}
+well_fill_gamma={:.2f}
+well_notch_depth={:.2f}

autocti/config/visualize/plots.ini

@@ -1,13 +1,13 @@
 [dataset]
-ci_pre_cti = False
-cosmic_ray_map = False
-noise_scaling_maps = False
+ci_pre_cti=False
+cosmic_ray_map=False
+noise_scaling_maps=False
 
 [fit]
-subplot_fit = False
-subplot_residual_maps = False
-subplot_normalized_residual_maps = False
-subplot_chi_squared_maps = False
-ci_pre_cti = False
-ci_post_cti = False
-noise_scaling_maps = False
+subplot_fit=False
+subplot_residual_maps=False
+subplot_normalized_residual_maps=False
+subplot_chi_squared_maps=False
+ci_pre_cti=False
+ci_post_cti=False
+noise_scaling_maps=False

autocti/plot/ci_fit_plots.py

@@ -73,7 +73,7 @@ def subplot_ci_fit(fit, include=None, sub_plotter=None):
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 @plotters.set_include_and_sub_plotter
@@ -99,7 +99,7 @@ def subplot_residual_maps(fits, include=None, sub_plotter=None):
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 @plotters.set_include_and_sub_plotter
@@ -125,7 +125,7 @@ def subplot_normalized_residual_maps(fits, include=None, sub_plotter=None):
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 @plotters.set_include_and_sub_plotter
@@ -151,7 +151,7 @@ def subplot_chi_squared_maps(fits, include=None, sub_plotter=None):
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 def individuals(
@@ -248,7 +248,7 @@ def subplot_fit_lines(fit, line_region, include=None, sub_plotter=None):
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 @plotters.set_include_and_sub_plotter
@@ -274,7 +274,7 @@ def subplot_residual_map_lines(fits, line_region, include=None, sub_plotter=None
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 @plotters.set_include_and_sub_plotter
@@ -302,7 +302,7 @@ def subplot_normalized_residual_map_lines(
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 @plotters.set_include_and_sub_plotter
@@ -329,7 +329,7 @@ def subplot_chi_squared_map_lines(fits, line_region, include=None, sub_plotter=N
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 def individuals_lines(
@@ -595,7 +595,7 @@ def noise_scaling_maps(fit, include=None, sub_plotter=None):
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 @plotters.set_include_and_plotter

autocti/plot/ci_imaging_plots.py

@@ -46,7 +46,7 @@ def subplot_ci_imaging(ci_imaging, include=None, sub_plotter=None):
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 def individual(
@@ -272,7 +272,7 @@ def subplot_ci_lines(ci_imaging, line_region, include=None, sub_plotter=None):
 
     sub_plotter.output.subplot_to_figure()
 
-    sub_plotter.figure.close()
+    sub_plotter.figure_2d.close()
 
 
 def individual_ci_lines(

eden.ini

@@ -1,3 +1,3 @@
 [eden]
-name = autocti
-prefix = ac
+name=autocti
+prefix=ac

test_autocti/config/non_linear/GridSearch.ini

@@ -1,3 +1,3 @@
 [general]
 number_of_cores=2
-step_size = 0.1
+step_size=0.1

test_autocti/config/non_linear/mcmc/Emcee.ini

@@ -3,14 +3,14 @@ nwalkers=50
 nsteps=2000
 
 [initialize]
-method = ball
-ball_lower_limit = 0.49
-ball_upper_limit = 0.51
+method=ball
+ball_lower_limit=0.49
+ball_upper_limit=0.51
 
 [auto_correlation]
-check_for_convergence = True
-check_size = 100
-required_length = 50
+check_for_convergence=True
+check_size=100
+required_length=50
 change_threshold=0.01
 
 [updates]

test_autocti/config/non_linear/nest/DynestyDynamic.ini

@@ -1,17 +1,17 @@
 [search]
-bound = multi
+bound=multi
 evidence_tolerance=0.01
-sample = auto
-bootstrap = 0
-enlarge = -1
-update_interval = -1.0
-vol_dec = 0.5
-vol_check = 2.0
-walks = 25
+sample=auto
+bootstrap=0
+enlarge=-1
+update_interval=-1.0
+vol_dec=0.5
+vol_check=2.0
+walks=25
 sampling_efficiency=0.5
-slices = 5
-fmove = 0.9
-max_move = 100
+slices=5
+fmove=0.9
+max_move=100
 maxiter=0
 maxcall=0
 logl_max=inf
@@ -41,7 +41,7 @@ use_errors=True
 use_widths=True
 
 [parallel]
-number_of_cores = 1
+number_of_cores=1
 
 [tag]
 name=dynesty_dynamic

test_autocti/config/non_linear/nest/DynestyStatic.ini

@@ -1,17 +1,17 @@
 [search]
-n_live_points = 150
-bound = multi
-sample = auto
-bootstrap = 0
-enlarge = -1
-update_interval = -1.0
-vol_dec = 0.5
-vol_check = 2.0
-walks = 25
+n_live_points=150
+bound=multi
+sample=auto
+bootstrap=0
+enlarge=-1
+update_interval=-1.0
+vol_dec=0.5
+vol_check=2.0
+walks=25
 sampling_efficiency=0.5
-slices = 5
-fmove = 0.9
-max_move = 100
+slices=5
+fmove=0.9
+max_move=100
 maxiter=0
 maxcall=0
 logl_max=inf
@@ -41,7 +41,7 @@ use_errors=True
 use_widths=True
 
 [parallel]
-number_of_cores = 1
+number_of_cores=1
 
 [tag]
 name=dynesty_static

test_autocti/config/non_linear/nest/MultiNest.ini

@@ -1,27 +1,27 @@
 [search]
-n_live_points = 50
-sampling_efficiency = 0.5
-const_efficiency_mode = False
-evidence_tolerance = 0.5
-multimodal = False
-importance_nested_sampling = False
-max_modes = 100
-mode_tolerance = -1e90
-max_iter = 0
+n_live_points=50
+sampling_efficiency=0.5
+const_efficiency_mode=False
+evidence_tolerance=0.5
+multimodal=False
+importance_nested_sampling=False
+max_modes=100
+mode_tolerance=-1e90
+max_iter=0
 
 [settings]
-n_iter_before_update = 5
-null_log_evidence = -1e90
-seed = -1
-verbose = False
-resume = True
-context = 0
-write_output = True
-log_zero = -1e100
-init_MPI = False
-terminate_at_acceptance_ratio = False
-acceptance_ratio_threshold = 1.0
-stagger_resampling_likelihood = True
+n_iter_before_update=5
+null_log_evidence=-1e90
+seed=-1
+verbose=False
+resume=True
+context=0
+write_output=True
+log_zero=-1e100
+init_MPI=False
+terminate_at_acceptance_ratio=False
+acceptance_ratio_threshold=1.0
+stagger_resampling_likelihood=True
 
 [updates]
 iterations_per_update=2500
@@ -48,31 +48,31 @@ sampling_efficiency=eff
 const_efficiency_mode=const
 multimodal=mm
 importance_nested_sampling=is
-stagger_resampling_value = 1e80
-terminate_at_acceptance_ratio = False
-acceptance_ratio_threshold = 1.0
+stagger_resampling_value=1e80
+terminate_at_acceptance_ratio=False
+acceptance_ratio_threshold=1.0
 
 [hyper_galaxy]
-const_efficiency_mode = False
-n_live_points = 30
-sampling_efficiency = 0.5
-multimodal = False
-evidence_tolerance = 0.1
+const_efficiency_mode=False
+n_live_points=30
+sampling_efficiency=0.5
+multimodal=False
+evidence_tolerance=0.1
 
 [inversion]
-const_efficiency_mode = True
-n_live_points = 50
-sampling_efficiency = 0.3
-multimodal = False
-evidence_tolerance = 100.0
-terminate_at_acceptance_ratio = False
-acceptance_ratio_threshold = 0.05
+const_efficiency_mode=True
+n_live_points=50
+sampling_efficiency=0.3
+multimodal=False
+evidence_tolerance=100.0
+terminate_at_acceptance_ratio=False
+acceptance_ratio_threshold=0.05
 
 [hyper_combined]
-const_efficiency_mode = True
-n_live_points = 50
-sampling_efficiency = 0.3
-multimodal = False
-evidence_tolerance = 10.0
-terminate_at_acceptance_ratio = False
-acceptance_ratio_threshold = 0.05
+const_efficiency_mode=True
+n_live_points=50
+sampling_efficiency=0.3
+multimodal=False
+evidence_tolerance=10.0
+terminate_at_acceptance_ratio=False
+acceptance_ratio_threshold=0.05