merge

autogalaxy/__init__.py

@@ -115,4 +115,4 @@
 
 conf.instance.register(__file__)
 
-__version__ = "2024.11.6.1"
+__version__ = "2024.11.13.2"

autogalaxy/aggregator/dataset_model.py

@@ -47,16 +47,17 @@ def _dataset_model_from(
         except AttributeError:
             dataset_model = None
 
-    if len(fit.children) > 0:
-        logger.info(
-            """
-            Using database for a fit with multiple summed Analysis objects.
-
-            DatasetModel objects do not fully support this yet (e.g. variables across Analysis objects may not be correct)
-            so proceed with caution!
-            """
-        )
-
-        return [dataset_model] * len(fit.children)
+    if fit.children is not None:
+        if len(fit.children) > 0:
+            logger.info(
+                """
+                Using database for a fit with multiple summed Analysis objects.
+    
+                DatasetModel objects do not fully support this yet (e.g. variables across Analysis objects may not be correct)
+                so proceed with caution!
+                """
+            )
+
+            return [dataset_model] * len(fit.children)
 
     return [dataset_model]

autogalaxy/analysis/plotter_interface.py

@@ -318,7 +318,7 @@ def should_plot(name):
             reconstructed_image=should_plot("reconstructed_image"),
             reconstruction=should_plot("reconstruction"),
             mesh_pixels_per_image_pixels=should_plot("mesh_pixels_per_image_pixels"),
-            errors=should_plot("errors"),
+            reconstruction_noise_map=should_plot("reconstruction_noise_map"),
             regularization_weights=should_plot("regularization_weights"),
         )
 
@@ -347,7 +347,7 @@ def should_plot(name):
                 pixelization_index=0,
                 reconstructed_image=True,
                 reconstruction=True,
-                errors=True,
+                reconstruction_noise_map=True,
                 regularization_weights=True,
             )
 
@@ -366,7 +366,7 @@ def should_plot(name):
                 pixelization_index=0,
                 reconstructed_image=True,
                 reconstruction=True,
-                errors=True,
+                reconstruction_noise_map=True,
                 regularization_weights=True,
                 interpolate_to_uniform=True,
             )

autogalaxy/config/visualize/plots.yaml

@@ -55,9 +55,9 @@ inversion:                                 # Settings for plots of inversions (e
   all_at_end_fits: true                    # Plot all individual plots listed below as .fits (even if False)?
   all_at_end_pdf: false                    # Plot all individual plots listed below as publication-quality .pdf (even if False)?
   data_subtracted: false                   # Plot individual plots of the data with the other inversion linear objects subtracted?
-  errors: false                            # Plot image of the errors of every mesh-pixel reconstructed value?
-  sub_pixels_per_image_pixels: false      # Plot the number of sub pixels per masked data pixels?
-  mesh_pixels_per_image_pixels: false     # Plot the number of image-plane mesh pixels per masked data pixels?
+  reconstruction_noise_map: false          # Plot image of the noise of every mesh-pixel reconstructed value?
+  sub_pixels_per_image_pixels: false       # Plot the number of sub pixels per masked data pixels?
+  mesh_pixels_per_image_pixels: false      # Plot the number of image-plane mesh pixels per masked data pixels?
   reconstructed_image: false               # Plot image of the reconstructed data (e.g. in the image-plane)?
   reconstruction: false                    # Plot the reconstructed inversion (e.g. the pixelization's mesh in the source-plane)?
   regularization_weights: false            # Plot the effective regularization weight of every inversion mesh pixel?

autogalaxy/gui/clicker.py

@@ -6,7 +6,7 @@
 
 
 class Clicker:
-    def __init__(self, image, pixel_scales, search_box_size, in_pixels : bool = False):
+    def __init__(self, image, pixel_scales, search_box_size, in_pixels: bool = False):
         self.image = image
 
         pixel_scales = aa.util.geometry.convert_pixel_scales_2d(

autogalaxy/gui/scribbler.py

@@ -2,9 +2,6 @@
 import numpy as np
 import matplotlib
 import matplotlib.pyplot as plt
-import matplotlib.colors as colors
-
-from skimage.transform import rescale
 
 
 class Scribbler:
@@ -16,6 +13,7 @@ def __init__(
         cmap=None,
         brush_width=0.05,
         backend="TkAgg",
+        mask_overlay=None
     ):
         """
 
@@ -33,18 +31,18 @@ def __init__(
         # create initial plot
         self.figure = plt.figure()
         self.ax = self.figure.add_subplot(111)
+
         if cmap is None:
             plt.imshow(image, interpolation="none")
         else:
             norm = cmap.norm_from(array=image)
+            plt.imshow(image, cmap=cmap.config_dict["cmap"], norm=norm)
 
-            if cmap.config_dict["cmap"] == "default":
-                from matplotlib.colors import LinearSegmentedColormap
-                from autoarray.plot.wrap.segmentdata import segmentdata
-
-                cmap = LinearSegmentedColormap(name="default", segmentdata=segmentdata)
+        if mask_overlay is not None:
+            grid = mask_overlay.derive_grid.edge
+            grid = mask_overlay.geometry.grid_pixel_centres_2d_from(grid_scaled_2d=grid)
+            plt.scatter(y=grid[:, 0], x=grid[:, 1], c="k", marker="x", s=10)
 
-            plt.imshow(image, cmap=cmap, norm=norm)
         plt.axis([0, image.shape[1], image.shape[0], 0])
         plt.axis("off")
         # if title:

autogalaxy/imaging/simulator.py

@@ -12,19 +12,29 @@ def via_galaxies_from(
         self, galaxies: List[Galaxy], grid: aa.type.Grid2DLike
     ) -> aa.Imaging:
         """
-        Simulate an `Imaging` dataset from an input plane and grid.
+        Simulate an `Imaging` dataset from an input list of `Galaxy` objects and a 2D grid of (y,x) coordinates.
 
-        The planbe is used to generate the image of the galaxies which is simulated.
+        The light profiles of each galaxy are used to generate the image of the galaxies which is simulated.
 
         The steps of the `SimulatorImaging` simulation process (e.g. PSF convolution, noise addition) are
-        described in the `SimulatorImaging` `__init__` method docstring.
+        described in the `SimulatorImaging` `__init__` method docstring, found in the PyAutoArray project.
+
+        If one of more galaxy light profiles are a `LightProfileSNR` object, the `intensity` of the light profile is
+        automatically set such that the signal-to-noise ratio of the light profile is equal to its input
+        `signal_to_noise_ratio` value.
+
+        For example, if a `LightProfileSNR` object has a `signal_to_noise_ratio` of 5.0, the intensity of the light
+        profile is set such that the peak surface brightness of the profile is 5.0 times the background noise level of
+        the image.
 
         Parameters
         ----------
         galaxies
-            The galaxies whose light is simulated.
+            The galaxies whose light profiles are evaluated using the input 2D grid of (y,x) coordinates in order to
+            generate the image of the galaxies which is then simulated.
         grid
-            The image-plane grid which the image of the strong lens is generated on.
+            The 2D grid of (y,x) coordinates which the light profiles of the galaxies are evaluated using in order
+            to generate the image of the galaxies.
         """
 
         galaxies = Galaxies(galaxies=galaxies)

autogalaxy/interferometer/simulator.py

@@ -22,7 +22,7 @@ def via_galaxies_from(self, galaxies: List[Galaxy], grid: aa.type.Grid2DLike):
             An arrays representing the effective exposure time of each pixel.
         psf: PSF
             An arrays describing the PSF the simulated image is blurred with.
-        add_poisson_noise: Bool
+        add_poisson_noise_to_data: Bool
             If `True` poisson noise_maps is simulated and added to the image, based on the total counts in each image
             pixel
         noise_seed: int

autogalaxy/plot/__init__.py

@@ -29,6 +29,7 @@
     VectorYXQuiver,
     PatchOverlay,
     InterpolatedReconstruction,
+    DelaunayDrawer,
     VoronoiDrawer,
     OriginScatter,
     MaskScatter,

autogalaxy/plot/mat_plot/two_d.py

@@ -30,6 +30,7 @@ def __init__(
         vector_yx_quiver: Optional[aplt.VectorYXQuiver] = None,
         patch_overlay: Optional[aplt.PatchOverlay] = None,
         interpolated_reconstruction: Optional[aplt.InterpolatedReconstruction] = None,
+        delaunay_drawer: Optional[aplt.DelaunayDrawer] = None,
         voronoi_drawer: Optional[aplt.VoronoiDrawer] = None,
         origin_scatter: Optional[aplt.OriginScatter] = None,
         mask_scatter: Optional[aplt.MaskScatter] = None,
@@ -120,6 +121,8 @@ def __init__(
         voronoi_drawer
             Interpolations the reconstruction of a `Mapper` object from its irregular grid (e.g. Delaunay, Voronoi) to a
             uniform 2D array and plots it via `plt.imshow()`.
+        delaunay_drawer
+            Draws a colored Delaunay mesh of pixels using `plt.tripcolor`.
         voronoi_drawer
             Draws a colored Voronoi mesh of pixels using `plt.fill`.
         origin_scatter
@@ -203,6 +206,7 @@ def __init__(
             contour=contour,
             grid_plot=grid_plot,
             interpolated_reconstruction=interpolated_reconstruction,
+            delaunay_drawer=delaunay_drawer,
             voronoi_drawer=voronoi_drawer,
             use_log10=use_log10,
         )

autogalaxy/profiles/mass/total/power_law_multipole.py

@@ -171,7 +171,7 @@ def deflections_yx_2d_from(
                 * self.einstein_radius ** (self.slope - 1.0)
                 * radial_grid ** (2.0 - self.slope)
             )
-            / (self.m**2.0 - (3.0 - self.slope)**2.0)
+            / (self.m**2.0 - (3.0 - self.slope) ** 2.0)
             * self.k_m
             * np.cos(self.m * (polar_angle_grid - self.angle_m))
         )
@@ -182,7 +182,7 @@ def deflections_yx_2d_from(
                 * self.einstein_radius ** (self.slope - 1.0)
                 * radial_grid ** (2.0 - self.slope)
             )
-            / (self.m**2.0 - (3.0 - self.slope)**2.0)
+            / (self.m**2.0 - (3.0 - self.slope) ** 2.0)
             * self.k_m
             * np.sin(self.m * (polar_angle_grid - self.angle_m))
         )

docs/overview/overview_1_start_here.rst

@@ -268,7 +268,7 @@ object.
         exposure_time=300.0,
         background_sky_level=1.0,
         psf=ag.Kernel2D.from_gaussian(shape_native=(11, 11), sigma=0.1, pixel_scales=0.05),
-        add_poisson_noise=True,
+        add_poisson_noise_to_data=True,
     )
 
 

test_autogalaxy/analysis/test_plotter_interface.py

@@ -90,7 +90,10 @@ def test__inversion(
 
     assert path.join(plot_path, "reconstructed_image.png") in plot_patch.paths
     assert path.join(plot_path, "reconstruction.png") in plot_patch.paths
-    assert path.join(plot_path, "inversion", "errors.png") not in plot_patch.paths
+    assert (
+        path.join(plot_path, "inversion", "reconstruction_noise_map.png")
+        not in plot_patch.paths
+    )
     assert path.join(plot_path, "regularization_weights.png") not in plot_patch.paths
 
 

test_autogalaxy/config/visualize.yaml

@@ -421,7 +421,7 @@ plots:
   inversion:
     all_at_end_png: false
     chi_squared_map: true
-    errors: false
+    reconstruction_noise_map: false
     interpolated_errors: true
     interpolated_reconstruction: true
     normalized_residual_map: false

test_autogalaxy/imaging/test_simulate_and_fit_imaging.py

@@ -23,7 +23,7 @@ def test__perfect_fit__chi_squared_0():
     )
 
     simulator = ag.SimulatorImaging(
-        exposure_time=300.0, psf=psf, add_poisson_noise=False
+        exposure_time=300.0, psf=psf, add_poisson_noise_to_data=False
     )
 
     dataset = simulator.via_galaxies_from(galaxies=[galaxy_0, galaxy_1], grid=grid)
@@ -146,7 +146,7 @@ def test__simulate_imaging_data_and_fit__linear_light_profiles_agree_with_standa
     )
 
     simulator = ag.SimulatorImaging(
-        exposure_time=300.0, psf=psf, add_poisson_noise=False
+        exposure_time=300.0, psf=psf, add_poisson_noise_to_data=False
     )
 
     dataset = simulator.via_galaxies_from(galaxies=[galaxy], grid=grid)

test_autogalaxy/imaging/test_simulator.py

@@ -85,7 +85,8 @@ def test__simulator__via_galaxies_from():
         psf=psf,
         exposure_time=10000.0,
         background_sky_level=100.0,
-        add_poisson_noise=False,
+        add_poisson_noise_to_data=False,
+        include_poisson_noise_in_noise_map=False,
     )
 
     dataset = simulator.via_galaxies_from(galaxies=[galaxy_0, galaxy_1], grid=grid)
@@ -130,7 +131,7 @@ def test__simulator__simulate_imaging_from_galaxy__source_galaxy__compare_to_ima
         psf=psf,
         exposure_time=10000.0,
         background_sky_level=100.0,
-        add_poisson_noise=True,
+        add_poisson_noise_to_data=True,
         noise_seed=1,
     )
 

test_autogalaxy/plot/mat_wrap/config/visualize/plots.ini

@@ -29,7 +29,7 @@ all_at_end_png=False
 subplot_inversion=True
 reconstructed_image=False
 reconstruction=False
-errors=False
+reconstruction_noise_map=False
 residual_map=False
 normalized_residual_map=False
 chi_squared_map=False