Overhaul plot styling and extract fits_* output functions

autogalaxy/analysis/plotter.py

@@ -1,15 +1,11 @@
 from __future__ import annotations
-import csv
-import matplotlib.pyplot as plt
-import numpy as np
 import os
 from typing import List, Union, TYPE_CHECKING
 
 if TYPE_CHECKING:
     from pathlib import Path
 
 from autoconf import conf
-from autoconf.fitsable import hdu_list_for_output_from
 
 import autoarray as aa
 import autoarray.plot as aplt
@@ -115,18 +111,10 @@ def should_plot(name):
             )
 
         if should_plot("fits_galaxy_images"):
-            image_list = [
-                galaxy.image_2d_from(grid=grid).native_for_fits for galaxy in galaxies
-            ]
-
-            hdu_list = hdu_list_for_output_from(
-                values_list=[image_list[0].mask.astype("float")] + image_list,
-                ext_name_list=["mask"] + [f"galaxy_{i}" for i in range(len(galaxies))],
-                header_dict=grid.mask.header_dict,
+            galaxies_plots.save_galaxy_images_fits(
+                galaxies=galaxies, grid=grid, output_path=self.image_path
             )
 
-            hdu_list.writeto(self.image_path / "galaxy_images.fits", overwrite=True)
-
     def inversion(self, inversion: aa.Inversion):
         """
         Output visualization of an ``Inversion``.
@@ -146,48 +134,23 @@ def should_plot(name):
         output = self.output_from()
 
         if should_plot("subplot_inversion"):
-            from autogalaxy.plot.plot_utils import _save_subplot
+            from autoarray.inversion.plot.inversion_plots import subplot_of_mapper
 
             mapper_list = inversion.cls_list_from(cls=aa.Mapper)
-
-            for i, mapper in enumerate(mapper_list):
-                suffix = f"_{i}"
-                reconstruction = inversion.reconstruction_dict[mapper]
-                grid = np.array(mapper.source_plane_mesh_grid)
-
-                fig, ax = plt.subplots(1, 1, figsize=(7, 7))
-                sc = ax.scatter(grid[:, 1], grid[:, 0], c=reconstruction, s=10)
-                plt.colorbar(sc, ax=ax)
-                ax.set_title("Reconstruction")
-                ax.set_aspect("equal")
-                _save_subplot(fig, output.path, f"subplot_inversion{suffix}", output.format_list[0] if output.format_list else "png")
+            fmt = output.format_list[0] if output.format_list else "png"
+
+            for i in range(len(mapper_list)):
+                subplot_of_mapper(
+                    inversion=inversion,
+                    mapper_index=i,
+                    output_path=output.path,
+                    output_filename=f"subplot_inversion_{i}",
+                    output_format=fmt,
+                )
 
         if should_plot("csv_reconstruction"):
-            mapper_list = inversion.cls_list_from(cls=aa.Mapper)
-
-            for i, mapper in enumerate(mapper_list):
-                y = mapper.source_plane_mesh_grid[:, 0]
-                x = mapper.source_plane_mesh_grid[:, 1]
-                reconstruction = inversion.reconstruction_dict[mapper]
-                noise_map = inversion.reconstruction_noise_map_dict[mapper]
-
-                with open(
-                    self.image_path / f"source_plane_reconstruction_{i}.csv",
-                    mode="w",
-                    newline="",
-                ) as file:
-                    writer = csv.writer(file)
-                    writer.writerow(["y", "x", "reconstruction", "noise_map"])
-
-                    for i in range(len(x)):
-                        writer.writerow(
-                            [
-                                float(y[i]),
-                                float(x[i]),
-                                float(reconstruction[i]),
-                                float(noise_map[i]),
-                            ]
-                        )
+            from autoarray.inversion.plot.inversion_plots import save_reconstruction_csv
+            save_reconstruction_csv(inversion=inversion, output_path=self.image_path)
 
     def adapt_images(self, adapt_images: AdaptImages):
         """
@@ -215,33 +178,6 @@ def should_plot(name):
                 )
 
         if should_plot("fits_adapt_images"):
-            if adapt_images.galaxy_name_image_dict is not None:
-                image_list = [
-                    adapt_images.galaxy_name_image_dict[name].native_for_fits
-                    for name in adapt_images.galaxy_name_image_dict.keys()
-                ]
-
-                hdu_list = hdu_list_for_output_from(
-                    values_list=[image_list[0].mask.astype("float")] + image_list,
-                    ext_name_list=["mask"] + list(adapt_images.galaxy_name_image_dict.keys()),
-                    header_dict=adapt_images.mask.header_dict,
-                )
-
-                hdu_list.writeto(self.image_path / "adapt_images.fits", overwrite=True)
-
-            if adapt_images.galaxy_name_image_plane_mesh_grid_dict is not None:
-                image_plane_mesh_grid_list = [
-                    adapt_images.galaxy_name_image_plane_mesh_grid_dict[name].native
-                    for name in adapt_images.galaxy_name_image_plane_mesh_grid_dict.keys()
-                ]
-
-                hdu_list = hdu_list_for_output_from(
-                    values_list=[np.array([1])] + image_plane_mesh_grid_list,
-                    ext_name_list=[""]
-                    + list(adapt_images.galaxy_name_image_plane_mesh_grid_dict.keys()),
-                )
-
-                hdu_list.writeto(
-                    self.image_path / "adapt_image_plane_mesh_grids.fits",
-                    overwrite=True,
-                )
+            adapt_plots.save_adapt_images_fits(
+                adapt_images=adapt_images, output_path=self.image_path
+            )

autogalaxy/config/visualize/general.yaml

@@ -6,4 +6,14 @@ inversion:
   reconstruction_vmax_factor: 0.5
 zoom:
   plane_percent: 0.01
-  inversion_percent: 0.01
+  inversion_percent: 0.01
+colormap: autoarray
+ticks:
+  extent_factor_2d: 0.75
+  number_of_ticks_2d: 3
+colorbar:
+  fraction: 0.047
+  pad: 0.01
+  labelrotation: 90
+  labelsize: 22
+  labelsize_subplot: 18

autogalaxy/ellipse/model/plotter.py

@@ -4,7 +4,7 @@
 
 import autoarray as aa
 
-from autoarray.dataset.plot.imaging_plots import subplot_imaging
+from autoarray.dataset.plot.imaging_plots import subplot_imaging_dataset
 
 from autogalaxy.ellipse.fit_ellipse import FitEllipse
 from autogalaxy.ellipse.plot import fit_ellipse_plots
@@ -29,7 +29,7 @@ def should_plot(name):
             return plot_setting(section=["dataset", "imaging"], name=name)
 
         if should_plot("subplot_dataset"):
-            subplot_imaging(
+            subplot_imaging_dataset(
                 dataset,
                 output_path=self.image_path,
                 output_format=self.fmt,

autogalaxy/galaxy/plot/adapt_plots.py

@@ -59,3 +59,54 @@ def subplot_adapt_images(
 
     plt.tight_layout()
     _save_subplot(fig, output_path, "subplot_adapt_images", output_format)
+
+
+def save_adapt_images_fits(adapt_images, output_path) -> None:
+    """Write FITS files for the adapt images and image-plane mesh grids.
+
+    Writes up to two FITS files into *output_path*:
+
+    * ``adapt_images.fits`` — one HDU per galaxy adapt image, plus a
+      ``mask`` extension, written when
+      ``adapt_images.galaxy_name_image_dict`` is not ``None``.
+    * ``adapt_image_plane_mesh_grids.fits`` — one HDU per galaxy
+      image-plane mesh grid, written when
+      ``adapt_images.galaxy_name_image_plane_mesh_grid_dict`` is not
+      ``None``.
+
+    Parameters
+    ----------
+    adapt_images : AdaptImages
+        The adapt images container holding per-galaxy image and mesh-grid
+        dictionaries.
+    output_path : str or Path
+        Directory in which to write the FITS files.
+    """
+    import numpy as np
+    from pathlib import Path
+    from autoconf.fitsable import hdu_list_for_output_from
+
+    output_path = Path(output_path)
+
+    if adapt_images.galaxy_name_image_dict is not None:
+        image_list = [
+            adapt_images.galaxy_name_image_dict[name].native_for_fits
+            for name in adapt_images.galaxy_name_image_dict
+        ]
+        hdu_list = hdu_list_for_output_from(
+            values_list=[image_list[0].mask.astype("float")] + image_list,
+            ext_name_list=["mask"] + list(adapt_images.galaxy_name_image_dict.keys()),
+            header_dict=adapt_images.mask.header_dict,
+        )
+        hdu_list.writeto(output_path / "adapt_images.fits", overwrite=True)
+
+    if adapt_images.galaxy_name_image_plane_mesh_grid_dict is not None:
+        mesh_grid_list = [
+            adapt_images.galaxy_name_image_plane_mesh_grid_dict[name].native
+            for name in adapt_images.galaxy_name_image_plane_mesh_grid_dict
+        ]
+        hdu_list = hdu_list_for_output_from(
+            values_list=[np.array([1])] + mesh_grid_list,
+            ext_name_list=[""] + list(adapt_images.galaxy_name_image_plane_mesh_grid_dict.keys()),
+        )
+        hdu_list.writeto(output_path / "adapt_image_plane_mesh_grids.fits", overwrite=True)

autogalaxy/galaxy/plot/galaxies_plots.py

@@ -5,6 +5,7 @@
 
 from autogalaxy.galaxy.galaxies import Galaxies
 from autogalaxy.plot.plot_utils import _to_lines, _to_positions, plot_array, plot_grid, _save_subplot, _critical_curves_from
+from autoarray.plot.utils import hide_unused_axes
 from autogalaxy import exc
 
 
@@ -154,6 +155,7 @@ def _defl_x():
             ax=axes_flat[i],
         )
 
+    hide_unused_axes(axes_flat)
     plt.tight_layout()
     _save_subplot(fig, output_path, auto_filename, output_format)
 
@@ -213,3 +215,36 @@ def subplot_galaxy_images(
 
     plt.tight_layout()
     _save_subplot(fig, output_path, "subplot_galaxy_images", output_format)
+
+
+def save_galaxy_images_fits(
+    galaxies,
+    grid: aa.type.Grid1D2DLike,
+    output_path,
+) -> None:
+    """Write a FITS file containing the 2D image of every galaxy.
+
+    Produces ``galaxy_images.fits`` in *output_path*.  The file contains one
+    HDU per galaxy, named ``galaxy_0``, ``galaxy_1``, …, plus a ``mask``
+    extension as the first extension.
+
+    Parameters
+    ----------
+    galaxies : Galaxies
+        The galaxies whose images are evaluated.  Must not contain
+        :class:`~autogalaxy.profiles.light.linear.LightProfileLinear` profiles.
+    grid : aa.type.Grid1D2DLike
+        The grid on which each galaxy image is evaluated.
+    output_path : str or Path
+        Directory in which to write ``galaxy_images.fits``.
+    """
+    from pathlib import Path
+    from autoconf.fitsable import hdu_list_for_output_from
+
+    image_list = [galaxy.image_2d_from(grid=grid).native_for_fits for galaxy in galaxies]
+    hdu_list = hdu_list_for_output_from(
+        values_list=[image_list[0].mask.astype("float")] + image_list,
+        ext_name_list=["mask"] + [f"galaxy_{i}" for i in range(len(galaxies))],
+        header_dict=grid.mask.header_dict,
+    )
+    hdu_list.writeto(Path(output_path) / "galaxy_images.fits", overwrite=True)

autogalaxy/imaging/model/plotter.py

@@ -5,7 +5,7 @@
 
 import autoarray as aa
 
-from autoarray.dataset.plot.imaging_plots import subplot_imaging, subplot_imaging_dataset_list
+from autoarray.dataset.plot.imaging_plots import subplot_imaging_dataset, subplot_imaging_dataset_list
 
 from autogalaxy.imaging.fit_imaging import FitImaging
 from autogalaxy.imaging.plot import fit_imaging_plots
@@ -91,7 +91,7 @@ def should_plot(name):
             return plot_setting(section=["dataset", "imaging"], name=name)
 
         if should_plot("subplot_dataset"):
-            subplot_imaging(
+            subplot_imaging_dataset(
                 dataset,
                 output_path=self.image_path,
                 output_format=self.fmt,

autogalaxy/plot/__init__.py

@@ -1,7 +1,7 @@
 from autogalaxy.plot.plot_utils import plot_array, plot_grid
 
 from autoarray.dataset.plot.imaging_plots import (
-    subplot_imaging,
+    subplot_imaging_dataset,
     subplot_imaging_dataset_list,
 )
 from autoarray.dataset.plot.interferometer_plots import subplot_interferometer_dirty_images

autogalaxy/plot/plot_utils.py

@@ -96,9 +96,10 @@ def _save_subplot(fig, output_path, output_filename, output_format="png",
 
 
 def _resolve_colormap(colormap):
-    """Resolve 'default' to the autoarray default colormap."""
-    if colormap == "default":
-        return "jet"
+    """Resolve 'default' or None to the autoarray default colormap."""
+    if colormap in ("default", None):
+        from autoarray.plot.utils import _default_colormap
+        return _default_colormap()
     return colormap
 
 

docs/general/workspace.rst

@@ -54,5 +54,5 @@ The **HowToGalaxy** lecture series are a collection of Jupyter notebooks describ
 fitting project and giving illustrations of different statistical methods and techniques.
 
 Checkout the
-`tutorials section <file:///Users/Jammy/Code/PyAuto/PyAutoGalaxy/docs/_build/howtogalaxy/howtogalaxy.html>`_ for a
+`tutorials section <file:///Users/Jammy/Code/PyAutoJAX/PyAutoGalaxy/docs/_build/howtogalaxy/howtogalaxy.html>`_ for a
 full description of the lectures and online examples of every notebook.

docs/index.rst

@@ -133,7 +133,7 @@ and `PyNUFFT` [@pynufft].
     We can use the grid and galaxies to perform many calculations, for example
     plotting the image of the galaxies.
     """
-    galaxies_plotter = aplt.GalaxiesPlotter(galaxies=[galaxy], grid=grid)
+    galaxies_plotter = aplt.Galaxies(galaxies=[galaxy], grid=grid)
     galaxies_plotter.figures_2d(image=True)