Tidies up Images.plot_and_save()

Closes #806

Whislt #806 was meant to address why no Matplotlib image was generated and tested/compared to a target image when
plotting without axes or colorbar I discovered this was because the image is saved with `Images.save_array_figure()`.

This in turn uses
[`matplotlib.pyplot.imsave()`](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.imsave.html) to save the
image and the test was using
[`skimage.io.imread()`](https://scikit-image.org/docs/stable/api/skimage.io.html#skimage.io.imread) to read the image
back as an array and test the `np.sum()` and `img.shape`.

We no longer need to save arrays nor images as readable arrays (see #804 / #802) and so the need to save the image in
this manner seemed redudant. The `Images.save_figure()` already has logic which excludes the axes and scale bars (see
lines 321 of current changeset).

Further the logic for deciding what to save within `Image.plot_and_save()` seemed overly complicated and if
`Images.save_array_figure()` were being called `Images.plot_and_save()` did not return a `fig` (Matplotlib Image) that
could be saved and tested using `pytest-mpl` extension.

To this end I have...

1. Removed `Images.save_array_figure()`.
2. Tweaked the plotting options under `Images.savefig()` starting at line 321 to use a [tight
   layout](https://matplotlib.org/2.0.2/users/tight_layout_guide.html) which ensures there is no border (see note
   below).
3. Simplified the logic in `Images.plot_and_save()` controlling whether images are saved so that `ValueError` are raised
   if `Images.savefig == False` or `if Images.image_set in ["all", "core"] or self.core_set:` evaluates to
   `False`. Ensures images are explicitly closed to reduce memory usage.
4. Added tests for the raising of `ValueError` exceptions in `Images.plot_and_save()`
5. Tidied up some test names to be consistent (resulted in image name change).
6. Tidied up passing of `plotting_config` into these tests.
7. Added a `pytest-mpl` test for `test_plot_and_save_no_axes_no_colorbar()`, adding the target image as required by #806

Note on Borders

The image generated by `pytest-mpl` against which comparisons are made _does_ have a border because it is saving the
returned `fig` object itself. The actual generated image doesn't have a border (manual checks have been made).

tests/test_plottingfuncs.py

@@ -8,7 +8,6 @@
 import pytest
 from matplotlib.axes import Axes
 from matplotlib.figure import Figure
-from skimage import io
 
 from topostats.grains import Grains
 from topostats.io import LoadScans
@@ -108,30 +107,19 @@ def test_save_figure(
     assert isinstance(ax, Axes)
 
 
-def test_save_array_figure(tmp_path: Path):
-    """Tests that the image array is saved."""
-    rng2 = np.random.default_rng()
-    Images(
-        data=rng2.random((10, 10)),
-        output_dir=tmp_path,
-        filename="result",
-    ).save_array_figure()
-    assert Path(tmp_path / "result.png").exists()
-
-
 @pytest.mark.mpl_image_compare(baseline_dir="resources/img/")
-def test_plot_and_save_no_colorbar(load_scan_data: LoadScans, tmp_path: Path) -> None:
+def test_plot_and_save_no_colorbar(load_scan_data: LoadScans, plotting_config: dict, tmp_path: Path) -> None:
     """Test plotting without colorbar."""
+    plotting_config["colorbar"] = False
     fig, _ = Images(
         data=load_scan_data.image,
         output_dir=tmp_path,
         filename="01-raw_heightmap",
         pixel_to_nm_scaling=load_scan_data.pixel_to_nm_scaling,
         title="Raw Height",
-        colorbar=False,
-        axes=True,
-        image_set="all",
+        **plotting_config,
     ).plot_and_save()
+    # pytest.fail()
     return fig
 
 
@@ -145,17 +133,15 @@ def test_plot_histogram_and_save(load_scan_data: LoadScans, tmp_path: Path) -> N
 
 
 @pytest.mark.mpl_image_compare(baseline_dir="resources/img/")
-def test_plot_and_save_colorbar(load_scan_data: LoadScans, tmp_path: Path) -> None:
-    """Test plotting with colorbar."""
+def test_plot_and_save_colorbar_and_axes(load_scan_data: LoadScans, plotting_config: dict, tmp_path: Path) -> None:
+    """Test plotting with colorbar and axes (True in default_config.yaml)."""
     fig, _ = Images(
         data=load_scan_data.image,
         output_dir=tmp_path,
         filename="01-raw_heightmap",
         pixel_to_nm_scaling=load_scan_data.pixel_to_nm_scaling,
         title="Raw Height",
-        colorbar=True,
-        axes=True,
-        image_set="all",
+        **plotting_config,
     ).plot_and_save()
     return fig
 
@@ -174,20 +160,43 @@ def test_plot_and_save_no_axes(load_scan_data: LoadScans, plotting_config: dict,
     return fig
 
 
+@pytest.mark.mpl_image_compare(baseline_dir="resources/img/")
 def test_plot_and_save_no_axes_no_colorbar(load_scan_data: LoadScans, plotting_config: dict, tmp_path: Path) -> None:
     """Test plotting without axes and without the colourbar."""
     plotting_config["axes"] = False
     plotting_config["colorbar"] = False
-    Images(
+    fig, _ = Images(
         data=load_scan_data.image,
         output_dir=tmp_path,
         filename="01-raw_heightmap",
         title="Raw Height",
         **plotting_config,
     ).plot_and_save()
-    img = io.imread(tmp_path / "01-raw_heightmap.png")
-    assert np.sum(img) == 1535334
-    assert img.shape == (64, 64, 4)
+    return fig
+
+
+@pytest.mark.parametrize(
+    ("save", "image_set", "core_set"),
+    [
+        pytest.param(False, "all", False, id="save option is false, no images can be plotted"),
+        pytest.param(True, "nothing", False, id="image_set is invalid, core_set false, no images can be plotted"),
+    ],
+)
+def test_plot_and_save_false_raises_exception(
+    load_scan_data: LoadScans, plotting_config: dict, save: bool, image_set: str, core_set: bool, tmp_path: Path
+) -> None:
+    """Test ValueError is raised if invalid save/image_set/core_set values are passed."""
+    plotting_config["save"] = save
+    plotting_config["image_set"] = image_set
+    plotting_config["core_set"] = core_set
+    with pytest.raises(ValueError):  # noqa: PT011
+        _, _ = Images(
+            data=load_scan_data.image,
+            output_dir=tmp_path,
+            filename="01-raw_heightmap",
+            title="Raw Height",
+            **plotting_config,
+        ).plot_and_save()
 
 
 @pytest.mark.mpl_image_compare(baseline_dir="resources/img/")

topostats/plottingfuncs.py

@@ -240,7 +240,7 @@ def plot_histogram_and_save(self):
 
     def plot_and_save(self):
         """
-        Plot and save the images with savefig or imsave depending on config file parameters.
+        Plot and save the image.
 
         Returns
         -------
@@ -251,19 +251,16 @@ def plot_and_save(self):
         """
         fig, ax = None, None
         if self.save:
-            if self.image_set == "all" or self.core_set:
-                if self.axes or self.colorbar:
-                    fig, ax = self.save_figure()
-                else:
-                    if isinstance(self.masked_array, np.ndarray) or self.region_properties:
-                        fig, ax = self.save_figure()
-                    else:
-                        self.save_array_figure()
-        LOGGER.info(
-            f"[{self.filename}] : Image saved to : {str(self.output_dir / self.filename)}.{self.savefig_format}\
- | DPI: {self.savefig_dpi}"
-        )
-        return fig, ax
+            if self.image_set in ["all", "core"] or self.core_set:
+                fig, ax = self.save_figure()
+                LOGGER.info(
+                    f"[{self.filename}] : Image saved to : {str(self.output_dir / self.filename)}.{self.savefig_format}"
+                    " | DPI: {self.savefig_dpi}"
+                )
+                plt.close()
+                return fig, ax
+            raise ValueError(f"Invalid image_set ({self.image_set=}) or core_set ({self.core_set=})")
+        raise ValueError(f"The 'save' option is False ({self.save=}), set to 'True' to save figures.")
 
     def save_figure(self):
         """Save figures as plt.savefig objects.
@@ -325,6 +322,8 @@ def save_figure(self):
             if not self.axes and not self.colorbar:
                 plt.title("")
                 fig.frameon = False
+                plt.box(False)
+                plt.tight_layout()
                 plt.savefig(
                     (self.output_dir / f"{self.filename}.{self.savefig_format}"),
                     bbox_inches="tight",
@@ -345,18 +344,6 @@ def save_figure(self):
         plt.close()
         return fig, ax
 
-    def save_array_figure(self) -> None:
-        """Save the image array as an image using plt.imsave()."""
-        plt.imsave(
-            (self.output_dir / f"{self.filename}.{self.savefig_format}"),
-            self.data,
-            cmap=self.cmap,
-            vmin=self.zrange[0],
-            vmax=self.zrange[1],
-            format=self.savefig_format,
-        )
-        plt.close()
-
 
 def add_bounding_boxes_to_plot(fig, ax, shape, region_properties: list, pixel_to_nm_scaling: float) -> None:
     """Add the bounding boxes to a plot.