Merge pull request #914 from AFM-SPM/ns-rse/fix-tests-test_plottingfuncs

tests/test_plottingfuncs.py

@@ -71,7 +71,6 @@ def test_load_mplstyle(style: str, axes_titlesize: int, font_size: float, image_
 def test_dilate_binary_image(binary_image: np.ndarray, dilation_iterations: int, expected: np.ndarray) -> None:
     """Test the dilate binary images function of plottingfuncs.py."""
     result = dilate_binary_image(binary_image=binary_image, dilation_iterations=dilation_iterations)
-
     np.testing.assert_array_equal(result, expected)
 
 
@@ -277,22 +276,6 @@ def test_high_dpi(minicircle_grain_gaussian_filter: Grains, plotting_config: dic
     return fig
 
 
-@pytest.mark.mpl_image_compare(baseline_dir="resources/img/")
-def test_mask_dilation(plotting_config: dict, tmp_path: Path) -> None:
-    """Test the plotting of a mask with a different colourmap (blu)."""
-    plotting_config["mask_cmap"] = "blue"
-    mask = np.zeros((1024, 1024))
-    mask[500, :] = 1
-    fig, _ = Images(
-        data=RNG.random((1024, 1024)),
-        output_dir=tmp_path,
-        filename="mask_dilation",
-        masked_array=mask,
-        **plotting_config,
-    ).plot_and_save()
-    return fig
-
-
 @pytest.mark.parametrize(
     ("n", "expected"),
     [

topostats/default_config.yaml

@@ -96,7 +96,7 @@ plotting:
   savefig_dpi: 600 # Options : null (defaults to the value in topostats/plotting_dictionary.yaml), see https://afm-spm.github.io/TopoStats/main/configuration.html#further-customisation and https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
   pixel_interpolation: null # Options : https://matplotlib.org/stable/gallery/images_contours_and_fields/interpolation_methods.html
   image_set: core # Options : all, core
-  zrange: [-2, 6] # low and high height range for core images (can take [null, null]). low <= high
+  zrange: [null, null] # low and high height range for core images (can take [null, null]). low <= high
   colorbar: true # Options : true, false
   axes: true # Options : true, false (due to off being a bool when parsed)
   num_ticks: [null, null] # Number of ticks to have along the x and y axes. Options : null (auto) or integer > 1

topostats/plottingfuncs.py

@@ -334,14 +334,6 @@ def save_figure(self):
                 vmax=self.zrange[1],
             )
             if isinstance(self.masked_array, np.ndarray):
-                # self.masked_array[self.masked_array != 0] = 1
-                # If the image is too large for singles to be resolved in the mask, then dilate the mask proportionally
-                # to image size to enable clear viewing.
-                # if np.max(self.masked_array.shape) > 500:
-                #     dilation_strength = int(np.max(self.masked_array.shape) / 256)
-                #     self.masked_array = dilate_binary_image(
-                #         binary_image=self.masked_array, dilation_iterations=dilation_strength
-                #     )
                 mask = np.ma.masked_where(self.masked_array == 0, self.masked_array)
                 ax.imshow(
                     mask,