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fix(plotting): remove dilation if images are large #914

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Sep 27, 2024
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fix(plotting): remove dilation if images are large #914

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17 changes: 0 additions & 17 deletions tests/test_plottingfuncs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)


Expand Down Expand Up @@ -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"),
[
Expand Down
2 changes: 1 addition & 1 deletion topostats/default_config.yaml
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Expand Up @@ -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
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8 changes: 0 additions & 8 deletions topostats/plottingfuncs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
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