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Tidies up Images.plot_and_save() #810

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Mar 12, 2024
Merged

Tidies up Images.plot_and_save() #810

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07db718
Tidies up Images.plot_and_save()
ns-rse Mar 4, 2024
ad4880b
Ensures target directories exist
ns-rse Mar 4, 2024
c30765a
Ensures target directories exist
ns-rse Mar 4, 2024
f2d0b78
Filter and grain image directory creation conditional on image_set
ns-rse Mar 5, 2024
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0 ...urces/img/test_plot_and_save_colorbar.png → .../test_plot_and_save_colorbar_and_axes.png
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34 changes: 9 additions & 25 deletions tests/test_plottingfuncs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -108,29 +107,17 @@ 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()
return fig

Expand All @@ -145,17 +132,15 @@ 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

Expand All @@ -174,20 +159,19 @@ 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.mpl_image_compare(baseline_dir="resources/img/")
Expand Down
19 changes: 12 additions & 7 deletions tests/test_processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -288,45 +288,50 @@ def test_check_run_steps(
@pytest.mark.parametrize(
("filter_run", "grains_run", "grainstats_run", "dnatracing_run", "log_msg1", "log_msg2"),
[
(
pytest.param(
False,
False,
False,
False,
"You have not included running the initial filter stage.",
"Please check your configuration file.",
id="All stages are disabled",
),
(
pytest.param(
True,
False,
False,
False,
"Detection of grains disabled, returning empty data frame.",
"16-gaussian_filtered",
"minicircle_small.png",
id="Only filtering enabled",
),
(
pytest.param(
True,
True,
False,
False,
"Calculation of grainstats disabled, returning empty dataframe.",
"25-labelled_image_bboxes",
"minicircle_small_above_masked.png",
id="Filtering and Grain enabled",
),
(
pytest.param(
True,
True,
True,
False,
"Processing grain",
"Calculation of DNA Tracing disabled, returning grainstats data frame.",
id="Filtering, Grain and GrainStats enabled",
),
(
pytest.param(
True,
True,
True,
True,
"Traced grain 3 of 3",
"Combining ['above'] grain statistics and dnatracing statistics",
id="Filtering, Grain, GrainStats and DNA Tracing enabled",
),
],
)
Expand Down
40 changes: 16 additions & 24 deletions topostats/plottingfuncs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,11 @@ def __init__(
"""
Initialise the class.

There are two key parameters that ensure whether and image is plotted that are passed in from the update
plotting dictionary. These are the `image_set` which defines whether to plot 'all' images or just the `core`
set. There is then the 'core_set' which defines whether an individual images belongs to the 'core_set' or not.
If it doesn't then it is not plotted when `image_set == "core"`.

Parameters
----------
data : np.array
Expand Down Expand Up @@ -240,7 +245,7 @@ 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
-------
Expand All @@ -251,18 +256,15 @@ def plot_and_save(self):
"""
fig, ax = None, None
if self.save:
# Only plot if image_set is "all" (i.e. user wants all images) or an image is in the core_set
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}"
)
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
return fig, ax

def save_figure(self):
Expand Down Expand Up @@ -325,6 +327,8 @@ 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",
Expand All @@ -345,18 +349,6 @@ 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.
Expand Down
21 changes: 15 additions & 6 deletions topostats/processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,17 +79,21 @@ def run_filters(
**filter_config,
)
filters.filter_image()

# Optionally plot filter stage
if plotting_config["run"]:
plotting_config.pop("run")
LOGGER.info(f"[{filename}] : Plotting Filtering Images")
if plotting_config["image_set"] == "all":
filter_out_path.mkdir(parents=True, exist_ok=True)
LOGGER.debug(f"[{filename}] : Target filter directory created : {filter_out_path}")
# Generate plots
for plot_name, array in filters.images.items():
if plot_name not in ["scan_raw"]:
if plot_name == "extracted_channel":
array = np.flipud(array.pixels)
plotting_config["plot_dict"][plot_name]["output_dir"] = filter_out_path
plotting_config["plot_dict"][plot_name]["output_dir"] = (
core_out_path if plotting_config["plot_dict"][plot_name]["core_set"] else filter_out_path
)
try:
Images(array, **plotting_config["plot_dict"][plot_name]).plot_and_save()
Images(array, **plotting_config["plot_dict"][plot_name]).plot_histogram_and_save()
Comment on lines +86 to 99
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The only other thing is that you've got an if image_set=='all' statement which is then used again within the plot_and_save() function, and I'm thinking would it make sense just to use it the once in processing?

We could pop it and re-add it like the plotting.run param and keep all the non-core images within this if statement, and the core image outside like it is? What do you think?

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@ns-rse ns-rse Mar 6, 2024 •
edited
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The logic here though is to create the sub-directory filter as held in filter_out_path (the same is true for grains). We then need to set the parameter in the current images plot_dict to whatever that is, hence the if/else.

When I simplified the logic within plot_and_save() for some reason I couldn't understand I got error messages about target directories not being present so I figured I needed to create them.

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Also having plot_and_save() know about image_set might be useful should anyone use the class/method interactively e.g. in a Notebook.

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Ok makes sense, thanks for explaining :)

Expand Down Expand Up @@ -184,18 +188,22 @@ def run_grains( # noqa: C901
LOGGER.info(f"[{filename}] : Plotting Grain Finding Images")
for direction, image_arrays in grains.directions.items():
LOGGER.info(f"[{filename}] : Plotting {direction} Grain Finding Images")
grain_out_path_direction = grain_out_path / f"{direction}"
if plotting_config["image_set"] == "all":
grain_out_path_direction.mkdir(parents=True, exist_ok=True)
LOGGER.debug(f"[{filename}] : Target grain directory created : {grain_out_path_direction}")
for plot_name, array in image_arrays.items():
LOGGER.info(f"[{filename}] : Plotting {plot_name} image")
plotting_config["plot_dict"][plot_name]["output_dir"] = grain_out_path / f"{direction}"
plotting_config["plot_dict"][plot_name]["output_dir"] = grain_out_path_direction
Images(array, **plotting_config["plot_dict"][plot_name]).plot_and_save()
# Make a plot of coloured regions with bounding boxes
plotting_config["plot_dict"]["bounding_boxes"]["output_dir"] = grain_out_path / f"{direction}"
plotting_config["plot_dict"]["bounding_boxes"]["output_dir"] = grain_out_path_direction
Images(
grains.directions[direction]["coloured_regions"],
**plotting_config["plot_dict"]["bounding_boxes"],
region_properties=grains.region_properties[direction],
).plot_and_save()
plotting_config["plot_dict"]["coloured_boxes"]["output_dir"] = grain_out_path / f"{direction}"
plotting_config["plot_dict"]["coloured_boxes"]["output_dir"] = grain_out_path_direction
Images(
grains.directions[direction]["labelled_regions_02"],
**plotting_config["plot_dict"]["coloured_boxes"],
Expand Down Expand Up @@ -534,7 +542,8 @@ def process_scan(
Parameters
----------
img_path_px2nm : Dict[str, Union[np.ndarray, Path, float]]
A dictionary with keys 'image', 'img_path' and 'px_2_nm' containing a file or frames' image, it's path and it's pixel to namometre scaling value.
A dictionary with keys 'image', 'img_path' and 'px_2_nm' containing a file or frames' image, it's path and it's
pixel to namometre scaling value.
base_dir : Union[str, Path]
Directory to recursively search for files, if not specified the current directory is scanned.
filter_config : dict
Expand Down
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