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Merge pull request #906 from AFM-SPM/ns-rse/reinstate-grains-try-except
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fix: reinstate grains try except
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@ns-rse
ns-rse committed Sep 17, 2024
2 parents 55deec3 + de37abb commit e9fc3ba
Showing 1 changed file with 72 additions and 73 deletions.
145 changes: 72 additions & 73 deletions topostats/processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,81 +158,82 @@ def run_grains( # noqa: C901
if grains_config["run"]:
grains_config.pop("run")

# try:
LOGGER.info(f"[{filename}] : *** Grain Finding ***")
grains = Grains(
image=image,
filename=filename,
pixel_to_nm_scaling=pixel_to_nm_scaling,
**grains_config,
)
grains.find_grains()
for direction, _ in grains.region_properties.items():
LOGGER.info(
f"[{filename}] : Grains found for direction {direction} : {len(grains.region_properties[direction])}"
try:
LOGGER.info(f"[{filename}] : *** Grain Finding ***")
grains = Grains(
image=image,
filename=filename,
pixel_to_nm_scaling=pixel_to_nm_scaling,
**grains_config,
)
if len(grains.region_properties[direction]) == 0:
LOGGER.warning(f"[{filename}] : No grains found for direction {direction}")
# except Exception as e:
# LOGGER.error(f"[{filename}] : An error occurred during grain finding, skipping grainstats and dnatracing.")
# LOGGER.error(f"[{filename}] : The error: {e}")
# else:
for direction, region_props in grains.region_properties.items():
if len(region_props) == 0:
LOGGER.warning(f"[{filename}] : No grains found for the {direction} direction.")
# Optionally plot grain finding stage if we have found grains and plotting is required
if plotting_config["run"]:
plotting_config.pop("run")
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():
if len(array.shape) == 3:
# Use the DNA class mask from the tensor. Hardcoded to 1 as this implementation is not yet generalised.
array = array[:, :, 1]
LOGGER.info(f"[{filename}] : Plotting {plot_name} image")
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_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_direction
# hard code to class index 1, as this implementation is not yet generalised.
Images(
grains.directions[direction]["labelled_regions_02"][:, :, 1],
**plotting_config["plot_dict"]["coloured_boxes"],
region_properties=grains.region_properties[direction],
).plot_and_save()
# Always want mask_overlay (aka "Height Thresholded with Mask") but in core_out_path
plot_name = "mask_overlay"
plotting_config["plot_dict"][plot_name]["output_dir"] = core_out_path
# hard code to class index 1, as this implementation is not yet generalised.
Images(
image,
filename=f"{filename}_{direction}_masked",
masked_array=grains.directions[direction]["removed_small_objects"][:, :, 1],
**plotting_config["plot_dict"][plot_name],
).plot_and_save()

plotting_config["run"] = True

grains.find_grains()
for direction, _ in grains.region_properties.items():
LOGGER.info(
f"[{filename}] : Grains found for direction {direction} : {len(grains.region_properties[direction])}"
)
if len(grains.region_properties[direction]) == 0:
LOGGER.warning(f"[{filename}] : No grains found for direction {direction}")
except Exception as e:
LOGGER.error(f"[{filename}] : An error occurred during grain finding, skipping grainstats and dnatracing.")
LOGGER.error(f"[{filename}] : The error: {e}")
else:
# Otherwise, return None and warn that plotting is disabled for grain finding images
LOGGER.info(f"[{filename}] : Plotting disabled for Grain Finding Images")
for direction, region_props in grains.region_properties.items():
if len(region_props) == 0:
LOGGER.warning(f"[{filename}] : No grains found for the {direction} direction.")
# Optionally plot grain finding stage if we have found grains and plotting is required
if plotting_config["run"]:
plotting_config.pop("run")
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():
if len(array.shape) == 3:
# Use the DNA class mask from the tensor. Hardcoded to 1 as this implementation is not yet generalised.
array = array[:, :, 1]
LOGGER.info(f"[{filename}] : Plotting {plot_name} image")
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_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_direction
# hard code to class index 1, as this implementation is not yet generalised.
Images(
grains.directions[direction]["labelled_regions_02"][:, :, 1],
**plotting_config["plot_dict"]["coloured_boxes"],
region_properties=grains.region_properties[direction],
).plot_and_save()
# Always want mask_overlay (aka "Height Thresholded with Mask") but in core_out_path
plot_name = "mask_overlay"
plotting_config["plot_dict"][plot_name]["output_dir"] = core_out_path
# hard code to class index 1, as this implementation is not yet generalised.
Images(
image,
filename=f"{filename}_{direction}_masked",
masked_array=grains.directions[direction]["removed_small_objects"][:, :, 1],
**plotting_config["plot_dict"][plot_name],
region_properties=grains.region_properties[direction],
).plot_and_save()

plotting_config["run"] = True

else:
# Otherwise, return None and warn that plotting is disabled for grain finding images
LOGGER.info(f"[{filename}] : Plotting disabled for Grain Finding Images")

grain_masks = {}
for direction in grains.directions:
grain_masks[direction] = grains.directions[direction]["labelled_regions_02"]
grain_masks = {}
for direction in grains.directions:
grain_masks[direction] = grains.directions[direction]["labelled_regions_02"]

return grain_masks
return grain_masks

# Otherwise, return None and warn grainstats is disabled
LOGGER.info(f"[{filename}] Detection of grains disabled, returning empty data frame.")
Expand Down Expand Up @@ -292,7 +293,6 @@ def run_grainstats(
height_profiles_dict = {}
# There are two layers to process those above the given threshold and those below
for direction, _ in grain_masks.items():

# Get the DNA class mask from the tensor
LOGGER.info(f"[{filename}] : Full Mask dimensions: {grain_masks[direction].shape}")
assert len(grain_masks[direction].shape) == 3, "Grain masks should be 3D tensors"
Expand Down Expand Up @@ -423,7 +423,6 @@ def run_dnatracing( # noqa: C901
tracing_stats = defaultdict()
grain_trace_data = defaultdict()
for direction, _ in grain_masks.items():

# Get the DNA class mask from the tensor
LOGGER.info(f"[{filename}] : Mask dimensions: {grain_masks[direction].shape}")
assert len(grain_masks[direction].shape) == 3, "Grain masks should be 3D tensors"
Expand Down

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