rahix/openflexure-microscope-server
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Spelling corrections and docstring improvements

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Co-authored by Joe Knapper <jaknapper@hotmail.com>
This commit is contained in:
Julian Stirling 2025-04-14 15:46:27 +00:00
parent bd411db5ea
commit 06632f195e
5 changed files with 33 additions and 29 deletions
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22
src/openflexure_microscope_server/things/smart_scan.py
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@ -67,7 +67,11 @@ def unpack_autofocus(scan_data):
def focus_change_acceptable(prev_pos, prev_z, new_pos, new_z, fractional_limit):
# limit is the largest ratio of change in z to change in xy that's allowed
"""Return true if the change in z-position is small enough.
A large change in z-position in an indication of focus failure.
fractional_limit is the largest ratio of change in z to change in xy that's allowed
"""
prev_xy = np.asarray(prev_pos, dtype="float64")
new_xy = np.asarray(new_pos, dtype="float64")
@ -100,7 +104,7 @@ def ensure_free_disk_space(path: str, min_space: int = 500000000) -> None:
default = 500,000,000 (500MiB)
Raises:
NotEnoughFreeSpaceError is the
NotEnoughFreeSpaceError if the remaining storage is below min_space
"""
du = shutil.disk_usage(path)
if du.free < min_space:
@ -449,7 +453,7 @@ class SmartScanThing(Thing):
)
autofocus_dz = 0
# Fix scan parameters in case UI is updates during scan.
# Fix scan parameters in case UI is updated during scan.
self._scan_data = {
"scan_name": self._ongoing_scan_name,
"overlap": overlap,
@ -464,7 +468,7 @@ class SmartScanThing(Thing):
}
@_scan_running
def _save_scan_inputs_jons(self):
def _save_scan_inputs_json(self):
# This should be a method of the scan_data dataclass
data = {
@ -504,7 +508,7 @@ class SmartScanThing(Thing):
try:
self._set_scan_data()
self._save_scan_inputs_jons()
self._save_scan_inputs_json()
if self._scan_images_taken != 0:
msg = "_scan_images_taken should be zero before starting scanning"
raise RuntimeError(msg)
@ -575,7 +579,7 @@ class SmartScanThing(Thing):
new_pos_xyz = self._move_to_next_point(next_pos_xy, z_est)
capture_image = True
# If skipping background, take and image to check if is background
# If skipping background, take an image to check if it is background
if self._scan_data["skip_background"]:
capture_image = self._background_detect.image_is_sample()
@ -583,7 +587,7 @@ class SmartScanThing(Thing):
route_planner.mark_location_visited(
new_pos_xyz, imaged=False, focused=False
)
# Background franction is actually a percentage
# Background fraction is actually a percentage
back_perc = round(self._background_detect.background_fraction(), 0)
msg = f"Skipping {new_pos_xyz} as it is {back_perc}% background."
self._scan_logger.info(msg)
@ -826,8 +830,8 @@ class SmartScanThing(Thing):
).encode("utf-8")
piexif.insert(piexif.dump(exif_dict), jpeg_path)
except: # noqa: E722
# We need to capture any exeption as there are many reasons metadata
# might not be added. We wern rather than log the error.
# We need to capture any exception as there are many reasons metadata
# might not be added. We warn rather than log the error.
self._scan_logger.warning(f"Failed to add metadata to {jpeg_path}")
except Exception as e:
raise IOError(f"An error occurred while saving {jpeg_path}") from e