Spelling corrections and docstring improvements
Co-authored by Joe Knapper <jaknapper@hotmail.com>
This commit is contained in:
Julian Stirling
parent
bd411db5ea
commit
06632f195e
5 changed files with 33 additions and 29 deletions
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@ -22,7 +22,7 @@ XYZPosList: TypeAlias = list[XYZPos]
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def enforce_xy_tuple(value: XYPos) -> XYPos:
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"""
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Used for enfocring that an input is a tuple and is the correct length
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Used for enforcing that an input is a tuple and is the correct length
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"""
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if not isinstance(value, (list, tuple)):
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raise ValueError("2 value tuple expected")
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@ -35,7 +35,7 @@ def enforce_xy_tuple(value: XYPos) -> XYPos:
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def enforce_xyz_tuple(value: XYZPos) -> XYZPos:
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"""
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Used for enfocring that an input is a tuple and is the correct length
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Used for enforcing that an input is a tuple and is the correct length
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"""
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if not isinstance(value, (list, tuple)):
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raise ValueError("3 value tuple expected")
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@ -64,7 +64,7 @@ class ScanPlanner:
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locations are adjusted.
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When subclassing be sure to use enforce_xy_tuple and enforce_xyz_tuple on any user
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data before
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data before running
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"""
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def __init__(self, intial_position: XYPos, planner_settings: Optional[dict] = None):
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@ -199,15 +199,15 @@ class ScanPlanner:
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path_pos = np.array(self._focused_locations, dtype="float64")[:, :2]
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# Use linalg.norm to calculate the direct distance bweween the points
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# Note linalg.norm always used float64
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# Note linalg.norm always uses float64
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dists = np.linalg.norm((path_pos - current_pos), axis=1)
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# Get indicies of all mimuma.
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# Get indices of all minima.
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# Note np.where always returns a tuple of arrays, hence the trailing [0]
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indicies = np.where(dists == np.min(dists))[0]
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indices = np.where(dists == np.min(dists))[0]
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# The last index is most recent
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return self._focused_locations[indicies[-1]]
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return self._focused_locations[indices[-1]]
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def mark_location_visited(
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self, xyz_pos: XYZPos, imaged: bool, focused: bool
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@ -216,7 +216,7 @@ class ScanPlanner:
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Mark the location as visited
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Args:
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xyz_pos: the x_y poistion
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xyz_pos: the x_y_z position
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imaged: true if an image was taken, false if not (due to background detect)
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focused: true if autofocus completed successfully
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"""
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@ -289,10 +289,10 @@ class SmartSpiral(ScanPlanner):
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self, xyz_pos: XYZPos, imaged: bool = True, focused: bool = True
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) -> None:
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"""
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Mark the location as visited. Adjust extra poisitons accordingly
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Mark the location as visited. Adjust extra positions accordingly
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Args:
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xyz_pos: the x_y poistion
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xyz_pos: the x_y_z position
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imaged: true if an image was taken, false if not (due to background detect)
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focused: true if autofocus completed successfully
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"""
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@ -306,9 +306,9 @@ class SmartSpiral(ScanPlanner):
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def _add_surrounding_positions(self, xy_pos: XYPos) -> None:
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"""
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This adds the surrounding (4 point connectivity) poistions
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This adds the surrounding (4 point connectivity) positions
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to the remaining locations if they are not too far away or
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or already planned or already visited
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already planned or already visited
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"""
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new_positions = [
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(xy_pos[0] - self._dx, xy_pos[1]),
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@ -318,7 +318,7 @@ class SmartSpiral(ScanPlanner):
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]
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for new_pos in new_positions:
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# Skip position if already planned or fixited
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# Skip position if already planned or visited
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if self.position_planned(new_pos) or self.position_visited(new_pos):
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continue
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@ -67,7 +67,11 @@ def unpack_autofocus(scan_data):
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def focus_change_acceptable(prev_pos, prev_z, new_pos, new_z, fractional_limit):
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# limit is the largest ratio of change in z to change in xy that's allowed
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"""Return true if the change in z-position is small enough.
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A large change in z-position in an indication of focus failure.
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fractional_limit is the largest ratio of change in z to change in xy that's allowed
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"""
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prev_xy = np.asarray(prev_pos, dtype="float64")
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new_xy = np.asarray(new_pos, dtype="float64")
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@ -100,7 +104,7 @@ def ensure_free_disk_space(path: str, min_space: int = 500000000) -> None:
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default = 500,000,000 (500MiB)
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Raises:
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NotEnoughFreeSpaceError is the
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NotEnoughFreeSpaceError if the remaining storage is below min_space
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"""
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du = shutil.disk_usage(path)
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if du.free < min_space:
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@ -449,7 +453,7 @@ class SmartScanThing(Thing):
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)
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autofocus_dz = 0
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# Fix scan parameters in case UI is updates during scan.
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# Fix scan parameters in case UI is updated during scan.
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self._scan_data = {
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"scan_name": self._ongoing_scan_name,
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"overlap": overlap,
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@ -464,7 +468,7 @@ class SmartScanThing(Thing):
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}
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@_scan_running
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def _save_scan_inputs_jons(self):
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def _save_scan_inputs_json(self):
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# This should be a method of the scan_data dataclass
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data = {
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@ -504,7 +508,7 @@ class SmartScanThing(Thing):
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try:
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self._set_scan_data()
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self._save_scan_inputs_jons()
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self._save_scan_inputs_json()
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if self._scan_images_taken != 0:
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msg = "_scan_images_taken should be zero before starting scanning"
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raise RuntimeError(msg)
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@ -575,7 +579,7 @@ class SmartScanThing(Thing):
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new_pos_xyz = self._move_to_next_point(next_pos_xy, z_est)
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capture_image = True
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# If skipping background, take and image to check if is background
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# If skipping background, take an image to check if it is background
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if self._scan_data["skip_background"]:
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capture_image = self._background_detect.image_is_sample()
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@ -583,7 +587,7 @@ class SmartScanThing(Thing):
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route_planner.mark_location_visited(
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new_pos_xyz, imaged=False, focused=False
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)
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# Background franction is actually a percentage
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# Background fraction is actually a percentage
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back_perc = round(self._background_detect.background_fraction(), 0)
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msg = f"Skipping {new_pos_xyz} as it is {back_perc}% background."
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self._scan_logger.info(msg)
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@ -826,8 +830,8 @@ class SmartScanThing(Thing):
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).encode("utf-8")
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piexif.insert(piexif.dump(exif_dict), jpeg_path)
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except: # noqa: E722
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# We need to capture any exeption as there are many reasons metadata
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# might not be added. We wern rather than log the error.
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# We need to capture any exception as there are many reasons metadata
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# might not be added. We warn rather than log the error.
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self._scan_logger.warning(f"Failed to add metadata to {jpeg_path}")
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except Exception as e:
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raise IOError(f"An error occurred while saving {jpeg_path}") from e
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