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Fixes to naming to make basic lint checks pass

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This commit is contained in:
Julian Stirling 2025-04-11 12:29:14 +01:00
parent e4cfcc76a7
commit 4eeff35e2d
4 changed files with 41 additions and 31 deletions
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12
src/openflexure_microscope_server/things/background_detect.py
View file

@ -88,8 +88,8 @@ class BackgroundDetectThing(Thing):
current_image = np.array(Image.open(current_image.open()))
# we're working in the LUV colourspace as it collect colours together in a human-intuitive way
current_image_LUV = cv2.cvtColor(current_image, cv2.COLOR_RGB2LUV)
mask = self.background_mask(current_image_LUV)
current_image_luv = cv2.cvtColor(current_image, cv2.COLOR_RGB2LUV)
mask = self.background_mask(current_image_luv)
return np.count_nonzero(mask) / np.prod(mask.shape) * 100
@thing_action
@ -114,11 +114,11 @@ class BackgroundDetectThing(Thing):
background = np.array(Image.open(background.open()))
# we're working in the LUV colourspace as it collect colours together in a human-intuitive way
background_LUV = cv2.cvtColor(background, cv2.COLOR_RGB2LUV)
background_luv = cv2.cvtColor(background, cv2.COLOR_RGB2LUV)
ch1 = (background_LUV.T[0]).flatten()
ch2 = (background_LUV.T[1]).flatten()
ch3 = (background_LUV.T[2]).flatten()
ch1 = (background_luv.T[0]).flatten()
ch2 = (background_luv.T[1]).flatten()
ch3 = (background_luv.T[2]).flatten()
points = np.array([np.asarray(ch1), np.asarray(ch2), np.asarray(ch3)]).T

10
src/openflexure_microscope_server/things/camera/simulation.py
View file

@ -71,18 +71,18 @@ class SimulatedCamera(BaseCamera):
sprite[rr < i] = 255
self.sprites.append(sprite)
def generate_blobs(self, N: int = 1000):
def generate_blobs(self, n_blobs: int = 1000):
"""Generate coordinates of blobs
Blobs are characterised by X, Y, sprite
We also generate a KD tree to rapidly find blobs in an image
"""
self.blobs = np.zeros((N, 3))
self.blobs = np.zeros((n_blobs, 3))
rng = np.random.default_rng()
w = np.max(self.glyph_shape)
self.blobs[:, 0] = rng.uniform(w / 2, self.canvas_shape[0] - w / 2, N)
self.blobs[:, 1] = rng.uniform(w / 2, self.canvas_shape[1] - w / 2, N)
self.blobs[:, 2] = rng.choice(len(self.sprites), N)
self.blobs[:, 0] = rng.uniform(w / 2, self.canvas_shape[0] - w / 2, n_blobs)
self.blobs[:, 1] = rng.uniform(w / 2, self.canvas_shape[1] - w / 2, n_blobs)
self.blobs[:, 2] = rng.choice(len(self.sprites), n_blobs)
def generate_canvas(self):
"""Generate a blank canvas"""

4
src/openflexure_microscope_server/things/camera_stage_mapping.py
View file

@ -296,7 +296,9 @@ class CameraStageMapper(Thing):
def assert_calibrated(self):
"""Raise an exception if the image_to_stage_displacement matrix is not set"""
if self.image_to_stage_displacement_matrix is None:
raise CSMUncalibratedError()
# Disable check of no message in raised exception as the message is explicitly
# added by CSMUncalibratedError
raise CSMUncalibratedError() # noqa: RSE102
@thing_property
def last_calibration(self) -> Optional[Dict]:

46
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -73,7 +73,7 @@ def unpack_autofocus(scan_data):
"""
jpeg_times = scan_data["jpeg_times"]
jpeg_sizes = scan_data["jpeg_sizes"]
jpeg_sizes_MB = [x / 10**3 for x in jpeg_sizes]
jpeg_sizes_mb = [x / 10**3 for x in jpeg_sizes]
stage_times = scan_data["stage_times"]
stage_positions = scan_data["stage_positions"]
stage_height = [pos[2] for pos in stage_positions]
@ -86,7 +86,7 @@ def unpack_autofocus(scan_data):
turning = np.where(turningpoints(jpeg_heights))[0] + 1
return jpeg_heights[turning[0] : turning[1]], jpeg_sizes_MB[turning[0] : turning[1]]
return jpeg_heights[turning[0] : turning[1]], jpeg_sizes_mb[turning[0] : turning[1]]
def limit_focus_change(prev_pos, prev_z, new_pos, new_z, limit):
@ -115,10 +115,12 @@ def steps_from_centre(current_loc, starting_loc, dx, dy):
return np.max(np.abs(np.divide(np.subtract(current_loc, starting_loc), step_size)))
def distance_to_site(current, next):
next = np.array(next, dtype="float64")
current = np.array(current, dtype="float64")
return np.sqrt((next[1] - current[1]) ** 2 + (next[0] - current[0]) ** 2)
def distance_to_site(current_pos, next_pos):
next_pos = np.array(next_pos, dtype="float64")
current_pos = np.array(current_pos, dtype="float64")
return np.sqrt(
(next_pos[1] - current_pos[1]) ** 2 + (next_pos[0] - current_pos[0]) ** 2
)
class NotEnoughFreeSpaceError(IOError):
@ -439,13 +441,21 @@ class SmartScanThing(Thing):
# TODO: Consider using CSM calibration size instead
# TODO: generalise to have 2D displacements for x and y (as the
# camera and stage may not be aligned).
CSM = self._csm.image_to_stage_displacement_matrix
csm_disp_matrix = self._csm.image_to_stage_displacement_matrix
dx = int(
np.abs(np.dot(np.array([0, arr.shape[1] * (1 - overlap)]), CSM)[0])
np.abs(
np.dot(
np.array([0, arr.shape[1] * (1 - overlap)]), csm_disp_matrix
)[0]
)
)
dy = int(
np.abs(np.dot(np.array([arr.shape[0] * (1 - overlap), 0]), CSM)[1])
np.abs(
np.dot(
np.array([arr.shape[0] * (1 - overlap), 0]), csm_disp_matrix
)[1]
)
)
self._scan_logger.info(
@ -1144,7 +1154,7 @@ class SmartScanThing(Thing):
# as some of them should only be added at the end (as we can't overwrite)
# them once they change
if not os.path.isfile(zip_fname):
with zipfile.ZipFile(zip_fname, mode="w") as zip:
with zipfile.ZipFile(zip_fname, mode="w") as scan_zip:
pass
# get a list of files in the existing zip
@ -1167,7 +1177,7 @@ class SmartScanThing(Thing):
]
tiff_name = ""
with zipfile.ZipFile(zip_fname, mode="a") as zip:
with zipfile.ZipFile(zip_fname, mode="a") as scan_zip:
for file in files:
if "stitched.jp" in file:
stitch_name = os.path.split(file)[1]
@ -1181,32 +1191,30 @@ class SmartScanThing(Thing):
pass
else:
logger.info(f"appending {file} to zip")
zip.write(os.path.join(scan_folder, file), arcname=file)
scan_zip.write(os.path.join(scan_folder, file), arcname=file)
# Promote key files to the top level of the zip only at the end of the scan (when downloading)
# and finally zip some of the final files
# TODO: if you download multiple times, you get duplicate files - is this a problem?
if download_zip:
with zipfile.ZipFile(zip_fname, mode="a") as zip:
with zipfile.ZipFile(zip_fname, mode="a") as scan_zip:
for fname in ["stitched_from_stage.jpg", stitch_name, tiff_name]:
fpath = os.path.join(images_folder, fname)
if os.path.exists(fpath):
logger.info(f"copying {fpath} to upper level")
zip.write(fpath, arcname=fname)
scan_zip.write(fpath, arcname=fname)
for file in files:
if any(banned_name in file for banned_name in files_to_delay):
logger.info(f"we are finally adding {file} into zip")
zip.write(os.path.join(scan_folder, file), arcname=file)
scan_zip.write(os.path.join(scan_folder, file), arcname=file)
logger.info("about to download zip")
return ZipBlob.from_file(zip_fname)
@thing_action
def get_files_in_zip(self, zip_path):
"""List the relative paths of all files and folders in the zip folder specified"""
zip = zipfile.ZipFile(zip_path)
zip = [os.path.normpath(i) for i in zip.namelist()]
return zip
scan_zip = zipfile.ZipFile(zip_path)
return [os.path.normpath(i) for i in scan_zip.namelist()]
class CaptureError(RuntimeError):