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Linter fixes

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NB I have permitted bare except: blocks in smart_scan. This should be reverted.
This commit is contained in:
Richard Bowman 2024-12-03 06:43:45 +00:00
parent 57177c6a56
commit 27aec769a2
4 changed files with 16 additions and 23 deletions
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35
src/openflexure_microscope_server/things/smart_scan.py
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@ -1,3 +1,5 @@
# ruff: noqa: E722
import shutil
import zipfile
import threading
@ -13,12 +15,10 @@ from pydantic import BaseModel
from scipy.stats import norm
from scipy.ndimage import zoom
from scipy.interpolate import interp1d
from copy import deepcopy
from datetime import datetime
from subprocess import CompletedProcess, Popen, PIPE, SubprocessError, run, STDOUT
from subprocess import CompletedProcess, Popen, PIPE, SubprocessError, STDOUT
from threading import Event, Thread
import glob
import zipfile
import json
import piexif
@ -109,14 +109,14 @@ def limit_focus_change(prev_pos, prev_z, new_pos, new_z, limit):
return "accept"
def distance_to_site(current, next):
current = np.array(current, dtype="float64")
next = np.array(next, dtype="float64")
if (next[1] - current[1]) ** 2 + (next[0] - current[0]) ** 2 < 0:
print(f"Negative distance between {next} and {current}")
return np.sqrt(
(next[1] - current[1]) ** 2 + (next[0] - current[0]) ** 2, dtype="float64"
)
# def distance_to_site(current, next):
# current = np.array(current, dtype="float64")
# next = np.array(next, dtype="float64")
# if (next[1] - current[1]) ** 2 + (next[0] - current[0]) ** 2 < 0:
# print(f"Negative distance between {next} and {current}")
# return np.sqrt(
# (next[1] - current[1]) ** 2 + (next[0] - current[0]) ** 2, dtype="float64"
# )
def steps_from_centre(current_loc, starting_loc, dx, dy):
step_size = np.array([dx,dy])
@ -455,7 +455,7 @@ class SmartScanThing(Thing):
max_dist = self.max_range
if self.autofocus_dz == 0:
logger.info(f'Running scan without autofocus')
logger.info('Running scan without autofocus')
elif self.autofocus_dz <= 200:
logger.warning(f'Your dz range is {self.autofocus_dz} steps, which is too short to attempt to focus. Running without autofocus')
@ -495,7 +495,7 @@ class SmartScanThing(Thing):
# TODO: generalise to have 2D displacements for x and y (as the
# camera and stage may not be aligned).
CSM = csm.image_to_stage_displacement_matrix
csm_calibration_width = csm.last_calibration["image_resolution"][1]
#csm_calibration_width = csm.last_calibration["image_resolution"][1]
overlap = self.overlap
@ -510,7 +510,6 @@ class SmartScanThing(Thing):
focused_path = [] # This holds a list of all points where focus succeeded
true_path = [] # This holds a list of all points visited
i = 0
ids = []
start_time = time.strftime("%H_%M_%S-%d_%m_%Y")
scan_folder = self.new_scan_folder(scan_name)
@ -628,9 +627,7 @@ class SmartScanThing(Thing):
# if more than 92% of the image is background, treat it as background and continue
if not image_is_sample:
logger.info(f"Skipping {stage.position} as it is {round(background_detect.background_fraction(),0)}% background.")
capture_image = False
else:
capture_image = True
# if not, it's sample. run an autofocus and use the updated height
new_pos = [
[stage.position["x"] - dx, stage.position["y"]],
@ -1017,10 +1014,10 @@ class SmartScanThing(Thing):
p = Popen(cmd, stdout=PIPE, stderr = STDOUT, bufsize=1, universal_newlines=True)
os.set_blocking(p.stdout.fileno(), False)
logger.info(time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(time.time())))
while p.poll() == None:
while p.poll() is None:
try:
output = p.stdout.readline()
if output != "" and output != None:
if output != "" and output is not None:
logger.info(output)
except:
pass
@ -1028,7 +1025,7 @@ class SmartScanThing(Thing):
for line in p.stdout:
try:
output = p.stdout.readline()
if output != "" and output != None:
if output != "" and output is not None:
logger.info(output)
except:
pass