rahix/openflexure-microscope-server
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Removed commented out code and unused functions

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This commit is contained in:
Joe Knapper 2025-04-09 15:32:13 +01:00
parent a5d1f1e965
commit f4db9b6e52
1 changed files with 2 additions and 23 deletions
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25
src/openflexure_microscope_server/things/smart_scan.py
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@ -156,25 +156,6 @@ def generate_config(
fp.write(f"{names[i]}; ; {loc[1], loc[0]} \n") fp.write(f"{names[i]}; ; {loc[1], loc[0]} \n")
def raw2rggb(raw):
"""Convert packed 10 bit raw to RGGB 8 bit"""
raw = np.asarray(raw) # ensure it's an array
rggb = np.empty((616, 820, 4), dtype=np.uint8)
raw_w = rggb.shape[1] // 2 * 5
for plane, offset in enumerate([(1, 1), (0, 1), (1, 0), (0, 0)]):
rggb[:, ::2, plane] = raw[offset[0] :: 2, offset[1] : raw_w + offset[1] : 5]
rggb[:, 1::2, plane] = raw[
offset[0] :: 2, offset[1] + 2 : raw_w + offset[1] + 2 : 5
]
return rggb
def rggb2rgb(rggb):
return np.stack(
[rggb[..., 0], rggb[..., 1] // 2 + rggb[..., 2] // 2, rggb[..., 3]], axis=2
)
class ChannelDistributions(BaseModel): class ChannelDistributions(BaseModel):
means: list[float] means: list[float]
standard_deviations: list[float] standard_deviations: list[float]
@ -428,7 +409,6 @@ class SmartScanThing(Thing):
metadata_getter: GetThingStates, metadata_getter: GetThingStates,
csm: CSMDep, csm: CSMDep,
background_detect: BackgroundDep, background_detect: BackgroundDep,
recentre: RecentreStage,
scan_name: str = "", scan_name: str = "",
): ):
"""Move the stage to cover an area, taking images that can be tiled together. """Move the stage to cover an area, taking images that can be tiled together.
@ -450,8 +430,6 @@ class SmartScanThing(Thing):
capture_thread = None capture_thread = None
self._scan_lock.acquire(timeout=0.1) self._scan_lock.acquire(timeout=0.1)
try: try:
# Before anything else, check that we've got a background set
# It's annoying to have to wait to find out!
max_dist = self.max_range max_dist = self.max_range
if self.autofocus_dz == 0: if self.autofocus_dz == 0:
@ -461,6 +439,8 @@ class SmartScanThing(Thing):
f"Your dz range is {self.autofocus_dz} steps, which is too short to attempt to focus. Running without autofocus" f"Your dz range is {self.autofocus_dz} steps, which is too short to attempt to focus. Running without autofocus"
) )
# Before anything else, check that we've got a background set
# It's annoying to have to wait to find out!
if self.skip_background: if self.skip_background:
d = background_detect.background_distributions d = background_detect.background_distributions
if not d: if not d:
@ -660,7 +640,6 @@ class SmartScanThing(Thing):
) )
capture_thread.start() capture_thread.start()
acquired.wait() # wait until the image is acquired acquired.wait() # wait until the image is acquired
# time.sleep(0.5)
positions.append(loc[:2]) positions.append(loc[:2])
names.append(name) names.append(name)