rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Formatted with Ruff

Browse source
This commit is contained in:
Richard Bowman 2024-12-03 06:46:08 +00:00
parent 27aec769a2
commit 9fd8fc37f1
19 changed files with 680 additions and 392 deletions
Download patch file Download diff file Expand all files Collapse all files

67
src/openflexure_microscope_server/things/autofocus.py
View file

@ -5,6 +5,7 @@ camera together to perform an autofocus routine.
See repository root for licensing information.
"""
from __future__ import annotations
from contextlib import contextmanager
import logging
@ -26,8 +27,10 @@ from pydantic import BaseModel
### Autofocus utilities
class JPEGSharpnessMonitor:
__globals__ = globals() # Required for FastAPI dependency
def __init__(self, stage: Stage, camera: Camera, portal: BlockingPortal):
self.camera = camera
self.stage = stage
@ -48,7 +51,7 @@ class JPEGSharpnessMonitor:
self.jpeg_sizes.append(len(frame))
if not self.running:
break
@contextmanager
def run(self):
"""Context manager, during which we will monitor sharpness from the camera"""
@ -73,7 +76,7 @@ class JPEGSharpnessMonitor:
# Index of the data for this movement
data_index: int = len(self.stage_positions) - 2
# Final z position after move
final_z_position: int = self.stage_positions[-1]['z']
final_z_position: int = self.stage_positions[-1]["z"]
return data_index, final_z_position
def move_data(
@ -84,12 +87,10 @@ class JPEGSharpnessMonitor:
istop = istart + 2
jpeg_times: np.ndarray = np.array(self.jpeg_times)
jpeg_sizes: np.ndarray = np.array(self.jpeg_sizes)
stage_times: np.ndarray = np.array(self.stage_times)[
istart:istop
]
stage_times: np.ndarray = np.array(self.stage_times)[istart:istop]
stage_zs: np.ndarray = np.array(
[p['z'] for p in self.stage_positions[istart:istop]]
)
[p["z"] for p in self.stage_positions[istart:istop]]
)
try:
start: int = int(np.argmax(jpeg_times > stage_times[0]))
stop: int = int(np.argmax(jpeg_times > stage_times[1]))
@ -128,6 +129,7 @@ class JPEGSharpnessMonitor:
SharpnessMonitorDep = Annotated[JPEGSharpnessMonitor, Depends()]
class SharpnessDataArrays(BaseModel):
jpeg_times: NDArray
jpeg_sizes: NDArray
@ -140,18 +142,18 @@ class AutofocusThing(Thing):
def fast_autofocus(
self,
m: SharpnessMonitorDep,
dz: int=2000,
start: str='centre',
dz: int = 2000,
start: str = "centre",
) -> SharpnessDataArrays:
"""Sweep the stage up and down, then move to the sharpest point
This method will will move down by dz/2, sweep up by dz, and then evaluate
the position where the image was sharpest. We'll then move back down, and
finally up to the sharpest point.
"""
with m.run():
# Move to (-dz / 2)
if start == 'centre':
if start == "centre":
m.focus_rel(-dz / 2)
# Move to dz while monitoring sharpness
# i: Sharpness monitor index for this move
@ -165,16 +167,16 @@ class AutofocusThing(Thing):
m.focus_rel(fz - z)
# Return all focus data
return m.data_dict()
@thing_action
def move_and_measure(
self,
m: SharpnessMonitorDep,
dz: Sequence[int],
wait: float=0,
wait: float = 0,
) -> SharpnessDataArrays:
"""Make a move (or a series of moves) and monitor sharpness
This method will will make a series of relative moves in z, and
return the sharpness (JPEG size) vs time, along with timestamps
for the moves. This can be used to calibrate autofocus.
@ -193,9 +195,11 @@ class AutofocusThing(Thing):
return m.data_dict()
@thing_action
def looping_autofocus(self, stage: Stage, m: SharpnessMonitorDep, dz=2000, start='centre'):
def looping_autofocus(
self, stage: Stage, m: SharpnessMonitorDep, dz=2000, start="centre"
):
"""Repeatedly autofocus the stage until it looks focused.
This action will run the `fast_autofocus` action until it settles on a point
in the middle 3/5 of its range. Such logic can be helpful if the microscope
is close to focus, but not quite within `dz/2`. It will attempt to autofocus
@ -207,14 +211,13 @@ class AutofocusThing(Thing):
with m.run():
while repeat and attempts < 10:
if start == 'centre':
stage.move_relative(x = 0, y = 0, z = -(backlash + dz / 2))
stage.move_relative(x = 0, y = 0, z = backlash)
if start == "centre":
stage.move_relative(x=0, y=0, z=-(backlash + dz / 2))
stage.move_relative(x=0, y=0, z=backlash)
i, z = m.focus_rel(dz, block_cancellation=True)
_, heights, sizes = m.move_data(i)
peak_height = heights[np.argmax(sizes)]
height_min = np.min(heights)
height_max = np.max(heights)
@ -224,25 +227,27 @@ class AutofocusThing(Thing):
or height_max - peak_height < dz / 5
):
attempts += 1
start = 'centre'
stage.move_absolute(z = peak_height-backlash)
stage.move_absolute(z = peak_height)
start = "centre"
stage.move_absolute(z=peak_height - backlash)
stage.move_absolute(z=peak_height)
else:
repeat = False
stage.move_relative(x = 0, y = 0, z = -(dz+backlash))
stage.move_absolute(z = peak_height)
stage.move_relative(x=0, y=0, z=-(dz + backlash))
stage.move_absolute(z=peak_height)
return heights.tolist(), sizes.tolist()
@thing_action
def verify_focus_sharpness(self, sweep_sizes: list, camera: WrappedCamera, threshold: float = 0.95):
'''Take the sharpness curve of the autofocus, and the size of the current frame
def verify_focus_sharpness(
self, sweep_sizes: list, camera: WrappedCamera, threshold: float = 0.95
):
"""Take the sharpness curve of the autofocus, and the size of the current frame
to see if the autofocus completed successfully. Returns True if current sharpness
is within "leniency" number of frames from the peak of the autofocus'''
is within "leniency" number of frames from the peak of the autofocus"""
current_sharpness = camera.grab_jpeg_size(stream_name='lores')
current_sharpness = camera.grab_jpeg_size(stream_name="lores")
peak = np.max(sweep_sizes)
base = np.min(sweep_sizes)
cutoff = threshold * (peak - base)
return current_sharpness >= base + cutoff
return current_sharpness >= base + cutoff