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Richard Bowman 2024-12-03 06:46:08 +00:00
parent 27aec769a2
commit 9fd8fc37f1
19 changed files with 680 additions and 392 deletions
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3
src/openflexure_microscope_server/things/auto_recentre_stage.py
View file

@ -11,6 +11,7 @@ from openflexure_microscope_server.things.camera_stage_mapping import CameraStag
CSMDep = direct_thing_client_dependency(CameraStageMapper, "/camera_stage_mapping/")
AutofocusDep = direct_thing_client_dependency(AutofocusThing, "/autofocus/")
class RecentringThing(Thing):
@thing_action
def recentre(
@ -27,7 +28,7 @@ class RecentringThing(Thing):
corresponds to the centre of the stage. This exploits the
fact that the OpenFlexure stage moves in an arc, i.e. its
height will vary with X and Y. The point where the variation
of Z with X and Y motion is smallest is the centre of its
of Z with X and Y motion is smallest is the centre of its
XY travel. This routine moves in X and Y, monitoring the
Z value of the focal plane, and attempts to find the point
where Z does not vary with X and Y, which is where it stops.

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

37
src/openflexure_microscope_server/things/camera/__init__.py
View file

@ -5,6 +5,7 @@ should enabe the server to work.
See repository root for licensing information.
"""
from __future__ import annotations
import logging
from typing import Literal, Protocol, runtime_checkable
@ -23,15 +24,14 @@ from labthings_fastapi.types.numpy import NDArray
class JPEGBlob(Blob):
media_type: str = "image/jpeg"
@runtime_checkable
class CameraProtocol(Protocol):
"""A Thing representing a camera"""
def __enter__(self) -> None:
...
def __exit__(self, _exc_type, _exc_value, _traceback) -> None:
...
def __enter__(self) -> None: ...
def __exit__(self, _exc_type, _exc_value, _traceback) -> None: ...
@property
def stream_active(self) -> bool:
@ -45,9 +45,8 @@ class CameraProtocol(Protocol):
def capture_array(
self,
resolution: Literal["lores", "main", "full"] = "main",
) -> NDArray:
...
) -> NDArray: ...
def capture_jpeg(
self,
metadata_getter: GetThingStates,
@ -78,9 +77,10 @@ class CameraProtocol(Protocol):
"""Acquire one image from the preview stream and return its size"""
...
class BaseCamera(Thing):
"""A Thing representing a camera
This is a concrete base class for `Thing`s implementing the `CameraProtocol`.
It provides the stream descriptors and actions to grab from the stream.
"""
@ -110,12 +110,16 @@ class BaseCamera(Thing):
stream (either "main" for the preview stream, or "lores" for the low
resolution preview). No metadata is returned.
"""
logging.info(f"StreamingPiCamera2.grab_jpeg(stream_name={stream_name}) starting")
logging.info(
f"StreamingPiCamera2.grab_jpeg(stream_name={stream_name}) starting"
)
stream = (
self.lores_mjpeg_stream if stream_name == "lores" else self.mjpeg_stream
)
frame = portal.call(stream.grab_frame)
logging.info(f"StreamingPiCamera2.grab_jpeg(stream_name={stream_name}) got frame")
logging.info(
f"StreamingPiCamera2.grab_jpeg(stream_name={stream_name}) got frame"
)
return JPEGBlob.from_bytes(frame)
@thing_action
@ -129,12 +133,12 @@ class BaseCamera(Thing):
self.lores_mjpeg_stream if stream_name == "lores" else self.mjpeg_stream
)
return portal.call(stream.next_frame_size)
class CameraStub(BaseCamera):
"""A stub for a camera, to allow dependencies
As of LabThings-FastAPI 0.0.7, we can't make a thing client dependency
based on a protocol, because the protocol is not a Thing, and its
methods/properties are not decorated as Affordances. This stub class
@ -142,9 +146,10 @@ class CameraStub(BaseCamera):
This stub class should be used for dependencies on the CameraProtocol.
"""
def __enter__(self) -> None:
raise NotImplementedError("Cameras must not inherit from CameraStub")
def __exit__(self, _exc_type, _exc_value, _traceback) -> None:
raise NotImplementedError("Cameras must not inherit from CameraStub")
@ -164,7 +169,7 @@ class CameraStub(BaseCamera):
resolution: Literal["lores", "main", "full"] = "main",
) -> NDArray:
raise NotImplementedError("Cameras must not inherit from CameraStub")
@thing_action
def capture_jpeg(
self,

27
src/openflexure_microscope_server/things/camera/opencv.py
View file

@ -1,10 +1,11 @@
"""OpenFlexure Microscope OpenCV Camera
This module defines a camera Thing that uses OpenCV's
This module defines a camera Thing that uses OpenCV's
`VideoCapture`.
See repository root for licensing information.
"""
from __future__ import annotations
import io
import json
@ -26,7 +27,8 @@ from . import BaseCamera, JPEGBlob
class OpenCVCamera(BaseCamera):
"""A Thing representing an OpenCV camera"""
def __init__(self, camera_index: int=0):
def __init__(self, camera_index: int = 0):
self.camera_index = camera_index
self._capture_thread: Optional[Thread] = None
self._capture_enabled = False
@ -37,7 +39,7 @@ class OpenCVCamera(BaseCamera):
self._capture_thread = Thread(target=self._capture_frames)
self._capture_thread.start()
return self
def __exit__(self, _exc_type, _exc_value, _traceback):
if self.stream_active:
self._capture_enabled = False
@ -50,6 +52,7 @@ class OpenCVCamera(BaseCamera):
if self._capture_enabled and self._capture_thread:
return self._capture_thread.is_alive()
return False
mjpeg_stream = MJPEGStreamDescriptor()
lores_mjpeg_stream = MJPEGStreamDescriptor()
@ -58,11 +61,15 @@ class OpenCVCamera(BaseCamera):
while self._capture_enabled:
ret, frame = self.cap.read()
if not ret:
logging.error(f"Failed to capture frame from camera {self.camera_index}")
logging.error(
f"Failed to capture frame from camera {self.camera_index}"
)
break
jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
self.mjpeg_stream.add_frame(jpeg, portal)
jpeg_lores = cv2.imencode(".jpg", cv2.resize(frame, (320, 240)))[1].tobytes()
jpeg_lores = cv2.imencode(".jpg", cv2.resize(frame, (320, 240)))[
1
].tobytes()
self.lores_mjpeg_stream.add_frame(jpeg_lores, portal)
@thing_action
@ -78,9 +85,11 @@ class OpenCVCamera(BaseCamera):
"""
ret, frame = self.cap.read()
if not ret:
raise RuntimeError(f"Failed to capture frame from camera {self.camera_index}")
raise RuntimeError(
f"Failed to capture frame from camera {self.camera_index}"
)
return frame
@thing_action
def capture_jpeg(
self,
@ -95,7 +104,9 @@ class OpenCVCamera(BaseCamera):
jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
exif_dict = {
"Exif": {
piexif.ExifIFD.UserComment: json.dumps(metadata_getter()).encode("utf-8")
piexif.ExifIFD.UserComment: json.dumps(metadata_getter()).encode(
"utf-8"
)
},
"GPS": {},
"Interop": {},

61
src/openflexure_microscope_server/things/camera/simulation.py
View file

@ -5,6 +5,7 @@ camera together to perform an autofocus routine.
See repository root for licensing information.
"""
from __future__ import annotations
import io
import json
@ -28,22 +29,26 @@ from pydantic import RootModel
from . import BaseCamera, JPEGBlob
from ..stage import StageProtocol as Stage
class ArrayModel(RootModel):
"""A model for an array"""
root: NDArray
class SimulatedCamera(BaseCamera):
"""A Thing representing an OpenCV camera"""
_stage: Optional[Stage] = None
_server: Optional[ThingServer] = None
def __init__(
self,
shape: tuple[int, int, int] = (600, 800, 3),
glyph_shape: tuple[int, int, int] = (51, 51, 3),
canvas_shape: tuple[int, int, int] = (3000, 4000, 3),
frame_interval: float = 0.1,
):
self,
shape: tuple[int, int, int] = (600, 800, 3),
glyph_shape: tuple[int, int, int] = (51, 51, 3),
canvas_shape: tuple[int, int, int] = (3000, 4000, 3),
frame_interval: float = 0.1,
):
self.shape = shape
self.glyph_shape = glyph_shape
self.canvas_shape = canvas_shape
@ -53,14 +58,14 @@ class SimulatedCamera(BaseCamera):
self.generate_sprites()
self.generate_blobs()
self.generate_canvas()
def generate_sprites(self):
"""Generate sprites to populate the image"""
self.sprites = []
black = np.zeros(self.glyph_shape, dtype=np.uint8)
x = np.arange(black.shape[0])
y = np.arange(black.shape[1])
rr = np.sqrt((x[:, None] - np.mean(x))**2 + (y[None, :] - np.mean(y))**2)
rr = np.sqrt((x[:, None] - np.mean(x)) ** 2 + (y[None, :] - np.mean(y)) ** 2)
for i in [5, 7, 9, 11, 13, 15]:
sprite = black.copy()
sprite[rr < i] = 255
@ -68,15 +73,15 @@ class SimulatedCamera(BaseCamera):
def generate_blobs(self, N: 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))
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[:, 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)
def generate_canvas(self):
@ -86,31 +91,34 @@ class SimulatedCamera(BaseCamera):
w, h, _ = self.glyph_shape
for x, y, sprite in self.blobs:
self.canvas[
int(x) - w//2:int(x) - w//2 + w,
int(y) - h//2:int(y) - h//2 + h,
int(x) - w // 2 : int(x) - w // 2 + w,
int(y) - h // 2 : int(y) - h // 2 + h,
] -= self.sprites[int(sprite)]
def generate_image(self, pos: tuple[int, int]):
"""Generate an image with blobs based on supplied coordinates"""
cw, ch, _ = self.canvas_shape
w, h, _ = self.shape
tl = (int(pos[0]) - w//2 - cw//2, int(pos[1]) - h//2 - ch//2)
tl = (int(pos[0]) - w // 2 - cw // 2, int(pos[1]) - h // 2 - ch // 2)
image = self.canvas[
tuple(slice(tl[i],tl[i] + self.shape[i]) for i in range(2)) + (slice(None),)
tuple(slice(tl[i], tl[i] + self.shape[i]) for i in range(2))
+ (slice(None),)
]
if image.shape != self.shape:
raise ValueError(f"Image shape {image.shape} does not match intended shape {self.shape}")
raise ValueError(
f"Image shape {image.shape} does not match intended shape {self.shape}"
)
return image
def attach_to_server(self, server: ThingServer, path: str):
self._server = server
return super().attach_to_server(server, path)
def get_stage_position(self):
if not self._stage and self._server:
self._stage = self._server.things["/stage/"]
return self._stage.instantaneous_position
def generate_frame(self):
"""Generate a frame with blobs based on the stage coordinates"""
try:
@ -118,14 +126,14 @@ class SimulatedCamera(BaseCamera):
except Exception as e:
print(f"Failed to get stage position: {e}")
pos = {"x": 0, "y": 0}
return self.generate_image((pos["x"]/10, pos["y"]/10))
return self.generate_image((pos["x"] / 10, pos["y"] / 10))
def __enter__(self):
self._capture_enabled = True
self._capture_thread = Thread(target=self._capture_frames)
self._capture_thread.start()
return self
def __exit__(self, _exc_type, _exc_value, _traceback):
if self.stream_active:
self._capture_enabled = False
@ -137,6 +145,7 @@ class SimulatedCamera(BaseCamera):
if self._capture_enabled and self._capture_thread:
return self._capture_thread.is_alive()
return False
mjpeg_stream = MJPEGStreamDescriptor()
lores_mjpeg_stream = MJPEGStreamDescriptor()
@ -148,7 +157,9 @@ class SimulatedCamera(BaseCamera):
frame = self.generate_frame()
jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
self.mjpeg_stream.add_frame(jpeg, portal)
jpeg_lores = cv2.imencode(".jpg", cv2.resize(frame, (320, 240)))[1].tobytes()
jpeg_lores = cv2.imencode(".jpg", cv2.resize(frame, (320, 240)))[
1
].tobytes()
self.lores_mjpeg_stream.add_frame(jpeg_lores, portal)
except Exception as e:
logging.error(f"Failed to capture frame: {e}, retrying...")
@ -165,7 +176,7 @@ class SimulatedCamera(BaseCamera):
binary image formats will be added in due course.
"""
return self.generate_frame()
@thing_action
def capture_jpeg(
self,
@ -180,7 +191,9 @@ class SimulatedCamera(BaseCamera):
jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
exif_dict = {
"Exif": {
piexif.ExifIFD.UserComment: json.dumps(metadata_getter()).encode("utf-8")
piexif.ExifIFD.UserComment: json.dumps(metadata_getter()).encode(
"utf-8"
)
},
"GPS": {},
"Interop": {},

92
src/openflexure_microscope_server/things/camera_stage_mapping.py
View file

@ -10,8 +10,20 @@ and return the calibration data.
This module is only intended to be called from the OpenFlexure Microscope
server, and depends on that server and its underlying LabThings library.
"""
import time
from typing import Annotated, Any, Callable, Dict, List, Mapping, NamedTuple, Optional, Sequence, Tuple
from typing import (
Annotated,
Any,
Callable,
Dict,
List,
Mapping,
NamedTuple,
Optional,
Sequence,
Tuple,
)
from fastapi import Depends, HTTPException
import numpy as np
@ -20,7 +32,10 @@ from camera_stage_mapping.camera_stage_calibration_1d import (
calibrate_backlash_1d,
image_to_stage_displacement_from_1d,
)
from labthings_fastapi.dependencies.invocation import InvocationCancelledError, InvocationLogger
from labthings_fastapi.dependencies.invocation import (
InvocationCancelledError,
InvocationLogger,
)
from labthings_fastapi.types.numpy import NDArray, denumpify, DenumpifyingDict
from labthings_fastapi.decorators import thing_action, thing_property
from labthings_fastapi.thing import Thing
@ -31,6 +46,7 @@ from .stage import StageDependency as Stage
CoordinateType = Tuple[float, float, float]
XYCoordinateType = Tuple[float, float]
class HardwareInterfaceModel(BaseModel):
move: Callable[[NDArray], None]
get_position: Callable[[], NDArray]
@ -41,7 +57,7 @@ class HardwareInterfaceModel(BaseModel):
def downsample(factor: int, image: np.ndarray) -> np.ndarray:
"""Downsample an image by taking the mean of each nxn region
This should be very efficient: we calculate the mean of each
`factor * factor` square, no interpolation. If the image is
not an integer multiple of the resampling factor, we discard
@ -53,46 +69,60 @@ def downsample(factor: int, image: np.ndarray) -> np.ndarray:
new_size = [d // factor for d in image.shape[:2]]
# First, we ensure we have something that's an integer multiple
# of `factor`
cropped = image[:new_size[0] * factor, :new_size[1] * factor, ...]
cropped = image[: new_size[0] * factor, : new_size[1] * factor, ...]
reshaped = cropped.reshape(
(new_size[0], factor, new_size[1], factor) + image.shape[2:]
)
return reshaped.mean(axis=(1,3))
return reshaped.mean(axis=(1, 3))
DEFAULT_SETTLING_TIME = 0.2
def make_hardware_interface(
stage: Stage, camera: Camera, downsample_factor: int = 2
) -> HardwareInterfaceModel:
stage: Stage, camera: Camera, downsample_factor: int = 2
) -> HardwareInterfaceModel:
"""Construct the functions we need to interface with the hardware"""
axes = stage.axis_names
def pos2dict(pos: Sequence[float]) -> Mapping[str, float]:
return {k: p for k, p in zip(axes, pos)}
def dict2pos(posd: Mapping[str, float]) -> Sequence[float]:
return tuple(posd[k] for k in axes if k in posd)
def move(pos: CoordinateType) -> None:
current_pos = stage.position
new_pos = pos2dict(pos)
displacement = {k: new_pos[k] - current_pos[k] for k in new_pos.keys()}
stage.move_relative(**displacement)
def get_position() -> CoordinateType:
return dict2pos(stage.position)
def grab_image() -> np.ndarray:
img = camera.capture_array()
return downsample(downsample_factor, img)
def settle() -> None:
time.sleep(DEFAULT_SETTLING_TIME)
try:
camera.capture_metadata # This discards frames on a picamera
except AttributeError:
pass # Don't raise an error for other cameras (may consider grabbing a frame)
return HardwareInterfaceModel(
move=move, get_position=get_position, grab_image=grab_image, settle=settle, grab_image_downsampling=downsample_factor
move=move,
get_position=get_position,
grab_image=grab_image,
settle=settle,
grab_image_downsampling=downsample_factor,
)
HardwareInterfaceDep = Annotated[HardwareInterfaceModel, Depends(make_hardware_interface)]
HardwareInterfaceDep = Annotated[
HardwareInterfaceModel, Depends(make_hardware_interface)
]
class MoveHistory(NamedTuple):
@ -102,11 +132,11 @@ class MoveHistory(NamedTuple):
class LoggingMoveWrapper:
"""Wrap a move function, and maintain a log position/time.
This class is callable, so it doesn't change the signature
of the function it wraps - it just makes it possible to get
a list of all the moves we've made, and how long they took.
Said list is intended to be useful for calibrating the stage
so we can estimate how long moves will take.
"""
@ -143,33 +173,39 @@ class CSMUncalibratedError(HTTPException):
(
"The camera_stage_mapping calibration is not yet available. "
"This probably means you need to run the calibration routine."
)
),
)
class CameraStageMapper(Thing):
"""A Thing to manage mapping between image and stage coordinates"""
def __enter__(self):
pass
def __exit__(self, exc_type, exc_value, traceback):
self.thing_settings.write_to_file()
@thing_action
def calibrate_1d(
self,
self,
hw: HardwareInterfaceDep,
stage: Stage,
logger: InvocationLogger,
direction: Tuple[float, float, float],
) -> DenumpifyingDict:
"""Move a microscope's stage in 1D, and figure out the relationship with the camera"""
move = LoggingMoveWrapper(hw.move) # log positions and times for stage calibration
move = LoggingMoveWrapper(
hw.move
) # log positions and times for stage calibration
tracker = Tracker(hw.grab_image, hw.get_position, settle=hw.settle)
direction_array: np.ndarray = np.array(direction)
starting_position = stage.position
try:
result: dict = calibrate_backlash_1d(tracker, move, direction_array, logger=logger)
result: dict = calibrate_backlash_1d(
tracker, move, direction_array, logger=logger
)
except InvocationCancelledError as e:
logger.info("Returning to starting position")
stage.move_absolute(**starting_position, block_cancellation=True)
@ -183,7 +219,7 @@ class CameraStageMapper(Thing):
self, hw: HardwareInterfaceDep, stage: Stage, logger: InvocationLogger
) -> DenumpifyingDict:
"""Move the microscope's stage in X and Y, to calibrate its relationship to the camera
This performs two 1d calibrations in x and y, then combines their results.
"""
logger.info("Calibrating X axis:")
@ -204,7 +240,7 @@ class CameraStageMapper(Thing):
self.thing_settings["image_resolution"] = corrected_resolution
csm_matrix = cal_xy["image_to_stage_displacement"]
csm_as_string = f'[{round(csm_matrix[0][0], 2)}, {round(csm_matrix[0][1], 2)},],[{round(csm_matrix[1][0], 2)}, {round(csm_matrix[1][1], 2)}]'
csm_as_string = f"[{round(csm_matrix[0][0], 2)}, {round(csm_matrix[0][1], 2)},],[{round(csm_matrix[1][0], 2)}, {round(csm_matrix[1][1], 2)}]"
logger.info(f"CSM matrix is {csm_as_string}.")
data: Dict[str, dict] = {
@ -221,14 +257,16 @@ class CameraStageMapper(Thing):
return data
@thing_property
def image_to_stage_displacement_matrix(self) -> Optional[List[List[float]]]: # 2x2 integer array
def image_to_stage_displacement_matrix(
self,
) -> Optional[List[List[float]]]: # 2x2 integer array
"""A 2x2 matrix that converts displacement in image coordinates to stage coordinates.
Note that this matrix is defined using "matrix coordinates", i.e. image coordinates
may be (y,x). This is an artifact of the way numpy, opencv, etc. define images. If
you are making use of this matrix in your own code, you will need to take care of
that conversion.
It is often helpful to give a concrete example: to make a move in image coordinates
(`dy`, `dx`), where `dx` is horizontal, i.e. the longer dimension of the image, you
should move the stage by:
@ -243,12 +281,12 @@ class CameraStageMapper(Thing):
if not displacement_matrix:
return None
return np.array(displacement_matrix).tolist()
@thing_property
def image_resolution(self) -> Optional[Tuple[float, float]]:
"""The image size used to calibrate the image_to_stage_displacement_matrix"""
return self.thing_settings.get("image_resolution", None)
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:
@ -256,10 +294,9 @@ class CameraStageMapper(Thing):
@thing_property
def last_calibration(self) -> Optional[Dict]:
"""The results of the last calibration that was run
"""
"""The results of the last calibration that was run"""
return self.thing_settings.get("last_calibration", None)
@thing_action
def move_in_image_coordinates(
self,
@ -268,7 +305,7 @@ class CameraStageMapper(Thing):
y: float,
):
"""Move by a given number of pixels on the camera
NB x and y here refer to what is usually understood to be the horizontal and
vertical axes of the image. In many toolkits, "matrix indices" are used, which
swap the order of these coordinates. This includes opencv and PIL. So, don't be
@ -280,8 +317,7 @@ class CameraStageMapper(Thing):
"""
self.assert_calibrated()
relative_move: np.ndarray = np.dot(
np.array([y, x]),
np.array(self.image_to_stage_displacement_matrix)
np.array([y, x]), np.array(self.image_to_stage_displacement_matrix)
)
stage.move_relative(x=relative_move[0], y=relative_move[1])

31
src/openflexure_microscope_server/things/settings_manager.py
View file

@ -5,6 +5,7 @@ This module provides some settings management across the other Things, and
for code that currently lives in clients but needs to persist settings on
the server.
"""
from collections.abc import Mapping
from socket import gethostname
from typing import Annotated, Any, MutableMapping, Optional, Sequence
@ -29,10 +30,7 @@ def recursive_update(old_dict: MutableMapping, update: Mapping):
"""Update a dictionary recursively"""
for k, v in update.items():
if isinstance(v, Mapping):
if (
k in old_dict
and isinstance(old_dict[k], MutableMapping)
):
if k in old_dict and isinstance(old_dict[k], MutableMapping):
recursive_update(old_dict[k], v)
else:
old_dict[k] = dict(**v)
@ -55,11 +53,13 @@ class SettingsManager(Thing):
def external_metadata(self) -> Mapping:
"""External metadata stored in the server's settings"""
return self.thing_settings.get("external_metadata", {})
@thing_action
def update_external_metadata(self, data: Mapping, key: Optional[str] = None) -> None:
def update_external_metadata(
self, data: Mapping, key: Optional[str] = None
) -> None:
"""Add or replace keys in the external metadata.
The data supplied will be merged into the existing dictionary
recursively, i.e. if a key exists, it will be added to rather than
replaced.
@ -80,7 +80,7 @@ class SettingsManager(Thing):
@thing_action
def delete_external_metadata(self, key: str) -> None:
"""Delete a key from the stored metadata.
The key may contain forward slashes, which are understood to separate
levels of the dictionary - i.e. `'a/c'` will remove the `c` key from a
dictionary that looks like: `{'a': {'c': 1}, 'b': {'d': 2}}`
@ -91,11 +91,10 @@ class SettingsManager(Thing):
del subdict[key.split("/")[-1]]
except KeyError:
raise HTTPException(
status_code=404,
detail="The specified key '{key}' was not found"
status_code=404, detail="The specified key '{key}' was not found"
)
self.thing_settings["external_metadata"] = metadata
@thing_property
def microscope_id(self) -> UUID:
"""A unique identifier for this microscope"""
@ -117,6 +116,7 @@ class SettingsManager(Thing):
def external_metadata_in_state(self) -> Sequence[str]:
"""A list of strings that are included in the "state" metadata"""
return self.thing_settings.get("external_metadata_in_state", [])
@external_metadata_in_state.setter
def external_metadata_in_state(self, keys: Sequence[str]):
"""Set the keys from external metadata that are returned in state"""
@ -140,7 +140,9 @@ class SettingsManager(Thing):
return state
@thing_action
def save_all_thing_settings(self, thing_server: ThingServerDep, logger: InvocationLogger) -> None:
def save_all_thing_settings(
self, thing_server: ThingServerDep, logger: InvocationLogger
) -> None:
"""Ensure all the Things sync their settings to disk.
Normally, each Thing has a `thing_settings` attribute that can be
@ -161,7 +163,4 @@ class SettingsManager(Thing):
f"Could not write {name} settings to disk: permission error."
)
except FileNotFoundError:
logger.warning(
f"Could not write {name} settings, folder not found"
)
logger.warning(f"Could not write {name} settings, folder not found")

520
src/openflexure_microscope_server/things/smart_scan.py
View file

File diff suppressed because it is too large Load diff

49
src/openflexure_microscope_server/things/stage/__init__.py
View file

@ -7,10 +7,11 @@ from labthings_fastapi.dependencies.invocation import CancelHook
from labthings_fastapi.dependencies.thing import direct_thing_client_dependency
from collections.abc import Sequence, Mapping
@runtime_checkable
class StageProtocol(Protocol):
"""A protocol for the OpenFlexure translation stage
"""
"""A protocol for the OpenFlexure translation stage"""
_axis_names: Sequence[str]
@property
@ -32,18 +33,28 @@ class StageProtocol(Protocol):
def thing_state(self) -> Mapping[str, Any]:
"""Summary metadata describing the current state of the stage"""
...
def move_relative(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
def move_relative(
self,
cancel: CancelHook,
block_cancellation: bool = False,
**kwargs: Mapping[str, int],
):
"""Make a relative move. Keyword arguments should be axis names."""
...
def move_absolute(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
def move_absolute(
self,
cancel: CancelHook,
block_cancellation: bool = False,
**kwargs: Mapping[str, int],
):
"""Make an absolute move. Keyword arguments should be axis names."""
...
def set_zero_position(self):
"""Make the current position zero in all axes
This action does not move the stage, but resets the position to zero.
It is intended for use after manually or automatically recentring the
stage.
@ -53,12 +64,13 @@ class StageProtocol(Protocol):
class BaseStage(Thing):
"""A base stage class for OpenFlexure translation stages
This can't be used directly but should reduce boilerplate code when
implementing new stages. A minimal working stage must implement
`move_relative` and `move_absolute` actions, which update the
`position` property on completion, and provide `set_zero_position`.
"""
_axis_names = ("x", "y", "z")
@thing_property
@ -85,9 +97,7 @@ class BaseStage(Thing):
@property
def thing_state(self):
"""Summary metadata describing the current state of the stage"""
return {
"position": self.position
}
return {"position": self.position}
class StageStub(BaseStage):
@ -98,20 +108,31 @@ class StageStub(BaseStage):
methods/properties are not decorated as Affordances. This stub class
is a workaround for that limitation, and should not be used directly.
"""
@thing_action
def move_relative(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
def move_relative(
self,
cancel: CancelHook,
block_cancellation: bool = False,
**kwargs: Mapping[str, int],
):
"""Make a relative move. Keyword arguments should be axis names."""
raise NotImplementedError("StageStub should not be used directly")
@thing_action
def move_absolute(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
def move_absolute(
self,
cancel: CancelHook,
block_cancellation: bool = False,
**kwargs: Mapping[str, int],
):
"""Make an absolute move. Keyword arguments should be axis names."""
raise NotImplementedError("StageStub should not be used directly")
@thing_action
def set_zero_position(self):
"""Make the current position zero in all axes
This action does not move the stage, but resets the position to zero.
It is intended for use after manually or automatically recentring the
stage.

36
src/openflexure_microscope_server/things/stage/dummy.py
View file

@ -1,6 +1,9 @@
from __future__ import annotations
from labthings_fastapi.decorators import thing_action
from labthings_fastapi.dependencies.invocation import CancelHook, InvocationCancelledError
from labthings_fastapi.dependencies.invocation import (
CancelHook,
InvocationCancelledError,
)
from collections.abc import Mapping
import time
@ -9,11 +12,12 @@ from . import BaseStage
class DummyStage(BaseStage):
"""A dummy stage for testing purposes
This stage should work similarly to a Sangaboard stage, but without any
hardware attached.
"""
def __init__(self, step_time: float=0.001, **kwargs):
def __init__(self, step_time: float = 0.001, **kwargs):
super().__init__(**kwargs)
self.step_time = step_time
@ -24,7 +28,12 @@ class DummyStage(BaseStage):
pass
@thing_action
def move_relative(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
def move_relative(
self,
cancel: CancelHook,
block_cancellation: bool = False,
**kwargs: Mapping[str, int],
):
"""Make a relative move. Keyword arguments should be axis names."""
displacement = [kwargs.get(k, 0) for k in self.axis_names]
self.moving = True
@ -50,7 +59,7 @@ class DummyStage(BaseStage):
# and to mark the invocation as "cancelled" rather than stopped.
raise e
finally:
self.moving=False
self.moving = False
self.position = {
k: self.position[k] + int(fraction_complete * v)
for k, v in zip(self.axis_names, displacement)
@ -58,19 +67,26 @@ class DummyStage(BaseStage):
self.instantaneous_position = self.position
@thing_action
def move_absolute(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
def move_absolute(
self,
cancel: CancelHook,
block_cancellation: bool = False,
**kwargs: Mapping[str, int],
):
"""Make an absolute move. Keyword arguments should be axis names."""
displacement = {
k: int(v) - self.position[k]
k: int(v) - self.position[k]
for k, v in kwargs.items()
if k in self.axis_names
}
self.move_relative(cancel, block_cancellation=block_cancellation, **displacement)
self.move_relative(
cancel, block_cancellation=block_cancellation, **displacement
)
@thing_action
def set_zero_position(self):
"""Make the current position zero in all axes
This action does not move the stage, but resets the position to zero.
It is intended for use after manually or automatically recentring the
stage.

71
src/openflexure_microscope_server/things/stitching.py
View file

@ -21,8 +21,10 @@ class Stitcher(Thing):
self._script = path_to_openflexure_stitch
def run_subprocess(
self, logger: InvocationLogger, cmd: list[str],
) -> CompletedProcess:
self,
logger: InvocationLogger,
cmd: list[str],
) -> CompletedProcess:
"""Run a subprocess and log any output"""
logger.info(f"Running command in subprocess: `{' '.join(cmd)}")
output = run(cmd, stdout=PIPE, stderr=PIPE, universal_newlines=True)
@ -31,19 +33,26 @@ class Stitcher(Thing):
logger.info(pipe)
output.check_returncode()
return output
def images_folder(self, smart_scan: SmartScanDep, scan_name: Optional[str]=None) -> str:
def images_folder(
self, smart_scan: SmartScanDep, scan_name: Optional[str] = None
) -> str:
scan_folder = smart_scan.scan_folder_path(scan_name=scan_name)
return os.path.join(scan_folder, "images")
@staticmethod
def output_up_to_date(folder: str, output_filename: str, image_prefix: str="image", image_suffix: str=".jpg") -> bool:
def output_up_to_date(
folder: str,
output_filename: str,
image_prefix: str = "image",
image_suffix: str = ".jpg",
) -> bool:
"""Check if any of the images in a folder are newer than a file
If there are no images (files with the prefix and suffix) newer than the
If there are no images (files with the prefix and suffix) newer than the
`output_filename`, we return `True`, i.e. the output is up to date. If
any image in the folder is newer, we return `False`.
This is not flawless logic - if an update process is slow, images might be
saved between starting that process and saving the output. Consequently,
a `True` from this function does not guarantee the output is up to date.
@ -61,24 +70,48 @@ class Stitcher(Thing):
return True
@thing_action
def stitch_scan_from_stage(self, logger: InvocationLogger, smart_scan: SmartScanDep, scan_name: Optional[str]=None, downsample: float=1.0) -> JPEGBlob:
def stitch_scan_from_stage(
self,
logger: InvocationLogger,
smart_scan: SmartScanDep,
scan_name: Optional[str] = None,
downsample: float = 1.0,
) -> JPEGBlob:
"""Generate a stitched image based on stage position metadata"""
output_fname = "stitched_from_stage.jpg"
images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
if self.output_up_to_date(images_folder, output_fname):
logger.info(f"No images are newer than {output_fname}, skipping.")
else:
self.run_subprocess(logger, [self._script, "--stitching_mode", "only_stage_stitch", images_folder])
self.run_subprocess(
logger,
[self._script, "--stitching_mode", "only_stage_stitch", images_folder],
)
return JPEGBlob.from_file(os.path.join(images_folder, output_fname))
@thing_action
def update_scan_correlations(self, logger: InvocationLogger, smart_scan: SmartScanDep, scan_name: Optional[str]=None) -> None:
"""Generate a stitched image based on stage position metadata"""
images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
self.run_subprocess(logger, [self._script, "--stitching_mode", "only_correlate", images_folder])
@thing_action
def stitch_scan(self, logger: InvocationLogger, smart_scan: SmartScanDep, scan_name: Optional[str]=None, downsample: float=1.0) -> None:
def update_scan_correlations(
self,
logger: InvocationLogger,
smart_scan: SmartScanDep,
scan_name: Optional[str] = None,
) -> None:
"""Generate a stitched image based on stage position metadata"""
images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
self.run_subprocess(logger, [self._script, "--stitching_mode", "all", images_folder])
self.run_subprocess(
logger, [self._script, "--stitching_mode", "only_correlate", images_folder]
)
@thing_action
def stitch_scan(
self,
logger: InvocationLogger,
smart_scan: SmartScanDep,
scan_name: Optional[str] = None,
downsample: float = 1.0,
) -> None:
"""Generate a stitched image based on stage position metadata"""
images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
self.run_subprocess(
logger, [self._script, "--stitching_mode", "all", images_folder]
)

6
src/openflexure_microscope_server/things/system_control.py
View file

@ -3,12 +3,14 @@ OpenFlexure Microscope system control Thing
This module defines a Thing that can shut down or restart the host computer.
"""
import subprocess
import os
from labthings_fastapi.thing import Thing
from labthings_fastapi.decorators import thing_action, thing_property
from pydantic import BaseModel
class CommandOutput(BaseModel):
output: str
error: str
@ -16,7 +18,7 @@ class CommandOutput(BaseModel):
class SystemControlThing(Thing):
"""
Attempt to shutdown the device
Attempt to shutdown the device
"""
@thing_action
@ -39,7 +41,7 @@ class SystemControlThing(Thing):
Checks if we are running on a Raspberry Pi.
"""
return os.path.exists("/usr/bin/raspi-config")
@thing_action
def reboot(self) -> CommandOutput:
"""Attempt to reboot the device"""

1
src/openflexure_microscope_server/things/test.py
View file

@ -3,6 +3,7 @@ OpenFlexure Microscope API test Thing
This Thing is intended only for use testing out the API and client(s).
"""
from labthings_fastapi.thing import Thing
from labthings_fastapi.decorators import thing_action, thing_property
from labthings_fastapi.dependencies.invocation import CancelHook, InvocationLogger