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Functional z stack Thing

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This commit is contained in:
jaknapper 2025-04-16 09:40:14 +01:00
parent 327a87e344
commit 1f3211e3ee
3 changed files with 182 additions and 41 deletions
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3
ofm_config_full.json
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@ -13,7 +13,8 @@
"path_to_openflexure_stitch": "application/openflexure-stitching/.venv/bin/openflexure-stitch"
}
},
"/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing"
"/background_detect/": "openflexure_microscope_server.things.background_detect:BackgroundDetectThing",
"/z_stack/": "openflexure_microscope_server.things.smart_scan:ZStackThing"
},
"settings_folder": "/var/openflexure/settings/"
}

83
src/openflexure_microscope_server/things/smart_scan.py
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@ -34,6 +34,7 @@ from openflexure_microscope_server.utilities import ErrorCapturingThread
from openflexure_microscope_server.things.autofocus import AutofocusThing
from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
from openflexure_microscope_server.things.background_detect import BackgroundDetectThing
from openflexure_microscope_server.things.z_stack import ZStackThing
from openflexure_microscope_server import scan_planners
CSMDep = direct_thing_client_dependency(CameraStageMapper, "/camera_stage_mapping/")
@ -41,7 +42,7 @@ AutofocusDep = direct_thing_client_dependency(AutofocusThing, "/autofocus/")
BackgroundDep = direct_thing_client_dependency(
BackgroundDetectThing, "/background_detect/"
)
ZStackDep = direct_thing_client_dependency(ZStackThing, "/z_stack/")
IMAGE_REGEX = re.compile(r"-?[0-9]+_-?[0-9]+\.jpeg$")
@ -159,6 +160,7 @@ class SmartScanThing(Thing):
self._background_detect: Optional[BackgroundDep] = None
self._ongoing_scan_name: Optional[str] = None
self._starting_position: Optional[Mapping[str, int]] = None
self._z_stack: Optional[ZStackDep] = None
self._capture_thread: Optional[ErrorCapturingThread] = None
self._scan_images_taken: Optional[int] = None
# TODO Scan data is a dict during refactoring, should become a dataclass
@ -175,6 +177,7 @@ class SmartScanThing(Thing):
metadata_getter: GetThingStates,
csm: CSMDep,
background_detect: BackgroundDep,
z_stack: ZStackDep,
scan_name: str = "",
):
"""Move the stage to cover an area, taking images that can be tiled together.
@ -198,6 +201,7 @@ class SmartScanThing(Thing):
self._csm = csm
self._background_detect = background_detect
self._capture_thread = None
self._z_stack = z_stack
self._scan_images_taken = 0
# Don't set self._scan_data dictionary. This is done at the start of _run_scan
@ -232,6 +236,7 @@ class SmartScanThing(Thing):
self._ongoing_scan_name = None
self._scan_images_taken = None
self._scan_data = None
self._z_stack = None
self._scan_lock.release()
@_scan_running
@ -586,22 +591,24 @@ class SmartScanThing(Thing):
)
# wait for the previous capture to be saved, i.e. don't leave more than one image saving in the background
if self._capture_thread:
self._wait_for_capture_thread()
# increment capure counter as thread has completed
self._scan_images_taken += 1
# Add it to the incremental zip
self.create_zip_of_scan(
logger=self._scan_logger,
scan_name=self._ongoing_scan_name,
download_zip=False,
)
# if self._capture_thread:
# self._wait_for_capture_thread()
# increment capure counter as thread has completed
self._scan_images_taken += 1
# Add it to the incremental zip
self.create_zip_of_scan(
logger=self._scan_logger,
scan_name=self._ongoing_scan_name,
download_zip=False,
)
name = f"image_{new_pos_xyz[0]}_{new_pos_xyz[1]}.jpg"
jpeg_path = os.path.join(self._ongoing_scan_images_dir, name)
self._capture_thread, acquired = self._start_capture_thread(jpeg_path)
# jpeg_path = os.path.join(self._ongoing_scan_images_dir, name)
self._z_stack.smart_stack(images_dir = self._ongoing_scan_images_dir)
# self._capture_thread = self._start_capture_thread(jpeg_path)
# wait until the image is acquired
acquired.wait()
# acquired.wait()
@_scan_running
def _try_autofocus(
@ -659,31 +666,31 @@ class SmartScanThing(Thing):
f"Waited {wait_time:.1f}s for the previous capture to finish saving."
)
@_scan_running
def _start_capture_thread(
self, jpeg_path: str
) -> tuple[ErrorCapturingThread, Event]:
"""
Start the capture thread.
# @_scan_running
# def _start_capture_thread(
# self, jpeg_path: str
# ) -> tuple[ErrorCapturingThread, Event]:
# """
# Start the capture thread.
Args:
jpeg_path, the path to save the image once aquired
# Args:
# jpeg_path, the path to save the image once aquired
Return the thread and an event that will be set when the image is aquired
"""
acquired = Event()
time.sleep(0.2)
# Return the thread and an event that will be set when the image is aquired
# """
# time.sleep(0.2)
# Acquire the image in a thread, and continue once it's acquired
# (i.e. leave saving in the background) Use ErrorCapturingThread
# intead of Thread. This will raise errors in the calling thread
# only when join() is called, allowing us to handle this appropriately.
capture_thread = ErrorCapturingThread(
target=self._capture_and_save,
kwargs={"acquired": acquired, "jpeg_path": jpeg_path},
)
capture_thread.start()
return capture_thread, acquired
# # Acquire the image in a thread, and continue once it's acquired
# # (i.e. leave saving in the background) Use ErrorCapturingThread
# # intead of Thread. This will raise errors in the calling thread
# # only when join() is called, allowing us to handle this appropriately.
# capture_thread = ErrorCapturingThread(
# # target=self._capture_and_save,
# target=self._z_stack.smart_stack(),
# kwargs={"images_dir": self._ongoing_scan_images_dir},
# )
# capture_thread.start()
# return capture_thread
@_scan_running
def _return_to_starting_position(self):
@ -1241,7 +1248,3 @@ class SmartScanThing(Thing):
"""List the relative paths of all files and folders in the zip folder specified"""
scan_zip = zipfile.ZipFile(zip_path)
return [os.path.normpath(i) for i in scan_zip.namelist()]
class CaptureError(RuntimeError):
"""An error trying to capture from Picamera"""

137
src/openflexure_microscope_server/things/z_stack.py Normal file
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@ -0,0 +1,137 @@
import os
from typing import Mapping, Optional
import cv2
import numpy as np
from PIL import Image
from pydantic import BaseModel
from scipy.stats import norm
import time
import piexif
import json
from labthings_fastapi.dependencies.metadata import GetThingStates
from labthings_fastapi.thing import Thing
from labthings_fastapi.decorators import thing_action, thing_property
from .camera import CameraDependency as CamDep
from .stage import StageDependency as StageDep
from labthings_fastapi.dependencies.invocation import (
CancelHook,
InvocationLogger,
InvocationCancelledError,
)
class CaptureError(RuntimeError):
"""An error trying to capture from Picamera"""
class ZStackThing(Thing):
@thing_property
def images_to_capture(self) -> int:
"""The number of images to capture and save in a stack
Defaults to 1 unless you need to see either side of focus"""
return self.thing_settings.get("stack_height", 9)
@images_to_capture.setter
def images_to_capture(self, value: int) -> None:
self.thing_settings["images_to_capture"] = value
@thing_property
def stack_dz(self) -> int:
"""Space in steps between images in a z-stack
Suggested is 50 for 60-100x
100 for 40x
200 for 20x"""
return self.thing_settings.get("stack_dz", 50)
@stack_dz.setter
def stack_dz(self, value: int) -> None:
self.thing_settings["stack_dz"] = value
@thing_action
def smart_stack(
self,
cam: CamDep,
stage: StageDep,
images_dir: str,
logger: InvocationLogger,
metadata_getter: GetThingStates,
) -> None:
stack_dz = self.stack_dz
images_to_capture = self.images_to_capture
stack_z_range = stack_dz * (images_to_capture - 1)
stage.move_relative(z=-stack_z_range / 2)
for capture_count in range(images_to_capture):
jpeg_path = os.path.join(
images_dir,
f"{capture_count}.jpeg",
)
self._capture_and_save(
jpeg_path, cam, logger, metadata_getter,
)
stage.move_relative(z=stack_dz)
def _capture_and_save(
self,
jpeg_path: str,
cam: CamDep,
logger: InvocationLogger,
metadata_getter: GetThingStates,
) -> None:
"""Capture an image and save it to disk
This will set the event `acquired` once the image has been acquired, so
that the stage may be moved while it's saved.
"""
capture_start = time.time()
image, metadata = self._capture_image(cam, metadata_getter,)
acquisition_time = time.time()
self._save_capture(jpeg_path, image, metadata)
save_time = time.time()
acquisition_duration = round(acquisition_time - capture_start, 1)
saving_duration = round(save_time - acquisition_time, 1)
logger.info(
f"Acquired {jpeg_path} in {acquisition_duration}s then {saving_duration}s saving to disk"
)
def _capture_image(self, cam, metadata_getter) -> tuple[np.ndarray, dict]:
"""Capture an image in memory and return it with metadata
This will set the event `acquired` once the image has been acquired, so
that the stage may be moved while it's saved.
CaptureError raised if the capture fails for any reason
returns tuple with numpy array of image data, and dict of metadata
"""
try:
metadata = metadata_getter()
image = cam.capture_array()[..., :3]
except Exception as e:
raise CaptureError("An error occurred while capturing") from e
return image, metadata
def _save_capture(
self,
jpeg_path: str,
image: np.ndarray,
metadata: dict,
) -> None:
"""Saving the captured image and metadata to disk
logger warning (via InvocationLogger) is raised if metadata is failed to be added
IOError is raised if the file cannot be saved
nothing is returned on success"""
try:
Image.fromarray(image.astype("uint8"), "RGB").save(
jpeg_path, quality=95, subsampling=0
)
try:
exif_dict = piexif.load(jpeg_path)
exif_dict["Exif"][piexif.ExifIFD.UserComment] = json.dumps(
metadata
).encode("utf-8")
piexif.insert(piexif.dump(exif_dict), jpeg_path)
except: # noqa: E722
# We need to capture any exception as there are many reasons metadata
# might not be added. We warn rather than log the error.
logger.warning(f"Failed to add metadata to {jpeg_path}")
except Exception as e:
raise IOError(f"An error occurred while saving {jpeg_path}") from e