Ruff formatting and removing all capturing from smart_scan
This commit is contained in:
jaknapper
parent
1f3211e3ee
commit
0b7a817674
2 changed files with 4 additions and 133 deletions
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@ -11,7 +11,6 @@ from PIL import Image
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from pydantic import BaseModel
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from datetime import datetime
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from subprocess import CompletedProcess, Popen, PIPE, SubprocessError, STDOUT
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from threading import Event
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import glob
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import json
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import piexif
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@ -590,9 +589,8 @@ class SmartScanThing(Thing):
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current_pos_xyz, imaged=True, focused=focused
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)
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# wait for the previous capture to be saved, i.e. don't leave more than one image saving in the background
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# if self._capture_thread:
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# self._wait_for_capture_thread()
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self._z_stack.smart_stack(images_dir = self._ongoing_scan_images_dir)
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# increment capure counter as thread has completed
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self._scan_images_taken += 1
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# Add it to the incremental zip
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@ -602,14 +600,6 @@ class SmartScanThing(Thing):
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download_zip=False,
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)
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name = f"image_{new_pos_xyz[0]}_{new_pos_xyz[1]}.jpg"
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# jpeg_path = os.path.join(self._ongoing_scan_images_dir, name)
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self._z_stack.smart_stack(images_dir = self._ongoing_scan_images_dir)
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# self._capture_thread = self._start_capture_thread(jpeg_path)
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# wait until the image is acquired
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# acquired.wait()
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@_scan_running
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def _try_autofocus(
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self,
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@ -646,52 +636,6 @@ class SmartScanThing(Thing):
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self._scan_logger.warning("Could not autofocus after 3 attempts.")
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return False, self._stage.position["z"]
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@_scan_running
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def _wait_for_capture_thread(self) -> None:
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"""
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Wait for the capture thread to be complete.
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"""
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wait_start = time.time()
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thread_was_alive = self._capture_thread.is_alive()
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# If the capture thread has thrown an exception it will be raised
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# when join is called, this will cause the scan to end. If we want
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# to retry captures at a later date this is where we will need to
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# catch the IOError or CaptureError from the thread.
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self._capture_thread.join()
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time.sleep(0.2)
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if thread_was_alive:
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wait_time = time.time() - wait_start
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self._scan_logger.info(
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f"Waited {wait_time:.1f}s for the previous capture to finish saving."
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)
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# @_scan_running
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# def _start_capture_thread(
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# self, jpeg_path: str
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# ) -> tuple[ErrorCapturingThread, Event]:
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# """
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# Start the capture thread.
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# Args:
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# jpeg_path, the path to save the image once aquired
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# Return the thread and an event that will be set when the image is aquired
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# """
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# time.sleep(0.2)
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# # Acquire the image in a thread, and continue once it's acquired
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# # (i.e. leave saving in the background) Use ErrorCapturingThread
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# # intead of Thread. This will raise errors in the calling thread
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# # only when join() is called, allowing us to handle this appropriately.
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# capture_thread = ErrorCapturingThread(
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# # target=self._capture_and_save,
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# target=self._z_stack.smart_stack(),
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# kwargs={"images_dir": self._ongoing_scan_images_dir},
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# )
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# capture_thread.start()
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# return capture_thread
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@_scan_running
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def _return_to_starting_position(self):
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self._scan_logger.info("Returning to starting position.")
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@ -750,74 +694,6 @@ class SmartScanThing(Thing):
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raise HTTPException(404, "File not found")
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return FileResponse(path)
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@_scan_running
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def _capture_and_save(
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self,
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acquired: Event,
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jpeg_path: str,
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) -> None:
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"""Capture an image and save it to disk
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This will set the event `acquired` once the image has been acquired, so
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that the stage may be moved while it's saved.
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"""
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try:
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capture_start = time.time()
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image, metadata = self._capture_image()
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finally:
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# Ensure aquired is set even if capture fails or program will hang forever.
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acquired.set()
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acquisition_time = time.time()
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self._save_capture(jpeg_path, image, metadata)
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save_time = time.time()
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acquisition_duration = round(acquisition_time - capture_start, 1)
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saving_duration = round(save_time - acquisition_time, 1)
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self._scan_logger.debug(
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f"Acquired {jpeg_path} in {acquisition_duration}s then {saving_duration}s saving to disk"
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)
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@_scan_running
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def _capture_image(self) -> tuple[np.ndarray, dict]:
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"""Capture an image in memory and return it with metadata
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This will set the event `acquired` once the image has been acquired, so
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that the stage may be moved while it's saved.
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CaptureError raised if the capture fails for any reason
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returns tuple with numpy array of image data, and dict of metadata
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"""
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try:
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metadata = self._metadata_getter()
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image = self._cam.capture_array()[..., :3]
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except Exception as e:
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raise CaptureError("An error occurred while capturing") from e
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return image, metadata
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@_scan_running
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def _save_capture(
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self,
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jpeg_path: str,
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image: np.ndarray,
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metadata: dict,
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) -> None:
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"""Saving the captured image and metadata to disk
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logger warning (via InvocationLogger) is raised if metadata is failed to be added
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IOError is raised if the file cannot be saved
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nothing is returned on success"""
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try:
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Image.fromarray(image.astype("uint8"), "RGB").save(
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jpeg_path, quality=95, subsampling=0
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)
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try:
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exif_dict = piexif.load(jpeg_path)
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exif_dict["Exif"][piexif.ExifIFD.UserComment] = json.dumps(
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metadata
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).encode("utf-8")
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piexif.insert(piexif.dump(exif_dict), jpeg_path)
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except: # noqa: E722
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# We need to capture any exception as there are many reasons metadata
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# might not be added. We warn rather than log the error.
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self._scan_logger.warning(f"Failed to add metadata to {jpeg_path}")
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except Exception as e:
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raise IOError(f"An error occurred while saving {jpeg_path}") from e
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@thing_property
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def max_range(self) -> int:
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@ -1,10 +1,6 @@
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import os
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from typing import Mapping, Optional
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import cv2
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import numpy as np
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from PIL import Image
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from pydantic import BaseModel
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from scipy.stats import norm
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import time
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import piexif
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import json
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@ -15,9 +11,7 @@ from labthings_fastapi.decorators import thing_action, thing_property
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from .camera import CameraDependency as CamDep
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from .stage import StageDependency as StageDep
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from labthings_fastapi.dependencies.invocation import (
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CancelHook,
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InvocationLogger,
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InvocationCancelledError,
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)
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@ -87,7 +81,7 @@ class ZStackThing(Thing):
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capture_start = time.time()
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image, metadata = self._capture_image(cam, metadata_getter,)
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acquisition_time = time.time()
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self._save_capture(jpeg_path, image, metadata)
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self._save_capture(jpeg_path, image, metadata, logger)
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save_time = time.time()
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acquisition_duration = round(acquisition_time - capture_start, 1)
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saving_duration = round(save_time - acquisition_time, 1)
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@ -114,6 +108,7 @@ class ZStackThing(Thing):
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jpeg_path: str,
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image: np.ndarray,
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metadata: dict,
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logger: InvocationLogger,
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) -> None:
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"""Saving the captured image and metadata to disk
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logger warning (via InvocationLogger) is raised if metadata is failed to be added
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