Merge branch 'master' into stage-calibration
This commit is contained in:
Richard Bowman
commit
70d4c7e950
23 changed files with 1285 additions and 138 deletions
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@ -1,10 +1,6 @@
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#!/usr/bin/env python
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from gevent import monkey
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# Patch most system modules. Leave threads untouched so we can still use them normally if needed.
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print("Monkey patching with Gevenet")
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monkey.patch_all()
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print("Monkey patching successful")
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import time
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import atexit
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@ -24,7 +24,3 @@ with handle_extension_error("camera stage mapping"):
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from .camera_stage_mapping import csm_extension
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with handle_extension_error("lens shading calibration"):
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from .picamera_autocalibrate import lst_extension_v2
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#FIXME: this oughtn't stay in the production version...
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with handle_extension_error("custom element example"):
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from ..example_extensions.custom_element import customelement_extension_v2
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@ -8,11 +8,13 @@ from openflexure_microscope.utilities import set_properties
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import time
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import numpy as np
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import threading
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import logging
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from scipy import ndimage
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from contextlib import contextmanager
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from threading import Thread, Event
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### Autofocus utilities
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@ -25,7 +27,7 @@ class JPEGSharpnessMonitor:
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self.jpeg_times = []
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self.stage_positions = []
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self.stage_times = []
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self.stop_event = threading.Event()
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self.stop_event = Event()
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self.timeout = timeout
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self.keep_alive()
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self.background_thread = None
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@ -48,26 +50,31 @@ class JPEGSharpnessMonitor:
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def start(self):
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"Start monitoring sharpness by looking at JPEG size"
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self.background_thread = threading.Thread(target=self._measure_jpegs)
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self.background_thread = Thread(target=self._measure_jpegs)
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self.background_thread.start()
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return self
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def stop(self):
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"Stop the background thread"
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self.stop_event.set()
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print("Joining JPEG thread")
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self.background_thread.join()
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def _measure_jpegs(self):
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"Function that runs in a background thread to record sharpness"
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logging.info("Starting sharpness measurement in background thread")
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logging.debug("Starting sharpness measurement in background thread")
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self.keep_alive()
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logging.debug(f"_measure_jpegs stop_event: {self.stop_event.is_set()}")
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while not self.stop_event.is_set() and not self.should_stop():
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self.jpeg_sizes.append(self.jpeg_size())
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self.jpeg_times.append(time.time())
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size_now = self.jpeg_size()
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time_now = time.time()
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self.jpeg_sizes.append(size_now)
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self.jpeg_times.append(time_now)
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print("Exited JPEG measure loop")
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if self.stop_event.is_set():
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logging.info("Cleanly stopped sharpness measurement in background thread")
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logging.debug("Cleanly stopped sharpness measurement in background thread")
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if self.should_stop():
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logging.info("Sharpness measurement timed out and has stopped")
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logging.debug("Sharpness measurement timed out and has stopped")
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def jpeg_size(self):
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"""Return the size of a frame from the MJPEG stream"""
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@ -195,7 +202,7 @@ def move_and_find_focus(microscope, dz):
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def fast_autofocus(microscope, dz=2000, backlash=None):
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"""Perform a down-up-down-up autofocus"""
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with monitor_sharpness(microscope) as m, microscope.camera.lock:
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with monitor_sharpness(microscope) as m, microscope.camera.lock, microscope.stage.lock:
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i, z = m.focus_rel(-dz / 2)
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i, z = m.focus_rel(dz)
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fz = m.sharpest_z_on_move(i)
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@ -245,17 +252,20 @@ def fast_up_down_up_autofocus(
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might slightly hurt accuracy, but is unlikely to be a big issue. Too big
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may cause you to overshoot, which is a problem.
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"""
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with monitor_sharpness(microscope) as m, microscope.camera.lock:
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with monitor_sharpness(microscope) as m, microscope.camera.lock, microscope.stage.lock:
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# Ensure the MJPEG stream has started
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microscope.camera.start_stream_recording()
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df = dz # TODO: refactor so I actually use dz in the code below!
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logging.debug("Initial move")
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if initial_move_up:
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m.focus_rel(df / 2)
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# move down
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logging.debug("Move down")
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i, z = m.focus_rel(-df)
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# now inspect where the sharpest point is, and estimate the sharpness
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# (JPEG size) that we should find at the start of the Z stack
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logging.debug("Get target_s")
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jt, jz, js = m.move_data(i)
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best_z = jz[np.argmax(js)]
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target_s = np.interp(
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@ -263,11 +273,13 @@ def fast_up_down_up_autofocus(
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) # NB jz is decreasing
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# now move to the start of the z stack
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logging.debug("Move to the start of the z stack")
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i, z = m.focus_rel(
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best_z + target_z - z + mini_backlash
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) # takes us to the start of the stack
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# We've deliberately undershot - figure out how much further we should move based on the curve
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logging.debug("Calculate remining movement")
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current_js = m.jpeg_size()
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imax = np.argmax(js) # we want to crop out just the bit below the peak
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js = js[imax:] # NB z is in DECREASING order
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@ -279,6 +291,7 @@ def fast_up_down_up_autofocus(
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# So, the Z position corresponding to our current sharpness value is zs[inow]
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# That means we should move forwards, by best_z - zs[inow]
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logging.debug("Correction move")
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correction_move = best_z + target_z - jz[inow]
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logging.debug(
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"Fast autofocus scan: correcting backlash by moving {} steps".format(
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@ -317,7 +330,7 @@ class AutofocusAPI(View):
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dz = payload.param("dz", default=np.linspace(-300, 300, 7), convert=np.array)
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if microscope.has_real_stage():
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logging.info("Running autofocus...")
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logging.debug("Running autofocus...")
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task = taskify(autofocus)(microscope, dz)
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# return a handle on the autofocus task
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@ -348,7 +361,7 @@ class FastAutofocusAPI(View):
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backlash = 0
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if microscope.has_real_stage():
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logging.info("Running autofocus...")
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logging.debug("Running autofocus...")
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task = taskify(fast_up_down_up_autofocus)(microscope, dz=dz, mini_backlash=backlash)
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# return a handle on the autofocus task
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@ -7,10 +7,35 @@ from labthings.core.tasks import taskify
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from flask import abort
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from contextlib import contextmanager
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import logging
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from .recalibrate_utils import recalibrate_camera, auto_expose_and_freeze_settings
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# Type hinting
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from typing import Tuple
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from .recalibrate_utils import recalibrate_camera, auto_expose_and_freeze_settings, flat_lens_shading_table
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@contextmanager
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def pause_stream(scamera, resolution: Tuple[int, int] = None):
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"""This context manager locks a streaming camera, and pauses the stream.
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The stream is re-enabled, with the original resolution, once the with
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block has finished.
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"""
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with scamera.lock:
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assert not scamera.record_active, "We can't pause the camera's video stream while a recording is in progress."
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streaming = scamera.stream_active
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old_resolution = scamera.camera.resolution
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if streaming:
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logging.info("Stopping stream in pause_stream context manager")
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scamera.stop_stream_recording(resolution=resolution)
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try:
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yield scamera
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finally:
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scamera.camera.resolution = old_resolution
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if streaming:
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logging.info("Restarting stream in pause_stream context manager")
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scamera.start_stream_recording()
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def recalibrate(microscope):
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"""Reset the camera's settings.
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@ -19,24 +44,10 @@ def recalibrate(microscope):
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table such that the background is as uniform as possible
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with a gray level of 230. It takes a little while to run.
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"""
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scamera = microscope.camera
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with scamera.lock:
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assert not scamera.record_active, "Can't recalibrate while recording!"
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streaming = scamera.stream_active
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if streaming:
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logging.info("Stopping stream before recalibration")
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scamera.stop_stream_recording(resolution=(640, 480))
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old_resolution = scamera.camera.resolution
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try:
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scamera.camera.resolution = (640, 480)
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auto_expose_and_freeze_settings(scamera.camera)
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recalibrate_camera(scamera.camera)
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finally:
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scamera.camera.resolution = old_resolution
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microscope.save_settings()
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if streaming:
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logging.info("Restarting stream after recalibration")
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scamera.start_stream_recording()
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with pause_stream(microscope.camera) as scamera:
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auto_expose_and_freeze_settings(scamera.camera) # scamera.camera is the PiCamera object
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recalibrate_camera(scamera.camera)
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microscope.save_settings()
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@ThingAction
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@ -52,9 +63,42 @@ class RecalibrateView(View):
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return taskify(recalibrate)(microscope)
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@ThingAction
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class FlattenLSTView(View):
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def post(self):
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microscope = find_component("org.openflexure.microscope")
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if not microscope:
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abort(503, "No microscope connected. Unable to flatten the lens shading table.")
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try:
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with pause_stream(microscope.camera) as scamera:
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flat_lst = flat_lens_shading_table(scamera.camera)
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scamera.camera.lens_shading_table = flat_lst
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microscope.save_settings()
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except:
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logging.exception("Error flattening the lens shading table.")
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abort(503, "Couldn't flatten the lens shading table - do you have the forked PiCamera library installed?")
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@ThingAction
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class DeleteLSTView(View):
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def post(self):
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microscope = find_component("org.openflexure.microscope")
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if not microscope:
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abort(503, "No microscope connected. Unable to flatten the lens shading table.")
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try:
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with pause_stream(microscope.camera) as scamera:
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scamera.camera.lens_shading_table = None
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microscope.save_settings()
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except:
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logging.exception("Error deleting the lens shading table.")
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abort(503, "Couldn't flatten the lens shading table - do you have the forked PiCamera library installed?")
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lst_extension_v2 = BaseExtension(
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"org.openflexure.calibration.picamera", version="2.0.0-beta.1"
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"org.openflexure.calibration.picamera", version="2.0.0-beta.1", description="Routines to perform flat-field correction on the camera."
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)
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lst_extension_v2.add_method(
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@ -62,3 +106,5 @@ lst_extension_v2.add_method(
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)
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lst_extension_v2.add_view(RecalibrateView, "/recalibrate")
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lst_extension_v2.add_view(FlattenLSTView, "/flatten_lens_shading_table")
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lst_extension_v2.add_view(DeleteLSTView, "/delete_lens_shading_table")
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|
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@ -198,6 +198,7 @@ def tile(
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else:
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# Run slow autofocus. Client should provide dz ~ 50
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autofocus_extension.autofocus(
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microscope,
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range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
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)
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logging.debug("Finished autofocus")
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|
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@ -42,13 +42,18 @@ customelement_extension_v2 = CustomElementExtension()
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def wc_func():
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return {
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"href": customelement_extension_v2.static_file_url("my-custom-element.min.js"),
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"name": "my-custom-element",
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"href": customelement_extension_v2.static_file_url("vue-web-component.min.js"),
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"name": "vue-web-component",
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}
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def gui_func():
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return {"icon": "pets", "title": "Element", "viewPanel": "stream", "wc": wc_func()}
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return {
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"icon": "grid_on",
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"title": "Med Scan",
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"viewPanel": "stream",
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"wc": wc_func(),
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}
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customelement_extension_v2.add_meta("wc", wc_func)
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|
|
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|
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@ -0,0 +1,22 @@
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# Example Web Component using Vue framework
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## Structure
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### Web component
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* `/src/components/VueWebComponent.vue`
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### Debug app
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* For debugging purposes, the component can be mounted into a demo app
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* `/src/App.vue` and `/src/main.js` provide demo app functionality, and do not affect the final built web component
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## Building
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* Run `npm run build`
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## Debugging
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* Run `npm run serve` to serve the demo app. This can be used to debug the component. Note, the base URL will be set to it's default value of a localhost microscope server
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|
|
@ -1,3 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:18020f0209272ab81d01b2d68da517fcff98dd07d2ad7fe738c66df75003f7cf
|
||||
oid sha256:e07e1d811b5182b4e96ab2a29d82db90c8de77d340844cf0acd284388154a671
|
||||
size 197
|
||||
|
|
|
|||
|
|
@ -1,3 +0,0 @@
|
|||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:94cc5b4e5b3ddb8c6b94ef9b81b49060c582935aedf6c7d1626f4166c1827442
|
||||
size 288006
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:ba98b02d051bf6f7d2d4302154512a72ae6ddc1eff261e171fd92a067e1bdf84
|
||||
size 92018
|
||||
|
|
@ -0,0 +1,3 @@
|
|||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:f03a6823dea074cef32557902c64407cf67899aaa7f6c0d19ff7746bd149fbe0
|
||||
size 288124
|
||||
|
|
@ -0,0 +1,3 @@
|
|||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:155a1dc5d6cbdc787012f83bf82c84b97944ab6b2141f9c566faa375571a3f4a
|
||||
size 92117
|
||||
File diff suppressed because it is too large
Load diff
|
|
@ -1,9 +1,10 @@
|
|||
{
|
||||
"name": "vue-web-component-project",
|
||||
"name": "vue-web-component",
|
||||
"version": "0.1.0",
|
||||
"private": true,
|
||||
"scripts": {
|
||||
"build": "vue-cli-service build --target wc --inline-vue --name my-custom-element ./src/components/VueWebComponent.vue"
|
||||
"serve": "vue-cli-service serve",
|
||||
"build": "cross-var vue-cli-service build --target wc --inline-vue --name $npm_package_name ./src/components/VueWebComponent.vue"
|
||||
},
|
||||
"dependencies": {
|
||||
"axios": "^0.19.2",
|
||||
|
|
@ -13,6 +14,7 @@
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|||
"devDependencies": {
|
||||
"@vue/cli-plugin-babel": "^4.1.0",
|
||||
"@vue/cli-service": "^4.1.0",
|
||||
"cross-var": "^1.1.0",
|
||||
"vue-template-compiler": "^2.6.10"
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,18 @@
|
|||
<template>
|
||||
<div id="app">
|
||||
<VueWebComponent/>
|
||||
</div>
|
||||
</template>
|
||||
|
||||
<script>
|
||||
import VueWebComponent from './components/VueWebComponent.vue'
|
||||
export default {
|
||||
name: 'app',
|
||||
components: {
|
||||
VueWebComponent
|
||||
}
|
||||
}
|
||||
</script>
|
||||
|
||||
<style>
|
||||
</style>
|
||||
|
|
@ -20,7 +20,7 @@ export default {
|
|||
props: {
|
||||
'componentBaseURL': {
|
||||
required: false,
|
||||
default: null,
|
||||
default: "http://localhost:5000/api/v2",
|
||||
type: String
|
||||
}
|
||||
},
|
||||
|
|
@ -33,7 +33,8 @@ export default {
|
|||
};
|
||||
},
|
||||
|
||||
mounted () {
|
||||
mounted: function() {
|
||||
console.log(this.componentBaseURL)
|
||||
if (this.componentBaseURL){
|
||||
axios
|
||||
.get(`${this.componentBaseURL}`)
|
||||
|
|
|
|||
|
|
@ -1,7 +1,6 @@
|
|||
import Vue from 'vue';
|
||||
import wrap from '@vue/web-component-wrapper';
|
||||
import VueWebComponent from './components/VueWebComponent';
|
||||
import App from './App.vue';
|
||||
|
||||
const CustomElement = wrap(Vue, VueWebComponent);
|
||||
|
||||
window.customElements.define('my-custom-element', CustomElement);
|
||||
new Vue({
|
||||
render: h => h(App)
|
||||
}).$mount('#app')
|
||||
|
|
@ -1,3 +1,4 @@
|
|||
process.env.VUE_APP_NAME = require('./package.json').name
|
||||
module.exports = {
|
||||
productionSourceMap: false
|
||||
};
|
||||
Loading…
Add table
Add a link
Reference in a new issue