Merge branch 'gain-exposure-settings' into 'master'
Gain & exposure settings See merge request openflexure/openflexure-microscope-server!8
This commit is contained in:
Joel Collins
commit
7088d78244
5 changed files with 20 additions and 174 deletions
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@ -2,6 +2,7 @@ from openflexure_microscope.api.utilities import gen, JsonPayload
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from openflexure_microscope.api.v1.views import MicroscopeView
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from flask import Response, Blueprint, jsonify, request
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import logging
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class StreamAPI(MicroscopeView):
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@ -99,8 +100,6 @@ class ConfigAPI(MicroscopeView):
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Content-Type: application/json
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{
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"analog_gain": 1.0,
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"digital_gain": 1.0,
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"image_resolution": [
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2592,
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1944
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@ -111,7 +110,9 @@ class ConfigAPI(MicroscopeView):
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1312,
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976
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],
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"picamera_params": {
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"picamera_settings": {
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"analog_gain": 1.0,
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"digital_gain": 1.0,
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"awb_gains": [
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0.92578125,
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2.94921875
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@ -125,7 +126,6 @@ class ConfigAPI(MicroscopeView):
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"plugins": [
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"openflexure_microscope.plugins.default:Plugin"
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],
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"shading_table_path": "/home/pi/.openflexure/microscopelst.npy",
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"video_resolution": [
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832,
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624
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@ -170,7 +170,7 @@ class ConfigAPI(MicroscopeView):
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"""
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payload = JsonPayload(request)
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print(payload.json)
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logging.debug("Updating settings from POST request.")
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self.microscope.write_config(payload.json)
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self.microscope.save_config()
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@ -125,6 +125,14 @@ class BaseCamera(object):
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self.images = self.load_capture_db(self.images_db)
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self.videos = self.load_capture_db(self.videos_db)
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def apply_config(self, config):
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"""Update settings from a config dictionary"""
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self.config.update(config)
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def read_config(self, config):
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"""Return the current settings as a dictionary"""
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return self.config
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def __enter__(self):
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"""Create camera on context enter."""
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return self
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@ -184,12 +184,18 @@ class StreamingCamera(BaseCamera):
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set_digital_gain(self.camera, value)
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elif key == 'analog_gain':
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set_analog_gain(self.camera, value)
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elif key == "shutter_speed":
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# TODO: use types from CONFIG_KEYS? @jtc42
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self.camera.shutter_speed = int(value)
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else:
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setattr(self.camera, key, value) # Write setting to camera
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# StreamingCamera parameters (applied via StreamingCamera config)
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for key, value in config.items(): # For each provided setting
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if key != 'picamera_settings': # We already handled this
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if key not in CONFIG_KEYS.keys():
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logging.warn("{} is not in the streaming camera settings dictionary - adding it.")
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#continue #TODO: filter settings somehow?
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logging.debug("Setting parameter {}: {}".format(key, value))
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self.config[key] = value
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@ -192,7 +192,7 @@ class Microscope(object):
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# If attached to a camera
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if self.camera:
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# Update camera config
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self.camera.config.update(config)
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self.camera.apply_config(config)
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# If attached to a stage
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# TODO: Convert stage settings into a config expansion
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@ -1,168 +0,0 @@
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import time
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import numpy as np
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import threading
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from openflexure_microscope.plugins import MicroscopePlugin
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from openflexure_microscope.utilities import set_properties
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from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
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from openflexure_microscope.api.utilities import JsonPayload
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from flask import request, jsonify, abort, current_app
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import logging
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from contextlib import contextmanager
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class JPEGSharpnessMonitor():
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def __init__(self, microscope, timeout=60):
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self.microscope = microscope
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self.camera = microscope.camera
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self.stage = microscope.stage
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self.jpeg_sizes = []
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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.timeout = timeout
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self.keep_alive()
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self.background_thread = None
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def is_alive(self):
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if self.background_thread is None:
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return False
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else:
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return self.background_thread.is_alive()
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def should_stop(self):
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import time
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return time.time() - self.kept_alive > self.timeout
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def keep_alive(self):
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import time
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self.kept_alive = time.time()
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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.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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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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self.keep_alive()
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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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if self.stop_event.is_set():
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logging.info("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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def jpeg_size(self):
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"""Return the size of a frame from the MJPEG stream"""
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return len(self.camera.get_frame())
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def focus_rel(self, dz, backlash=False, **kwargs):
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self.keep_alive()
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self.stage_times.append(time.time())
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self.stage_positions.append(self.stage.position)
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self.stage.move_rel([0, 0, dz], backlash=backlash, **kwargs)
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self.stage_times.append(time.time())
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self.stage_positions.append(self.stage.position)
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i = len(self.stage_positions) - 2
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return i, self.stage_positions[-1][2]
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def move_data(self, istart, istop=None):
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"Extract sharpness as a function of (interpolated) z"
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global np, logging
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if istop is None:
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istop = istart + 2
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jpeg_times = np.array(self.jpeg_times)
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jpeg_sizes = np.array(self.jpeg_sizes)
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stage_times = np.array(self.stage_times)[istart:istop]
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stage_zs = np.array(self.stage_positions)[istart:istop, 2]
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start = np.argmax(jpeg_times > stage_times[0])
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stop = np.argmax(jpeg_times > stage_times[1])
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if stop < 1:
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stop = len(jpeg_times)
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logging.debug("changing stop to {}".format(stop))
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jpeg_times = jpeg_times[start:stop]
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jpeg_zs = np.interp(jpeg_times, stage_times, stage_zs)
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return jpeg_times, jpeg_zs, jpeg_sizes[start:stop]
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def sharpest_z_on_move(self, index):
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"""Return the z position of the sharpest image on a given move"""
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jt, jz, js = self.move_data(index)
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return jz[np.argmax(js)]
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def data_dict(self):
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"""Return the gathered data as a single convenient dictionary"""
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data = {}
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for k in ['jpeg_times', 'jpeg_sizes', 'stage_times', 'stage_positions']:
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data[k] = getattr(self, k)
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return data
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class FastAutofocusAPI(MicroscopeViewPlugin):
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def post(self):
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payload = JsonPayload(request)
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# Figure out the parameters to use
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dz = payload.param("dz", default=2000, convert=int)
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backlash = payload.param("backlash", default=None, convert=int)
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if backlash < 0:
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backlash = None
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print("Running autofocus...")
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task = self.microscope.task.start(self.plugin.fast_autofocus, dz, backlash=backlash)
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# return a handle on the autofocus task
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return jsonify(task.state), 202
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class Plugin(MicroscopePlugin):
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"""
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Plugin to provide fast autofocus
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"""
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JPEGSharpnessMonitor = JPEGSharpnessMonitor # make the class available
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def sharpness_monitor(self):
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return JPEGSharpnessMonitor(self.microscope)
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@contextmanager
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def monitor_sharpness(self):
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m = self.sharpness_monitor()
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m.start()
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try:
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yield m
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finally:
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m.stop()
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def move_and_find_focus(self, dz):
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"""Make a relative Z move and return the peak sharpness position"""
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with self.monitor_sharpness() as m:
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m.focus_rel(dz)
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return m.sharpest_z_on_move(0)
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def fast_autofocus(self, dz=2000, backlash=None):
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"""Perform a down-up-down-up autofocus"""
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with self.monitor_sharpness() as m:
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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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if backlash is None:
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i, z = m.focus_rel(-dz) # move all the way to the start so it's consistent
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else:
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i, z = m.focus_rel(fz - z - backlash)
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m.focus_rel(fz - z)
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return m.data_dict()
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api_views = {
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'/fast_autofocus': FastAutofocusAPI,
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}
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