Updated docs
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jtc42
parent
fdbba08b66
commit
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12 changed files with 143 additions and 77 deletions
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@ -148,6 +148,12 @@ app.register_blueprint(task_blueprint, url_prefix=uri('/task', 'v1'))
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def routes():
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"""
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List of all connected API routes
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.. :quickref: System; Routes
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:>header Accept: application/json
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:>header Content-Type: application/json
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:status 200: stream active
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"""
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return jsonify(list_routes(app))
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@ -156,6 +162,12 @@ def routes():
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def err_log():
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"""
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Most recent 1mb of log output
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.. :quickref: System; Log
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:>header Accept: application/json
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:>header Content-Type: application/json
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:status 200: stream active
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"""
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timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
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return send_file(
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@ -100,35 +100,36 @@ class ConfigAPI(MicroscopeView):
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Content-Type: application/json
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{
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"image_resolution": [
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2592,
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1944
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],
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"jpeg_quality": 75,
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"name": "0e2c6fac5421429aac67c7903107bdd8",
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"numpy_resolution": [
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1312,
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976
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],
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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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],
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"awb_mode": "off",
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"exposure_mode": "off",
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"framerate": 24.0,
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"saturation": 0,
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"shutter_speed": 5378
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},
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"id": "0e2c6fac5421429aac67c7903107bdd8",
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"name": "docuscope-2000",
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"fov": [4100, 3146],
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"camera_settings": {
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"image_resolution": [2592, 1944],
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"numpy_resolution": [1312, 976],
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"video_resolution": [832, 624],
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"jpeg_quality": 75,
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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": [0.92578125, 2.94921875],
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"awb_mode": "off",
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"exposure_mode": "off",
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"framerate": 24.0,
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"saturation": 0,
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"shutter_speed": 5378
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},
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},
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"stage_settings": {
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"backlash": {
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"x": 256,
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"y": 256,
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"z": 0
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}
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}
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"plugins": [
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"openflexure_microscope.plugins.default:Plugin"
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],
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"stream_resolution": [
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832,
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624
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"openflexure_microscope.plugins.default.autofocus:AutofocusPlugin",
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"openflexure_microscope.plugins.default.scan:ScanPlugin",
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"openflexure_microscope.plugins.default.camera_calibration:Plugin"
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]
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}
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@ -152,18 +153,52 @@ class ConfigAPI(MicroscopeView):
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Accept: 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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"jpeg_quality": 75,
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"picamera_params": {
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"framerate": 24.0,
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"saturation": 0,
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"shutter_speed": 5000
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"id": "0e2c6fac5421429aac67c7903107bdd8",
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"name": "docuscope-2000",
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"fov": [4100, 3146],
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"camera_settings": {
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"image_resolution": [2592, 1944],
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"numpy_resolution": [1312, 976],
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"video_resolution": [832, 624],
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"jpeg_quality": 75,
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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": [0.92578125, 2.94921875],
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"awb_mode": "off",
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"exposure_mode": "off",
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"framerate": 24.0,
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"saturation": 0,
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"shutter_speed": 5378
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},
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},
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"stage_settings": {
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"backlash": {
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"x": 256,
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"y": 256,
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"z": 0
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}
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}
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"plugins": [
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"openflexure_microscope.plugins.default.autofocus:AutofocusPlugin",
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"openflexure_microscope.plugins.default.scan:ScanPlugin",
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"openflexure_microscope.plugins.default.camera_calibration:Plugin"
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]
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}
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:>header Accept: application/json
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:<json string id: Unique string identifier of the microscope.
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:<json string name: Friendly name for the microscope
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:<json array fov: Field of view (motor steps per full width and height of frame)
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:<json json camera_settings: - **image_resolution** *(array)*: Resolution of full image captures
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- **numpy_resolution** *(array)*: Resolution of full numpy array captures
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- **video_resolution** *(array)*: Resolution of video recordings, low res image captures, and the preview stream
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- **jpeg_quality** *(int)*: Quality in which to store JPEG capture data
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- **picamera_settings** *(json)*: Key-value pairs to apply directly to any attached PiCamera object
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:<json json stage_settings: - **backlash** *(json)*: x, y, and z backlash compensation, in motor steps
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:<json array plugins: Array of plugin paths to load. Requires reloading the microscope object after applying
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:<header Content-Type: application/json
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:status 200: capture created
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@ -6,9 +6,9 @@ import logging
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import pkg_resources
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import uuid
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from openflexure_stage import OpenFlexureStage
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from .stage.base import BaseStage
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from .camera.pi import StreamingCamera
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from .camera.base import BaseCamera
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from .plugins import PluginMount
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from .utilities import axes_to_array
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@ -28,8 +28,8 @@ class Microscope:
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automatically created if None.
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lock (:py:class:`openflexure_microscope.lock.CompositeLock`): Composite lock controlling thread access
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to multiple pieces of hardware.
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camera (:py:class:`openflexure_microscope.camera.pi.StreamingCamera`): Camera object
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stage (:py:class:`openflexure_stage.stage.OpenFlexureStage`): Stage object
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camera (:py:class:`openflexure_microscope.camera.base.BaseCamera`): Camera object
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stage (:py:class:`openflexure_microscope.stage.base.BaseStage`): Stage object
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task: (:py:class:`openflexure_microscope.task.TaskOrchestrator`): Threaded ask orchestrator for managing
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background tasks using microscope hardware
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plugin (:py:class:`openflexure_microscope.plugins.PluginMount`): Mounting point for all microscope plugins
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@ -76,7 +76,7 @@ class Microscope:
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self.stage.close()
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logging.info("Closed {}".format(self))
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def attach(self, camera: StreamingCamera, stage: OpenFlexureStage):
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def attach(self, camera: BaseCamera, stage: BaseStage):
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"""
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Retroactively attaches a camera and stage to the microscope object.
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@ -84,8 +84,8 @@ class Microscope:
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opened at a later time.
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Args:
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camera (:py:class:`openflexure_microscope.camera.pi.StreamingCamera`): camera object
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stage (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
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camera (:py:class:`openflexure_microscope.camera.base.BaseCamera`): camera object
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stage (:py:class:`openflexure_microscope.stage.base.BaseStage`): stage object
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"""
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settings_full = self.read_config()
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@ -94,7 +94,7 @@ class Microscope:
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# Maybe even attach dummy hardware at __init__, and replace with real hardware if it exists
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logging.debug("Attaching camera...")
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self.camera = camera #: :py:class:`openflexure_microscope.camera.pi.StreamingCamera`: Picamera object
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self.camera = camera #: :py:class:`openflexure_microscope.camera.base.BaseCamera`: Picamera object
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if not self.camera:
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logging.info("No camera attached.")
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else:
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@ -106,7 +106,7 @@ class Microscope:
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self.lock.locks.append(self.camera.lock)
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logging.debug("Attaching stage...")
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self.stage = stage #: :py:class:`openflexure_stage.stage.OpenFlexureStage`: OpenFlexure stage object
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self.stage = stage #: :py:class:`openflexure_microscope.stage.base.BaseStage`: OpenFlexure stage object
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if not self.stage:
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logging.info("No stage attached.")
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else:
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@ -1 +1,2 @@
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__all__ = ['AutofocusPlugin']
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from .plugin import AutofocusPlugin
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@ -89,28 +89,36 @@ class AutofocusPlugin(MicroscopePlugin):
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This autofocus method is very efficient, as it only passes the peak once.
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The sequence of moves it performs is:
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1. Move to the top of the range `dz/2` (can be disabled)
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2. Move down by `dz` while monitoring JPEG size to find the focus.
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3. Move back up to the `target_z` position, relative to the sharpest image.
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4. Measure the sharpness, and compare against the curve recorded in (2) to
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estimate how much further we need to go. Make this move, to reach our
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target position.
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1. Move to the top of the range `dz/2` (can be disabled)
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2. Move down by `dz` while monitoring JPEG size to find the focus.
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3. Move back up to the `target_z` position, relative to the sharpest image.
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4. Measure the sharpness, and compare against the curve recorded in (2) to \\
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estimate how much further we need to go. Make this move, to reach our \\
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target position.
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Moving back to the target position in two steps allows us to correct for
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backlash, by using the sharpness-vs-z curve as a rough encoder for Z.
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Parameters:
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dz: number of steps over which to scan (optional, default 2000)
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target_z: we aim to finish at this position, relative to focus. This may
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be useful if, for example, you want to acquire a stack of images in Z.
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It is optional, and the default value of 0 will finish at the focus.
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initial_move_up: (optional, default True) set this to `False` to move down
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from the starting position. Mostly useful if you're able to combine
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the initial move with something else, e.g. moving to the next scan point.
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mini_backlash: (optional, default 50) is a small extra move made in step
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3 to help counteract backlash. It should be small enough that you
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would always expect there to be greater backlash than this. Too small
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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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dz: number of steps over which to scan (optional, default 2000)
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target_z: we aim to finish at this position, relative to focus. This may
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be useful if, for example, you want to acquire a stack of images in Z.
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It is optional, and the default value of 0 will finish at the focus.
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initial_move_up: (optional, default True) set this to `False` to move down
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from the starting position. Mostly useful if you're able to combine
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the initial move with something else, e.g. moving to the next scan point.
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mini_backlash: (optional, default 50) is a small extra move made in step
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3 to help counteract backlash. It should be small enough that you
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would always expect there to be greater backlash than this. Too small
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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 self.monitor_sharpness() as m, self.microscope.camera.lock:
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# Ensure the MJPEG stream has started
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@ -1 +1,2 @@
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__all__ = ['Plugin']
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from .plugin import Plugin
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@ -1 +1,2 @@
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__all__ = ['ScanPlugin']
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from .plugin import ScanPlugin
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