Restructured entire API into blueprints
This commit is contained in:
Joel Collins
parent
aede078eb9
commit
c995a15fdc
13 changed files with 739 additions and 1024 deletions
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@ -1,187 +1,118 @@
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#!/usr/bin/env python
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#!/usr/bin/env python
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"""
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TODO: Implement API route to cleanly shut down server
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TODO: Implement plugin API routes somehow
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"""
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from pprint import pprint
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import numpy as np
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from importlib import import_module
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from importlib import import_module
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import time
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import time
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import datetime
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import datetime
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import os
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from flask import (
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from flask import (
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Flask, render_template, Response,
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Flask, render_template, Response, url_for,
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redirect, request, jsonify, send_file)
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redirect, request, jsonify, send_file, abort,
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make_response)
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import numpy as np
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from flask.views import MethodView
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from werkzeug.exceptions import default_exceptions
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from openflexure_microscope.api.utilities import parse_payload, get_from_payload, gen, get_bool, list_routes
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from openflexure_microscope import Microscope, config
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from openflexure_microscope.camera.pi import StreamingCamera
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from openflexure_microscope.camera.pi import StreamingCamera
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from openflexure_stage import OpenFlexureStage
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import atexit
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import logging, sys
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logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
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# Create a dummy microscope object, with no hardware attachments
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api_microscope = Microscope(None, None)
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logging.debug("Created an empty microscope in global.")
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# Generate API URI based on version from filename
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def uri(suffix, api_version, base=None):
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if not base:
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base = "/api/{}".format(api_version)
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uri = base + suffix
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logging.debug("Created app route: {}".format(uri))
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return uri
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# Create flask app
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app = Flask(__name__)
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app = Flask(__name__)
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cam = StreamingCamera()
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app.url_map.strict_slashes = False
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def parse_payload(request):
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# Make errors more API friendly
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"""Convert request to JSON. Will eventually handle error-checking."""
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# TODO: Handle invalid JSON payloads
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def _handle_http_exception(e):
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state = request.get_json()
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return make_response(
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return state
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jsonify({
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'status_code': e.code,
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'error': e.name,
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'details': e.description
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}),
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e.code)
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for code in default_exceptions:
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app.errorhandler(code)(_handle_http_exception)
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def gen(camera):
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# After app starts, but before first request, attach hardware to global microscope
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"""Video streaming generator function."""
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@app.before_first_request
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while True:
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def attach_microscope():
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# the obtained frame is a jpeg
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# Create the microscope object globally (common to all spawned server threads)
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frame = camera.get_frame()
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global api_microscope
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logging.debug("First request made. Populating microscope with hardware...")
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openflexurerc = config.load_config() # Load default user config
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yield (b'--frame\r\n'
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api_microscope.attach(
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b'Content-Type: image/jpeg\r\n\r\n' + frame + b'\r\n')
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StreamingCamera(config=openflexurerc),
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OpenFlexureStage("/dev/ttyUSB0")
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)
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logging.debug("Microscope successfully attached!")
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##### WEBAPP ROUTES ######
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@app.route('/')
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@app.route('/')
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def index():
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def index():
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"""Video streaming home page."""
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cam.start_worker() # Start the stream
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return render_template('index.html')
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@app.route('/stream')
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def stream():
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"""Video streaming route. Put this in the src attribute of an img tag."""
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return Response(
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gen(cam),
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mimetype='multipart/x-mixed-replace; boundary=frame')
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# TODO: Be able to change the image resolution with an option
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@app.route('/capture/', methods=['GET', 'POST', 'PUT'])
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def capture():
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"""
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"""
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POST/PUT: Capture a single image.
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API demo app
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GET: Return capture status, or download latest capture.
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"""
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"""
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if request.method == 'POST' or request.method == 'PUT':
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return render_template(
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state = parse_payload(request)
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'index_v1.html'
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print(state)
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)
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# Handle filename argument
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##### API ROUTES ######
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if 'filename' in state:
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from openflexure_microscope.api.v1 import blueprints
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filename = state['filename']
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else:
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filename = None
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if 'write_to_file' in state:
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# Base routes
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write_to_file = bool(state['write_to_file'])
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base_blueprint = blueprints.base.construct_blueprint(api_microscope)
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else:
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app.register_blueprint(base_blueprint, url_prefix=uri('', 'v1'))
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write_to_file = False
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if 'use_video_port' in state:
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# Stage routes
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use_video_port = bool(state['use_video_port'])
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stage_blueprint = blueprints.stage.construct_blueprint(api_microscope)
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else:
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app.register_blueprint(stage_blueprint, url_prefix=uri('/stage', 'v1'))
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use_video_port = False
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if 'resize' in state:
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# Camera routes
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resize_h = int(state['resize'])
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camera_blueprint = blueprints.camera.construct_blueprint(api_microscope)
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resize_w = int(resize_h*(4/3))
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app.register_blueprint(camera_blueprint, url_prefix=uri('/camera', 'v1'))
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resize = (resize_w, resize_h)
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else:
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resize = None
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response = cam.capture(
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# List all routes
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write_to_file=write_to_file,
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list_routes(app)
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use_video_port=use_video_port,
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filename=filename,
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resize=resize)
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return str(response) + "\n"
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# Automatically clean up microscope at exit
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def cleanup():
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global api_microscope
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api_microscope.close()
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else: # If GET request
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atexit.register(cleanup)
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download = request.args.get('download')
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if __name__ == "__main__":
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app.run(host='0.0.0.0', port="5000", threaded=True, debug=True, use_reloader=False)
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state = cam.state
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if ((
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download == 'true' or
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download == 'True' or
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download == '1') and
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cam.image is not None):
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return send_file(cam.image.data, mimetype='image/jpeg')
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else:
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return jsonify(state)
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@app.route('/record/', methods=['GET', 'POST', 'PUT'])
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def record():
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"""
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POST/PUT: Start or stop a video recording.
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GET: Return recording status, or download latest recording
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"""
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if request.method == 'POST' or request.method == 'PUT':
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state = request.get_json()
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print(state)
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# Handle filename argument
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if 'filename' in state:
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filename = state['filename']
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else:
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filename = None
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# Handle status argument
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if 'status' in state:
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status = bool(state['status'])
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# synchronise the arduino_time
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if status is True:
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response = cam.start_recording(filename=filename)
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return str(response)
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elif status is False:
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response = cam.stop_recording()
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return str(response)
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else:
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download = request.args.get('download')
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state = cam.state
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if ((
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download == 'true' or
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download == 'True' or
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download == '1') and
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cam.state['recent_video'] is not None):
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return send_file(
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cam.state['recent_video'],
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mimetype='video/H264',
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as_attachment=True)
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else:
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return jsonify(state)
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@app.route('/preview/', methods=['GET', 'POST', 'PUT'])
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def preview():
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"""
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POST/PUT: Start or stop the direct-to-GPU camera preview on the Pi.
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GET: Return preview status
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"""
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if request.method == 'POST' or request.method == 'PUT':
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state = request.get_json()
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print(state)
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if 'status' in state:
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status = bool(state['status'])
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if status is False:
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response = cam.stop_preview()
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else:
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response = cam.start_preview()
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return str(response)
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else:
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# Get args passed via URL (not useful here. Just for reference.)
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state = cam.state
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return jsonify(state)
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if __name__ == '__main__':
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app.run(host='0.0.0.0', threaded=True, debug=True, use_reloader=False)
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@ -1,3 +1,5 @@
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import pprint
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def parse_payload(request):
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def parse_payload(request):
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"""Convert request to JSON. Will eventually handle error-checking."""
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"""Convert request to JSON. Will eventually handle error-checking."""
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# TODO: Handle invalid JSON payloads
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# TODO: Handle invalid JSON payloads
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@ -32,3 +34,8 @@ def get_bool(get_arg):
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return True
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return True
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else:
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else:
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return False
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return False
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def list_routes(app):
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"""Print available functions."""
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pprint.pprint(list(map(lambda x: repr(x), app.url_map.iter_rules())))
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@ -1,172 +0,0 @@
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#!/usr/bin/env python
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from pprint import pprint
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from importlib import import_module
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import time
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import datetime
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from flask import (
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Flask, render_template, Response,
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redirect, request, jsonify, send_file)
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import numpy as np
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from openflexure_microscope.api.utilities import parse_payload, gen
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from openflexure_microscope.camera.pi import StreamingCamera
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app = Flask(__name__)
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cam = StreamingCamera()
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@app.route('/')
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def index():
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"""Video streaming home page."""
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cam.start_worker() # Start the stream
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return render_template('index_v0.html')
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@app.route('/stream')
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def stream():
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"""Video streaming route. Put this in the src attribute of an img tag."""
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return Response(
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gen(cam),
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mimetype='multipart/x-mixed-replace; boundary=frame')
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# TODO: Be able to change the image resolution with an option
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@app.route('/capture/', methods=['GET', 'POST', 'PUT'])
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def capture():
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"""
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POST/PUT: Capture a single image.
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GET: Return capture status, or download latest capture.
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"""
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if request.method == 'POST' or request.method == 'PUT':
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state = parse_payload(request)
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print(state)
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# Handle filename argument
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if 'filename' in state:
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filename = state['filename']
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else:
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filename = None
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if 'write_to_file' in state:
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write_to_file = bool(state['write_to_file'])
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else:
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write_to_file = False
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if 'use_video_port' in state:
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use_video_port = bool(state['use_video_port'])
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else:
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use_video_port = False
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if 'resize' in state:
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resize_h = int(state['resize'])
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resize_w = int(resize_h*(4/3))
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resize = (resize_w, resize_h)
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else:
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resize = None
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response = cam.capture(
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write_to_file=write_to_file,
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use_video_port=use_video_port,
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filename=filename,
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resize=resize)
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return str(response) + "\n"
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else: # If GET request
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download = request.args.get('download')
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state = cam.state
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if ((
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download == 'true' or
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download == 'True' or
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download == '1') and
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cam.image is not None):
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return send_file(cam.image.data, mimetype='image/jpeg')
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else:
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return jsonify(state)
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@app.route('/record/', methods=['GET', 'POST', 'PUT'])
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def record():
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"""
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POST/PUT: Start or stop a video recording.
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GET: Return recording status, or download latest recording
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"""
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if request.method == 'POST' or request.method == 'PUT':
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state = request.get_json()
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print(state)
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# Handle filename argument
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if 'filename' in state:
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filename = state['filename']
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else:
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filename = None
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# Handle status argument
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if 'status' in state:
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status = bool(state['status'])
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# synchronise the arduino_time
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if status is True:
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response = cam.start_recording(filename=filename)
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return str(response)
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elif status is False:
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response = cam.stop_recording()
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return str(response)
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else:
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download = request.args.get('download')
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state = cam.state
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if ((
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download == 'true' or
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download == 'True' or
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download == '1') and
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cam.state['recent_video'] is not None):
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return send_file(
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cam.state['recent_video'],
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mimetype='video/H264',
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as_attachment=True)
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else:
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return jsonify(state)
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@app.route('/preview/', methods=['GET', 'POST', 'PUT'])
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def preview():
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"""
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POST/PUT: Start or stop the direct-to-GPU camera preview on the Pi.
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GET: Return preview status
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"""
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if request.method == 'POST' or request.method == 'PUT':
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state = request.get_json()
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print(state)
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if 'status' in state:
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||||||
status = bool(state['status'])
|
|
||||||
|
|
||||||
if status is False:
|
|
||||||
response = cam.stop_preview()
|
|
||||||
else:
|
|
||||||
response = cam.start_preview()
|
|
||||||
|
|
||||||
return str(response)
|
|
||||||
|
|
||||||
else:
|
|
||||||
# Get args passed via URL (not useful here. Just for reference.)
|
|
||||||
state = cam.state
|
|
||||||
return jsonify(state)
|
|
||||||
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
app.run(host='0.0.0.0', threaded=True, debug=True, use_reloader=False)
|
|
||||||
|
|
@ -1,695 +0,0 @@
|
||||||
#!/usr/bin/env python
|
|
||||||
"""
|
|
||||||
TODO: Add proper docstrings
|
|
||||||
TODO: Implement API route to cleanly shut down server
|
|
||||||
TODO: Implement microscope function API routes (autofocus etc)
|
|
||||||
"""
|
|
||||||
|
|
||||||
import numpy as np
|
|
||||||
from importlib import import_module
|
|
||||||
import time
|
|
||||||
import datetime
|
|
||||||
import os
|
|
||||||
|
|
||||||
from flask import (
|
|
||||||
Flask, render_template, Response, url_for,
|
|
||||||
redirect, request, jsonify, send_file, abort,
|
|
||||||
make_response)
|
|
||||||
|
|
||||||
from flask.views import MethodView
|
|
||||||
from werkzeug.exceptions import default_exceptions
|
|
||||||
|
|
||||||
from openflexure_microscope.api.utilities import parse_payload, get_from_payload, gen, get_bool
|
|
||||||
|
|
||||||
from openflexure_microscope import Microscope, config
|
|
||||||
from openflexure_microscope.camera.pi import StreamingCamera
|
|
||||||
from openflexure_stage import OpenFlexureStage
|
|
||||||
|
|
||||||
import atexit
|
|
||||||
import logging, sys
|
|
||||||
|
|
||||||
logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
|
|
||||||
|
|
||||||
# Create a dummy microscope object, with no hardware attachments
|
|
||||||
api_microscope = Microscope(None, None)
|
|
||||||
logging.debug("Created an empty microscope in global.")
|
|
||||||
|
|
||||||
# Generate API URI based on version from filename
|
|
||||||
def uri(suffix, base=None):
|
|
||||||
if not base:
|
|
||||||
api_ver = os.path.splitext(os.path.basename(__file__))[0]
|
|
||||||
base = "/api/{}".format(api_ver)
|
|
||||||
uri = base + suffix
|
|
||||||
logging.debug("Created app route: {}".format(uri))
|
|
||||||
return uri
|
|
||||||
|
|
||||||
# Create flask app
|
|
||||||
app = Flask(__name__)
|
|
||||||
app.url_map.strict_slashes = False
|
|
||||||
|
|
||||||
|
|
||||||
# Make errors more API friendly
|
|
||||||
|
|
||||||
def _handle_http_exception(e):
|
|
||||||
return make_response(
|
|
||||||
jsonify({
|
|
||||||
'status_code': e.code,
|
|
||||||
'error': e.name,
|
|
||||||
'details': e.description
|
|
||||||
}),
|
|
||||||
e.code)
|
|
||||||
|
|
||||||
for code in default_exceptions:
|
|
||||||
app.errorhandler(code)(_handle_http_exception)
|
|
||||||
|
|
||||||
|
|
||||||
# After app starts, but before first request, attach hardware to global microscope
|
|
||||||
@app.before_first_request
|
|
||||||
def attach_microscope():
|
|
||||||
# Create the microscope object globally (common to all spawned server threads)
|
|
||||||
global api_microscope
|
|
||||||
logging.debug("First request made. Populating microscope with hardware...")
|
|
||||||
openflexurerc = config.load_config() # Load default user config
|
|
||||||
|
|
||||||
api_microscope.attach(
|
|
||||||
StreamingCamera(config=openflexurerc),
|
|
||||||
OpenFlexureStage("/dev/ttyUSB0")
|
|
||||||
)
|
|
||||||
|
|
||||||
logging.debug("Microscope successfully attached!")
|
|
||||||
|
|
||||||
|
|
||||||
##### WEBAPP ROUTES ######
|
|
||||||
|
|
||||||
@app.route('/')
|
|
||||||
def index():
|
|
||||||
"""
|
|
||||||
API demo app
|
|
||||||
"""
|
|
||||||
return render_template(
|
|
||||||
'index_v1.html'
|
|
||||||
)
|
|
||||||
|
|
||||||
##### API ROUTES ######
|
|
||||||
|
|
||||||
|
|
||||||
# Basic microscope view
|
|
||||||
|
|
||||||
class MicroscopeView(MethodView):
|
|
||||||
|
|
||||||
def __init__(self, microscope, **kwargs):
|
|
||||||
"""
|
|
||||||
Create a generic MethodView with a globally available
|
|
||||||
microscope object passed as an argument.
|
|
||||||
"""
|
|
||||||
self.microscope = microscope
|
|
||||||
|
|
||||||
MethodView.__init__(self, **kwargs)
|
|
||||||
|
|
||||||
|
|
||||||
class StreamAPI(MicroscopeView):
|
|
||||||
|
|
||||||
def get(self):
|
|
||||||
"""
|
|
||||||
Real-time MJPEG stream from the microscope camera
|
|
||||||
|
|
||||||
.. :quickref: State; Camera stream
|
|
||||||
|
|
||||||
:>header Accept: image/jpeg
|
|
||||||
:>header Content-Type: image/jpeg
|
|
||||||
:status 200: stream active
|
|
||||||
"""
|
|
||||||
# Restart stream worker thread
|
|
||||||
self.microscope.camera.start_worker()
|
|
||||||
|
|
||||||
return Response(
|
|
||||||
gen(self.microscope.camera),
|
|
||||||
mimetype='multipart/x-mixed-replace; boundary=frame')
|
|
||||||
|
|
||||||
app.add_url_rule(
|
|
||||||
uri('/stream/'),
|
|
||||||
view_func=StreamAPI.as_view('stream', microscope=api_microscope))
|
|
||||||
|
|
||||||
|
|
||||||
class StateAPI(MicroscopeView):
|
|
||||||
|
|
||||||
def get(self):
|
|
||||||
"""
|
|
||||||
JSON representation of the microscope object.
|
|
||||||
|
|
||||||
.. :quickref: State; Microscope state
|
|
||||||
|
|
||||||
**Example request**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
GET /state/ HTTP/1.1
|
|
||||||
Accept: application/json
|
|
||||||
|
|
||||||
**Example response**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
HTTP/1.1 200 OK
|
|
||||||
Vary: Accept
|
|
||||||
Content-Type: application/json
|
|
||||||
|
|
||||||
{
|
|
||||||
"camera": {
|
|
||||||
"preview_active": false,
|
|
||||||
"record_active": false,
|
|
||||||
"stream_active": true
|
|
||||||
},
|
|
||||||
"plugin": {},
|
|
||||||
"stage": {
|
|
||||||
"backlash": {
|
|
||||||
"x": 128,
|
|
||||||
"y": 128,
|
|
||||||
"z": 128
|
|
||||||
},
|
|
||||||
"position": {
|
|
||||||
"x": -8080,
|
|
||||||
"y": 5665,
|
|
||||||
"z": -12600
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
:>header Accept: application/json
|
|
||||||
:>header Content-Type: application/json
|
|
||||||
:status 200: state available
|
|
||||||
"""
|
|
||||||
return jsonify(self.microscope.state)
|
|
||||||
|
|
||||||
app.add_url_rule(
|
|
||||||
uri('/state/'),
|
|
||||||
view_func=StateAPI.as_view('state', microscope=api_microscope))
|
|
||||||
|
|
||||||
|
|
||||||
class PositionAPI(MicroscopeView):
|
|
||||||
|
|
||||||
def get(self):
|
|
||||||
"""
|
|
||||||
Return current x, y and z positions of the stage.
|
|
||||||
|
|
||||||
.. :quickref: Position; Get current position
|
|
||||||
|
|
||||||
**Example request**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
GET /stage/position/ HTTP/1.1
|
|
||||||
Accept: application/json
|
|
||||||
|
|
||||||
**Example response**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
HTTP/1.1 200 OK
|
|
||||||
Vary: Accept
|
|
||||||
Content-Type: application/json
|
|
||||||
|
|
||||||
{
|
|
||||||
"x": 0,
|
|
||||||
"y": 0,
|
|
||||||
"z": 0
|
|
||||||
}
|
|
||||||
|
|
||||||
:>json int x: x steps
|
|
||||||
:>json int y: y steps
|
|
||||||
:>json int z: z steps
|
|
||||||
"""
|
|
||||||
return jsonify(self.microscope.state['stage']['position'])
|
|
||||||
|
|
||||||
def post(self):
|
|
||||||
"""
|
|
||||||
Set x, y and z positions of the stage.
|
|
||||||
|
|
||||||
.. :quickref: Position; Update current position
|
|
||||||
|
|
||||||
:reqheader Accept: application/json
|
|
||||||
:<json boolean absolute: (true) move to absolute position, (false) move by relative amount
|
|
||||||
:<json boolean force: allow moving by more than programmed limit
|
|
||||||
:<json int x: x steps
|
|
||||||
:<json int y: y steps
|
|
||||||
:<json int z: z steps
|
|
||||||
|
|
||||||
"""
|
|
||||||
# Get payload
|
|
||||||
state = parse_payload(request)
|
|
||||||
logging.debug(state)
|
|
||||||
|
|
||||||
# Construct position array
|
|
||||||
position = [0, 0, 0]
|
|
||||||
|
|
||||||
# Handle absolute positioning
|
|
||||||
if 'absolute' in state and state['absolute'] is True:
|
|
||||||
# Get coordinates from payload
|
|
||||||
for axis, key in enumerate(['x', 'y', 'z']):
|
|
||||||
if key in state:
|
|
||||||
position[axis] = int(state[key]-self.microscope.stage.position[axis])
|
|
||||||
|
|
||||||
else:
|
|
||||||
# Get coordinates from payload
|
|
||||||
for axis, key in enumerate(['x', 'y', 'z']):
|
|
||||||
if key in state:
|
|
||||||
position[axis] = int(state[key])
|
|
||||||
|
|
||||||
logging.debug(position)
|
|
||||||
|
|
||||||
# Safeguard to prevent moving to an absolute position beyond a fixed limit
|
|
||||||
if 'force' not in state or state['force'] is False: # Allow for override
|
|
||||||
# TODO: Make travel_limit a property of the stage or microscope
|
|
||||||
# TODO: Make travel_limit a 3-axis list
|
|
||||||
travel_limit = 20000
|
|
||||||
for axis, pos in enumerate(position):
|
|
||||||
if abs(pos) > travel_limit:
|
|
||||||
# Respond with 400 Bad Request
|
|
||||||
response = {'error': 'Cannot move to absolute position beyond the safeguard limit.'}
|
|
||||||
return jsonify(response), 400
|
|
||||||
|
|
||||||
self.microscope.stage.move_rel(position)
|
|
||||||
|
|
||||||
return jsonify(self.microscope.state['stage']['position'])
|
|
||||||
|
|
||||||
app.add_url_rule(
|
|
||||||
uri('/stage/position/'),
|
|
||||||
view_func=PositionAPI.as_view('position', microscope=api_microscope))
|
|
||||||
|
|
||||||
|
|
||||||
class StageParamsAPI(MicroscopeView):
|
|
||||||
|
|
||||||
def get(self):
|
|
||||||
"""
|
|
||||||
Return current parameters of the stage.
|
|
||||||
|
|
||||||
.. :quickref: Stage params; Get current stage parameters
|
|
||||||
|
|
||||||
**Example request**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
GET /stage/params HTTP/1.1
|
|
||||||
Accept: application/json
|
|
||||||
|
|
||||||
**Example response**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
HTTP/1.1 200 OK
|
|
||||||
Vary: Accept
|
|
||||||
Content-Type: application/json
|
|
||||||
|
|
||||||
{
|
|
||||||
"backlash": {
|
|
||||||
"x": 0,
|
|
||||||
"y": 0,
|
|
||||||
"z": 128
|
|
||||||
},
|
|
||||||
}
|
|
||||||
|
|
||||||
"""
|
|
||||||
|
|
||||||
return jsonify(self.microscope.state['stage'])
|
|
||||||
|
|
||||||
def post(self):
|
|
||||||
"""
|
|
||||||
Set parameters of the stage.
|
|
||||||
|
|
||||||
.. :quickref: Stage params; Set current stage parameters
|
|
||||||
|
|
||||||
:reqheader Accept: application/json
|
|
||||||
:<json json backlash: - **x** *(int)*: x-axis backlash in steps
|
|
||||||
- **y** *(int)*: y-axis backlash in steps
|
|
||||||
- **z** *(int)*: x-axis backlash in steps
|
|
||||||
|
|
||||||
"""
|
|
||||||
# Get payload
|
|
||||||
state = parse_payload(request)
|
|
||||||
logging.debug(state)
|
|
||||||
|
|
||||||
# BACKLASH
|
|
||||||
if 'backlash' in state:
|
|
||||||
# Construct backlash array
|
|
||||||
backlash = [0, 0, 0]
|
|
||||||
|
|
||||||
# Get backlash coordinates from payload
|
|
||||||
for axis, key in enumerate(['x', 'y', 'z']):
|
|
||||||
if key in state['backlash']:
|
|
||||||
backlash[axis] = int(state['backlash'][key])
|
|
||||||
|
|
||||||
# Apply backlash
|
|
||||||
self.microscope.stage.backlash = backlash
|
|
||||||
|
|
||||||
return jsonify(self.microscope.state['stage'])
|
|
||||||
|
|
||||||
app.add_url_rule(
|
|
||||||
uri('/stage/params/'),
|
|
||||||
view_func=StageParamsAPI.as_view('stage_params', microscope=api_microscope))
|
|
||||||
|
|
||||||
|
|
||||||
class CaptureListAPI(MicroscopeView):
|
|
||||||
|
|
||||||
def get(self):
|
|
||||||
"""
|
|
||||||
Get list of image captures.
|
|
||||||
|
|
||||||
.. :quickref: Capture collection; Get collection of captures
|
|
||||||
|
|
||||||
:>header Accept: application/json
|
|
||||||
:query include_unavailable: return json representations of captures that have been completely deleted
|
|
||||||
|
|
||||||
:>jsonarr boolean available: availability of capture data
|
|
||||||
:>jsonarr string filename: filename of capture
|
|
||||||
:>jsonarr string id: unique id of the capture object
|
|
||||||
:>jsonarr boolean keep_on_disk: keep the capture file on microscope after closing
|
|
||||||
:>jsonarr boolean locked: file locked for modifications (mostly used for video recording)
|
|
||||||
:>jsonarr string path: path on pi storage to the capture file, if available
|
|
||||||
:>jsonarr boolean stream: capture stored in-memory as a BytesIO stream
|
|
||||||
:>jsonarr json uri: - **download** *(string)*: api uri to the capture file download
|
|
||||||
- **metadata** *(string)*: api uri to the capture json representation
|
|
||||||
|
|
||||||
:>header Content-Type: application/json
|
|
||||||
:status 200: capture found
|
|
||||||
:status 404: no capture found with that id
|
|
||||||
"""
|
|
||||||
include_unavailable = get_bool(request.args.get('include_unavailable'))
|
|
||||||
|
|
||||||
if include_unavailable:
|
|
||||||
captures = [image.metadata for image in self.microscope.camera.images]
|
|
||||||
else:
|
|
||||||
captures = [image.metadata for image in self.microscope.camera.images if image.metadata['available']]
|
|
||||||
|
|
||||||
return jsonify(captures)
|
|
||||||
|
|
||||||
def delete(self):
|
|
||||||
"""
|
|
||||||
Delete all captures (not yet implemented)
|
|
||||||
|
|
||||||
.. :quickref: Capture collection; Delete all captures
|
|
||||||
"""
|
|
||||||
for image in self.microscope.camera.images:
|
|
||||||
image.delete()
|
|
||||||
|
|
||||||
captures = [image.metadata for image in self.microscope.camera.images]
|
|
||||||
|
|
||||||
return jsonify(captures)
|
|
||||||
|
|
||||||
def post(self):
|
|
||||||
"""
|
|
||||||
Create a new image capture.
|
|
||||||
|
|
||||||
.. :quickref: Capture collection; New capture
|
|
||||||
|
|
||||||
**Example request**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
POST /camera/capture HTTP/1.1
|
|
||||||
Accept: application/json
|
|
||||||
|
|
||||||
{
|
|
||||||
"filename": "myfirstcapture",
|
|
||||||
"keep_on_disk": true,
|
|
||||||
"use_video_port": true,
|
|
||||||
"size": {
|
|
||||||
"x": 640,
|
|
||||||
"y": 480
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
:>header Accept: application/json
|
|
||||||
|
|
||||||
:<json string filename: filename of stored capture
|
|
||||||
:<json boolean keep_on_disk: keep the capture file on microscope after closing
|
|
||||||
:<json boolean use_video_port: capture still image from the video port
|
|
||||||
:<json json size: - **x** *(int)*: x-axis resize
|
|
||||||
- **y** *(int)*: y-axis resize
|
|
||||||
|
|
||||||
:>json boolean available: availability of capture data
|
|
||||||
:>json string filename: filename of capture
|
|
||||||
:>json string id: unique id of the capture object
|
|
||||||
:>json boolean keep_on_disk: keep the capture file on microscope after closing
|
|
||||||
:>json boolean locked: file locked for modifications (mostly used for video recording)
|
|
||||||
:>json string path: path on pi storage to the capture file, if available
|
|
||||||
:>json boolean stream: capture stored in-memory as a BytesIO stream
|
|
||||||
:>json json uri: - **download** *(string)*: api uri to the capture file download
|
|
||||||
- **metadata** *(string)*: api uri to the capture json representation
|
|
||||||
|
|
||||||
:<header Content-Type: application/json
|
|
||||||
:status 200: capture created
|
|
||||||
"""
|
|
||||||
state = parse_payload(request)
|
|
||||||
logging.info(state)
|
|
||||||
|
|
||||||
filename = get_from_payload(state, 'filename', default=None)
|
|
||||||
keep_on_disk = bool(get_from_payload(state, 'keep_on_disk', default=True))
|
|
||||||
use_video_port = bool(get_from_payload(state, 'use_video_port', default=False))
|
|
||||||
|
|
||||||
resize = get_from_payload(state, 'size', default=None)
|
|
||||||
if resize:
|
|
||||||
if ('width' in resize) and ('height' in resize):
|
|
||||||
resize = (int(resize['width']), int(resize['height'])) # Convert dict to tuple
|
|
||||||
else:
|
|
||||||
abort(400)
|
|
||||||
|
|
||||||
capture_obj = self.microscope.camera.capture(
|
|
||||||
write_to_file=True, # Always write data to disk when using API
|
|
||||||
keep_on_disk=keep_on_disk,
|
|
||||||
use_video_port=use_video_port,
|
|
||||||
filename=filename,
|
|
||||||
resize=resize)
|
|
||||||
|
|
||||||
return jsonify(capture_obj.metadata)
|
|
||||||
|
|
||||||
app.add_url_rule(
|
|
||||||
uri('/camera/capture/'),
|
|
||||||
view_func=CaptureListAPI.as_view('capture_list', microscope=api_microscope))
|
|
||||||
|
|
||||||
|
|
||||||
class CaptureAPI(MicroscopeView):
|
|
||||||
|
|
||||||
def get(self, capture_id):
|
|
||||||
"""
|
|
||||||
Get JSON representation of a capture
|
|
||||||
|
|
||||||
.. :quickref: Capture; Get capture
|
|
||||||
|
|
||||||
**Example request**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/ HTTP/1.1
|
|
||||||
Accept: application/json
|
|
||||||
|
|
||||||
**Example response**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
HTTP/1.1 200 OK
|
|
||||||
Vary: Accept
|
|
||||||
Content-Type: application/json
|
|
||||||
|
|
||||||
{
|
|
||||||
"available": true,
|
|
||||||
"filename": "2018-11-16_10-21-53.jpeg",
|
|
||||||
"id": "d0b2067abbb946f19351e075c5e7cd5b",
|
|
||||||
"keep_on_disk": false,
|
|
||||||
"locked": false,
|
|
||||||
"path": "capture/2018-11-16_10-21-53.jpeg",
|
|
||||||
"stream": false,
|
|
||||||
"uri": {
|
|
||||||
"download": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/download",
|
|
||||||
"metadata": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/"
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
:>json boolean available: availability of capture data
|
|
||||||
:>json string filename: filename of capture
|
|
||||||
:>json string id: unique id of the capture object
|
|
||||||
:>json boolean keep_on_disk: keep the capture file on microscope after closing
|
|
||||||
:>json boolean locked: file locked for modifications (mostly used for video recording)
|
|
||||||
:>json string path: path on pi storage to the capture file, if available
|
|
||||||
:>json boolean stream: capture stored in-memory as a BytesIO stream
|
|
||||||
:>json json uri: - **download** *(string)*: api uri to the capture file download
|
|
||||||
- **metadata** *(string)*: api uri to the capture json representation
|
|
||||||
|
|
||||||
"""
|
|
||||||
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
||||||
|
|
||||||
if not capture_obj:
|
|
||||||
return abort(404) # 404 Not Found
|
|
||||||
|
|
||||||
# Get capture metadata
|
|
||||||
capture_metadata = capture_obj.metadata
|
|
||||||
|
|
||||||
# TODO: Tidy up adding URI to metadata
|
|
||||||
# Add API routes to returned metadata
|
|
||||||
uri_dict = {
|
|
||||||
'uri': {'metadata': uri('/capture/{}/'.format(capture_id))}
|
|
||||||
}
|
|
||||||
|
|
||||||
# If available, also add download link
|
|
||||||
if capture_metadata['available']:
|
|
||||||
uri_dict['uri']['download'] = uri('/capture/{}/download/{}'.format(capture_obj.id, capture_obj.filename))
|
|
||||||
|
|
||||||
capture_metadata.update(uri_dict)
|
|
||||||
|
|
||||||
return jsonify(capture_metadata)
|
|
||||||
|
|
||||||
def delete(self, capture_id):
|
|
||||||
"""
|
|
||||||
Delete all capture data from the Pi, even if `keep_on_disk=true;`.
|
|
||||||
|
|
||||||
.. :quickref: Capture; Delete capture.
|
|
||||||
"""
|
|
||||||
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
||||||
|
|
||||||
if not capture_obj:
|
|
||||||
return abort(404) # 404 Not Found
|
|
||||||
|
|
||||||
capture_obj.delete()
|
|
||||||
|
|
||||||
return jsonify({"return": capture_id})
|
|
||||||
|
|
||||||
def put(self, capture_id):
|
|
||||||
"""
|
|
||||||
Modify the metadata of a capture (not yet implemented)
|
|
||||||
|
|
||||||
.. :quickref: Capture; Update capture metadata
|
|
||||||
"""
|
|
||||||
return jsonify({"return": capture_id})
|
|
||||||
|
|
||||||
app.add_url_rule(
|
|
||||||
uri('/camera/capture/<capture_id>/'),
|
|
||||||
view_func=CaptureAPI.as_view('capture', microscope=api_microscope))
|
|
||||||
|
|
||||||
|
|
||||||
class CaptureDownloadRedirectAPI(MicroscopeView):
|
|
||||||
def get(self, capture_id):
|
|
||||||
"""
|
|
||||||
Redirect to download the capture under it's currently set filename.
|
|
||||||
I.e., `/(capture_id)/download` will
|
|
||||||
redirect to `/(capture_id)/download/(filename)`.
|
|
||||||
|
|
||||||
Note: This route may be deprecated in the future. Where at all
|
|
||||||
possible, please include a filename to download as.
|
|
||||||
|
|
||||||
.. :quickref: Capture; Redirect to download
|
|
||||||
"""
|
|
||||||
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
||||||
|
|
||||||
if not capture_obj or not capture_obj.metadata['available']:
|
|
||||||
return abort(404) # 404 Not Found
|
|
||||||
|
|
||||||
as_attachment = get_bool(request.args.get('as_attachment'))
|
|
||||||
thumbnail = get_bool(request.args.get('thumbnail'))
|
|
||||||
|
|
||||||
return redirect(url_for('capture_download', capture_id=capture_id, filename=capture_obj.filename, as_attachment=as_attachment, thumbnail=thumbnail), code=307)
|
|
||||||
|
|
||||||
# Route for shortcut where no filename is specified
|
|
||||||
app.add_url_rule(
|
|
||||||
uri('/camera/capture/<capture_id>/download'),
|
|
||||||
view_func=CaptureDownloadRedirectAPI.as_view('capture_download_redirect', microscope=api_microscope))
|
|
||||||
|
|
||||||
|
|
||||||
class CaptureDownloadAPI(MicroscopeView):
|
|
||||||
def get(self, capture_id, filename):
|
|
||||||
"""
|
|
||||||
Return image data for a capture.
|
|
||||||
|
|
||||||
Return capture data as an image file with the requested filename.
|
|
||||||
I.e., `/(capture_id)/download/foo.jpeg` will download the image as
|
|
||||||
`foo.jpeg`, regardless of the capture's initially set filename.
|
|
||||||
|
|
||||||
.. :quickref: Capture; Download capture file
|
|
||||||
|
|
||||||
**Example request**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/download/2018-11-20_16-04-17.jpeg HTTP/1.1
|
|
||||||
Accept: image/jpeg
|
|
||||||
|
|
||||||
:>header Accept: image/jpeg
|
|
||||||
:query thumbnail: return an image thumbnail e.g. ?thumbnail=true
|
|
||||||
:query as_attachment: return the image as an attachment download e.g. ?as_attachment=true
|
|
||||||
|
|
||||||
:>header Content-Type: image/jpeg
|
|
||||||
:status 200: capture data found
|
|
||||||
:status 404: no capture found with that id
|
|
||||||
"""
|
|
||||||
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
||||||
|
|
||||||
if not capture_obj or not capture_obj.metadata['available']:
|
|
||||||
return abort(404) # 404 Not Found
|
|
||||||
|
|
||||||
as_attachment = get_bool(request.args.get('as_attachment'))
|
|
||||||
thumbnail = get_bool(request.args.get('thumbnail'))
|
|
||||||
|
|
||||||
# If no filename is specified, redirect to the capture's currently set filename
|
|
||||||
if not filename:
|
|
||||||
return redirect(url_for('capture_download', capture_id=capture_id, filename=capture_obj.filename, as_attachment=as_attachment, thumbnail=thumbnail), code=307)
|
|
||||||
|
|
||||||
# Download the image data using the requested filename
|
|
||||||
if thumbnail:
|
|
||||||
img = capture_obj.thumbnail
|
|
||||||
else:
|
|
||||||
img = capture_obj.data
|
|
||||||
|
|
||||||
return send_file(
|
|
||||||
img,
|
|
||||||
mimetype='image/jpeg',
|
|
||||||
as_attachment=as_attachment,
|
|
||||||
attachment_filename=filename)
|
|
||||||
|
|
||||||
app.add_url_rule(
|
|
||||||
uri('/camera/capture/<capture_id>/download/<filename>'),
|
|
||||||
view_func=CaptureDownloadAPI.as_view('capture_download', microscope=api_microscope))
|
|
||||||
|
|
||||||
|
|
||||||
# Preview
|
|
||||||
class GPUPreviewAPI(MicroscopeView):
|
|
||||||
|
|
||||||
def post(self, operation):
|
|
||||||
"""
|
|
||||||
Create a new image capture.
|
|
||||||
|
|
||||||
.. :quickref: GPU Preview; Start/stop preview
|
|
||||||
|
|
||||||
**Example requests**:
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
POST /camera/preview/start HTTP/1.1
|
|
||||||
Accept: application/json
|
|
||||||
|
|
||||||
.. sourcecode:: http
|
|
||||||
|
|
||||||
POST /camera/preview/stop HTTP/1.1
|
|
||||||
Accept: application/json
|
|
||||||
|
|
||||||
:>header Accept: application/json
|
|
||||||
|
|
||||||
:<header Content-Type: application/json
|
|
||||||
:status 200: preview started/stopped
|
|
||||||
"""
|
|
||||||
if operation == "start":
|
|
||||||
self.microscope.camera.start_preview()
|
|
||||||
elif operation == "stop":
|
|
||||||
self.microscope.camera.stop_preview()
|
|
||||||
return jsonify(self.microscope.state)
|
|
||||||
|
|
||||||
app.add_url_rule(
|
|
||||||
uri('/camera/preview/<string:operation>'),
|
|
||||||
view_func=GPUPreviewAPI.as_view('gpu_preview', microscope=api_microscope))
|
|
||||||
|
|
||||||
# Automatically clean up microscope at exit
|
|
||||||
def cleanup():
|
|
||||||
global api_microscope
|
|
||||||
api_microscope.close()
|
|
||||||
|
|
||||||
atexit.register(cleanup)
|
|
||||||
|
|
||||||
if __name__ == "__main__":
|
|
||||||
app.run(host='0.0.0.0', port="5000", threaded=True, debug=True, use_reloader=False)
|
|
||||||
0
openflexure_microscope/api/v1/__init__.py
Normal file
0
openflexure_microscope/api/v1/__init__.py
Normal file
1
openflexure_microscope/api/v1/blueprints/__init__.py
Normal file
1
openflexure_microscope/api/v1/blueprints/__init__.py
Normal file
|
|
@ -0,0 +1 @@
|
||||||
|
from . import camera, stage, base
|
||||||
92
openflexure_microscope/api/v1/blueprints/base.py
Normal file
92
openflexure_microscope/api/v1/blueprints/base.py
Normal file
|
|
@ -0,0 +1,92 @@
|
||||||
|
from openflexure_microscope.api.utilities import parse_payload, get_from_payload, gen, get_bool
|
||||||
|
from openflexure_microscope.api.v1.views import MicroscopeView
|
||||||
|
|
||||||
|
from flask import Response, Blueprint, jsonify
|
||||||
|
|
||||||
|
|
||||||
|
class StreamAPI(MicroscopeView):
|
||||||
|
|
||||||
|
def get(self):
|
||||||
|
"""
|
||||||
|
Real-time MJPEG stream from the microscope camera
|
||||||
|
|
||||||
|
.. :quickref: State; Camera stream
|
||||||
|
|
||||||
|
:>header Accept: image/jpeg
|
||||||
|
:>header Content-Type: image/jpeg
|
||||||
|
:status 200: stream active
|
||||||
|
"""
|
||||||
|
# Restart stream worker thread
|
||||||
|
self.microscope.camera.start_worker()
|
||||||
|
|
||||||
|
return Response(
|
||||||
|
gen(self.microscope.camera),
|
||||||
|
mimetype='multipart/x-mixed-replace; boundary=frame')
|
||||||
|
|
||||||
|
|
||||||
|
class StateAPI(MicroscopeView):
|
||||||
|
|
||||||
|
def get(self):
|
||||||
|
"""
|
||||||
|
JSON representation of the microscope object.
|
||||||
|
|
||||||
|
.. :quickref: State; Microscope state
|
||||||
|
|
||||||
|
**Example request**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
GET /state/ HTTP/1.1
|
||||||
|
Accept: application/json
|
||||||
|
|
||||||
|
**Example response**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
HTTP/1.1 200 OK
|
||||||
|
Vary: Accept
|
||||||
|
Content-Type: application/json
|
||||||
|
|
||||||
|
{
|
||||||
|
"camera": {
|
||||||
|
"preview_active": false,
|
||||||
|
"record_active": false,
|
||||||
|
"stream_active": true
|
||||||
|
},
|
||||||
|
"plugin": {},
|
||||||
|
"stage": {
|
||||||
|
"backlash": {
|
||||||
|
"x": 128,
|
||||||
|
"y": 128,
|
||||||
|
"z": 128
|
||||||
|
},
|
||||||
|
"position": {
|
||||||
|
"x": -8080,
|
||||||
|
"y": 5665,
|
||||||
|
"z": -12600
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
:>header Accept: application/json
|
||||||
|
:>header Content-Type: application/json
|
||||||
|
:status 200: state available
|
||||||
|
"""
|
||||||
|
return jsonify(self.microscope.state)
|
||||||
|
|
||||||
|
|
||||||
|
def construct_blueprint(microscope_obj):
|
||||||
|
|
||||||
|
blueprint = Blueprint('base_blueprint', __name__)
|
||||||
|
|
||||||
|
blueprint.add_url_rule(
|
||||||
|
'/stream',
|
||||||
|
view_func=StreamAPI.as_view('stream', microscope=microscope_obj)
|
||||||
|
)
|
||||||
|
|
||||||
|
blueprint.add_url_rule(
|
||||||
|
'/state',
|
||||||
|
view_func=StateAPI.as_view('state', microscope=microscope_obj)
|
||||||
|
)
|
||||||
|
|
||||||
|
return(blueprint)
|
||||||
34
openflexure_microscope/api/v1/blueprints/camera/__init__.py
Normal file
34
openflexure_microscope/api/v1/blueprints/camera/__init__.py
Normal file
|
|
@ -0,0 +1,34 @@
|
||||||
|
from openflexure_microscope.api.v1.views import MicroscopeView
|
||||||
|
|
||||||
|
from flask import Blueprint
|
||||||
|
|
||||||
|
from . import capture, record, preview
|
||||||
|
|
||||||
|
|
||||||
|
def construct_blueprint(microscope_obj):
|
||||||
|
|
||||||
|
blueprint = Blueprint('camera_blueprint', __name__)
|
||||||
|
|
||||||
|
# Capture routes
|
||||||
|
blueprint.add_url_rule(
|
||||||
|
'/capture/<capture_id>/download/<filename>',
|
||||||
|
view_func=capture.DownloadAPI.as_view('capture_download', microscope=microscope_obj))
|
||||||
|
|
||||||
|
blueprint.add_url_rule(
|
||||||
|
'/capture/<capture_id>/download',
|
||||||
|
view_func=capture.DownloadRedirectAPI.as_view('capture_download_redirect', microscope=microscope_obj))
|
||||||
|
|
||||||
|
blueprint.add_url_rule(
|
||||||
|
'/capture/<capture_id>/',
|
||||||
|
view_func=capture.CaptureAPI.as_view('capture', microscope=microscope_obj))
|
||||||
|
|
||||||
|
blueprint.add_url_rule(
|
||||||
|
'/capture/',
|
||||||
|
view_func=capture.ListAPI.as_view('capture_list', microscope=microscope_obj))
|
||||||
|
|
||||||
|
# Preview routes
|
||||||
|
blueprint.add_url_rule(
|
||||||
|
'/preview/<string:operation>',
|
||||||
|
view_func=preview.GPUPreviewAPI.as_view('gpu_preview', microscope=microscope_obj))
|
||||||
|
|
||||||
|
return(blueprint)
|
||||||
289
openflexure_microscope/api/v1/blueprints/camera/capture.py
Normal file
289
openflexure_microscope/api/v1/blueprints/camera/capture.py
Normal file
|
|
@ -0,0 +1,289 @@
|
||||||
|
from openflexure_microscope.api.utilities import parse_payload, get_from_payload, gen, get_bool
|
||||||
|
from openflexure_microscope.api.v1.views import MicroscopeView
|
||||||
|
|
||||||
|
from flask import Response, Blueprint, jsonify, request, abort, url_for, redirect, send_file
|
||||||
|
|
||||||
|
import logging
|
||||||
|
|
||||||
|
|
||||||
|
class ListAPI(MicroscopeView):
|
||||||
|
|
||||||
|
def get(self):
|
||||||
|
"""
|
||||||
|
Get list of image captures.
|
||||||
|
|
||||||
|
.. :quickref: Capture collection; Get collection of captures
|
||||||
|
|
||||||
|
:>header Accept: application/json
|
||||||
|
:query include_unavailable: return json representations of captures that have been completely deleted
|
||||||
|
|
||||||
|
:>jsonarr boolean available: availability of capture data
|
||||||
|
:>jsonarr string filename: filename of capture
|
||||||
|
:>jsonarr string id: unique id of the capture object
|
||||||
|
:>jsonarr boolean keep_on_disk: keep the capture file on microscope after closing
|
||||||
|
:>jsonarr boolean locked: file locked for modifications (mostly used for video recording)
|
||||||
|
:>jsonarr string path: path on pi storage to the capture file, if available
|
||||||
|
:>jsonarr boolean stream: capture stored in-memory as a BytesIO stream
|
||||||
|
:>jsonarr json uri: - **download** *(string)*: api uri to the capture file download
|
||||||
|
- **metadata** *(string)*: api uri to the capture json representation
|
||||||
|
|
||||||
|
:>header Content-Type: application/json
|
||||||
|
:status 200: capture found
|
||||||
|
:status 404: no capture found with that id
|
||||||
|
"""
|
||||||
|
include_unavailable = get_bool(request.args.get('include_unavailable'))
|
||||||
|
|
||||||
|
if include_unavailable:
|
||||||
|
captures = [image.metadata for image in self.microscope.camera.images]
|
||||||
|
else:
|
||||||
|
captures = [image.metadata for image in self.microscope.camera.images if image.metadata['available']]
|
||||||
|
|
||||||
|
return jsonify(captures)
|
||||||
|
|
||||||
|
def delete(self):
|
||||||
|
"""
|
||||||
|
Delete all captures (not yet implemented)
|
||||||
|
|
||||||
|
.. :quickref: Capture collection; Delete all captures
|
||||||
|
"""
|
||||||
|
for image in self.microscope.camera.images:
|
||||||
|
image.delete()
|
||||||
|
|
||||||
|
captures = [image.metadata for image in self.microscope.camera.images]
|
||||||
|
|
||||||
|
return jsonify(captures)
|
||||||
|
|
||||||
|
def post(self):
|
||||||
|
"""
|
||||||
|
Create a new image capture.
|
||||||
|
|
||||||
|
.. :quickref: Capture collection; New capture
|
||||||
|
|
||||||
|
**Example request**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
POST /camera/capture HTTP/1.1
|
||||||
|
Accept: application/json
|
||||||
|
|
||||||
|
{
|
||||||
|
"filename": "myfirstcapture",
|
||||||
|
"keep_on_disk": true,
|
||||||
|
"use_video_port": true,
|
||||||
|
"size": {
|
||||||
|
"x": 640,
|
||||||
|
"y": 480
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
:>header Accept: application/json
|
||||||
|
|
||||||
|
:<json string filename: filename of stored capture
|
||||||
|
:<json boolean keep_on_disk: keep the capture file on microscope after closing
|
||||||
|
:<json boolean use_video_port: capture still image from the video port
|
||||||
|
:<json json size: - **x** *(int)*: x-axis resize
|
||||||
|
- **y** *(int)*: y-axis resize
|
||||||
|
|
||||||
|
:>json boolean available: availability of capture data
|
||||||
|
:>json string filename: filename of capture
|
||||||
|
:>json string id: unique id of the capture object
|
||||||
|
:>json boolean keep_on_disk: keep the capture file on microscope after closing
|
||||||
|
:>json boolean locked: file locked for modifications (mostly used for video recording)
|
||||||
|
:>json string path: path on pi storage to the capture file, if available
|
||||||
|
:>json boolean stream: capture stored in-memory as a BytesIO stream
|
||||||
|
:>json json uri: - **download** *(string)*: api uri to the capture file download
|
||||||
|
- **metadata** *(string)*: api uri to the capture json representation
|
||||||
|
|
||||||
|
:<header Content-Type: application/json
|
||||||
|
:status 200: capture created
|
||||||
|
"""
|
||||||
|
state = parse_payload(request)
|
||||||
|
logging.info(state)
|
||||||
|
|
||||||
|
filename = get_from_payload(state, 'filename', default=None)
|
||||||
|
keep_on_disk = bool(get_from_payload(state, 'keep_on_disk', default=True))
|
||||||
|
use_video_port = bool(get_from_payload(state, 'use_video_port', default=False))
|
||||||
|
|
||||||
|
resize = get_from_payload(state, 'size', default=None)
|
||||||
|
if resize:
|
||||||
|
if ('width' in resize) and ('height' in resize):
|
||||||
|
resize = (int(resize['width']), int(resize['height'])) # Convert dict to tuple
|
||||||
|
else:
|
||||||
|
abort(400)
|
||||||
|
|
||||||
|
capture_obj = self.microscope.camera.capture(
|
||||||
|
write_to_file=True, # Always write data to disk when using API
|
||||||
|
keep_on_disk=keep_on_disk,
|
||||||
|
use_video_port=use_video_port,
|
||||||
|
filename=filename,
|
||||||
|
resize=resize)
|
||||||
|
|
||||||
|
return jsonify(capture_obj.metadata)
|
||||||
|
|
||||||
|
|
||||||
|
class CaptureAPI(MicroscopeView):
|
||||||
|
|
||||||
|
def get(self, capture_id):
|
||||||
|
"""
|
||||||
|
Get JSON representation of a capture
|
||||||
|
|
||||||
|
.. :quickref: Capture; Get capture
|
||||||
|
|
||||||
|
**Example request**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/ HTTP/1.1
|
||||||
|
Accept: application/json
|
||||||
|
|
||||||
|
**Example response**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
HTTP/1.1 200 OK
|
||||||
|
Vary: Accept
|
||||||
|
Content-Type: application/json
|
||||||
|
|
||||||
|
{
|
||||||
|
"available": true,
|
||||||
|
"filename": "2018-11-16_10-21-53.jpeg",
|
||||||
|
"id": "d0b2067abbb946f19351e075c5e7cd5b",
|
||||||
|
"keep_on_disk": false,
|
||||||
|
"locked": false,
|
||||||
|
"path": "capture/2018-11-16_10-21-53.jpeg",
|
||||||
|
"stream": false,
|
||||||
|
"uri": {
|
||||||
|
"download": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/download",
|
||||||
|
"metadata": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/"
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
:>json boolean available: availability of capture data
|
||||||
|
:>json string filename: filename of capture
|
||||||
|
:>json string id: unique id of the capture object
|
||||||
|
:>json boolean keep_on_disk: keep the capture file on microscope after closing
|
||||||
|
:>json boolean locked: file locked for modifications (mostly used for video recording)
|
||||||
|
:>json string path: path on pi storage to the capture file, if available
|
||||||
|
:>json boolean stream: capture stored in-memory as a BytesIO stream
|
||||||
|
:>json json uri: - **download** *(string)*: api uri to the capture file download
|
||||||
|
- **metadata** *(string)*: api uri to the capture json representation
|
||||||
|
|
||||||
|
"""
|
||||||
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
||||||
|
|
||||||
|
if not capture_obj:
|
||||||
|
return abort(404) # 404 Not Found
|
||||||
|
|
||||||
|
# Get capture metadata
|
||||||
|
capture_metadata = capture_obj.metadata
|
||||||
|
|
||||||
|
# TODO: Tidy up adding URI to metadata
|
||||||
|
# Add API routes to returned metadata
|
||||||
|
uri_dict = {
|
||||||
|
'uri': {'metadata': '{}/{}'.format(url_for(self), capture_id)}
|
||||||
|
}
|
||||||
|
|
||||||
|
# If available, also add download link
|
||||||
|
if capture_metadata['available']:
|
||||||
|
uri_dict['uri']['download'] = '{}/{}/download/{}'.format(url_for(self), capture_obj.id, capture_obj.filename)
|
||||||
|
|
||||||
|
capture_metadata.update(uri_dict)
|
||||||
|
|
||||||
|
return jsonify(capture_metadata)
|
||||||
|
|
||||||
|
def delete(self, capture_id):
|
||||||
|
"""
|
||||||
|
Delete all capture data from the Pi, even if `keep_on_disk=true;`.
|
||||||
|
|
||||||
|
.. :quickref: Capture; Delete capture.
|
||||||
|
"""
|
||||||
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
||||||
|
|
||||||
|
if not capture_obj:
|
||||||
|
return abort(404) # 404 Not Found
|
||||||
|
|
||||||
|
capture_obj.delete()
|
||||||
|
|
||||||
|
return jsonify({"return": capture_id})
|
||||||
|
|
||||||
|
def put(self, capture_id):
|
||||||
|
"""
|
||||||
|
Modify the metadata of a capture (not yet implemented)
|
||||||
|
|
||||||
|
.. :quickref: Capture; Update capture metadata
|
||||||
|
"""
|
||||||
|
return jsonify({"return": capture_id})
|
||||||
|
|
||||||
|
|
||||||
|
class DownloadRedirectAPI(MicroscopeView):
|
||||||
|
def get(self, capture_id):
|
||||||
|
"""
|
||||||
|
Redirect to download the capture under it's currently set filename.
|
||||||
|
I.e., `/(capture_id)/download` will
|
||||||
|
redirect to `/(capture_id)/download/(filename)`.
|
||||||
|
|
||||||
|
Note: This route may be deprecated in the future. Where at all
|
||||||
|
possible, please include a filename to download as.
|
||||||
|
|
||||||
|
.. :quickref: Capture; Redirect to download
|
||||||
|
"""
|
||||||
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
||||||
|
|
||||||
|
if not capture_obj or not capture_obj.metadata['available']:
|
||||||
|
return abort(404) # 404 Not Found
|
||||||
|
|
||||||
|
as_attachment = get_bool(request.args.get('as_attachment'))
|
||||||
|
thumbnail = get_bool(request.args.get('thumbnail'))
|
||||||
|
|
||||||
|
return redirect(url_for('.capture_download', capture_id=capture_id, filename=capture_obj.filename, as_attachment=as_attachment, thumbnail=thumbnail), code=307)
|
||||||
|
|
||||||
|
|
||||||
|
class DownloadAPI(MicroscopeView):
|
||||||
|
def get(self, capture_id, filename):
|
||||||
|
"""
|
||||||
|
Return image data for a capture.
|
||||||
|
|
||||||
|
Return capture data as an image file with the requested filename.
|
||||||
|
I.e., `/(capture_id)/download/foo.jpeg` will download the image as
|
||||||
|
`foo.jpeg`, regardless of the capture's initially set filename.
|
||||||
|
|
||||||
|
.. :quickref: Capture; Download capture file
|
||||||
|
|
||||||
|
**Example request**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/download/2018-11-20_16-04-17.jpeg HTTP/1.1
|
||||||
|
Accept: image/jpeg
|
||||||
|
|
||||||
|
:>header Accept: image/jpeg
|
||||||
|
:query thumbnail: return an image thumbnail e.g. ?thumbnail=true
|
||||||
|
:query as_attachment: return the image as an attachment download e.g. ?as_attachment=true
|
||||||
|
|
||||||
|
:>header Content-Type: image/jpeg
|
||||||
|
:status 200: capture data found
|
||||||
|
:status 404: no capture found with that id
|
||||||
|
"""
|
||||||
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
||||||
|
|
||||||
|
if not capture_obj or not capture_obj.metadata['available']:
|
||||||
|
return abort(404) # 404 Not Found
|
||||||
|
|
||||||
|
as_attachment = get_bool(request.args.get('as_attachment'))
|
||||||
|
thumbnail = get_bool(request.args.get('thumbnail'))
|
||||||
|
|
||||||
|
# If no filename is specified, redirect to the capture's currently set filename
|
||||||
|
if not filename:
|
||||||
|
return redirect(url_for('capture_download', capture_id=capture_id, filename=capture_obj.filename, as_attachment=as_attachment, thumbnail=thumbnail), code=307)
|
||||||
|
|
||||||
|
# Download the image data using the requested filename
|
||||||
|
if thumbnail:
|
||||||
|
img = capture_obj.thumbnail
|
||||||
|
else:
|
||||||
|
img = capture_obj.data
|
||||||
|
|
||||||
|
return send_file(
|
||||||
|
img,
|
||||||
|
mimetype='image/jpeg',
|
||||||
|
as_attachment=as_attachment,
|
||||||
|
attachment_filename=filename)
|
||||||
38
openflexure_microscope/api/v1/blueprints/camera/preview.py
Normal file
38
openflexure_microscope/api/v1/blueprints/camera/preview.py
Normal file
|
|
@ -0,0 +1,38 @@
|
||||||
|
from openflexure_microscope.api.utilities import parse_payload, get_from_payload, gen, get_bool
|
||||||
|
from openflexure_microscope.api.v1.views import MicroscopeView
|
||||||
|
|
||||||
|
from flask import Response, Blueprint, jsonify, request, abort, url_for, redirect, send_file
|
||||||
|
|
||||||
|
import logging
|
||||||
|
|
||||||
|
|
||||||
|
class GPUPreviewAPI(MicroscopeView):
|
||||||
|
|
||||||
|
def post(self, operation):
|
||||||
|
"""
|
||||||
|
Create a new image capture.
|
||||||
|
|
||||||
|
.. :quickref: GPU Preview; Start/stop preview
|
||||||
|
|
||||||
|
**Example requests**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
POST /camera/preview/start HTTP/1.1
|
||||||
|
Accept: application/json
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
POST /camera/preview/stop HTTP/1.1
|
||||||
|
Accept: application/json
|
||||||
|
|
||||||
|
:>header Accept: application/json
|
||||||
|
|
||||||
|
:<header Content-Type: application/json
|
||||||
|
:status 200: preview started/stopped
|
||||||
|
"""
|
||||||
|
if operation == "start":
|
||||||
|
self.microscope.camera.start_preview()
|
||||||
|
elif operation == "stop":
|
||||||
|
self.microscope.camera.stop_preview()
|
||||||
|
return jsonify(self.microscope.state)
|
||||||
177
openflexure_microscope/api/v1/blueprints/stage.py
Normal file
177
openflexure_microscope/api/v1/blueprints/stage.py
Normal file
|
|
@ -0,0 +1,177 @@
|
||||||
|
from openflexure_microscope.api.utilities import parse_payload, get_from_payload, gen, get_bool
|
||||||
|
from openflexure_microscope.api.v1.views import MicroscopeView
|
||||||
|
|
||||||
|
from flask import Response, Blueprint, jsonify, request
|
||||||
|
|
||||||
|
import logging
|
||||||
|
|
||||||
|
|
||||||
|
class PositionAPI(MicroscopeView):
|
||||||
|
|
||||||
|
def get(self):
|
||||||
|
"""
|
||||||
|
Return current x, y and z positions of the stage.
|
||||||
|
|
||||||
|
.. :quickref: Position; Get current position
|
||||||
|
|
||||||
|
**Example request**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
GET /stage/position/ HTTP/1.1
|
||||||
|
Accept: application/json
|
||||||
|
|
||||||
|
**Example response**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
HTTP/1.1 200 OK
|
||||||
|
Vary: Accept
|
||||||
|
Content-Type: application/json
|
||||||
|
|
||||||
|
{
|
||||||
|
"x": 0,
|
||||||
|
"y": 0,
|
||||||
|
"z": 0
|
||||||
|
}
|
||||||
|
|
||||||
|
:>json int x: x steps
|
||||||
|
:>json int y: y steps
|
||||||
|
:>json int z: z steps
|
||||||
|
"""
|
||||||
|
return jsonify(self.microscope.state['stage']['position'])
|
||||||
|
|
||||||
|
def post(self):
|
||||||
|
"""
|
||||||
|
Set x, y and z positions of the stage.
|
||||||
|
|
||||||
|
.. :quickref: Position; Update current position
|
||||||
|
|
||||||
|
:reqheader Accept: application/json
|
||||||
|
:<json boolean absolute: (true) move to absolute position, (false) move by relative amount
|
||||||
|
:<json boolean force: allow moving by more than programmed limit
|
||||||
|
:<json int x: x steps
|
||||||
|
:<json int y: y steps
|
||||||
|
:<json int z: z steps
|
||||||
|
|
||||||
|
"""
|
||||||
|
# Get payload
|
||||||
|
state = parse_payload(request)
|
||||||
|
logging.debug(state)
|
||||||
|
|
||||||
|
# Construct position array
|
||||||
|
position = [0, 0, 0]
|
||||||
|
|
||||||
|
# Handle absolute positioning
|
||||||
|
if 'absolute' in state and state['absolute'] is True:
|
||||||
|
# Get coordinates from payload
|
||||||
|
for axis, key in enumerate(['x', 'y', 'z']):
|
||||||
|
if key in state:
|
||||||
|
position[axis] = int(state[key]-self.microscope.stage.position[axis])
|
||||||
|
|
||||||
|
else:
|
||||||
|
# Get coordinates from payload
|
||||||
|
for axis, key in enumerate(['x', 'y', 'z']):
|
||||||
|
if key in state:
|
||||||
|
position[axis] = int(state[key])
|
||||||
|
|
||||||
|
logging.debug(position)
|
||||||
|
|
||||||
|
# Safeguard to prevent moving to an absolute position beyond a fixed limit
|
||||||
|
if 'force' not in state or state['force'] is False: # Allow for override
|
||||||
|
# TODO: Make travel_limit a property of the stage or microscope
|
||||||
|
# TODO: Make travel_limit a 3-axis list
|
||||||
|
travel_limit = 20000
|
||||||
|
for axis, pos in enumerate(position):
|
||||||
|
if abs(pos) > travel_limit:
|
||||||
|
# Respond with 400 Bad Request
|
||||||
|
response = {'error': 'Cannot move to absolute position beyond the safeguard limit.'}
|
||||||
|
return jsonify(response), 400
|
||||||
|
|
||||||
|
self.microscope.stage.move_rel(position)
|
||||||
|
|
||||||
|
return jsonify(self.microscope.state['stage']['position'])
|
||||||
|
|
||||||
|
|
||||||
|
class StageParamsAPI(MicroscopeView):
|
||||||
|
|
||||||
|
def get(self):
|
||||||
|
"""
|
||||||
|
Return current parameters of the stage.
|
||||||
|
|
||||||
|
.. :quickref: Stage params; Get current stage parameters
|
||||||
|
|
||||||
|
**Example request**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
GET /stage/params HTTP/1.1
|
||||||
|
Accept: application/json
|
||||||
|
|
||||||
|
**Example response**:
|
||||||
|
|
||||||
|
.. sourcecode:: http
|
||||||
|
|
||||||
|
HTTP/1.1 200 OK
|
||||||
|
Vary: Accept
|
||||||
|
Content-Type: application/json
|
||||||
|
|
||||||
|
{
|
||||||
|
"backlash": {
|
||||||
|
"x": 0,
|
||||||
|
"y": 0,
|
||||||
|
"z": 128
|
||||||
|
},
|
||||||
|
}
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
return jsonify(self.microscope.state['stage'])
|
||||||
|
|
||||||
|
def post(self):
|
||||||
|
"""
|
||||||
|
Set parameters of the stage.
|
||||||
|
|
||||||
|
.. :quickref: Stage params; Set current stage parameters
|
||||||
|
|
||||||
|
:reqheader Accept: application/json
|
||||||
|
:<json json backlash: - **x** *(int)*: x-axis backlash in steps
|
||||||
|
- **y** *(int)*: y-axis backlash in steps
|
||||||
|
- **z** *(int)*: x-axis backlash in steps
|
||||||
|
|
||||||
|
"""
|
||||||
|
# Get payload
|
||||||
|
state = parse_payload(request)
|
||||||
|
logging.debug(state)
|
||||||
|
|
||||||
|
# BACKLASH
|
||||||
|
if 'backlash' in state:
|
||||||
|
# Construct backlash array
|
||||||
|
backlash = [0, 0, 0]
|
||||||
|
|
||||||
|
# Get backlash coordinates from payload
|
||||||
|
for axis, key in enumerate(['x', 'y', 'z']):
|
||||||
|
if key in state['backlash']:
|
||||||
|
backlash[axis] = int(state['backlash'][key])
|
||||||
|
|
||||||
|
# Apply backlash
|
||||||
|
self.microscope.stage.backlash = backlash
|
||||||
|
|
||||||
|
return jsonify(self.microscope.state['stage'])
|
||||||
|
|
||||||
|
|
||||||
|
def construct_blueprint(microscope_obj):
|
||||||
|
|
||||||
|
blueprint = Blueprint('stage_blueprint', __name__)
|
||||||
|
|
||||||
|
blueprint.add_url_rule(
|
||||||
|
'/position',
|
||||||
|
view_func=PositionAPI.as_view('position', microscope=microscope_obj)
|
||||||
|
)
|
||||||
|
|
||||||
|
blueprint.add_url_rule(
|
||||||
|
'/params',
|
||||||
|
view_func=StageParamsAPI.as_view('stage_params', microscope=microscope_obj)
|
||||||
|
)
|
||||||
|
|
||||||
|
return(blueprint)
|
||||||
13
openflexure_microscope/api/v1/views.py
Normal file
13
openflexure_microscope/api/v1/views.py
Normal file
|
|
@ -0,0 +1,13 @@
|
||||||
|
from flask.views import MethodView
|
||||||
|
|
||||||
|
|
||||||
|
class MicroscopeView(MethodView):
|
||||||
|
|
||||||
|
def __init__(self, microscope, **kwargs):
|
||||||
|
"""
|
||||||
|
Create a generic MethodView with a globally available
|
||||||
|
microscope object passed as an argument.
|
||||||
|
"""
|
||||||
|
self.microscope = microscope
|
||||||
|
|
||||||
|
MethodView.__init__(self, **kwargs)
|
||||||
Loading…
Add table
Add a link
Reference in a new issue