697 lines
21 KiB
Python
697 lines
21 KiB
Python
#!/usr/bin/env python
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"""
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TODO: Add proper docstrings
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TODO: Implement API route to cleanly shut down server
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TODO: Implement microscope function API routes (autofocus etc)
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"""
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import numpy as np
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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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import os
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from flask import (
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Flask, render_template, Response, url_for,
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redirect, request, jsonify, send_file, abort,
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make_response)
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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
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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_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, base=None):
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if not base:
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api_ver = os.path.splitext(os.path.basename(__file__))[0]
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base = "/api/{}".format(api_ver)
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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.url_map.strict_slashes = False
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# Make errors more API friendly
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def _handle_http_exception(e):
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return make_response(
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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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# After app starts, but before first request, attach hardware to global microscope
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@app.before_first_request
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def attach_microscope():
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# Create the microscope object globally (common to all spawned server threads)
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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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api_microscope.attach(
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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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def index():
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"""
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API demo app
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"""
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return render_template(
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'index_v1.html'
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)
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##### API ROUTES ######
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# Basic microscope view
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class MicroscopeView(MethodView):
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def __init__(self, microscope):
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"""
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Create a generic MethodView with a globally available
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microscope object passed as an argument.
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"""
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self.microscope = microscope
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MethodView.__init__(self)
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class StreamAPI(MicroscopeView):
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def get(self):
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"""
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Real-time MJPEG stream from the microscope camera
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.. :quickref: State; Camera stream
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:>header Accept: image/jpeg
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:>header Content-Type: image/jpeg
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:status 200: stream active
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"""
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# Restart stream worker thread
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self.microscope.camera.start_worker()
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return Response(
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gen(self.microscope.camera),
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mimetype='multipart/x-mixed-replace; boundary=frame')
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app.add_url_rule(
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uri('/stream/'),
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view_func=StreamAPI.as_view('stream', microscope=api_microscope))
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class StateAPI(MicroscopeView):
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def get(self):
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"""
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JSON representation of the microscope object.
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.. :quickref: State; Microscope state
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**Example request**:
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.. sourcecode:: http
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GET /state/ HTTP/1.1
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Accept: application/json
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**Example response**:
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.. sourcecode:: http
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HTTP/1.1 200 OK
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Vary: Accept
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Content-Type: application/json
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{
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"camera": {
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"preview_active": false,
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"record_active": false,
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"stream_active": true
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},
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"plugin": {},
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"stage": {
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"backlash": {
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"x": 128,
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"y": 128,
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"z": 128
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},
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"position": {
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"x": -8080,
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"y": 5665,
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"z": -12600
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}
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}
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}
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:>header Accept: application/json
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:>header Content-Type: application/json
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:status 200: state available
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"""
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return jsonify(self.microscope.state)
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app.add_url_rule(
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uri('/state/'),
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view_func=StateAPI.as_view('state', microscope=api_microscope))
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class PositionAPI(MicroscopeView):
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def get(self):
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"""
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Return current x, y and z positions of the stage.
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.. :quickref: Position; Get current position
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**Example request**:
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.. sourcecode:: http
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GET /stage/position/ HTTP/1.1
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Accept: application/json
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**Example response**:
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.. sourcecode:: http
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HTTP/1.1 200 OK
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Vary: Accept
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Content-Type: application/json
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{
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"x": 0,
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"y": 0,
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"z": 0
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}
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:>json int x: x steps
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:>json int y: y steps
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:>json int z: z steps
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"""
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return jsonify(self.microscope.state['stage']['position'])
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def post(self):
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"""
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Set x, y and z positions of the stage.
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.. :quickref: Position; Update current position
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:reqheader Accept: application/json
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:<json boolean absolute: (true) move to absolute position, (false) move by relative amount
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:<json boolean force: allow moving by more than programmed limit
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:<json int x: x steps
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:<json int y: y steps
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:<json int z: z steps
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"""
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# Get payload
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state = parse_payload(request)
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logging.debug(state)
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# Construct position array
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position = [0, 0, 0]
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# Handle absolute positioning
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if 'absolute' in state and state['absolute'] is True:
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# Get coordinates from payload
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for axis, key in enumerate(['x', 'y', 'z']):
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if key in state:
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position[axis] = int(state[key]-self.microscope.stage.position[axis])
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else:
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# Get coordinates from payload
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for axis, key in enumerate(['x', 'y', 'z']):
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if key in state:
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position[axis] = int(state[key])
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logging.debug(position)
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# Safeguard to prevent moving to an absolute position beyond a fixed limit
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if 'force' not in state or state['force'] is False: # Allow for override
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# TODO: Make travel_limit a property of the stage or microscope
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# TODO: Make travel_limit a 3-axis list
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travel_limit = 20000
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for axis, pos in enumerate(position):
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if abs(pos) > travel_limit:
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# Respond with 400 Bad Request
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response = {'error': 'Cannot move to absolute position beyond the safeguard limit.'}
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return jsonify(response), 400
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self.microscope.stage.move_rel(position)
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return jsonify(self.microscope.state['stage']['position'])
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app.add_url_rule(
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uri('/stage/position/'),
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view_func=PositionAPI.as_view('position', microscope=api_microscope))
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class StageParamsAPI(MicroscopeView):
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def get(self):
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"""
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Return current parameters of the stage.
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.. :quickref: Stage params; Get current stage parameters
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**Example request**:
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.. sourcecode:: http
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GET /stage/params HTTP/1.1
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Accept: application/json
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**Example response**:
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.. sourcecode:: http
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HTTP/1.1 200 OK
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Vary: Accept
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Content-Type: application/json
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{
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"backlash": {
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"x": 0,
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"y": 0,
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"z": 128
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},
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}
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"""
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return jsonify(self.microscope.state['stage'])
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def post(self):
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"""
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Set parameters of the stage.
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.. :quickref: Stage params; Set current stage parameters
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:reqheader Accept: application/json
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:<json json backlash: - **x** *(int)*: x-axis backlash in steps
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- **y** *(int)*: y-axis backlash in steps
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- **z** *(int)*: x-axis backlash in steps
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"""
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# Get payload
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state = parse_payload(request)
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logging.debug(state)
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# BACKLASH
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if 'backlash' in state:
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# Construct backlash array
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backlash = [0, 0, 0]
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# Get backlash coordinates from payload
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for axis, key in enumerate(['x', 'y', 'z']):
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if key in state['backlash']:
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backlash[axis] = int(state['backlash'][key])
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# Apply backlash
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self.microscope.stage.backlash = backlash
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return jsonify(self.microscope.state['stage'])
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app.add_url_rule(
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uri('/stage/params/'),
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view_func=StageParamsAPI.as_view('stage_params', microscope=api_microscope))
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class CaptureListAPI(MicroscopeView):
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def get(self):
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"""
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Get list of image captures.
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.. :quickref: Capture collection; Get collection of captures
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:>header Accept: application/json
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:query include_unavailable: return json representations of captures that have been completely deleted
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:>jsonarr boolean available: availability of capture data
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:>jsonarr string filename: filename of capture
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:>jsonarr string id: unique id of the capture object
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:>jsonarr boolean keep_on_disk: keep the capture file on microscope after closing
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:>jsonarr boolean locked: file locked for modifications (mostly used for video recording)
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:>jsonarr string path: path on pi storage to the capture file, if available
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:>jsonarr boolean stream: capture stored in-memory as a BytesIO stream
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:>jsonarr json uri: - **download** *(string)*: api uri to the capture file download
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- **metadata** *(string)*: api uri to the capture json representation
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:>header Content-Type: application/json
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:status 200: capture found
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:status 404: no capture found with that id
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"""
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include_unavailable = get_bool(request.args.get('include_unavailable'))
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if include_unavailable:
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captures = [image.metadata for image in self.microscope.camera.images]
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else:
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captures = [image.metadata for image in self.microscope.camera.images if image.metadata['available']]
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return jsonify(captures)
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def delete(self):
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"""
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Delete all captures (not yet implemented)
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.. :quickref: Capture collection; Delete all captures
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"""
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for image in self.microscope.camera.images:
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image.delete()
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captures = [image.metadata for image in self.microscope.camera.images]
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return jsonify(captures)
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def post(self):
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"""
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Create a new image capture.
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.. :quickref: Capture collection; New capture
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**Example request**:
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.. sourcecode:: http
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POST /camera/capture HTTP/1.1
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Accept: application/json
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{
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"filename": "myfirstcapture",
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"keep_on_disk": true,
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"use_video_port": true,
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"size": {
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"x": 640,
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"y": 480
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}
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}
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:>header Accept: application/json
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:<json string filename: filename of stored capture
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:<json boolean keep_on_disk: keep the capture file on microscope after closing
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:<json boolean use_video_port: capture still image from the video port
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:<json json size: - **x** *(int)*: x-axis resize
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- **y** *(int)*: y-axis resize
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:>json boolean available: availability of capture data
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:>json string filename: filename of capture
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:>json string id: unique id of the capture object
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:>json boolean keep_on_disk: keep the capture file on microscope after closing
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:>json boolean locked: file locked for modifications (mostly used for video recording)
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:>json string path: path on pi storage to the capture file, if available
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:>json boolean stream: capture stored in-memory as a BytesIO stream
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:>json json uri: - **download** *(string)*: api uri to the capture file download
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- **metadata** *(string)*: api uri to the capture json representation
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:<header Content-Type: application/json
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:status 200: capture created
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"""
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state = parse_payload(request)
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logging.info(state)
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filename = get_from_payload(state, 'filename', default=None)
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keep_on_disk = bool(get_from_payload(state, 'keep_on_disk', default=True))
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use_video_port = bool(get_from_payload(state, 'use_video_port', default=False))
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resize = get_from_payload(state, 'size', default=None)
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if resize:
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if ('width' in resize) and ('height' in resize):
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resize = (int(resize['width']), int(resize['height'])) # Convert dict to tuple
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else:
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abort(400)
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capture_obj = self.microscope.camera.capture(
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write_to_file=True, # Always write data to disk when using API
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keep_on_disk=keep_on_disk,
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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 jsonify(capture_obj.metadata)
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app.add_url_rule(
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uri('/camera/capture/'),
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view_func=CaptureListAPI.as_view('capture_list', microscope=api_microscope))
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class CaptureAPI(MicroscopeView):
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def get(self, capture_id):
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"""
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Get JSON representation of a capture
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.. :quickref: Capture; Get capture
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**Example request**:
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.. sourcecode:: http
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GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/ HTTP/1.1
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Accept: application/json
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**Example response**:
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.. sourcecode:: http
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HTTP/1.1 200 OK
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Vary: Accept
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Content-Type: application/json
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{
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"available": true,
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"filename": "2018-11-16_10-21-53.jpeg",
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"id": "d0b2067abbb946f19351e075c5e7cd5b",
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"keep_on_disk": false,
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"locked": false,
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"path": "capture/2018-11-16_10-21-53.jpeg",
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"stream": false,
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"uri": {
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"download": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/download",
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"metadata": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/"
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}
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}
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:>json boolean available: availability of capture data
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:>json string filename: filename of capture
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:>json string id: unique id of the capture object
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:>json boolean keep_on_disk: keep the capture file on microscope after closing
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:>json boolean locked: file locked for modifications (mostly used for video recording)
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:>json string path: path on pi storage to the capture file, if available
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:>json boolean stream: capture stored in-memory as a BytesIO stream
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:>json json uri: - **download** *(string)*: api uri to the capture file download
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- **metadata** *(string)*: api uri to the capture json representation
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"""
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capture_obj = self.microscope.camera.image_from_id(capture_id)
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if not capture_obj:
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return abort(404) # 404 Not Found
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# Get capture metadata
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capture_metadata = capture_obj.metadata
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# TODO: Tidy up adding URI to metadata
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# Add API routes to returned metadata
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uri_dict = {
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'uri': {'metadata': uri('/capture/{}/'.format(capture_id))}
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}
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# If available, also add download link
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if capture_metadata['available']:
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uri_dict['uri']['download'] = uri('/capture/{}/download/{}'.format(capture_obj.id, capture_obj.filename))
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capture_metadata.update(uri_dict)
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return jsonify(capture_metadata)
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def delete(self, capture_id):
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"""
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Delete all capture data from the Pi, even if `keep_on_disk=true;`.
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.. :quickref: Capture; Delete capture.
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"""
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capture_obj = self.microscope.camera.image_from_id(capture_id)
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if not capture_obj:
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return abort(404) # 404 Not Found
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capture_obj.delete()
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return jsonify({"return": capture_id})
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def put(self, capture_id):
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"""
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Modify the metadata of a capture (not yet implemented)
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.. :quickref: Capture; Update capture metadata
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"""
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return jsonify({"return": capture_id})
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app.add_url_rule(
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uri('/camera/capture/<capture_id>/'),
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view_func=CaptureAPI.as_view('capture', microscope=api_microscope))
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class CaptureDownloadRedirectAPI(MicroscopeView):
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def get(self, capture_id):
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"""
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Redirect to download the capture under it's currently set filename.
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I.e., `/(capture_id)/download` will
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redirect to `/(capture_id)/download/(filename)`.
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Note: This route may be deprecated in the future. Where at all
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possible, please include a filename to download as.
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.. :quickref: Capture; Redirect to download
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"""
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capture_obj = self.microscope.camera.image_from_id(capture_id)
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if not capture_obj or not capture_obj.metadata['available']:
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return abort(404) # 404 Not Found
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as_attachment = get_bool(request.args.get('as_attachment'))
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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
|
|
|
|
:>header 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)
|