247 lines
7 KiB
Python
247 lines
7 KiB
Python
#!/usr/bin/env python
|
|
"""
|
|
TODO: Add proper docstrings
|
|
TODO: Bind to port 80
|
|
TODO: Reimplement capture methods
|
|
TODO: Implement API route to cleanly shut down server
|
|
TODO: Implement microscope function API routes (autofocus etc)
|
|
"""
|
|
|
|
from pprint import pprint
|
|
from importlib import import_module
|
|
import time
|
|
import datetime
|
|
|
|
from flask import (
|
|
Flask, render_template, Response,
|
|
redirect, request, jsonify, send_file, abort)
|
|
|
|
|
|
import numpy as np
|
|
|
|
from openflexure_microscope.api.utilities import parse_payload, gen, get_bool
|
|
|
|
from openflexure_microscope import Microscope
|
|
from openflexure_microscope.camera.pi import StreamingCamera
|
|
from openflexure_stage import OpenFlexureStage
|
|
|
|
import logging, sys
|
|
logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
|
|
|
|
|
|
# Create the microscope object globally (common to all spawned server threads)
|
|
microscope = Microscope(
|
|
StreamingCamera(),
|
|
OpenFlexureStage("/dev/ttyUSB0")
|
|
)
|
|
|
|
# Create flask app
|
|
app = Flask(__name__)
|
|
|
|
# Some useful functions
|
|
def uri(suffix, base='/api/v1'):
|
|
return base + suffix
|
|
|
|
# Define front-end routes
|
|
|
|
@app.route('/')
|
|
def index():
|
|
"""Video streaming home page."""
|
|
return render_template(
|
|
'index_v1.html'
|
|
)
|
|
|
|
# Define API routes
|
|
|
|
# Basic routes
|
|
|
|
@app.route(uri('/stream'))
|
|
def stream():
|
|
"""Video streaming route. Put this in the src attribute of an img tag."""
|
|
global microscope
|
|
|
|
# Restart stream worker thread
|
|
microscope.camera.start_worker()
|
|
|
|
return Response(
|
|
gen(microscope.camera),
|
|
mimetype='multipart/x-mixed-replace; boundary=frame')
|
|
|
|
@app.route(uri('/state'))
|
|
def state():
|
|
"""Return JSONified microscope state"""
|
|
global microscope
|
|
|
|
return jsonify(microscope.state)
|
|
|
|
# Positioning routes
|
|
|
|
@app.route(uri('/position'), methods=['GET', 'POST', 'PUT'])
|
|
def position():
|
|
"""Set and get the microscope stage position"""
|
|
global microscope
|
|
|
|
if request.method == 'POST' or request.method == 'PUT':
|
|
# 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]-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 not 'force' 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 = 2000
|
|
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
|
|
|
|
microscope.stage.move_rel(position)
|
|
|
|
return jsonify(microscope.state['position'])
|
|
|
|
|
|
# Capture routes
|
|
|
|
@app.route(uri('/capture/'), methods=['GET', 'POST', 'PUT'])
|
|
def capture():
|
|
"""Return JSONified microscope state"""
|
|
global microscope
|
|
|
|
if request.method == 'POST' or request.method == 'PUT':
|
|
state = parse_payload(request)
|
|
print(state)
|
|
|
|
if 'filename' in state:
|
|
filename = state['filename']
|
|
else:
|
|
filename = None
|
|
|
|
if 'keep_on_disk' in state:
|
|
keep_on_disk = bool(state['keep_on_disk'])
|
|
else:
|
|
keep_on_disk = True
|
|
|
|
if 'use_video_port' in state:
|
|
use_video_port = bool(state['use_video_port'])
|
|
else:
|
|
use_video_port = False
|
|
|
|
if 'size' in state:
|
|
if 'width' in state['size'] and 'height' in state['size']:
|
|
resize = (state['size']['width'], state['size']['height'])
|
|
else:
|
|
raise Exception("Invalid resize parameters passed. Ensure both width and height are specified.")
|
|
else:
|
|
resize = None
|
|
|
|
capture_obj = 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)
|
|
|
|
else: # GET requests
|
|
include_unavailable = get_bool(request.args.get('include_unavailable'))
|
|
|
|
if include_unavailable:
|
|
captures = [image for image in microscope.camera.images if image.metadata['available']]
|
|
else:
|
|
captures = microscope.camera.images
|
|
|
|
metadata_array = [capture.metadata for capture in captures]
|
|
|
|
return jsonify(metadata_array)
|
|
|
|
|
|
@app.route(uri('/capture/<capture_uuid>/'), methods=['GET', 'DELETE'])
|
|
def get_capture(capture_uuid):
|
|
"""Return JSONified capture by UUID"""
|
|
global microscope
|
|
|
|
print(capture_uuid)
|
|
capture_obj = microscope.camera.image_from_id(capture_uuid)
|
|
|
|
if not capture_obj:
|
|
return abort(404) # 404 Not Found
|
|
|
|
# Get capture metadata
|
|
capture_metadata = capture_obj.metadata
|
|
|
|
# Add API routes to returned metadata
|
|
uri_dict = {
|
|
'uri': {'metadata': uri('/capture/{}/'.format(capture_uuid))}
|
|
}
|
|
|
|
# If available, also add download link
|
|
if capture_metadata['available']:
|
|
uri_dict['uri']['download'] = uri('/capture/{}/download'.format(capture_uuid))
|
|
|
|
capture_metadata.update(uri_dict)
|
|
|
|
if request.method == 'DELETE':
|
|
print("DELETE NOT YET IMPLEMENETED")
|
|
return jsonify(capture_metadata)
|
|
|
|
else: # GET requests
|
|
return jsonify(capture_metadata)
|
|
|
|
|
|
@app.route(uri('/capture/<capture_uuid>/download'), methods=['GET'])
|
|
def download_capture(capture_uuid):
|
|
"""Return capture file by UUID"""
|
|
global microscope
|
|
|
|
print(capture_uuid)
|
|
capture_obj = microscope.camera.image_from_id(capture_uuid)
|
|
|
|
if not capture_obj:
|
|
return abort(404) # 404 Not Found
|
|
|
|
as_attachment = get_bool(request.args.get('as_attachment'))
|
|
|
|
return send_file(
|
|
capture_obj.data,
|
|
mimetype='image/jpeg',
|
|
as_attachment=as_attachment,
|
|
attachment_filename=capture_obj.filename)
|
|
|
|
@app.route(uri('/capture/<capture_uuid>/thumbnail'), methods=['GET'])
|
|
def thumb_capture(capture_uuid):
|
|
"""Return capture thumbnail by UUID"""
|
|
global microscope
|
|
|
|
print(capture_uuid)
|
|
capture_obj = microscope.camera.image_from_id(capture_uuid)
|
|
|
|
if not capture_obj:
|
|
return abort(404) # 404 Not Found
|
|
|
|
return send_file(
|
|
capture_obj.thumbnail,
|
|
mimetype='image/jpeg')
|
|
|
|
if __name__ == '__main__':
|
|
app.run(host='0.0.0.0', threaded=True, debug=True, use_reloader=False)
|