Merge remote-tracking branch 'planktonplanet/master'
This commit is contained in:
Romain Bazile
commit
20e3026856
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@ -1,439 +0,0 @@
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import paho.mqtt.client as mqtt
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from picamera import PiCamera
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from datetime import datetime, timedelta
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from adafruit_motor import stepper
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from adafruit_motorkit import MotorKit
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from time import sleep
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import json
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import os
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import subprocess
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from skimage.util import img_as_ubyte
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from morphocut import Call
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from morphocut.contrib.ecotaxa import EcotaxaWriter
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from morphocut.contrib.zooprocess import CalculateZooProcessFeatures
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from morphocut.core import Pipeline
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from morphocut.file import Find
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from morphocut.image import (
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ExtractROI,
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FindRegions,
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ImageReader,
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ImageWriter,
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RescaleIntensity,
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RGB2Gray,
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)
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from morphocut.stat import RunningMedian
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from morphocut.str import Format
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from morphocut.stream import TQDM, Enumerate, FilterVariables
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from skimage.feature import canny
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from skimage.color import rgb2gray, label2rgb
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from skimage.morphology import disk
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from skimage.morphology import erosion, dilation, closing
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from skimage.measure import label, regionprops
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import cv2, shutil
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import smbus
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#fan
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bus = smbus.SMBus(1)
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################################################################################
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kit = MotorKit()
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pump_stepper = kit.stepper1
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pump_stepper.release()
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focus_stepper = kit.stepper2
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focus_stepper.release()
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################################################################################
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camera = PiCamera()
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camera.resolution = (3280, 2464)
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camera.iso = 60
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camera.shutter_speed = 500
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camera.exposure_mode = 'fixedfps'
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################################################################################
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message = ''
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topic = ''
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count=''
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################################################################################
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def on_connect(client, userdata, flags, rc):
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print("Connected! - " + str(rc))
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client.subscribe("actuator/#")
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rgb(0,255,0)
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def on_subscribe(client, obj, mid, granted_qos):
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print("Subscribed! - "+str(mid)+" "+str(granted_qos))
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def on_message(client, userdata, msg):
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print(msg.topic+" "+str(msg.qos)+" "+str(msg.payload))
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global message
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global topic
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global count
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message=str(msg.payload.decode())
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topic=msg.topic.split("/")[1]
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count=0
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def on_log(client, obj, level, string):
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print(string)
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def rgb(R,G,B):
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bus.write_byte_data(0x0d, 0x00, 0)
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bus.write_byte_data(0x0d, 0x01, R)
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bus.write_byte_data(0x0d, 0x02, G)
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bus.write_byte_data(0x0d, 0x03, B)
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bus.write_byte_data(0x0d, 0x00, 1)
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bus.write_byte_data(0x0d, 0x01, R)
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bus.write_byte_data(0x0d, 0x02, G)
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bus.write_byte_data(0x0d, 0x03, B)
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bus.write_byte_data(0x0d, 0x00, 2)
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bus.write_byte_data(0x0d, 0x01, R)
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bus.write_byte_data(0x0d, 0x02, G)
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bus.write_byte_data(0x0d, 0x03, B)
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cmd="i2cdetect -y 1"
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subprocess.Popen(cmd.split(),stdout=subprocess.PIPE)
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################################################################################
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client = mqtt.Client()
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client.connect("127.0.0.1",1883,60)
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client.on_connect = on_connect
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client.on_subscribe = on_subscribe
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client.on_message = on_message
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client.on_log = on_log
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client.loop_start()
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################################################################################
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while True:
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################################################################################
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if (topic=="pump"):
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rgb(0,0,255)
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direction=message.split(" ")[0]
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delay=float(message.split(" ")[1])
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nb_step=int(message.split(" ")[2])
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client.publish("receiver/pump", "Start");
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while True:
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if direction == "BACKWARD":
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direction=stepper.BACKWARD
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if direction == "FORWARD":
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direction=stepper.FORWARD
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count+=1
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# print(count,nb_step)
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pump_stepper.onestep(direction=direction, style=stepper.DOUBLE)
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sleep(delay)
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if topic!="pump":
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pump_stepper.release()
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print("The pump has been interrompted.")
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client.publish("receiver/pump", "Interrompted");
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rgb(0,255,0)
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break
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if count>nb_step:
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pump_stepper.release()
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print("The pumping is done.")
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topic="wait"
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client.publish("receiver/pump", "Done");
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rgb(0,255,0)
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break
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################################################################################
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elif (topic=="focus"):
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rgb(255,255,0)
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direction=message.split(" ")[0]
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nb_step=int(message.split(" ")[1])
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client.publish("receiver/focus", "Start");
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while True:
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if direction == "FORWARD":
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direction=stepper.FORWARD
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if direction == "BACKWARD":
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direction=stepper.BACKWARD
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count+=1
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# print(count,nb_step)
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focus_stepper.onestep(direction=direction, style=stepper.MICROSTEP)
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if topic!="focus":
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focus_stepper.release()
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print("The stage has been interrompted.")
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client.publish("receiver/focus", "Interrompted");
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rgb(0,255,0)
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break
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if count>nb_step:
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focus_stepper.release()
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print("The focusing is done.")
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topic="wait"
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client.publish("receiver/focus", "Done");
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rgb(0,255,0)
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break
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################################################################################
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elif (topic=="image"):
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camera.start_preview(fullscreen=False, window = (160, 0, 640, 480))
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sleep_before=int(message.split(" ")[0])
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nb_step=int(message.split(" ")[1])
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path=str(message.split(" ")[2])
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nb_frame=int(message.split(" ")[3])
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sleep_during=int(message.split(" ")[4])
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#sleep a duration before to start
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sleep(sleep_before)
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client.publish("receiver/image", "Start");
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#flushing before to begin
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rgb(0,0,255)
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for i in range(nb_step):
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pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
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sleep(0.01)
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rgb(0,255,0)
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directory = os.path.join(path, "PlanktonScope")
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os.makedirs(directory, exist_ok=True)
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export = os.path.join(directory, "export")
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os.makedirs(export, exist_ok=True)
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date=datetime.now().strftime("%m_%d_%Y")
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time=datetime.now().strftime("%H_%M")
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path_date = os.path.join(directory, date)
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os.makedirs(path_date, exist_ok=True)
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path_time = os.path.join(path_date,time)
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os.makedirs(path_time, exist_ok=True)
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while True:
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count+=1
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# print(count,nb_frame)
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filename = os.path.join(path_time,datetime.now().strftime("%M_%S_%f")+".jpg")
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rgb(0,255,255)
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camera.capture(filename)
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rgb(0,255,0)
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client.publish("receiver/image", datetime.now().strftime("%M_%S_%f")+".jpg has been imaged.");
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rgb(0,0,255)
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for i in range(10):
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pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
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sleep(0.01)
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sleep(0.5)
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rgb(0,255,0)
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if(count>nb_frame):
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camera.stop_preview()
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client.publish("receiver/image", "Completed");
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# Meta data that is added to every object
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local_metadata = {
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"process_datetime": datetime.now(),
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"acq_camera_resolution" : camera.resolution,
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"acq_camera_iso" : camera.iso,
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"acq_camera_shutter_speed" : camera.shutter_speed
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}
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global_metadata = None
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config_txt = None
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RAW = None
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CLEAN = None
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ANNOTATED = None
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OBJECTS = None
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archive_fn = None
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config_txt = open('/home/pi/PlanktonScope/config.txt','r')
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node_red_metadata = json.loads(config_txt.read())
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global_metadata = {**local_metadata, **node_red_metadata}
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RAW = os.path.join(path_time, "RAW")
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os.makedirs(RAW, exist_ok=True)
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os.system("mv "+str(path_time)+"/*.jpg "+str(RAW))
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CLEAN = os.path.join(path_time, "CLEAN")
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os.makedirs(CLEAN, exist_ok=True)
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ANNOTATED = os.path.join(path_time, "ANNOTATED")
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os.makedirs(ANNOTATED, exist_ok=True)
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OBJECTS = os.path.join(path_time, "OBJECTS")
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os.makedirs(OBJECTS, exist_ok=True)
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archive_fn = os.path.join(directory,"export", str(date)+"_"+str(time)+"_ecotaxa_export.zip")
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client.publish("receiver/segmentation", "Start");
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# Define processing pipeline
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# Define processing pipeline
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with Pipeline() as p:
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# Recursively find .jpg files in import_path.
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# Sort to get consective frames.
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abs_path = Find(RAW, [".jpg"], sort=True, verbose=True)
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FilterVariables(abs_path)
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# Extract name from abs_path
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name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)
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Call(rgb, 0,255,0)
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# Read image
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img = ImageReader(abs_path)
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||||||
# Show progress bar for frames
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||||||
#TQDM(Format("Frame {name}", name=name))
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|
||||||
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|
||||||
# Apply running median to approximate the background image
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|
||||||
flat_field = RunningMedian(img, 5)
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||||||
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||||||
# Correct image
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img = img / flat_field
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FilterVariables(name,img)
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|
||||||
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|
||||||
# Rescale intensities and convert to uint8 to speed up calculations
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|
||||||
img = RescaleIntensity(img, in_range=(0, 1.1), dtype="uint8")
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|
||||||
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|
||||||
frame_fn = Format(os.path.join(CLEAN, "{name}.jpg"), name=name)
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|
||||||
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||||||
ImageWriter(frame_fn, img)
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|
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|
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FilterVariables(name,img)
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|
||||||
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|
||||||
# Convert image to uint8 gray
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|
||||||
img_gray = RGB2Gray(img)
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|
||||||
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|
||||||
# ?
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|
||||||
img_gray = Call(img_as_ubyte, img_gray)
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|
||||||
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|
||||||
#Canny edge detection
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|
||||||
img_canny = Call(cv2.Canny, img_gray, 50,100)
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|
||||||
|
|
||||||
#Dilate
|
|
||||||
kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
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|
||||||
img_dilate = Call(cv2.dilate, img_canny, kernel, iterations=2)
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|
||||||
|
|
||||||
#Close
|
|
||||||
kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (5, 5))
|
|
||||||
img_close = Call(cv2.morphologyEx, img_dilate, cv2.MORPH_CLOSE, kernel, iterations=1)
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|
||||||
|
|
||||||
#Erode
|
|
||||||
kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
|
|
||||||
mask = Call(cv2.erode, img_close, kernel, iterations=2)
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|
||||||
|
|
||||||
FilterVariables(name,img,img_gray,mask)
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|
||||||
|
|
||||||
# Find objects
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|
||||||
regionprops = FindRegions(
|
|
||||||
mask, img_gray, min_area=1000, padding=10, warn_empty=name
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|
||||||
)
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|
||||||
|
|
||||||
Call(rgb, 255,0,255)
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|
||||||
# For an object, extract a vignette/ROI from the image
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|
||||||
roi_orig = ExtractROI(img, regionprops, bg_color=255)
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|
||||||
|
|
||||||
# Generate an object identifier
|
|
||||||
i = Enumerate()
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|
||||||
#Call(print,i)
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|
||||||
|
|
||||||
object_id = Format("{name}_{i:d}", name=name, i=i)
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|
||||||
#Call(print,object_id)
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|
||||||
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|
||||||
object_fn = Format(os.path.join(OBJECTS, "{name}.jpg"), name=object_id)
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|
||||||
|
|
||||||
ImageWriter(object_fn, roi_orig)
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|
||||||
|
|
||||||
# Calculate features. The calculated features are added to the global_metadata.
|
|
||||||
# Returns a Variable representing a dict for every object in the stream.
|
|
||||||
meta = CalculateZooProcessFeatures(
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|
||||||
regionprops, prefix="object_", meta=global_metadata
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|
||||||
)
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|
||||||
json_meta = Call(json.dumps,meta, sort_keys=True, default=str)
|
|
||||||
|
|
||||||
Call(client.publish, "receiver/segmentation/metric", json_meta)
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|
||||||
|
|
||||||
# Add object_id to the metadata dictionary
|
|
||||||
meta["object_id"] = object_id
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|
||||||
|
|
||||||
# Generate object filenames
|
|
||||||
orig_fn = Format("{object_id}.jpg", object_id=object_id)
|
|
||||||
|
|
||||||
FilterVariables(orig_fn,roi_orig,meta,object_id)
|
|
||||||
# Write objects to an EcoTaxa archive:
|
|
||||||
# roi image in original color, roi image in grayscale, metadata associated with each object
|
|
||||||
EcotaxaWriter(archive_fn, (orig_fn, roi_orig), meta)
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|
||||||
|
|
||||||
# Progress bar for objects
|
|
||||||
TQDM(Format("Object {object_id}", object_id=object_id))
|
|
||||||
|
|
||||||
Call(client.publish, "receiver/segmentation/object_id", object_id)
|
|
||||||
|
|
||||||
meta=None
|
|
||||||
FilterVariables(meta)
|
|
||||||
|
|
||||||
|
|
||||||
p.run()
|
|
||||||
|
|
||||||
#remove directory
|
|
||||||
#shutil.rmtree(import_path)
|
|
||||||
|
|
||||||
client.publish("receiver/segmentation", "Completed");
|
|
||||||
|
|
||||||
rgb(255,255,255)
|
|
||||||
sleep(sleep_during)
|
|
||||||
rgb(0,255,0)
|
|
||||||
|
|
||||||
date=datetime.now().strftime("%m_%d_%Y")
|
|
||||||
time=datetime.now().strftime("%H_%M")
|
|
||||||
|
|
||||||
path_date = os.path.join(directory, date)
|
|
||||||
os.makedirs(path_date, exist_ok=True)
|
|
||||||
|
|
||||||
path_time = os.path.join(path_date,time)
|
|
||||||
os.makedirs(path_time, exist_ok=True)
|
|
||||||
|
|
||||||
rgb(0,0,255)
|
|
||||||
for i in range(nb_step):
|
|
||||||
pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
|
|
||||||
sleep(0.01)
|
|
||||||
rgb(0,255,0)
|
|
||||||
|
|
||||||
os.makedirs(path_time, exist_ok=True)
|
|
||||||
count=0
|
|
||||||
|
|
||||||
if topic!="image":
|
|
||||||
pump_stepper.release()
|
|
||||||
print("The imaging has been interrompted.")
|
|
||||||
client.publish("receiver/image", "Interrompted");
|
|
||||||
rgb(0,255,0)
|
|
||||||
count=0
|
|
||||||
break
|
|
||||||
|
|
||||||
else:
|
|
||||||
# print("Waiting")
|
|
||||||
sleep(1)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -1,529 +0,0 @@
|
||||||
################################################################################
|
|
||||||
#Actuator Libraries
|
|
||||||
################################################################################
|
|
||||||
|
|
||||||
#Library for exchaning messages with Node-RED
|
|
||||||
import paho.mqtt.client as mqtt
|
|
||||||
|
|
||||||
#Library to control the PiCamera
|
|
||||||
from picamera import PiCamera
|
|
||||||
|
|
||||||
#Libraries to control the steppers for focusing and pumping
|
|
||||||
from adafruit_motor import stepper
|
|
||||||
from adafruit_motorkit import MotorKit
|
|
||||||
|
|
||||||
#Library to send command over I2C for the light module on the fan
|
|
||||||
import smbus
|
|
||||||
|
|
||||||
################################################################################
|
|
||||||
#Practical Libraries
|
|
||||||
################################################################################
|
|
||||||
|
|
||||||
#Library to get date and time for folder name and filename
|
|
||||||
from datetime import datetime, timedelta
|
|
||||||
|
|
||||||
#Library to be able to sleep for a duration
|
|
||||||
from time import sleep
|
|
||||||
|
|
||||||
#Libraries manipulate json format, execute bash commands
|
|
||||||
import json, shutil, os, subprocess
|
|
||||||
|
|
||||||
################################################################################
|
|
||||||
#Morphocut Libraries
|
|
||||||
################################################################################
|
|
||||||
|
|
||||||
from skimage.util import img_as_ubyte
|
|
||||||
from morphocut import Call
|
|
||||||
from morphocut.contrib.ecotaxa import EcotaxaWriter
|
|
||||||
from morphocut.contrib.zooprocess import CalculateZooProcessFeatures
|
|
||||||
from morphocut.core import Pipeline
|
|
||||||
from morphocut.file import Find
|
|
||||||
from morphocut.image import (ExtractROI,
|
|
||||||
FindRegions,
|
|
||||||
ImageReader,
|
|
||||||
ImageWriter,
|
|
||||||
RescaleIntensity,
|
|
||||||
RGB2Gray
|
|
||||||
)
|
|
||||||
from morphocut.stat import RunningMedian
|
|
||||||
from morphocut.str import Format
|
|
||||||
from morphocut.stream import TQDM, Enumerate, FilterVariables
|
|
||||||
|
|
||||||
################################################################################
|
|
||||||
#Other image processing Libraries
|
|
||||||
################################################################################
|
|
||||||
|
|
||||||
from skimage.feature import canny
|
|
||||||
from skimage.color import rgb2gray, label2rgb
|
|
||||||
from skimage.morphology import disk
|
|
||||||
from skimage.morphology import erosion, dilation, closing
|
|
||||||
from skimage.measure import label, regionprops
|
|
||||||
#pip3 install opencv-python
|
|
||||||
import cv2
|
|
||||||
|
|
||||||
|
|
||||||
################################################################################
|
|
||||||
#STREAMING
|
|
||||||
################################################################################
|
|
||||||
import io
|
|
||||||
import picamera
|
|
||||||
import logging
|
|
||||||
import socketserver
|
|
||||||
from threading import Condition
|
|
||||||
from http import server
|
|
||||||
import threading
|
|
||||||
|
|
||||||
PAGE="""\
|
|
||||||
<html>
|
|
||||||
<head>
|
|
||||||
<title>picamera MJPEG streaming demo</title>
|
|
||||||
</head>
|
|
||||||
<body>
|
|
||||||
<img src="stream.mjpg" width="640" height="480" />
|
|
||||||
</body>
|
|
||||||
</html>
|
|
||||||
"""
|
|
||||||
|
|
||||||
class StreamingOutput(object):
|
|
||||||
def __init__(self):
|
|
||||||
self.frame = None
|
|
||||||
self.buffer = io.BytesIO()
|
|
||||||
self.condition = Condition()
|
|
||||||
|
|
||||||
def write(self, buf):
|
|
||||||
if buf.startswith(b'\xff\xd8'):
|
|
||||||
# New frame, copy the existing buffer's content and notify all
|
|
||||||
# clients it's available
|
|
||||||
self.buffer.truncate()
|
|
||||||
with self.condition:
|
|
||||||
self.frame = self.buffer.getvalue()
|
|
||||||
self.condition.notify_all()
|
|
||||||
self.buffer.seek(0)
|
|
||||||
return self.buffer.write(buf)
|
|
||||||
|
|
||||||
class StreamingHandler(server.BaseHTTPRequestHandler):
|
|
||||||
def do_GET(self):
|
|
||||||
if self.path == '/':
|
|
||||||
self.send_response(301)
|
|
||||||
self.send_header('Location', '/index.html')
|
|
||||||
self.end_headers()
|
|
||||||
elif self.path == '/index.html':
|
|
||||||
content = PAGE.encode('utf-8')
|
|
||||||
self.send_response(200)
|
|
||||||
self.send_header('Content-Type', 'text/html')
|
|
||||||
self.send_header('Content-Length', len(content))
|
|
||||||
self.end_headers()
|
|
||||||
self.wfile.write(content)
|
|
||||||
elif self.path == '/stream.mjpg':
|
|
||||||
self.send_response(200)
|
|
||||||
self.send_header('Age', 0)
|
|
||||||
self.send_header('Cache-Control', 'no-cache, private')
|
|
||||||
self.send_header('Pragma', 'no-cache')
|
|
||||||
self.send_header('Content-Type', 'multipart/x-mixed-replace; boundary=FRAME')
|
|
||||||
self.end_headers()
|
|
||||||
try:
|
|
||||||
while True:
|
|
||||||
with output.condition:
|
|
||||||
output.condition.wait()
|
|
||||||
frame = output.frame
|
|
||||||
self.wfile.write(b'--FRAME\r\n')
|
|
||||||
self.send_header('Content-Type', 'image/jpeg')
|
|
||||||
self.send_header('Content-Length', len(frame))
|
|
||||||
self.end_headers()
|
|
||||||
self.wfile.write(frame)
|
|
||||||
self.wfile.write(b'\r\n')
|
|
||||||
except Exception as e:
|
|
||||||
logging.warning(
|
|
||||||
'Removed streaming client %s: %s',
|
|
||||||
self.client_address, str(e))
|
|
||||||
else:
|
|
||||||
self.send_error(404)
|
|
||||||
self.end_headers()
|
|
||||||
|
|
||||||
class StreamingServer(socketserver.ThreadingMixIn, server.HTTPServer):
|
|
||||||
allow_reuse_address = True
|
|
||||||
daemon_threads = True
|
|
||||||
################################################################################
|
|
||||||
#MQTT core functions
|
|
||||||
################################################################################
|
|
||||||
#Run this function in order to connect to the client (Node-RED)
|
|
||||||
def on_connect(client, userdata, flags, rc):
|
|
||||||
#Print when connected
|
|
||||||
print("Connected! - " + str(rc))
|
|
||||||
#When connected, run subscribe()
|
|
||||||
client.subscribe("actuator/#")
|
|
||||||
#Turn green the light module
|
|
||||||
rgb(0,255,0)
|
|
||||||
|
|
||||||
#Run this function in order to subscribe to all the topics begining by actuator
|
|
||||||
def on_subscribe(client, obj, mid, granted_qos):
|
|
||||||
#Print when subscribed
|
|
||||||
print("Subscribed! - "+str(mid)+" "+str(granted_qos))
|
|
||||||
|
|
||||||
#Run this command when Node-RED is sending a message on the subscribed topic
|
|
||||||
def on_message(client, userdata, msg):
|
|
||||||
#Print the topic and the message
|
|
||||||
print(msg.topic+" "+str(msg.qos)+" "+str(msg.payload))
|
|
||||||
#Update the global variables command, args and counter
|
|
||||||
global command
|
|
||||||
global args
|
|
||||||
global counter
|
|
||||||
#Parse the topic to find the command. ex : actuator/pump -> pump
|
|
||||||
command=msg.topic.split("/")[1]
|
|
||||||
#Decode the message to find the arguments
|
|
||||||
args=str(msg.payload.decode())
|
|
||||||
#Reset the counter to 0
|
|
||||||
counter=0
|
|
||||||
|
|
||||||
################################################################################
|
|
||||||
#Actuators core functions
|
|
||||||
################################################################################
|
|
||||||
def rgb(R,G,B):
|
|
||||||
#Update LED n°1
|
|
||||||
bus.write_byte_data(0x0d, 0x00, 0)
|
|
||||||
bus.write_byte_data(0x0d, 0x01, R)
|
|
||||||
bus.write_byte_data(0x0d, 0x02, G)
|
|
||||||
bus.write_byte_data(0x0d, 0x03, B)
|
|
||||||
|
|
||||||
#Update LED n°2
|
|
||||||
bus.write_byte_data(0x0d, 0x00, 1)
|
|
||||||
bus.write_byte_data(0x0d, 0x01, R)
|
|
||||||
bus.write_byte_data(0x0d, 0x02, G)
|
|
||||||
bus.write_byte_data(0x0d, 0x03, B)
|
|
||||||
|
|
||||||
#Update LED n°3
|
|
||||||
bus.write_byte_data(0x0d, 0x00, 2)
|
|
||||||
bus.write_byte_data(0x0d, 0x01, R)
|
|
||||||
bus.write_byte_data(0x0d, 0x02, G)
|
|
||||||
bus.write_byte_data(0x0d, 0x03, B)
|
|
||||||
|
|
||||||
#Update the I2C Bus in order to really update the LEDs new values
|
|
||||||
cmd="i2cdetect -y 1"
|
|
||||||
subprocess.Popen(cmd.split(),stdout=subprocess.PIPE)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
################################################################################
|
|
||||||
#Init function - executed only once
|
|
||||||
################################################################################
|
|
||||||
|
|
||||||
#define the bus used to actuate the light module on the fan
|
|
||||||
bus = smbus.SMBus(1)
|
|
||||||
|
|
||||||
#define the names for the 2 exsting steppers
|
|
||||||
kit = MotorKit()
|
|
||||||
pump_stepper = kit.stepper1
|
|
||||||
pump_stepper.release()
|
|
||||||
focus_stepper = kit.stepper2
|
|
||||||
focus_stepper.release()
|
|
||||||
|
|
||||||
#Precise the settings of the PiCamera
|
|
||||||
camera = PiCamera()
|
|
||||||
camera.resolution = (3280, 2464)
|
|
||||||
camera.iso = 60
|
|
||||||
camera.shutter_speed = 500
|
|
||||||
camera.exposure_mode = 'fixedfps'
|
|
||||||
|
|
||||||
#Declare the global variables command, args and counter
|
|
||||||
command = ''
|
|
||||||
args = ''
|
|
||||||
counter=''
|
|
||||||
|
|
||||||
client = mqtt.Client()
|
|
||||||
client.connect("127.0.0.1",1883,60)
|
|
||||||
client.on_connect = on_connect
|
|
||||||
client.on_subscribe = on_subscribe
|
|
||||||
client.on_message = on_message
|
|
||||||
client.loop_start()
|
|
||||||
|
|
||||||
################################################################################
|
|
||||||
|
|
||||||
local_metadata = {
|
|
||||||
"process_datetime": datetime.now(),
|
|
||||||
"acq_camera_resolution" : camera.resolution,
|
|
||||||
"acq_camera_iso" : camera.iso,
|
|
||||||
"acq_camera_shutter_speed" : camera.shutter_speed
|
|
||||||
}
|
|
||||||
|
|
||||||
config_txt = open('/home/pi/PlanktonScope/config.txt','r')
|
|
||||||
node_red_metadata = json.loads(config_txt.read())
|
|
||||||
|
|
||||||
global_metadata = {**local_metadata, **node_red_metadata}
|
|
||||||
|
|
||||||
archive_fn = os.path.join("/home/pi/PlanktonScope/","export", "ecotaxa_export.zip")
|
|
||||||
# Define processing pipeline
|
|
||||||
|
|
||||||
with Pipeline() as p:
|
|
||||||
# Recursively find .jpg files in import_path.
|
|
||||||
# Sort to get consective frames.
|
|
||||||
abs_path = Find("/home/pi/PlanktonScope/tmp", [".jpg"], sort=True, verbose=True)
|
|
||||||
|
|
||||||
|
|
||||||
# Extract name from abs_path
|
|
||||||
name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)
|
|
||||||
|
|
||||||
Call(rgb, 0,255,0)
|
|
||||||
|
|
||||||
# Read image
|
|
||||||
img = ImageReader(abs_path)
|
|
||||||
|
|
||||||
# Show progress bar for frames
|
|
||||||
TQDM(Format("Frame {name}", name=name))
|
|
||||||
|
|
||||||
# Apply running median to approximate the background image
|
|
||||||
flat_field = RunningMedian(img, 5)
|
|
||||||
|
|
||||||
# Correct image
|
|
||||||
img = img / flat_field
|
|
||||||
|
|
||||||
# Rescale intensities and convert to uint8 to speed up calculations
|
|
||||||
img = RescaleIntensity(img, in_range=(0, 1.1), dtype="uint8")
|
|
||||||
|
|
||||||
FilterVariables(name,img)
|
|
||||||
# frame_fn = Format(os.path.join("/home/pi/PlanktonScope/tmp","CLEAN", "{name}.jpg"), name=name)
|
|
||||||
|
|
||||||
# ImageWriter(frame_fn, img)
|
|
||||||
|
|
||||||
# Convert image to uint8 gray
|
|
||||||
img_gray = RGB2Gray(img)
|
|
||||||
|
|
||||||
# ?
|
|
||||||
img_gray = Call(img_as_ubyte, img_gray)
|
|
||||||
|
|
||||||
#Canny edge detection
|
|
||||||
img_canny = Call(cv2.Canny, img_gray, 50,100)
|
|
||||||
|
|
||||||
#Dilate
|
|
||||||
kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
|
|
||||||
img_dilate = Call(cv2.dilate, img_canny, kernel, iterations=2)
|
|
||||||
|
|
||||||
#Close
|
|
||||||
kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (5, 5))
|
|
||||||
img_close = Call(cv2.morphologyEx, img_dilate, cv2.MORPH_CLOSE, kernel, iterations=1)
|
|
||||||
|
|
||||||
#Erode
|
|
||||||
kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
|
|
||||||
mask = Call(cv2.erode, img_close, kernel, iterations=2)
|
|
||||||
|
|
||||||
# Find objects
|
|
||||||
regionprops = FindRegions(
|
|
||||||
mask, img_gray, min_area=1000, padding=10, warn_empty=name
|
|
||||||
)
|
|
||||||
|
|
||||||
Call(rgb, 255,0,255)
|
|
||||||
# For an object, extract a vignette/ROI from the image
|
|
||||||
roi_orig = ExtractROI(img, regionprops, bg_color=255)
|
|
||||||
|
|
||||||
# Generate an object identifier
|
|
||||||
i = Enumerate()
|
|
||||||
#Call(print,i)
|
|
||||||
|
|
||||||
object_id = Format("{name}_{i:d}", name=name, i=i)
|
|
||||||
#Call(print,object_id)
|
|
||||||
object_fn = Format(os.path.join("/home/pi/PlanktonScope/","OBJECTS", "{name}.jpg"), name=object_id)
|
|
||||||
|
|
||||||
ImageWriter(object_fn, roi_orig)
|
|
||||||
|
|
||||||
# Calculate features. The calculated features are added to the global_metadata.
|
|
||||||
# Returns a Variable representing a dict for every object in the stream.
|
|
||||||
meta = CalculateZooProcessFeatures(
|
|
||||||
regionprops, prefix="object_", meta=global_metadata
|
|
||||||
)
|
|
||||||
|
|
||||||
json_meta = Call(json.dumps,meta, sort_keys=True, default=str)
|
|
||||||
|
|
||||||
Call(client.publish, "receiver/segmentation/metric", json_meta)
|
|
||||||
|
|
||||||
# Add object_id to the metadata dictionary
|
|
||||||
meta["object_id"] = object_id
|
|
||||||
|
|
||||||
# Generate object filenames
|
|
||||||
orig_fn = Format("{object_id}.jpg", object_id=object_id)
|
|
||||||
|
|
||||||
# Write objects to an EcoTaxa archive:
|
|
||||||
# roi image in original color, roi image in grayscale, metadata associated with each object
|
|
||||||
EcotaxaWriter(archive_fn, (orig_fn, roi_orig), meta)
|
|
||||||
|
|
||||||
# Progress bar for objects
|
|
||||||
TQDM(Format("Object {object_id}", object_id=object_id))
|
|
||||||
|
|
||||||
Call(client.publish, "receiver/segmentation/object_id", object_id)
|
|
||||||
|
|
||||||
|
|
||||||
output = StreamingOutput()
|
|
||||||
address = ('', 8000)
|
|
||||||
server = StreamingServer(address, StreamingHandler)
|
|
||||||
|
|
||||||
threading.Thread(target=server.serve_forever).start()
|
|
||||||
################################################################################
|
|
||||||
|
|
||||||
camera.start_recording(output, format='mjpeg', resize=(640, 480))
|
|
||||||
while True:
|
|
||||||
|
|
||||||
if (command=="pump"):
|
|
||||||
rgb(0,0,255)
|
|
||||||
direction=args.split(" ")[0]
|
|
||||||
delay=float(args.split(" ")[1])
|
|
||||||
nb_step=int(args.split(" ")[2])
|
|
||||||
|
|
||||||
client.publish("receiver/pump", "Start");
|
|
||||||
|
|
||||||
|
|
||||||
while True:
|
|
||||||
|
|
||||||
if direction == "BACKWARD":
|
|
||||||
direction=stepper.BACKWARD
|
|
||||||
if direction == "FORWARD":
|
|
||||||
direction=stepper.FORWARD
|
|
||||||
pump_stepper.onestep(direction=direction, style=stepper.DOUBLE)
|
|
||||||
counter+=1
|
|
||||||
sleep(delay)
|
|
||||||
|
|
||||||
if command!="pump":
|
|
||||||
pump_stepper.release()
|
|
||||||
print("The pump has been interrompted.")
|
|
||||||
client.publish("receiver/pump", "Interrompted");
|
|
||||||
rgb(0,255,0)
|
|
||||||
break
|
|
||||||
|
|
||||||
if counter>nb_step:
|
|
||||||
pump_stepper.release()
|
|
||||||
print("The pumping is done.")
|
|
||||||
command="wait"
|
|
||||||
client.publish("receiver/pump", "Done");
|
|
||||||
rgb(0,255,0)
|
|
||||||
break
|
|
||||||
|
|
||||||
################################################################################
|
|
||||||
|
|
||||||
elif (command=="focus"):
|
|
||||||
|
|
||||||
rgb(255,255,0)
|
|
||||||
direction=args.split(" ")[0]
|
|
||||||
nb_step=int(args.split(" ")[1])
|
|
||||||
client.publish("receiver/focus", "Start");
|
|
||||||
|
|
||||||
|
|
||||||
while True:
|
|
||||||
|
|
||||||
if direction == "FORWARD":
|
|
||||||
direction=stepper.FORWARD
|
|
||||||
if direction == "BACKWARD":
|
|
||||||
direction=stepper.BACKWARD
|
|
||||||
counter+=1
|
|
||||||
focus_stepper.onestep(direction=direction, style=stepper.MICROSTEP)
|
|
||||||
|
|
||||||
if command!="focus":
|
|
||||||
focus_stepper.release()
|
|
||||||
print("The stage has been interrompted.")
|
|
||||||
client.publish("receiver/focus", "Interrompted");
|
|
||||||
rgb(0,255,0)
|
|
||||||
break
|
|
||||||
|
|
||||||
if counter>nb_step:
|
|
||||||
focus_stepper.release()
|
|
||||||
print("The focusing is done.")
|
|
||||||
command="wait"
|
|
||||||
client.publish("receiver/focus", "Done");
|
|
||||||
rgb(0,255,0)
|
|
||||||
break
|
|
||||||
|
|
||||||
################################################################################
|
|
||||||
|
|
||||||
elif (command=="image"):
|
|
||||||
|
|
||||||
|
|
||||||
sleep_before=int(args.split(" ")[0])
|
|
||||||
|
|
||||||
nb_step=int(args.split(" ")[1])
|
|
||||||
|
|
||||||
path=str(args.split(" ")[2])
|
|
||||||
|
|
||||||
nb_frame=int(args.split(" ")[3])
|
|
||||||
|
|
||||||
sleep_during=int(args.split(" ")[4])
|
|
||||||
|
|
||||||
#sleep a duration before to start
|
|
||||||
sleep(sleep_before)
|
|
||||||
|
|
||||||
|
|
||||||
client.publish("receiver/image", "Start");
|
|
||||||
|
|
||||||
#flushing before to begin
|
|
||||||
|
|
||||||
rgb(0,0,255)
|
|
||||||
for i in range(nb_step):
|
|
||||||
if (command=="image"):
|
|
||||||
pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
|
|
||||||
sleep(0.01)
|
|
||||||
else:
|
|
||||||
break
|
|
||||||
rgb(0,255,0)
|
|
||||||
|
|
||||||
while True:
|
|
||||||
|
|
||||||
counter+=1
|
|
||||||
print(datetime.now().strftime("%H_%M_%S_%f"))
|
|
||||||
filename = os.path.join("/home/pi/PlanktonScope/tmp",datetime.now().strftime("%M_%S_%f")+".jpg")
|
|
||||||
|
|
||||||
rgb(0,255,255)
|
|
||||||
camera.capture(filename)
|
|
||||||
rgb(0,255,0)
|
|
||||||
|
|
||||||
client.publish("receiver/image", datetime.now().strftime("%M_%S_%f")+".jpg has been imaged.");
|
|
||||||
|
|
||||||
rgb(0,0,255)
|
|
||||||
for i in range(10):
|
|
||||||
pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
|
|
||||||
sleep(0.01)
|
|
||||||
sleep(0.5)
|
|
||||||
rgb(0,255,0)
|
|
||||||
|
|
||||||
if(counter>nb_frame):
|
|
||||||
|
|
||||||
# camera.stop_preview()
|
|
||||||
|
|
||||||
client.publish("receiver/image", "Completed");
|
|
||||||
# Meta data that is added to every object
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
client.publish("receiver/segmentation", "Start");
|
|
||||||
# Define processing pipeline
|
|
||||||
|
|
||||||
|
|
||||||
p.run()
|
|
||||||
|
|
||||||
#remove directory
|
|
||||||
#shutil.rmtree(import_path)
|
|
||||||
|
|
||||||
client.publish("receiver/segmentation", "Completed");
|
|
||||||
|
|
||||||
|
|
||||||
cmd = os.popen("rm -rf /home/pi/PlanktonScope/tmp/*.jpg")
|
|
||||||
|
|
||||||
rgb(255,255,255)
|
|
||||||
sleep(sleep_during)
|
|
||||||
rgb(0,255,0)
|
|
||||||
|
|
||||||
|
|
||||||
rgb(0,0,255)
|
|
||||||
for i in range(nb_step):
|
|
||||||
pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
|
|
||||||
sleep(0.01)
|
|
||||||
rgb(0,255,0)
|
|
||||||
|
|
||||||
counter=0
|
|
||||||
|
|
||||||
|
|
||||||
if command!="image":
|
|
||||||
pump_stepper.release()
|
|
||||||
print("The imaging has been interrompted.")
|
|
||||||
client.publish("receiver/image", "Interrompted");
|
|
||||||
rgb(0,255,0)
|
|
||||||
counter=0
|
|
||||||
break
|
|
||||||
|
|
||||||
else:
|
|
||||||
# print("Waiting")
|
|
||||||
sleep(1)
|
|
||||||
Loading…
Reference in a new issue