Update Acquisition.rst
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7430000772
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@ -125,383 +125,3 @@ D) Define simple sequence for I2C modules (Valves and pump)
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if feedback == 9:
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if feedback == 9:
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if verbose is True:
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if verbose is True:
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print("Pumping : Fast")
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print("Pumping : Fast")
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################################################################################
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def valve(state, verbose=True):
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sleep(0.2)
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if state is 'open_all':
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bus.write_byte(0x20, 1)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 1:
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if verbose:
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print("Valve : All open")
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if state is 'close_all':
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bus.write_byte(0x20, 0)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 0:
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if verbose:
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print("Valve : All closed")
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if state is 'open_in_sample':
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bus.write_byte(0x20, 2)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 2:
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if verbose:
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print("Valve : In sample open")
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if state is 'close_in_sample':
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bus.write_byte(0x20, 3)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 3:
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if verbose:
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print("Valve : In sample closed")
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if state is 'open_in_air':
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bus.write_byte(0x20, 4)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 4:
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if verbose:
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print("Valve : In air open")
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if state is 'close_in_air':
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bus.write_byte(0x20, 5)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 5:
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if verbose:
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print("Valve : In air closed")
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if state is 'open_in_bleach':
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bus.write_byte(0x20, 6)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 6:
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if verbose:
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print("Valve : In bleach open")
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if state is 'close_in_bleach':
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bus.write_byte(0x20, 7)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 7:
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if verbose:
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print("Valve : In bleach closed")
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if state is 'open_out_bleach':
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bus.write_byte(0x20, 8)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 8:
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if verbose:
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print("Valve : Out bleach open")
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if state is 'close_out_bleach':
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bus.write_byte(0x20, 9)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 9:
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if verbose:
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print("Valve : Out bleach closed")
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if state is 'open_out_sample':
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bus.write_byte(0x20, 10)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 10:
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if verbose:
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print("Valve : Out sample open")
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if state is 'close_out_sample':
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bus.write_byte(0x20, 11)
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sleep(1)
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feedback=bus.read_byte(0x20)
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if feedback == 11:
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if verbose:
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print("Valve : Out sample closed")
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################################################################################
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# E) Define simple functions making the whole sequence
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################################################################################
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#First function to run in order to turn on the blue LED as well as the relay to make the I2C operationnal
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def start():
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print("###############")
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print("STARTING")
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print("###############")
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#Inform on the statut of the operation
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print("Starting : engaged")
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#turn the blue LED ON (even if it's written off here)
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BLUE.off()
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print("Led : Blue on")
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#turn the circuit ON (even if it's written off here)
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RELAY.off()
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print("Relay : Activated")
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for i in range(3):
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GREEN.off()
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print("Led : Green on")
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RED.off()
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print("Led : Red on")
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sleep(0.1)
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GREEN.on()
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print("Led : Green off")
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RED.on()
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print("Led : Red off")
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sleep(0.1)
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directory="/pi/home/Desktop/PlanktonScope_acquisition/"
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#create a directory if the directory doesn't exist yet
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if not os.path.exists(directory):
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os.makedirs(directory)
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GREEN.off()
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#Inform on the statut of the operation
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print("Starting : done")
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################################################################################
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#This function will prepare the pump and the valves to realize the loading operation
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def init():
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print("###############")
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print("INITIALIZING")
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print("###############")
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#Inform on the statut of the operation
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print("Initializing : engaged")
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pump('forward', True)
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pump('stop', True)
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valve('open_in_sample', True)
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valve('open_out_sample', True)
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valve('close_in_air', True)
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valve('close_in_bleach', True)
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valve('close_out_bleach', True)
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#Inform on the statut of the operation
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print("Initializing : done")
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################################################################################
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#The load will simply load a sample by pumping fast during a long period
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def load():
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print("###############")
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print("LOADING")
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print("###############")
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#Inform on the statut of the operation
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print("Loading : engaged")
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pump('fast', True)
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#wait to complete the loading process and print info on the terminal
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for i in range(duration_loading):
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print("Loading : "+str(i)+"/"+str(duration_loading))
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sleep(1)
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#Inform on the statut of the operation
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print("Loading : done")
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################################################################################
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#flush will create some valving sequence to remove potential air trapped in the tubes
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def flush():
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print("###############")
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print("FLUSHING")
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print("###############")
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#Inform on the statut of the operation
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print("Flushing : engaged")
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valve('close_in_sample', True)
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valve('open_in_sample', True)
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valve('close_in_sample', True)
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valve('open_in_sample', True)
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pump('slow', True)
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#wait to complete the flushing process and print info on the terminal
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for i in range(duration_flushing):
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print("Flushing : "+str(i)+"/"+str(duration_flushing))
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sleep(1)
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#Inform on the statut of the operation
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print("Flushing : done")
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################################################################################
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#image is very a basci way to take images
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def image():
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print("###############")
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print("IMAGING")
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print("###############")
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#Inform on the statut of the operation
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print("Imaging : engaged")
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#start the preview only during the acquisition
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camera.start_preview(fullscreen=False, window = (160, 0, 640, 480))
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#allow the camera to warm up
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sleep(2)
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for frame in range(nb_frame):
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#turn the green LED ON (even if it's written off here)
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GREEN.off()
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sleep(0.5)
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#get the actual date
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date = datetime.now().strftime("%m_%d_%Y")
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directory="/pi/home/Desktop/PlanktonScope_acquisition/"+str(date)
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#create a directory if the directory doesn't exist yet
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if not os.path.exists(directory):
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os.makedirs(directory)
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#get the time now
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time = datetime.now().strftime("%H_%M_%S_%f")
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#create a filename from the date and the time
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filename="/pi/home/Desktop/PlanktonScope_acquisition/"+str(date)+"/"+str(time)+".jpg"
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#capture an image with the specified filename
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camera.capture(filename)
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#wait to complete the imaging process and print info on the terminal
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print("Imaging : "+str(frame)+"/"+str(nb_frame))
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#turn the green LED OFF (even if it's written on here)
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GREEN.on()
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sleep(0.5)
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#stop the preview during the rest of the sequence
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camera.stop_preview()
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GREEN.off()
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pump('stop', True)
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#Inform on the statut of the operation
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print("Imaging : done")
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################################################################################
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#aeration will remove the liquid from the tube and replace it by air
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def aeration():
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print("###############")
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print("AERATION")
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print("###############")
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#Inform on the statut of the operation
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print("Aeration : engaged")
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#remove liquid from tubes
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pump('stop', True)
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valve('close_all', True)
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valve('open_in_air', True)
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valve('open_out_sample', True)
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pump('medium', True)
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#wait to complete the aeration process and print info on the terminal
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for i in range(duration_aeration):
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print("Aerating : "+str(i)+"/"+str(duration_aeration))
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sleep(1)
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pump('stop', True)
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#Inform on the statut of the operation
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print("Aeration : done")
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################################################################################
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#wait will make the pi sleep until the next hour
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def wait():
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print("###############")
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print("WAITING")
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print("###############")
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#Inform on the statut of the operation
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print("Waiting : engaged")
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# Calculate the delay to the start of the next hour
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next_hour = (datetime.now() + timedelta(hour=1)).replace(
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minute=0, second=0, microsecond=0)
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delay = (next_hour - datetime.now()).seconds
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#wait to complete the waiting process and print info on the terminal
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for i in range(delay):
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print("Waiting : "+str(i)+"/"+str(delay))
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sleep(1)
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#Inform on the statut of the operation
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print("Waiting : done")
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################################################################################
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#stop will turn off the green LED and turn on the red one
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def stop():
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GREEN.on()
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print("Led : Green off")
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RED.off()
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print("Led : Red on")
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#Inform on the statut of the operation
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print("The sequence is done.")
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################################################################################
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# F) Execute the sequence
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################################################################################
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start()
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while True:
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init()
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load()
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flush()
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image()
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aeration()
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wait()
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stop()
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