diff --git a/docs/Acquisition.rst b/docs/Acquisition.rst index 4e5f3ca..83e5041 100644 --- a/docs/Acquisition.rst +++ b/docs/Acquisition.rst @@ -1,499 +1,22 @@ .. _install: ============ -Acquisition +Installation ============ - #!/usr/bin/env python - # coding: utf-8 +.. currentmodule:: picamera - ################################################################################ - # A) Import the librairies needed to execute the script - ################################################################################ +.. _raspbian_install: - #Activate pinout to control the LEDs and the RELAY - from gpiozero import LED - - #Allow to access the I2C BUS from the Raspberry Pi - import smbus2 as smbus - - #Time librairy in order to sleep when need - from time import sleep - - #Picamera library to take images - from picamera import PiCamera - - #Enable calculation of remaining duration and datetime - from datetime import datetime, timedelta - - #Enable creation of new folders - import os - - - ################################################################################ - # B) Define the used pinout - ################################################################################ - - - #Affiliate pin to var for the LEDs - GREEN = LED(16) - RED = LED(12) - BLUE = LED(26) - - #Affiliate pin to var for the RELAY - RELAY = LED(14) - - - ################################################################################ - # C) Configuration file - ################################################################################ - - - camera = PiCamera() - - camera.resolution = (2592, 1944) - camera.iso = 60 - camera.exposure_mode = 'off' - camera.shutter_speed = 100 - camera.awb_mode = 'off' - camera.awb_gains = (2,1) - - nb_frame=300 - - duration_loading=120 #(sec) - duration_flushing=20 #(sec) - duration_aeration=30 #(sec) - - ################################################################################ - # D) Define simple sequence for I2C modules (Valves and pump) - ################################################################################ - - - def pump(state, verbose=True): - - sleep(0.2) - - if state is 'forward': - # Stop pumping - bus.write_byte(0x30, 1) - sleep(1) - feedback=bus.read_byte(0x30) - if feedback == 1: - if verbose is True: - print("Pumping : Forward") - - if state is 'backward': - # Stop pumping - bus.write_byte(0x30, 2) - sleep(1) - feedback=bus.read_byte(0x30) - if feedback == 2: - if verbose is True: - print("Pumping : Backward") - - if state is 'stop': - # Stop pumping - bus.write_byte(0x30, 0) - sleep(1) - feedback=bus.read_byte(0x30) - if feedback == 0: - if verbose is True: - print("Pumping : Stop") - - if state is 'slow': - # Start pumping - bus.write_byte(0x30, 3) - sleep(1) - feedback=bus.read_byte(0x30) - if feedback == 3: - if verbose is True: - print("Pumping : Slow") - - if state is 'medium': - # Start pumping - bus.write_byte(0x30, 5) - sleep(1) - feedback=bus.read_byte(0x30) - if feedback == 5: - if verbose is True: - print("Pumping : Medium") - - if state is 'fast': - # Start pumping - bus.write_byte(0x30, 9) - sleep(1) - feedback=bus.read_byte(0x30) - if feedback == 9: - if verbose is True: - print("Pumping : Fast") - - ################################################################################ - - - def valve(state, verbose=True): - - sleep(0.2) - - if state is 'open_all': - bus.write_byte(0x20, 1) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 1: - if verbose: - print("Valve : All open") - - if state is 'close_all': - bus.write_byte(0x20, 0) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 0: - if verbose: - print("Valve : All closed") - - - if state is 'open_in_sample': - bus.write_byte(0x20, 2) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 2: - if verbose: - print("Valve : In sample open") - - if state is 'close_in_sample': - bus.write_byte(0x20, 3) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 3: - if verbose: - print("Valve : In sample closed") - - if state is 'open_in_air': - bus.write_byte(0x20, 4) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 4: - if verbose: - print("Valve : In air open") - - if state is 'close_in_air': - bus.write_byte(0x20, 5) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 5: - if verbose: - print("Valve : In air closed") - - if state is 'open_in_bleach': - bus.write_byte(0x20, 6) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 6: - if verbose: - print("Valve : In bleach open") - - if state is 'close_in_bleach': - bus.write_byte(0x20, 7) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 7: - if verbose: - print("Valve : In bleach closed") - - if state is 'open_out_bleach': - bus.write_byte(0x20, 8) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 8: - if verbose: - print("Valve : Out bleach open") - - if state is 'close_out_bleach': - bus.write_byte(0x20, 9) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 9: - if verbose: - print("Valve : Out bleach closed") - - if state is 'open_out_sample': - bus.write_byte(0x20, 10) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 10: - if verbose: - print("Valve : Out sample open") - - if state is 'close_out_sample': - bus.write_byte(0x20, 11) - sleep(1) - feedback=bus.read_byte(0x20) - if feedback == 11: - if verbose: - print("Valve : Out sample closed") - - - ################################################################################ - # E) Define simple functions making the whole sequence - ################################################################################ - - - #First function to run in order to turn on the blue LED as well as the relay to make the I2C operationnal - def start(): - - print("###############") - print("STARTING") - print("###############") - - #Inform on the statut of the operation - print("Starting : engaged") - - #turn the blue LED ON (even if it's written off here) - BLUE.off() - print("Led : Blue on") - #turn the circuit ON (even if it's written off here) - RELAY.off() - print("Relay : Activated") - - for i in range(3): - GREEN.off() - print("Led : Green on") - RED.off() - print("Led : Red on") - sleep(0.1) - - GREEN.on() - print("Led : Green off") - RED.on() - print("Led : Red off") - sleep(0.1) - - - directory="/pi/home/Desktop/PlanktonScope_acquisition/" - #create a directory if the directory doesn't exist yet - if not os.path.exists(directory): - os.makedirs(directory) - - GREEN.off() - - #Inform on the statut of the operation - print("Starting : done") - - - ################################################################################ - - #This function will prepare the pump and the valves to realize the loading operation - def init(): - - print("###############") - print("INITIALIZING") - print("###############") - - #Inform on the statut of the operation - print("Initializing : engaged") - - pump('forward', True) - - pump('stop', True) - - valve('open_in_sample', True) - valve('open_out_sample', True) - - valve('close_in_air', True) - - valve('close_in_bleach', True) - valve('close_out_bleach', True) - - #Inform on the statut of the operation - print("Initializing : done") - - - ################################################################################ - - #The load will simply load a sample by pumping fast during a long period - def load(): - - print("###############") - print("LOADING") - print("###############") - - #Inform on the statut of the operation - print("Loading : engaged") - - pump('fast', True) - - #wait to complete the loading process and print info on the terminal - for i in range(duration_loading): - print("Loading : "+str(i)+"/"+str(duration_loading)) - sleep(1) - - #Inform on the statut of the operation - print("Loading : done") - - - ################################################################################ - - #flush will create some valving sequence to remove potential air trapped in the tubes - def flush(): - - print("###############") - print("FLUSHING") - print("###############") - - #Inform on the statut of the operation - print("Flushing : engaged") - - valve('close_in_sample', True) - valve('open_in_sample', True) - - valve('close_in_sample', True) - valve('open_in_sample', True) - - pump('slow', True) - - #wait to complete the flushing process and print info on the terminal - for i in range(duration_flushing): - print("Flushing : "+str(i)+"/"+str(duration_flushing)) - sleep(1) - - #Inform on the statut of the operation - print("Flushing : done") - - - ################################################################################ - - #image is very a basci way to take images - def image(): - - print("###############") - print("IMAGING") - print("###############") - - #Inform on the statut of the operation - print("Imaging : engaged") - - #start the preview only during the acquisition - camera.start_preview(fullscreen=False, window = (160, 0, 640, 480)) - #allow the camera to warm up - sleep(2) - - for frame in range(nb_frame): - - #turn the green LED ON (even if it's written off here) - GREEN.off() - sleep(0.5) - - #get the actual date - date = datetime.now().strftime("%m_%d_%Y") - directory="/pi/home/Desktop/PlanktonScope_acquisition/"+str(date) - - #create a directory if the directory doesn't exist yet - if not os.path.exists(directory): - os.makedirs(directory) - - #get the time now - time = datetime.now().strftime("%H_%M_%S_%f") - #create a filename from the date and the time - filename="/pi/home/Desktop/PlanktonScope_acquisition/"+str(date)+"/"+str(time)+".jpg" - - #capture an image with the specified filename - camera.capture(filename) - - #wait to complete the imaging process and print info on the terminal - print("Imaging : "+str(frame)+"/"+str(nb_frame)) - - #turn the green LED OFF (even if it's written on here) - GREEN.on() - sleep(0.5) - - #stop the preview during the rest of the sequence - camera.stop_preview() - - GREEN.off() - pump('stop', True) - - #Inform on the statut of the operation - print("Imaging : done") - - - ################################################################################ - - #aeration will remove the liquid from the tube and replace it by air - def aeration(): - - print("###############") - print("AERATION") - print("###############") - - #Inform on the statut of the operation - print("Aeration : engaged") - - #remove liquid from tubes - pump('stop', True) - - valve('close_all', True) - - valve('open_in_air', True) - valve('open_out_sample', True) - - pump('medium', True) - - #wait to complete the aeration process and print info on the terminal - for i in range(duration_aeration): - print("Aerating : "+str(i)+"/"+str(duration_aeration)) - sleep(1) - - pump('stop', True) - - #Inform on the statut of the operation - print("Aeration : done") - - - ################################################################################ - - #wait will make the pi sleep until the next hour - def wait(): - - print("###############") - print("WAITING") - print("###############") - - #Inform on the statut of the operation - print("Waiting : engaged") - - # Calculate the delay to the start of the next hour - next_hour = (datetime.now() + timedelta(hour=1)).replace( - minute=0, second=0, microsecond=0) - delay = (next_hour - datetime.now()).seconds - - #wait to complete the waiting process and print info on the terminal - for i in range(delay): - print("Waiting : "+str(i)+"/"+str(delay)) - sleep(1) - - #Inform on the statut of the operation - print("Waiting : done") - - - ################################################################################ - - #stop will turn off the green LED and turn on the red one - def stop(): - - GREEN.on() - print("Led : Green off") - RED.off() - print("Led : Red on") - - #Inform on the statut of the operation - print("The sequence is done.") - - - ################################################################################ - # F) Execute the sequence - ################################################################################ - +Raspbian installation +===================== +If you are using the `Raspbian`_ distro, it is best to install picamera using +the system's package manager: apt. This will ensure that picamera is easy to +keep up to date, and easy to remove should you wish to do so. It will also make +picamera available for all users on the system. To install picamera using apt +simply:: start() while True: