auto_image_nikon_jobs.py

# -*- coding: utf-8 -*-
"""
On the fly drift correction interfacing with MyPIC
"""

import time
import os
from datetime import date
import logging
import json
import win32event

def update_status(new_data, filename='status.json'):
    '''
    Update selected field(s) in status.json file.
    Input:
        new_data: Dictionary with status commands.
        filename: Path to status json file.
    '''
    connected = False
    while not connected:
        try:
            with open(filename,'r') as f:
                data=json.load(f)
            for k,v in new_data.items():
                data[k]=new_data[k]
            with open(filename, 'w') as f:
                json.dump(data, f)
            logging.info('Status updated to: '+str(data))
            connected = True
            return
        except (json.decoder.JSONDecodeError, FileNotFoundError):
            print('status.json could not be opened, retrying...')
            time.sleep(5)

def read_status(filename='status.json'):
    '''
    Read out the status.json file.
    Also return the last modification time.
    '''
    connected = False
    while not connected:
        try:
            with open(filename,'r') as f:
                status = json.load(f)
                mtime = os.stat(filename).st_mtime
            connected = True
            return status, mtime
        except (json.decoder.JSONDecodeError, FileNotFoundError):
            print('status.json could not be opened, retrying...')
            time.sleep(5)

def set_command(command, filename='status.json'):
    '''
    Convenience function for setting current command in status json file.
    Input:
        command: string with text to go in command key dict in status json.
    '''
    update_status({'command':command}, filename)

def imaging_loop():
    '''
    Loop for automated imaging based on json input. Runs as follows:
        - Check if status json reports imaging.
        - Try to click resume button.
        - Starts loop to wait for completion of imaging.
        - Once complete, pause imaging again.
        - Send command for fluidics sequence to start to json.
    '''
    
    event_image_available = win32event.CreateEvent(None,0,0,"NIS_Image_Available")
    event_image_processed = win32event.CreateEvent(None,0,0,"NIS_Image_Processed")
    
    # Set original file modification time, only check status if file changed.
    _, status_mod_time_old = read_status()
    while True:
        status_mod_time_new = os.stat('status.json').st_mtime
        if status_mod_time_new != status_mod_time_old:
            time.sleep(2)
            status, _ = read_status()
            if status['command'] == 'image':
                logging.info('Image command found, starting imaging.')
                set_command('imaging')
                win32event.SetEvent(event_image_processed)
                win32event.ResetEvent(event_image_available)
                time.sleep(5)
                
                while True:
                    print("waiting for imaging completion...")
                    time.sleep(1)
                    win32event.WaitForSingleObject(event_image_available,-1)
                    print("Imaging completion event detected.")
                    break
                     
                logging.info('Imaging complete.')
                set_command('robot')
                _, status_mod_time_old = read_status()
        else:
            time.sleep(3)
 

def main_loop():
    
    '''
    Running function. Performs the following tasks:
    Checks if myPIC registry entries and status json files are available.    
    Initiate logging function. (Small modification for PIL in pyautogui to prevent internal DEBUG logging.)
    Launches automated imaging loop in seperate thread.
    Checks if new image available for analysis from myPIC. Perform drift correction on the fly, updating the stage position if so.
    '''
    if not os.path.isdir('logging'):
        os.mkdir('logging')
    logging.basicConfig(level=logging.DEBUG, filename='logging'+os.sep+str(date.today())+'_imaging.log',
                        filemode="a+", format="%(asctime)-15s %(levelname)-8s %(message)s")
    if len(logging.getLogger().handlers) < 2:
        logging.getLogger().addHandler(logging.StreamHandler())
    logging.getLogger('PIL').setLevel(logging.INFO)
    
    logging.info('AutoImage script initialized')
            
    imaging_loop()

if __name__ == '__main__':
    main_loop()