pixelScan_injection.py

"""
Script to loop through pixels enabling one at a time, using astropix.py. 
Loop over full array and record from each pixel individually. 
Based off beam_test.py and example_loop.py

Author: Amanda Steinhebel

02/2023 Jihee Kim fixed injection enabled
        example) python3.9 pixelScan_injection.py -n "filename" -C 0 0 -R 0 0 -v 300.
"""

from astropix import astropix2
import modules.hitplotter as hitplotter
import os
import binascii
import pandas as pd
import numpy as np
import time
import logging
import argparse

from modules.setup_logger import logger


# This sets the logger name.
logdir = "./runlogs/"
if os.path.exists(logdir) == False:
    os.mkdir(logdir)
logname = "./runlogs/AstropixRunlog_" + time.strftime("%Y%m%d-%H%M%S") + ".log"



#Init 
def main(args,row,col, fpgaCon:bool=True, fpgaDiscon:bool=True):

    # Ensures output directory exists
    if os.path.exists(args.outdir) == False:
        os.mkdir(args.outdir)

    if fpgaCon:
        # Prepare everything, create the object
        global astro 
        logger.info('Initiate FPGA connection')
        if boolInj:
            astro = astropix2(inject=[row,col]) 
        else:        
            astro = astropix2()

    astro.init_voltages(vthreshold=args.threshold) 

    #Define YAML path variables
    pathdelim=os.path.sep #determine if Mac or Windows separators in path name
    ymlpath="config"+pathdelim+args.yaml+".yml"

    #Initiate asic with pixel mask as defined in yaml 
    #Updates injection pixel
    astro.asic_init(yaml=ymlpath, analog_col=col)

    #Enable single pixel in (col,row)
    #Updates asic by default
    astro.enable_pixel(col,row)

    #If injection, ensure injection pixel is enabled and initialize
    if boolInj is not None:
        astro.enable_injection(col,row)
        astro.init_injection(inj_voltage=args.vinj)

    astro.enable_spi() 
    logger.info("Chip configured")
    astro.dump_fpga()

    if boolInj is not None:
        astro.start_injection()

    i=0
    if args.maxtime is not None: 
        end_time=time.time()+(args.maxtime*60.)
    strPix = "_col"+str(col)+"_row"+str(row)+"_"
    fname=strPix if not args.name else args.name+strPix+"_"

    # Prepares the file paths 
    if args.saveascsv: # Here for csv
        csvpath = args.outdir +'/' + fname + time.strftime("%Y%m%d-%H%M%S") + '.csv'
        csvframe =pd.DataFrame(columns = [
                'readout',
                'Chip ID',
                'payload',
                'location',
                'isCol',
                'timestamp',
                'tot_msb',
                'tot_lsb',
                'tot_total',
                'tot_us',
                'hittime'
        ])

    # Prepares the file paths 
    # Save final configuration to output file    
    ymlpathout=args.outdir+pathdelim+args.yaml+"_"+fname+time.strftime("%Y%m%d-%H%M%S")+".yml"
    astro.write_conf_to_yaml(ymlpathout)
    # And here for the text files/logs
    bitpath = args.outdir + pathdelim + fname + time.strftime("%Y%m%d-%H%M%S") + '.log'
    bitfile = open(bitpath,'w')
    # Writes all the config information to the file
    bitfile.write(astro.get_log_header())
    bitfile.write(str(args))
    bitfile.write("\n")

    try: # By enclosing the main loop in try/except we are able to capture keyboard interupts cleanly    
        while (True): # Loop continues 
            # Break conditions
            if args.maxtime is not None:
                if time.time() >= end_time: break
            
            if astro.hits_present(): # Checks if hits are present
    
                time.sleep(.001) # this is probably not needed, will ask Nicolas

                readout = astro.get_readout(3) # Gets the bytearray from the chip

                # Writes the hex version to hits
                bitfile.write(f"{i}\t{str(binascii.hexlify(readout))}\n")
                print(binascii.hexlify(readout))

                # Added fault tolerance for decoding, the limits of which are set through arguments
                try:
                    hits = astro.decode_readout(readout, i, printer = True)
                finally:
                    i += 1
                    # If we are saving a csv this will write it out. 
                    if args.saveascsv:
                        csvframe = pd.concat([csvframe, hits])
            # If no hits are present this waits for some to accumulate
            else: time.sleep(.001)
    # Ends program cleanly when a keyboard interupt is sent.
    except KeyboardInterrupt:
        logger.info("Keyboard interupt. Program halt!")
    # Catches other exceptions
    except Exception as e:
        logger.exception(f"Encountered Unexpected Exception! \n{e}")
    finally:  
        if args.saveascsv: 
            csvframe.index.name = "dec_order"
            csvframe.to_csv(csvpath) 
        if boolInj is not None: astro.stop_injection() 
        bitfile.close() # Close open file       
        if fpgaDiscon:
            astro.close_connection() # Closes SPI
            logger.info('FPGA Connection ended')
        logger.info("Program terminated successfully")
    # END OF PROGRAM


    

if __name__ == "__main__":

    parser = argparse.ArgumentParser(description='Astropix Driver Code')
    parser.add_argument('-n', '--name', default='', required=False,
                    help='Option to give additional name to output files upon running')

    parser.add_argument('-o', '--outdir', default='.', required=False,
                    help='Output Directory for all datafiles')

    parser.add_argument('-y', '--yaml', action='store', required=False, type=str, default = 'testconfig',
                    help = 'filepath (in config/ directory) .yml file containing chip configuration. Default: config/testconfig.yml (All pixels off)')

    parser.add_argument('-t', '--threshold', type = float, action='store', default=None,
                    help = 'Threshold voltage for digital ToT (in mV). DEFAULT 100mV')

    parser.add_argument('-M', '--maxtime', type=float, action='store', default=None,
                    help = 'Maximum run time (in minutes)')

    parser.add_argument('-C', '--colrange', action='store', default=[0,34], type=int, nargs=2,
                    help =  'Loop over given range of columns. Default: 0 34')

    parser.add_argument('-R', '--rowrange', action='store', default=[0,34], type=int, nargs=2,
                    help =  'Loop over given range of rows. Default: 0 34')
                    
    parser.add_argument('-v','--vinj', action='store', default = None, type=float,
                    help = 'Specify injection voltage (in mV) to turn on injection. If argument not used, injection not enabled. DEFAULT None')
    
    parser.add_argument('-c', '--saveascsv', action='store_true', default=False, required=False, 
                    help='save output files as CSV. If False, save as txt. Default: FALSE')
    

    parser.add_argument
    args = parser.parse_args()
    
    # Logging
    loglevel = logging.INFO
    formatter = logging.Formatter('%(asctime)s:%(msecs)d.%(name)s.%(levelname)s:%(message)s')
    fh = logging.FileHandler(logname)
    fh.setFormatter(formatter)
    sh = logging.StreamHandler()
    sh.setFormatter(formatter)

    logging.getLogger().addHandler(sh) 
    logging.getLogger().addHandler(fh)
    logging.getLogger().setLevel(loglevel)

    logger = logging.getLogger(__name__)

    boolInj = True if args.vinj is not None else False

    #loop over full array by default, unless bounds are given as argument
    for c in range(args.colrange[0],args.colrange[1]+1,1):
        for r in range(args.rowrange[0],args.rowrange[1]+1,1):
            if r==args.rowrange[0] and c==args.colrange[0]:#first pixel probed - connect to FPGA but leave open
                main(args,r,c, fpgaDiscon=False)
            elif r==args.rowrange[1] and c==args.colrange[1]: #final pixel probed - disconnect from FPGA upon completion
                main(args,r,c, fpgaCon=False)
            else: #for bulk of pixels, FPGA is already open. Do not reconnect and do not disconnect when completed, leave it open for the next pixel
                main(args,r,c, fpgaCon=False, fpgaDiscon=False)