AES_plot.py

import matplotlib.pyplot as plt
from drawnow import drawnow, figure
import datetime
import csv
import numpy as np
from time import sleep
import pandas as pd

df=pd.read_csv('reference/elem_aes.csv',delimiter=',')

def peak_interval(Emin,Emax,df):
    '''Finds the 5 peak widths closest to the average energy of the current window and returns their lower bound, maximum, and upper bound. For derivative mode.'''
# in case all peaks within interval are desired
#    c1=df['DiffPeak'] < Emax
#    c2=df['DiffPeak'] > Emin
#    df=df[c1&c2]
    Eavg=(Emin+Emax)/2.
    df['|DiffPeak-Eavg|']=abs(df['DiffPeak']-Eavg)
    df=df.sort_values(by='|DiffPeak-Eavg|')
    df=df.iloc[0:5]
    l=(-df['LowerEnergy']).tolist()
    u=(-df['UpperEnergy']).tolist()
    dpeak=(-df['DiffPeak']).tolist()
    names=df['Element'].tolist()
    return [names,list(zip(l,dpeak,u))]

now=datetime.datetime.now()
time_stamp=str(now.year) +'-'+ str(now.month) +'-'+ str(now.day) +'-'+ str(now.hour)
time_stamp='2018-12-11-18'
time_plot_update=0.25
num_items=400

plotQ=True
AESx_lst=[]
AESy_lst=[]

def draw():
    plt.subplot(2,2,1)
    plt.plot(t,-1.*np.array(x),'bo-')
    plt.ylabel('Electron Beam Energy (eV)')
    plt.subplot(2,2,3)
    plt.ylabel('Counts (a.u.)')
    plt.xlabel('Time (s)')
    plt.plot(t,y,'bo-')
    plt.subplot(2,2,2)
    plt.plot(x,y)
    plt.xticks(np.linspace(min(x),max(x),10),
            [int(val) for val in np.round(-np.linspace(min(x),max(x),10))])
    plt.xlabel('Electron Beam Energy (eV)')
    plt.ylabel('Counts (a.u.)')
    interval=max(y)-min(y)
    for n,peak in enumerate(peaks):
        plt.plot(peak,[n*interval/len(peaks)]*3,'o-')
    plt.legend(names)

while plotQ:
    try:
        do_plot=open('setpoints/do_plot.control','r')
        for line in do_plot:
            plotQ=bool(line.rstrip('\n'))
        do_plot.close()
    except:
        plotQ=False

    time_lst=[]
    AESx_lst=[]
    AESy_lst=[]
    with open('out/AES_hist-'+time_stamp,'r') as AES_csv:
        AES_reader=csv.reader(AES_csv)
        for line in AES_reader:
            time,AESx,AESy=line
            time_lst.append(float(time))
            AESx_lst.append(float(AESx))
            AESy_lst.append(float(AESy))

    if len(time_lst) > num_items:
        time_lst=time_lst[-num_items:]
        AESx_lst=AESx_lst[-num_items:]
        AESy_lst=AESy_lst[-num_items:]
    t=time_lst #short-hand references
    x=AESx_lst
    y=AESy_lst
    names,peaks=peak_interval(min(-np.array(x)),max(-np.array(x)),df) #recall the signal voltage is negative
    drawnow(draw)
    sleep(time_plot_update)