# Berendsen's code 2.5 for Fig.2.7

import matplotlib.pyplot as plt
import numpy as np 

fname = 'tab2.5.csv'
time = []
conc = []
err = []

def readMyFile(fname):
    dx = np.arange(4,dtype='f')
    file = open(fname, 'r', encoding='utf-8')
    a_line = file.readline()
    l = len(a_line)
    a_line = a_line[:l-1]
    result = a_line.split(',')
    print("Header of the file '" + fname + "': " + a_line)
   
    for x in reversed(result):  # remove ""
        if len(x)>0:
            break
        else:
            result.remove(x)
            
    n_item = len(result)
#    print(result, ', ', n_item, ' items')

    i = 0
    while (True):
        a_line = file.readline()
        l = len(a_line)
        a_line = a_line[:l-1]
        if len(a_line)==0:            # end of file
            break
        result = a_line.split(',')
#        print(i+1,') ',result)
        print('(',i+1,') ', end='')
        for j in range(n_item):
#            print(j,n_item)
            dx[j] = float(result[j])
            print(f"{dx[j]:,.2f}  ", end="")
        print() 
        i += 1
 
        time.append(dx[0])  
        conc.append(dx[1])
        err.append(dx[2])  
    file.close()
    print('data =',i,', item=',n_item,', file =',fname)
    
#--------- Main program starts here -----------
readMyFile(fname)    # vectors are read from file

fig, ax = plt.subplots()
ax.plot(time,conc,lw=2,ls='-',marker='o',ms=5,mec='r',mew=2,mfc='r')
ax.set_yscale('log')

pos = [1, 10, 100] 
# ax.set_yticks(pos)
# ticks = ['1', '10', '100']
# ax.set_yticklabels(ticks)

# plt.semilogy(time, conc)')
plt.errorbar(time, conc, err)
plt.grid(axis='y', which='both')
plt.grid(axis='x', which='major')

font1 = {'family':'serif','color':'blue','size':13}

plt.xlabel('time $t$/s',fontdict = font1 )
plt.ylabel('concentration $c$/mmol L$^{-1}$',fontdict = font1)
plt.title('Code 2.5 for Fig.2.7')

plt.show()
# fig.savefig('plot of fig.2.7.png')