commit d6416a4977709edf6496401e5b22b9902d6774f8
Author: Aloma Blanch <aloma_b@hotmail.com>
Date:   Thu Jul 16 19:41:59 2020 -0500

    First part of the post process script. Error and periodicity

diff --git a/functions.py b/functions.py
new file mode 100644
index 0000000..886d970
--- /dev/null
+++ b/functions.py
@@ -0,0 +1,78 @@
+ #!/usr/bin/env python
+
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.ticker as mtick
+from tkinter import Tk
+from tkinter.filedialog import askopenfilename, asksaveasfile, askdirectory
+import pandas as pd
+import tkinter as tk
+from scipy.signal import find_peaks
+
+
+def error_plot(folder,t_step,r_criteria,save):
+    # Load iterations and residual error
+    histor = folder + '/histor.dat'
+    input = open(histor, 'r')
+    output = open(folder + "/histor_better.dat", 'w')
+    output.writelines(line.strip() +'\n' for line in input)
+    input.close()
+    output.close()
+    error_info = pd.read_csv(folder + "/histor_better.dat", sep=' ', header=None, usecols=(0,1,2))
+
+    # Select only last iteration of residual error
+    error=[] 
+    for n in range(1,error_info.shape[0]):
+        if (error_info[0][n]>error_info[0][n-1]):
+            error.append(error_info[2][n-1])
+
+    time = np.linspace(start = t_step, stop = len(error)*t_step, num = len(error))
+    
+    # Plots of interest
+    # Liniar Scale
+    plt.figure()  
+    plt.plot(time,error)
+    plt.plot(time,r_criteria*np.ones(len(error)),'r')
+    plt.ylabel('Residual error')
+    plt.xlabel('Time steps')
+    plt.title('Last nonlinear residual error for each time step')
+    plt.grid(True)
+    if save: plt.savefig(plt_folder + case + '_Last_nonlin_res_error.pdf')
+
+    # Semilog scale
+    plt.figure()  
+    plt.semilogy(time,error)
+    plt.semilogy(time,r_criteria*np.ones(len(error)),'r:')
+    plt.ylabel('Residual error')
+    plt.xlabel('Time steps')
+    plt.title('Log - Last nonlinear residual error for each time step')
+    plt.grid(True)
+    if save: plt.savefig(plt_folder + case + '_Log_Last_nonlin_res_error.pdf')
+    
+
+def periodicity(project,folder,dt,T_cyc,n_cyc):
+    pressure = np.loadtxt(folder+'/PHistRCR.dat',skiprows=2,)
+    time = np.linspace(0,T_cyc*n_cyc,round(T_cyc/dt*n_cyc))
+    peak_P = []
+    peak_P_pos = []
+    Nc = round(T_cyc/dt)
+    for i in range(0,n_cyc):
+        peak_P.append(np.amax(pressure[i*Nc:Nc*(i+1),-1])/1333.22)
+        peak_P_pos.append(np.where(pressure[i*Nc:Nc*(i+1),-1] == np.amax(pressure[i*Nc:Nc*(i+1),-1]))[0][0]+Nc*i)
+    
+    peak_Pdiff = [peak_P[n]-peak_P[n-1] for n in range(1,len(peak_P))]
+    peak_Pdiff = list(map(abs, peak_Pdiff)) 
+    
+    fig, ax = plt.subplots()
+    ax.plot(time,pressure[:,-1]/1333.22)
+    ax.plot(time[peak_P_pos], peak_P,'ro',label='Cylce pike')
+    ax.set(xlabel='time [s]', ylabel='Pressure [mmHg]',
+        title='Pressure @ last outlet')
+    ax.spines['right'].set_visible(False)
+    ax.spines['top'].set_visible(False)
+    ax.legend(loc=0)
+    plt.show()
+    
+    if (peak_Pdiff[-1]<=1): print('The numerical simulation \'{0}\' has achieve periodicity!\nSystolic Blood Pressure (SBP):\nsecond-last cycle = {1:.2f} mmHg,\nlast cycle = {2:.2f} mmHg,\n\u0394mmHg = {3:.2f} mmHg'.format(project,peak_P[-2],peak_P[-1],peak_Pdiff[-1]))  
+
+
diff --git a/main.py b/main.py
new file mode 100644
index 0000000..d48278c
--- /dev/null
+++ b/main.py
@@ -0,0 +1,51 @@
+ #!/usr/bin/env python
+
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.ticker as mtick
+from tkinter import Tk
+from tkinter.filedialog import askopenfilename, asksaveasfile, askdirectory
+import pandas as pd
+import tkinter as tk
+import os.path
+from scipy.signal import find_peaks_cwt
+from scipy import signal
+import statistics
+
+
+from functions import error_plot, periodicity
+  
+# Selct dir 
+Tk().withdraw()
+folder = askdirectory()
+project_folder = os.path.dirname(folder)
+project = os.path.basename(project_folder)
+
+# Input parameters
+T_cyc = 0.477
+n_cyc = 5
+
+
+# Read important parameters from - solver.inp file
+mylines = []                             # Declare an empty list named mylines.
+with open (project_folder + '/solver.inp', 'rt') as myfile: # Open lorem.txt for reading text data.
+    for myline in myfile:                # For each line, stored as myline,
+        mylines.append(myline)           # add its contents to mylines.
+# print(mylines)
+
+
+# Number of Timesteps - idx 3
+# Idea: remove the text to extract the number, the text part will be the same no matter the simulation
+N_ts = int(mylines[3][20:-1])
+
+# Time Step Size - idx 4
+dt = float(mylines[4][16:-1])
+
+# Residual criteria - idx 4
+rc = float(mylines[26][18:-1])
+
+# Cehcking convergency and periodicity
+error_plot(folder,dt,rc,False)
+periodicity(project,folder,dt,T_cyc,n_cyc)
+
+