adding function that calcualtes number of cardiac cycles and period of cardiac cycle

functions.py

@@ -5,14 +5,49 @@ Created on Thu Jul 16 15:08:27 2020
 @author: Aloma Blanch
 """
 
-
 import numpy as np
-import matplotlib.pyplot as plt
 import pandas as pd
-from statistics import mean 
+import matplotlib.pyplot as plt
-# from scipy.signal import find_peaks
 import matplotlib.transforms as mtransforms
 
+from math import floor
+from statistics import mean 
+from scipy.signal import find_peaks
+
+def cycle(folder,dt,save_path):
+    pressure = np.loadtxt(folder + '/PHistRCR.dat',skiprows=2)
+    N_ts = pressure.shape[0]
+    T = round(dt*N_ts,3)
+    time = np.linspace(0,T,N_ts)
+    # Find peaks, keep only the maximums
+    peaks, _ = find_peaks(pressure[:,-1])
+    idx = np.where(pressure[peaks,-1] >= np.mean(pressure))
+    peaks_loc = peaks[idx]
+    P_peaks = pressure[peaks,-1][pressure[peaks,-1] >= np.mean(pressure)]
+    # Rmove the multiple picks found in the same location
+    idx_del  = []
+    t_pk_loc = time[peaks_loc].tolist()
+    peak_tdiff = [t_pk_loc[n]-t_pk_loc[n-1] for n in range(1,len(t_pk_loc))]
+    for i in range(0,len(peak_tdiff)):
+        if peak_tdiff[i]<= dt*10:
+            idx_del.append(i)
+            t_pk_loc[i] = []
+            peak_tdiff[i] = []    
+    t_pk_loc[:] = [x for x in t_pk_loc if x]
+    peak_tdiff[:] = [x for x in peak_tdiff if x]
+    P_peaks = np.delete(P_peaks,idx_del)
+
+    fig, ax = plt.subplots()
+    ax.plot(time,pressure[:,-1]/1333.22,'b')
+    ax.plot(t_pk_loc, P_peaks/1333.22, "or",label='peak location')
+    ax.set(xlabel='time [s]', ylabel='Pressure [mmHg]',
+	   title='Pressure at last outlet')
+    ax.spines['right'].set_visible(False)
+    ax.spines['top'].set_visible(False)
+    ax.legend(loc=0)
+    # plt.show()
+    plt.savefig(save_path + '/Pressure_max_n_cycles.pdf')
+    return (floor(mean(peak_tdiff)*1000)/1000,len(t_pk_loc))
 
 def error_plot(folder,t_step,r_criteria,save_path):
     # Load iterations and residual error

main.py

@@ -20,7 +20,7 @@ import os.path
 # from fpdf import FPDF
 
 
-from functions import error_plot, periodicity, pressure, flow, inlet_flow_waveform, rcr
+from functions import error_plot, periodicity, pressure, flow, inlet_flow_waveform, rcr, cycle
 from generatePDF import generatePDF  
 
 
@@ -33,11 +33,6 @@ save_path = folder+'/'+project+'-report'
 os.mkdir(save_path)
 save_pdf = save_path + '/' + project + '-report.pdf'
 
-# 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.
@@ -56,6 +51,9 @@ t_btw_rst = int(mylines[6][37:-1])
 # Extracting Outlet Boundary Conditions from - rcrt.dat fle
 Rc_C_Rd = rcr(project_folder)
 
+# Extracting number of cycles and period of cardiac cycle
+(T_cyc,n_cyc) = cycle(folder,dt,save_path)
+        
 # Cehcking convergency and periodicity
 error_plot(folder,dt,rc,save_path)
 txt1 = periodicity(project,folder,dt,T_cyc,n_cyc,save_path)