Change: flow inlet plot, skyprow, +1...
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Aloma Blanch
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c3c570764b
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74
functions.py
74
functions.py
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@ -15,11 +15,10 @@ from math import floor
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from statistics import mean
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from scipy.signal import find_peaks
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def cycle(folder,dt,save_path):
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pressure = np.loadtxt(folder + '/PHistRCR.dat',skiprows=2)
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N_ts = pressure.shape[0]
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def cycle(folder,dt,N_ts,save_path):
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pressure = np.loadtxt(folder + '/PHistRCR.dat',skiprows=1)
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T = round(dt*N_ts,3)
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time = np.linspace(0,T,N_ts)
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time = np.linspace(0,T,N_ts+1)
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# Find peaks, keep only the maximums
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peaks, _ = find_peaks(pressure[:,-1])
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idx = np.where(pressure[peaks,-1] >= np.mean(pressure))
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@ -92,8 +91,8 @@ def error_plot(folder,t_step,r_criteria,save_path):
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def periodicity(project,folder,dt,T_cyc,n_cyc,save_path):
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pressure = np.loadtxt(folder+'/PHistRCR.dat',skiprows=2,)
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time = np.linspace(0,T_cyc*n_cyc,round(T_cyc/dt*n_cyc))
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pressure = np.loadtxt(folder+'/PHistRCR.dat',skiprows=1,)
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time = np.linspace(0,T_cyc*n_cyc,round(T_cyc/dt*n_cyc)+1)
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peak_P = []
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peak_P_pos = []
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Nc = round(T_cyc/dt)
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@ -119,10 +118,13 @@ def periodicity(project,folder,dt,T_cyc,n_cyc,save_path):
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if (peak_Pdiff[-1]<=1):
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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]))
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txt = ['The numerical simulation \'{0}\' has achieved periodicity.'.format(project), 'Systolic Blood Pressure (SBP):', 'Second-last cycle = {0:.2f} mmHg'.format(peak_P[-2]), 'Last cycle = {0:.2f} mmHg'.format(peak_P[-1]), 'Delta_mmHg = {0:.2f} mmHg'.format(peak_Pdiff[-1])]
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else:
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print('The numerical simulation \'{0}\' has not 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]))
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txt = ['The numerical simulation \'{0}\' has achieved periodicity.'.format(project), 'Systolic Blood Pressure (SBP):', 'Second-last cycle = {0:.2f} mmHg'.format(peak_P[-2]), 'Last cycle = {0:.2f} mmHg'.format(peak_P[-1]), 'Delta_mmHg = {0:.2f} mmHg'.format(peak_Pdiff[-1])]
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return txt
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def pressure(folder,N_ts,T_cyc,dt,n_cyc,save_path):
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pressure = np.loadtxt(folder+'/PHistRCR.dat',skiprows=2,)
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pressure = np.loadtxt(folder+'/PHistRCR.dat',skiprows=1,)
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Nc = round(T_cyc/dt)
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time = np.linspace(0,T_cyc,Nc)
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fig, ax = plt.subplots()
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@ -147,14 +149,14 @@ def pressure(folder,N_ts,T_cyc,dt,n_cyc,save_path):
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def flow(folder,N_ts,T_cyc,dt,n_cyc,save_path):
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flow = np.loadtxt(folder+'/QHistRCR.dat',skiprows=2,)
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flow = np.loadtxt(folder+'/QHistRCR.dat',skiprows=1,)
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Nc = round(T_cyc/dt)
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time = np.linspace(0,T_cyc,Nc)
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fig, ax = plt.subplots()
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Q = np.empty(flow.shape[1])
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for i in range(0,flow.shape[1]):
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ax.plot(time,flow[N_ts-Nc:N_ts,i],label='ROI-'+str(i+2))
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Q[i] = (mean(flow[N_ts-Nc:N_ts,i]))
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ax.plot(time,flow[N_ts-Nc+1:N_ts+1,i],label='ROI-'+str(i+2))
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Q[i] = (mean(flow[N_ts-Nc+1:N_ts+1,i]))
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ax.set(xlabel='time [s]', ylabel='Flow [mL/s]',
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title='Flow at each outlet')
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@ -169,7 +171,10 @@ def flow(folder,N_ts,T_cyc,dt,n_cyc,save_path):
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def inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc,save_path):
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x = np.loadtxt(project_folder+'/ROI-1.flow')
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t = x[:,0]
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Q = -x[:,1]
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if (x[4,1] < 0):
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Q = -x[:,1]
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else:
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Q = x[:,1]
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Nt_pts = np.linspace(t_btw_rst,N_ts,int(N_ts/t_btw_rst))
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t_pts = Nt_pts*dt
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# Put all the time values on a single cardiac cylce
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@ -224,10 +229,11 @@ def barPlot(project_folder,DBP,MBP,SBP,PP,Q_avg,save_path):
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aimed_all = [1] #No li agrada fer append en una llista buida, no recordo perquè i segur que es pot fer millor
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f = open(project_folder+'/aimed.txt', 'r') #obrir el fitxer
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for line in f:
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aimed_all = line.split() #fas una llista amb cada valor de la línia carregan-te els espais buits
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del aimed_all[0] #esborrar el primer valor que has posat perquè no estigues buida la llista
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aimed_all.append(line.split()) #fas una llista amb cada valor de la línia carregan-te els espais buits
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def plot_bar(CFD,aimed,name,save_path,unit):
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del aimed_all[0] #esborrar el primer valor que has posat perquè no estigues buida la llista
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def plot_bar(CFD,aimed,name,save_path,unit,decimals):
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labels = []
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for i in range(0,len(CFD)):
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labels.append('ROI-'+str(i+2))
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@ -243,19 +249,19 @@ def barPlot(project_folder,DBP,MBP,SBP,PP,Q_avg,save_path):
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ax.legend()
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high = max(max(aimed,CFD))
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ax.set_ylim(top = 1.7*high)
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def autolabel(rects):
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def autolabel(rects,decimals):
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"""Attach a text label above each bar in *rects*, displaying its height."""
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for rect in rects:
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height = rect.get_height()
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ax.annotate('{}'.format(height),
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ax.annotate(decimals.format(height),
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xy=(rect.get_x() + rect.get_width() / 2, height),
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xytext=(0,3), # 3 points vertical offset
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textcoords="offset points",
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ha='center', va='bottom',
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fontsize = 7.5)
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autolabel(rects1)
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autolabel(rects2)
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autolabel(rects1,decimals)
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autolabel(rects2,decimals)
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# Create labels
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err = []
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zip_object = zip(CFD, aimed)
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@ -272,26 +278,26 @@ def barPlot(project_folder,DBP,MBP,SBP,PP,Q_avg,save_path):
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fig.savefig(save_path + '/'+name+'_bar.jpg',dpi=150)
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# DBP
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CFD = [round(float(i),1) for i in DBP]
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aimed = [round(float(i),1) for i in aimed_all[0]]
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plot_bar(CFD,aimed,'DBP',save_path,' [mmHg]')
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CFD = [float(i) for i in DBP]
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aimed = [float(i) for i in aimed_all[0]]
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plot_bar(CFD,aimed,'DBP',save_path,' [mmHg]','{0:.1f}')
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# MBP
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CFD = [round(float(i),1) for i in MBP]
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aimed = [round(float(i),1) for i in aimed_all[1]]
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plot_bar(CFD,aimed,'MBP',save_path,' [mmHg]')
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CFD = [float(i) for i in MBP]
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aimed = [float(i) for i in aimed_all[1]]
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plot_bar(CFD,aimed,'MBP',save_path,' [mmHg]','{0:.1f}')
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# SBP
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CFD = [round(float(i),1) for i in SBP]
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aimed = [round(float(i),1) for i in aimed_all[2]]
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plot_bar(CFD,aimed,'SBP',save_path,' [mmHg]')
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CFD = [float(i) for i in SBP]
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aimed = [float(i) for i in aimed_all[2]]
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plot_bar(CFD,aimed,'SBP',save_path,' [mmHg]','{0:.1f}')
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# PP
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CFD = [round(float(i),1) for i in PP]
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aimed = [round(float(i),1) for i in aimed_all[3]]
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plot_bar(CFD,aimed,'PP',save_path,' [mmHg]')
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CFD = [float(i) for i in PP]
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aimed = [float(i) for i in aimed_all[3]]
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plot_bar(CFD,aimed,'PP',save_path,' [mmHg]','{0:.1f}')
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# DBP
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CFD = [round(float(i),1) for i in Q_avg]
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aimed = [round(float(i),1) for i in aimed_all[4]]
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plot_bar(CFD,aimed,'Q_avg',save_path,' [mL/s]')
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# Q_avg
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CFD = [float(i) for i in Q_avg]
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aimed = [float(i) for i in aimed_all[4]]
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plot_bar(CFD,aimed,'Q_avg',save_path,' [mL/s]','{0:.2f}')
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