Added plot bars for DBP, MBP, SBP, Q
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Aloma Blanch
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880667e488
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71
functions.py
71
functions.py
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@ -5,6 +5,7 @@ Created on Thu Jul 16 15:08:27 2020
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@author: Aloma Blanch
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"""
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import matplotlib
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import numpy as np
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import pandas as pd
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import matplotlib.pyplot as plt
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@ -47,7 +48,7 @@ def cycle(folder,dt,save_path):
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ax.legend(loc=0)
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# plt.show()
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plt.savefig(save_path + '/Pressure_max_n_cycles.pdf')
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return (floor(mean(peak_tdiff)*1000)/1000,len(t_pk_loc))
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return (floor(mean(peak_tdiff[1:])*1000)/1000,len(t_pk_loc))
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def error_plot(folder,t_step,r_criteria,save_path):
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# Load iterations and residual error
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@ -105,7 +106,7 @@ def periodicity(project,folder,dt,T_cyc,n_cyc,save_path):
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fig, ax = plt.subplots()
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ax.plot(time,pressure[:,-1]/1333.22,'b')
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ax.plot(time[peak_P_pos], peak_P,'ro',label='Cylce pike')
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ax.plot(time[peak_P_pos], peak_P,'ro',label='Cycle pike')
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ax.set(xlabel='time [s]', ylabel='Pressure [mmHg]',
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title='Pressure at last outlet')
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ax.spines['right'].set_visible(False)
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@ -219,4 +220,68 @@ def rcr(project_folder):
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Rc_C_Rd[i][2] = float(rcr_lines[4+i*6][:-1])
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return Rc_C_Rd
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def barPlot(project_folder,DBP,MBP,SBP,PP,Q_avg,save_path):
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import csv
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with open(project_folder+'/aimed.csv', 'r') as f:
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aimed_all = list(csv.reader(f, delimiter=';'))
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def plot_bar(CFD,aimed,name,save_path,unit):
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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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x = np.arange(len(labels)) # the label locations
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width = 0.38 # the width of the bars
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fig, ax = plt.subplots()
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rects1 = ax.bar(x - width/2, CFD, width, label='CFD',color='k')
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rects2 = ax.bar(x + width/2, aimed, width, label='Aimed',color='white', edgecolor='black', hatch='/')
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ax.set_ylabel(name + unit)
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ax.set_title(name)
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ax.set_xticks(x)
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ax.set_xticklabels(labels)
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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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"""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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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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fig.tight_layout()
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# plt.show()
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plt.savefig(save_path + '/'+name+'_bar.pdf')
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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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# 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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# 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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# 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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# 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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@ -135,14 +135,23 @@ def generatePDF(save_path,project,DBP,MBP,SBP,PP,Q_avg,txt1,txt2,Rc_C_Rd,T_cyc,n
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pdf.cell(width_cell[0],10,'ROI-'+ str(i+2),1,0,'C')
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pdf.cell(width_cell[1],10,str(round(Q_avg[i],3)),1,1,'C')
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pdf.print_section(4, 'Checking CFD values vs aimed')
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pdf.image(save_path +'/DBP_bar.jpg', x = 40, y = 50, w = 140, h = 100, type = '', link = '')
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pdf.image(save_path +'/MBP_bar.jpg', x = 40, y = 170, w = 140, h = 100, type = '', link = '')
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pdf.print_section(4, 'Checking CFD values vs aimed')
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pdf.image(save_path +'/SBP_bar.jpg', x = 40, y = 50, w = 140, h = 100, type = '', link = '')
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pdf.image(save_path +'/PP_bar.jpg', x = 40, y = 170, w = 140, h = 100, type = '', link = '')
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pdf.print_section(4, 'Checking CFD values vs aimed')
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pdf.image(save_path +'/Q_avg_bar.jpg', x = 40, y = 50, w = 140, h = 100, type = '', link = '')
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pdf.cell(0, 10,'', 0, 1)
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pdf.print_section(4, 'Checking Inlet Flow Waveform and time steps saved')
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pdf.print_section(5, 'Checking Inlet Flow Waveform and time steps saved')
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pdf.image(save_path +'/inlet_waveform.jpg', x = 40, y = 50, w = 140, h = 100, type = '', link = '')
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pdf.set_font('Arial', '', 10)
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pdf.cell(0, 5,txt2, 0, 1)
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width_cell=[30,20,110];
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pdf.print_section(5, 'Outlet Boundary Condition Applied')
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pdf.print_section(6, 'Outlet Boundary Condition Applied')
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pdf.set_font('Arial', '', 10)
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pdf.cell(0, 10,'3-Element Windkessel model outlet boundary condition applied in SimVascular', 0, 1)
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pdf.cell(0, 5,' ', 0, 1)
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@ -162,7 +171,7 @@ def generatePDF(save_path,project,DBP,MBP,SBP,PP,Q_avg,txt1,txt2,Rc_C_Rd,T_cyc,n
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pdf.cell(width_cell[0],10,str(Rc_C_Rd[i][1]),1,0,'C') # Third column of row 1
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pdf.cell(width_cell[0],10,str(Rc_C_Rd[i][2]),1,1,'C') # Third column of row 1
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pdf.print_section(6, 'Solver Parameters')
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pdf.print_section(7, 'Solver Parameters')
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pdf.set_font('Arial', '', 10)
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pdf.cell(0, 10,'Cardiac cycle period - ' + str(T_cyc) + 's', 0, 1)
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pdf.cell(0, 10,'Number of cycles - ' + str(n_cyc), 0, 1)
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7
main.py
7
main.py
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@ -20,7 +20,7 @@ import os.path
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# from fpdf import FPDF
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from functions import error_plot, periodicity, pressure, flow, inlet_flow_waveform, rcr, cycle
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from functions import error_plot, periodicity, pressure, flow, inlet_flow_waveform, rcr, cycle, barPlot
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from generatePDF import generatePDF
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@ -53,7 +53,7 @@ Rc_C_Rd = rcr(project_folder)
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# Extracting number of cycles and period of cardiac cycle
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(T_cyc,n_cyc) = cycle(folder,dt,save_path)
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T_cyc=0.477
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# Cehcking convergency and periodicity
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error_plot(folder,dt,rc,save_path)
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txt1 = periodicity(project,folder,dt,T_cyc,n_cyc,save_path)
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@ -67,5 +67,8 @@ txt1 = periodicity(project,folder,dt,T_cyc,n_cyc,save_path)
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# Inlet Flow Rate + and t saved
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txt2 = inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc,save_path)
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# Extract bar plots CFD vs. aimed
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barPlot(project_folder,DBP,MBP,SBP,PP,Q_avg,save_path)
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# Create PDF report
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generatePDF(save_path,project,DBP,MBP,SBP,PP,Q_avg,txt1,txt2,Rc_C_Rd,T_cyc,n_cyc,N_ts,dt)
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