Creating the PDF output
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Aloma Blanch
parent
e079927b84
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1e4ef53bc6
88
functions.py
88
functions.py
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@ -12,7 +12,7 @@ from scipy.signal import find_peaks
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import matplotlib.transforms as mtransforms
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def error_plot(folder,t_step,r_criteria,save):
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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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histor = folder + '/histor.dat'
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input = open(histor, 'r')
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@ -29,30 +29,31 @@ def error_plot(folder,t_step,r_criteria,save):
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error.append(error_info[2][n-1])
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time = np.linspace(start = t_step, stop = len(error)*t_step, num = len(error))
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# Plots of interest
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# Liniar Scale
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plt.figure()
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plt.plot(time,error)
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plt.plot(time,r_criteria*np.ones(len(error)),'r')
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plt.ylabel('Residual error')
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plt.xlabel('Time steps')
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plt.title('Last nonlinear residual error for each time step')
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plt.grid(True)
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if save: plt.savefig(plt_folder + case + '_Last_nonlin_res_error.pdf')
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fig, ax = plt.subplots()
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ax.plot(time,error)
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ax.plot(time,r_criteria*np.ones(len(error)),'r')
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ax.set(xlabel='Time steps', ylabel='Residual error',
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title='Last nonlinear residual error for each time step')
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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plt.show()
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plt.savefig(save_path + '/Last_nonlin_res_error.pdf')
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# Semilog scale
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plt.figure()
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plt.semilogy(time,error)
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plt.semilogy(time,r_criteria*np.ones(len(error)),'r')
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plt.ylabel('Residual error')
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plt.xlabel('Time steps')
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plt.title('Log - Last nonlinear residual error for each time step')
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plt.grid(True)
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if save: plt.savefig(plt_folder + case + '_Log_Last_nonlin_res_error.pdf')
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fig, ax = plt.subplots()
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ax.semilogy(time,error)
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ax.semilogy(time,r_criteria*np.ones(len(error)),'r')
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ax.set(xlabel='Time steps', ylabel='Residual error',
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title='Log - Last nonlinear residual error for each time step')
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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plt.show()
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plt.savefig(save_path + '/Log_Last_nonlin_res_error.pdf')
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fig.savefig(save_path + '/Log_Last_nonlin_res_error.jpg',dpi=150)
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def periodicity(project,folder,dt,T_cyc,n_cyc):
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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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peak_P = []
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@ -66,19 +67,23 @@ def periodicity(project,folder,dt,T_cyc,n_cyc):
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peak_Pdiff = list(map(abs, peak_Pdiff))
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fig, ax = plt.subplots()
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ax.plot(time,pressure[:,-1]/1333.22)
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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.set(xlabel='time [s]', ylabel='Pressure [mmHg]',
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title='Pressure @ last outlet')
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title='Pressure at last outlet')
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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ax.legend(loc=0)
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plt.show()
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plt.savefig(save_path + '/periodicity.pdf')
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fig.savefig(save_path + '/periodicity.jpg',dpi=150)
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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]))
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def pressure(folder,N_ts,T_cyc,dt,n_cyc):
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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 achieve periodicity!\nSystolic Blood Pressure (SBP):\nsecond-last cycle = {1:.2f} mmHg,\nlast cycle = {2:.2f} mmHg,\nDelta_mmHg = {3:.2f} mmHg'.format(project,peak_P[-2],peak_P[-1],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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Nc = round(T_cyc/dt)
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time = np.linspace(0,T_cyc,Nc)
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@ -93,15 +98,17 @@ def pressure(folder,N_ts,T_cyc,dt,n_cyc):
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MBP[i] = (mean(pressure[N_ts-Nc:N_ts,i]/1333.22))
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PP = SBP-DBP
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ax.set(xlabel='time [s]', ylabel='Pressure [mmHg]',
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title='Pressure @ each outlet')
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title='Pressure at each outlet')
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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ax.legend(loc=0)
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plt.show()
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plt.savefig(save_path + '/pressure.pdf')
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fig.savefig(save_path + '/pressure.jpg',dpi=150)
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return (DBP,MBP,SBP,PP)
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def flow(folder,N_ts,T_cyc,dt,n_cyc):
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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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Nc = round(T_cyc/dt)
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time = np.linspace(0,T_cyc,Nc)
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@ -112,14 +119,16 @@ def flow(folder,N_ts,T_cyc,dt,n_cyc):
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Q[i] = (mean(flow[N_ts-Nc:N_ts,i]))
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ax.set(xlabel='time [s]', ylabel='Flow [mL/s]',
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title='Flow @ each outlet')
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title='Flow at each outlet')
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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ax.legend(loc=0)
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plt.show()
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plt.savefig(save_path + '/flow.pdf')
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fig.savefig(save_path + '/flow.jpg',dpi=150)
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return Q
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def inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc):
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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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@ -136,12 +145,11 @@ def inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc):
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fig, ax = plt.subplots()
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ax.plot(t, Q, 'r')
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ax.plot(t_pts, Q_pts, 'ob')
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ax.plot(t_pts, Q_pts, 'ob',label='Time steps saved')
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trans_offset = mtransforms.offset_copy(ax.transData, fig=fig,
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x=-0, y=0.15, units='inches')
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ax.set(xlabel='Time [s]', ylabel='Flow Rate - Q [mL/s]',
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title='Inlet Flow rate Waveform - 1 cycle')
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title='Inlet Flow Rate Waveform')
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ax.set_ylim([-10, 90])
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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@ -151,8 +159,14 @@ def inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc):
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for i in range(0,np.unique(np.round(t_pts,3)).shape[0]):
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time.append('$t_'+str(i+1)+'$')
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for x, y, t in zip(t_pts[(-n_cyc-1):], Q_pts[(-n_cyc-1):], time):
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plt.text(x, y, t, transform=trans_offset, fontsize=12)
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plt.text(x, y, t, transform=trans_offset, fontsize=12)
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ax.legend(loc=0)
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plt.show()
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plt.savefig(save_path + '/inlet_waveform.pdf')
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fig.savefig(save_path + '/inlet_waveform.jpg',dpi=150)
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print('{0} time steps saved, available to visualize in ParaView.'.format(np.unique(np.round(t_pts,3)).shape[0]))
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txt = '{0} time steps saved, available to visualize in ParaView.'.format(np.unique(np.round(t_pts,3)).shape[0])
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return txt
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36
main.py
36
main.py
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@ -11,6 +11,7 @@ import os.path
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from scipy.signal import find_peaks_cwt
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from scipy import signal
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import statistics
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from fpdf import FPDF
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from functions import error_plot, periodicity, pressure, flow, inlet_flow_waveform
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@ -20,6 +21,9 @@ Tk().withdraw()
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folder = askdirectory()
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project_folder = os.path.dirname(folder)
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project = os.path.basename(project_folder)
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save_path = folder+'/'+project+'-report'
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# os.mkdir(save_path)
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save_pdf = save_path + '/' + project + '-report.pdf'
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# Input parameters
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T_cyc = 0.477
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@ -42,14 +46,36 @@ rc = float(mylines[26][18:-1])
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t_btw_rst = int(mylines[6][37:-1])
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# Cehcking convergency and periodicity
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error_plot(folder,dt,rc,False)
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periodicity(project,folder,dt,T_cyc,n_cyc)
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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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# Pressure - Outlets
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(DBP,MBP,SBP,PP) = pressure(folder,N_ts,T_cyc,dt,n_cyc)
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(DBP,MBP,SBP,PP) = pressure(folder,N_ts,T_cyc,dt,n_cyc,save_path)
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# Flow Rate - Outlets
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(Q_avg) = flow(folder,N_ts,T_cyc,dt,n_cyc)
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(Q_avg) = flow(folder,N_ts,T_cyc,dt,n_cyc,save_path)
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# Inlet Flow Rate + and t saved
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inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc)
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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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# Create PDF report
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pdf = FPDF('P','mm','Letter')
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pdf.add_page()
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pdf.set_font('Times', 'B', 18)
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pdf.cell(200, 20, 'Project name: '+ project, 0, 1, 'C')
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# Keep this ratio - 5.42/3.86
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pdf.set_font('Times', '', 14)
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pdf.cell(200, 30, 'Cehcking convergency and periodicity:', 0, 1, 'L')
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pdf.image(save_path +'/Log_Last_nonlin_res_error.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '')
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pdf.image(save_path +'/periodicity.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '')
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pdf.cell(200, 20, 'Cehcking Pressures at each outlet:', 0, 1, 'L')
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pdf.image(save_path +'/pressure.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '')
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pdf.cell(200, 20, 'Cehcking Flow Rate at each outlet:', 0, 1, 'L')
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pdf.image(save_path +'/flow.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '')
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pdf.image(save_path +'/inlet_waveform.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '')
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pdf.output(save_pdf, 'F')
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