aloma/SimVascular_report_PostProcess
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Compare commits

base: aloma:ca94398ec87ada97abd627996f8109a5618975d8
Branches Tags
aloma:master
..
compare: aloma:e77d6f0d9a513a8bd5ffa6aae72e5cf60d8027e4
Branches Tags
aloma:master

2 Commits
ca94398ec8 ... e77d6f0d9a

Author SHA1 Message Date
Aloma Blanch
e77d6f0d9a Improve the looking of the PDF output, centering figures and tables, changing font... 2020-07-17 07:44:15 -05:00
Aloma Blanch
6dcd1a4641 Removing unnecessary libraries 2020-07-17 06:48:51 -05:00
3 changed files with 48 additions and 39 deletions
Show Stats Expand all files Collapse all files

18
functions.py
View File

@ -8,13 +8,9 @@ Created on Thu Jul 16 15:08:27 2020
import numpy as np import numpy as np
import matplotlib.pyplot as plt 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 pandas as pd
import tkinter as tk
from statistics import mean from statistics import mean
from scipy.signal import find_peaks # from scipy.signal import find_peaks
import matplotlib.transforms as mtransforms import matplotlib.transforms as mtransforms
@ -44,7 +40,7 @@ def error_plot(folder,t_step,r_criteria,save_path):
title='Last nonlinear residual error for each time step') title='Last nonlinear residual error for each time step')
ax.spines['right'].set_visible(False) ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False) ax.spines['top'].set_visible(False)
plt.show() # plt.show()
plt.savefig(save_path + '/Last_nonlin_res_error.pdf') plt.savefig(save_path + '/Last_nonlin_res_error.pdf')
# Semilog scale # Semilog scale
fig, ax = plt.subplots() fig, ax = plt.subplots()
@ -54,7 +50,7 @@ def error_plot(folder,t_step,r_criteria,save_path):
title='Log - Last nonlinear residual error for each time step') title='Log - Last nonlinear residual error for each time step')
ax.spines['right'].set_visible(False) ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False) ax.spines['top'].set_visible(False)
plt.show() # plt.show()
plt.savefig(save_path + '/Log_Last_nonlin_res_error.pdf') plt.savefig(save_path + '/Log_Last_nonlin_res_error.pdf')
fig.savefig(save_path + '/Log_Last_nonlin_res_error.jpg',dpi=150) fig.savefig(save_path + '/Log_Last_nonlin_res_error.jpg',dpi=150)
@ -80,7 +76,7 @@ def periodicity(project,folder,dt,T_cyc,n_cyc,save_path):
ax.spines['right'].set_visible(False) ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False) ax.spines['top'].set_visible(False)
ax.legend(loc=0) ax.legend(loc=0)
plt.show() # plt.show()
plt.savefig(save_path + '/periodicity.pdf') plt.savefig(save_path + '/periodicity.pdf')
fig.savefig(save_path + '/periodicity.jpg',dpi=150) fig.savefig(save_path + '/periodicity.jpg',dpi=150)
@ -109,7 +105,7 @@ def pressure(folder,N_ts,T_cyc,dt,n_cyc,save_path):
ax.spines['right'].set_visible(False) ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False) ax.spines['top'].set_visible(False)
ax.legend(loc=0) ax.legend(loc=0)
plt.show() # plt.show()
plt.savefig(save_path + '/pressure.pdf') plt.savefig(save_path + '/pressure.pdf')
fig.savefig(save_path + '/pressure.jpg',dpi=150) fig.savefig(save_path + '/pressure.jpg',dpi=150)
return (DBP,MBP,SBP,PP) return (DBP,MBP,SBP,PP)
@ -130,7 +126,7 @@ def flow(folder,N_ts,T_cyc,dt,n_cyc,save_path):
ax.spines['right'].set_visible(False) ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False) ax.spines['top'].set_visible(False)
ax.legend(loc=0) ax.legend(loc=0)
plt.show() # plt.show()
plt.savefig(save_path + '/flow.pdf') plt.savefig(save_path + '/flow.pdf')
fig.savefig(save_path + '/flow.jpg',dpi=150) fig.savefig(save_path + '/flow.jpg',dpi=150)
return Q return Q
@ -168,7 +164,7 @@ def inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc,save_path):
for x, y, t in zip(t_pts[(-n_cyc-1):], Q_pts[(-n_cyc-1):], time): for x, y, t in zip(t_pts[(-n_cyc-1):], Q_pts[(-n_cyc-1):], time):
plt.text(x, y, t, transform=trans_offset, fontsize=12) plt.text(x, y, t, transform=trans_offset, fontsize=12)
ax.legend(loc=0) ax.legend(loc=0)
plt.show() # plt.show()
plt.savefig(save_path + '/inlet_waveform.pdf') plt.savefig(save_path + '/inlet_waveform.pdf')
fig.savefig(save_path + '/inlet_waveform.jpg',dpi=150) fig.savefig(save_path + '/inlet_waveform.jpg',dpi=150)
print('{0} time steps saved, available to visualize in ParaView.'.format(np.unique(np.round(t_pts,3)).shape[0])) print('{0} time steps saved, available to visualize in ParaView.'.format(np.unique(np.round(t_pts,3)).shape[0]))

45
generatePDF.py
View File

@ -83,19 +83,26 @@ def generatePDF(save_path,project,DBP,MBP,SBP,PP,Q_avg,txt1,txt2):
pdf.set_title(title) pdf.set_title(title)
pdf.set_author('Aloma Blanch Granada') pdf.set_author('Aloma Blanch Granada')
pdf.print_section(1, 'Cehcking convergency and periodicity') pdf.print_section(1, 'Checking convergency and periodicity')
pdf.image(save_path +'/Log_Last_nonlin_res_error.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '') pdf.image(save_path +'/Log_Last_nonlin_res_error.jpg', x = 40, y = None, w = 140, h = 100, type = '', link = '')
pdf.image(save_path +'/periodicity.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '') pdf.image(save_path +'/periodicity.jpg', x = 40, y = None, w = 140, h = 100, type = '', link = '')
pdf.cell(0, 10,txt1[0], 0, 1) pdf.set_font('Arial', '', 10)
pdf.cell(0, 10,txt1[1], 0, 1) pdf.cell(0, 10,' ', 0, 1)
pdf.cell(0, 10,txt1[2], 0, 1) pdf.cell(0, 5,txt1[0], 0, 1)
pdf.cell(0, 5,txt1[1], 0, 1)
pdf.cell(0, 5,txt1[2], 0, 1)
pdf.cell(0, 5,txt1[3], 0, 1)
pdf.cell(0, 5,txt1[4], 0, 1)
pdf.print_section(2, 'Cehcking Pressures at each outlet') pdf.print_section(2, 'Checking Pressures at each outlet')
pdf.image(save_path +'/pressure.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '') pdf.image(save_path +'/pressure.jpg', x = 40, y = None, w = 140, h = 100, type = '', link = '')
width_cell=[20,30,30,30,30,30,30]; width_cell=[20,30,30,30,30,30,30];
# pfd.SetFillColor(193,229,252); # Background color of header # pfd.SetFillColor(193,229,252); # Background color of header
pdf.set_font('Times', '', 10)
# Header starts # Header starts
pdf.cell(0, 25,' ', 0, 1)
pdf.set_x(35)
pdf.cell(width_cell[0],10,'ROI',1,0,'C') # First header column pdf.cell(width_cell[0],10,'ROI',1,0,'C') # First header column
pdf.cell(width_cell[1],10,'DBP [mmHg]',1,0,'C') # Second header column pdf.cell(width_cell[1],10,'DBP [mmHg]',1,0,'C') # Second header column
pdf.cell(width_cell[2],10,'MBP [mmHg]',1,0,'C') # Third header column pdf.cell(width_cell[2],10,'MBP [mmHg]',1,0,'C') # Third header column
@ -103,6 +110,7 @@ def generatePDF(save_path,project,DBP,MBP,SBP,PP,Q_avg,txt1,txt2):
pdf.cell(width_cell[4],10,'PP [mmHg]',1,1,'C') # Fourth header column pdf.cell(width_cell[4],10,'PP [mmHg]',1,1,'C') # Fourth header column
# Rows # Rows
for i in range(0,len(SBP)): for i in range(0,len(SBP)):
pdf.set_x(35)
pdf.cell(width_cell[0],10,'ROI-'+ str(i+2),1,0,'C') # First column of row 1 pdf.cell(width_cell[0],10,'ROI-'+ str(i+2),1,0,'C') # First column of row 1
pdf.cell(width_cell[1],10,str(round(DBP[i],2)),1,0,'C') # Second column of row 1 pdf.cell(width_cell[1],10,str(round(DBP[i],2)),1,0,'C') # Second column of row 1
pdf.cell(width_cell[2],10,str(round(MBP[i],2)),1,0,'C') # Third column of row 1 pdf.cell(width_cell[2],10,str(round(MBP[i],2)),1,0,'C') # Third column of row 1
@ -110,21 +118,26 @@ def generatePDF(save_path,project,DBP,MBP,SBP,PP,Q_avg,txt1,txt2):
pdf.cell(width_cell[4],10,str(round(PP[i],2)),1,1,'C') # Fourth column of row 1 pdf.cell(width_cell[4],10,str(round(PP[i],2)),1,1,'C') # Fourth column of row 1
pdf.print_section(3, 'Cehcking Flow Rate at each outlet') pdf.print_section(3, 'Checking Flow Rate at each outlet')
pdf.image(save_path +'/flow.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '') pdf.image(save_path +'/flow.jpg', x = 40, y = None, w = 140, h = 100, type = '', link = '')
width_cell=[20,60]; width_cell=[20,45];
# pfd.SetFillColor(193,229,252); # Background color of header # pfd.SetFillColor(193,229,252); # Background color of header
pdf.set_font('Times', '', 10)
# Header starts # Header starts
pdf.cell(0, 25,' ', 0, 1)
pdf.set_x(80)
pdf.cell(width_cell[0],10,'ROI',1,0,'C') # First header column pdf.cell(width_cell[0],10,'ROI',1,0,'C') # First header column
pdf.cell(width_cell[1],10,'Average Flow rate [mL/s]',1,1,'C') # Second header column pdf.cell(width_cell[1],10,'Average Flow rate [mL/s]',1,1,'C') # Second header column
# Rows # Rows
for i in range(0,len(Q_avg)): for i in range(0,len(Q_avg)):
pdf.set_x(80)
pdf.cell(width_cell[0],10,'ROI-'+ str(i+2),1,0,'C') pdf.cell(width_cell[0],10,'ROI-'+ str(i+2),1,0,'C')
pdf.cell(width_cell[1],10,str(round(Q_avg[i],2)),1,1,'C') pdf.cell(width_cell[1],10,str(round(Q_avg[i],2)),1,1,'C')
pdf.print_section(4, 'Cehcking Inlet Flow Waveform and time steps saved') pdf.print_section(4, 'Checking Inlet Flow Waveform and time steps saved')
pdf.image(save_path +'/inlet_waveform.jpg', x = None, y = None, w = 140, h = 100, type = '', link = '') pdf.image(save_path +'/inlet_waveform.jpg', x = 40, y = 50, w = 140, h = 100, type = '', link = '')
pdf.cell(0, 10,txt2, 0, 1) pdf.set_font('Arial', '', 10)
pdf.cell(0, 5,txt2, 0, 1)
pdf.output(save_path + '/' + project + '-report.pdf', 'F') pdf.output(save_path + '/' + project + '-report.pdf', 'F')

24
main.py
View File

@ -5,18 +5,19 @@ Created on Thu Jul 16 15:08:27 2020
@author: Aloma Blanch @author: Aloma Blanch
""" """
import numpy as np # import numpy as np
import matplotlib.pyplot as plt # import matplotlib.pyplot as plt
import matplotlib.ticker as mtick # import matplotlib.ticker as mtick
from tkinter import Tk from tkinter import Tk
from tkinter.filedialog import askopenfilename, asksaveasfile, askdirectory # from tkinter.filedialog import askopenfilename, asksaveasfile, askdirectory
import pandas as pd from tkinter.filedialog import askdirectory
import tkinter as tk # import pandas as pd
# import tkinter as tk
import os.path import os.path
from scipy.signal import find_peaks_cwt # from scipy.signal import find_peaks_cwt
from scipy import signal # from scipy import signal
import statistics # import statistics
from fpdf import FPDF # from fpdf import FPDF
from functions import error_plot, periodicity, pressure, flow, inlet_flow_waveform from functions import error_plot, periodicity, pressure, flow, inlet_flow_waveform
@ -65,6 +66,5 @@ txt1 = periodicity(project,folder,dt,T_cyc,n_cyc,save_path)
# Inlet Flow Rate + and t saved # Inlet Flow Rate + and t saved
txt2 = inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc,save_path) txt2 = inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc,save_path)
# Create PDF report # Create PDF report
generatePDF(save_path,project,DBP,MBP,SBP,PP,Q_avg,txt1,txt2) generatePDF(save_path,project,DBP,MBP,SBP,PP,Q_avg,txt1,txt2)