minor change

report_main.py

@@ -0,0 +1,99 @@
+ #!/usr/bin/env python
+"""
+Created on Thu Jul 16 15:08:27 2020
+
+@author: Aloma Blanch
+"""
+
+# import numpy as np
+# import matplotlib.pyplot as plt
+# import matplotlib.ticker as mtick
+from tkinter import Tk
+# from tkinter.filedialog import askopenfilename, asksaveasfile, askdirectory
+from tkinter.filedialog import askdirectory
+# import pandas as pd
+# import tkinter as tk
+import os.path
+# from scipy.signal import find_peaks_cwt
+# from scipy import signal
+# import statistics
+# from fpdf import FPDF
+
+
+from functions import error_plot, periodicity, pressure, flow, inlet_flow_waveform, rcr, cycle, barPlot
+from generatePDF import generatePDF  
+
+
+# Selct dir 
+Tk().withdraw()
+folder = askdirectory()
+project_folder = os.path.dirname(folder)
+project = os.path.basename(project_folder)
+save_path = folder+'/'+project+'-report'
+os.mkdir(save_path)
+save_pdf = save_path + '/' + project + '-report.pdf'
+
+# 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.
+    for myline in myfile:                # For each line, stored as myline,
+        mylines.append(myline)           # add its contents to mylines.
+# Number of Timesteps - idx 3
+# Idea: remove the text to extract the number, the text part will be the same no matter the simulation
+N_ts = int(mylines[3][20:-1])
+# Time Step Size - idx 4
+dt = float(mylines[4][16:-1])
+# Residual criteria - idx 4
+rc = float(mylines[26][18:-1])
+# Imesteps between Restarts - idx 6
+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,N_ts,save_path)
+T_cyc=0.4769
+n_cyc=4   
+# Cehcking convergency and periodicity
+error_plot(folder,dt,rc,save_path)
+txt1 = periodicity(project,folder,dt,T_cyc,n_cyc,save_path)
+
+# Pressure - Outlets
+(DBP,MBP,SBP,PP) = pressure(folder,N_ts,T_cyc,dt,n_cyc,save_path)
+ 
+# Flow Rate - Outlets
+(Q_avg) = flow(folder,N_ts,T_cyc,dt,n_cyc,save_path)
+
+# Inlet Flow Rate + and t saved
+txt2 = inlet_flow_waveform(project_folder,t_btw_rst,N_ts,dt,T_cyc,n_cyc,save_path)
+
+# Extract bar plots CFD vs. aimed
+barPlot(project_folder,DBP,MBP,SBP,PP,Q_avg,save_path)
+
+# # Flow comparison specific for patient 120.
+# # Only ROI-5,6,8 because that is the PC-MRA data that we have.
+# def flow_comparison(folder,N_ts,T_cyc,dt,n_cyc,save_path):
+#     flow_sim = np.loadtxt(folder+'/QHistRCR.dat',skiprows=2,)
+#     flow_doc = np.loadtxt(os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(folder)))))+'/Data/flow_waveforms.txt',skiprows=2,)
+    
+#     Nc = round(T_cyc/dt)
+#     time_sim = np.linspace(0,T_cyc,Nc)
+#     time_doc = np.linspace(0,T_cyc,flow_doc.shape[0])
+#     Q = np.empty(flow_sim.shape[1])
+#     for i in range(0,flow_sim.shape[1]):
+#         fig, ax = plt.subplots()
+#         ax.plot(time_sim,flow_sim[N_ts-Nc:N_ts,i],label='sim ROI-'+str(i+2))
+#         ax.plot(time_doc,flow_doc[:,1+i],label='doc ROI-'+str(i+2))
+   
+#     ax.set(xlabel='time [s]', ylabel='Flow [mL/s]',
+#         title='Flow at each outlet')
+#     ax.spines['right'].set_visible(False)
+#     ax.spines['top'].set_visible(False)
+#     ax.legend(loc=0)
+#     # plt.show()
+#     plt.savefig(save_path + '/flow_comparison.pdf')
+#     fig.savefig(save_path + '/flow_comparison.jpg',dpi=150)
+
+# Create PDF report
+generatePDF(save_path,project,DBP,MBP,SBP,PP,Q_avg,txt1,txt2,Rc_C_Rd,T_cyc,n_cyc,N_ts,dt)