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main.py
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main.py
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# -*- coding: utf-8 -*-
"""
@author: jl
"""
import sys
import os
import numpy as np
from PyQt4 import QtGui
import matplotlib.pyplot as plt
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
from solvers.rk4_N import rk4_N
from solvers.euler_method import euler_method
import csv
class MainWindow(QtGui.QMainWindow):
def __init__(self, parent=None):
super(MainWindow, self).__init__(parent)
self.setGeometry(600, 300, 1000, 600)
self.setWindowTitle('Disease Simulator')
self.setWindowIcon(QtGui.QIcon('pythonlogo.png'))
self.ODE_simulator()
#self.CA_simulator()
extractAction = QtGui.QAction("&Exit", self)
extractAction.setShortcut("Ctrl+Q")
extractAction.setStatusTip('Leave The App')
extractAction.triggered.connect(self.close_application)
resetAction = QtGui.QAction("&New ", self)
resetAction.setShortcut("Ctrl+N")
resetAction.setStatusTip('New Simulation')
resetAction.triggered.connect(self.form_widget.new_sim)
saveAction = QtGui.QAction("&Save ", self)
saveAction.setShortcut("Ctrl+S")
saveAction.setStatusTip('Save Simulation')
saveAction.triggered.connect(self.form_widget.save_sim)
CA_Action = QtGui.QAction("&C.A. ", self)
CA_Action.setShortcut("Ctrl+A")
CA_Action.setStatusTip('Cellular Automaton Simulator')
CA_Action.triggered.connect(self.CA_simulator)
ODE_Action = QtGui.QAction("&ODE ", self)
ODE_Action.setShortcut("Ctrl+O")
ODE_Action.setStatusTip('ODE Simulator')
ODE_Action.triggered.connect(self.ODE_simulator)
mainMenu = self.menuBar()
mainMenu = mainMenu.addMenu('&File')
mainMenu.addAction(extractAction)
mainMenu.addAction(resetAction)
fileMenu = self.menuBar()
fileMenu = fileMenu.addMenu('&Simulation')
fileMenu.addAction(ODE_Action)
fileMenu.addAction(CA_Action)
def CA_simulator(self):
self.form_widget = CAWidget(self)
_widget = QtGui.QWidget()
_layout = QtGui.QVBoxLayout(_widget)
_layout.addWidget(self.form_widget)
self.setCentralWidget(_widget)
def ODE_simulator(self):
self.form_widget = PWidget(self)
_widget = QtGui.QWidget()
_layout = QtGui.QVBoxLayout(_widget)
_layout.addWidget(self.form_widget)
self.setCentralWidget(_widget)
#def type_simulator(self, type):
# if type == 'ODE':
# self.form_widget = PWidget(self)
# elif type == 'CA':
# self.form_widget = CAWidget(self)
def close_application(self):
choice = QtGui.QMessageBox.question(self, 'Close!',
"Are you sure you want to exit?",
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
if choice == QtGui.QMessageBox.Yes:
sys.exit()
else:
pass
class CAWidget(QtGui.QWidget):
def __init__(self,parent):
super(CAWidget, self).__init__(parent)
self.center()
# Dropdown button ODE Models
self.Box_models_ca = QtGui.QComboBox(self)
self.Box_models_ca.addItem("SI model")
self.Box_models_ca.addItem("SIR model")
self.Box_models_ca.addItem("Other")
self.Box_models_ca.currentIndexChanged.connect(self.selection_model)
# Solver parameters grid
initial_time = QtGui.QLabel('Initial time ')
final_time = QtGui.QLabel('Final time')
self.val_ti = QtGui.QDoubleSpinBox()
self.val_ti.setRange(0, 1e9)
self.val_ti.setValue(0)
self.val_ti.setSingleStep(0.0001)
self.val_ti.setDecimals(4)
self.val_tf = QtGui.QDoubleSpinBox()
self.val_tf.setRange(0.001, 1e9)
self.val_tf.setValue(20)
self.val_tf.setSingleStep(0.0001)
self.val_tf.setDecimals(4)
# initial conditions grid
x01 = QtGui.QLabel('x1(0)')
x02 = QtGui.QLabel('x2(0)')
x03 = QtGui.QLabel('x3(0)')
self.val_x01 = QtGui.QDoubleSpinBox()
self.val_x01.setRange(0, 1e12)
self.val_x01.setValue(10)
self.val_x01.setDecimals(4)
self.val_x02 = QtGui.QDoubleSpinBox()
self.val_x02.setRange(0, 1e12)
self.val_x02.setValue(2)
self.val_x02.setDecimals(4)
self.val_x03 = QtGui.QDoubleSpinBox()
self.val_x03.setRange(0, 1e12)
self.val_x03.setValue(1)
self.val_x03.setDecimals(4)
grid_i = QtGui.QGridLayout()
grid_i.addWidget(x01, 0, 0)
grid_i.addWidget(self.val_x01, 0, 1)
grid_i.addWidget(x02, 1, 0)
grid_i.addWidget(self.val_x02, 1, 1)
grid_i.addWidget(x03, 2, 0)
grid_i.addWidget(self.val_x03, 2, 1)
grid_p = QtGui.QGridLayout()
grid_p.addWidget(initial_time, 0, 0)
grid_p.addWidget(self.val_ti, 0, 1)
grid_p.addWidget(final_time, 1, 0)
grid_p.addWidget(self.val_tf, 1, 1)
# button Save
btn_save = QtGui.QPushButton('Save Data', self)
btn_save.resize(btn_save.sizeHint())
btn_save.clicked.connect(self.save_sim)
# button Solve
btn_play = QtGui.QPushButton('PLAY', self)
btn_play.resize(btn_play.sizeHint())
btn_play.clicked.connect(self.play)
# grid Layout
grid = QtGui.QGridLayout()
self.setLayout(grid)
grid.setSpacing(10)
grid.addWidget(btn_save, 3, 1)
grid.addWidget(btn_play, 3, 0)
# pyplot
self.figure = plt.figure(figsize=(15, 10))
self.canvas = FigureCanvas(self.figure)
self.toolbar = NavigationToolbar(self.canvas, self)
grid.addWidget(self.toolbar, 0, 0, 1, 2)
grid.addWidget(self.canvas, 1, 0, 1, 2)
grid.addWidget(self.Box_models_ca, 0, 1)
def center(self):
qr = self.frameGeometry()
cp = QtGui.QDesktopWidget().availableGeometry().center()
qr.moveCenter(cp)
self.move(qr.topLeft())
def selection_model(self):
pass
def save_sim(self):
pass
def play(self):
plt.cla() #this clears the plot
ax1 = self.figure.add_subplot(121)
ax2 = self.figure.add_subplot(122)
ax1.set_title('Simulation Results')
plt.xlabel('Simulation time')
plt.ylabel('Population')
self.canvas.draw()
return y[0], solutions
class PWidget(QtGui.QWidget):
def __init__(self,parent):
super(PWidget, self).__init__(parent)
self.center()
# vertical Box Layout
solver = QtGui.QLabel('Solver:')
parameters = QtGui.QLabel('parameters')
ode_model = QtGui.QLabel('ODE Model:')
initial_conditions = QtGui.QLabel('Initial Conditions')
parameters_model = QtGui.QLabel('Parameters model')
# Dropdown button Solvers
self.Box_solver = QtGui.QComboBox(self)
self.Box_solver.addItem("Runge Kuta 4")
self.Box_solver.addItem("Euler")
self.Box_solver.addItem("Other")
self.Box_solver.currentIndexChanged.connect(self.selection_solver)
# Dropdown button ODE Models
self.Box_models = QtGui.QComboBox(self)
self.Box_models.addItem("SI model")
self.Box_models.addItem("SIR model")
self.Box_models.addItem("SI model 2")
self.Box_models.addItem("Other")
self.Box_models.currentIndexChanged.connect(self.selection_model)
# Solver parameters grid
initial_time = QtGui.QLabel('Initial time ')
final_time = QtGui.QLabel('Final time')
simulation_steps = QtGui.QLabel('Simulation steps')
self.val_ti = QtGui.QDoubleSpinBox()
self.val_ti.setRange(0, 1e9)
self.val_ti.setValue(0)
self.val_ti.setSingleStep(0.0001)
self.val_ti.setDecimals(4)
self.val_tf = QtGui.QDoubleSpinBox()
self.val_tf.setRange(0.001, 1e9)
self.val_tf.setValue(30)
self.val_tf.setSingleStep(0.0001)
self.val_tf.setDecimals(4)
self.val_num_steps = QtGui.QDoubleSpinBox()
self.val_num_steps.setRange(0, 1e12)
self.val_num_steps.setValue(100)
self.val_tf.setSingleStep(1)
self.val_tf.setDecimals(0)
grid_p = QtGui.QGridLayout()
grid_p.addWidget(initial_time, 0, 0)
grid_p.addWidget(self.val_ti, 0, 1)
grid_p.addWidget(final_time, 1, 0)
grid_p.addWidget(self.val_tf, 1, 1)
grid_p.addWidget(simulation_steps, 2, 0)
grid_p.addWidget(self.val_num_steps, 2, 1)
# initial conditions grid
x01 = QtGui.QLabel('x1(0)')
x02 = QtGui.QLabel('x2(0)')
x03 = QtGui.QLabel('x3(0)')
x04 = QtGui.QLabel('x4(0)')
self.val_x01 = QtGui.QDoubleSpinBox()
self.val_x01.setRange(0, 1e12)
self.val_x01.setValue(1)
self.val_x01.setDecimals(4)
self.val_x02 = QtGui.QDoubleSpinBox()
self.val_x02.setRange(0, 1e12)
self.val_x02.setValue(0.01)
self.val_x02.setDecimals(4)
self.val_x03 = QtGui.QDoubleSpinBox()
self.val_x03.setRange(0, 1e12)
self.val_x03.setValue(0)
self.val_x03.setDecimals(4)
self.val_x04 = QtGui.QDoubleSpinBox()
self.val_x04.setRange(0, 1e12)
self.val_x04.setValue(0)
self.val_x04.setDecimals(4)
grid_i = QtGui.QGridLayout()
grid_i.addWidget(x01, 0, 0)
grid_i.addWidget(self.val_x01, 0, 1)
grid_i.addWidget(x02, 1, 0)
grid_i.addWidget(self.val_x02, 1, 1)
grid_i.addWidget(x03, 2, 0)
grid_i.addWidget(self.val_x03, 2, 1)
grid_i.addWidget(x04, 3, 0)
grid_i.addWidget(self.val_x04, 3, 1)
# Model parameters grid
alpha_p = QtGui.QLabel('alpha')
beta_p = QtGui.QLabel('beta')
gamma_p = QtGui.QLabel('gamma')
self.val_alpha=QtGui.QDoubleSpinBox()
self.val_alpha.setRange(-1e7, 1e7)
self.val_alpha.setValue(0.01)
self.val_alpha.setDecimals(4)
self.val_alpha.setSingleStep(0.0001)
self.val_beta=QtGui.QDoubleSpinBox()
self.val_beta.setRange(-1e7, 1e7)
self.val_beta.setValue(0.9)
self.val_beta.setDecimals(4)
self.val_beta.setSingleStep(0.0001)
self.val_gamma = QtGui.QDoubleSpinBox()
self.val_gamma.setRange(-1e7, 1e7)
self.val_gamma.setValue(1)
self.val_gamma.setDecimals(4)
self.val_gamma.setSingleStep(0.0001)
grid_pm = QtGui.QGridLayout()
grid_pm.addWidget(alpha_p, 0, 0)
grid_pm.addWidget(self.val_alpha, 0, 1)
grid_pm.addWidget(beta_p, 1, 0)
grid_pm.addWidget(self.val_beta, 1, 1)
grid_pm.addWidget(gamma_p, 2, 0)
grid_pm.addWidget(self.val_gamma, 2, 1)
vbox = QtGui.QVBoxLayout()
vbox.addStretch(1)
vbox.addWidget(solver)
vbox.addWidget(self.Box_solver)
vbox.addLayout(grid_p)
vbox.addWidget(ode_model)
vbox.addWidget(self.Box_models)
vbox.addLayout(grid_i)
vbox.addLayout(grid_pm)
# grid Layout
grid = QtGui.QGridLayout()
self.setLayout(grid)
grid.setSpacing(10)
grid.addLayout(vbox,1, 2)
# button Erase
btn1 = QtGui.QPushButton('Erase', self)
btn1.resize(btn1.sizeHint())
btn1.clicked.connect(self.errase)
grid.addWidget(btn1, 3, 0)
# button Save
btn2 = QtGui.QPushButton('Save Data', self)
btn2.resize(btn2.sizeHint())
btn2.clicked.connect(self.save_sim)
grid.addWidget(btn2, 3, 1)
# button Solve
btn3 = QtGui.QPushButton('SOLVE', self)
btn3.resize(btn3.sizeHint())
btn3.clicked.connect(self.solve)
grid.addWidget(btn3, 2, 2)
# progress bar
#progress_bar = QtGui.QProgressBar(self)
#grid.addWidget(progress_bar, 2, 0, 1, 2)
self.checkBox = QtGui.QCheckBox('Labels', self)
grid.addWidget(self.checkBox, 2, 1)
# pyplot
self.figure = plt.figure(figsize=(15, 10))
self.canvas = FigureCanvas(self.figure)
self.toolbar = NavigationToolbar(self.canvas, self)
grid.addWidget(self.toolbar, 0, 0, 1, 2)
grid.addWidget(self.canvas, 1, 0, 1, 2)
def center(self):
qr = self.frameGeometry()
cp = QtGui.QDesktopWidget().availableGeometry().center()
qr.moveCenter(cp)
self.move(qr.topLeft())
def new_sim(self):
plt.cla()
ax = self.figure.add_subplot(111)
self.canvas.draw()
self.val_ti.setValue(0)
self.val_tf.setValue(100)
self.val_num_steps.setValue(100)
self.val_alpha.setValue(0.5)
self.val_beta.setValue(0.5)
self.val_gamma.setValue(0.5)
self.val_x01.setValue(1)
self.val_x02.setValue(0.0)
self.val_x03.setValue(0)
self.val_x04.setValue(0)
def errase(self):
plt.cla()
ax = self.figure.add_subplot(111)
self.canvas.draw()
def file_open(self):
name = QtGui.QFileDialog.getOpenFileName(self, 'Open File')
if name[-3:]!='.py':
choice = QtGui.QMessageBox.question(self, 'Attention!',
"You must choose a .py file",
QtGui.QMessageBox.Ok)
else:
return name
def selection_solver(self):
ti = np.float(self.val_ti.value())
tf = np.float(self.val_tf.value())
num_steps = np.int(self.val_num_steps.value())
f, X0, consts = self.selection_model()
if self.Box_solver.currentText() == 'Runge Kuta 4':
S = rk4_N
elif self.Box_solver.currentText() == 'Euler':
S = euler_method
elif self.Box_solver.currentText() == 'Other':
filename = str(self.file_open())
directory, module_name = os.path.split(filename)
module_name = os.path.splitext(module_name)[0]
path = list(sys.path)
sys.path.insert(0, directory)
try:
module = __import__(module_name)
finally:
sys.path[:] = path # restore
name = (filename.replace(os.getcwd() + '/solvers/', ''))[:-3]
S = getattr(module, name)
y = S(f, X0, consts, ti, tf, num_steps)
return y
def selection_model(self):
alpha = np.float(self.val_alpha.value())
beta = np.float(self.val_beta.value())
gamma = np.float(self.val_gamma.value())
x01 = np.float(self.val_x01.value())
x02 = np.float(self.val_x02.value())
x03 = np.float(self.val_x03.value())
x04 = np.float(self.val_x04.value())
if self.Box_models.currentText() == 'SI model':
consts = [alpha, beta]
X0 = [x01, x02]
from models.SI_model import SI_model as model
elif self.Box_models.currentText() == 'SIR model':
consts = [alpha, beta]
X0 = [x01, x02, x03]
from models.SIR_model import SIR_model as model
elif self.Box_models.currentText() == 'SI model 2':
consts = [alpha, beta, gamma]
X0 = [x01, x02]
from models.SIS_model2 import SIS_model2 as model
elif self.Box_models.currentText() == 'Other':
filename = str(self.file_open())
directory, module_name = os.path.split(filename)
module_name = os.path.splitext(module_name)[0]
path = list(sys.path)
sys.path.insert(0, directory)
try:
module = __import__(module_name)
finally:
sys.path[:] = path # restore
name = (filename.replace(os.getcwd()+'/models/', ''))[:-3]
model = getattr(module, name)
#X0 = import it from a file
#consts = also import them from a file
return model, X0, consts
def save_sim(self):
time_s, results = self.solve()
name = QtGui.QFileDialog.getSaveFileName(self, 'Save File')+'.csv'
A = []
for i in range(len(results[0])):
a = []
a.append(time_s[i])
for j in range(len(results)):
a.append(results[j][i])
A.append(a)
#rows = zip(time_s, A)
with open(name, 'w') as csvfile:
writer = csv.writer(csvfile)
for r, row in enumerate(A):
writer.writerow(row)
def solve(self):
#plt.cla() #this clears the plot
ax = self.figure.add_subplot(111)
y = self.selection_solver()
solutions = [[] for j in range(len(y[1][0]))]
for ye in y[1]:
for j in range(len(solutions)):
solutions[j].append(ye[j])
consts_names = "".join(['$alpha$=', str(self.val_alpha.value()), ' $beta$=', str(self.val_beta.value()), ' $gamma$=',
str(self.val_gamma.value()), '\n', '$S$'])
labels = [consts_names, '$I$', '$R$']
for ind, solution in enumerate(solutions):
ax.plot(y[0], solution, '-o', label=labels[ind])
if self.checkBox.isChecked() is True:
ax.legend(loc='best', prop={'size': 10})
ax.set_title('Simulation Results')
plt.xlabel('Simulation time')
plt.ylabel('Population')
self.canvas.draw()
return y[0], solutions
def main():
app = QtGui.QApplication(sys.argv)
w = MainWindow()
w.show()
app.exec_()
if __name__ == '__main__':
main()