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CoronaSimulationDialog.py
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import datetime
import numpy as np
from PyQt5.QtCore import pyqtSlot, QSettings
from matplotlib.ticker import FuncFormatter
from PyQt5.QtWidgets import QDialog, QFileDialog, QMessageBox
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
from matplotlib.figure import Figure
from ActualData import ActualData
from ConnectivityData import ConnectivityData
from RData import RData
from RtEstimator import RtEstimator
from gen.Ui_CoronaSimulationDialog import Ui_CoronaSimulationDialog
from GlobalModel import GlobalModel
class CoronaSimulationDialog(QDialog):
def __init__(self):
super().__init__(None)
self.sir = GlobalModel()
self.ui = Ui_CoronaSimulationDialog()
self.ui.setupUi(self)
self.fig = Figure()
self.canvas = FigureCanvasQTAgg(self.fig)
self.ax = self.canvas.figure.add_subplot(111)
self.ax2 = self.ax.twinx()
self.ui.figuresLayout.addWidget(self.canvas)
self.showMaximized()
self.simulation_days = 30
self.days = []
self.first_day = ''
actual_data_file = QSettings().value("actual_data_file", "")
if actual_data_file:
self.load_actual_data_file(actual_data_file)
r_data_file = QSettings().value("r_data_file", "")
if r_data_file:
self.load_r_data_file(r_data_file)
connectivity_data_file = QSettings().value("connectivity_data_file", "")
if connectivity_data_file:
self.load_connectivity_data_file(connectivity_data_file)
self.start_execution()
# noinspection PyUnusedLocal
def x_formatter(self, x, pos):
x = int(x)
if 0 < x < len(self.days):
return self.days[x]
return ''
# noinspection PyUnusedLocal
@staticmethod
def y_formatter(x, pos):
return '{:,}'.format(int(x))
def start_execution(self):
if ActualData.empty():
QMessageBox.warning(None, 'Warning', 'Actual data is empty')
return
if RData.empty():
QMessageBox.warning(None, 'Warning', 'R data is empty')
return
base = datetime.datetime.strptime(ActualData.first_day, '%Y-%m-%d')
self.days = [(base + datetime.timedelta(days=x)).strftime('%Y-%m-%d') for x in range(len(ActualData.actual_data) + self.simulation_days)]
t0 = len(ActualData.actual_infected)
t = np.linspace(t0, t0 + self.simulation_days - 1, self.simulation_days)
i = self.sir.execute(t)
self.ax.cla()
self.ax.xaxis.grid()
self.ax.yaxis.grid()
self.ax.minorticks_on()
self.ax.set_xticklabels(self.days, rotation=90)
self.ax.xaxis.set_major_formatter(FuncFormatter(self.x_formatter))
self.ax.yaxis.set_major_formatter(FuncFormatter(self.y_formatter))
self.ax.plot(list(range(len(ActualData.actual_infected))), ActualData.actual_infected, label='Actual')
t_for_i = [int(i) for i in t]
t_for_i = t_for_i[:len(t_for_i) - 1]
self.ax.plot(t_for_i, i, label='Expected')
self.ax.set_xlim(0, len(ActualData.actual_data) + self.simulation_days)
self.ax.legend(loc="upper right")
self.canvas.draw_idle()
def load_actual_data_file(self, file_name):
if ActualData.load_file(file_name):
self.ui.actualDataFileLineEdit.setText(file_name)
def load_r_data_file(self, file_name):
if RData.load_file(file_name):
self.ui.RDataFileLineEdit.setText(file_name)
def load_connectivity_data_file(self, file_name):
if ConnectivityData.load_file(file_name):
self.ui.connectivityFileLineEdit.setText(file_name)
@pyqtSlot()
def actual_data_file_selected(self):
t = QFileDialog.getOpenFileName(self, filter="csv(*.csv)")
file_name = t[0]
if file_name:
QSettings().setValue("actual_data_file", file_name)
self.load_actual_data_file(file_name)
self.start_execution()
@pyqtSlot()
def r_data_file_selected(self):
t = QFileDialog.getOpenFileName(self, filter="csv(*.csv)")
file_name = t[0]
if file_name:
QSettings().setValue("r_data_file", file_name)
self.load_r_data_file(file_name)
self.start_execution()
@pyqtSlot()
def connectivity_data_file_selected(self):
t = QFileDialog.getOpenFileName(self, filter="csv(*.csv)")
file_name = t[0]
if file_name:
QSettings().setValue("connectivity_data_file", file_name)
self.load_connectivity_data_file(file_name)
self.start_execution()
@pyqtSlot()
def estimate_R(self):
if ActualData.empty():
QMessageBox.warning(None, 'Warning', 'Actual data is empty')
return
communities_count = ActualData.actual_data.shape[1] // 3
time_for_r = []
super_r = None
for i in range(communities_count):
actual_infected = ActualData.actual_data[:, i * 3 + 1]
actual_infected = [int(i) for i in actual_infected]
incidents = [actual_infected[0]]
incidents.extend(np.diff(actual_infected))
r, rt = RtEstimator(incidents, 5.1, 1).estimR()
rt = np.trim_zeros(rt)
r = r[:len(rt)]
time_for_r = rt
if super_r is None:
super_r = np.empty([len(rt), communities_count])
super_r[:, i] = r
t = QFileDialog.getSaveFileName(self, filter="csv(*.csv)")
file_name = t[0]
if file_name:
RData.Rt, RData.Rt_t1 = super_r, time_for_r
if RData.save_r_data_file(file_name):
QSettings().setValue("r_data_file", file_name)
self.load_r_data_file(file_name)
self.start_execution()
@pyqtSlot()
def simulationDaysChanged(self):
default = 30
str = self.ui.lineEditSimulationDays.text()
x = int(str)
if x < 10:
x = default
if self.simulation_days != x:
self.simulation_days = x
self.start_execution()