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covid19-VuongSimulator.py
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covid19-VuongSimulator.py
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import sys, getopt
import matplotlib.pyplot as plt
import matplotlib.dates
from datetime import datetime
from datetime import date
import csv
from lib.tavuong_visual import *
from lib.tavuong_model import *
from lib.tavuong_readfile import *
from lib.tavuong_simulator import *
#from lib.vuong_covid19_visual import *
#from lib.vuong_covid19_model import *
from lib.user_visual import *
def main(argv):
# VUONG SIMULATION
# ---LIB of system
# ---VUONG ALGORITHM
# Author: Dr. The Anh Vuong
# (c) 2020 by Dr.-The Anh Vuong
# Licence: MIT
# ------------------------------------------
# ARGUMENT Processing
inputfile = ''
outputfile = ''
country_in = ''
mode_in = ""
gesund_in =""
ncasesfile=''
deathsfile =''
tau_in =''
recP_in=''
simu_mode =''
try:
opts, args = getopt.getopt(argv,"hi:o:c:m:g:n:d:t:r:s:",["ifile=","ofile=","country=","mode=", "recover=",\
"nfile=","dfile=", "tau=", "recP=","simu="])
except getopt.GetoptError:
print ('test.py -i <inputfile> -o <outputfile>')
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print ('VuongSimulation: \n -n <new_Cases_file> -d <new_Deaths_file> -o outputfile \n -c country'+ \
'\n -t Incubation Periode Tau \n -r Recovery Period \n -s simulation mode \n')
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-n", "--nfile"):
ncasesfile = arg
elif opt in ("-d", "--dfile"):
deathsfile = arg
elif opt in ("-c", "--country"):
country_in = arg
elif opt in ("-m", "--mode"):
mode_in = arg
elif opt in ("-g", "--recover"):
gesund_in = arg
elif opt in ("-t", "--tau"):
tau_in = arg
elif opt in ("-r", "--recP"):
recP_in = arg
elif opt in ("-s", "--simu"):
simu_mode = arg
# input control
# print (argv)
# if argv[0] != "": print (argv)
# --------------------------------------
# DIALOG
# Data-files amd country ( colum Name) choise
print("---------------------------------------|")
print("| VUONG Covid19 Simulator |")
print("| Data Simulation |")
print("| Data Analysis |")
print("| Author: Dr.-Ing. The Anh Vuong |")
print("---------------------------------------\n")
# covid19-data-kit: CSV Data reading
# source https://ourworldindata.org/coronavirus-source-data
# download put to ./data, eg. new_casesC.csv
# VMODEL input file is now -n and -nd, -i is commented
sname = inputfile
# if sname == "":
# sname = input ('VMODEL > Case data file? ')
# if sname =="":
# sname = './data/new_casesC.csv'
# icountry = 0
# iland = 0
# fig, ax = plt.subplots()
sname = ncasesfile
# --------- mono country
# namecountry =""
# namecountry = country_in
# if namecountry == "": namecountry = input("VMODEL > country? ")
#-------------------------------------
# print ('Country' , namecountry)
print ('Covid19-VUONG SIMULATOR')
print (argv)
# DIALOG
# Mode select
# use covid19 -datakit for development
# set direct to VUONG MODEL ta
mode =""
mode = mode_in
mode ="ta"
if mode == "":
print("| Visualization models: |")
print("| ac : actual cases |")
print("| sr : daily sum of cases |")
print("| gc : actual incl. estim. recovery rate |")
print("| gs : accum. incl. estim. recovery rate|")
print("| me : my model |")
print("| t2 : test plot |")
print("| ta : VuongModell |")
mode = input('KIT > What is your calculate-model? ')
# print ('KIT > VuongModell' + mode)
# RECOVERED SECLECT
gesund = 0.0
if ((mode == "ac") or mode == "sr"or mode == "ta"):
gesund ='0.0'
else:
if (gesund_in == ""):
gesund_in = input('KIT > Recovered factor? ')
gesund = float(str(gesund_in))
gesund = 0.0
# gesund = gesund_in
# print ('Recovered factor : ' + str(gesund))
fig, ax = plt.subplots()
if (mode in 'me'):
my_collection_1(x,y,y1,y2,namecountry,gesund)
# EXAMPLE MODEL
if (mode in 'ac'):
tavuong_collection_ac(x,y,y1,y2)
if (mode in 'sr'):
tavuong_collection_sr(x,y,y1,y2)
# IN DEVELOPING
if (mode in 'gc'):
# gesund = 0.8
tavuong_collection_gc(x,y,y1,y2,gesund)
if (mode in 'gs'):
# gesund = 0.8
tavuong_collection_gs(x,y,y1,y2,gesund)
if (mode in 'rf'):
tavuong_collection_rf1(x,y,y1,y2,gesund)
# TEST
if (mode in 't2'):
kit_plot_test2(x,y)
if (mode in 'ta'):
# simu_mode = int(input('VMODEL > Simulation Stufe ? '))
# if (simu_mode == ''):
# simu_mode -----------------------------------------------------------------
sread = ta_para_read('VMODEL > new_case-file ? ',ncasesfile, './data/new_cases.csv')
ncasesfile = sread
print ('new_case-file', ncasesfile)
sread = ta_para_read('VMODEL > deaths-file ? ',deathsfile, './data/new_deaths.csv')
deathsfile = sread
print ('deaths-file', deathsfile)
sread = ta_para_read('VMODEL > VuongSimualtion mode ? ',simu_mode, 6)
simu_mode = sread
print ('VuongSimualtion mode' , simu_mode)
# sread = ta_para_read('VMODEL > Simulation Stufe ? ',gesund, '0.90')
# gesund = float(str(sread))
# print (sread , gesund)
sread = ta_para_read('VMODEL > Incubation Period? ',tau_in, 7)
tau_in = sread
print ('Incubation Period' , tau_in)
sread = ta_para_read('VMODEL > Recovery Period ? ',recP_in, 14)
recP_in = sread
print ('Recovery Period' , recP_in)
gesund = 0.0
if (gesund_in == ""):
gesund_in = input('VMODEL > Fix factor? ')
gesund = float(str(gesund_in))
# One Country - Mode 1-6
if (int(simu_mode) <= 6):
namecountry =""
namecountry = country_in
if namecountry == "": namecountry = input("VMODEL > country? ")
vuong_covid_Model (ncasesfile,deathsfile,namecountry, gesund, int(simu_mode), int(tau_in),int(recP_in),5)
# MUlti Country - Mode 7-9
# ----List von Country ./data/country:list.csv
# ----new parameter for mode 7
else:
switch7 = '5'
# ------dialog for mode 7
if (int(simu_mode) == 7):
switch7 = ''
sread = ta_para_read('VMODEL > Mode Switch ? ',switch7, '5')
switch7 = sread
print ('Mode ', simu_mode, 'switch: ', switch7)
#-------command line for mode 7
if (int(simu_mode) > 70) and (int(simu_mode) < 79):
switch7 = int(simu_mode) - 70
simu_mode = '7'
# listn = ['Germany', 'Italy', 'France', 'Sweden', 'Belgium', 'United Kingdom', 'Russia']
listn = []
listn = tavuong_country_name('./data/vmodel_testlist.csv')
print (listn)
for ncc in listn:
namecountry = ncc
# print ('VMODEL > ', ncc, namecountry)
vuong_covid_Model (ncasesfile,deathsfile,namecountry, gesund, int(simu_mode), int(tau_in),int(recP_in),int(switch7))
namecountry = "Multi countries - IncuP=" + tau_in + ' recP='+ recP_in
#-------command line for mode 8
if (int(simu_mode) > 80) and (int(simu_mode) < 89):
namecountry =""
namecountry = country_in
if namecountry == "": namecountry = input("VMODEL > country? ")
switch7 = int(simu_mode) - 80
simu_mode = '8'
listTau = ['0', '2', '5', '7', '10']
# listn = []
# listn = tavuong_country_name('./data/vmodel_testlist.csv')
print (listTau)
for ncc in listTau:
tau_in = ncc
# print ('VMODEL > ', ncc, tau_in)
vuong_covid_Model (ncasesfile,deathsfile,namecountry, gesund, int(simu_mode), int(tau_in),int(recP_in),int(switch7))
namecountry = "Variable IncuP - recP="+ recP_in
#-------command line for mode 9
if (int(simu_mode) > 90) and (int(simu_mode) < 99):
namecountry =""
namecountry = country_in
if namecountry == "": namecountry = input("VMODEL > country? ")
switch7 = int(simu_mode) - 90
simu_mode = '9'
listTau = ['14', '21', '28']
# listn = []
# listn = tavuong_country_name('./data/vmodel_testlist.csv')
print (listTau)
for ncc in listTau:
recP_in = ncc
# print ('VMODEL > ', ncc, recP_in)
vuong_covid_Model (ncasesfile,deathsfile,namecountry, gesund, int(simu_mode), int(tau_in),int(recP_in),int(switch7))
namecountry = "Variable RecP -IncuP=" + tau_in
# show
# picstore = 0
show_curve(ax,"Dr.Vuong-COVID19-SIMULATOR",namecountry,outputfile)
# main()
main(sys.argv[1:])