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dataCreateByState.py
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import re
import csv
from datetime import datetime
import numpy as np
from numpy import savetxt
def cell2TwoNumbersByBracket(inStr):
withoutComma = re.compile("^[0-9]+$")
withComma = re.compile("^\d{1,3}(,\d{3})*(\.\d+)?$")
if inStr == "":
firstNumber, secondNumber = 0, 0
elif type(inStr) == int:
firstNumber, secondNumber = inStr, 0
elif withoutComma.fullmatch(inStr):
firstNumber, secondNumber = int(process_num(inStr)), 0
elif withComma.fullmatch(inStr):
firstNumber, secondNumber = int(process_num(str(inStr).replace(",",""))), 0
else:
withNewCaseInBracket = re.compile("^[0-9]+\([^\)][0-9]+\)")
idxBra = inStr.find('(')
idxKet = inStr.find(')')
firstNumber = int(process_num(inStr[0:idxBra]))
secondNumber = int(process_num(inStr[(idxBra+1):idxKet]))
return firstNumber, secondNumber
def cumulNewCases2Cell(cumulNewCases):
return cumulAndNewCases2Cell(cumulNewCases[0], cumulNewCases[1])
def cumulAndNewCases2Cell(cumulCases, newCases):
if newCases == 0:
return cumulCases
else:
return str(cumulCases) + "(" + str(newCases) + ")"
def process_num(num):
return float(re.sub(r'[^\w\s.]','',num))
def processColumnNames(columnRaw):
switcher={
"Date":"Date",
"JH":"Johor",
"KD":"Kedah",
"KE":"Kelantan",
"ML":"Malacca",
"NS":"Negeri Sembilan",
"PH":"Pahang",
"PG":"Penang",
"PK":"Perak",
"PR":"Perlis",
"SB":"Sabah",
"SR":"Sarawak",
"SE":"Selangor",
"TR":"Terengganu",
"KL":"Kuala Lumpur",
"PT":"Putrajaya",
"LB":"Labuan"
}
return switcher.get(columnRaw, "Invalid input column")
def createByStateData(rawCSVFilename):
with open(rawCSVFilename, newline='', encoding='utf-8') as csvfile:
data = list(csv.reader(csvfile))
# below is specific to the table on Malaysia's Wikipedia page
# remove line with date "4/3/2020-12/3/2020" and "15/3/2020"
data = [row for row in data if '4/3/2020-12/3/2020' not in row]
data = [row for row in data if '15/3/2020' not in row]
data = [row for row in data if '15/03/2020' not in row]
# For 16/3/2020, 17/3/2020, 18/3/2020, split KL+PT proportionally
for i in range(len(data)):
if(data[i][0] == '14/3/2020' or data[i][0] == '14/03/2020'):
idx14_3 = i
if(data[i][0] == '16/3/2020' or data[i][0] == '16/03/2020'):
idx16_3 = i
if(data[i][0] == '17/3/2020' or data[i][0] == '17/03/2020'):
idx17_3 = i
if(data[i][0] == '18/3/2020' or data[i][0] == '18/03/2020'):
idx18_3 = i
if(data[i][0] == '19/3/2020' or data[i][0] == '19/03/2020'):
idx19_3 = i
idxKL = data[0].index('KL')
dataKL14_3 = cell2TwoNumbersByBracket(data[idx14_3][idxKL])
dataPT14_3 = cell2TwoNumbersByBracket(data[idx14_3][idxKL+1])
data16_3 = cell2TwoNumbersByBracket(data[idx16_3][idxKL])
data17_3 = cell2TwoNumbersByBracket(data[idx17_3][idxKL])
data18_3 = cell2TwoNumbersByBracket(data[idx18_3][idxKL])
dataKL19_3 = cell2TwoNumbersByBracket(data[idx19_3][idxKL])
dataPT19_3 = cell2TwoNumbersByBracket(data[idx19_3][idxKL+1])
ratioKL14_3 = dataKL14_3[0]/(dataKL14_3[0]+dataPT14_3[0])
ratioKL19_3 = dataKL19_3[0]/(dataKL19_3[0]+dataPT19_3[0])
ratioKL16_3 = ((19-16)*ratioKL14_3 + (16-14)*ratioKL19_3)/(19-14)
ratioKL17_3 = ((19-17)*ratioKL14_3 + (17-14)*ratioKL19_3)/(19-14)
ratioKL18_3 = ((19-18)*ratioKL14_3 + (18-14)*ratioKL19_3)/(19-14)
dataKL16_3 = (int(ratioKL16_3*data16_3[0]), int (ratioKL16_3*data16_3[1]))
dataKL17_3 = (int(ratioKL17_3*data17_3[0]), int (ratioKL17_3*data17_3[1]))
dataKL18_3 = (int(ratioKL18_3*data18_3[0]), int (ratioKL18_3*data18_3[1]))
ratioPT16_3 = 1 - ratioKL16_3
ratioPT17_3 = 1 - ratioKL17_3
ratioPT18_3 = 1 - ratioKL18_3
dataPT16_3 = (int(ratioPT16_3*data16_3[0]), int (ratioPT16_3*data16_3[1]))
dataPT17_3 = (int(ratioPT17_3*data17_3[0]), int (ratioPT17_3*data17_3[1]))
dataPT18_3 = (int(ratioPT18_3*data18_3[0]), int (ratioPT18_3*data18_3[1]))
data[idx16_3][idxKL] = cumulNewCases2Cell(dataKL16_3)
data[idx16_3].insert(idxKL+1, cumulNewCases2Cell(dataPT16_3))
data[idx17_3][idxKL] = cumulNewCases2Cell(dataKL17_3)
data[idx17_3].insert(idxKL+1, cumulNewCases2Cell(dataPT17_3))
data[idx18_3][idxKL] = cumulNewCases2Cell(dataKL18_3)
data[idx18_3].insert(idxKL+1, cumulNewCases2Cell(dataPT18_3))
# Remove the final "Source" column
for singleData in data:
del singleData[len(singleData)-1]
# Store variables: dates, cumulCases
columnsRaw = data[0]
columns = [""] * len(columnsRaw)
for i in range(len(columnsRaw)):
columns[i] = processColumnNames(columnsRaw[i])
datesStr = [""] * (len(data)-1)
cumulCases = [[0 for x in range(len(columns)-1)] for y in range (len(data)-1)]
for i in range(1, len(data)):
dateStr = data[i][0]
day, month, year = dateStr.split("/")
datesStr[i-1] = str(year) + "-" + str(month).zfill(2) + "-" + str (day).zfill(2)
for j in range(1, len(columns)):
cumulCase, newCase = cell2TwoNumbersByBracket(data[i][j])
cumulCases[i-1][j-1] = cumulCase
# save cumulative infecteds CSV
with open('./data/totalInfectedByStates.csv', 'w') as csvfile:
for j in range(len(columns)-1):
csvfile.write(str(columns[j]) + ',')
csvfile.write(str(columns[len(columns)-1]) + '\n')
for i in range(len(cumulCases)):
csvfile.write(datesStr[i] + ',')
for j in range(len(cumulCases[0])-1):
csvfile.write(str(cumulCases[i][j]) + ',')
csvfile.write(str(cumulCases[i][len(cumulCases[0])-1]) + '\n')
# save daily new infecteds CSV
with open('./data/newDailyInfectedByStates.csv', 'w') as csvfile:
newDailyCases = [[0 for x in range(len(cumulCases[0]))] for y in range(len(cumulCases))]
newDailyCases[0] = cumulCases[0]
prevDate = datetime.strptime(datesStr[0], "%Y-%m-%d")
for i in range(1, len(datesStr)):
nowDate = datetime.strptime(datesStr[i], "%Y-%m-%d")
days = (nowDate - prevDate).days
for j in range(len(newDailyCases[0])):
newDailyCases[i][j] = (cumulCases[i][j] - cumulCases [i-1][j]) / days
prevDate = nowDate
for j in range(len(columns)-1):
csvfile.write(str(columns[j]) + ',')
csvfile.write(str(columns[len(columns)-1]) + '\n')
for i in range(len(newDailyCases)):
csvfile.write(datesStr[i] + ',')
for j in range(len(newDailyCases[0])-1):
csvfile.write(str(newDailyCases[i][j]) + ',')
csvfile.write(str(newDailyCases[i][len(newDailyCases [0])-1]) + '\n')
# dynamics talbe by states (x=cumulative cases, y1, y2, .... = new cases per day for each states, z = date just for tooltip)
dynamicsTableHeader = []
dynamicsTableHeader.append("Total cases")
for j in range(1, len(columns)):
dynamicsTableHeader.append(columns[j])
dynamicsTableHeader.append(columns[0])
dynamicTableNp = []
cumulCasesInt = []
for i in range(len(cumulCases)):
for j in range(1, len(columns)):
dynamicsTableRow = []
cumulCase = cumulCases[i][j-1] #cumulCase axis is always integer, so no problem in vstack
if cumulCase > 0:
newCase = str(newDailyCases[i][j-1])
dynamicsTableRow.append(cumulCase)
dynamicsTableRowData = [''] * len(cumulCases[i]) # new cases is None or integer
dynamicsTableRow.extend(dynamicsTableRowData)
dynamicsTableRow[j] = newCase
dynamicsTableRow.append(datesStr[i])
if len(dynamicTableNp) == 0:
dynamicTableNp = np.array(dynamicsTableRow)
cumulCasesInt = [cumulCase]
else:
dynamicTableNp = np.vstack((dynamicTableNp, dynamicsTableRow))
cumulCasesInt.append(cumulCase)
dynamicTableNp = dynamicTableNp[np.argsort(cumulCasesInt)]
dynamicTableNp = np.vstack((dynamicsTableHeader, dynamicTableNp))
savetxt('./data/byStateDynamics.csv', dynamicTableNp, delimiter = ',', fmt = '%s')