I have a 14MB Excel file with five worksheets that I’m reading into a Pandas dataframe, and although the code below works, it takes 9 minutes!
Does anyone have suggestions for speeding it up?
import pandas as pd def OTT_read(xl,site_name): df = pd.read_excel(xl.io,site_name,skiprows=2,parse_dates=0,index_col=0, usecols=[0,1,2],header=None, names=['date_time','%s_depth'%site_name,'%s_temp'%site_name]) return df def make_OTT_df(FILEDIR,OTT_FILE): xl = pd.ExcelFile(FILEDIR + OTT_FILE) site_names = xl.sheet_names df_list = [OTT_read(xl,site_name) for site_name in site_names] return site_names,df_list FILEDIR='c:/downloads/' OTT_FILE='OTT_Data_All_stations.xlsx' site_names_OTT,df_list_OTT = make_OTT_df(FILEDIR,OTT_FILE)
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Answer
As others have suggested, csv reading is faster. So if you are on windows and have Excel, you could call a vbscript to convert the Excel to csv and then read the csv. I tried the script below and it took about 30 seconds.
# create a list with sheet numbers you want to process sheets = map(str,range(1,6)) # convert each sheet to csv and then read it using read_csv df={} from subprocess import call excel='C:\Users\rsignell\OTT_Data_All_stations.xlsx' for sheet in sheets: csv = 'C:\Users\rsignell\test' + sheet + '.csv' call(['cscript.exe', 'C:\Users\rsignell\ExcelToCsv.vbs', excel, csv, sheet]) df[sheet]=pd.read_csv(csv)
Here’s a little snippet of python to create the ExcelToCsv.vbs script:
#write vbscript to file vbscript="""if WScript.Arguments.Count < 3 Then WScript.Echo "Please specify the source and the destination files. Usage: ExcelToCsv <xls/xlsx source file> <csv destination file> <worksheet number (starts at 1)>" Wscript.Quit End If csv_format = 6 Set objFSO = CreateObject("Scripting.FileSystemObject") src_file = objFSO.GetAbsolutePathName(Wscript.Arguments.Item(0)) dest_file = objFSO.GetAbsolutePathName(WScript.Arguments.Item(1)) worksheet_number = CInt(WScript.Arguments.Item(2)) Dim oExcel Set oExcel = CreateObject("Excel.Application") Dim oBook Set oBook = oExcel.Workbooks.Open(src_file) oBook.Worksheets(worksheet_number).Activate oBook.SaveAs dest_file, csv_format oBook.Close False oExcel.Quit """; f = open('ExcelToCsv.vbs','w') f.write(vbscript.encode('utf-8')) f.close()
This answer benefited from Convert XLS to CSV on command line and csv & xlsx files import to pandas data frame: speed issue