ArcPy runs slow outside ArcMap?

Question

I'm running a fairly small script to get height differences. The scripts gets the height in a point based on a DTM. Running the script in the ArcMap python window uses 1 min 30 seconds for 1000 points, while running it in the python window outside Arcmap (C:\Python27\ArcGIS10.5\python.exe) uses 2 min 40 seconds for the same 1000 points. What causes this big difference? There can be many points for each dataset, so I want it to be able to run outside ArcMap so it doesn't run out if memory.

import arcpy 
import datetime

arcpy.env.workspace =  r'\\path\Laserdata.gdb'
arcpy.env.scratchWorkspace =  r'\\path\Temp_data.gdb'
# laserline 
laser = 'L0380_2m_Vertice_selection'

# 1 x 1 m raster
raster_1m = r'\\path\Connection to sde.sde\DTM1'

def main():
    i = 1
    print "Starttime: " + str(datetime.datetime.now())
    start = datetime.datetime.now()
    fields = arcpy.ListFields(laser)

    if len(arcpy.ListFields(laser,"DTMZ"))>0:  
        print "Field exist"  
    else:  
        print "Does not exist"
        arcpy.AddField_management(laser, "DTMZ", "FLOAT")

    with arcpy.da.UpdateCursor(laser, ['SHAPE@X','SHAPE@Y' ,'DTMZ']) as curs:
        for row in curs:
            X = str(row[0]).replace(".",",")
            Y = str(row[1]).replace(".",",")
            XY = str(X + " " + Y)

            hoydeDTM  = arcpy.GetCellValue_management(raster_1m, XY)
            if str(hoydeDTM) == 'NoData':
                hoydeDTM = -9999
            else:
                hoydeDTM = hoydeDTM

            row[2] = str(hoydeDTM)
            i = i + 1 
            if i % 1000 == 0:
                print i
                print datetime.datetime.now() - start
            curs.updateRow(row)

    print "Endtime: "  + str(datetime.datetime.now())
    print  datetime.datetime.now() - start

if __name__ == '__main__':
    main()

Answer 1

@AlexTereshenkov idea that it could be down to it being a layer may be the source of this problem, if you look at the help file for the Get Cell Value Tool what does the Syntax section tell you that it wants as input? A raster layer, you are not providing it with a layer but a string which is the full path to a raster dataset. I would imagine internally it is having to convert that to a layer object on every cycle of the loop.

That being said you have written a whole load of unnecessary code which can all be done in just one tool! I suggest you explore the Extract Values to Points tool? I would expect this to be much faster as it is a system tool (compiled code).