Python: passing coordinates from list to function

Question

I am using some code from a workshop to extract data from netCDF files by the coordinates closest to my specified coordinates. When using just one set of coordinates I am able to extract the values I need without trouble as below:

import numpy as np
import netCDF4
from math import pi
from numpy import cos, sin

def tunnel_fast(latvar,lonvar,lat0,lon0):
    '''
    Find closest point in a set of (lat,lon) points to specified point
    latvar - 2D latitude variable from an open netCDF dataset
    lonvar - 2D longitude variable from an open netCDF dataset
    lat0,lon0 - query point
    Returns iy,ix such that the square of the tunnel distance
    between (latval[it,ix],lonval[iy,ix]) and (lat0,lon0)
    is minimum.
    '''

    rad_factor = pi/180.0 # for trignometry, need angles in radians
    # Read latitude and longitude from file into numpy arrays
    latvals = latvar[:] * rad_factor
    lonvals = lonvar[:] * rad_factor
    ny,nx = latvals.shape
    lat0_rad = lat0 * rad_factor
    lon0_rad = lon0 * rad_factor
    # Compute numpy arrays for all values, no loops
    clat,clon = cos(latvals),cos(lonvals)
    slat,slon = sin(latvals),sin(lonvals)
    delX = cos(lat0_rad)*cos(lon0_rad) - clat*clon
    delY = cos(lat0_rad)*sin(lon0_rad) - clat*slon
    delZ = sin(lat0_rad) - slat;
    dist_sq = delX**2 + delY**2 + delZ**2
    minindex_1d = dist_sq.argmin()  # 1D index of minimum element
    iy_min,ix_min = np.unravel_index(minindex_1d, latvals.shape)
    return iy_min,ix_min

ncfile = netCDF4.Dataset('E:\wind_level2_1.nc', 'r')
latvar = ncfile.variables['latitude']
lonvar = ncfile.variables['longitude']

#_________GG turbine_________GAD10  Latitude    51.735516, GAD10    Longitude   1.942656

iy,ix = tunnel_fast(latvar, lonvar, 51.735516, 1.942656)
print('Closest lat lon:', latvar[iy,ix], lonvar[iy,ix])

refLAT=latvar[iy,ix]
refLON = lonvar[iy,ix]
#try to find the data for this location

SARwind = ncfile.variables['sar_wind'][:,:]
ModelWind = ncfile.variables['model_speed'][:,:]

print 'iy,ix' #appears to be the index of the value of Lat,lon
print SARwind[iy,ix]


ncfile.close()

Now I am trying to loop through a text file containing coordinates coord_list to extract sets of coordinates, find the data then move to the next set of coordinates in the list. This code works on it's own as below:

import csv
from decimal import Decimal
with open('Turbine_locs_no_header.csv','rb') as f:
    reader = csv.reader(f)
    #coord_list = list(reader)
    coord_list = [reader]
    end_row = len(coord_list)

    lon_ind=1
    lat_ind=2

for row in range(0, end_row-1):#end_row - 1 due to the 0 index
    turbine_lat = coord_list[row][lat_ind]
    turbine_lon = coord_list[row][lon_ind]
    turbine_lat = [Decimal(turbine_lat)]
    print 'lat',turbine_lat, 'lon',turbine_lon, row

However, I want to pass coordinates from the text file to this part of the original code iy,ix = tunnel_fast(latvar, lonvar, 51.94341, 1.922094888), replacing the numbers with variables iy, ix = tunnel_fast(latvar, lonvar, turbine_lat, turbine_lon). I try to combine the two codes by creating a function get_coordinates, I get the following errors

  File "C:/Users/mm/test_nc_bycoords_GG_turbines_AGW.py", line 65, in <module>
    get_coordinates(coord_list, latvar, lonvar)
  File "C:/Users/mm/test_nc_bycoords_GG_turbines_AGW.py", line 51, in get_coordinates
    iy, ix = tunnel_fast(latvar, lonvar, turbine_lat, turbine_lon)
  File "C:/Users/mm/test_nc_bycoords_GG_turbines_AGW.py", line 27, in tunnel_fast
    lat0_rad = lat0 * rad_factor
TypeError: can't multiply sequence by non-int of type 'float'

I thought this is because the turbine_lat and turbine_lon are list items so cannot be used, but this doesn't seem to be connected to the errors. I know this code needs more work anyway, but if anyone could help me spot where I am going wrong that would be very helpful. My attempt to combine the two codes is below.

import numpy as np
import netCDF4
from math import pi
from numpy import cos, sin
import csv

# edited from https://github.com/Unidata/unidata-python-workshop/blob/a56daa50d7b343c7debe93968683613642d6b9f7/notebooks/netcdf-by-coordinates.ipynb

def tunnel_fast(latvar,lonvar,lat0,lon0):
    '''
    Find closest point in a set of (lat,lon) points to specified point
    latvar - 2D latitude variable from an open netCDF dataset
    lonvar - 2D longitude variable from an open netCDF dataset
    lat0,lon0 - query point
    Returns iy,ix such that the square of the tunnel distance
    between (latval[it,ix],lonval[iy,ix]) and (lat0,lon0)
    is minimum.
    '''

    rad_factor = pi/180.0 # for trignometry, need angles in radians
    # Read latitude and longitude from file into numpy arrays
    latvals = latvar[:] * rad_factor
    lonvals = lonvar[:] * rad_factor
    ny,nx = latvals.shape
    lat0_rad = lat0 * rad_factor
    lon0_rad = lon0 * rad_factor
    # Compute numpy arrays for all values, no loops
    clat,clon = cos(latvals),cos(lonvals)
    slat,slon = sin(latvals),sin(lonvals)
    delX = cos(lat0_rad)*cos(lon0_rad) - clat*clon
    delY = cos(lat0_rad)*sin(lon0_rad) - clat*slon
    delZ = sin(lat0_rad) - slat;
    dist_sq = delX**2 + delY**2 + delZ**2
    minindex_1d = dist_sq.argmin()  # 1D index of minimum element
    iy_min,ix_min = np.unravel_index(minindex_1d, latvals.shape)
    return iy_min,ix_min
#________________my edits___________________________________________________
def get_coordinates(coord_list, latvar, lonvar):
    "this takes coordinates from a .csv and assigns them to variables"

    end_row = len(coord_list)

    lon_ind=1
    lat_ind=2

    for row in range(0, end_row-1):#end_row - 1 due to the 0 index
        turbine_lat = coord_list[row][lat_ind]
        turbine_lon = coord_list[row][lon_ind]
        iy, ix = tunnel_fast(latvar, lonvar, turbine_lat, turbine_lon)
        print('Closest lat lon:', latvar[iy, ix], lonvar[iy, ix])

#________________________________________________________________________________________________________________________
ncfile = netCDF4.Dataset('NOGAPS_wind_level2_1.nc', 'r')
latvar = ncfile.variables['latitude']
lonvar = ncfile.variables['longitude']

#____added in to pass to get coordinates function
with open('Turbine_locs_no_header.csv','rb') as f:
    reader = csv.reader(f)
    coord_list = list(reader)
#_________take latitude from coordinateas function

get_coordinates(coord_list, latvar, lonvar)

#iy,ix = tunnel_fast(latvar, lonvar, turbine_lat, turbine_lon)#get these from the 'assign_coordinates_fromlist.py
#print('Closest lat lon:', latvar[iy,ix], lonvar[iy,ix])

SARwind = ncfile.variables['sar_wind'][:,:]
ModelWind = ncfile.variables['model_speed'][:,:]

print 'iy,ix' #appears to be the index of the value of Lat,lon
print SARwind[iy,ix]


ncfile.close()

When I try to convert

Answer 1

Thanks to help from a_guest

It was a simple problem of lat0 and lon0 being passed as <type 'str'> to tunnel_fast when it requires <type 'float'>. This appears to come from loading the coord_list as a list.

with open('Turbine_locs_no_header.csv','rb') as f:
    reader = csv.reader(f)
    coord_list = list(reader)

The workaround I used was to convert lat0 and lon0 to floats at the beginning of tunnel_fast

lat0 = float(lat0) 
lon0 = float(lon0)

I am sure there is a more elegant way to do this, but it works.

Answer 2

You can unpack an argument list using *args (see the docs). In your case you could do tunnel_fast(latvar, lonvar, *coord_list[row]). You need to make sure that the order of arguments in coord_list[row] is correct and if coord_list[row] contains more than the two values then you need to slice it appropriately.