# Obtain coordinates and corresponding pixel values from GeoTiff using python gdal and save them as numpy array

This should get you going. The raster values are read using rasterio, and pixel centre coordinates are converted to Eastings/Northings using affine, which are then converted to Latitude/Longitude using pyproj. Most arrays have the same shape as the input raster.

```
import rasterio
import numpy as np
from affine import Affine
from pyproj import Proj, transform
fname = '/path/to/your/raster.tif'
# Read raster
with rasterio.open(fname) as r:
T0 = r.transform # upper-left pixel corner affine transform
p1 = Proj(r.crs)
A = r.read() # pixel values
# All rows and columns
cols, rows = np.meshgrid(np.arange(A.shape[2]), np.arange(A.shape[1]))
# Get affine transform for pixel centres
T1 = T0 * Affine.translation(0.5, 0.5)
# Function to convert pixel row/column index (from 0) to easting/northing at centre
rc2en = lambda r, c: (c, r) * T1
# All eastings and northings (there is probably a faster way to do this)
eastings, northings = np.vectorize(rc2en, otypes=[np.float, np.float])(rows, cols)
# Project all longitudes, latitudes
p2 = Proj(proj='latlong',datum='WGS84')
longs, lats = transform(p1, p2, eastings, northings)
```

would add as comment, but a bit long - in case you wanted to use gdal/ogr within python - something like this might work (hacked together from some other code i had - not tested!) This also assumes that rather than finding the nearest raster pixel to a polygon centroid, you simply query the raster at the xy of the centroid. i have no idea what the speed tradeoff might be...

```
from osgeo import gdal,ogr
fc='PathtoYourVector'
rast='pathToYourRaster'
def GetCentroidValue(fc,rast):
#open vector layer
drv=ogr.GetDriverByName('ESRI Shapefile') #assuming shapefile?
ds=drv.Open(fc,True) #open for editing
lyr=ds.GetLayer(0)
#open raster layer
src_ds=gdal.Open(rast)
gt=src_ds.GetGeoTransform()
rb=src_ds.GetRasterBand(1)
gdal.UseExceptions() #so it doesn't print to screen everytime point is outside grid
for feat in lyr:
geom=feat.GetGeometryRef()
mx=geom.Centroid().GetX()
my=geom.Centroid().GetY()
px = int((mx - gt[0]) / gt[1]) #x pixel
py = int((my - gt[3]) / gt[5]) #y pixel
try: #in case raster isnt full extent
structval=rb.ReadRaster(px,py,1,1,buf_type=gdal.GDT_Float32) #Assumes 32 bit int- 'float'
intval = struct.unpack('f' , structval) #assume float
val=intval[0]
except:
val=-9999 #or some value to indicate a fail
feat.SetField('YOURFIELD',val)
lyr.SetFeature(feat)
src_ds=None
ds=None
GetCentroidValue(fc,rast)
```