I'm working with 52 rasters of a specific region over a period of one year in python. I also have a mask raster of the same area that is a binary color (250 black pixels for disparate areas of interest, nothing for everything else).

I'm trying to use a black pixel from the mask raster as bounds to grab a single pixel over time (52 rasters/weeks) as a numpy array, and I'd like to do this for all 250 black pixels, grabbing their corresponding pixels over time into separate arrays.

Unfortunately I cannot seem to find a method to pull this off. The closest thing I've found is using a shapefile to clip a raster. Any suggestions on how to achieve this in python would be golden.

  • In particular GIS?
    – FelixIP
    Commented Aug 22, 2018 at 18:59
  • Yeah trying to do temporal analysis on the pixels. Commented Aug 22, 2018 at 19:05
  • Do the 52 rasters and the mask have the same size/boundaries? Commented Sep 29, 2018 at 10:31
  • They have the exact same dimensions. Commented Sep 29, 2018 at 10:47

1 Answer 1


Hope this helps!

import rasterio
import numpy as np
import os

mask_path = r"mask.tif"
tiff_paths = [r"tiff1.tif", r"tiff2.tif", ...]
# tiff_paths = os.listdir(folderpath_with_tiffs)

with rasterio.open(mask_path) as src:
    mask = src.read(1)

stack = None
for tiff_path in tiff_paths:
    with rasterio.open(tiff_path) as src:
        array = src.read(1)
        extract = array[mask==0]  # [3 4]
        if stack is None:
            stack = extract.copy()
            stack = np.vstack((stack, extract))


If this is our binary mask

[[0 1 1]
 [0 1 1]
 [1 1 1]] 

and this is the array of the first tiff raster

[[3 5 2]
 [4 7 6]
 [8 8 1]]

and we want to extract the pixel values at the positions where the mask is 0

[3 4]

we would get a stack like this after looping through all tiffs.

[[3 4]    # extract of first tiff
 [1 6]    # second
 [2 1]]   # third and so on

We can get the time series of the first mask pixel by

# [3 1 2]
  • Question wouldn't np.dstack be a better choice than np.vstack? Commented Oct 1, 2018 at 10:29
  • Really depends on how you want to arrange and later access your results array. np.dstack would give you a third array dimension to deal with though. Give np.column_stack() a try, this would give you one pixel time series per row. Commented Oct 1, 2018 at 12:18

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