Tuesday, February 22, 2011

Clip a Raster using a Shapefile

Clipping a satellite image: Rasterize, Mask, Clip, Save
If you read this blog you see most of the material covers shapefiles.  The intent of this blog is to cover remote sensing as well and this article provides a great foundation for remote sensing in Python. In this post I'll demonstrate how to use several Python libraries to to create a script which can take any polygon shapefile and use it as a mask to clip a geospatial image.  Although I'm demonstrating a fairly basic process, this article and the accompanying sample script is densely-packed with lots of good information and tips that would take you hours if not days to piece together reading forum posts, mailing lists, blogs, and trial and error.  This post will get you well on your way to doing whatever you want to do with Python and Remote Sensing.

Satellite and aerial images are usually collected in square tiles more or less the same way your digital camera frames and captures a picture.  Geospatial images are data capturing different wavelengths of light reflected from known points on the Earth or even other planets.  GIS professionals routinely clip these image tiles to a specific area of interest to provide context for vector layers within a GIS map.  This technique may also be used for remote sensing to narrow down image processing to specific areas to reduce the amount of time it takes to analyze the image.

The Process

Clipping a raster is a series of simple button clicks in high-end geospatial software packages.  In terms of computing, geospatial images are actually very large, multi-dimensional arrays.  Remote Sensing at its simplest is performing mathematical operations on these arrays to extract information from the data. Behind the scenes here is what the software is doing (give or take a few steps):
  1. Convert the vector shapefile to a matrix which can be used as mask
  2. Load the geospatial image into a matrix
  3. Throw out any image cells outside of the shapefile extent
  4. Set all values outside the shapefile boundary to NODATA (null) values
  5. OPTIONAL: Perform a histogram stretch on the image for better visualization
  6. Save the resulting image as a new raster.
Geospatial Python Raster Clipping Workflow

Two things I try to do on this blog are build on techniques used in previous posts and focus on pure-Python solutions as much as possible.  The script featured in this post will use one of the shapefile rasterization techniques I've written about in the past.  However I did not go pure-Python on this for several reasons.  Geospatial image formats tend to be extremely complex.  You could make a career out of reading and writing the dozens of evolving image formats out there.  As the old saying goes TIFF stands for "Thousands of Incompatible File Formats".  So for this reason I use the Python bindings for GDAL when dealing with geospatial raster data.  The other issue is the size of most geospatial raster data.  Satellite and high-resolution aerial images can easily be in the 10's to 100's of megabytes size range.  Doing math on these images and the memory required to follow the six step process outlined above exceeds the capability of Python's native libraries in many instances.  For this reason I use the Numpy library which is dedicated to large, multi-dimensional matrix math.  Another reason to use Numpy is tight integration with GDAL in the form of the "GDALNumeric" module. (Numeric was the predecessor to Numpy) In past posts I showed a pure-Python way to rasterize a shapefile.  However I use the Python Imaging Library (PIL) in this example because it provides convenient methods to move data back and forth between Numpy.

Library Installation

So in summary you will need to install the following packages to make the sample script work.  Usually the Python Disutils system (i.e. the "easy_install" script) is the fastest and simplest way to install a Python library.  Because of the complexity and dependencies of some of these tools you may need to track down a pre-compiled binary for your platform.  Both Numpy and GDAL have them linked from their respective websites or the Python Package Index.

The Example

# - clip a geospatial image using a shapefile

import operator
from osgeo import gdal, gdalnumeric, ogr, osr
import Image, ImageDraw

# Raster image to clip
raster = "SatImage.tif"

# Polygon shapefile used to clip
shp = "county"

# Name of clip raster file(s)
output = "clip"

# This function will convert the rasterized clipper shapefile 
# to a mask for use within GDAL.    
def imageToArray(i):
    Converts a Python Imaging Library array to a 
    gdalnumeric image.
    return a

def arrayToImage(a):
    Converts a gdalnumeric array to a 
    Python Imaging Library Image.
    return i
def world2Pixel(geoMatrix, x, y):
  Uses a gdal geomatrix (gdal.GetGeoTransform()) to calculate
  the pixel location of a geospatial coordinate 
  ulX = geoMatrix[0]
  ulY = geoMatrix[3]
  xDist = geoMatrix[1]
  yDist = geoMatrix[5]
  rtnX = geoMatrix[2]
  rtnY = geoMatrix[4]
  pixel = int((x - ulX) / xDist)
  line = int((ulY - y) / yDist)
  return (pixel, line) 

def histogram(a, bins=range(0,256)):
  Histogram function for multi-dimensional array.
  a = array
  bins = range of numbers to match 
  fa = a.flat
  n = gdalnumeric.searchsorted(gdalnumeric.sort(fa), bins)
  n = gdalnumeric.concatenate([n, [len(fa)]])
  hist = n[1:]-n[:-1] 
  return hist

def stretch(a):
  Performs a histogram stretch on a gdalnumeric array image.
  hist = histogram(a)
  im = arrayToImage(a)   
  lut = []
  for b in range(0, len(hist), 256):
    # step size
    step = reduce(operator.add, hist[b:b+256]) / 255
    # create equalization lookup table
    n = 0
    for i in range(256):
      lut.append(n / step)
      n = n + hist[i+b]
  im = im.point(lut)
  return imageToArray(im)

# Load the source data as a gdalnumeric array
srcArray = gdalnumeric.LoadFile(raster)

# Also load as a gdal image to get geotransform 
# (world file) info
srcImage = gdal.Open(raster)
geoTrans = srcImage.GetGeoTransform()

# Create an OGR layer from a boundary shapefile
shapef = ogr.Open("%s.shp" % shp)
lyr = shapef.GetLayer(shp)
poly = lyr.GetNextFeature()

# Convert the layer extent to image pixel coordinates
minX, maxX, minY, maxY = lyr.GetExtent()
ulX, ulY = world2Pixel(geoTrans, minX, maxY)
lrX, lrY = world2Pixel(geoTrans, maxX, minY)

# Calculate the pixel size of the new image
pxWidth = int(lrX - ulX)
pxHeight = int(lrY - ulY)

clip = srcArray[:, ulY:lrY, ulX:lrX]

# Create a new geomatrix for the image
geoTrans = list(geoTrans)
geoTrans[0] = minX
geoTrans[3] = maxY

# Map points to pixels for drawing the 
# boundary on a blank 8-bit, 
# black and white, mask image.
points = []
pixels = []
geom = poly.GetGeometryRef()
pts = geom.GetGeometryRef(0)
for p in range(pts.GetPointCount()):
  points.append((pts.GetX(p), pts.GetY(p)))
for p in points:
  pixels.append(world2Pixel(geoTrans, p[0], p[1]))
rasterPoly ="L", (pxWidth, pxHeight), 1)
rasterize = ImageDraw.Draw(rasterPoly)
rasterize.polygon(pixels, 0)
mask = imageToArray(rasterPoly)   

# Clip the image using the mask
clip = gdalnumeric.choose(mask, \
    (clip, 0)).astype(gdalnumeric.uint8)

# This image has 3 bands so we stretch each one to make them
# visually brighter
for i in range(3):
  clip[i,:,:] = stretch(clip[i,:,:])

# Save ndvi as tiff
gdalnumeric.SaveArray(clip, "%s.tif" % output, \
    format="GTiff", prototype=raster)

# Save ndvi as an 8-bit jpeg for an easy, quick preview
clip = clip.astype(gdalnumeric.uint8)
gdalnumeric.SaveArray(clip, "%s.jpg" % output, format="JPEG")

Tips and Further Reading

The utility functions at the beginning of this script are useful whenever you are working with remotely sensed data in Python using GDAL, PIL, and Numpy.

If you're in a hurry be sure to look at the GDAL utility programs.  This collection has a tool for just about any simple operation including clipping a raster to a rectangle.  Technically you could accomplish the above polygon clip using only GDAL utilities but for complex operations like this Python is much easier.

The data referenced in the above script are a shapefile and a 7-4-1 Path 22, Row 39 Landsat image from 2006. You can download the data and the above sample script from the GeospatialPython Google Code project here.

I would normally use the Python Shapefile Library to grab the polygon shape instead of OGR but because I used GDAL, OGR is already there. So why bother with another library?

If you are going to get serious about Remote Sensing and Python you should check out OpenEV.  This package is a complete remote sensing platform including an ERDAS Imagine-style viewer.  It comes with all the GDAL tools, mapserver and tools, and a ready-to-run Python environment.

I've written about it before but Spectral Python is worth a look and worth mentioning again. I also recently found PyResample on Google Code but I haven't tried it yet.  

Beyond the above you will find bits and pieces of Python remote sensing code scattered around the web.  Good places to look are:
More to come!

UPDATE (May 4, 2011): I usually provide a link to example source code and data for instructional posts. I set up the download for this one but forgot to post it.  This zip file contains everything you need to perform the example above except the installation of GDAL, Numpy, and PIL:

Make sure the required libraries are installed and working before you attempt this example.  As I mention above the OpenEV package has a Python environment with all required packages except PIL.  It may take a little work to get PIL into this unofficial Python environment but in my experience it's less work than wrangling GDAL into place.


  1. Hi.
    Your code is very impressing but I'm trying to use it and it doesn't working.
    Do you have a py file and tif and shp file to make a test?


  2. Lucas,

    Yes I do. I forgot to add it to the post. Please go to:

    Go do the "Downloads" section and download "". It has all of the files you need to make this work. However you will still need to install the Numpy, GDAL, and PIL libraries.

  3. Hi Joel, thanks for the answer

    I would like to use the code to clip a 1-band raster file based on a multi-features polygon shapefile, but some errors are happening, like:

    clip = srcArray[:, ulY:lrY, ulX:lrX]
    IndexError: too many indices

    for p in range(pts.GetPointCount()):
    AttributeError: 'NoneType' object has no attribute 'GetPointCount'

    1. If it helps someone

      The array here has a shape of (1,rows,col) but you just have (rows, col)
      Fix the line with clip = srcArray[np.newaxis,ulY:lrY, ulX:lrX]
      This should potentially work

  4. Hi,
    This tool is very useful. I am wondering if you can help me to modify it such that we can clip several raster files in a given directory (batch processing). Thanks

  5. To batch process and clip a bunch of rasters do the following:

    1. Get the example in this blog post working.

    2. Change the source image to one of your images and make any adjustments needed to get the script working with a sample of your data.

    3. Collect a list of image files in your directory using the Python glob module.

    4. Iterate through that list applying the whole script beginning with the "srcArray" variable which is assigned to the current file name.

    5. Post to if you are having troubles.

    Let us know how it goes!

  6. Nice hack, but you could do the same thing using about 4 lines of code by using ArcObjects!

    1. Yes, but this solution does not require an ESRI license and is subsequently ~$8000 cheaper.

  7. Does anyone know how to do this in R?

  8. Thank you for the post,

    If I have a single shapefile with several polygons inside it how can I make several clips for each of that polyon? I have to extract them from a shapefile and iterate over them?

    1. Hi Antonio, were you able to do this? If yes, could you share your code?

  9. Antonio,

    You shouldn't have to extract the polygons to separate files.

    This script could be modified to do that. Instead of "poly = lyr.GetNextFeature()", you would build and array of polygons for each feature in the shapefile.

    And then you would need to put the "Map Points to Pixels" section in a loop to apply each polygon to the clipping mask.

    I haven't tried this trick but it should work.

    When I have more time I can try to create an example. If you get it working let me know.

  10. I would like to use the code to clip a 1-band raster file based on a multi-features polygon shapefile, but some errors are happening, like:

    clip = srcArray[:, ulY:lrY, ulX:lrX]
    IndexError: too many indices

  11. Hi, thanks for your great page!

    I am not sure I understand gdalnumeric versus numpy. If I understand this link correctly, gdalnumeric just imports numpy and parts of gdalor am I misunderstanding something?

    Sorry if this is a stupid question, but the widely spread info on the net makes it not that easy to get an overview on gdal, ogr, etc etc...

  12. Hi, in the world2Pixel method, you should divide 'ulY - y' by yDist instead of xDist.

  13. Hi, is it possible to use this code to clip ECW images? I.e. can I associate a vector poly (reduced poly of the image footprint poly) and "visually mask" the pixels outside of the vector poly? My online research shows that it isn't possible with ECW images. I failed trying in Global Mapper and with GDAL and QGIS; it works on TIFF but as soon as I export to ECW, I get unwanted edge pixels...

    1. Arun, ECW images are highly compressed and designed for fast viewing. You must uncompress them to perform any geospatial analysis.

  14. Hi
    How can I clip DEM from Shape file. Is this same code will be working ?

  15. Hi, I required help in your code

    I am getting an error in the last line of the code i.e.

    "gdalnumeric.SaveArray(clip, "%s.tif" % output, format="GTiff", prototype=raster)"


    File "E:\code\PyCode\GlapTop2_code", line 108, in
    gdalnumeric.SaveArray(clip, "%s.tif" % output, format="GTiff", prototype=raster)
    File "C:\Python27\lib\site-packages\osgeo\", line 204, in SaveArray
    return driver.CreateCopy( filename, OpenArray(src_array,prototype) )
    File "C:\Python27\lib\site-packages\osgeo\", line 396, in CreateCopy
    return _gdal.Driver_CreateCopy(self, *args, **kwargs)
    ValueError: Received a NULL pointer.

  16. Hey Joel, nice tutorial. Do you have any advice how to implement this if you are processing raster on blocks that covers only part of the shapefile?

  17. HI Joel,

    As several others have suggested, attempting to perform this operation on a 1-2 band image produces an error on this line:

    clip = srcArray[:, ulY:lrY, ulX:lrX]

    I altered my code to
    clip = srcArray[:, ulY:lrY, ulX:lrX],

    however I then encounter an error at this line:
    clip = gdalnumeric.choose(mask, (clip, 0)).astype(gdalnumeric.uint8)

    ValueError: shape mismatch: objects cannot be broadcast to a single shape

    Do you have advice for overcoming this?

  18. Apologies- I altered the line with the original error to:
    clip = srcArray[ulY:lrY, ulX:lrX]


  19. Hi.. got to know many things from your post. One thing that I see amiss in my interpolation routine is the shapefile. May I know how did you create those county.* shapefiles? I'd like to do that for a particular country of interest.
    Thank you!

    1. Yes - please see this post on how to subset a shapefile by attributes which should allow you to isolate your country of interest from a world boundaries shapefile:

  20. really nice tool!! the only problem i am seeing is that after the clipping the resulting image coordinates are not correct any more. Did anybody already solve that problem?


  21. Nice post. This is very useful. Thank you so much for sharing.
    clipping path services

  22. Hey, I am try to clip the raster from a vector polygon. And I set no data as 255 on QGIS, and it also deletes 255 values in raster within the boundary. Thus leaving transparent artifacts in the image. I wonder if your tool fix that problem as well.. Please let me know if you have solution for such. Thank you.


    1. you can choose a different no data value. or you want to see the no data values.

  23. When I cut raster the SRC was lost. How can I clip raster without lose SRC of file?

  24. This is a wonderful post on clipping a raster using a Shapefile. Really, it is a very informative and beneficial article. I’m very glad to read this article. Before reading this post I didn’t have clear idea about clipping a raster. Now I have vast knowledge about it. Thanks for posting such an excellent article. Now I want to learn raster to vector service.

  25. HI, I am getting error of too many indices for Array on "clip = srcArray[:, ulY:lrY, ulX:lrX]"

    when i change this line of code as suggeste above with "clip = srcArray[ulY:lrY, ulX:lrX]
    i get the erro of "Width and Height must be > 0"
    any suggestion would be helpful.
    thank you

  26. I am also getting error of too many indices for Array on "clip = srcArray[:, ulY:lrY, ulX:lrX]"
    Are there any pre-conditions for the geotiff and shapefile?


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  28. Hi Joel,
    I like this tutorial.
    One question , what I need to modify in script to keep the clipped image with the original size of input raster ? After running the script the clipped image is smaller than the original. I'd like to keep the original height and width.

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