title: mask and extract cell values from a vrt file?
body: <p>I have raster data for built up areas around the globe with 40m resolution as vrt file, <a href="http://cidportal.jrc.ec.europa.eu/ftp/jrc-opendata/GHSL/GHS_BUILT_LDSMT_GLOBE_R2015B/GHS_BUILT_LDSMT_GLOBE_R2015B_3857_38/V1-0/" rel="nofollow noreferrer">download data from here</a> , and I am trying to crop the data by a mask and then extract color index value for each cell.</p>
  
  <p>Note: another 2 files exist with the data: <code>vrt.clr</code> and <code>vrt.ovr</code></p>
  
  <p>Here is a sample of data:
  <a href="https://i.stack.imgur.com/knfS7.jpg" rel="nofollow noreferrer">view of vrt data in arcmap</a>.</p>
  
  <p><strong>My question: why I am getting empty cells values when I crop by mask ?</strong></p>
  
  <p>I have tried the following:</p>
  
  <ul>
  <li>extract by mask using arcmap toolbox</li>
  <li><p>using gdal in python 2.7</p>
  
  <p><code>import gdal
  ds = gdal.Open('input.vrt')
  ds = gdal.Translate('output.vrt', ds, projWin = 
  [80.439,5.341,81.048,4.686])
  ds = None</code></p></li>
  <li><p>I have also try to save the data as tif </p></li>
  </ul>
  
  <p>Also, is there any way to read the color index value at given coordinates (x,y) after masking the data?</p>