I am generating a simple two-class (binary) geotiff from a numpy array with 3 values: 1, 2, and NaN. I wanted to display the geotiff with distinct colors so I used the color table. However, color table only supports the Byte or UInt16 datatype, which will convert the NaN to zeros.

Is there a way to write a binary geotiff including the NaN with colors?

filename = 'test.tif'
ds = gdal.Open(filename, gdal.GA_ReadOnly)
outfile = 'classify.tif'
driver = gdal.GetDriverByName("GTiff")
outdata = driver.Create(outfile, cols, rows, 1, gdal.GDT_Byte)     
outband = outdata.GetRasterBand(1)
ct = gdal.ColorTable()
ct.SetColorEntry(1, (0,0,102,255))      
ct.SetColorEntry(2, (0,255,255,255))    
outdata = None
outband = None
ds = None
  • Could you set NaN into third palette entry (0,0,0,255) and mark that as NoData?
    – user30184
    Commented Aug 28, 2017 at 18:52
  • Nope. Color Table only supports Byte or UInt16. However, NaN supports float datatype but not Byte or UInt16. So I had to write the file to Byte and it converts all the NaN elements into zeros.
    – J.Wang
    Commented Aug 28, 2017 at 20:43
  • What does it matter if you know that all zeros mean NaN and you set metadata to show that as nodata?
    – user30184
    Commented Aug 28, 2017 at 21:05
  • Good question. It is not a big issue but when I display it in GIS/RS software, I want those areas to be shown as NaN and I can easily get a percentage of each class.
    – J.Wang
    Commented Aug 28, 2017 at 21:20
  • So your NaN does not mean missing data but it is a meaningful class? Sorry but I do not understand your use case yet.
    – user30184
    Commented Aug 28, 2017 at 21:36

1 Answer 1


you can convert the NaNs to a real value (e.g. 255) and then set your Geotiffs NoData value to this real value.


More info on the conversion can be found here: Reclassify a raster value to -9999 and set it to the nodata value using python and or gdal

  • But I need to write it to a float type, right? The color table doesn't support float type. I wonder if there's another way to write the geotiff with color.
    – J.Wang
    Commented Aug 28, 2017 at 23:26
  • can't you just use an integer, UInt16 ?
    – RutgerH
    Commented Aug 29, 2017 at 2:18
  • Then I wouldn't be able to produce a colored geotiff?
    – J.Wang
    Commented Aug 29, 2017 at 15:51
  • ct.SetColorEntry(255, (0,0,0,0))
    – RutgerH
    Commented Aug 29, 2017 at 16:16
  • can you share your file, then I can give it a try
    – RutgerH
    Commented Aug 29, 2017 at 16:20

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