Python-gdal write a GeoTiff with binary color and NaN

Question

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) 
outdata.SetGeoTransform(ds.GetGeoTransform())
outdata.SetProjection(ds.GetProjection())
outband = outdata.GetRasterBand(1)
ct = gdal.ColorTable()
ct.SetColorEntry(1, (0,0,102,255)) 
ct.SetColorEntry(2, (0,255,255,255)) 
outband.SetColorTable(ct)
outband.WriteArray(result)
outband.FlushCache() 
outdata = None
outband = None
ds = None

• user30184: Could you set NaN into third palette entry (0,0,0,255) and mark that as NoData?
• J.Wang: 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.
• user30184: What does it matter if you know that all zeros mean NaN and you set metadata to show that as nodata?
• J.Wang: 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.
• user30184: So your NaN does not mean missing data but it is a meaningful class? Sorry but I do not understand your use case yet.

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.

dst_ds.GetRasterBand(1).SetNoDataValue(255)

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

• J.Wang: 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.
• RutgerH: can't you just use an integer, UInt16 ?
• J.Wang: Then I wouldn't be able to produce a colored geotiff?
• RutgerH: ct.SetColorEntry(255, (0,0,0,0))
• RutgerH: can you share your file, then I can give it a try