Convert NAN to NODATA in QGIS

Question

I have come across a set of poorly generated rasters which I need to align and regularize. I am open to any quick and dirty way to do this, but prefer QGIS since I have been using it for all my operations thus far.

The rasters contain positive ranges of floating point values, have a NODATA value defined, but also have many cells containing nan values. I would like to convert all nan values to the currently defined NODATA value. To achieve this, I tried many combinations of using the following:

• gdal raster calculator (using numpy where and isnan functions)
• raster calculator
• GRASS r.null tool

However I can't seem to get a workflow going. The gdal raster calc with numpy functions was close, but unfortunately theres no way of referring to the currently defined NODATA value by variable (as far as I know).

I would like to avoid using Python tools like rasterio since rasters should not be delivered in this format anyway (no use scripting this).

Does anyone have a way of achieving this?

Answer 1

Here's a lazy script I wrote to do this:

import rasterio
import os
import numpy as np


raster = 'Waterways_dist_clipped_30m.tif'

ds = rasterio.open(os.path.join('main_input',raster))
profile = ds.profile

data = ds.read(1)
new_data = np.where(np.isnan(data), profile['nodata'], data).astype(profile['dtype'])

with rasterio.Env():
    with rasterio.open(os.path.join('D:\\TEMP\\rasters', raster), 'w', **profile) as dst:
        dst.write(new_data, 1)

ds.close()
print('don')

Lord knows I didn't enjoy writing it....

Answer 2

If still useful for someone, I solved this problem using the raster calculator. For a raster called 'RAST':

RAST/(abs(RAST)+1>0)

The denominator gives zero at not a number (nan) pixels, and thus the equation gives 'no data'