Excluding nodata value in band calculation with Rasterio?

Question

How do I exclude no data values when doing a raster calculation with rasterio. I realise that the files are read into an array, and that "0" is a nodata value. However, when I do a simple sum like "image + 1" it applies the math to the nodata value as well. So what is the best way to 'ignore' nodata values in the calculation?

FYI: I am calibrating the Landsat bands to reflectance and this is what my current snippet of the band math looks like:

    if "B1.TIF" in band:
        print band
        image = "%s" % (band)
        with rasterio.open(image) as src:
            image_read = src.read(1)
        #np.seterr(divide='ignore', invalid='ignore')
        constant = 0.01745329251994444444444444444444 #Constant is calculated (3.14/180) which is converting the sun-angle to sun_radians which was suggested by WOlfgang
        set_mb = "{:.16f}".format(float(mult_band1))
        set_ab = "{:.16f}".format(float(add_band1))
        toa_1 = (float(set_mb) * image_read.astype(float)) + (float(set_ab))
        solar_z = np.cos((90-float(sun_elevation))*float(constant))
        toa_2 = (toa_1.astype(float) / solar_z) * 100000
        kwargs = src.meta
        with rasterio.open(outfile, 'w', **kwargs) as dst:
            dst.write_band(1, toa_2.astype(rasterio.uint16))
        #print image_read.mask, toa_2

Is there a simple way to ignore nodata values in the calculation?

Answer 1

You can get a Numpy masked array that covers up nodata values from Rasterio by adding a keyword argument: src.read(1, masked=True). Operations on a masked array do not use the covered up elements.

If your dataset has no defined nodata value, but you want to use for example 0, read out a non-masked array and mask it yourself:

image_read = src.read(1)
image_read_masked = numpy.ma.masked_array(image_read, mask=(image_read == 0))