Rasterio showing single band images wrong

Question

I'm using rasterio in Python at the moment, and I have no problem when I'm dealing with RGB satellite images. However, if I try using singleband Sentinel 2 images, or a singleband Sentinel 1 image, something happens. As this figure here shows, you can see that the image on the left, is suddenly green. Whilst the exact same image on the right in QGIS, looks at it should. Any suggestions?

I use the following code:

dataset = rasterio.open(project_dir + '/data/satellite_data/S1/merged/S1HH.tiff')
img=dataset.read()
fig=show(img)

Answer 1

This isn't rasterio reading the raster incorrectly. It's whatever you are using to display the data (matplotlib?) applying a default colour ramp. By saving as an RGBA in QGIS you are changing (and destroying) the data.

Instead, assuming you're using matplotlib, use the cmap argument in pyplot.imshow to specify a grayscale colourmap, something like:

from matplotlib import pyplot
import rasterio

dataset = rasterio.open(project_dir + '/data/satellite_data/S1/merged/S1HH.tiff')
img=dataset.read()
img_plt = pyplot.imshow(img, cmap='gray')
pyplot.show()

For a (very) basic contrast stretch:

import numpy as np

img[img == dataset.nodata] = np.nan  # Convert NoData to NaN
vmin, vmax = np.nanpercentile(img, (5,95))  # 5-95% stretch
img_plt = pyplot.imshow(img, cmap='gray', vmin=vmin, vmax=vmax)
pyplot.show()