I work with Sentinel-2 images. I wanted to plot a histogram of a cloudmask, but it showed non-existent values.

I used the MSK_CLDPRB_20m.jp2 layer, which is a raster that shows the probability of there being a cloud on that pixel. This is a value between 0 (no clouds) and 100 (clouds). When classifying the symbology (unique values), Qgis says there are only values between 0 and 100. When manually inspecting I also wasn't able to find any values higher than 100.

But when I plot the histogram of the layer, it shows the following. enter image description here 'Frequentie' = Frequency, 'Pixelwaarde' = Pixelvalue

This specific image doesn't contains that much clouds, so the value 0 is present a lot (which is expected). The problem is that it also shows there are values above 100?

What's the reason for this?

I use QGIS 3.22.5

  • Have you tried using the Raster Calculator to remove any value superior to 100 and then plot the histogram again? (with an expression such as IF(raster_name > 100, raster_name*0, raster_name), to set all values superior to 100 to 0 for instance)
    – Sken2107
    Commented Jun 15, 2022 at 7:59
  • Same observation here forum.step.esa.int/t/what-exactly-is-in-msk-cldprb/23908/2. Could there be calibration involved somewhere, telling that min raw value means 0 and max raw value means 100? Does gdalinfo show anything about scale and offset?
    – user30184
    Commented Jun 15, 2022 at 8:39
  • By developers.google.com/earth-engine/datasets/catalog/… value 100 should be the maximum. Compare QGIS with gdalinfo -stats. I wonder if QGIS is using some overview level of the image for making the computation of the histogram faster.
    – user30184
    Commented Jun 15, 2022 at 8:53
  • 1
    I used the Raster Calculator to remove values higher than 100. After this the histogram did show up correctly without any values higher than 100.
    – Niek
    Commented Jun 15, 2022 at 10:35
  • I used gdalinfo - stats to look at the file. GDAL doesn't show anything about scale or offset. It does specify a min and max of 0.000 and 100.000 which is correct...
    – Niek
    Commented Jun 15, 2022 at 10:52

1 Answer 1


I found that using the raster calculator option to set all the values below/above one specific value to 0 produces a nice histogram

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