Changing of pixel values when clipping raster by mask in QGIS

clipraster

I am using 'Clip raster by mask layer' in QGIS to clip a raster temperature layer down to the size of the area I'm interested in using a polygon. The resulting clipped layer is a raster that has pixel values significantly different from the original.

I am doing this same process with different raster layers and it usually works fine, but some clipped layers come out with pixel values totally off. This is not an issue of values display. It's just that the pixels have different values. For example, when I right-click with 'identifier features' option on a random pixel it gives me values of 26.95 in the original (which makes complete sense as this is the value of mean annual temperature) and a value of 3001 in the clipped raster.

Does anyone know what's going wrong?

I couldn't attach the image in my previous comment. Here it is:

Best Answer

Before you run the mask tool, use the GDAL Translate (convert format) tool to unscale your input raster as follows:

Select tool from toolbox under GDAL->Raster conversion -> Translate
Choose your input raster as the input layer for the translate tool
Type -unscale -co DECIMAL_PRECISION=2 in the Additional command-line parameters (don't forget the leading hyphen)
Choose output filename and location
Run the Translate tool and use the output (unscaled tiff) as the input to 'clip raster from mask' as you did before.

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The simple way to do this in QGIS is to use the Raster Calculator (Raster->Raster Calculator). You have a couple of options. The easiest to explain/understand is to make a unitary raster from your mask (all data set to either 1 or NoData) and then multiply your clip layer by the unitary mask layer.

To ensure the extents match the mask layer, in the raster calculator window select the mask layer in the 'Raster bands' list on the left and then click the 'Current layer extent' button on the right.

You can create a unitary mask on the fly by using a conditional statement (see the link) something like this:

(maskLayer@1 >= 0) * clipLayer@1

This statement basically says: treat everything in my mask layer that is not NoData as being equal to 1 (NoData stays as NoData). Just be sure to remember to set the extent (see above)!

Raster Calculator and paletted data:

Any output from the raster calculator will be just values and not carry over any information contained within a colour pallet. You have a couple of options to 'get your palette back':

Go to the style tab of the original layer's properties and (making sure it is paletted), click on Save Style button at the bottom. You can then apply this same style to your new layer and if you have only clipped it as per the above instructions, it will appear the same as before. This is easy but your raster is not paletted in a persistent way outside of the QGIS project.
To make the presentation persistent, you can right-click the layer and 'Save As'. Check the 'Rendered Image' radio button at the top of the save-dialog box. This will make a new raster with the exact colour scheme as your palatted layer BUT it will no longer be a single band raster but a four band RGBA raster.
If you MUST have an actual stand-alone single-band raster with a persistent palette (and not RGBA), then I don't know of a way of doing this in QGIS but you could take the output of step 2 above and open it in GIMP (or Photoshop) and change the mode from RGB to Indexed Colour. But you will need to create a world file as saving the image in GIMP/Photoshop will destroy the georeferencing.

Best Answer

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