Question: Given two input layers

1. The clip layer - an arbitrary layer (though in my case it's a float 1 band geotiff)
2. The mask layer - a paletted *raster* in which every pixel is either NO DATA or a single "color" value, same for every pixel.

I want to create an output raster whose overall extent matches the extent of the mask layer and each pixel is either NO DATA if the corresponding pixel of the mask layer is NO DATA or the value of the corresponding pixel from the clip layer if the corresponding pixel of the mask layer is not NO DATA.

I know I can mask the clip layer with a polygon, but the mask layer is a raster. Polygonizing the raster layer is possible in principle, but would result in a polygon with a lot of very short edges.

Is there a direct way to do this in QGIS?

I suppose there's probably a path that involves creating a new layer and using the raster calculator, but I'm hoping there's something more direct. Further complicating the matter is that the two rasters might not have the same resolution and origin.

I believe this is equivalent to [Extract by Mask](http://help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#/Extract_by_Mask/009z0000002n000000/) in ArcMap.

Answer: 
The simple way to do this in QGIS is to use the [Raster Calculator](http://www.qgis.org/en/docs/user_manual/working_with_raster/raster_calculator.html) (`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':

1. 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.
2. 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.
3. 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.
I don't have enough rep to comment, but I would like to share what worked with me after spending quite some time! After following @MappaGnosis advice, I used raster calculator 4 times (because I had a 4-band image) and following the exact same process, changing the bands used in the raster calculator, ended up with 4 images whose extent were equal to the raster we wanted to clip by and (as each resulting raster has only 1 band) the value of those bands were from the raster we wanted to clip.

To sum it up, all I did was:

```
(maskLayer@1 >= 0) * clipLayer@1
(maskLayer@2 >= 0) * clipLayer@2
(maskLayer@3 >= 0) * clipLayer@3
(maskLayer@4 >= 0) * clipLayer@4

```

Then, we can build a virtual raster with those 4 files (don't forget to tick the "place each file in separate band") and voilá! Export the virtual raster and it's done.