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Put your gradient on a new layer and use a mask to show the area you want. You can make a layer mask from a selection (menu Layer - Layer Mask - Reveal Selection). You can also alter the mask later to adjust what it shows and hides if required.
Example below :
You can also do the same with a Gradient Fill Layer (menu Layer - New Fill Layer - Gradient)
This has the advantage that you can go back and change the gradient parameters as well as the mask
I hope that helps you
While that is useful to know (I didn't know about that previously), but it's not quite what I was asking, sorry I guess I was a bit unclear, but basically what I want to know how to do is that if I had something like this on one layer:
How would I be able to turn it into something like this without having to manually select the green square with the magic wand and use the gradient tool.
For this it wouldn't be too much of an issue to manually select an area and apply the gradient to it as it was only one operation, but If I wanted to apply 12 gradients onto the white square to get something like this:
Then it would be a lot of work to manually select each area before applying the gradient.
So what I was wondering is if you could get a gradient to fill an area by colour rather than by selection. This is possible to do on other adobe applications, which is why I think there would be a way to do it on photoshop.