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I have a set of image files ordered by file names and another group just like the other one, with the same number of files. I want to get a new file with two layers, having the first layer as the first image of the first group and the second layer as the first image of of the second group, being the first layer visiblein multiply mode or some other mode of layer mixing. Problem is I want to do this operation with more than 100 pairs, each pair making a new file. Is there any batch process to perform something like this?

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If the images are not too big (otherwise work with smaller groups), and if the file names in both sets are ordered the same way, using scripts that exist:

  1. Load N images of the first group as layers in one single image (open the first normally, and use File>Open as layers for the rest (the file selector in open-as-layers lets you select multiple files, so this is only two operations, whatever the number of files).
  2. Do the same to open the 2nd set of layers in a second image.
  3. Use ofn-interleave-layers to interleave the layers of the 2nd image between the layers of the first, and merge them down with a given layer blend mode. The script requires the images to have the same canvas size, and all involved layers to be also at that size ( if necessary you can use ofn-layers-to-image-size for this). This creates a third image.
  4. Use another script to export all the layers of the 3rd image to files (for instance ofn-export-layers).

All three mentioned scripts can be found here.

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