I am new at using Whitebox GAT, which I find very interesting.

When one runs an analysis, is there any possibility to limit the processing to a section of the input DTM, or does the latter have to be clipped exactly to the extent of the study area?


No, unfortunately there is no concept of a global work area in Whitebox GAT. Your best way forward is simply to clip the data layers to your area of interest using the Clip Raster To Polygon (raster data clipped to vector polygon) or Clip (vector clipped to vector polygon) tools.

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