I am using the BirdLife International .gdb file (polygons) of bird species distributions to try and make a species richness map across the Brazilian Amazon. To do this I have clipped the global distributions file to my study area. I have also created a hexagonal grid of my study area.

My method so far has been to intersect these two layers to split the distributions into the hexagonal grid cells. From this I am getting the polygon centroids and counting the number of points in each of the original hexagon cells. This has already worked for the IUCN mammal and amphibian shapefiles.

However, when I try to intersect the birdlife distribution layer with the hexagonal cells I get an invalid geometry error even though I have validated the geometries using the QGis Validate geometries tool, and removed invalid geometries.

error invalid geometry detected in input layer A, feature 42

I have also tried checking the geometries in ArcMap10 and they appear to be valid. The problem also continued after deleting the features the error message highlighted.

Is there a method that would avoid this error or would solve this problem?

  • What is the precise error message that you receive?
    – PolyGeo
    Feb 20, 2017 at 20:04
  • i don't have the exact message but it was something along the lines of "error invalid geometry detected in input layer A, feature 42." I tried deleting this but it still returned the same error.
    – Tom
    Feb 20, 2017 at 21:18
  • Did you try to rebuild that specific feature? Or just export everything to a new shape. Do the projections match?
    – DirkB.
    Feb 20, 2017 at 21:23
  • I just deleted the feature from the shapefile and tried again with the result. The projections match up.
    – Tom
    Feb 20, 2017 at 21:37
  • What happens if you save out a new shapefile from that shapefile and try the process on the new one?
    – artwork21
    Feb 21, 2017 at 13:52

1 Answer 1


Try to find and fix the problematic features. I find that when intersecting most errors occur from a) remaining points from inner rings b) folded geometries or "cropped" polygons that result in bad nodes order along the perimeter of the polygon. Some cases of these 2 categories produce valid geometries. What i find helpfull is intersecting through postgres which returns errors in coordinates albeit one by one (it does not list them all at once) and go fix them manually. If you expect many errors other methods are required.

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