Problems intersecting large polygon shapefiles in QGIS (V2.18.2)

Question

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?

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.