[GIS] Clustering of multiple raster layers to create sub-regions using QGIS

clusteringpolygonqgisraster

I'm attempting to create n sub-regions from a polygon based on a cluster analysis of a bunch of overlapping raster layers (physical layers, eg: depth, currents, waves).

Currently, I can create a regular grid across the polygon, then extract physical attributes from the physical raster layers (eg: Gridspot or equivalent tool) then, run a cluster analysis restricted to n number of clusters (in R or other stats package).

Then, I can identify each cluster-group, and plot them back in GIS (QGIS or ArcMap). I envisage however, that some cluster-groups will be dispersed (spatial outliers and not meaningful), whereas some will be clumped (worthy of being a sub-region).

I could then manually draw around representative clumps to create n sub-regions.

Is there a tool like ArcMap 10.1 Grouping Analysis that can be run in QGIS? I'm only running 10.0.

Are there suggestions of a better way to do cluster analysis of multiple raster layers, to create n sub-regions (bio-regions)?

Best Answer

It seems that your problem is that cluster analysis processes such as k-means in R do not consider spatial information, hence the output is likely to be dispersed (spatially at least!). Have you considered adding the raster row and column values in as additional variables, this would make the clustering algorithm 'aware' of the spatial configuration of the data?

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[GIS] Segmenting rasters into sub-regions and sample using R without using extract()

You could crop and mask the raster to each region and then use "sampleRandom" to create a random sample of the specific region(s). This should speed things up considerably.

        require(raster)

        r1 <- raster(ncol=10, nrow=10, xmn=0, ymn =0, xmx=100, ymx=100)
          r1[] <- runif(ncell(r1),0,100)
        r2 <- raster(ncol=10, nrow=10, xmn=0, ymn =0, xmx=100, ymx=100)
          r2[] <- runif(ncell(r1),100,200)
        r3 <- raster(ncol=10, nrow=10, xmn=0, ymn =0, xmx=100, ymx=100)
          r3[] <- runif(ncell(r1),200,300)

        r <- stack(r1, r2, r3)
          names(r) <- c("r1", "r2", "r3")  

        region1 <- rbind(c(0,0), c(50,0), c(50,50), c(0,50), c(0,0))
          region2 <- rbind(c(50,0), c(100,0), c(100,50), c(50,50), c(50,0))
            region3 <- rbind(c(0,50), c(50,50), c(50,100), c(0,100), c(0,50))
              region4 <- rbind(c(50,50), c(100,50), c(100,100), c(50,100), c(50,50))
        polys <- SpatialPolygons(list(Polygons(list(Polygon(region1)), "region1"),
                                 Polygons(list(Polygon(region2)), "region2"), 
                                 Polygons(list(Polygon(region3)), "region3"), 
                                 Polygons(list(Polygon(region4)), "region4")))

 rs <- as.data.frame(array(0, dim=c( 0, length(names(r))+1 )))  
      names(rs) <- c("REGION", names(r))                 
  for(i in 1:length(polys)){
      region <- polys[i]
        cr <- crop(r, extent(region), snap="out")                   
          m <- rasterize(region, cr)
           mr <- mask(x=cr, mask=m)
             rs.mat <- sampleRandom(mr, 10, na.rm=TRUE)
               rs.mat <- cbind(REGION=i, rs.mat)
        rs <- rbind(rs, as.data.frame(rs.mat) ) 
      }
    print( rs )

[GIS] Dividing an irregular polygon into sub-regions

You might try the Editor, Copy Parallel tool to create lines the same distance apart. This would be a Polyline feature class. The Advanced Editing Tool bar has Split Polygon tool. First, Select the lines overlapping your polygon, then execute the tool. Your Polygon will be cut by each line. The lines need to extend beyond the edges of your polygon.

Best Answer

Related Solutions

[GIS] Segmenting rasters into sub-regions and sample using R without using extract()

[GIS] Dividing an irregular polygon into sub-regions

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