I have a raster layer (coloured squares) and a vector layer that represents water bodies (blue coloured polygones; see image below). I am looking for a way to exclude / remove the cells that are covered by more than a certain percentage of water (say 60%). How can I do it using gdal and / or python?

enter image description here

1 Answer 1


Next code can be used to do that:

from osgeo import gdal, osr

registry = QgsMapLayerRegistry.instance()

raster = registry.mapLayersByName('my_raster')
provider = raster[0].dataProvider()
filename = provider.dataSourceUri()
water_bodies = registry.mapLayersByName('water_bodies_mult')

dataset = gdal.Open(filename)
band = dataset.GetRasterBand(1)
transform = dataset.GetGeoTransform()
data = band.ReadAsArray()

feat_wb = water_bodies[0].getFeatures().next() 

extent = raster[0].extent()

xmin, ymin, xmax, ymax = extent.toRectF().getCoords()

xsize = raster[0].rasterUnitsPerPixelX()
ysize = raster[0].rasterUnitsPerPixelY()

pixel_area = xsize*ysize

rows = raster[0].height()
cols = raster[0].width()

x1 = xmin
y1 = ymax

for i in range(rows):
    for j in range(cols):
        p1 = QgsPoint(x1, y1)
        p2 = QgsPoint(x1 + xsize, y1 - ysize)
        rect = QgsRectangle(p1, p2)
        geom = QgsGeometry.fromWkt(rect.asWktPolygon())
        if geom.intersects(feat_wb.geometry()):
            new_geom = geom.intersection(feat_wb.geometry())
            perc = (new_geom.area()/pixel_area)*100
            if perc >= 60.:
                data[i][j] = -9999

        x1 += xsize
    x1 = xmin
    y1 -= ysize

# Create gtif file 
driver = gdal.GetDriverByName("GTiff")

output_file = "/home/zeito/pyqgis_data/new_raster.tif"

dst_ds = driver.Create(output_file, 

#writting output raster
dst_ds.GetRasterBand(1).WriteArray( data )

#setting extension of output raster
# top left x, w-e pixel resolution, rotation, top left y, rotation, n-s pixel resolution

wkt = dataset.GetProjection()

# setting spatial reference of output raster 
srs = osr.SpatialReference()
dst_ds.SetProjection( srs.ExportToWkt() )

#Close output raster dataset 
dataset = None
dst_ds = None

For a situation represented by next image:

enter image description here

after running above code and load resulting raster (new_raster.tif), it can be observed, at next image, that the cells that were covered by more than 60 % of water were excluded (resulting raster is transparent in these areas).

enter image description here

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