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I want to use GDAL/OGR to extract pixel values from a raster file. The extraction should be based on polygons, stored in a shapefile. My thought was to iterate over the features in the shapefile, extract the pixel values of those pixels that have there center point within the polygon and calculate a percentile from those values. When this is done I want to write the calculated percentile back to the polygon and go on with the next polygon.

Iterating over the polygons is easy, but what I do not get is how to extract the pixel values from the pixels, covered by the polygon.

PS: I'm using Python.

Could somebody help me at this point?

Cheers Thomas

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If I iterate over the features and while one is 'selected', can I call the GetExtent function of the shapefile layer and will the returned extent only represent the extent of the current feature? – Thomas Becker Aug 13 '13 at 11:37
It sounds as though you are wanting to do zonal statistics. Have a look at…; – MappaGnosis Aug 13 '13 at 11:56
@MappaGnosis That version of zonal stats appears extremely limited; I see no evidence from the documentation that it computes percentiles. Do you know of a zonal stats solution for QGIS that does compute specified percentiles by zone? – whuber Aug 13 '13 at 15:13
alright, the percentile is no problem for me since I had to define a function for it anyway. My issue goes with the Python coding using GDAL/OGR... I'm used to do the stuff using ArcGIS and their Python classes. However, it takes ages and in the end the script is crashing. So, I'm on my way to re-write the script without arcpy. Can anybody point me to some code snippet where I can learn on how to do the stuff? – Thomas Becker Aug 13 '13 at 16:04
@WHuber Offhand I don't know of a more extensive Zonal Stats Plugin for QGIS. However, my link was meant to point to the programmed Python + GDAL solution in my reply in that thread. My example there is just looking at getting the minimum value, but being a programmed solution, it shouldn't be too hard to extend it a bit to calculate percentiles of the zone data. Instead of going for the 'easy statistics' options there is also a scipy.ndimage.filters.percentile_filter function available. – MappaGnosis Aug 14 '13 at 15:07

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