I want to be able to write pixel values of each pixel falling under a polygon onto a polygon attribute table or a CSV. I have about 1200 polygons and a georefernced GeoTiff file with NDVI values. While I understand there are many tools available to calculate zonal stats and I have tried zonal statistics, LecoS and rasterstats plugin (all QGIS), they all provide only summary statistics (mean, median, min, max, etc.) but not individual pixel values. So pretty much are of no use here. I also took a look at rasterstats source code but could not find a quick way to modify the zonal output parameters to suit my needs. So I'm wondering if there is a GDAL, QGIS, python based solution out there?
TL;DR: I would like to write pixel values of all the pixels falling under a poylgon onto a CSV or a shapefile attribute table (1200 polygons).