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I have two rasters in a PostGIS database that I want to be able to compare. The first raster is at 5m pixel resolution and the second raster is at 30m pixel resolution and is on a different grid.

How I can align the rasters to the same grid based on the pixels, not on the rasters themselves?

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If you want to actually move one raster so that the cells of both rasters align (i.e., 36 cells from the first raster fit perfectly over one cell of the second), then you can register one raster to perfectly overly the other. This overwrites that raster's georeferencing data though. You can also resample one raster with the environment settings such that the output raster perfectly overlies the other raster.

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If you can load the two rasters into GDAL and extract their geotransforms, this is easy to do without warping the rasters in any way (such as resampling):

def pixToGeoToPix(x1_index, y1_index, gt1, gt2):
    '''
    x1_index: x index of pixel in first image
    y1_index: y index of pixel in first image
    gt1: geotransform tuple of first image
    gt2: geotransform tuple of second image
    '''
    geo_x = gt1[0] + gt1[1]*x1_index
    geo_y = gt1[3] + gt1[5]*y1_index
    x2_index = int((geo_x-gt2[0])/gt2[1])
    y2_index = int((gt2[3]-geo_y)/gt2[5])
    return x2_index, y2_index

This function uses the geotransforms of both images to map a pixel index of one image to the equivalent pixel index in the second image by using the pixel's geo-coordinate to translate the pixel index between images. Once you have the matching indices you can easily use numpy to compare the two pixels.

Note that this doesn't necessarily require GDAL. The only information you need is the top left x/y coordinate and x/y spatial resolution of both images, and there are many ways to extract those values.

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