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The Remove rasters from Mosaic Dataset tool does not have the option for spatial query. The code below illustrates the use of ArcPy to remove rasters based on a polygon area of interest.
The code sample can be used as a stand alone Python script to remove rasters from a mosaic dataset based on a spatial query. A polygon is used in this example.
from arcpy import env
env.workspace = r"D:\Documents\Northwest.gdb"
clipShape = "parks"
mosaicDataset = "CityOfPortland"
# Make a mosaic layer to be able to select the footprint
# Select the footprint based on polygon clipShape using the intersect method
arcpy.SelectLayerByLocation_management("mdlayer", "INTERSECT", clipShape)
# Run the remove rasters tool without any query on the selection
arcpy.RemoveRastersFromMosaicDataset_management("mdlayer", "#", "UPDATE_BOUNDARY", "MARK_OVERVIEW_ITEMS")