tandemx_mask.py

#! /usr/bin/env python

"""
Script to mask TanDEM-X DEMs to isolate good elevation values
Documentation of AUX products is here: https://tandemx-science.dlr.de/pdfs/TD-GS-PS-0021_DEM-Product-Specification_v3.1.pdf
"""

import sys
import os
import glob
from pygeotools.lib import iolib
import numpy as np
import scipy.ndimage as ndimage

if len(sys.argv) != 2:
    sys.exit("Usage: '%s tiledir'" % sys.argv[0])
else:
    tiledir = sys.argv[1]

print(tiledir)
dem_fn = glob.glob(os.path.join(tiledir, 'DEM/*DEM.tif'))[0]
print(dem_fn)
dem_ds = iolib.fn_getds(dem_fn)
dem = iolib.ds_getma(dem_ds)
print(dem.count())

#Get original mask, True where masked
mask = np.ma.getmaskarray(dem)

#Theoretical height error
err_fn = glob.glob(os.path.join(tiledir, 'AUXFILES/*HEM.tif'))[0]
err = iolib.fn_getma(err_fn)
max_err_multi = 1.5
mask = np.logical_or(mask, (err.data > max_err_multi))

#Water mask
wam_fn = glob.glob(os.path.join(tiledir, 'AUXFILES/*WAM.tif'))[0]
wam = iolib.fn_getma(wam_fn)
wam_clim = (33,127)
#wam_clim = (3,127)
mask = np.logical_or(mask, (wam >= wam_clim[0]) & (wam <= wam_clim[1]))

#Consistency mask
com_fn = glob.glob(os.path.join(tiledir, 'AUXFILES/*COM.tif'))[0]
com = iolib.fn_getma(com_fn)
com_valid = (8,9,10)
#4 is only one obs
#com_invalid = (0,1,2,4)
com_invalid = (0,1,2)
mask = np.logical_or(mask, np.isin(com.data, com_invalid))

#More stringent error threshold for single strip pixels
#max_err_single = 1.0
#mask = np.logical_or(mask, (com.data == 4) & (err.data > max_err_single))

#Apply
dem_masked = np.ma.array(dem, mask=mask)
print(dem_masked.count())
out_fn = os.path.splitext(dem_fn)[0]+'_masked.tif'
iolib.writeGTiff(dem_masked, out_fn, dem_ds)

#Dilate mask by n_iter px to remove isolated pixels and values around nodata 
n_iter = 1
mask = ndimage.morphology.binary_dilation(mask, iterations=n_iter)
#To keep valid edges, do subsequent erosion 
mask = ndimage.morphology.binary_erosion(mask, iterations=n_iter)
#(dilation of inverted mask, to avoid maasking outer edge)
#mask = ~(ndimage.morphology.binary_dilation(~mask, iterations=n_iter))

#Apply
dem_masked = np.ma.array(dem, mask=mask)
print(dem_masked.count())
out_fn = os.path.splitext(dem_fn)[0]+'_masked_erode.tif'
iolib.writeGTiff(dem_masked, out_fn, dem_ds)