Restrict VI calculation to non-cloud pixles

[madhuksridhar]

Description

Restrict VI calculations to pixels that meet the following conditions:

• Pixel Fmask is NOT cloud, cloud shadow, or adjacent to cloud. Cloud related pixels should be set to mask value (-9999). This requires refactoring to read the Fmask raster along with the rest of the bands

[madhuksridhar]

Fmask rasters for test S30 and L30 granules uploaded here

[madhuksridhar]

Description of bits in the Fmask QA layer is given in HLS user guide Table 9

One way to read Fmask raster and mask out cloud related pixels

def retrieve_permutations(f, repeat=0):
    import itertools
    perm= itertools.product(*[f.get(i, [0, 1]) for i in range(repeat)])
    possible_bin=[] ## binary
    possible_int = [] ## int
    for i in list(perm): 
        my_bin = ''.join((str(v) for v in i))
        my_bin.replace("'","")
        possible_bin.append(my_bin)
        possible_int.append(int(my_bin,2))
    return possible_bin, possible_int

def get_cloud_mask(fmask_ds):
    """
      See Table 9 in the HLS v2 user guide 
      https://lpdaac.usgs.gov/documents/1698/HLS_User_Guide_V2.pdf
    """
    cloud_shadow_fixed = {4: [1]}
    adj_cloud_fixed = {5: [1]}
    cloud_fixed   = {6: [1]}

    cloud_shadow_ignore = retrieve_permutations(cloud_shadow_fixed, 8)
    adj_cloud_ignore = retrieve_permutations(adj_cloud_fixed, 8)
    cloud_ignore   = retrieve_permutations(cloud_fixed, 8)

    ## take the integer output
    fmask_ignore =np.concatenate([cloud_ignore[1], cloud_shadow_ignore[1], adj_cloud_ignore[1]])
    mask = fmask_ds.isin(fmask_ignore)

    # check unique clear values after masking
    #clear = fmask_ds.where(~fmask_ds.isin(fmask_ignore))
    #print("unique cloud fmask values :", np.unique(clear))

    return mask

[chuckwondo]

Fixed by #10