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---

Raster masks from vector masks

xsar.Sentinel1Dataset.dataset has a land_mask variable by default, rasterized from cartopy.feature.NaturalEarthFeature(‘physical’, ‘land’, ‘10m’)

Mask sigma0 over land

Replacing sigma0 values with nan over ocean can be done with xarray.where

import xarray as xr
import xsar
import numpy as np
import os
ds = xsar.open_dataset(xsar.get_test_file('S1B_IW_GRDH_1SDV_20181013T062322_20181013T062347_013130_018428_Z010.SAFE'), resolution='1000m')

# apply land_mask. The final transpose is done to preserve dimensions ordering
ds['sigma0_land'] = xr.where(ds['land_mask'], ds['sigma0'], np.nan).transpose(*ds['sigma0'].dims)
ds['sigma0_land']

<xarray.DataArray 'sigma0_land' (pol: 2, line: 166, sample: 265)>
dask.array<transpose, shape=(2, 166, 265), dtype=float64, chunksize=(1, 166, 265), chunktype=numpy.ndarray>
Coordinates:
  * pol          (pol) object 'VV' 'VH'
  * line         (line) float64 49.5 149.5 249.5 ... 1.645e+04 1.655e+04
  * sample       (sample) float64 49.5 149.5 249.5 ... 2.635e+04 2.645e+04
    spatial_ref  int64 0

xarray.DataArray

'sigma0_land'

• pol: 2
• line: 166
• sample: 265

• dask.array<chunksize=(1, 166, 265), meta=np.ndarray>

  Array Chunk Bytes 687.34 kiB 343.67 kiB Shape (2, 166, 265) (1, 166, 265) Count 64 Tasks 2 Chunks Type float64 numpy.ndarray

• Coordinates: (4)
  • pol
    (pol)
    object
    'VV' 'VH'

    array(['VV', 'VH'], dtype=object)

  • line
    (line)
    float64
    49.5 149.5 ... 1.645e+04 1.655e+04

    array([   49.5,   149.5,   249.5,   349.5,   449.5,   549.5,   649.5,   749.5,
             849.5,   949.5,  1049.5,  1149.5,  1249.5,  1349.5,  1449.5,  1549.5,
            1649.5,  1749.5,  1849.5,  1949.5,  2049.5,  2149.5,  2249.5,  2349.5,
            2449.5,  2549.5,  2649.5,  2749.5,  2849.5,  2949.5,  3049.5,  3149.5,
            3249.5,  3349.5,  3449.5,  3549.5,  3649.5,  3749.5,  3849.5,  3949.5,
            4049.5,  4149.5,  4249.5,  4349.5,  4449.5,  4549.5,  4649.5,  4749.5,
            4849.5,  4949.5,  5049.5,  5149.5,  5249.5,  5349.5,  5449.5,  5549.5,
            5649.5,  5749.5,  5849.5,  5949.5,  6049.5,  6149.5,  6249.5,  6349.5,
            6449.5,  6549.5,  6649.5,  6749.5,  6849.5,  6949.5,  7049.5,  7149.5,
            7249.5,  7349.5,  7449.5,  7549.5,  7649.5,  7749.5,  7849.5,  7949.5,
            8049.5,  8149.5,  8249.5,  8349.5,  8449.5,  8549.5,  8649.5,  8749.5,
            8849.5,  8949.5,  9049.5,  9149.5,  9249.5,  9349.5,  9449.5,  9549.5,
            9649.5,  9749.5,  9849.5,  9949.5, 10049.5, 10149.5, 10249.5, 10349.5,
           10449.5, 10549.5, 10649.5, 10749.5, 10849.5, 10949.5, 11049.5, 11149.5,
           11249.5, 11349.5, 11449.5, 11549.5, 11649.5, 11749.5, 11849.5, 11949.5,
           12049.5, 12149.5, 12249.5, 12349.5, 12449.5, 12549.5, 12649.5, 12749.5,
           12849.5, 12949.5, 13049.5, 13149.5, 13249.5, 13349.5, 13449.5, 13549.5,
           13649.5, 13749.5, 13849.5, 13949.5, 14049.5, 14149.5, 14249.5, 14349.5,
           14449.5, 14549.5, 14649.5, 14749.5, 14849.5, 14949.5, 15049.5, 15149.5,
           15249.5, 15349.5, 15449.5, 15549.5, 15649.5, 15749.5, 15849.5, 15949.5,
           16049.5, 16149.5, 16249.5, 16349.5, 16449.5, 16549.5])

  • sample
    (sample)
    float64
    49.5 149.5 ... 2.635e+04 2.645e+04

    array([   49.5,   149.5,   249.5, ..., 26249.5, 26349.5, 26449.5])

  • spatial_ref
    ()
    int64
    0

    crs_wkt :

    GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]

    semi_major_axis :

    6378137.0

    semi_minor_axis :

    6356752.314245179

    inverse_flattening :

    298.257223563

    reference_ellipsoid_name :

    WGS 84

    longitude_of_prime_meridian :

    0.0

    prime_meridian_name :

    Greenwich

    geographic_crs_name :

    WGS 84

    grid_mapping_name :

    latitude_longitude

    spatial_ref :

    GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]

    gcps :

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{'type': 'Point', 'coordinates': [-1.9512233801366998, 47.5478051288588, 0]}}, {'type': 'Feature', 'properties': {'id': '8bbae664-f5cb-49a5-a1bc-4a73a1dd428c', 'info': None, 'row': 144, 'col': 28}, 'geometry': {'type': 'Point', 'coordinates': [-2.133861380601548, 47.571730880010165, 0]}}, {'type': 'Feature', 'properties': {'id': 'c1a38bcf-a038-48b9-8ed1-d7c1c9713ab8', 'info': None, 'row': 144, 'col': 42}, 'geometry': {'type': 'Point', 'coordinates': [-2.316664291621321, 47.595366666751275, 0]}}, {'type': 'Feature', 'properties': {'id': 'eab65a23-9b9b-4d8e-869f-1b915efa8570', 'info': None, 'row': 144, 'col': 56}, 'geometry': {'type': 'Point', 'coordinates': [-2.4996303808294655, 47.61871199451519, 0]}}, {'type': 'Feature', 'properties': {'id': '8f535c63-988f-4701-9bec-5673df78afca', 'info': None, 'row': 144, 'col': 70}, 'geometry': {'type': 'Point', 'coordinates': [-2.682757903325378, 47.6417663738237, 0]}}, {'type': 'Feature', 'properties': {'id': 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'aa65cd02-ebbc-46c4-98b7-59fb5e01060e', 'info': None, 'row': 153, 'col': 14}, 'geometry': {'type': 'Point', 'coordinates': [-1.974498608918433, 47.46702978289763, 0]}}, {'type': 'Feature', 'properties': {'id': 'fde55381-04e6-40a6-a732-ef5a65ba0bc0', 'info': None, 'row': 153, 'col': 28}, 'geometry': {'type': 'Point', 'coordinates': [-2.1568602013032736, 47.49094759819954, 0]}}, {'type': 'Feature', 'properties': {'id': 'ef2ed555-cd59-42f5-a4f9-3fd722ac806c', 'info': None, 'row': 153, 'col': 42}, 'geometry': {'type': 'Point', 'coordinates': [-2.3393858849882414, 47.51457624661245, 0]}}, {'type': 'Feature', 'properties': {'id': 'e43d43e2-750c-41e5-a900-cbdd29b6fa3a', 'info': None, 'row': 153, 'col': 56}, 'geometry': {'type': 'Point', 'coordinates': [-2.5220739449750202, 47.53791523676965, 0]}}, {'type': 'Feature', 'properties': {'id': '37d76bff-33af-49a2-907a-458d40152110', 'info': None, 'row': 153, 'col': 70}, 'geometry': {'type': 'Point', 'coordinates': [-2.704922653222464, 47.56096408224515, 0]}}, {'type': 'Feature', 'properties': {'id': 'f68a3c50-4a0b-4f9a-920a-b57d03e182bf', 'info': None, 'row': 153, 'col': 84}, 'geometry': {'type': 'Point', 'coordinates': [-2.8879302689424406, 47.58372230162321, 0]}}, {'type': 'Feature', 'properties': {'id': '2f5d2bd6-3c34-4bcb-8da5-6ea0d86edf26', 'info': None, 'row': 153, 'col': 98}, 'geometry': {'type': 'Point', 'coordinates': [-3.071095038639031, 47.60618941853424, 0]}}, {'type': 'Feature', 'properties': {'id': 'bc51d58e-718e-4044-9a98-1154bcb893a8', 'info': None, 'row': 153, 'col': 112}, 'geometry': {'type': 'Point', 'coordinates': [-3.254415196106645, 47.62836496168582, 0]}}, {'type': 'Feature', 'properties': {'id': '5b1be6ae-667a-4dae-8b72-ea84fbdc37e3', 'info': None, 'row': 153, 'col': 126}, 'geometry': {'type': 'Point', 'coordinates': [-3.4378889624781337, 47.65024846490036, 0]}}, {'type': 'Feature', 'properties': {'id': '9e2ba141-a3da-490a-9170-bb58a11d7100', 'info': None, 'row': 153, 'col': 140}, 'geometry': {'type': 'Point', 'coordinates': [-3.621514546338247, 47.671839467160524, 0]}}, {'type': 'Feature', 'properties': {'id': '51bca8c3-2923-485f-abb2-54e8a7d26f6d', 'info': None, 'row': 153, 'col': 154}, 'geometry': {'type': 'Point', 'coordinates': [-3.8052901438793234, 47.69313751265892, 0]}}, {'type': 'Feature', 'properties': {'id': '913a4b78-4e13-4eb0-af0b-4c4ac139d766', 'info': None, 'row': 153, 'col': 168}, 'geometry': {'type': 'Point', 'coordinates': [-3.989213939061151, 47.71414215084755, 0]}}, {'type': 'Feature', 'properties': {'id': '25b24b1a-5d29-4086-88bd-96276e876740', 'info': None, 'row': 153, 'col': 182}, 'geometry': {'type': 'Point', 'coordinates': [-4.173284103742063, 47.73485293648277, 0]}}, {'type': 'Feature', 'properties': {'id': '4db65b8d-cab1-4bb5-b5e9-202afab5570a', 'info': None, 'row': 153, 'col': 196}, 'geometry': {'type': 'Point', 'coordinates': [-4.357498797765099, 47.75526942966488, 0]}}, {'type': 'Feature', 'properties': {'id': 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47.3620631634341, 0]}}, {'type': 'Feature', 'properties': {'id': 'dec9e199-b04d-4cf1-b319-2b25891db313', 'info': None, 'row': 162, 'col': 14}, 'geometry': {'type': 'Point', 'coordinates': [-1.997815707307867, 47.386260833551944, 0]}}, {'type': 'Feature', 'properties': {'id': '8fc31159-d70e-4149-a2d4-63eee6dbabb4', 'info': None, 'row': 162, 'col': 28}, 'geometry': {'type': 'Point', 'coordinates': [-2.179901170015012, 47.41017062812458, 0]}}, {'type': 'Feature', 'properties': {'id': '4bb7a863-fe8d-4980-ac5e-1314525c146d', 'info': None, 'row': 162, 'col': 42}, 'geometry': {'type': 'Point', 'coordinates': [-2.3621499151248466, 47.43379205418162, 0]}}, {'type': 'Feature', 'properties': {'id': '3590b046-a9d8-4ad5-a222-0f3cce153551', 'info': None, 'row': 162, 'col': 56}, 'geometry': {'type': 'Point', 'coordinates': [-2.5445602440647237, 47.45712462339094, 0]}}, {'type': 'Feature', 'properties': {'id': '0f4df75d-1343-41a4-ad9d-e830c62d833a', 'info': None, 'row': 162, 'col': 70}, 'geometry': 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47.67445927462697, 0]}}, {'type': 'Feature', 'properties': {'id': 'acfb274b-9835-4231-adfd-aed5175a1d88', 'info': None, 'row': 162, 'col': 210}, 'geometry': {'type': 'Point', 'coordinates': [-4.561239545593567, 47.69458360643476, 0]}}, {'type': 'Feature', 'properties': {'id': 'ce48bba9-9c88-4e38-9024-dab7d224d276', 'info': None, 'row': 162, 'col': 224}, 'geometry': {'type': 'Point', 'coordinates': [-4.745451682767867, 47.71441361265866, 0]}}, {'type': 'Feature', 'properties': {'id': '88a6a5fb-9e6c-48da-bfaf-22ae32d73b87', 'info': None, 'row': 162, 'col': 238}, 'geometry': {'type': 'Point', 'coordinates': [-4.929802160827342, 47.73394887163518, 0]}}, {'type': 'Feature', 'properties': {'id': 'e4f6b04a-8903-4887-8a03-e84e1acdaea8', 'info': None, 'row': 162, 'col': 252}, 'geometry': {'type': 'Point', 'coordinates': [-5.114289107350792, 47.75318896717446, 0]}}]}

    array(0)

• Attributes: (0)

Adding masks

Masks can be added with xsar.Sentinel1Meta.set_mask_feature, providing a shapefile or a cartopy.feature.Feature object.

For a default mask for all SAFE, use classmethod xsar.Sentinel1Meta.set_mask_feature

Here, we add a ocean_mask dataset variable:

xsar.Sentinel1Meta.set_mask_feature('ocean', os.path.join(xsar.get_test_file('water-polygons-split-4326'), 'water_polygons.shp'))


s1meta = xsar.Sentinel1Meta(xsar.get_test_file('S1B_IW_GRDH_1SDV_20181013T062322_20181013T062347_013130_018428_Z010.SAFE'))
ds = xsar.open_dataset(s1meta, resolution='200m')
ds['sigma0_ocean'] = xr.where(ds['ocean_mask'], ds['sigma0'], np.nan).transpose(*ds['sigma0'].dims)
ds[['sigma0_ocean','ocean_mask']]

<xarray.Dataset>
Dimensions:       (pol: 2, line: 834, sample: 1329)
Coordinates:
  * pol           (pol) object 'VV' 'VH'
  * line          (line) float64 9.5 29.5 49.5 ... 1.663e+04 1.665e+04 1.667e+04
  * sample        (sample) float64 9.5 29.5 49.5 ... 2.655e+04 2.657e+04
    spatial_ref   int64 0
Data variables:
    sigma0_ocean  (pol, line, sample) float64 dask.array<chunksize=(1, 834, 1329), meta=np.ndarray>
    ocean_mask    (line, sample) int8 dask.array<chunksize=(834, 1329), meta=np.ndarray>
Attributes: (12/17)
    name:              SENTINEL1_DS:/tmp/S1B_IW_GRDH_1SDV_20181013T062322_201...
    short_name:        SENTINEL1_DS:S1B_IW_GRDH_1SDV_20181013T062322_20181013...
    product:           GRDH
    safe:              S1B_IW_GRDH_1SDV_20181013T062322_20181013T062347_01313...
    swath:             IW
    multidataset:      False
    ...                ...
    footprint:         POLYGON ((-1.371244242212007 48.8181227490355, -4.9521...
    coverage:          168km * 265km (line * sample )
    pixel_line_m:      <xarray.DataArray 'azimuthPixelSpacing' ()>\narray(10....
    pixel_sample_m:    <xarray.DataArray 'groundRangePixelSpacing' ()>\narray...
    orbit_pass:        Descending
    platform_heading:  -165.3526446468305

xarray.Dataset

• Dimensions:
  • pol: 2
  • line: 834
  • sample: 1329
• Coordinates: (4)
  • pol
    (pol)
    object
    'VV' 'VH'

    array(['VV', 'VH'], dtype=object)

  • line
    (line)
    float64
    9.5 29.5 ... 1.665e+04 1.667e+04

    array([9.50000e+00, 2.95000e+01, 4.95000e+01, ..., 1.66295e+04, 1.66495e+04,
           1.66695e+04])

  • sample
    (sample)
    float64
    9.5 29.5 ... 2.655e+04 2.657e+04

    array([9.50000e+00, 2.95000e+01, 4.95000e+01, ..., 2.65295e+04, 2.65495e+04,
           2.65695e+04])

  • spatial_ref
    ()
    int64
    0

    crs_wkt :

    GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]

    semi_major_axis :

    6378137.0

    semi_minor_axis :

    6356752.314245179

    inverse_flattening :

    298.257223563

    reference_ellipsoid_name :

    WGS 84

    longitude_of_prime_meridian :

    0.0

    prime_meridian_name :

    Greenwich

    geographic_crs_name :

    WGS 84

    grid_mapping_name :

    latitude_longitude

    spatial_ref :

    GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]

    gcps :

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    array(0)

• Data variables: (2)
  • sigma0_ocean
    (pol, line, sample)
    float64
    dask.array<chunksize=(1, 834, 1329), meta=np.ndarray>

    Array Chunk Bytes 16.91 MiB 8.46 MiB Shape (2, 834, 1329) (1, 834, 1329) Count 64 Tasks 2 Chunks Type float64 numpy.ndarray

  • ocean_mask
    (line, sample)
    int8
    dask.array<chunksize=(834, 1329), meta=np.ndarray>

    history :

    ocean_mask: /tmp/water-polygons-split-4326/water_polygons.shp

    Array Chunk Bytes 1.06 MiB 1.06 MiB Shape (834, 1329) (834, 1329) Count 3 Tasks 1 Chunks Type int8 numpy.ndarray

• Attributes: (17)

  name :

  SENTINEL1_DS:/tmp/S1B_IW_GRDH_1SDV_20181013T062322_20181013T062347_013130_018428_Z010.SAFE:IW

  short_name :

  SENTINEL1_DS:S1B_IW_GRDH_1SDV_20181013T062322_20181013T062347_013130_018428_Z010.SAFE:IW

  product :

  GRDH

  safe :

  S1B_IW_GRDH_1SDV_20181013T062322_20181013T062347_013130_018428_Z010.SAFE

  swath :

  IW

  multidataset :

  False

  ipf :

  2.91

  platform :

  SENTINEL-1B

  pols :

  VV VH

  start_date :

  2018-10-13 06:23:22.317102

  stop_date :

  2018-10-13 06:23:47.315227

  footprint :

  POLYGON ((-1.371244242212007 48.8181227490355, -4.952180073180092 49.22908720976283, -5.299019842440263 47.73223932854375, -1.820918145395446 47.32222709505006, -1.371244242212007 48.8181227490355))

  coverage :

  168km * 265km (line * sample )

  pixel_line_m :

  <xarray.DataArray 'azimuthPixelSpacing' ()> array(10.) Attributes: source: /product/imageAnnotation/imageInformation/azimuthPixelSpacing

  pixel_sample_m :

  <xarray.DataArray 'groundRangePixelSpacing' ()> array(10.) Attributes: source: /product/imageAnnotation/imageInformation/rangePixelSpacing

  orbit_pass :

  Descending

  platform_heading :

  -165.3526446468305

Masks are available as a shapely object (lon/lat coordinates), with xsar.Sentinel1Meta.get_mask:

When using this s1meta object with xsar.Sentinel1Meta.footprint, mask are rasterized over the dataset, and variables postfixed with _mask are created.

Convert a mask to dataset coordinates

xsar.Sentinel1Meta.ll2coords allow converting lon/lat coordinates on shapely objects.

So it’s possible to plot the vector mask on a raster variable:

import holoviews as hv
import geoviews.feature as gf
hv.extension('bokeh')
from holoviews.operation.datashader import datashade,rasterize


# get the shapely polygon of the mask (on the footprint, lon/lat)
land_poly = s1meta.get_mask('ocean')

# convert lon/lat to line/sample
land_poly_coords = s1meta.ll2coords(s1meta.get_mask('ocean'))

# plot masked sigma0, with coastline

(
    hv.Image(ds['sigma0_ocean'].sel(pol='VV')).opts(cmap='gray',clim=(0,0.2), colorbar=True,tools=['hover'],title="xsar") \
    * hv.Path(land_poly_coords).opts(color='lightgreen',width=800,height=800)
).opts(invert_axes=True)