Custom stacks#

Let’s use EOReader with custom stacks.

# EOReader Imports
import os
import xarray as xr
from eoreader.reader import Reader
from eoreader.products import SensorType
from eoreader.bands import BLUE, GREEN, RED, NIR, SWIR_1, VV, VV_DSPK, SLOPE, HILLSHADE
from sertit import display

reader = Reader()

# Create logger
import logging
from sertit import logs

logs.init_logger(logging.getLogger("eoreader"))

# Set a DEM
from eoreader.env_vars import DEM_PATH

os.environ[DEM_PATH] = os.path.join("/home", "data", "DS2", "BASES_DE_DONNEES", "GLOBAL", "COPDEM_30m",
                                    "COPDEM_30m.vrt")

Custom stack with minimum data#

For both SAR and optical stacks, the two minimum keywords to provide are:

  • band_map: a dictionary mapping the satellite band to the band number (starting to 1, in GDAL style)

  • sensor_type: Either SAR or OPTICAL (a string or a SensorType Enum)

# Paths
stack_folder = os.path.join("/home", "data", "DS3", "CI", "eoreader", "others")
opt_path = os.path.join(stack_folder, "20200310T030415_WV02_Ortho_BGRN_STK.tif")
sar_path = os.path.join(stack_folder, "20210827T162210_ICEYE_SC_GRD_STK.tif")

# Optical minimum example
opt_prod = reader.open(opt_path,
                       custom=True,
                       sensor_type="OPTICAL",  # With a string
                       band_map={BLUE: 1, GREEN: 2, RED: 3, NIR: 4, SWIR_1: 5})
opt_prod

---------------------------------------------------------------------------
CPLE_OpenFailedError                      Traceback (most recent call last)
File rasterio/_base.pyx:307, in rasterio._base.DatasetBase.__init__()

File rasterio/_base.pyx:218, in rasterio._base.open_dataset()

File rasterio/_err.pyx:221, in rasterio._err.exc_wrap_pointer()

CPLE_OpenFailedError: /home/data/DS3/CI/eoreader/others/20200310T030415_WV02_Ortho_BGRN_STK.tif: No such file or directory

During handling of the above exception, another exception occurred:

RasterioIOError                           Traceback (most recent call last)
Cell In[5], line 2
      1 # Optical minimum example
----> 2 opt_prod = reader.open(opt_path,
      3                        custom=True,
      4                        sensor_type="OPTICAL",  # With a string
      5                        band_map={BLUE: 1, GREEN: 2, RED: 3, NIR: 4, SWIR_1: 5})
      6 opt_prod

File ~/checkouts/readthedocs.org/user_builds/eoreader/checkouts/latest/eoreader/reader.py:467, in Reader.open(self, product_path, archive_path, output_path, method, remove_tmp, custom, constellation, **kwargs)
    464 if custom:
    465     from eoreader.products import CustomProduct
--> 467     prod = CustomProduct(
    468         product_path=product_path,
    469         archive_path=archive_path,
    470         output_path=output_path,
    471         remove_tmp=remove_tmp,
    472         constellation=constellation,
    473         **kwargs,
    474     )
    475 else:
    476     prod = None

File ~/checkouts/readthedocs.org/user_builds/eoreader/checkouts/latest/eoreader/products/custom_product.py:107, in CustomProduct.__init__(self, product_path, archive_path, output_path, remove_tmp, **kwargs)
    105 super_kwargs = kwargs.copy()
    106 super_kwargs.pop("constellation", None)
--> 107 super().__init__(
    108     product_path, archive_path, output_path, remove_tmp, **super_kwargs
    109 )

File ~/checkouts/readthedocs.org/user_builds/eoreader/checkouts/latest/eoreader/products/product.py:244, in Product.__init__(self, product_path, archive_path, output_path, remove_tmp, **kwargs)
    241 self._set_instrument()
    243 # Post initialization
--> 244 self._post_init(**kwargs)
    246 # Set product type, needs to be done after the post-initialization
    247 self._set_product_type()

File ~/checkouts/readthedocs.org/user_builds/eoreader/checkouts/latest/eoreader/products/custom_product.py:177, in CustomProduct._post_init(self, **kwargs)
    175 # Check CRS
    176 try:
--> 177     crs = self.crs()  # noqa
    178 except InvalidProductError as msg:
    179     LOGGER.warning(msg)

File ~/checkouts/readthedocs.org/user_builds/eoreader/envs/latest/lib/python3.8/site-packages/methodtools.py:72, in _LruCacheWire.__call__(self, *args, **kwargs)
     70 def __call__(self, *args, **kwargs):
     71     # descriptor detection support - never called
---> 72     return self.__call__(*args, **kwargs)

File ~/checkouts/readthedocs.org/user_builds/eoreader/checkouts/latest/eoreader/__init__.py:34, in cache.<locals>.wrapper(*args, **kwargs)
     31 @lru_cache()
     32 @wraps(func)
     33 def wrapper(*args, **kwargs):
---> 34     return func(*args, **kwargs)

File ~/checkouts/readthedocs.org/user_builds/eoreader/checkouts/latest/eoreader/products/custom_product.py:310, in CustomProduct.crs(self)
    302 @cache
    303 def crs(self) -> crs.CRS:
    304     """
    305     Get UTM projection of stack.
    306 
    307     Returns:
    308         crs.CRS: CRS object
    309     """
--> 310     with rasterio.open(str(self.path)) as ds:
    311         def_crs = ds.crs
    313     if def_crs.is_projected:

File ~/checkouts/readthedocs.org/user_builds/eoreader/envs/latest/lib/python3.8/site-packages/rasterio/env.py:451, in ensure_env_with_credentials.<locals>.wrapper(*args, **kwds)
    448     session = DummySession()
    450 with env_ctor(session=session):
--> 451     return f(*args, **kwds)

File ~/checkouts/readthedocs.org/user_builds/eoreader/envs/latest/lib/python3.8/site-packages/rasterio/__init__.py:304, in open(fp, mode, driver, width, height, count, crs, transform, dtype, nodata, sharing, **kwargs)
    301 path = _parse_path(raw_dataset_path)
    303 if mode == "r":
--> 304     dataset = DatasetReader(path, driver=driver, sharing=sharing, **kwargs)
    305 elif mode == "r+":
    306     dataset = get_writer_for_path(path, driver=driver)(
    307         path, mode, driver=driver, sharing=sharing, **kwargs
    308     )

File rasterio/_base.pyx:309, in rasterio._base.DatasetBase.__init__()

RasterioIOError: /home/data/DS3/CI/eoreader/others/20200310T030415_WV02_Ortho_BGRN_STK.tif: No such file or directory

opt_stack = opt_prod.stack([BLUE, GREEN, RED])

xr.plot.imshow(opt_stack.copy(data=display.scale(opt_stack.data)))

<matplotlib.image.AxesImage at 0x7f3f735a6be0>
../_images/44453e1eb0d99d646ebde8136d6be3d466c6e5bf97ff60f078fc9bc2ce5132ca.png 
opt_stack

<xarray.DataArray 'BLUE GREEN RED' (z: 3, y: 2237, x: 1244)>
array([[[       nan,        nan,        nan, ..., 0.02729181,
         0.03021449, 0.0321508 ],
        [       nan,        nan,        nan, ..., 0.03289769,
         0.03252383, 0.03231718],
        [       nan,        nan,        nan, ..., 0.03253607,
         0.03250813, 0.03260763],
        ...,
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan]],

       [[       nan,        nan,        nan, ..., 0.0325688 ,
         0.03575394, 0.03786882],
        [       nan,        nan,        nan, ..., 0.03874811,
         0.0377332 , 0.0372853 ],
        [       nan,        nan,        nan, ..., 0.03795209,
         0.03785328, 0.03810363],
...
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan]],

       [[       nan,        nan,        nan, ..., 0.02202989,
         0.02403895, 0.02508134],
        [       nan,        nan,        nan, ..., 0.02564428,
         0.02424301, 0.02346394],
        [       nan,        nan,        nan, ..., 0.0244639 ,
         0.02421321, 0.02448287],
        ...,
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan]]], dtype=float32)
Coordinates:
    spatial_ref  int64 0
  * x            (x) float64 3.044e+05 3.044e+05 ... 3.143e+05 3.143e+05
  * y            (y) float64 1.459e+06 1.459e+06 ... 1.441e+06 1.441e+06
  * z            (z) MultiIndex
  - variable     (z) object 'BLUE' 'GREEN' 'RED'
  - band         (z) int64 1 1 1
Attributes:
    long_name:         BLUE GREEN RED
    sensor:            CUSTOM
    sensor_id:         CUSTOM
    product_path:      /home/data/DS3/CI/eoreader/others/20200310T030415_WV02...
    product_name:      20200310T030415_WV02_Ortho_BGRN_STK
    product_filename:  20200310T030415_WV02_Ortho_BGRN_STK
    product_type:      CUSTOM
    acquisition_date:  20220111T142955
    condensed_name:    20220111T142955_CUSTOM_CUSTOM
# SAR minimum example
sar_prod = reader.open(sar_path,
                       custom=True,
                       sensor_type=SensorType.SAR,  # With the Enum
                       band_map={VV: 1, VV_DSPK: 2})
sar_prod

2022-01-11 14:29:57,786 - [DEBUG] - Warping DEM for 20220111T142956_CUSTOM_CUSTOM
2022-01-11 14:29:57,791 - [DEBUG] - Using DEM: /home/data/DS2/BASES_DE_DONNEES/GLOBAL/COPDEM_30m/COPDEM_30m.vrt
2022-01-11 14:30:00,399 - [DEBUG] - Computing slope for 20220111T142956_CUSTOM_CUSTOM

sar_stack = sar_prod.stack([SLOPE, VV, VV_DSPK])

xr.plot.imshow(sar_stack.copy(data=display.scale(sar_stack.data)))

<matplotlib.image.AxesImage at 0x7f3f6cbd9940>
../_images/fa8389038f78527a2fe1f16ef8f5bae084b8bd6a854596366c11b4cfe1df78dd.png 
sar_stack

<xarray.DataArray 'SLOPE VV VV_DSPK' (z: 3, y: 2748, x: 2967)>
array([[[1.1417845 , 0.9661645 , 0.88848215, ..., 0.        ,
         0.        , 0.        ],
        [0.91908467, 0.8988768 , 0.9166924 , ..., 0.        ,
         0.        , 0.        ],
        [1.0019214 , 0.84933126, 0.86957526, ..., 0.        ,
         0.        , 0.        ],
        ...,
        [0.        , 0.        , 0.        , ..., 0.        ,
         0.        , 0.        ],
        [0.        , 0.        , 0.        , ..., 0.        ,
         0.        , 0.        ],
        [0.        , 0.        , 0.        , ..., 0.        ,
         0.        , 0.        ]],

       [[       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
...
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan]],

       [[       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        ...,
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan],
        [       nan,        nan,        nan, ...,        nan,
                nan,        nan]]], dtype=float32)
Coordinates:
    spatial_ref  int64 0
  * x            (x) float64 6.7e+05 6.701e+05 6.701e+05 ... 8.124e+05 8.124e+05
  * y            (y) float64 1.113e+04 1.109e+04 ... -1.206e+05 -1.207e+05
  * z            (z) MultiIndex
  - variable     (z) object 'SLOPE' 'VV' 'VV_DSPK'
  - band         (z) int64 1 1 1
Attributes:
    long_name:         SLOPE VV VV_DSPK
    sensor:            CUSTOM
    sensor_id:         CUSTOM
    product_path:      /home/data/DS3/CI/eoreader/others/20210827T162210_ICEY...
    product_name:      20210827T162210_ICEYE_SC_GRD_STK
    product_filename:  20210827T162210_ICEYE_SC_GRD_STK
    product_type:      CUSTOM
    acquisition_date:  20220111T142956
    condensed_name:    20220111T142956_CUSTOM_CUSTOM
# You can compute the footprint and the extent
extent = opt_prod.extent()
footprint = opt_prod.footprint()
base = extent.plot(color='cyan', edgecolor='black')
footprint.plot(ax=base, color='blue', edgecolor='black', alpha=0.5)

<AxesSubplot:>
../_images/091ec07f19d92f67f45a3ed4e0927ac55ab1f7f0fb98baa02b3e511b0434fe27.png 
extent = sar_prod.extent()
footprint = sar_prod.footprint()
base = extent.plot(color='cyan', edgecolor='black')
footprint.plot(ax=base, color='blue', edgecolor='black', alpha=0.5)

<AxesSubplot:>
../_images/ee66d92953b495ea5712f1c1ce5203b1ee9a2dc8364d8cca09bd29c62e15cf1f.png

Custom stack with full data#

If you know them, it is best to give EOReader all the data you know about your stack:

  • name: product name. If not provided, the filename will be used

  • acquisition_datetime: product acquisition datetime. If not provided, the datetime of the creation of the object will be used

  • platform: product platform. If not provided, CUSTOM will be set. Either a string of a Platform enum.

  • product_type: product type. If not provided, CUSTOM will be set.

  • default_resolution: product default resolution. If not provided, the stack resolution will be used.

For optical products, two additional keyword can be set to compute the hillshade band:

  • sun_azimuth

  • sun_zenith

# Optical
opt_prod = reader.open(
    opt_path,
    custom=True,
    name="20200310T030415_WV02_Ortho",
    acquisition_datetime="20200310T030415",
    sensor_type=SensorType.OPTICAL,
    platform="WV02",
    product_type="Ortho",
    default_resolution=2.0,
    sun_azimuth=10.0,
    sun_zenith=20.0,
    band_map={BLUE: 1, GREEN: 2, RED: 3, NIR: 4, SWIR_1: 5},
)
hillshade = opt_prod.load(HILLSHADE)[HILLSHADE]

2022-01-11 14:30:03,394 - [DEBUG] - Warping DEM for 20200310T030415_WV02_Ortho
2022-01-11 14:30:03,397 - [DEBUG] - Using DEM: /home/data/DS2/BASES_DE_DONNEES/GLOBAL/COPDEM_30m/COPDEM_30m.vrt
2022-01-11 14:30:03,953 - [DEBUG] - Computing hillshade DEM for 20200310T030415_WV02_Ortho

hillshade.plot()

<matplotlib.collections.QuadMesh at 0x7f3f507e9640>
../_images/702a6085d2ba942f958a5b2277c72ae0fc509c486d93150dd0855c18b4755019.png 
hillshade

<xarray.DataArray 'HILLSHADE' (band: 1, y: 2237, x: 1244)>
array([[[243.5148 , 244.15515, 244.76294, ..., 239.26723, 239.37088,
         239.47406],
        [241.75117, 242.62433, 243.46106, ..., 239.39891, 239.43938,
         239.48117],
        [239.7554 , 240.88208, 241.96498, ..., 239.66376, 239.59615,
         239.53004],
        ...,
        [247.74507, 248.3067 , 246.9472 , ..., 239.20195, 239.27254,
         239.39708],
        [247.93413, 248.49562, 246.84186, ..., 239.26035, 239.3623 ,
         239.51692],
        [248.09465, 248.6562 , 246.72041, ..., 239.2324 , 239.33617,
         239.4908 ]]], dtype=float32)
Coordinates:
  * band         (band) int64 1
  * x            (x) float64 3.044e+05 3.044e+05 ... 3.143e+05 3.143e+05
  * y            (y) float64 1.459e+06 1.459e+06 ... 1.441e+06 1.441e+06
    spatial_ref  int64 0
Attributes:
    scale_factor:      1.0
    add_offset:        0.0
    long_name:         HILLSHADE
    sensor:            WorldView-2
    sensor_id:         WV02
    product_path:      /home/data/DS3/CI/eoreader/others/20200310T030415_WV02...
    product_name:      20200310T030415_WV02_Ortho
    product_filename:  20200310T030415_WV02_Ortho_BGRN_STK
    product_type:      Ortho
    acquisition_date:  20200310T030415
    condensed_name:    20200310T030415_WV02_Ortho
# SAR
sar_prod = reader.open(
    sar_path,
    custom=True,
    sensor_type=SensorType.SAR,
    name="20210827T162210_ICEYE_SC_GRD",
    acquisition_datetime="20210827T162210",
    platform="ICEYE",
    product_type="GRD",
    default_resolution=6.0,
    band_map={VV: 1, VV_DSPK: 2},
)

{<SarBandNames.VV: 'VV'>: <xarray.DataArray 'VV' (band: 1, y: 2748, x: 2967)>
 array([[[nan, nan, nan, ..., nan, nan, nan],
         [nan, nan, nan, ..., nan, nan, nan],
         [nan, nan, nan, ..., nan, nan, nan],
         ...,
         [nan, nan, nan, ..., nan, nan, nan],
         [nan, nan, nan, ..., nan, nan, nan],
         [nan, nan, nan, ..., nan, nan, nan]]], dtype=float32)
 Coordinates:
   * band         (band) int64 1
   * x            (x) float64 6.7e+05 6.701e+05 6.701e+05 ... 8.124e+05 8.124e+05
   * y            (y) float64 1.113e+04 1.109e+04 ... -1.206e+05 -1.207e+05
     spatial_ref  int64 0
 Attributes:
     scale_factor:      1.0
     add_offset:        0.0
     long_name:         VV
     sensor:            ICEYE
     sensor_id:         ICEYE
     product_path:      /home/data/DS3/CI/eoreader/others/20210827T162210_ICEY...
     product_name:      20210827T162210_ICEYE_SC_GRD
     product_filename:  20210827T162210_ICEYE_SC_GRD_STK
     product_type:      GRD
     acquisition_date:  20210827T162210
     condensed_name:    20210827T162210_ICEYE_GRD}

from pprint import pprint
from eoreader import utils

# Read and display metadata
mtd, _ = sar_prod.read_mtd()
pprint(utils.quick_xml_to_dict(mtd))