eoio.readers.flex.reader module

eoio.readers.flex.reader

Reader for FLEX L2 FLXSYN products (NetCDF4).

The product is a synergy of FLORIS, OLCI and SLSTR data on a common 300 m UTM grid. Variables are exposed under the following vars_sel selections:

meas

All science variables: OLCI/SLSTR/FLORIS apparent reflectance, FLORIS real reflectance, SIF (spectrum, integrated, peaks, O2 bands), and the vegetation products. Shortcuts: "all", "olci", "slstr", "floris", "fluorescence", "vegetation".

aux

Retrieved atmospheric state (water vapour, AOT, Angstrom exponent, asymmetry parameter, cloud probability, LST, PAR), at-surface direct/diffuse irradiance, elevation and view geometry. Shortcuts: "all", "atmosphere", "irradiance", "geometry".

mask

cirrus_cloud_mask (the only mask in the product).

Every dataset also carries the x/y (projected, from the product’s GeoTransform) and 2-D latitude/longitude coordinates; the CRS comes from the file (crs attribute), as the UTM zone differs between products.

Wavelength information is kept as in the product: each spectral grid has its own dimension (wavelength_olci, wavelength_floris, …). Use the resample_wavelength processor to put spectra on a common grid. FLORIS wavelengths are stored per across-track sample but are treated as a single vector, as only the first sample is populated in the products seen so far; this is provisional until real products show whether a spectral smile (per-row wavelengths) must be handled (it is expected to be corrected in L1).

Values outside the product’s stated valid_min/valid_max are not altered (e.g. cloud_probability below 0 and total_integrated_sif far above valid_max in the test products). These are considered product issues to be raised with the producers, not corrected in the reader.

The split of variables between meas, aux and mask follows the product’s science/auxiliary division. Placement of cloud_probability (aux) relative to cloud masks is to be revisited as part of a wider consistency discussion across readers.

The files carry no acquisition time, so product_datetime is taken from the start time in the filename. Whether a start/stop range is needed is still to be confirmed.

Memory: by default the selected (subsetted) variables are loaded into memory. With read_params={"use_chunks": True} (optionally "chunks": {"y": ..., "x": ...}, default 64 x 64) they stay lazy, dask-backed arrays and are only read when computed, so a full product can be opened and then reduced without holding it all in memory. The file stays open while the dataset is in use.

Uncertainties (include_uncertainties) are registered through obsarray as ds.unc components. The product documents no error-correlation model, so a placeholder is assumed (random across y/x, systematic across wavelength); see eoio.readers.flex.data_io.err_corr_for(). The spectral error correlation is computed and passed to the L2B retrieval but is not stored per product (too expensive), so it cannot be read from the files; typical matrices per land-cover type may replace the placeholder in future.

Classes

FLEXL2Reader(path[, vars_sel, subset, ...])

Reader for FLEX L2 FLXSYN products.

class eoio.readers.flex.reader.FLEXL2Reader(path: Path | str, vars_sel: Dict[str, Any] | None = None, subset: Dict[str, Any] | None = None, read_params: Dict[str, Any] | None = None)

Bases: BaseReader

Reader for FLEX L2 FLXSYN products.

all_read_params = {'chunks': "None/{'x':X,'y':Y}: dask chunk sizes (default 64 x 64 when use_chunks is True)", 'include_uncertainties': 'True/False', 'metadata_level': 'all/basic/None', 'save_extracted': 'True/False', 'use_chunks': 'True/False: keep variables lazy (dask-backed) instead of loading them into memory'}

all_subset: Dict[str, Any] = {'roi': 'Primary/shapely geometry/bounding box tuple (xmin, ymin, xmax, ymax)/GeoJSON-like ``dict`` with a ``type`` key/list of ``[x, y]`` coordinate pairs defining a polygon/``((x, y), half_width_m)`` defining a square box around a point', 'roi_crs': 'Any EPSG Code', 'wavelength': ['min', 'max', 'nearest', 'tolerance']}

aux_def: Dict[str, List[str]] = {'all': ['elevation', 'sun_zenith_angle', 'viewing_zenith_angle', 'relative_azimuth_angle', 'columnar_water_vapor', 'aerosol_optical_thickness', 'angstrom_exponent', 'asymmetry_parameter', 'cloud_probability', 'land_surface_temperature', 'integrated_par', 'direct_irradiance', 'diffuse_irradiance'], 'atmosphere': ['columnar_water_vapor', 'aerosol_optical_thickness', 'angstrom_exponent', 'asymmetry_parameter', 'cloud_probability', 'land_surface_temperature', 'integrated_par', 'direct_irradiance', 'diffuse_irradiance'], 'geometry': ['sun_zenith_angle', 'viewing_zenith_angle', 'relative_azimuth_angle'], 'irradiance': ['direct_irradiance', 'diffuse_irradiance']}

default_read_params: Dict[str, Any] = {'chunks': None, 'include_uncertainties': True, 'metadata_level': 'all', 'save_extracted': False, 'use_chunks': False}

default_subset: Dict[str, Any] = {'roi': None, 'roi_crs': 4326, 'wavelength': None}

default_vars_sel = {'aux': None, 'mask': None, 'meas': 'all'}

static get_extension() → str

Return the file extension of FLEX products.

list_uncertainty_vars() → List[str]

Uncertainty variables of the selected meas/aux variables only.

mask_def: Dict[str, List[str]] = {'all': ['cirrus_cloud_mask']}

meas_def: Dict[str, List[str]] = {'all': ['olci_apparent_reflectance', 'slstr_apparent_reflectance', 'floris_apparent_reflectance', 'sif_emission_spectrum', 'total_integrated_sif', 'sif_peak_values', 'sif_peak_positions', 'sif_O2_bands_value', 'floris_real_reflectance', 'leaf_area_index', 'leaf_chlorophyll_content', 'leaf_carotenoid_content', 'fapar_chlorophyll', 'apar_chlorophyll_photons', 'fraction_of_absorbed_photosynthetically_active_radiation', 'electron_transport_rate', 'fluorescence_quantum_efficiency', 'fluorescence_escape_probability', 'reversible_energy_dissipation', 'PSI_PSII_relative_contribution'], 'floris': ['floris_apparent_reflectance', 'floris_real_reflectance'], 'fluorescence': ['sif_emission_spectrum', 'total_integrated_sif', 'sif_peak_values', 'sif_peak_positions', 'sif_O2_bands_value', 'floris_real_reflectance'], 'olci': ['olci_apparent_reflectance'], 'slstr': ['slstr_apparent_reflectance'], 'vegetation': ['leaf_area_index', 'leaf_chlorophyll_content', 'leaf_carotenoid_content', 'fapar_chlorophyll', 'apar_chlorophyll_photons', 'fraction_of_absorbed_photosynthetically_active_radiation', 'electron_transport_rate', 'fluorescence_quantum_efficiency', 'fluorescence_escape_probability', 'reversible_energy_dissipation', 'PSI_PSII_relative_contribution']}

open_dataset() → Dataset

Open the FLEX product as an xarray.Dataset according to the request parameters.

Returns:

the opened and subsetted dataset.

uncertainty_vars: List[str] = ['direct_irradiance_uncertainty', 'diffuse_irradiance_uncertainty', 'floris_apparent_reflectance_uncertainty', 'sif_emission_spectrum_uncertainty', 'total_integrated_sif_uncertainty', 'sif_peak_values_uncertainty', 'sif_peak_positions_uncertainty', 'sif_O2_bands_value_uncertainty', 'floris_real_reflectance_uncertainty', 'leaf_area_index_uncertainty', 'leaf_chlorophyll_content_uncertainty', 'leaf_carotenoid_content_uncertainty', 'fapar_chlorophyll_uncertainty', 'apar_chlorophyll_photons_uncertainty', 'fraction_of_absorbed_photosynthetically_active_radiation_uncertainty', 'electron_transport_rate_uncertainty', 'fluorescence_quantum_efficiency_uncertainty', 'fluorescence_escape_probability_uncertainty']