Add OCI L2 BGC reader

doc/source/reading.rst

@@ -305,6 +305,13 @@ time etc. The following attributes are standardized across all readers:
   should happen and when they actually do. See :ref:`time_metadata` below for
   details.
 * ``raw_metadata``: Raw, unprocessed metadata from the reader.
+* ``rows_per_scan``: Optional integer indicating how many rows of data
+  represent a single scan of the instrument. This is primarily used by
+  some resampling algorithms (ex. EWA) to produce better results and only
+  makes sense for swath-based (usually polar-orbiting) instruments. For
+  example, MODIS 1km data has 10 rows of data per scan. If an instrument
+  does not have multiple rows per scan this should usually be set to 0 rather
+  than 1 to indicate that the entire swath should be treated as a whole.
 
 Note that the above attributes are not necessarily available for each dataset.
 

satpy/etc/enhancements/generic.yaml

@@ -1192,6 +1192,18 @@ enhancements:
           factor: 21.0
           min_stretch: 0.0
           max_stretch: 20.0
+  chlor_a_bgc:
+    name: chlor_a
+    reader: oci_l2_bgc
+    operations:
+      - name: stretch
+        method: !!python/name:satpy.enhancements.stretch
+        kwargs:
+          stretch: log
+          base: "10"
+          factor: 21.0
+          min_stretch: 0.0
+          max_stretch: 20.0
 
   cimss_cloud_type:
     standard_name: cimss_cloud_type

satpy/etc/readers/oci_l2_bgc.yaml

@@ -0,0 +1,37 @@
+reader:
+  name: oci_l2_bgc
+  short_name: PACE OCI L2 BGC
+  long_name: PACE OCI L2 Biogeochemical in NetCDF format
+  description: PACE OCI L2 Biogeochemical Reader
+  status: Beta
+  supports_fsspec: false
+  reader: !!python/name:satpy.readers.yaml_reader.FileYAMLReader
+  sensors: [oci]
+
+file_types:
+  bgc_nc:
+    file_patterns:
+    # Example: PACE_OCI.20240907T191809.L2.OC_BGC.V2_0.NRT.nc4
+      - '{platform:s}_{sensor:s}.{start_time:%Y%m%dT%H%M%S}.L2.OC_BGC.V{sw_version:s}.{processing_type:s}nc4'
+    file_reader: !!python/name:satpy.readers.seadas_l2.SEADASL2NetCDFFileHandler
+    geo_resolution: 1000
+
+datasets:
+  longitude:
+    name: longitude
+    file_type: [bgc_nc]
+    file_key: ["navigation_data/longitude", "longitude"]
+    resolution: 1000
+
+  latitude:
+    name: latitude
+    file_type: [bgc_nc]
+    file_key: ["navigation_data/latitude", "latitude"]
+    resolution: 1000
+
+  chlor_a:
+    name: chlor_a
+    file_type: [bgc_nc]
+    file_key: ["geophysical_data/chlor_a", "chlor_a"]
+    resolution: 1000
+    coordinates: [longitude, latitude]

satpy/readers/seadas_l2.py

@@ -54,6 +54,8 @@ def _rows_per_scan(self):
             return 10
         if "viirs" in self.sensor_names:
             return 16
+        if "oci" in self.sensor_names:
+            return 0
         raise ValueError(f"Don't know how to read data for sensors: {self.sensor_names}")
 
     def _platform_name(self):
@@ -82,7 +84,10 @@ def sensor_names(self):
         sensor_name = self[self.sensor_attr_name].lower()
         if sensor_name.startswith("modis"):
             return {"modis"}
-        return {"viirs"}
+        if sensor_name.startswith("viirs"):
+            return {"viirs"}
+        # Example: OCI
+        return {sensor_name}
 
     def get_dataset(self, data_id, dataset_info):
         """Get DataArray for the specified DataID."""

satpy/tests/reader_tests/test_oci_l2_bgc.py

@@ -0,0 +1,72 @@
+# Copyright (c) 2024 Satpy developers
+#
+# This file is part of satpy.
+#
+# satpy is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# satpy is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# satpy.  If not, see <http://www.gnu.org/licenses/>.
+"""Tests for the 'oci_l2_bgc' reader."""
+
+import numpy as np
+import pytest
+from pyresample.geometry import SwathDefinition
+
+from satpy import Scene, available_readers
+
+from .test_seadas_l2 import _create_seadas_chlor_a_netcdf_file
+
+# NOTE:
+# The following fixtures are not defined in this file, but are used and injected by Pytest:
+# - tmp_path_factory
+
+
+@pytest.fixture(scope="module")
+def oci_l2_bgc_netcdf(tmp_path_factory):
+    """Create MODIS SEADAS NetCDF file."""
+    filename = "PACE_OCI.20211118T175853.L2.OC_BGC.V2_0.NRT.nc4"
+    full_path = str(tmp_path_factory.mktemp("oci_l2_bgc") / filename)
+    return _create_seadas_chlor_a_netcdf_file(full_path, "PACE", "OCI")
+
+
+class TestSEADAS:
+    """Test the OCI L2 file reader."""
+
+    def test_available_reader(self):
+        """Test that OCI L2 reader is available."""
+        assert "oci_l2_bgc" in available_readers()
+
+    def test_scene_available_datasets(self, oci_l2_bgc_netcdf):
+        """Test that datasets are available."""
+        scene = Scene(reader="oci_l2_bgc", filenames=oci_l2_bgc_netcdf)
+        available_datasets = scene.all_dataset_names()
+        assert len(available_datasets) > 0
+        assert "chlor_a" in available_datasets
+
+    @pytest.mark.parametrize("apply_quality_flags", [False, True])
+    def test_load_chlor_a(self, oci_l2_bgc_netcdf, apply_quality_flags):
+        """Test that we can load 'chlor_a'."""
+        reader_kwargs = {"apply_quality_flags": apply_quality_flags}
+        scene = Scene(reader="oci_l2_bgc", filenames=oci_l2_bgc_netcdf, reader_kwargs=reader_kwargs)
+        scene.load(["chlor_a"])
+        data_arr = scene["chlor_a"]
+        assert data_arr.dims == ("y", "x")
+        assert data_arr.attrs["platform_name"] == "PACE"
+        assert data_arr.attrs["sensor"] == {"oci"}
+        assert data_arr.attrs["units"] == "mg m^-3"
+        assert data_arr.dtype.type == np.float32
+        assert isinstance(data_arr.attrs["area"], SwathDefinition)
+        assert data_arr.attrs["rows_per_scan"] == 0
+        data = data_arr.data.compute()
+        if apply_quality_flags:
+            assert np.isnan(data[2, 2])
+            assert np.count_nonzero(np.isnan(data)) == 1
+        else:
+            assert np.count_nonzero(np.isnan(data)) == 0

satpy/tests/reader_tests/test_seadas_l2.py

@@ -190,6 +190,7 @@ def _create_seadas_chlor_a_netcdf_file(full_path, mission, sensor):
     geophys_group = nc.createGroup("geophysical_data")
     _add_variable_to_netcdf_file(geophys_group, "chlor_a", chlor_a_info)
     _add_variable_to_netcdf_file(geophys_group, "l2_flags", l2_flags_info)
+    nc.close()
     return [full_path]