Merge pull request #1410 from adybbroe/fix-osisaf-reader

Fix osisaf SST reader

doc/source/index.rst

@@ -181,7 +181,7 @@ the base Satpy installation.
       - `slstr_l1b`
       - In development
     * - OSISAF SST data in GHRSST (netcdf) format
-      - `ghrsst_l3c_sst`
+      - `ghrsst_l2`
       - In development
     * - NUCAPS EDR Retrieval in NetCDF4 format
       - `nucaps`
@@ -245,7 +245,7 @@ the base Satpy installation.
       - `glm_l2`
       - Beta
     * - Sentinel-3 SLSTR SST data in NetCDF4 format
-      - `slstr_l2`
+      - `ghrsst_l2`
       - Beta
     * - IASI level 2 SO2 in BUFR format
       - `iasi_l2_so2_bufr`

satpy/composites/__init__.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-# Copyright (c) 2015-2020 Satpy developers
+# Copyright (c) 2015-2022 Satpy developers
 #
 # This file is part of satpy.
 #
@@ -495,7 +495,7 @@ def build_colormap(palette, dtype, info):
         Colormaps come in different forms, but they are all supposed to have
         color values between 0 and 255. The following cases are considered:
 
-        - Palettes comprised of only a list on colors. If *dtype* is uint8,
+        - Palettes comprised of only a list of colors. If *dtype* is uint8,
           the values of the colormap are the enumeration of the colors.
           Otherwise, the colormap values will be spread evenly from the min
           to the max of the valid_range provided in `info`.

satpy/etc/readers/ghrsst_l2.yaml

@@ -0,0 +1,97 @@
+reader:
+  description: NC Reader for GHRSST Level 2 data
+  name: ghrsst_l2
+  sensors: ['slstr', 'avhrr/3', 'viirs']
+  default_channels: []
+  reader: !!python/name:satpy.readers.yaml_reader.FileYAMLReader
+
+file_types:
+    GHRSST_OSISAF:
+        file_reader: !!python/name:satpy.readers.ghrsst_l2.GHRSSTL2FileHandler
+        # S-OSI_-FRA_-NPP_-NARSST_FIELD-202010141300Z.nc
+        file_patterns: ['S-OSI_-{generating_centre:4s}-{satid:s}-{field_type:s}_FIELD-{valid_time:%Y%m%d%H%M}Z.nc']
+
+    SLSTR:
+        file_reader: !!python/name:satpy.readers.ghrsst_l2.GHRSSTL2FileHandler
+        file_patterns: ['{dt1:%Y%m%d%H%M%S}-{generating_centre:3s}-{type_id:3s}_GHRSST-SSTskin-SLSTR{something:1s}-{dt2:%Y%m%d%H%M%S}-{version}.nc',
+        '{mission_id:3s}_SL_{processing_level:1s}_WST____{start_time:%Y%m%dT%H%M%S}_{end_time:%Y%m%dT%H%M%S}_{creation_time:%Y%m%dT%H%M%S}_{duration:4d}_{cycle:3d}_{relative_orbit:3d}_{frame:4s}_{centre:3s}_{mode:1s}_{timeliness:2s}_{collection:3s}.SEN3.tar']
+
+datasets:
+  # SLSTR SST and Sea Ice products
+  longitude_slstr:
+    name: longitude_slstr
+    resolution: 1000
+    view: nadir
+    file_type: SLSTR
+    standard_name: lon
+    units: degree
+
+  latitude_slstr:
+    name: latitude_slstr
+    resolution: 1000
+    view: nadir
+    file_type: SLSTR
+    standard_name: lat
+    units: degree
+
+  sea_surface_temperature_slstr:
+    name: sea_surface_temperature
+    sensor: slstr
+    coordinates: [longitude_slstr, latitude_slstr]
+    file_type: SLSTR
+    resolution: 1000
+    view: nadir
+    units: kelvin
+    standard_name: sea_surface_temperature
+
+  sea_ice_fraction_slstr:
+    name: sea_ice_fraction
+    sensor: slstr
+    coordinates: [longitude_slstr, latitude_slstr]
+    file_type: SLSTR
+    resolution: 1000
+    view: nadir
+    units: "%"
+    standard_name: sea_ice_fraction
+
+  # Quality estimation 0-5: no data, cloud, worst, low, acceptable, best
+  quality_level_slstr:
+    name: quality_level
+    sensor: slstr
+    coordinates: [longitude_slstr, latitude_slstr]
+    file_type: SLSTR
+    resolution: 1000
+    view: nadir
+    standard_name: quality_level
+
+
+  # OSISAF SST:
+  longitude_osisaf:
+    name: longitude_osisaf
+    resolution: 2000
+    file_type: GHRSST_OSISAF
+    standard_name: lon
+    units: degree
+
+  latitude_osisaf:
+    name: latitude_osisaf
+    resolution: 2000
+    file_type: GHRSST_OSISAF
+    standard_name: lat
+    units: degree
+
+  sea_surface_temperature_osisaf:
+    name: sea_surface_temperature
+    coordinates: [longitude_osisaf, latitude_osisaf]
+    file_type: GHRSST_OSISAF
+    resolution: 2000
+    units: kelvin
+    standard_name: sea_surface_temperature
+
+  sea_ice_fraction_osisaf:
+    name: sea_ice_fraction
+    coordinates: [longitude_osisaf, latitude_osisaf]
+    file_type: GHRSST_OSISAF
+    resolution: 2000
+    units: "%"
+    standard_name: sea_ice_fraction

satpy/readers/ghrsst_l2.py

@@ -0,0 +1,97 @@
+# -*- coding: utf-8 -*-
+# Copyright (c) 2017 - 2022 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/>.
+"""Reader for the GHRSST level-2 formatted data."""
+
+import os
+import tarfile
+from contextlib import suppress
+from datetime import datetime
+from functools import cached_property
+
+import xarray as xr
+
+from satpy import CHUNK_SIZE
+from satpy.readers.file_handlers import BaseFileHandler
+
+
+class GHRSSTL2FileHandler(BaseFileHandler):
+    """File handler for GHRSST L2 netCDF files."""
+
+    def __init__(self, filename, filename_info, filetype_info, engine=None):
+        """Initialize the file handler for GHRSST L2 netCDF data."""
+        super().__init__(filename, filename_info, filetype_info)
+        self._engine = engine
+        self._tarfile = None
+
+        self.filename_info['start_time'] = datetime.strptime(
+            self.nc.start_time, '%Y%m%dT%H%M%SZ')
+        self.filename_info['end_time'] = datetime.strptime(
+            self.nc.stop_time, '%Y%m%dT%H%M%SZ')
+
+    @cached_property
+    def nc(self):
+        """Get the xarray Dataset for the filename."""
+        if os.fspath(self.filename).endswith('tar'):
+            file_obj = self._open_tarfile()
+        else:
+            file_obj = self.filename
+
+        nc = xr.open_dataset(file_obj,
+                             decode_cf=True,
+                             mask_and_scale=True,
+                             engine=self._engine,
+                             chunks={'ni': CHUNK_SIZE,
+                                     'nj': CHUNK_SIZE})
+
+        return nc.rename({'ni': 'x', 'nj': 'y'})
+
+    def _open_tarfile(self):
+        self._tarfile = tarfile.open(name=self.filename, mode='r')
+        sst_filename = next((name for name in self._tarfile.getnames()
+                             if self._is_sst_file(name)))
+        file_obj = self._tarfile.extractfile(sst_filename)
+        return file_obj
+
+    @staticmethod
+    def _is_sst_file(name):
+        """Check if file in the tar archive is a valid SST file."""
+        return name.endswith('nc') and 'GHRSST-SSTskin' in name
+
+    def get_dataset(self, key, info):
+        """Get any available dataset."""
+        stdname = info.get('standard_name')
+        return self.nc[stdname].squeeze()
+
+    @property
+    def start_time(self):
+        """Get start time."""
+        return self.filename_info['start_time']
+
+    @property
+    def end_time(self):
+        """Get end time."""
+        return self.filename_info['end_time']
+
+    @property
+    def sensor(self):
+        """Get the sensor name."""
+        return self.nc.attrs['sensor'].lower()
+
+    def __del__(self):
+        """Close the tarfile object."""
+        with suppress(AttributeError):
+            self._tarfile.close()