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) 2015-2020, 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/slstr_l2.py → satpy/readers/ghrsst_l2.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
-# Copyright (c) 2017 Satpy developers
+# Copyright (c) 2017 - 2022 Satpy developers
 #
-# This file is part of satpy.
+# 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
@@ -14,8 +14,11 @@
 #
 # 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 Sentinel-3 SLSTR SST data."""
+"""Reader for the GHRSST level-2 formatted data."""
 
+import os
+import tarfile
+from contextlib import suppress
 from datetime import datetime
 
 import xarray as xr
@@ -24,29 +27,24 @@
 from satpy.readers.file_handlers import BaseFileHandler
 
 
-class SLSTRL2FileHandler(BaseFileHandler):
-    """File handler for Sentinel-3 SSL L2 netCDF files."""
+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 Sentinel-3 SSL L2 netCDF data."""
-        super(SLSTRL2FileHandler, self).__init__(filename, filename_info, filetype_info)
+        """Initialize the file handler for GHRSST L2 netCDF data."""
+        super().__init__(filename, filename_info, filetype_info)
 
-        if filename.endswith('tar'):
-            import os
-            import tarfile
-            import tempfile
-            with tempfile.TemporaryDirectory() as tempdir:
-                with tarfile.open(name=filename, mode='r') as tf:
-                    sst_filename = next((name for name in tf.getnames()
-                                        if name.endswith('nc') and 'GHRSST-SSTskin' in name))
-                    tf.extract(sst_filename, tempdir)
-                    fullpath = os.path.join(tempdir, sst_filename)
-                    self.nc = xr.open_dataset(fullpath,
-                                              decode_cf=True,
-                                              mask_and_scale=True,
-                                              engine=engine,
-                                              chunks={'ni': CHUNK_SIZE,
-                                                      'nj': CHUNK_SIZE})
+        if os.fspath(filename).endswith('tar'):
+            self._tarfile = tarfile.open(name=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)
+            self.nc = xr.open_dataset(file_obj,
+                                      decode_cf=True,
+                                      mask_and_scale=True,
+                                      engine=engine,
+                                      chunks={'ni': CHUNK_SIZE,
+                                              'nj': CHUNK_SIZE})
         else:
             self.nc = xr.open_dataset(filename,
                                       decode_cf=True,
@@ -61,6 +59,13 @@ def __init__(self, filename, filename_info, filetype_info, engine=None):
         self.filename_info['end_time'] = datetime.strptime(
             self.nc.stop_time, '%Y%m%dT%H%M%SZ')
 
+    @staticmethod
+    def _is_sst_file(name):
+        """Check if file in the tar archive is a valid SST file."""
+        if name.endswith('nc') and 'GHRSST-SSTskin' in name:
+            return True
+        return False
+
     def get_dataset(self, key, info):
         """Get any available dataset."""
         stdname = info.get('standard_name')
@@ -75,3 +80,13 @@ def start_time(self):
     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()

satpy/tests/reader_tests/test_ghrsst_l2.py

@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# Copyright (c) 2018, 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/>.
+"""Module for testing the satpy.readers.ghrsst_l2 module."""
+
+import os
+import tarfile
+import tempfile
+import unittest
+from datetime import datetime
+from pathlib import Path
+from unittest import mock
+
+import numpy as np
+import xarray as xr
+
+from satpy.readers.ghrsst_l2 import GHRSSTL2FileHandler
+
+
+class TestGHRSSTL2Reader(unittest.TestCase):
+    """Test Sentinel-3 SST L2 reader."""
+
+    @mock.patch('satpy.readers.ghrsst_l2.xr')
+    def setUp(self, xr_):
+        """Create a fake osisaf ghrsst dataset."""
+        self.base_data = np.array(([-32768, 1135, 1125], [1138, 1128, 1080]))
+        self.lon_data = np.array(([-13.43, 1.56, 11.25], [-11.38, 1.28, 10.80]))
+        self.lat_data = np.array(([43.43, 55.56, 61.25], [41.38, 50.28, 60.80]))
+        self.lon = xr.DataArray(
+            self.lon_data,
+            dims=('nj', 'ni'),
+            attrs={'standard_name': 'longitude',
+                   'units': 'degrees_east',
+                   }
+        )
+        self.lat = xr.DataArray(
+            self.lat_data,
+            dims=('nj', 'ni'),
+            attrs={'standard_name': 'latitude',
+                   'units': 'degrees_north',
+                   }
+        )
+        self.sst = xr.DataArray(
+            self.base_data,
+            dims=('nj', 'ni'),
+            attrs={'scale_factor': 0.01, 'add_offset': 273.15,
+                   '_FillValue': -32768, 'units': 'kelvin',
+                   }
+        )
+        self.fake_dataset = xr.Dataset(
+            data_vars={
+                'sea_surface_temperature': self.sst,
+                'longitude': self.lon,
+                'latitude': self.lat,
+            },
+            attrs={
+                "start_time": "20220321T112640Z",
+                "stop_time": "20220321T145711Z",
+                "platform": 'NOAA20',
+                "sensor": "VIIRS",
+            },
+        )
+        self._tmpfile = tempfile.NamedTemporaryFile(suffix='.nc')
+        self.fake_dataset.to_netcdf(self._tmpfile.name)
+
+        self._create_tarfile_with_testdata()
+
+    def _create_tarfile_with_testdata(self):
+        """Create a 'fake' testdata set in a tar file."""
+        self._tmpdir = tempfile.TemporaryDirectory()
+
+        slstr_fakename = "S3A_SL_2_WST_MAR_O_NR_003.SEN3"
+        tarfile_fakename = "S3A_SL_2_WST_MAR_O_NR_003.SEN3.tar"
+        self._slstrdir = Path(self._tmpdir.name) / slstr_fakename
+        self._slstrdir.mkdir(parents=True, exist_ok=True)
+        self._tarfile_path = Path(self._tmpdir.name) / tarfile_fakename
+
+        with tempfile.NamedTemporaryFile(suffix='.nc',
+                                         prefix='L2P_GHRSST-SSTskin', dir=self._slstrdir) as ncfilename:
+            self.fake_dataset.to_netcdf(ncfilename.name)
+            xmlfile_path = tempfile.NamedTemporaryFile(prefix='xfdumanifest', suffix='.xml',
+                                                       dir=Path(self._tmpdir.name) / slstr_fakename)
+
+            with tarfile.open(name=self._tarfile_path, mode='w') as tar:
+                tar.add(ncfilename.name, arcname=Path(slstr_fakename) / os.path.basename(ncfilename.name))
+                tar.add(xmlfile_path.name, arcname=Path(slstr_fakename) / os.path.basename(xmlfile_path.name))
+
+    def test_instantiate(self):
+        """Test initialization of file handlers."""
+        filename_info = {}
+        GHRSSTL2FileHandler(self._tmpfile.name, filename_info, None)
+        GHRSSTL2FileHandler(os.fspath(self._tarfile_path), filename_info, None)
+
+    def test_get_dataset(self):
+        """Test retrieval of datasets."""
+        filename_info = {}
+        test = GHRSSTL2FileHandler(self._tmpfile.name, filename_info, None)
+        test.get_dataset('longitude', {'standard_name': 'longitude'})
+        test.get_dataset('latitude', {'standard_name': 'latitude'})
+        test.get_dataset('sea_surface_temperature', {'standard_name': 'sea_surface_temperature'})
+
+        with self.assertRaises(KeyError):
+            test.get_dataset('erroneous dataset', {'standard_name': 'erroneous dataset'})
+
+    def test_get_sensor(self):
+        """Test retrieval of the sensor name from the netCDF file."""
+        dt_valid = datetime(2022, 3, 21, 11, 26, 40)  # 202203211200Z
+        filename_info = {'field_type': 'NARSST', 'generating_centre': 'FRA_',
+                         'satid': 'NOAA20_', 'valid_time': dt_valid}
+
+        test = GHRSSTL2FileHandler(self._tmpfile.name, filename_info, None)
+        assert test.sensor == 'viirs'
+
+    def test_get_start_and_end_times(self):
+        """Test retrieval of the sensor name from the netCDF file."""
+        dt_valid = datetime(2022, 3, 21, 11, 26, 40)  # 202203211200Z
+        good_start_time = datetime(2022, 3, 21, 11, 26, 40)  # 20220321T112640Z
+        good_stop_time = datetime(2022, 3, 21, 14, 57, 11)  # 20220321T145711Z
+
+        filename_info = {'field_type': 'NARSST', 'generating_centre': 'FRA_',
+                         'satid': 'NOAA20_', 'valid_time': dt_valid}
+
+        test = GHRSSTL2FileHandler(self._tmpfile.name, filename_info, None)
+
+        assert test.start_time == good_start_time
+        assert test.end_time == good_stop_time
+
+    def tearDown(self):
+        """Clean up."""
+        print(self._tmpfile.name)
+        self._tmpfile.close()
+        self._tmpdir.cleanup()