Fix osisaf SST reader

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/enhancements/generic.yaml

@@ -930,3 +930,39 @@ enhancements:
           factor: 21.0
           min_stretch: 0.0
           max_stretch: 20.0
+
+  osisaf_sst_smhi_colormap:
+    standard_name: sea_surface_subskin_temperature
+    operations:
+    - name: osisaf_sst
+      method: !!python/name:satpy.enhancements.colorize
+      kwargs:
+          palettes:
+            - colors: [
+              [255, 0, 255],
+              [195, 0, 129],
+              [129, 0, 47],
+              [195, 0, 0],
+              [255, 0, 0],
+              [236, 43, 0],
+              [217, 86, 0],
+              [200, 128, 0],
+              [211, 154, 13],
+              [222, 180, 26],
+              [233, 206, 39],
+              [244, 232, 52],
+              [255.99609375, 255.99609375, 63.22265625],
+              [203.125, 255.99609375, 52.734375],
+              [136.71875, 255.99609375, 27.34375],
+              [0, 255.99609375, 0],
+              [0, 207.47265625, 0],
+              [0, 158.94921875, 0],
+              [0, 110.42578125, 0],
+              [0, 82.8203125, 63.99609375],
+              [0, 55.21484375, 127.9921875],
+              [0, 27.609375, 191.98828125],
+              [0, 0, 255.99609375],
+              [100.390625, 100.390625, 255.99609375],
+              [150.5859375, 150.5859375, 255.99609375]]
+              min_value: 296.55
+              max_value: 273.55

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 - 2020, 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
+import tempfile
 from datetime import datetime
 
 import xarray as xr
@@ -24,21 +27,18 @@
 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(GHRSSTL2FileHandler, self).__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))
+                                         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,
@@ -75,3 +75,8 @@ 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()

satpy/tests/reader_tests/test_ghrsst_l2.py

@@ -0,0 +1,121 @@
+#!/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 unittest
+from datetime import datetime
+from unittest import mock
+from unittest.mock import MagicMock, patch
+
+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.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,
+            },
+            attrs={
+                "start_time": "20220321T112640Z",
+                "stop_time": "20220321T145711Z",
+                "platform": 'NOAA20',
+                "sensor": "VIIRS",
+            },
+        )
+
+    @mock.patch('xarray.open_dataset')
+    def test_instantiate(self, mocked_dataset):
+        """Test initialization of file handlers."""
+        filename_info = {}
+        tmp = MagicMock(start_time='20191120T125002Z', stop_time='20191120T125002Z')
+        tmp.rename.return_value = tmp
+        xr.open_dataset.return_value = tmp
+        GHRSSTL2FileHandler('somedir/somefile.nc', filename_info, None)
+        mocked_dataset.assert_called()
+        mocked_dataset.reset_mock()
+
+        with patch('tarfile.open') as tf:
+            tf.return_value.__enter__.return_value = MagicMock(getnames=lambda *a: ["GHRSST-SSTskin.nc"])
+            GHRSSTL2FileHandler('somedir/somefile.tar', filename_info, None)
+        mocked_dataset.assert_called()
+        mocked_dataset.reset_mock()
+
+    @mock.patch('xarray.open_dataset')
+    def test_get_dataset(self, mocked_dataset):
+        """Test retrieval of datasets."""
+        filename_info = {}
+        tmp = MagicMock(start_time='20191120T125002Z', stop_time='20191120T125002Z')
+        tmp.rename.return_value = tmp
+        xr.open_dataset.return_value = tmp
+        test = GHRSSTL2FileHandler('somedir/somefile.nc', filename_info, None)
+        test.nc = {'longitude': xr.Dataset(),
+                   'latitude': xr.Dataset(),
+                   'sea_surface_temperature': xr.Dataset(),
+                   'sea_ice_fraction': xr.Dataset(),
+                   }
+        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'})
+        test.get_dataset('sea_ice_fraction', {'standard_name': 'sea_ice_fraction'})
+        with self.assertRaises(KeyError):
+            test.get_dataset('erroneous dataset', {'standard_name': 'erroneous dataset'})
+        mocked_dataset.assert_called()
+        mocked_dataset.reset_mock()
+
+    @mock.patch('xarray.open_dataset')
+    def test_get_sensor(self, mocked_dataset):
+        """Test retrieval of the sensor name from the netCDF file."""
+        mocked_dataset.return_value = self.fake_dataset
+        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('somedir/somefile.nc', filename_info, None)
+        assert test.sensor == 'viirs'
+
+    @mock.patch('xarray.open_dataset')
+    def test_get_start_and_end_times(self, mocked_dataset):
+        """Test retrieval of the sensor name from the netCDF file."""
+        mocked_dataset.return_value = self.fake_dataset
+        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('somedir/somefile.nc', filename_info, None)
+
+        assert test.start_time == good_start_time
+        assert test.end_time == good_stop_time