Merge pull request #1020 from eysteinn/feature-slstr_l2

Feature Sentinel-3 Level-2 SST

doc/source/index.rst

@@ -228,6 +228,9 @@ the base Satpy installation.
     * - GOES-R GLM Grided Level 2 in NetCDF4 format
       - `glm_l2`
       - Beta
+    * - Sentinel-3 SLSTR SST data in NetCDF4 format
+      - `slstr_l2`
+      - Beta
 
 
 Indices and tables

satpy/etc/readers/slstr_l2.yaml

@@ -0,0 +1,59 @@
+reader:
+  description: NC Reader for Sentinel-3 SLSTR Level 2 data
+  name: slstr_l2
+  sensors: [slstr_l2]
+  default_channels: []
+  reader: !!python/name:satpy.readers.yaml_reader.FileYAMLReader
+
+file_types:
+    SLSTRB:
+        file_reader: !!python/name:satpy.readers.slstr_l2.SLSTRL2FileHandler
+        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:
+  longitude:
+    name: longitude
+    resolution: 1000
+    view: nadir
+    file_type: SLSTRB
+    standard_name: lon
+    units: degree
+
+  latitude:
+    name: latitude
+    resolution: 1000
+    view: nadir
+    file_type: SLSTRB
+    standard_name: lat
+    units: degree
+
+  sea_surface_temperature:
+    name: sea_surface_temperature
+    sensor: slstr_l2
+    coordinates: [longitude, latitude]
+    file_type: SLSTRB
+    resolution: 1000
+    view: nadir
+    units: kelvin
+    standard_name: sea_surface_temperature
+
+  sea_ice_fraction:
+    name: sea_ice_fraction
+    sensor: slstr_l2
+    coordinates: [longitude, latitude]
+    file_type: SLSTRB
+    resolution: 1000
+    view: nadir
+    units: "%"
+    standard_name: sea_ice_fraction
+
+  # Quality estimation 0-5: no data, cloud, worst, low, acceptable, best
+  quality_level:
+    name: quality_level
+    sensor: slstr_l2
+    coordinates: [longitude, latitude]
+    file_type: SLSTRB
+    resolution: 1000
+    view: nadir
+    standard_name: sea_ice_fraction

satpy/readers/slstr_l2.py

@@ -0,0 +1,75 @@
+# -*- coding: utf-8 -*-
+# Copyright (c) 2017 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 Sentinel-3 SLSTR SST data."""
+
+from datetime import datetime
+from satpy.readers.file_handlers import BaseFileHandler
+from satpy import CHUNK_SIZE
+import xarray as xr
+
+
+class SLSTRL2FileHandler(BaseFileHandler):
+    """File handler for Sentinel-3 SSL 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)
+
+        if filename.endswith('tar'):
+            import tarfile
+            import os
+            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})
+        else:
+            self.nc = xr.open_dataset(filename,
+                                      decode_cf=True,
+                                      mask_and_scale=True,
+                                      engine=engine,
+                                      chunks={'ni': CHUNK_SIZE,
+                                              'nj': CHUNK_SIZE})
+
+        self.nc = self.nc.rename({'ni': 'x', 'nj': 'y'})
+        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')
+
+    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']

satpy/tests/reader_tests/__init__.py

@@ -41,7 +41,7 @@
                                       test_hsaf_grib, test_abi_l2_nc, test_eum_base,
                                       test_ami_l1b, test_viirs_compact, test_seviri_l2_bufr,
                                       test_geos_area, test_nwcsaf_msg, test_glm_l2,
-                                      test_seviri_l1b_icare, test_mimic_TPW2_nc,)
+                                      test_seviri_l1b_icare, test_mimic_TPW2_nc, test_slstr_l2,)
 
 if sys.version_info < (2, 7):
     import unittest2 as unittest
@@ -106,5 +106,6 @@ def suite():
     mysuite.addTests(test_mimic_TPW2_nc.suite())
     mysuite.addTests(test_glm_l2.suite())
     mysuite.addTests(test_seviri_l1b_icare.suite())
+    mysuite.addTests(test_slstr_l2.suite())
 
     return mysuite

satpy/tests/reader_tests/test_slstr_l2.py

@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# Copyright (c) 2018 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.slstr_l2 module."""
+
+import unittest
+from unittest import mock
+from unittest.mock import MagicMock
+from unittest.mock import patch
+import xarray as xr
+from satpy.readers.slstr_l2 import SLSTRL2FileHandler
+
+
+class TestSLSTRL2Reader(unittest.TestCase):
+    """Test Sentinel-3 SST L2 reader."""
+
+    @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
+        SLSTRL2FileHandler('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"])
+            SLSTRL2FileHandler('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 = SLSTRL2FileHandler('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()
+
+
+def suite():
+    """Test suite for test_slstr_l2."""
+    loader = unittest.TestLoader()
+    mysuite = unittest.TestSuite()
+    mysuite.addTest(loader.loadTestsFromTestCase(TestSLSTRL2Reader))
+    return mysuite
+
+
+if __name__ == '__main__':
+    unittest.main()