fix #523 new mapper

nansat/mappers/mapper_sentinel1_l2_iw.py

@@ -0,0 +1,225 @@
+# ------------------------------------------------------------------------------
+# Name:     mapper_sentinel1_iw_l2_odl.py
+# Purpose:  Mapper for Sentinel-1 IW L2 OCN products provided by ODL
+#
+# Author:       Artem Moiseev
+#
+# Created:  28.05.2021
+# Copyright:    (c) NERSC
+# License: GPL V3
+# ------------------------------------------------------------------------------
+
+
+import os
+import re   
+from datetime import datetime, timezone
+
+from nansat.vrt import VRT
+from nansat import Domain, NSR
+from nansat.exceptions import WrongMapperError
+
+import json
+import pythesint as pti
+from netCDF4 import Dataset, date2num
+import numpy as np
+
+
+class Mapper(VRT):
+    """"""
+
+    def __init__(self, file_src, gdal_dataset, gdal_metadata, *args, **kwargs):
+        # Check if an input file can be read with this mapper, else raise error
+        # Check the filename
+        Mapper.check_input(file_src)
+
+        # Check if the subswath number [1, 2, 3] is provided
+        # Subswath number is required for mapping the RVL products
+        if 'subswath_n' in kwargs.keys():
+            subswath_id = kwargs['subswath_n'] - 1
+        else:
+            subswath_id = 0
+        # Check if the product type is provided: rvl 
+        if 'product_type' in kwargs.keys():
+            product = kwargs['product_type']
+        else:
+            product = 'rvl'
+
+        if 'dop_time' in kwargs.keys():
+            dop_time = kwargs['dop_time']
+        else:
+            dop_time = False
+        # Read the NetCDF dataset
+        nc_dataset = Dataset(file_src)
+        # Generate a domain for the required subswath
+        # (1) Import lon lat arrays for the required subswath from the file
+        if product == 'rvl':
+            lon = nc_dataset.variables[product + 'Lon'][:, :, subswath_id]
+            lat = nc_dataset.variables[product + 'Lat'][:, :, subswath_id]
+        elif product == 'owi':
+            lon = nc_dataset.variables[product + 'Lon'][:, :]
+            lat = nc_dataset.variables[product + 'Lat'][:, :]
+        else:
+            raise ValueError
+
+        # (2) Filter part not covered with data following the data mask from the product
+        lon = self.filter_data(lon)
+        lat = self.filter_data(lat)
+        # (3) Generale the subswath domain from the lon lat arrays
+        self._init_from_lonlat(lon=lon, lat=lat)
+        # Get GCPs from the created domain and set them for the input file
+        dom = Domain.from_lonlat(lon, lat)
+        self.dataset.SetGCPs(dom.vrt.dataset.GetGCPs(), NSR().wkt)
+
+        # Add bands
+        for subdataset_name in nc_dataset.variables.keys():
+            # The ODL Sentinel-1 data contain several products. eact var name 
+            # starts with the name of the generic product e.g.: rvlDoppler or oswAngularBinSize
+            # Use only required type of products e.g., rvl
+            if not str.startswith(subdataset_name, product):
+                continue
+            # Import band data
+            band = nc_dataset.variables[subdataset_name]
+
+            if product == 'rvl':
+                if band.dimensions[:2] != ('rvlAzSize', 'rvlRaSize'):
+                    continue
+                elif subdataset_name == 'rvlZeroDopplerTime':
+                    if dop_time:
+                        band_data, band_metadata = self.process_zero_doppler_time_band(
+                            nc_dataset, band, subswath_id)
+                else:
+                    band_data = self.filter_data(nc_dataset.variables[subdataset_name][:, :, subswath_id])
+                    band_metadata = {}
+
+            elif product == 'owi':
+                # Process only part of the OWI product which prowided on the OWI grid 
+                # Some part of the OWI product is provided on the OSW grid and will be ignored
+                if len(band.dimensions) < 2:
+                    continue 
+                elif band.dimensions[:2] != ('owiAzSize', 'owiRaSize'):
+                    continue
+                elif len(band.dimensions) == 2:
+                    band_data = self.filter_data(nc_dataset.variables[subdataset_name][:, :])
+                    band_metadata = {}
+                else:
+                    continue
+            else:
+                raise ValueError
+
+            # Create band VRT
+            # NOTE: The try/except routine was added to fix the issue with the mask in the UssX/UssY bands
+            # TODO: Fix the issue. Use a SAR mask while filtering the data instead of using the mask from each NetCDF band
+            try:
+                band_vrt = VRT.from_array(band_data)
+            except RuntimeError:
+                continue
+            # Add VRT to the list of all dataset vrts
+            self.band_vrts[subdataset_name + 'VRT'] = band_vrt
+            src = {'SourceFilename': self.band_vrts[subdataset_name + 'VRT'].filename, 
+                   'SourceBand': 1}
+            # Add band specific metadata
+            dst = {'name': subdataset_name}
+            if len(band_metadata.keys()) != 0:
+                for key, value in band_metadata.items():
+                    dst[key] = value
+
+            for subdataset_att in nc_dataset.variables[subdataset_name].ncattrs():
+                dst[subdataset_att] = nc_dataset.variables[subdataset_name].getncattr(subdataset_att)
+            # Create band
+            self.create_band(src, dst)
+            self.dataset.FlushCache()
+
+        # Set generic metadata
+        try:
+            platform = nc_dataset.getncattr('missionName').replace('S', 'Sentinel-')
+            self.dataset.SetMetadataItem('platform', json.dumps(pti.get_gcmd_platform(platform)))
+            self.dataset.SetMetadataItem('instrument', json.dumps(pti.get_gcmd_instrument('SAR')))
+            self.dataset.SetMetadataItem('data_center', json.dumps(
+                pti.get_gcmd_provider('FR/IFREMER/CERSAT')))
+            self.dataset.SetMetadataItem('ISO_topic_category',
+                                         json.dumps(pti.get_iso19115_topic_category('Oceans')))
+            self.dataset.SetMetadataItem('summary', '')
+            self.dataset.SetMetadataItem('entry_title', '')
+        except json.JSONDecodeError:
+            pass
+        # Add metadata from the product
+        for key, value in nc_dataset.__dict__.items():
+            if isinstance(value, str):
+                self.dataset.SetMetadataItem(key, value)
+            elif isinstance(value, np.ndarray):
+                self.dataset.SetMetadataItem(key, ','.join([str(a) for a in value]))
+            else:
+                continue
+
+        # Set time coverage metadata
+        time_coverage_start = datetime.strptime(nc_dataset.getncattr('firstMeasurementTime')[:-1], '%Y-%m-%dT%H:%M:%S')
+        time_coverage_end = datetime.strptime(nc_dataset.getncattr('lastMeasurementTime')[:-1], '%Y-%m-%dT%H:%M:%S')
+        self.dataset.SetMetadataItem('time_coverage_start', time_coverage_start.isoformat())
+        self.dataset.SetMetadataItem('time_coverage_end', time_coverage_end.isoformat())
+
+    def process_zero_doppler_time_band(self, nc_ds, band, subswath_id, calendar_start='seconds since 2010-01-01'):
+        zero_dop_time_raw = np.char.decode(self.filter_data(band[:, :, :, subswath_id]))
+        timeseries = zero_dop_time_raw.reshape(
+            (zero_dop_time_raw.shape[0] * zero_dop_time_raw.shape[1], -1))
+        # Assemble raw timestamp strings and convert it to datetime objects
+        zero_dop_time_datetime = np.array(list(map(self._join_test, timeseries)))
+
+        zero_dop_time_datetime_2d = zero_dop_time_datetime.reshape(zero_dop_time_raw.shape[:2])
+
+        band_data = date2num(zero_dop_time_datetime_2d, calendar_start, calendar='standard')
+        band_metadata = {'units': calendar_start,
+                         'long_name': band.long_name}
+        return band_data, band_metadata
+
+    def _convert_time(self, time_str):
+        try:
+            time_stamp = datetime.strptime(time_str, '%Y-%m-%d %H:%M:%S.%f')
+        except:
+            time_stamp = datetime(1999, 1, 1, 0, 0, 0)
+        return time_stamp
+
+    def _join_test(self, arr):
+        """Assemble the time string"""
+        return self._convert_time(''.join(arr)[:-3])
+
+    def filter_data(self, arr):
+        # Remove data covered by mask from the array
+        if isinstance(arr.mask, np.ndarray):
+            unmasked_data = arr.data[:, arr.mask[0] == False]
+        else:
+            unmasked_data = arr
+        return unmasked_data
+
+    @staticmethod
+    def check_input(file_src):
+        """Check that input file (according to file_src) can be read by the mapper
+        Parameters
+        ----------
+        file_src : str
+            path of input Sentinel-1 IW file
+        """
+        # Extract filename and file format for the src
+        filename_base, file_format = Mapper.parse_filename(file_src.strip())
+
+        if file_format != '.nc':
+            raise WrongMapperError('Only netCDF format is supported')
+        elif not re.match(r's1.-iw-ocn-vv*', filename_base):
+            raise WrongMapperError()
+
+    @staticmethod
+    def parse_filename(file_src):
+        """Parse input file src to extract file name and format
+        Parameters
+        ----------
+        file_src : str
+            path of input Sentinel-1 IW file
+        Returns
+        -------
+        filename_base: str
+            filename without format (i.e. without '.nc')
+        file_format: str
+            format of the file (i.e '.nc')
+        """
+        _, filename = os.path.split(file_src)
+        filename_base, file_format = os.path.splitext(filename)
+        return filename_base, file_format