Source code for satpy.readers.hdfeos_base

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2019 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/>.
"""Base HDF-EOS reader."""

from __future__ import annotations

import logging
import re
from ast import literal_eval
from contextlib import suppress
from datetime import datetime

import numpy as np
import xarray as xr
from pyhdf.error import HDF4Error
from pyhdf.SD import SD

from satpy import DataID
from satpy.readers.file_handlers import BaseFileHandler
from satpy.utils import normalize_low_res_chunks

logger = logging.getLogger(__name__)


[docs] def interpolate(clons, clats, csatz, src_resolution, dst_resolution): """Interpolate two parallel datasets jointly.""" if csatz is None: return _interpolate_no_angles(clons, clats, src_resolution, dst_resolution) return _interpolate_with_angles(clons, clats, csatz, src_resolution, dst_resolution)
[docs] def _interpolate_with_angles(clons, clats, csatz, src_resolution, dst_resolution): from geotiepoints.modisinterpolator import modis_1km_to_250m, modis_1km_to_500m, modis_5km_to_1km # (src_res, dst_res, is satz not None) -> interp function interpolation_functions = { (5000, 1000): modis_5km_to_1km, (1000, 500): modis_1km_to_500m, (1000, 250): modis_1km_to_250m } return _find_and_run_interpolation(interpolation_functions, src_resolution, dst_resolution, (clons, clats, csatz))
[docs] def _interpolate_no_angles(clons, clats, src_resolution, dst_resolution): interpolation_functions = {} try: from geotiepoints.simple_modis_interpolator import modis_1km_to_250m as simple_1km_to_250m from geotiepoints.simple_modis_interpolator import modis_1km_to_500m as simple_1km_to_500m except ImportError: raise NotImplementedError( f"Interpolation from {src_resolution}m to {dst_resolution}m " "without satellite zenith angle information is not " "implemented. Try updating your version of " "python-geotiepoints.") else: interpolation_functions[(1000, 500)] = simple_1km_to_500m interpolation_functions[(1000, 250)] = simple_1km_to_250m return _find_and_run_interpolation(interpolation_functions, src_resolution, dst_resolution, (clons, clats))
[docs] def _find_and_run_interpolation(interpolation_functions, src_resolution, dst_resolution, args): try: interpolation_function = interpolation_functions[(src_resolution, dst_resolution)] except KeyError: error_message = "Interpolation from {}m to {}m not implemented".format( src_resolution, dst_resolution) raise NotImplementedError(error_message) logger.debug("Interpolating from {} to {}".format(src_resolution, dst_resolution)) return interpolation_function(*args)
[docs] class HDFEOSBaseFileReader(BaseFileHandler): """Base file handler for HDF EOS data for both L1b and L2 products.""" def __init__(self, filename, filename_info, filetype_info, **kwargs): """Initialize the base reader.""" BaseFileHandler.__init__(self, filename, filename_info, filetype_info) try: self.sd = SD(self.filename) except HDF4Error as err: error_message = "Could not load data from file {}: {}".format(self.filename, err) raise ValueError(error_message) self.metadata = self._load_all_metadata_attributes()
[docs] def _load_all_metadata_attributes(self): metadata = {} attrs = self.sd.attributes() for md_key in ("CoreMetadata.0", "StructMetadata.0", "ArchiveMetadata.0"): try: str_val = attrs[md_key] except KeyError: continue else: metadata.update(self.read_mda(str_val)) return metadata
[docs] @classmethod def read_mda(cls, attribute): """Read the EOS metadata.""" line_iterator = iter(attribute.split('\n')) return cls._read_mda(line_iterator)
[docs] @classmethod def _read_mda(cls, lines, element=None): current_dict = {} for line in lines: if not line: continue if line == 'END': return current_dict key, val = cls._split_line(line, lines) if key in ['GROUP', 'OBJECT']: current_dict[val] = cls._read_mda(lines, val) elif key in ['END_GROUP', 'END_OBJECT']: if val != element: raise SyntaxError("Non-matching end-tag") return current_dict elif key in ['CLASS', 'NUM_VAL']: pass else: current_dict[key] = val logger.warning("Malformed EOS metadata, missing an END.") return current_dict
[docs] @classmethod def _split_line(cls, line, lines): key, val = line.split('=') key = key.strip() val = val.strip() try: with suppress(ValueError): val = literal_eval(val) except SyntaxError: key, val = cls._split_line(line + next(lines), lines) return key, val
@property def metadata_platform_name(self): """Platform name from the internal file metadata.""" try: # Example: 'Terra' or 'Aqua' return self.metadata['INVENTORYMETADATA']['ASSOCIATEDPLATFORMINSTRUMENTSENSOR'][ 'ASSOCIATEDPLATFORMINSTRUMENTSENSORCONTAINER']['ASSOCIATEDPLATFORMSHORTNAME']['VALUE'] except KeyError: return self._platform_name_from_filename()
[docs] def _platform_name_from_filename(self): platform_indicator = self.filename_info["platform_indicator"] if platform_indicator in ("t", "O"): # t1.* or MOD* return "Terra" # a1.* or MYD* return "Aqua"
@property def start_time(self): """Get the start time of the dataset.""" try: date = (self.metadata['INVENTORYMETADATA']['RANGEDATETIME']['RANGEBEGINNINGDATE']['VALUE'] + ' ' + self.metadata['INVENTORYMETADATA']['RANGEDATETIME']['RANGEBEGINNINGTIME']['VALUE']) return datetime.strptime(date, '%Y-%m-%d %H:%M:%S.%f') except KeyError: return self._start_time_from_filename()
[docs] def _start_time_from_filename(self): return self.filename_info["start_time"]
@property def end_time(self): """Get the end time of the dataset.""" try: date = (self.metadata['INVENTORYMETADATA']['RANGEDATETIME']['RANGEENDINGDATE']['VALUE'] + ' ' + self.metadata['INVENTORYMETADATA']['RANGEDATETIME']['RANGEENDINGTIME']['VALUE']) return datetime.strptime(date, '%Y-%m-%d %H:%M:%S.%f') except KeyError: return self.start_time
[docs] def _read_dataset_in_file(self, dataset_name): if dataset_name not in self.sd.datasets(): error_message = "Dataset name {} not included in available datasets {}".format( dataset_name, self.sd.datasets() ) raise KeyError(error_message) dataset = self.sd.select(dataset_name) return dataset
[docs] def load_dataset(self, dataset_name, is_category=False): """Load the dataset from HDF EOS file.""" from satpy.readers.hdf4_utils import from_sds dataset = self._read_dataset_in_file(dataset_name) chunks = self._chunks_for_variable(dataset) dask_arr = from_sds(dataset, chunks=chunks) dims = ('y', 'x') if dask_arr.ndim == 2 else None data = xr.DataArray(dask_arr, dims=dims, attrs=dataset.attributes()) data = self._scale_and_mask_data_array(data, is_category=is_category) return data
[docs] def _chunks_for_variable(self, hdf_dataset): scan_length_250m = 40 var_shape = hdf_dataset.info()[2] res_multiplier = self._get_res_multiplier(var_shape) num_nonyx_dims = len(var_shape) - 2 return normalize_low_res_chunks( (1,) * num_nonyx_dims + ("auto", -1), var_shape, (1,) * num_nonyx_dims + (scan_length_250m, -1), (1,) * num_nonyx_dims + (res_multiplier, res_multiplier), np.float32, )
[docs] @staticmethod def _get_res_multiplier(var_shape): num_columns_to_multiplier = { 271: 20, # 5km 1354: 4, # 1km 2708: 2, # 500m 5416: 1, # 250m } for max_columns, res_multiplier in num_columns_to_multiplier.items(): if var_shape[-1] <= max_columns: return res_multiplier return 1
[docs] def _scale_and_mask_data_array(self, data, is_category=False): """Unscale byte data and mask invalid/fill values. MODIS requires unscaling the in-file bytes in an unexpected way:: data = (byte_value - add_offset) * scale_factor See the below L1B User's Guide Appendix C for more information: https://mcst.gsfc.nasa.gov/sites/default/files/file_attachments/M1054E_PUG_2017_0901_V6.2.2_Terra_V6.2.1_Aqua.pdf """ good_mask, new_fill = self._get_good_data_mask(data, is_category=is_category) scale_factor = data.attrs.pop('scale_factor', None) add_offset = data.attrs.pop('add_offset', None) # don't scale category products, even though scale_factor may equal 1 # we still need to convert integers to floats if scale_factor is not None and not is_category: if add_offset is not None and add_offset != 0: data = data - np.float32(add_offset) data = data * np.float32(scale_factor) if good_mask is not None: data = data.where(good_mask, new_fill) return data
[docs] def _get_good_data_mask(self, data_arr, is_category=False): try: fill_value = data_arr.attrs["_FillValue"] except KeyError: return None, None # preserve integer data types if possible if is_category and np.issubdtype(data_arr.dtype, np.integer): # no need to mask, the fill value is already what it needs to be return None, None new_fill = np.nan data_arr.attrs.pop('_FillValue', None) good_mask = data_arr != fill_value return good_mask, new_fill
[docs] def _add_satpy_metadata(self, data_id: DataID, data_arr: xr.DataArray): """Add metadata that is specific to Satpy.""" new_attrs = { 'platform_name': 'EOS-' + self.metadata_platform_name, 'sensor': 'modis', } res = data_id["resolution"] rps = self._resolution_to_rows_per_scan(res) new_attrs["rows_per_scan"] = rps data_arr.attrs.update(new_attrs)
[docs] def _resolution_to_rows_per_scan(self, resolution: int) -> int: known_rps = { 5000: 2, 1000: 10, 500: 20, 250: 40, } return known_rps.get(resolution, 10)
[docs] class HDFEOSGeoReader(HDFEOSBaseFileReader): """Handler for the geographical datasets.""" # list of geographical datasets handled by the georeader # mapping to the default variable name if not specified in YAML DATASET_NAMES = { 'longitude': 'Longitude', 'latitude': 'Latitude', 'satellite_azimuth_angle': ('SensorAzimuth', 'Sensor_Azimuth'), 'satellite_zenith_angle': ('SensorZenith', 'Sensor_Zenith'), 'solar_azimuth_angle': ('SolarAzimuth', 'SolarAzimuth'), 'solar_zenith_angle': ('SolarZenith', 'Solar_Zenith'), } def __init__(self, filename, filename_info, filetype_info, **kwargs): """Initialize the geographical reader.""" HDFEOSBaseFileReader.__init__(self, filename, filename_info, filetype_info, **kwargs) self.cache = {}
[docs] @staticmethod def is_geo_loadable_dataset(dataset_name: str) -> bool: """Determine if this dataset should be loaded as a Geo dataset.""" return dataset_name in HDFEOSGeoReader.DATASET_NAMES
[docs] @staticmethod def read_geo_resolution(metadata): """Parse metadata to find the geolocation resolution.""" # level 1 files try: return HDFEOSGeoReader._geo_resolution_for_l1b(metadata) except KeyError: try: return HDFEOSGeoReader._geo_resolution_for_l2_l1b(metadata) except (AttributeError, KeyError): raise RuntimeError("Could not determine resolution from file metadata")
[docs] @staticmethod def _geo_resolution_for_l1b(metadata): ds = metadata['INVENTORYMETADATA']['COLLECTIONDESCRIPTIONCLASS']['SHORTNAME']['VALUE'] if ds.endswith('D03') or ds.endswith('HKM') or ds.endswith('QKM'): return 1000 # 1km files have 5km geolocation usually return 5000
[docs] @staticmethod def _geo_resolution_for_l2_l1b(metadata): # data files probably have this level 2 files # this does not work for L1B 1KM data files because they are listed # as 1KM data but the geo data inside is at 5km latitude_dim = metadata['SwathStructure']['SWATH_1']['DimensionMap']['DimensionMap_2']['GeoDimension'] resolution_regex = re.compile(r'(?P<resolution>\d+)(km|KM)') resolution_match = resolution_regex.search(latitude_dim) return int(resolution_match.group('resolution')) * 1000
@property def geo_resolution(self): """Resolution of the geographical data retrieved in the metadata.""" return self.read_geo_resolution(self.metadata)
[docs] def _load_ds_by_name(self, ds_name): """Attempt loading using multiple common names.""" var_names = self.DATASET_NAMES[ds_name] if isinstance(var_names, (list, tuple)): try: return self.load_dataset(var_names[0]) except KeyError: return self.load_dataset(var_names[1]) return self.load_dataset(var_names)
[docs] def get_interpolated_dataset(self, name1, name2, resolution, offset=0): """Load and interpolate datasets.""" try: result1 = self.cache[(name1, resolution)] result2 = self.cache[(name2, resolution)] except KeyError: result1 = self._load_ds_by_name(name1) result2 = self._load_ds_by_name(name2) - offset try: sensor_zenith = self._load_ds_by_name('satellite_zenith_angle') except KeyError: # no sensor zenith angle, do "simple" interpolation sensor_zenith = None result1, result2 = interpolate( result1, result2, sensor_zenith, self.geo_resolution, resolution ) self.cache[(name1, resolution)] = result1 self.cache[(name2, resolution)] = result2 + offset
[docs] def get_dataset(self, dataset_id: DataID, dataset_info: dict) -> xr.DataArray: """Get the geolocation dataset.""" # Name of the dataset as it appears in the HDF EOS file in_file_dataset_name = dataset_info.get('file_key') # Name of the dataset in the YAML file dataset_name = dataset_id['name'] # Resolution asked resolution = dataset_id['resolution'] if in_file_dataset_name is not None: # if the YAML was configured with a specific name use that data = self.load_dataset(in_file_dataset_name) else: # otherwise use the default name for this variable data = self._load_ds_by_name(dataset_name) if resolution != self.geo_resolution: if in_file_dataset_name is not None: # they specified a custom variable name but # we don't know how to interpolate this yet raise NotImplementedError( "Interpolation for variable '{}' is not " "configured".format(dataset_name)) # The data must be interpolated logger.debug("Loading %s", dataset_name) if dataset_name in ['longitude', 'latitude']: self.get_interpolated_dataset('longitude', 'latitude', resolution) elif dataset_name in ['satellite_azimuth_angle', 'satellite_zenith_angle']: # Sensor dataset names differs between L1b and L2 products self.get_interpolated_dataset('satellite_azimuth_angle', 'satellite_zenith_angle', resolution, offset=90) elif dataset_name in ['solar_azimuth_angle', 'solar_zenith_angle']: # Sensor dataset names differs between L1b and L2 products self.get_interpolated_dataset('solar_azimuth_angle', 'solar_zenith_angle', resolution, offset=90) data = self.cache[dataset_name, resolution] for key in ('standard_name', 'units'): if key in dataset_info: data.attrs[key] = dataset_info[key] self._add_satpy_metadata(dataset_id, data) return data