#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2021 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 SEADAS L2 products.
This reader currently only supports MODIS and VIIRS Chlorophyll A from SEADAS.
The reader includes an additional keyword argument ``apply_quality_flags``
which can be used to mask out low-quality pixels based on quality flags
contained in the file (``l2_flags``). This option defaults to ``False``, but
when set to ``True`` the "CHLWARN" pixels of the ``l2_flags`` variable
are masked out. These pixels represent data where the chlorophyll algorithm
warned about the quality of the result.
"""
from datetime import datetime
from .hdf4_utils import HDF4FileHandler
from .netcdf_utils import NetCDF4FileHandler
[docs]
class _SEADASL2Base:
"""Simple handler of SEADAS L2 files."""
def __init__(self, filename, filename_info, filetype_info, apply_quality_flags=False):
"""Initialize file handler and determine if data quality flags should be applied."""
super().__init__(filename, filename_info, filetype_info)
self.apply_quality_flags = apply_quality_flags and self.l2_flags_var_name in self
[docs]
def _rows_per_scan(self):
if "modis" in self.sensor_names:
return 10
if "viirs" in self.sensor_names:
return 16
raise ValueError(f"Don't know how to read data for sensors: {self.sensor_names}")
@property
def start_time(self):
"""Get the starting observation time of this file's data."""
start_time = self[self.start_time_attr_name]
return datetime.strptime(start_time[:-3], self.time_format)
@property
def end_time(self):
"""Get the ending observation time of this file's data."""
end_time = self[self.end_time_attr_name]
return datetime.strptime(end_time[:-3], self.time_format)
@property
def sensor_names(self):
"""Get sensor for the current file's data."""
# Example: MODISA or VIIRSN or VIIRSJ1
sensor_name = self[self.sensor_attr_name].lower()
if sensor_name.startswith("modis"):
return {"modis"}
return {"viirs"}
[docs]
def get_dataset(self, data_id, dataset_info):
"""Get DataArray for the specified DataID."""
file_key, data = self._get_file_key_and_variable(data_id, dataset_info)
data = self._filter_by_valid_min_max(data)
data = self._rename_2d_dims_if_necessary(data)
data = self._mask_based_on_l2_flags(data)
for attr_name in ("standard_name", "long_name", "units"):
val = data.attrs[attr_name]
if val[-1] == "\x00":
data.attrs[attr_name] = data.attrs[attr_name][:-1]
data = self._add_satpy_metadata(data)
return data
[docs]
def _get_file_key_and_variable(self, data_id, dataset_info):
file_keys = dataset_info.get("file_key", data_id["name"])
if not isinstance(file_keys, list):
file_keys = [file_keys]
for file_key in file_keys:
try:
data = self[file_key]
return file_key, data
except KeyError:
continue
raise KeyError(f"Unable to find any of the possible keys for {data_id}: {file_keys}")
[docs]
def _rename_2d_dims_if_necessary(self, data_arr):
if data_arr.ndim != 2 or data_arr.dims == ("y", "x"):
return data_arr
return data_arr.rename(dict(zip(data_arr.dims, ("y", "x"))))
[docs]
def _filter_by_valid_min_max(self, data_arr):
valid_range = self._valid_min_max(data_arr)
data_arr = data_arr.where(valid_range[0] <= data_arr)
data_arr = data_arr.where(data_arr <= valid_range[1])
return data_arr
[docs]
def _valid_min_max(self, data_arr):
try:
return data_arr.attrs["valid_range"]
except KeyError:
return data_arr.attrs["valid_min"], data_arr.attrs["valid_max"]
[docs]
def _mask_based_on_l2_flags(self, data_arr):
standard_name = data_arr.attrs.get("standard_name", "")
if self.apply_quality_flags and not ("lon" in standard_name or "lat" in standard_name):
l2_flags = self[self.l2_flags_var_name]
l2_flags = self._rename_2d_dims_if_necessary(l2_flags)
mask = (l2_flags & 0b00000000010000000000000000000000) != 0
data_arr = data_arr.where(~mask)
return data_arr
[docs]
class SEADASL2NetCDFFileHandler(_SEADASL2Base, NetCDF4FileHandler):
"""Simple handler of SEADAS L2 NetCDF4 files."""
start_time_attr_name = "/attr/time_coverage_start"
end_time_attr_name = "/attr/time_coverage_end"
time_format = "%Y-%m-%dT%H:%M:%S.%f"
platform_attr_name = "/attr/platform"
sensor_attr_name = "/attr/instrument"
l2_flags_var_name = "geophysical_data/l2_flags"
[docs]
class SEADASL2HDFFileHandler(_SEADASL2Base, HDF4FileHandler):
"""Simple handler of SEADAS L2 HDF4 files."""
start_time_attr_name = "/attr/Start Time"
end_time_attr_name = "/attr/End Time"
time_format = "%Y%j%H%M%S"
platform_attr_name = "/attr/Mission"
sensor_attr_name = "/attr/Sensor Name"
l2_flags_var_name = "l2_flags"