-
Notifications
You must be signed in to change notification settings - Fork 292
Implementing a reader for satpy
David Hoese edited this page Apr 15, 2019
·
6 revisions
DEPRECATED: See https://satpy.readthedocs.io/en/latest/dev_guide/custom_reader.html for the newest version.
In order to add a reader to satpy, you will need to implement two files:
- a YAML file for describing the files to read and the datasets that are available
- a python file implementing the actual reading of the datasets and metadata
For this tutorial, we will use the already implemented NWCSAF reader as an example
The yaml file is composed of three sections:
- the
readersection, that gives a general parameters of the reader - the
file_typessection, which gives the patterns of the files this reader can handle - the
datasetssection, describing the datasets available from this reader
reader:
description: NetCDF4 reader for the NWCSAF MSG 2016 format
name: nc_nwcsaf_msg
sensors: [seviri]
default_channels: []
reader: !!python/name:satpy.readers.yaml_reader.FileYAMLReaderEach file type needs to provide:
-
file_reader, the class that will handle the files for this reader, that you will implement in the corresponding python file (see next section) -
file_patterns, the patterns to match to find files this reader can handle. The syntax to use is basically the same asformatwith the addition of time. See the trollsift package info for more details.
file_types:
nc_nwcsaf_cma:
file_reader: !!python/name:satpy.readers.nc_nwcsaf.NcNWCSAF
file_patterns: ['S_NWC_CMA_{platform_id}_{region_id}_{start_time:%Y%m%dT%H%M%S}Z.nc']
nc_nwcsaf_ct:
file_reader: !!python/name:satpy.readers.nc_nwcsaf.NcNWCSAF
file_patterns: ['S_NWC_CT_{platform_id}_{region_id}_{start_time:%Y%m%dT%H%M%S}Z.nc']
The datasets section describes each dataset available in the files. The parameters provided are made available to the methods of the implementing class.
Parameters you can define for example are:
- name
- sensor
- resolution
- wavelength
- polarization
- file_type
datasets:
# ---- CMA products ------------
cma:
name: cma
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_cma
cma_pal:
name: cma_pal
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_cma
cma_cloudsnow:
name: cma_cloudsnow
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_cma
cma_cloudsnow_pal:
name: cma_cloudsnow_pal
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_cma
cma_dust:
name: cma_dust
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_cma
cma_dust_pal:
name: cma_dust_pal
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_cma
cma_volcanic:
name: cma_volcanic
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_cma
cma_volcanic_pal:
name: cma_volcanic_pal
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_cma
# ---- CT products ------------
ct:
name: ct
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_ct
ct_pal:
name: ct_pal
sensor: seviri
resolution: 3000
file_type: nc_nwcsaf_ctThe methods that have to be implemented are:
get_dataset-
get_area_deffor datasets that can have navigation defined as a proj.4 string and an area extent The attributes the class must have: start_timeend_time
import logging
from datetime import datetime
import os
import numpy as np
import xarray as xr
from pyresample.utils import get_area_def
from satpy.readers.file_handlers import BaseFileHandler
from satpy.readers.utils import unzip_file
from satpy import CHUNK_SIZE
logger = logging.getLogger(__name__)
SENSOR = {'NOAA-19': 'avhrr/3',
'NOAA-18': 'avhrr/3',
'NOAA-15': 'avhrr/3',
'Metop-A': 'avhrr/3',
'Metop-B': 'avhrr/3',
'Metop-C': 'avhrr/3',
'EOS-Aqua': 'modis',
'EOS-Terra': 'modis',
'Suomi-NPP': 'viirs',
'NOAA-20': 'viirs',
'JPSS-1': 'viirs', }
PLATFORM_NAMES = {'MSG1': 'Meteosat-8',
'MSG2': 'Meteosat-9',
'MSG3': 'Meteosat-10',
'MSG4': 'Meteosat-11', }
class NcNWCSAF(BaseFileHandler):
"""NWCSAF PPS&MSG NetCDF reader."""
def __init__(self, filename, filename_info, filetype_info):
"""Init method."""
super(NcNWCSAF, self).__init__(filename, filename_info,
filetype_info)
self._unzipped = unzip_file(filename)
if self._unzipped:
filename = self._unzipped
self.cache = {}
self.nc = xr.open_dataset(filename,
decode_cf=True,
mask_and_scale=False,
engine='h5netcdf',
chunks=CHUNK_SIZE)
self.nc = self.nc.rename({'nx': 'x', 'ny': 'y'})
self.pps = False
try:
# MSG:
sat_id = self.nc.attrs['satellite_identifier']
try:
self.platform_name = PLATFORM_NAMES[sat_id]
except KeyError:
self.platform_name = PLATFORM_NAMES[sat_id.astype(str)]
except KeyError:
# PPS:
self.platform_name = self.nc.attrs['platform']
self.pps = True
self.sensor = SENSOR.get(self.platform_name, 'seviri')
def remove_timedim(self, var):
"""Remove time dimension from dataset"""
if self.pps and var.dims[0] == 'time':
data = var[0, :, :]
data.attrs = var.attrs
var = data
return var
def get_dataset(self, dsid, info):
"""Load a dataset."""
dsid_name = dsid.name
if dsid_name in self.cache:
logger.debug('Get the data set from cache: %s.', dsid_name)
return self.cache[dsid_name]
if dsid_name in ['lon', 'lat'] and dsid_name not in self.nc.keys():
dsid_name = dsid_name + '_reduced'
logger.debug('Reading %s.', dsid_name)
variable = self.nc[dsid_name]
variable = self.remove_timedim(variable)
variable = self.scale_dataset(dsid, variable, info)
if dsid_name.endswith('_reduced'):
# Get full resolution lon,lat from the reduced (tie points) grid
self.upsample_geolocation(dsid, info)
return self.cache[dsid.name]
return variable
def scale_dataset(self, dsid, variable, info):
"""Scale the data set, applying the attributes from the netCDF file"""
variable = remove_empties(variable)
scale = variable.attrs.get('scale_factor', np.array(1))
offset = variable.attrs.get('add_offset', np.array(0))
if np.issubdtype((scale + offset).dtype, np.floating):
if '_FillValue' in variable.attrs:
variable = variable.where(
variable != variable.attrs['_FillValue'])
variable.attrs['_FillValue'] = np.nan
if 'valid_range' in variable.attrs:
variable = variable.where(
variable <= variable.attrs['valid_range'][1])
variable = variable.where(
variable >= variable.attrs['valid_range'][0])
if 'valid_max' in variable.attrs:
variable = variable.where(
variable <= variable.attrs['valid_max'])
if 'valid_min' in variable.attrs:
variable = variable.where(
variable >= variable.attrs['valid_min'])
attrs = variable.attrs
variable = variable * scale + offset
variable.attrs = attrs
variable.attrs.update({'platform_name': self.platform_name,
'sensor': self.sensor})
variable.attrs.setdefault('units', '1')
ancillary_names = variable.attrs.get('ancillary_variables', '')
try:
variable.attrs['ancillary_variables'] = ancillary_names.split()
except AttributeError:
pass
if 'standard_name' in info:
variable.attrs.setdefault('standard_name', info['standard_name'])
if self.pps and dsid.name == 'ctth_alti':
# pps valid range and palette don't match
variable.attrs['valid_range'] = (0., 9000.)
if self.pps and dsid.name == 'ctth_alti_pal':
# pps palette has the nodata color (black) first
variable = variable[1:, :]
return variable
def upsample_geolocation(self, dsid, info):
"""Upsample the geolocation (lon,lat) from the tiepoint grid"""
from geotiepoints import SatelliteInterpolator
# Read the fields needed:
col_indices = self.nc['nx_reduced'].values
row_indices = self.nc['ny_reduced'].values
lat_reduced = self.scale_dataset(dsid, self.nc['lat_reduced'], info)
lon_reduced = self.scale_dataset(dsid, self.nc['lon_reduced'], info)
shape = (self.nc['y'].shape[0], self.nc['x'].shape[0])
cols_full = np.arange(shape[1])
rows_full = np.arange(shape[0])
satint = SatelliteInterpolator((lon_reduced.values, lat_reduced.values),
(row_indices,
col_indices),
(rows_full, cols_full))
lons, lats = satint.interpolate()
self.cache['lon'] = xr.DataArray(lons, attrs=lon_reduced.attrs, dims=['y', 'x'])
self.cache['lat'] = xr.DataArray(lats, attrs=lat_reduced.attrs, dims=['y', 'x'])
return
def get_area_def(self, dsid):
"""Get the area definition of the datasets in the file.
Only applicable for MSG products!
"""
if self.pps:
# PPS:
raise NotImplementedError
if dsid.name.endswith('_pal'):
raise NotImplementedError
try:
proj_str = self.nc.attrs['gdal_projection'] + ' +units=km'
except TypeError:
proj_str = self.nc.attrs['gdal_projection'].decode() + ' +units=km'
nlines, ncols = self.nc[dsid.name].shape
area_extent = (float(self.nc.attrs['gdal_xgeo_up_left']) / 1000,
float(self.nc.attrs['gdal_ygeo_low_right']) / 1000,
float(self.nc.attrs['gdal_xgeo_low_right']) / 1000,
float(self.nc.attrs['gdal_ygeo_up_left']) / 1000)
area = get_area_def('some_area_name',
"On-the-fly area",
'geosmsg',
proj_str,
ncols,
nlines,
area_extent)
return area
def __del__(self):
if self._unzipped:
try:
os.remove(self._unzipped)
except (IOError, OSError):
pass
@property
def start_time(self):
"""Return the start time of the object."""
try:
# MSG:
try:
return datetime.strptime(self.nc.attrs['time_coverage_start'],
'%Y-%m-%dT%H:%M:%SZ')
except TypeError:
return datetime.strptime(self.nc.attrs['time_coverage_start'].astype(str),
'%Y-%m-%dT%H:%M:%SZ')
except ValueError:
# PPS:
return datetime.strptime(self.nc.attrs['time_coverage_start'],
'%Y%m%dT%H%M%S%fZ')
@property
def end_time(self):
"""Return the end time of the object."""
try:
# MSG:
try:
return datetime.strptime(self.nc.attrs['time_coverage_end'],
'%Y-%m-%dT%H:%M:%SZ')
except TypeError:
return datetime.strptime(self.nc.attrs['time_coverage_end'].astype(str),
'%Y-%m-%dT%H:%M:%SZ')
except ValueError:
# PPS:
return datetime.strptime(self.nc.attrs['time_coverage_end'],
'%Y%m%dT%H%M%S%fZ')
def remove_empties(variable):
"""Remove empty objects from the *variable*'s attrs."""
import h5py
for key, val in variable.attrs.items():
if isinstance(val, h5py._hl.base.Empty):
variable.attrs.pop(key)
return variable