Source code for satpy.readers.modis_l1b

#!/usr/bin/env python
# -*- coding: utf-8 -*-
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"""Modis level 1b hdf-eos format reader.

Introduction
------------

The ``modis_l1b`` reader reads and calibrates Modis L1 image data in hdf-eos format. Files often have
a pattern similar to the following one:

.. parsed-literal::

    M[O/Y]D02[1/H/Q]KM.A[date].[time].[collection].[processing_time].hdf

Other patterns where "collection" and/or "proccessing_time" are missing might also work
(see the readers yaml file for details). Geolocation files (MOD03) are also supported.
The IMAPP direct broadcast naming format is also supported with names like:
``a1.12226.1846.1000m.hdf``.

Saturation Handling
-------------------

Band 2 of the MODIS sensor is available in 250m, 500m, and 1km resolutions.
The band data may include a special fill value to indicate when the detector
was saturated in the 250m version of the data. When the data is aggregated to
coarser resolutions this saturation fill value is converted to a
"can't aggregate" fill value. By default, Satpy will replace these fill values
with NaN to indicate they are invalid. This is typically undesired when
generating images for the data as they appear as "holes" in bright clouds.
To control this the keyword argument ``mask_saturated`` can be passed and set
to ``False`` to set these two fill values to the maximum valid value.

.. code-block:: python

    scene = satpy.Scene(filenames=filenames,
                        reader='modis_l1b',
                        reader_kwargs={'mask_saturated': False})
    scene.load(['2'])

Note that the saturation fill value can appear in other bands (ex. bands 7-19)
in addition to band 2. Also, the "can't aggregate" fill value is a generic
"catch all" for any problems encountered when aggregating high resolution bands
to lower resolutions. Filling this with the max valid value could replace
non-saturated invalid pixels with valid values.

Geolocation files
-----------------

For the 1km data (mod021km) geolocation files (mod03) are optional. If not given to the reader
1km geolocations will be interpolated from the 5km geolocation contained within the file.

For the 500m and 250m data geolocation files are needed.


References:
    - Modis gelocation description: http://www.icare.univ-lille1.fr/wiki/index.php/MODIS_geolocation
"""
import logging

import numpy as np
import xarray as xr

from satpy.readers.hdf4_utils import from_sds
from satpy.readers.hdfeos_base import HDFEOSBaseFileReader, HDFEOSGeoReader

logger = logging.getLogger(__name__)


[docs] class HDFEOSBandReader(HDFEOSBaseFileReader): """Handler for the regular band channels.""" res = {"1": 1000, "Q": 250, "H": 500} res_to_possible_variable_names = { 1000: ['EV_250_Aggr1km_RefSB', 'EV_500_Aggr1km_RefSB', 'EV_1KM_RefSB', 'EV_1KM_Emissive'], 500: ['EV_250_Aggr500_RefSB', 'EV_500_RefSB'], 250: ['EV_250_RefSB'], } def __init__(self, filename, filename_info, filetype_info, mask_saturated=True, **kwargs): """Init the file handler.""" super().__init__(filename, filename_info, filetype_info, **kwargs) self._mask_saturated = mask_saturated ds = self.metadata['INVENTORYMETADATA'][ 'COLLECTIONDESCRIPTIONCLASS']['SHORTNAME']['VALUE'] self.resolution = self.res[ds[-3]]
[docs] def get_dataset(self, key, info): """Read data from file and return the corresponding projectables.""" if self.resolution != key['resolution']: return var_name, band_index = self._get_band_variable_name_and_index(key["name"]) subdata = self.sd.select(var_name) var_attrs = subdata.attributes() uncertainty = self.sd.select(var_name + "_Uncert_Indexes") chunks = self._chunks_for_variable(subdata) array = xr.DataArray(from_sds(subdata, chunks=chunks)[band_index, :, :], dims=['y', 'x']).astype(np.float32) valid_range = var_attrs['valid_range'] valid_min = np.float32(valid_range[0]) valid_max = np.float32(valid_range[1]) if not self._mask_saturated: array = self._fill_saturated(array, valid_max) array = self._mask_invalid(array, valid_min, valid_max) array = self._mask_uncertain_pixels(array, uncertainty, band_index) projectable = self._calibrate_data(key, info, array, var_attrs, band_index) # if ((platform_name == 'Aqua' and key['name'] in ["6", "27", "36"]) or # (platform_name == 'Terra' and key['name'] in ["29"])): # height, width = projectable.shape # row_indices = projectable.mask.sum(1) == width # if row_indices.sum() != height: # projectable.mask[row_indices, :] = True # Get the orbit number # if not satscene.orbit: # mda = self.data.attributes()["CoreMetadata.0"] # orbit_idx = mda.index("ORBITNUMBER") # satscene.orbit = mda[orbit_idx + 111:orbit_idx + 116] # Trimming out dead sensor lines (detectors) on terra: # (in addition channel 27, 30, 34, 35, and 36 are nosiy) # if satscene.satname == "terra": # for band in ["29"]: # if not satscene[band].is_loaded() or satscene[band].data.mask.all(): # continue # width = satscene[band].data.shape[1] # height = satscene[band].data.shape[0] # indices = satscene[band].data.mask.sum(1) < width # if indices.sum() == height: # continue # satscene[band] = satscene[band].data[indices, :] # satscene[band].area = geometry.SwathDefinition( # lons=satscene[band].area.lons[indices, :], # lats=satscene[band].area.lats[indices, :]) self._add_satpy_metadata(key, projectable) return projectable
[docs] def _get_band_variable_name_and_index(self, band_name): variable_names = self.res_to_possible_variable_names[self.resolution] for variable_name in variable_names: subdata = self.sd.select(variable_name) var_attrs = subdata.attributes() try: band_index = self._get_band_index(var_attrs, band_name) except ValueError: # can't find band in list of bands continue return variable_name, band_index
[docs] def _get_band_index(self, var_attrs, band_name): """Get the relative indices of the desired channel.""" band_names = var_attrs["band_names"].split(",") index = band_names.index(band_name) return index
[docs] def _fill_saturated(self, array, valid_max): """Replace saturation-related values with max reflectance. If the file handler was created with ``mask_saturated`` set to ``True`` then all invalid/fill values are set to NaN. If ``False`` then the fill values 65528 and 65533 are set to the maximum valid value. These values correspond to "can't aggregate" and "saturation". Fill values: * 65535 Fill Value (includes reflective band data at night mode and completely missing L1A scans) * 65534 L1A DN is missing within a scan * 65533 Detector is saturated * 65532 Cannot compute zero point DN, e.g., SV is saturated * 65531 Detector is dead (see comments below) * 65530 RSB dn** below the minimum of the scaling range * 65529 TEB radiance or RSB dn exceeds the maximum of the scaling range * 65528 Aggregation algorithm failure * 65527 Rotation of Earth view Sector from nominal science collection position * 65526 Calibration coefficient b1 could not be computed * 65525 Subframe is dead * 65524 Both sides of the PCLW electronics on simultaneously * 65501 - 65523 (reserved for future use) * 65500 NAD closed upper limit """ return array.where((array != 65533) & (array != 65528), valid_max)
[docs] def _mask_invalid(self, array, valid_min, valid_max): """Replace fill values with NaN.""" return array.where((array >= valid_min) & (array <= valid_max))
[docs] def _mask_uncertain_pixels(self, array, uncertainty, band_index): if not self._mask_saturated: return array uncertainty_chunks = self._chunks_for_variable(uncertainty) band_uncertainty = from_sds(uncertainty, chunks=uncertainty_chunks)[band_index, :, :] array = array.where(band_uncertainty < 15) return array
[docs] def _calibrate_data(self, key, info, array, var_attrs, index): if key['calibration'] == 'brightness_temperature': projectable = calibrate_bt(array, var_attrs, index, key['name']) info.setdefault('units', 'K') info.setdefault('standard_name', 'toa_brightness_temperature') elif key['calibration'] == 'reflectance': projectable = calibrate_refl(array, var_attrs, index) info.setdefault('units', '%') info.setdefault('standard_name', 'toa_bidirectional_reflectance') elif key['calibration'] == 'radiance': projectable = calibrate_radiance(array, var_attrs, index) info.setdefault('units', var_attrs.get('radiance_units')) info.setdefault('standard_name', 'toa_outgoing_radiance_per_unit_wavelength') elif key['calibration'] == 'counts': projectable = calibrate_counts(array, var_attrs, index) info.setdefault('units', 'counts') info.setdefault('standard_name', 'counts') # made up else: raise ValueError("Unknown calibration for " "key: {}".format(key)) projectable.attrs = info return projectable
[docs] class MixedHDFEOSReader(HDFEOSGeoReader, HDFEOSBandReader): """A file handler for the files that have both regular bands and geographical information in them.""" def __init__(self, filename, filename_info, filetype_info, **kwargs): """Init the file handler.""" HDFEOSGeoReader.__init__(self, filename, filename_info, filetype_info, **kwargs) HDFEOSBandReader.__init__(self, filename, filename_info, filetype_info, **kwargs)
[docs] def get_dataset(self, key, info): """Get the dataset.""" if key['name'] in HDFEOSGeoReader.DATASET_NAMES: return HDFEOSGeoReader.get_dataset(self, key, info) return HDFEOSBandReader.get_dataset(self, key, info)
[docs] def calibrate_counts(array, attributes, index): """Calibration for counts channels.""" offset = np.float32(attributes["corrected_counts_offsets"][index]) scale = np.float32(attributes["corrected_counts_scales"][index]) array = (array - offset) * scale return array
[docs] def calibrate_radiance(array, attributes, index): """Calibration for radiance channels.""" offset = np.float32(attributes["radiance_offsets"][index]) scale = np.float32(attributes["radiance_scales"][index]) array = (array - offset) * scale return array
[docs] def calibrate_refl(array, attributes, index): """Calibration for reflective channels.""" offset = np.float32(attributes["reflectance_offsets"][index]) scale = np.float32(attributes["reflectance_scales"][index]) # convert to reflectance and convert from 1 to % array = (array - offset) * scale * 100 return array
[docs] def calibrate_bt(array, attributes, index, band_name): """Calibration for the emissive channels.""" offset = np.float32(attributes["radiance_offsets"][index]) scale = np.float32(attributes["radiance_scales"][index]) array = (array - offset) * scale # Planck constant (Joule second) h__ = np.float32(6.6260755e-34) # Speed of light in vacuum (meters per second) c__ = np.float32(2.9979246e+8) # Boltzmann constant (Joules per Kelvin) k__ = np.float32(1.380658e-23) # Derived constants c_1 = 2 * h__ * c__ * c__ c_2 = (h__ * c__) / k__ # Effective central wavenumber (inverse centimeters) cwn = np.array([ 2.641775E+3, 2.505277E+3, 2.518028E+3, 2.465428E+3, 2.235815E+3, 2.200346E+3, 1.477967E+3, 1.362737E+3, 1.173190E+3, 1.027715E+3, 9.080884E+2, 8.315399E+2, 7.483394E+2, 7.308963E+2, 7.188681E+2, 7.045367E+2], dtype=np.float32) # Temperature correction slope (no units) tcs = np.array([ 9.993411E-1, 9.998646E-1, 9.998584E-1, 9.998682E-1, 9.998819E-1, 9.998845E-1, 9.994877E-1, 9.994918E-1, 9.995495E-1, 9.997398E-1, 9.995608E-1, 9.997256E-1, 9.999160E-1, 9.999167E-1, 9.999191E-1, 9.999281E-1], dtype=np.float32) # Temperature correction intercept (Kelvin) tci = np.array([ 4.770532E-1, 9.262664E-2, 9.757996E-2, 8.929242E-2, 7.310901E-2, 7.060415E-2, 2.204921E-1, 2.046087E-1, 1.599191E-1, 8.253401E-2, 1.302699E-1, 7.181833E-2, 1.972608E-2, 1.913568E-2, 1.817817E-2, 1.583042E-2], dtype=np.float32) # Transfer wavenumber [cm^(-1)] to wavelength [m] cwn = 1. / (cwn * 100) # Some versions of the modis files do not contain all the bands. emmissive_channels = ["20", "21", "22", "23", "24", "25", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36"] global_index = emmissive_channels.index(band_name) cwn = cwn[global_index] tcs = tcs[global_index] tci = tci[global_index] array = c_2 / (cwn * np.log(c_1 / (1000000 * array * cwn ** 5) + 1)) array = (array - tci) / tcs return array