Rayleigh._do_interp() - Code Metrics - Inspection of "Fix Rayleigh corrector to work with dask" - pytroll/pyspectral - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — develop (#33)

by Adam

created 2018-04-17 08:17 UTC

Rayleigh._do_interp() A

↳ Parent: Rayleigh.get_reflectance()

Complexity

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Importance

Changes	5
Bugs	0	Features	0

Metric	Value
cc	1
c	5
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dl	0
loc	6
rs	9.4285

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Copyright (c) 2016-2018 Pytroll

# Author(s):

#   Adam.Dybbroe <[email protected]>
#   Martin Raspaud <[email protected]>

# This program 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.

# This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.

"""Atmospheric correction of shortwave imager bands in the wavelength range 400
to 800 nm

"""

import os
import time
import logging
from six import integer_types

import h5py
import numpy as np

try:
    from dask.array import (where, zeros, clip, rad2deg, deg2rad, cos, arccos,
                            atleast_2d, Array, map_blocks, from_array)
    HAVE_DASK = True
    try:
        # use serializable h5py wrapper to make sure files are closed properly
        import h5pickle as h5py
    except ImportError:
        pass
except ImportError:
    from numpy import where, zeros, clip, rad2deg, deg2rad, cos, arccos, atleast_2d
    map_blocks = None
    from_array = None
    Array = None
    HAVE_DASK = False

from geotiepoints.multilinear import MultilinearInterpolator
from pyspectral.rsr_reader import RelativeSpectralResponse
from pyspectral.utils import (INSTRUMENTS, RAYLEIGH_LUT_DIRS,
                              AEROSOL_TYPES, ATMOSPHERES,
                              BANDNAMES,
                              download_luts, get_central_wave,
                              get_bandname_from_wavelength)

LOG = logging.getLogger(__name__)


class BandFrequencyOutOfRange(ValueError):

    """Exception when the band frequency is out of the visible range"""

    pass


class Rayleigh(object):

    """Container for the atmospheric correction of satellite imager bands.

    This class removes background contributions of Rayleigh scattering of
    molecules and Mie scattering and absorption by aerosols.

    """

    def __init__(self, platform_name, sensor, **kwargs):
        """Initialize class and determine LUT to use."""
        self.platform_name = platform_name
        self.sensor = sensor
        self.coeff_filename = None

        atm_type = kwargs.get('atmosphere', 'us-standard')
        if atm_type not in ATMOSPHERES:
            raise AttributeError('Atmosphere type not supported! ' +
                                 'Need to be one of {}'.format(str(ATMOSPHERES)))

        aerosol_type = kwargs.get('aerosol_type', 'marine_clean_aerosol')

        if aerosol_type not in AEROSOL_TYPES:
            raise AttributeError('Aerosol type not supported! ' +
                                 'Need to be one of {0}'.format(str(AEROSOL_TYPES)))

        rayleigh_dir = RAYLEIGH_LUT_DIRS[aerosol_type]

        if atm_type not in ATMOSPHERES.keys():
            LOG.error("Atmosphere type %s not supported", atm_type)

        LOG.info("Atmosphere chosen: %s", atm_type)

        # Try fix instrument naming
        instr = INSTRUMENTS.get(platform_name, sensor)
        if instr != sensor:
            sensor = instr
            LOG.warning("Inconsistent sensor/satellite input - " +
                        "sensor set to %s", sensor)

        self.sensor = sensor.replace('/', '')

        ext = atm_type.replace(' ', '_')
        lutname = "rayleigh_lut_{0}.h5".format(ext)
        self.reflectance_lut_filename = os.path.join(rayleigh_dir, lutname)
        if not os.path.exists(self.reflectance_lut_filename):
            LOG.warning(
                "No lut file %s on disk", self.reflectance_lut_filename)
            LOG.info("Will download from internet...")
            download_luts(aerosol_type=aerosol_type)

        if (not os.path.exists(self.reflectance_lut_filename) or
                not os.path.isfile(self.reflectance_lut_filename)):
            raise IOError('pyspectral file for Rayleigh scattering correction ' +
                          'does not exist! Filename = ' +
                          str(self.reflectance_lut_filename))

        LOG.debug('LUT filename: %s', str(self.reflectance_lut_filename))
        self._rayl = None
        self._wvl_coord = None
        self._azid_coord = None
        self._satz_sec_coord = None
        self._sunz_sec_coord = None

    def get_effective_wavelength(self, bandname):
        """Get the effective wavelength with Rayleigh scattering in mind"""
        try:
            rsr = RelativeSpectralResponse(self.platform_name, self.sensor)
        except IOError:
            LOG.exception(
                "No spectral responses for this platform and sensor: %s %s", self.platform_name, self.sensor)
            if isinstance(bandname, (float, integer_types)):
                LOG.warning(
                    "Effective wavelength is set to the requested band wavelength = %f", bandname)
                return bandname
            raise

        if isinstance(bandname, str):
            bandname = BANDNAMES.get(self.sensor, BANDNAMES['generic']).get(bandname, bandname)
        elif isinstance(bandname, (float, integer_types)):
            if not(0.4 < bandname < 0.8):
                raise BandFrequencyOutOfRange(
                    'Requested band frequency should be between 0.4 and 0.8 microns!')
            bandname = get_bandname_from_wavelength(self.sensor, bandname, rsr.rsr)

        wvl, resp = rsr.rsr[bandname][
            'det-1']['wavelength'], rsr.rsr[bandname]['det-1']['response']

        cwvl = get_central_wave(wvl, resp, weight=1. / wvl**4)
        LOG.debug("Band name: %s  Effective wavelength: %f", bandname, cwvl)

        return cwvl

    def get_reflectance_lut(self):
        """Read the LUT with reflectances as a function of wavelength, satellite zenith
        secant, azimuth difference angle, and sun zenith secant

        """
        if self._rayl is None:
            lut_vars = get_reflectance_lut(self.reflectance_lut_filename)
            self._rayl = lut_vars[0]
            self._wvl_coord = lut_vars[1]
            self._azid_coord = lut_vars[2]
            self._satz_sec_coord = lut_vars[3]
            self._sunz_sec_coord = lut_vars[4]
        return self._rayl, self._wvl_coord, self._azid_coord,\
            self._satz_sec_coord, self._sunz_sec_coord

    def get_reflectance(self, sun_zenith, sat_zenith, azidiff, bandname,
                        redband=None):
        """Get the reflectance from the three sun-sat angles."""
        # Get wavelength in nm for band:
        wvl = self.get_effective_wavelength(bandname) * 1000.0
        rayl, wvl_coord, azid_coord, satz_sec_coord, sunz_sec_coord = \
            self.get_reflectance_lut()

        # force dask arrays
        compute = False
        if HAVE_DASK and not isinstance(sun_zenith, Array):
            compute = True
            sun_zenith = from_array(sun_zenith, chunks=sun_zenith.shape)
            sat_zenith = from_array(sat_zenith, chunks=sat_zenith.shape)
            azidiff = from_array(azidiff, chunks=azidiff.shape)
            if redband is not None:
                redband = from_array(redband, chunks=redband.shape)

        clip_angle = rad2deg(arccos(1. / sunz_sec_coord.max()))
        sun_zenith = clip(sun_zenith, 0, clip_angle)
        sunzsec = 1. / cos(deg2rad(sun_zenith))
        clip_angle = rad2deg(arccos(1. / satz_sec_coord.max()))
        sat_zenith = clip(sat_zenith, 0, clip_angle)
        satzsec = 1. / cos(deg2rad(sat_zenith))
        shape = sun_zenith.shape

        if not(wvl_coord.min() < wvl < wvl_coord.max()):
            LOG.warning(
                "Effective wavelength for band %s outside 400-800 nm range!",
                str(bandname))
            LOG.info(
                "Set the rayleigh/aerosol reflectance contribution to zero!")
            if HAVE_DASK:
                chunks = sun_zenith.chunks if redband is None \
                    else redband.chunks
                res = zeros(shape, chunks=chunks)
                return res.compute() if compute else res
            else:
                return zeros(shape)

        idx = np.searchsorted(wvl_coord, wvl)
        wvl1 = wvl_coord[idx - 1]
        wvl2 = wvl_coord[idx]

        fac = (wvl2 - wvl) / (wvl2 - wvl1)
        raylwvl = fac * rayl[idx - 1, :, :, :] + (1 - fac) * rayl[idx, :, :, :]
        tic = time.time()

        smin = [sunz_sec_coord[0], azid_coord[0], satz_sec_coord[0]]
        smax = [sunz_sec_coord[-1], azid_coord[-1], satz_sec_coord[-1]]
        orders = [
            len(sunz_sec_coord), len(azid_coord), len(satz_sec_coord)]
        minterp = MultilinearInterpolator(smin, smax, orders)

        f_3d_grid = raylwvl
        minterp.set_values(atleast_2d(f_3d_grid.ravel()))

        def _do_interp(minterp, sunzsec, azidiff, satzsec):
            interp_points2 = np.vstack((sunzsec.ravel(),
                                        180 - azidiff.ravel(),
                                        satzsec.ravel()))
            res = minterp(interp_points2)
            return res.reshape(sunzsec.shape)

        if HAVE_DASK:
            ipn = map_blocks(_do_interp, minterp, sunzsec, azidiff,
                             satzsec, dtype=raylwvl.dtype,
                             chunks=azidiff.chunks)
        else:
            ipn = _do_interp(minterp, sunzsec, azidiff, satzsec)

        LOG.debug("Time - Interpolation: {0:f}".format(time.time() - tic))

        ipn *= 100
        res = ipn
        if redband is not None:
            res = where(redband < 20., res,
                        (1 - (redband - 20) / 80) * res)

        res = clip(res, 0, 100)
        if compute:
            res = res.compute()
        return res


def get_reflectance_lut(filename):
    """Read the LUT with reflectances as a function of wavelength, satellite
    zenith secant, azimuth difference angle, and sun zenith secant

    """

    h5f = h5py.File(filename, 'r')

    tab = h5f['reflectance']
    wvl = h5f['wavelengths']
    azidiff = h5f['azimuth_difference']
    satellite_zenith_secant = h5f['satellite_zenith_secant']
    sun_zenith_secant = h5f['sun_zenith_secant']

    if HAVE_DASK:
        tab = from_array(tab, chunks=(10, 10, 10, 10))
        # wvl_coord is used in a lot of non-dask functions, keep in memory
        wvl = from_array(wvl, chunks=(100,)).persist()
        azidiff = from_array(azidiff, chunks=(1000,))
        satellite_zenith_secant = from_array(satellite_zenith_secant,
                                             chunks=(1000,))
        sun_zenith_secant = from_array(sun_zenith_secant,
                                       chunks=(1000,))
    else:
        # load all of the data we are going to use in to memory
        tab = tab[:]
        wvl = wvl[:]
        azidiff = azidiff[:]
        satellite_zenith_secant = satellite_zenith_secant[:]
        sun_zenith_secant = sun_zenith_secant[:]
        h5f.close()

    return tab, wvl, azidiff, satellite_zenith_secant, sun_zenith_secant


# if __name__ == "__main__":
#     SHAPE = (1000, 3000)
#     NDIM = SHAPE[0] * SHAPE[1]
#     SUNZ = np.ma.arange(
#         NDIM / 2, NDIM + NDIM / 2).reshape(SHAPE) * 60. / float(NDIM)
#     SATZ = np.ma.arange(NDIM).reshape(SHAPE) * 60. / float(NDIM)
#     AZIDIFF = np.ma.arange(NDIM).reshape(SHAPE) * 179.9 / float(NDIM)
#     rfl = this.get_reflectance(SUNZ, SATZ, AZIDIFF, 'M4')


1			#!/usr/bin/env python
2			# -- coding: utf-8 --
3
4			# Copyright (c) 2016-2018 Pytroll
5
6			# Author(s):
7
8			# Adam.Dybbroe <[email protected]>
9			# Martin Raspaud <[email protected]>
10
11			# This program is free software: you can redistribute it and/or modify
12			# it under the terms of the GNU General Public License as published by
13			# the Free Software Foundation, either version 3 of the License, or
14			# (at your option) any later version.
15
16			# This program is distributed in the hope that it will be useful,
17			# but WITHOUT ANY WARRANTY; without even the implied warranty of
18			# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19			# GNU General Public License for more details.
20
21			# You should have received a copy of the GNU General Public License
22			# along with this program. If not, see <http://www.gnu.org/licenses/>.
23
24			"""Atmospheric correction of shortwave imager bands in the wavelength range 400
25			to 800 nm
26
27			"""
28
29			import os
30			import time
31			import logging
32			from six import integer_types
33
34			import h5py
35			import numpy as np
36
37			try:
38			from dask.array import (where, zeros, clip, rad2deg, deg2rad, cos, arccos,
39			atleast_2d, Array, map_blocks, from_array)
40			HAVE_DASK = True
41			try:
42			# use serializable h5py wrapper to make sure files are closed properly
43			import h5pickle as h5py
44			except ImportError:
45			pass
46			except ImportError:
47			from numpy import where, zeros, clip, rad2deg, deg2rad, cos, arccos, atleast_2d
48			map_blocks = None
49			from_array = None
50			Array = None
51			HAVE_DASK = False
52
53			from geotiepoints.multilinear import MultilinearInterpolator
54			from pyspectral.rsr_reader import RelativeSpectralResponse
55			from pyspectral.utils import (INSTRUMENTS, RAYLEIGH_LUT_DIRS,
56			AEROSOL_TYPES, ATMOSPHERES,
57			BANDNAMES,
58			download_luts, get_central_wave,
59			get_bandname_from_wavelength)
60
61			LOG = logging.getLogger(__name__)
62
63
64			class BandFrequencyOutOfRange(ValueError):
65
66			"""Exception when the band frequency is out of the visible range"""
67
68			pass
69
70
71			class Rayleigh(object):
72
73			"""Container for the atmospheric correction of satellite imager bands.
74
75			This class removes background contributions of Rayleigh scattering of
76			molecules and Mie scattering and absorption by aerosols.
77
78			"""
79
80			def __init__(self, platform_name, sensor, **kwargs):
81			"""Initialize class and determine LUT to use."""
82			self.platform_name = platform_name
83			self.sensor = sensor
84			self.coeff_filename = None
85
86			atm_type = kwargs.get('atmosphere', 'us-standard')
87			if atm_type not in ATMOSPHERES:
88			raise AttributeError('Atmosphere type not supported! ' +
89			'Need to be one of {}'.format(str(ATMOSPHERES)))
90
91			aerosol_type = kwargs.get('aerosol_type', 'marine_clean_aerosol')
92
93			if aerosol_type not in AEROSOL_TYPES:
94			raise AttributeError('Aerosol type not supported! ' +
95			'Need to be one of {0}'.format(str(AEROSOL_TYPES)))
96
97			rayleigh_dir = RAYLEIGH_LUT_DIRS[aerosol_type]
98
99			if atm_type not in ATMOSPHERES.keys():
100			LOG.error("Atmosphere type %s not supported", atm_type)
101
102			LOG.info("Atmosphere chosen: %s", atm_type)
103
104			# Try fix instrument naming
105			instr = INSTRUMENTS.get(platform_name, sensor)
106			if instr != sensor:
107			sensor = instr
108			LOG.warning("Inconsistent sensor/satellite input - " +
109			"sensor set to %s", sensor)
110
111			self.sensor = sensor.replace('/', '')
112
113			ext = atm_type.replace(' ', '_')
114			lutname = "rayleigh_lut_{0}.h5".format(ext)
115			self.reflectance_lut_filename = os.path.join(rayleigh_dir, lutname)
116			if not os.path.exists(self.reflectance_lut_filename):
117			LOG.warning(
118			"No lut file %s on disk", self.reflectance_lut_filename)
119			LOG.info("Will download from internet...")
120			download_luts(aerosol_type=aerosol_type)
121
122			if (not os.path.exists(self.reflectance_lut_filename) or
123			not os.path.isfile(self.reflectance_lut_filename)):
124			raise IOError('pyspectral file for Rayleigh scattering correction ' +
125			'does not exist! Filename = ' +
126			str(self.reflectance_lut_filename))
127
128			LOG.debug('LUT filename: %s', str(self.reflectance_lut_filename))
129			self._rayl = None
130			self._wvl_coord = None
131			self._azid_coord = None
132			self._satz_sec_coord = None
133			self._sunz_sec_coord = None
134
135			def get_effective_wavelength(self, bandname):
136			"""Get the effective wavelength with Rayleigh scattering in mind"""
137			try:
138			rsr = RelativeSpectralResponse(self.platform_name, self.sensor)
139			except IOError:
140			LOG.exception(
141			"No spectral responses for this platform and sensor: %s %s", self.platform_name, self.sensor)
142			if isinstance(bandname, (float, integer_types)):
143			LOG.warning(
144			"Effective wavelength is set to the requested band wavelength = %f", bandname)
145			return bandname
146			raise
147
148			if isinstance(bandname, str):
149			bandname = BANDNAMES.get(self.sensor, BANDNAMES['generic']).get(bandname, bandname)
150			elif isinstance(bandname, (float, integer_types)):
151			if not(0.4 < bandname < 0.8):
152			raise BandFrequencyOutOfRange(
153			'Requested band frequency should be between 0.4 and 0.8 microns!')
154			bandname = get_bandname_from_wavelength(self.sensor, bandname, rsr.rsr)
155
156			wvl, resp = rsr.rsr[bandname][
157			'det-1']['wavelength'], rsr.rsr[bandname]['det-1']['response']
158
159			cwvl = get_central_wave(wvl, resp, weight=1. / wvl**4)
160			LOG.debug("Band name: %s Effective wavelength: %f", bandname, cwvl)
161
162			return cwvl
163
164			def get_reflectance_lut(self):
165			"""Read the LUT with reflectances as a function of wavelength, satellite zenith
166			secant, azimuth difference angle, and sun zenith secant
167
168			"""
169			if self._rayl is None:
170			lut_vars = get_reflectance_lut(self.reflectance_lut_filename)
171			self._rayl = lut_vars[0]
172			self._wvl_coord = lut_vars[1]
173			self._azid_coord = lut_vars[2]
174			self._satz_sec_coord = lut_vars[3]
175			self._sunz_sec_coord = lut_vars[4]
176			return self._rayl, self._wvl_coord, self._azid_coord,\
177			self._satz_sec_coord, self._sunz_sec_coord
178
179			def get_reflectance(self, sun_zenith, sat_zenith, azidiff, bandname,
180			redband=None):
181			"""Get the reflectance from the three sun-sat angles."""
182			# Get wavelength in nm for band:
183			wvl = self.get_effective_wavelength(bandname) * 1000.0
184			rayl, wvl_coord, azid_coord, satz_sec_coord, sunz_sec_coord = \
185			self.get_reflectance_lut()
186
187			# force dask arrays
188			compute = False
189			if HAVE_DASK and not isinstance(sun_zenith, Array):
190			compute = True
191			sun_zenith = from_array(sun_zenith, chunks=sun_zenith.shape)
192			sat_zenith = from_array(sat_zenith, chunks=sat_zenith.shape)
193			azidiff = from_array(azidiff, chunks=azidiff.shape)
194			if redband is not None:
195			redband = from_array(redband, chunks=redband.shape)
196
197			clip_angle = rad2deg(arccos(1. / sunz_sec_coord.max()))
198			sun_zenith = clip(sun_zenith, 0, clip_angle)
199			sunzsec = 1. / cos(deg2rad(sun_zenith))
200			clip_angle = rad2deg(arccos(1. / satz_sec_coord.max()))
201			sat_zenith = clip(sat_zenith, 0, clip_angle)
202			satzsec = 1. / cos(deg2rad(sat_zenith))
203			shape = sun_zenith.shape
204
205			if not(wvl_coord.min() < wvl < wvl_coord.max()):
206			LOG.warning(
207			"Effective wavelength for band %s outside 400-800 nm range!",
208			str(bandname))
209			LOG.info(
210			"Set the rayleigh/aerosol reflectance contribution to zero!")
211			if HAVE_DASK:
212			chunks = sun_zenith.chunks if redband is None \
213			else redband.chunks
214			res = zeros(shape, chunks=chunks)
215			return res.compute() if compute else res
216			else:
217			return zeros(shape)
218
219			idx = np.searchsorted(wvl_coord, wvl)
220			wvl1 = wvl_coord[idx - 1]
221			wvl2 = wvl_coord[idx]
222
223			fac = (wvl2 - wvl) / (wvl2 - wvl1)
224			raylwvl = fac * rayl[idx - 1, :, :, :] + (1 - fac) * rayl[idx, :, :, :]
225			tic = time.time()
226
227			smin = [sunz_sec_coord[0], azid_coord[0], satz_sec_coord[0]]
228			smax = [sunz_sec_coord[-1], azid_coord[-1], satz_sec_coord[-1]]
229			orders = [
230			len(sunz_sec_coord), len(azid_coord), len(satz_sec_coord)]
231			minterp = MultilinearInterpolator(smin, smax, orders)
232
233			f_3d_grid = raylwvl
234			minterp.set_values(atleast_2d(f_3d_grid.ravel()))
235
236			def _do_interp(minterp, sunzsec, azidiff, satzsec):
237			interp_points2 = np.vstack((sunzsec.ravel(),
238			180 - azidiff.ravel(),
239			satzsec.ravel()))
240			res = minterp(interp_points2)
241			return res.reshape(sunzsec.shape)
242
243			if HAVE_DASK:
244			ipn = map_blocks(_do_interp, minterp, sunzsec, azidiff,
245			satzsec, dtype=raylwvl.dtype,
246			chunks=azidiff.chunks)
247			else:
248			ipn = _do_interp(minterp, sunzsec, azidiff, satzsec)
249
250			LOG.debug("Time - Interpolation: {0:f}".format(time.time() - tic))
251
252			ipn *= 100
253			res = ipn
254			if redband is not None:
255			res = where(redband < 20., res,
256			(1 - (redband - 20) / 80) * res)
257
258			res = clip(res, 0, 100)
259			if compute:
260			res = res.compute()
261			return res
262
263
264			def get_reflectance_lut(filename):
265			"""Read the LUT with reflectances as a function of wavelength, satellite
266			zenith secant, azimuth difference angle, and sun zenith secant
267
268			"""
269
270			h5f = h5py.File(filename, 'r')
271
272			tab = h5f['reflectance']
273			wvl = h5f['wavelengths']
274			azidiff = h5f['azimuth_difference']
275			satellite_zenith_secant = h5f['satellite_zenith_secant']
276			sun_zenith_secant = h5f['sun_zenith_secant']
277
278			if HAVE_DASK:
279			tab = from_array(tab, chunks=(10, 10, 10, 10))
280			# wvl_coord is used in a lot of non-dask functions, keep in memory
281			wvl = from_array(wvl, chunks=(100,)).persist()
282			azidiff = from_array(azidiff, chunks=(1000,))
283			satellite_zenith_secant = from_array(satellite_zenith_secant,
284			chunks=(1000,))
285			sun_zenith_secant = from_array(sun_zenith_secant,
286			chunks=(1000,))
287			else:
288			# load all of the data we are going to use in to memory
289			tab = tab[:]
290			wvl = wvl[:]
291			azidiff = azidiff[:]
292			satellite_zenith_secant = satellite_zenith_secant[:]
293			sun_zenith_secant = sun_zenith_secant[:]
294			h5f.close()
295
296			return tab, wvl, azidiff, satellite_zenith_secant, sun_zenith_secant
297
298
299			# if __name__ == "__main__":
300			# SHAPE = (1000, 3000)
301			# NDIM = SHAPE[0] * SHAPE[1]
302			# SUNZ = np.ma.arange(
303			# NDIM / 2, NDIM + NDIM / 2).reshape(SHAPE) * 60. / float(NDIM)
304			# SATZ = np.ma.arange(NDIM).reshape(SHAPE) * 60. / float(NDIM)
305			# AZIDIFF = np.ma.arange(NDIM).reshape(SHAPE) * 179.9 / float(NDIM)
306			# rfl = this.get_reflectance(SUNZ, SATZ, AZIDIFF, 'M4')
307

pytroll / pyspectral

Pull Request — develop (#33)

Rayleigh._do_interp() A

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