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Daskify NIR reflectance calculations #59

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merged 13 commits into from
Apr 9, 2019
Merged

Daskify NIR reflectance calculations #59

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d94cb88
Use dask instead of Numpy where suitable
pnuu Nov 28, 2018
4b88bdb
Use np.testing.assert_allclose instead of assertAlmostEqual
pnuu Nov 29, 2018
a695588
Revert back to use numpy operations
pnuu Nov 29, 2018
71ff135
Use np.asanyarray instead of np.array
pnuu Nov 29, 2018
45e38b1
Remove references to masked array attributes
pnuu Nov 29, 2018
654e3e7
Change documentation to use plain Numpy arrays instead of masked arrays
pnuu Nov 29, 2018
01933a7
Remove obsolete commented-out lines
pnuu Nov 29, 2018
b977c21
Don't rely on dask to be available
pnuu Nov 29, 2018
92b743c
Compute the results if the input is not dask array
pnuu Nov 29, 2018
b22d176
Fix da.log and da.exp to np.log and da.log
pnuu Nov 30, 2018
500dc7f
Convert the result to masked array if also the input is masked
pnuu Nov 30, 2018
781e477
Add tests for checking output for masked and dask arrays stay the same
pnuu Nov 30, 2018
86086df
Ensure that radiance from planck() isn't masked
pnuu Nov 30, 2018
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26 changes: 13 additions & 13 deletions doc/37_reflectance.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ expressed in :math:`W/m^2 sr^{-1} \mu m^{-1}`, or using SI units :math:`W/m^2 sr
>>> tb37 = np.array([298.07385254, 297.15478516, 294.43276978, 281.67633057, 273.7923584])
>>> viirs = RadTbConverter('Suomi-NPP', 'viirs', 'M12')
>>> rad37 = viirs.tb2radiance(tb37)
>>> print([np.round(rad, 7) for rad in rad37['radiance'].data])
>>> print([np.round(rad, 7) for rad in rad37['radiance']])
[369717.4765726, 355110.5207853, 314684.2788726, 173143.5424898, 116408.0007877]
>>> rad37['unit']
'W/m^2 sr^-1 m^-1'
Expand All @@ -58,7 +58,7 @@ In order to get the total radiance over the band one has to multiply with the eq
>>> tb37 = np.array([298.07385254, 297.15478516, 294.43276978, 281.67633057, 273.7923584])
>>> viirs = RadTbConverter('Suomi-NPP', 'viirs', 'M12')
>>> rad37 = viirs.tb2radiance(tb37, normalized=False)
>>> print([np.round(rad, 8) for rad in rad37['radiance'].data])
>>> print([np.round(rad, 8) for rad in rad37['radiance']])
[0.07037968, 0.06759909, 0.05990352, 0.03295972, 0.02215951]
>>> rad37['unit']
'W/m^2 sr^-1'
Expand Down Expand Up @@ -127,7 +127,7 @@ where :math:`S(\lambda)` is the spectral solar irradiance.
>>> viirs = RelativeSpectralResponse('Suomi-NPP', 'viirs')
>>> solar_irr = SolarIrradianceSpectrum(TOTAL_IRRADIANCE_SPECTRUM_2000ASTM, dlambda=0.005)
>>> sflux = solar_irr.inband_solarflux(viirs.rsr['M12'])
>>> print(round(sflux, 7))
>>> print(np.round(sflux, 7))
2.2428119

Derive the reflective part of the observed 3.7 micron radiance
Expand Down Expand Up @@ -197,9 +197,9 @@ In Python this becomes:
>>> tb37 = np.array([298.07385254, 297.15478516, 294.43276978, 281.67633057, 273.7923584])
>>> tb11 = np.array([271.38806152, 271.38806152, 271.33453369, 271.98553467, 271.93609619])
>>> m12r = refl_m12.reflectance_from_tbs(sunz, tb37, tb11)
>>> print(m12r.mask)
>>> print(np.any(np.isnan(m12r)))
False
>>> print([round(refl, 8) for refl in m12r.data])
>>> print([np.round(refl, 8) for refl in m12r])
[0.21432927, 0.20285153, 0.17063976, 0.05408903, 0.00838111]

We can try decompose equation :eq:`refl37` above using the example of VIIRS M12 band:
Expand All @@ -215,19 +215,19 @@ We can try decompose equation :eq:`refl37` above using the example of VIIRS M12
>>> rad11 = viirs.tb2radiance(tb11, normalized=False)
>>> sflux = 2.242817881698326
>>> nomin = rad37['radiance'] - rad11['radiance']
>>> print(nomin.mask)
>>> print(np.isnan(nomin))
[False False False False False]
>>> print([np.round(val, 8) for val in nomin.data])
>>> print([np.round(val, 8) for val in nomin])
[0.05083677, 0.04805618, 0.0404157, 0.01279279, 0.00204485]
>>> denom = np.cos(np.deg2rad(sunz))/np.pi * sflux - rad11['radiance']
>>> print(denom.mask)
>>> print(np.isnan(denom))
[False False False False False]
>>> print([np.round(val, 8) for val in denom.data])
>>> print([np.round(val, 8) for val in denom])
[0.23646313, 0.23645682, 0.23650559, 0.23582015, 0.2358661]
>>> res = nomin/denom
>>> print(res.mask)
>>> print(np.isnan(res))
[False False False False False]
>>> print([round(val, 8) for val in res.data])
>>> print([np.round(val, 8) for val in res])
[0.21498817, 0.2032345, 0.17088689, 0.05424807, 0.00866955]


Expand All @@ -252,8 +252,8 @@ Using the example of the VIIRS M12 band from above this gives the following spec
>>> tb11 = np.array([271.38806152, 271.38806152, 271.33453369, 271.98553467, 271.93609619])
>>> m12r = refl_m12.reflectance_from_tbs(sunz, tb37, tb11)
>>> tb = refl_m12.emissive_part_3x()
>>> ['{tb:6.3f}'.format(tb=round(t, 4)) for t in tb.data]
>>> ['{tb:6.3f}'.format(tb=np.round(t, 4)) for t in tb]
['266.996', '267.262', '267.991', '271.033', '271.927']
>>> rad = refl_m12.emissive_part_3x(tb=False)
>>> ['{rad:6.3f}'.format(rad=round(r, 4)) for r in rad.data]
>>> ['{rad:6.3f}'.format(rad=np.round(r, 4)) for r in rad]
['80285.149', '81458.022', '84749.639', '99761.400', '104582.030']
8 changes: 5 additions & 3 deletions doc/usage.rst
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Expand Up @@ -22,9 +22,11 @@ Now, you can work with the data as you wish, make some simple plot for instance:
>>> import matplotlib.pyplot as plt
>>> dummy = plt.figure(figsize=(10, 5))
>>> import numpy as np
>>> resp = np.ma.masked_less_equal(olci.rsr['Oa01']['det-1']['response'], 0.015)
>>> wvl = np.ma.masked_array(olci.rsr['Oa01']['det-1']['wavelength'], resp.mask)
>>> dummy = plt.plot(wvl.compressed(), resp.compressed())
>>> rsr = olci.rsr['Oa01']['det-1']['response']
>>> resp = np.where(rsr < 0.015, np.nan, rsr)
>>> wl_ = olci.rsr['Oa01']['det-1']['wavelength']
>>> wvl = np.where(np.isnan(resp), np.nan, wl_)
>>> dummy = plt.plot(wvl, resp)
>>> plt.show() # doctest: +SKIP

.. image:: _static/olci_ch1.png
Expand Down
1 change: 1 addition & 0 deletions pyspectral/blackbody.py
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Expand Up @@ -182,6 +182,7 @@ def planck(wave, temp, wavelength=True):

denom = np.exp(exp_arg) - 1
rad = nom / denom
rad = np.where(rad.mask, np.nan, rad.data)
radshape = rad.shape
if wln.shape[0] == 1:
if temperature.shape[0] == 1:
Expand Down
40 changes: 30 additions & 10 deletions pyspectral/near_infrared_reflectance.py
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Expand Up @@ -28,6 +28,11 @@

import os
import numpy as np
try:
from dask.array import where, logical_or
except ImportError:
from numpy import where, logical_or

from pyspectral.solar import (SolarIrradianceSpectrum,
TOTAL_IRRADIANCE_SPECTRUM_2000ASTM)
from pyspectral.utils import BANDNAMES, get_bandname_from_wavelength
Expand Down Expand Up @@ -195,15 +200,25 @@ def reflectance_from_tbs(self, sun_zenith, tb_near_ir, tb_thermal, **kwargs):
absorption correction will be applied.

"""
# Check for dask arrays
if hasattr(tb_near_ir, 'compute') or hasattr(tb_thermal, 'compute'):
compute = False
else:
compute = True
if hasattr(tb_near_ir, 'mask') or hasattr(tb_thermal, 'mask'):
is_masked = True
else:
is_masked = False

if np.isscalar(tb_near_ir):
tb_nir = np.array([tb_near_ir, ])
else:
tb_nir = np.array(tb_near_ir)
tb_nir = np.asanyarray(tb_near_ir)
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Does np.asanyarray convert dask arrays to numpy arrays?

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It does:

In [1]: import dask.array as da                                                                                                                                      

In [2]: a = da.arange(5., chunks=2)                                                                                                                                  

In [3]: import numpy as np                                                                                                                                           

In [4]: type(np.asanyarray(a))                                                                                                                                       
Out[4]: numpy.ndarray

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@djhoese what do you suggest?

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As mentioned on slack, I'd prefer if everything could be kept as dask arrays for as long as possible and if things have to be computed they should be done in a map_blocks or delayed function. As @pnuu mentioned on slack converting to numpy here made the code faster and use less memory in his test cases. I'm fairly certain this is because the array is used later on in a non-dask-friendly way and the dask array is actually being computed multiple times. I think I pointed them out on slack during the PCW.

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As this part of pyspectral wasn't dask friendly before, could we perhaps merge this PR now and make sure things works and then work further to improve the daskfriendliness?
@mraspaud @djhoese @pnuu ?

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I'm fine with merging. Then we could also merge pytroll/satpy#529 so this PR would be usable via SatpY.

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So this is working now ?

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I think there hasn't been anything that didn't work since I last touched this, just that it might not be quite optimal in performance and how things should be done with dask.

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Fine. +0

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Fine, I will just try do some system testing off line first to be sure. Any suggested recipes/tests @pnuu ?


if np.isscalar(tb_thermal):
tb_therm = np.array([tb_thermal, ])
else:
tb_therm = np.array(tb_thermal)
tb_therm = np.asanyarray(tb_thermal)

if tb_therm.shape != tb_nir.shape:
errmsg = 'Dimensions do not match! {0} and {1}'.format(
Expand All @@ -221,7 +236,7 @@ def reflectance_from_tbs(self, sun_zenith, tb_near_ir, tb_thermal, **kwargs):
if np.isscalar(tb_ir_co2):
tbco2 = np.array([tb_ir_co2, ])
else:
tbco2 = np.array(tb_ir_co2)
tbco2 = np.asanyarray(tb_ir_co2)

if not self.rsr:
raise NotImplementedError("Reflectance calculations without "
Expand All @@ -239,9 +254,8 @@ def reflectance_from_tbs(self, sun_zenith, tb_near_ir, tb_thermal, **kwargs):
if l_nir.ravel().shape[0] < 10:
LOG.info('l_nir = %s', str(l_nir))

sunz = np.ma.masked_outside(sun_zenith, 0.0, 88.0)
sunzmask = sunz.mask
sunz = sunz.filled(88.)
sunzmask = (sun_zenith < 0.0) | (sun_zenith > 88.0)
sunz = where(sunzmask, 88.0, sun_zenith)

mu0 = np.cos(np.deg2rad(sunz))
# mu0 = np.where(np.less(mu0, 0.1), 0.1, mu0)
Expand All @@ -262,12 +276,18 @@ def reflectance_from_tbs(self, sun_zenith, tb_near_ir, tb_thermal, **kwargs):
mask = (self._solar_radiance - thermal_emiss_one *
self._rad3x_correction) < EPSILON

np.logical_or(sunzmask, mask, out=mask)
np.logical_or(mask, np.isnan(tb_nir), out=mask)
logical_or(sunzmask, mask, out=mask)
logical_or(mask, np.isnan(tb_nir), out=mask)

self._r3x = np.ma.masked_where(mask, data)
self._r3x = where(mask, np.nan, data)

# Reflectances should be between 0 and 1, but values above 1 is
# perfectly possible and okay! (Multiply by 100 to get reflectances
# in percent)
return self._r3x
if hasattr(self._r3x, 'compute') and compute:
res = self._r3x.compute()
else:
res = self._r3x
if is_masked:
res = np.ma.masked_array(res, mask=np.isnan(res))
return res
2 changes: 1 addition & 1 deletion pyspectral/radiance_tb_conversion.py
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Expand Up @@ -228,7 +228,7 @@ def make_tb2rad_lut(self, filepath, normalized=True):
tb_ = np.arange(TB_MIN, TB_MAX, self.tb_resolution)
retv = self.tb2radiance(tb_, normalized=normalized)
rad = retv['radiance']
np.savez(filepath, tb=tb_, radiance=rad.compressed())
np.savez(filepath, tb=tb_, radiance=rad)

@staticmethod
def read_tb2rad_lut(filepath):
Expand Down
32 changes: 24 additions & 8 deletions pyspectral/tests/test_reflectance.py
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Expand Up @@ -116,7 +116,7 @@ def test_rsr_integral(self):
refl37 = Calculator('EOS-Aqua', 'modis', '20')

expected = 1.8563451e-07 # unit = 'm' (meter)
self.assertAlmostEqual(refl37.rsr_integral, expected)
np.testing.assert_allclose(refl37.rsr_integral, expected)

with patch('pyspectral.radiance_tb_conversion.RelativeSpectralResponse') as mymock:
instance = mymock.return_value
Expand All @@ -128,7 +128,7 @@ def test_rsr_integral(self):

expected = 13000.385 # SI units = 'm-1' (1/meter)
res = refl37.rsr_integral
self.assertAlmostEqual(res / expected, 1.0, 6)
np.testing.assert_allclose(res / expected, 1.0, 6)

def test_reflectance(self):
"""Test the derivation of the reflective part of a 3.7 micron band"""
Expand Down Expand Up @@ -158,28 +158,44 @@ def test_reflectance(self):
tb3 = np.array([290.])
tb4 = np.array([282.])
refl = refl37.reflectance_from_tbs(sunz, tb3, tb4)
self.assertAlmostEqual(refl.data[0], 0.251245010648, 6)
np.testing.assert_allclose(refl[0], 0.251245010648, 6)

tb3x = refl37.emissive_part_3x()
self.assertAlmostEqual(tb3x, 276.213054, 6)
np.testing.assert_allclose(tb3x, 276.213054, 6)

sunz = np.array([80.])
tb3 = np.array([295.])
tb4 = np.array([282.])
refl = refl37.reflectance_from_tbs(sunz, tb3, tb4)
self.assertAlmostEqual(refl.data[0], 0.452497961, 6)
np.testing.assert_allclose(refl[0], 0.452497961, 6)

tb3x = refl37.emissive_part_3x()
self.assertAlmostEqual(tb3x, 270.077268, 6)
np.testing.assert_allclose(tb3x, 270.077268, 6)

sunz = np.array([50.])
tb3 = np.array([300.])
tb4 = np.array([285.])
refl = refl37.reflectance_from_tbs(sunz, tb3, tb4)
self.assertAlmostEqual(refl.data[0], 0.1189217, 6)
np.testing.assert_allclose(refl[0], 0.1189217, 6)

tb3x = refl37.emissive_part_3x()
self.assertAlmostEqual(tb3x, 282.455426, 6)
np.testing.assert_allclose(tb3x, 282.455426, 6)

sunz = np.array([50.])
tb3 = np.ma.masked_array([300.], mask=False)
tb4 = np.ma.masked_array([285.], mask=False)
refl = refl37.reflectance_from_tbs(sunz, tb3, tb4)
self.assertTrue(hasattr(refl, 'mask'))

try:
import dask.array as da
sunz = da.from_array([50.], chunks=10)
tb3 = da.from_array([300.], chunks=10)
tb4 = da.from_array([285.], chunks=10)
refl = refl37.reflectance_from_tbs(sunz, tb3, tb4)
self.assertTrue(hasattr(refl, 'compute'))
except ImportError:
pass

def tearDown(self):
"""Clean up"""
Expand Down