def test_opt_functions_OPTAA_vectorization_with_tscor_nans(self):
"""
Test the vectorized OPTAA wrapper functions in the opt_functions.py module;
include "a" and "c" test wavelengths outside of the (original) range of the
wavelength keys in the tscor.py file, which contains the dictionary of the
temperature and salinity correction coefficients. The dictionary keys have
been extended from [400.0 755.0] to [380.0 775.0] with entries of np.nan.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Initial code by Russell Desiderio, 29-Apr-2014. Added tests for when OPTAA
wavelengths are outside the range of the empirically derived temperature
and salinity correction wavelength keys in the original tscor.py dictionary
by modifying def test_opt_functions_OPTAA_vectorization test data.
"""
# test inputs:
# replicate the inputs to represent 3 data packets
npackets = 3
# tbins will become a 2D array.
tbins = np.array([14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565])
tbins = np.tile(tbins, (npackets, 1))
# nrows of tarr = length(nwlngth); ncols of tarr = length(tbins)
tarr = np.array([
[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]
])
# tarr will become a 3D array
# dimensions will be (npackets, nwavelengths, ntempbins)
tarr = np.tile(tarr, (npackets, 1, 1))
# valid tscor dictionary entries (those without nan values) are
# keyed at [400.0 755.0] nm. The dictionary has been extended to
# to [380.0 775.0] using np.nan as fill values. test:
cwlngth = np.array([398.5, 540., 580., 630., 670., 710.])
awlngth = np.array([500., 550., 600., 650., 700., 761.2])
c_sig = np.array([150., 225., 200., 350., 450., 495.])
c_ref = np.array([550., 540., 530., 520., 510., 500.])
c_off = np.array([1.35, 1.30, 1.25, 1.20, 1.15, 1.10])
a_sig = np.array([250., 300., 210., 430., 470., 495.])
a_ref = np.array([450., 460., 470., 480., 490., 500.])
a_off = np.array([0.35, 0.30, 0.25, 0.20, 0.15, 0.10])
# make all of the previous vectors 2-D
for str in ['cwlngth', 'awlngth', 'c_sig', 'c_ref', 'c_off', 'a_sig', 'a_ref', 'a_off']:
exec(str + ' = np.tile(' + str + ', (npackets,1))')
# traw, Tcal, T, and PS will now be vectors, so:
traw = np.array([48355])
Tcal = np.array([20.0])
T = np.array([12.0])
PS = np.array([35.0])
for str in ['traw', 'Tcal', 'T', 'PS']:
exec(str + ' = np.tile(' + str + ', (npackets,1))')
# expected outputs:
# 1st c wavelength is out-of-range of the empirical TS corrections, so the DPA
# should return the fill value.
cpd_ts = np.array([fill_value, 4.807914, 5.156010, 2.788715, 1.655607, 1.171965])
# to scatter-correct the 1st abs wavelength value, the c values are interpolated;
# because the 1st c value is out-of-TScor-range, the 1st abs value will also be
# a fill value. and, the last abs value will also be a fill value because 761.2>755.0.
apd_ts_s_ref700 = np.array([fill_value, 1.021574, 3.235057, 0.099367, 0.000000, fill_value])
for str in ['cpd_ts', 'apd_ts_s_ref700']:
exec(str + ' = np.tile(' + str + ', (npackets,1))')
# beam attenuation (beam c) test
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off, Tcal,
tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption test
a_ts_s700 = np.zeros(6)
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_s700, apd_ts_s_ref700, rtol=1e-6, atol=1e-6)
def test_opt_functions_OPTAA_a_and_c_wavelength_sets(self):
"""
Test the OPTAA wrapper functions in the opt_functions.py module.
Test a-c dataset with different wavelength values for the absorption versus
beam c optical channels. Included to test that the c optical values are correctly
interpolated onto the abs wavelengths in the scatter correction algorithm.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Implemented by Russell Desiderio, 26-Feb-2014. Additional unit test data
constructed as documented in the OPTAA Unit Test document artifact
reference above.
"""
# test inputs:
tbins = np.array([14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565])
# nrows of tarr = length(wlngth); ncols of tarr = length(tbins)
tarr = np.array([
[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]
])
# a_off and c_off must have same dimensions as wlngth.
cwlngth = np.array([510., 540., 580., 630., 670., 710.])
awlngth = np.array([500., 550., 600., 650., 700., 715.])
c_sig = np.array([150., 225., 200., 350., 450., 495.])
c_ref = np.array([550., 540., 530., 520., 510., 500.])
c_off = np.array([1.35, 1.30, 1.25, 1.20, 1.15, 1.10])
a_sig = np.array([250., 300., 210., 430., 470., 495.])
a_ref = np.array([450., 460., 470., 480., 490., 500.])
a_off = np.array([0.35, 0.30, 0.25, 0.20, 0.15, 0.10])
# traw, T, and PS must be scalar (before vectorization).
traw = 48355.0
Tcal = 20.0
T = 12.0
PS = 35.0
# also test case of user selected reference wavelength for abs scatter correction
ref_wave = 695 # nearest abs wavelength (700nm) should become reference wavelength
# expected outputs
cpd_ts = np.array([6.553771, 4.807914, 5.156010, 2.788715, 1.655607, 1.171965], ndmin=2)
apd_ts_s_ref715 = np.array([1.990992, 1.479089, 3.350109, 0.350108, 0.152712, 0.000000],
ndmin=2)
apd_ts_s_ref700 = np.array([1.379858, 1.021574, 3.235057, 0.099367, 0.000000, -0.156972],
ndmin=2)
# beam attenuation (beam c) wrapper test
c_ts = np.zeros(6)
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off, Tcal,
tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption wrapper test
# case: default reference wavelength for scatter correction
a_ts_sdef = np.zeros(6)
a_ts_sdef = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_sdef, apd_ts_s_ref715, rtol=1e-6, atol=1e-6)
# case: user selected reference wavelength for scatter correction
a_ts_s700 = np.zeros(6)
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS, ref_wave)
np.testing.assert_allclose(a_ts_s700, apd_ts_s_ref700, rtol=1e-6, atol=1e-6)
def test_opt_functions_OPTAA_vectorization(self):
"""
Test the vectorization of the OPTAA wrapper functions in the opt_functions.py module.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Implemented by Russell Desiderio, 05-Mar-2014. Additional unit test data
constructed as documented in the OPTAA Unit Test document artifact
reference above.
"""
# test inputs:
# replicate the inputs to represent 3 data packets
npackets = 3
# tbins will become a 2D array.
tbins = np.array([14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565])
tbins = np.tile(tbins, (npackets, 1))
# nrows of tarr = length(nwlngth); ncols of tarr = length(tbins)
tarr = np.array([
[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]
])
# tarr will become a 3D array
# dimensions will be (npackets, nwavelengths, ntempbins)
tarr = np.tile(tarr, (npackets, 1, 1))
###
# note that "tarr = np.tile(tarr, (1, 1, npackets))" results in the
# array tarr.shape = (1,6,7*npackets)
###
# a_off and c_off must have same dimensions as wlngth.
cwlngth = np.array([510., 540., 580., 630., 670., 710.])
awlngth = np.array([500., 550., 600., 650., 700., 715.])
c_sig = np.array([150., 225., 200., 350., 450., 495.])
c_ref = np.array([550., 540., 530., 520., 510., 500.])
c_off = np.array([1.35, 1.30, 1.25, 1.20, 1.15, 1.10])
a_sig = np.array([250., 300., 210., 430., 470., 495.])
a_ref = np.array([450., 460., 470., 480., 490., 500.])
a_off = np.array([0.35, 0.30, 0.25, 0.20, 0.15, 0.10])
# make all of the previous vectors 2-D
for str in ['cwlngth', 'awlngth', 'c_sig', 'c_ref', 'c_off', 'a_sig', 'a_ref', 'a_off']:
exec(str + ' = np.tile(' + str + ', (npackets,1))')
# traw, Tcal, T, and PS will now be vectors, so:
traw = np.array([48355])
Tcal = np.array([20.0])
T = np.array([12.0])
PS = np.array([35.0])
for str in ['traw', 'Tcal', 'T', 'PS']:
exec(str + ' = np.tile(' + str + ', (npackets,1))')
# also test case of user selected reference wavelength for abs scatter correction
ref_wave = 695 # nearest abs wavelength (700nm) should become reference wavelength
# expected outputs
cpd_ts = np.array([6.553771, 4.807914, 5.156010, 2.788715, 1.655607, 1.171965])
apd_ts_s_ref715 = np.array([1.990992, 1.479089, 3.350109, 0.350108, 0.152712, 0.000000])
apd_ts_s_ref700 = np.array([1.379858, 1.021574, 3.235057, 0.099367, 0.000000, -0.156972])
for str in ['cpd_ts', 'apd_ts_s_ref715', 'apd_ts_s_ref700']:
exec(str + ' = np.tile(' + str + ', (npackets,1))')
# beam attenuation (beam c) test
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off, Tcal,
tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption test
# case: default reference wavelength for scatter correction
a_ts_sdef = np.zeros(6)
a_ts_sdef = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_sdef, apd_ts_s_ref715, rtol=1e-6, atol=1e-6)
# case: user selected reference wavelength for scatter correction
a_ts_s700 = np.zeros(6)
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS, ref_wave)
np.testing.assert_allclose(a_ts_s700, apd_ts_s_ref700, rtol=1e-6, atol=1e-6)
def test_opt_functions_OPTAA_vectorization_with_tscor_nans(self):
"""
Test the vectorized OPTAA wrapper functions in the opt_functions.py module;
include "a" and "c" test wavelengths outside of the (original) range of the
wavelength keys in the tscor.py file, which contains the dictionary of the
temperature and salinity correction coefficients. The dictionary keys have
been extended from [400.0 755.0] to [380.0 775.0] with entries of np.nan.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Initial code by Russell Desiderio, 29-Apr-2014. Added tests for when OPTAA
wavelengths are outside the range of the empirically derived temperature
and salinity correction wavelength keys in the original tscor.py dictionary
by modifying def test_opt_functions_OPTAA_vectorization test data.
2015-04-17: Russell Desiderio. Use np.nan instead of fill_value.
Changed signal and reference count input from float to fix.
Replaced 'exec' statements.
2015-04-21: Russell Desiderio. Cosmetic statement re-ordering and shaping of input arrays.
"""
# test inputs:
# replicate the inputs to represent 3 data packets
npackets = 3
## natively scalar inputs
traw = np.array([48355])
Tcal = np.array([20.0])
T = np.array([12.0])
PS = np.array([35.0])
# time-vectorize
[traw, Tcal, T,
PS] = [np.tile(xarray, npackets) for xarray in [traw, Tcal, T, PS]]
## natively 1D inputs
# valid tscor dictionary entries (those without nan values) are
# keyed at [400.0 755.0] nm. The dictionary has been extended to
# to [380.0 775.0] using np.nan as fill values. test:
cwlngth = np.array([[398.5, 540., 580., 630., 670., 710.]])
awlngth = np.array([[500., 550., 600., 650., 700., 761.2]])
c_sig = np.array([[150, 225, 200, 350, 450, 495]])
c_ref = np.array([[550, 540, 530, 520, 510, 500]])
c_off = np.array([[1.35, 1.30, 1.25, 1.20, 1.15, 1.10]])
a_sig = np.array([[250, 300, 210, 430, 470, 495]])
a_ref = np.array([[450, 460, 470, 480, 490, 500]])
a_off = np.array([[0.35, 0.30, 0.25, 0.20, 0.15, 0.10]])
tbins = np.array(
[[14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565]])
# time-vectorize
[cwlngth, awlngth, c_sig, c_ref, c_off, a_sig, a_ref, a_off, tbins] = [
np.tile(xarray, (npackets, 1)) for xarray in [
cwlngth, awlngth, c_sig, c_ref, c_off, a_sig, a_ref, a_off,
tbins
]
]
# nrows of tarr = length(nwlngth); ncols of tarr = length(tbins)
tarr = np.array([[[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]]])
# time-vectorize
# dimensions will be (npackets, nwavelengths, ntempbins)
tarr = np.tile(tarr, (npackets, 1, 1))
# expected outputs:
# 1st c wavelength is out-of-range of the empirical TS corrections, so the DPA
# should return nan.
cpd_ts = np.array(
[[np.nan, 4.807914, 5.156010, 2.788715, 1.655607, 1.171965]])
# to scatter-correct the 1st abs wavelength value, the c values are interpolated;
# because the 1st c value is out-of-TScor-range, the 1st abs value will also be
# a nan value. and, the last abs value will also be a nan value because 761.2>755.0.
apd_ts_s_ref700 = np.array(
[[np.nan, 1.021574, 3.235057, 0.099367, 0.000000, np.nan]])
cpd_ts = np.tile(cpd_ts, (npackets, 1))
apd_ts_s_ref700 = np.tile(apd_ts_s_ref700, (npackets, 1))
# beam attenuation (beam c) test
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off,
Tcal, tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption test
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth,
a_off, Tcal, tbins, tarr,
cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_s700,
apd_ts_s_ref700,
rtol=1e-6,
atol=1e-6)
def test_opt_functions_OPTAA_wrapper_functions(self):
"""
Test the OPTAA wrapper functions in the opt_functions.py module.
Use realistically shaped ac-s data arrays in the calling arguments:
offsets are dimensioned at the number of wavelengths;
for internal temperature, L1 temperature, and salinity,
one value per a-c dataset.
Values based on test data in DPSs and available on Alfresco.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Implemented by Russell Desiderio, 21-Feb-2014. Additional unit test data
constructed as documented in the OPTAA Unit Test document artifact
reference above.
"""
# test inputs:
tbins = np.array([14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565])
# nrows of tarr = length(wlngth); ncols of tarr = length(tbins)
tarr = np.array([
[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]
])
# a_off and c_off must have same dimensions as wlngth.
wlngth = np.array([500., 550., 600., 650., 700., 715.])
c_sig = np.array([150., 225., 200., 350., 450., 495.])
c_ref = np.array([550., 540., 530., 520., 510., 500.])
c_off = np.array([1.35, 1.30, 1.25, 1.20, 1.15, 1.10])
a_sig = np.array([250., 300., 210., 430., 470., 495.])
a_ref = np.array([450., 460., 470., 480., 490., 500.])
a_off = np.array([0.35, 0.30, 0.25, 0.20, 0.15, 0.10])
# traw, T, and PS must be scalar (before vectorization).
traw = 48355.0
Tcal = 20.0
T = 12.0
PS = 35.0
# also test case of user selected reference wavelength for abs scatter correction
ref_wave = 695 # nearest wavelength (700nm) should become reference wavelength
# expected outputs
cpd_ts = np.array([6.553646, 4.807949, 5.161655, 2.788220, 1.666362, 1.184530], ndmin=2)
apd_ts_s_ref715 = np.array([1.999989, 1.501766, 3.177048, 0.249944, 0.086438, 0.000000],
ndmin=2)
apd_ts_s_ref700 = np.array([1.750859, 1.320885, 3.068470, 0.111075, 0.000000, -0.064806],
ndmin=2)
# beam attenuation (beam c) wrapper test
c_ts = np.zeros(6)
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, wlngth, c_off, Tcal,
tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption wrapper test
# case: default reference wavelength for scatter correction
a_ts_sdef = np.zeros(6)
a_ts_sdef = optfunc.opt_optical_absorption(a_ref, a_sig, traw, wlngth, a_off, Tcal,
tbins, tarr, cpd_ts, wlngth, T, PS)
np.testing.assert_allclose(a_ts_sdef, apd_ts_s_ref715, rtol=1e-6, atol=1e-6)
# case: user selected reference wavelength for scatter correction
a_ts_s700 = np.zeros(6)
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, wlngth, a_off, Tcal,
tbins, tarr, cpd_ts, wlngth, T, PS, ref_wave)
np.testing.assert_allclose(a_ts_s700, apd_ts_s_ref700, rtol=1e-6, atol=1e-6)
def test_opt_functions_OPTAA_vectorization(self):
"""
Test the vectorization of the OPTAA wrapper functions in the opt_functions.py module.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Implemented by Russell Desiderio, 05-Mar-2014. Additional unit test data
constructed as documented in the OPTAA Unit Test document artifact
reference above.
2015-04-17: Russell Desiderio. Changed signal and reference count input from float to fix.
Replaced 'exec' statements.
2015-04-21: Russell Desiderio. Corrected input data shapes to current CI implementation.
Added scalar time record case.
"""
### set test inputs: scalar (that is, 1) time record case
# native scalars will come into the DPA with shape (1,)
traw = np.array([48355])
Tcal = np.array([20.0])
T = np.array([12.0])
PS = np.array([35.0])
# native 1D arrays will come in as 2D row vectors
cwlngth = np.array([[510., 540., 580., 630., 670., 710.]])
awlngth = np.array([[500., 550., 600., 650., 700., 715.]])
c_sig = np.array([[150, 225, 200, 350, 450, 495]])
c_ref = np.array([[550, 540, 530, 520, 510, 500]])
c_off = np.array([[1.35, 1.30, 1.25, 1.20, 1.15, 1.10]])
a_sig = np.array([[250, 300, 210, 430, 470, 495]])
a_ref = np.array([[450, 460, 470, 480, 490, 500]])
a_off = np.array([[0.35, 0.30, 0.25, 0.20, 0.15, 0.10]])
tbins = np.array(
[[14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565]])
# native 2D arrays will come in as 3D arrays, for this single time record case;
# a singleton dimension will be prepended to the native 2D array.
# native dimensions of tarr are (nwavelengths, ntempbins),
# so that tarr.shape = (1,6,7)
tarr = np.array([[[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]]])
## expected outputs to scalar time record test: 2D row vectors
# beam attenuation (beam c) test
# expected:
cpd_ts = np.array(
[[6.553771, 4.807914, 5.156010, 2.788715, 1.655607, 1.171965]])
# calculated:
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off,
Tcal, tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption test
# case: default reference wavelength for scatter correction
apd_ts_s_ref715 = np.array(
[[1.990992, 1.479089, 3.350109, 0.350108, 0.152712, 0.000000]])
a_ts_sdef = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth,
a_off, Tcal, tbins, tarr,
cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_sdef,
apd_ts_s_ref715,
rtol=1e-6,
atol=1e-6)
# absorption test
# case: user selected reference wavelength for scatter correction to abs values
ref_wave = 695 # nearest abs wavelength (700nm) should become reference wavelength
apd_ts_s_ref700 = np.array(
[[1.379858, 1.021574, 3.235057, 0.099367, 0.000000, -0.156972]])
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth,
a_off, Tcal, tbins, tarr,
cpd_ts, cwlngth, T, PS,
ref_wave)
np.testing.assert_allclose(a_ts_s700,
apd_ts_s_ref700,
rtol=1e-6,
atol=1e-6)
### multiple time records case
# replicate the inputs to represent 3 data packets
npackets = 3
[traw, Tcal, T,
PS] = [np.tile(xarray, npackets) for xarray in [traw, Tcal, T, PS]]
[cwlngth, awlngth, c_sig, c_ref, c_off, a_sig, a_ref, a_off, tbins] = [
np.tile(xarray, (npackets, 1)) for xarray in [
cwlngth, awlngth, c_sig, c_ref, c_off, a_sig, a_ref, a_off,
tbins
]
]
tarr = np.tile(tarr, (npackets, 1, 1))
# replicate the expected output data products
cpd_ts = np.tile(cpd_ts, (npackets, 1))
apd_ts_s_ref715 = np.tile(apd_ts_s_ref715, (npackets, 1))
apd_ts_s_ref700 = np.tile(apd_ts_s_ref700, (npackets, 1))
# beam attenuation (beam c) test
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off,
Tcal, tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption test
# case: default reference wavelength for scatter correction
a_ts_sdef = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth,
a_off, Tcal, tbins, tarr,
cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_sdef,
apd_ts_s_ref715,
rtol=1e-6,
atol=1e-6)
# case: user selected reference wavelength for scatter correction
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth,
a_off, Tcal, tbins, tarr,
cpd_ts, cwlngth, T, PS,
ref_wave)
np.testing.assert_allclose(a_ts_s700,
apd_ts_s_ref700,
rtol=1e-6,
atol=1e-6)
def test_opt_functions_OPTAA_a_and_c_wavelength_sets(self):
"""
Test the OPTAA wrapper functions in the opt_functions.py module.
Test a-c dataset with different wavelength values for the absorption versus
beam c optical channels. Included to test that the c optical values are correctly
interpolated onto the abs wavelengths in the scatter correction algorithm.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Implemented by Russell Desiderio, 26-Feb-2014. Additional unit test data
constructed as documented in the OPTAA Unit Test document artifact
reference above.
2015-04-17: Russell Desiderio. Changed signal and reference count input from float to fix.
"""
# test inputs:
tbins = np.array(
[14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565])
# nrows of tarr = length(wlngth); ncols of tarr = length(tbins)
tarr = np.array([[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]])
# a_off and c_off must have same dimensions as wlngth.
cwlngth = np.array([510., 540., 580., 630., 670., 710.])
awlngth = np.array([500., 550., 600., 650., 700., 715.])
c_sig = np.array([150, 225, 200, 350, 450, 495])
c_ref = np.array([550, 540, 530, 520, 510, 500])
c_off = np.array([1.35, 1.30, 1.25, 1.20, 1.15, 1.10])
a_sig = np.array([250, 300, 210, 430, 470, 495])
a_ref = np.array([450, 460, 470, 480, 490, 500])
a_off = np.array([0.35, 0.30, 0.25, 0.20, 0.15, 0.10])
# traw, T, and PS must be scalar (before vectorization).
traw = 48355
Tcal = 20.0
T = 12.0
PS = 35.0
# also test case of user selected reference wavelength for abs scatter correction
ref_wave = 695 # nearest abs wavelength (700nm) should become reference wavelength
# expected outputs
cpd_ts = np.array(
[6.553771, 4.807914, 5.156010, 2.788715, 1.655607, 1.171965],
ndmin=2)
apd_ts_s_ref715 = np.array(
[1.990992, 1.479089, 3.350109, 0.350108, 0.152712, 0.000000],
ndmin=2)
apd_ts_s_ref700 = np.array(
[1.379858, 1.021574, 3.235057, 0.099367, 0.000000, -0.156972],
ndmin=2)
# beam attenuation (beam c) wrapper test
c_ts = np.zeros(6)
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off,
Tcal, tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption wrapper test
# case: default reference wavelength for scatter correction
a_ts_sdef = np.zeros(6)
a_ts_sdef = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth,
a_off, Tcal, tbins, tarr,
cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_sdef,
apd_ts_s_ref715,
rtol=1e-6,
atol=1e-6)
# case: user selected reference wavelength for scatter correction
a_ts_s700 = np.zeros(6)
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth,
a_off, Tcal, tbins, tarr,
cpd_ts, cwlngth, T, PS,
ref_wave)
np.testing.assert_allclose(a_ts_s700,
apd_ts_s_ref700,
rtol=1e-6,
atol=1e-6)
def test_opt_functions_OPTAA_wrapper_functions(self):
"""
Test the OPTAA wrapper functions in the opt_functions.py module.
Use realistically shaped ac-s data arrays in the calling arguments:
offsets are dimensioned at the number of wavelengths;
for internal temperature, L1 temperature, and salinity,
one value per a-c dataset.
Values based on test data in DPSs and available on Alfresco.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Implemented by Russell Desiderio, 21-Feb-2014. Additional unit test data
constructed as documented in the OPTAA Unit Test document artifact
reference above.
2015-04-17: Russell Desiderio. Changed signal and reference count input from float to fix.
"""
# test inputs:
tbins = np.array(
[14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565])
# nrows of tarr = length(wlngth); ncols of tarr = length(tbins)
tarr = np.array([[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]])
# a_off and c_off must have same dimensions as wlngth.
wlngth = np.array([500., 550., 600., 650., 700., 715.])
c_sig = np.array([150, 225, 200, 350, 450, 495])
c_ref = np.array([550, 540, 530, 520, 510, 500])
c_off = np.array([1.35, 1.30, 1.25, 1.20, 1.15, 1.10])
a_sig = np.array([250, 300, 210, 430, 470, 495])
a_ref = np.array([450, 460, 470, 480, 490, 500])
a_off = np.array([0.35, 0.30, 0.25, 0.20, 0.15, 0.10])
# traw, T, and PS must be scalar (before vectorization).
traw = 48355
Tcal = 20.0
T = 12.0
PS = 35.0
# also test case of user selected reference wavelength for abs scatter correction
ref_wave = 695 # nearest wavelength (700nm) should become reference wavelength
# expected outputs
cpd_ts = np.array(
[6.553646, 4.807949, 5.161655, 2.788220, 1.666362, 1.184530],
ndmin=2)
apd_ts_s_ref715 = np.array(
[1.999989, 1.501766, 3.177048, 0.249944, 0.086438, 0.000000],
ndmin=2)
apd_ts_s_ref700 = np.array(
[1.750859, 1.320885, 3.068470, 0.111075, 0.000000, -0.064806],
ndmin=2)
# beam attenuation (beam c) wrapper test
c_ts = np.zeros(6)
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, wlngth, c_off,
Tcal, tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption wrapper test
# case: default reference wavelength for scatter correction
a_ts_sdef = np.zeros(6)
a_ts_sdef = optfunc.opt_optical_absorption(a_ref, a_sig, traw, wlngth,
a_off, Tcal, tbins, tarr,
cpd_ts, wlngth, T, PS)
np.testing.assert_allclose(a_ts_sdef,
apd_ts_s_ref715,
rtol=1e-6,
atol=1e-6)
# case: user selected reference wavelength for scatter correction
a_ts_s700 = np.zeros(6)
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, wlngth,
a_off, Tcal, tbins, tarr,
cpd_ts, wlngth, T, PS,
ref_wave)
np.testing.assert_allclose(a_ts_s700,
apd_ts_s_ref700,
rtol=1e-6,
atol=1e-6)
def test_opt_functions_OPTAA_vectorization_with_tscor_nans(self):
"""
Test the vectorized OPTAA wrapper functions in the opt_functions.py module;
include "a" and "c" test wavelengths outside of the (original) range of the
wavelength keys in the tscor.py file, which contains the dictionary of the
temperature and salinity correction coefficients. The dictionary keys have
been extended from [400.0 755.0] to [380.0 775.0] with entries of np.nan.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Initial code by Russell Desiderio, 29-Apr-2014. Added tests for when OPTAA
wavelengths are outside the range of the empirically derived temperature
and salinity correction wavelength keys in the original tscor.py dictionary
by modifying def test_opt_functions_OPTAA_vectorization test data.
2015-04-17: Russell Desiderio. Use np.nan instead of fill_value.
Changed signal and reference count input from float to fix.
Replaced 'exec' statements.
2015-04-21: Russell Desiderio. Cosmetic statement re-ordering and shaping of input arrays.
"""
# test inputs:
# replicate the inputs to represent 3 data packets
npackets = 3
## natively scalar inputs
traw = np.array([48355])
Tcal = np.array([20.0])
T = np.array([12.0])
PS = np.array([35.0])
# time-vectorize
[traw, Tcal, T, PS] = [np.tile(xarray, npackets) for xarray in [traw, Tcal, T, PS]]
## natively 1D inputs
# valid tscor dictionary entries (those without nan values) are
# keyed at [400.0 755.0] nm. The dictionary has been extended to
# to [380.0 775.0] using np.nan as fill values. test:
cwlngth = np.array([[398.5, 540., 580., 630., 670., 710.]])
awlngth = np.array([[500., 550., 600., 650., 700., 761.2]])
c_sig = np.array([[150, 225, 200, 350, 450, 495]])
c_ref = np.array([[550, 540, 530, 520, 510, 500]])
c_off = np.array([[1.35, 1.30, 1.25, 1.20, 1.15, 1.10]])
a_sig = np.array([[250, 300, 210, 430, 470, 495]])
a_ref = np.array([[450, 460, 470, 480, 490, 500]])
a_off = np.array([[0.35, 0.30, 0.25, 0.20, 0.15, 0.10]])
tbins = np.array([[14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565]])
# time-vectorize
[cwlngth, awlngth, c_sig, c_ref, c_off, a_sig, a_ref, a_off, tbins] = [
np.tile(xarray, (npackets, 1)) for xarray in [
cwlngth, awlngth, c_sig, c_ref, c_off, a_sig, a_ref, a_off, tbins]]
# nrows of tarr = length(nwlngth); ncols of tarr = length(tbins)
tarr = np.array([[
[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]
]])
# time-vectorize
# dimensions will be (npackets, nwavelengths, ntempbins)
tarr = np.tile(tarr, (npackets, 1, 1))
# expected outputs:
# 1st c wavelength is out-of-range of the empirical TS corrections, so the DPA
# should return nan.
cpd_ts = np.array([[np.nan, 4.807914, 5.156010, 2.788715, 1.655607, 1.171965]])
# to scatter-correct the 1st abs wavelength value, the c values are interpolated;
# because the 1st c value is out-of-TScor-range, the 1st abs value will also be
# a nan value. and, the last abs value will also be a nan value because 761.2>755.0.
apd_ts_s_ref700 = np.array([[np.nan, 1.021574, 3.235057, 0.099367, 0.000000, np.nan]])
cpd_ts = np.tile(cpd_ts, (npackets, 1))
apd_ts_s_ref700 = np.tile(apd_ts_s_ref700, (npackets, 1))
# beam attenuation (beam c) test
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off, Tcal,
tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption test
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_s700, apd_ts_s_ref700, rtol=1e-6, atol=1e-6)
def test_opt_functions_OPTAA_vectorization(self):
"""
Test the vectorization of the OPTAA wrapper functions in the opt_functions.py module.
OOI (2013). Data Product Specification for Optical Beam Attenuation
Coefficient. Document Control Number 1341-00690.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00690_Data_Product_SPEC_OPTATTN_OOI.pdf)
OOI (2013). Data Product Specification for Optical Absorption
Coefficient. Document Control Number 1341-00700.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI
>> Controlled >> 1000 System Level >>
1341-00700_Data_Product_SPEC_OPTABSN_OOI.pdf)
OOI (2014). OPTAA Unit Test. 1341-00700_OPTABSN Artifact.
https://alfresco.oceanobservatories.org/ (See: Company Home >> OOI >>
>> REFERENCE >> Data Product Specification Artifacts >> 1341-00700_OPTABSN >>
OPTAA_unit_test.xlsx)
Implemented by Russell Desiderio, 05-Mar-2014. Additional unit test data
constructed as documented in the OPTAA Unit Test document artifact
reference above.
2015-04-17: Russell Desiderio. Changed signal and reference count input from float to fix.
Replaced 'exec' statements.
2015-04-21: Russell Desiderio. Corrected input data shapes to current CI implementation.
Added scalar time record case.
"""
### set test inputs: scalar (that is, 1) time record case
# native scalars will come into the DPA with shape (1,)
traw = np.array([48355])
Tcal = np.array([20.0])
T = np.array([12.0])
PS = np.array([35.0])
# native 1D arrays will come in as 2D row vectors
cwlngth = np.array([[510., 540., 580., 630., 670., 710.]])
awlngth = np.array([[500., 550., 600., 650., 700., 715.]])
c_sig = np.array([[150, 225, 200, 350, 450, 495]])
c_ref = np.array([[550, 540, 530, 520, 510, 500]])
c_off = np.array([[1.35, 1.30, 1.25, 1.20, 1.15, 1.10]])
a_sig = np.array([[250, 300, 210, 430, 470, 495]])
a_ref = np.array([[450, 460, 470, 480, 490, 500]])
a_off = np.array([[0.35, 0.30, 0.25, 0.20, 0.15, 0.10]])
tbins = np.array([[14.5036, 15.5200, 16.4706, 17.4833, 18.4831, 19.5196, 20.5565]])
# native 2D arrays will come in as 3D arrays, for this single time record case;
# a singleton dimension will be prepended to the native 2D array.
# native dimensions of tarr are (nwavelengths, ntempbins),
# so that tarr.shape = (1,6,7)
tarr = np.array([[
[0.0, -0.004929, -0.004611, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004611, -0.004418, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004418, -0.004355, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004355, -0.004131, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.004131, -0.003422, 0.0, 0.0, 0.0, 0.0],
[0.0, -0.003422, -0.002442, 0.0, 0.0, 0.0, 0.0]
]])
## expected outputs to scalar time record test: 2D row vectors
# beam attenuation (beam c) test
# expected:
cpd_ts = np.array([[6.553771, 4.807914, 5.156010, 2.788715, 1.655607, 1.171965]])
# calculated:
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off, Tcal,
tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption test
# case: default reference wavelength for scatter correction
apd_ts_s_ref715 = np.array([[1.990992, 1.479089, 3.350109, 0.350108, 0.152712, 0.000000]])
a_ts_sdef = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_sdef, apd_ts_s_ref715, rtol=1e-6, atol=1e-6)
# absorption test
# case: user selected reference wavelength for scatter correction to abs values
ref_wave = 695 # nearest abs wavelength (700nm) should become reference wavelength
apd_ts_s_ref700 = np.array([[1.379858, 1.021574, 3.235057, 0.099367, 0.000000, -0.156972]])
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS, ref_wave)
np.testing.assert_allclose(a_ts_s700, apd_ts_s_ref700, rtol=1e-6, atol=1e-6)
### multiple time records case
# replicate the inputs to represent 3 data packets
npackets = 3
[traw, Tcal, T, PS] = [np.tile(xarray, npackets) for xarray in [traw, Tcal, T, PS]]
[cwlngth, awlngth, c_sig, c_ref, c_off, a_sig, a_ref, a_off, tbins] = [
np.tile(xarray, (npackets, 1)) for xarray in [
cwlngth, awlngth, c_sig, c_ref, c_off, a_sig, a_ref, a_off, tbins]]
tarr = np.tile(tarr, (npackets, 1, 1))
# replicate the expected output data products
cpd_ts = np.tile(cpd_ts, (npackets, 1))
apd_ts_s_ref715 = np.tile(apd_ts_s_ref715, (npackets, 1))
apd_ts_s_ref700 = np.tile(apd_ts_s_ref700, (npackets, 1))
# beam attenuation (beam c) test
c_ts = optfunc.opt_beam_attenuation(c_ref, c_sig, traw, cwlngth, c_off, Tcal,
tbins, tarr, T, PS)
np.testing.assert_allclose(c_ts, cpd_ts, rtol=1e-6, atol=1e-6)
# absorption test
# case: default reference wavelength for scatter correction
a_ts_sdef = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS)
np.testing.assert_allclose(a_ts_sdef, apd_ts_s_ref715, rtol=1e-6, atol=1e-6)
# case: user selected reference wavelength for scatter correction
a_ts_s700 = optfunc.opt_optical_absorption(a_ref, a_sig, traw, awlngth, a_off, Tcal,
tbins, tarr, cpd_ts, cwlngth, T, PS, ref_wave)
np.testing.assert_allclose(a_ts_s700, apd_ts_s_ref700, rtol=1e-6, atol=1e-6)