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Commit fa46ae1f authored by Harmel Tristan's avatar Harmel Tristan
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clean up package

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build/lib/process/process.py deleted 100644 → 0
View file @ c9a02a96
import numpy as np
import pandas as pd
from scipy import interpolate, integrate
from scipy.optimize import curve_fit
import plotly.plotly as py
# import plotly.graph_objs as go
from plotly.graph_objs import *
from utils.utils import reshape as r
import utils.auxdata as ua
from ..config import *
class awr_process:
def __init__(self, df=None, wl=None):
self.df = df
self.aot = 0.1
self.ws = 2
self.wl = wl
self.rhosoaa_fine_file = rhosoaa_fine_file
self.rhosoaa_coarse_file = rhosoaa_coarse_file
self.M1999_file = M1999_file
self.M2015_file = M2015_file
self.load_rho_lut()
self.rho = self.rhosoaa_fine
def load_rho_lut(self):
self.rhosoaa_fine = pd.read_csv(self.rhosoaa_fine_file, index_col=[0, 1, 2, 3, 4, 5])
self.rhosoaa_coarse = pd.read_csv(self.rhosoaa_coarse_file, index_col=[0, 1, 2, 3, 4, 5])
self.rhoM1999 = pd.read_csv(self.M1999_file, skiprows=7, index_col=[0, 1, 2, 3])
self.rhoM2015 = pd.read_csv(self.M2015_file, skiprows=8, index_col=[0, 1, 2, 3])
self.rhoM1999.dropna(inplace=True)
self.rhoM2015.dropna(inplace=True)
def get_rho_values(self, sza, vza, azi, ws=[2], aot=[0.1], wl=[550], sunglint=False):
'''
Interpolate the rho factor values from tabulated data
:param sza: solar zenith angle in deg, array-like
:param vza: view zenith angle in deg, array-like
:param azi: relative azimuth in deg (=0 when looking at Sun), array-like
:param ws: wind speed, m/s,(based on Cox-Munk parametrization of surface roughness) array-like
:param aot: aerosol optical thickness at 550 nm, array-like
:param wl: wavelength in nm, array-like
:param sunglint: add sunglint component in rho calculation if True
:return:
'''
grid = self.rho.rho.index.levels
# convert pandas dataframe into 6D array of the tabulated rho values for interpolation
rhoname = 'rho'
if sunglint:
rhoname = 'rho_g'
rho_6d = r().df2ndarray(self.rho, rhoname)
rho_ = calc().spline_2d(grid[-2:], rho_6d, (azi, vza))
rho_wl = calc().spline_4d(grid[:-2], rho_, (ws, aot, wl, sza))
return rho_wl.squeeze()
def get_rho_mobley(self, rhodf, sza, vza, azi, ws):
'''
Get the Mobley rho factor from cubic interpolation in the tabulated values
:param rhodf:
:param sza:
:param vza:
:param azi:
:param ws:
:return:
'''
rhodf = rhodf.query('sza<75 & vza >0')
rhodf.index = rhodf.index.remove_unused_levels()
# grid {wind, sza, vza, azi}
grid = rhodf.index.levels
rho_ = r().df2ndarray(rhodf, 'rho')
rho_mobley = calc().spline_4d(grid, rho_, (ws, sza, vza, azi))
return rho_mobley
def call_process(self, vza=[40], azi=[135], ws=2, aot=0.1):
wl = self.wl
Lt = self.df.loc[:, ("Lt")]
Lsky = self.df.loc[:, ("Lsky")]
Ed = self.df.loc[:, ("Ed")]
sza = self.df.loc[:, ("sza")].values.mean()
Rrs = self.process(wl, Lt, Lsky, Ed, sza, vza, azi, ws, aot)
Rrs.columns = pd.MultiIndex.from_product([['Rrs(awr)'], self.Rrs.columns], names=['param', 'wl'])
self.Rrs = Rrs
return self.Rrs
def process(self, wl, Lt, Lsky, Ed, sza, vza=[40], azi=[135], ws=[2], aot=[0.1]):
'''
:param wl:
:param Lt:
:param Lsky:
:param Ed:
:param sza:
:param vza:
:param azi:
:param ws:
:param aot:
:return:
'''
rho = self.get_rho_values([sza], vza, azi, wl=wl, ws=ws, aot=aot)
self.Rrs = (Lt - rho * Lsky) / Ed
return self.Rrs, rho
class swr_process:
def __init__(self, df=None, wl=None, ):
self.df = df
self.wl = wl
def call_process(self, shade_corr=False):
wl = self.wl
Lu = self.df.loc[:, ("Lu0+")]
Ed = self.df.loc[:, ("Ed")]
sza = self.df.loc[:, ("sza")].values.mean()
Rrs = self.process(Lu, Ed, sza, wl, shade_corr=shade_corr)
Rrs.columns = pd.MultiIndex.from_product([['Rrs(swr)'], Rrs.columns], names=['param', 'wl'])
self.Rrs = Rrs
return Rrs
def process(self, Lu, Ed, sza, wl, R=0.05, shade_corr=False):
Rrs = Lu / Ed
ang_w = calc().angle_w(sza)
iopw = ua.iopw()
iopw.load_iopw()
iopw.get_iopw(wl)
a, bb = iopw.aw, iopw.bbw
# TODO add particulate and dissolved component to a and bb values
# a,bb = aux.get_iop(..., withwater=True)
acdom = ua.cdom(0.5, wl).get_acdom()
a = a + acdom + 0.4
bb = bb + 0.05
if shade_corr:
Rrs = self.shade_corr(Rrs, R, ang_w, a, bb, wl)
# Rrs.columns = pd.MultiIndex.from_product([['Rrs(swr)'], Rrs.columns], names=['param', 'wl'])
self.Rrs = Rrs
self.a = a
self.bb = bb
self.acdom = acdom
return self.Rrs
def epsilon(self, K, R, ang_w):
'''
epsilon from Shang et al, 2017, Applied Optics
:param K:
:param R:
:param ang_w: Sun zenith angle below surface (in deg)
:return:
'''
self.eps = np.array(1 - np.exp(-K * R / np.tan(np.radians(ang_w))))
return self.eps
def K(self, a, bb, ang_w):
'''
K (sum attenuation coef. of Lu in and outside the shade) from Shang et al, 2017, Applied Optics
:param a: total absorption coefficient (m-1)
:param bb: total backscattering coefficient (m-1)
:param ang_w: Sun zenith angle below surface (in deg)
:return:
'''
sin_ang_w = np.sin(np.radians(ang_w))
self.K_ = (3.15 * sin_ang_w + 1.15) * a * np.exp(-1.57 * bb) \
+ (5.62 * sin_ang_w - 0.23) * bb * np.exp(-0.5 * a)
return self.K_
def shade_corr(self, Rrs, R, ang_w, a, bb, wl, wl_cutoff=900):
'''
Correction of shading error from Shang et al, 2017, Applied Optics
:param Rrs:
:param R:
:param ang_w:
:param a:
:param bb:
:return:
'''
K = self.K(a, bb, ang_w)
eps = self.epsilon(K, R, ang_w)
eps[wl > wl_cutoff] = 0
self.Rrs = Rrs / (1 - eps)
return self.Rrs
class iwr_process:
def __init__(self, df=None, wl=None, ):
self.df = df
self.wl = wl
def process(self):
wl = self.wl
df = self.df
reflectance = df.loc[:, ("Luz")] / df.loc[:, ("Edz")]
reflectance.columns = pd.MultiIndex.from_product([['reflectance'], reflectance.columns], names=['param', 'wl'])
self.reflectance = reflectance
df['rounded_depth', ''] = df.prof_Edz.round(1)
df.groupby('rounded_depth').mean()
return self.reflectance
@staticmethod
def f_Edz(depth, Kd, Ed0):
'''simple Edz model for homogeneous water column'''
return Ed0 * np.exp(-Kd*depth)
@staticmethod
def f_logEdz(depth, Kd, Ed0):
'''simple Edz model for homogeneous water column'''
return np.log(1 + iwr_process.f_Edz(depth, Kd, Ed0)) #Ed0) -Kd*depth
def Kd(self, depth, Edz):
Kd = np.diff(Edz) / np.diff(depth)
def plot_raw(self,x='Luz',y='prof_Luz'):
trace = Scattergl(
x=self.df[x].values,
y=self.df[y].values,
text=self.df.index.get_level_values(0),
hoverinfo="text",
marker={
'size': 7,
'opacity': 0.5,
# 'color': 'rgba({}, {}, {}, {})'.format(*s_m.to_rgba(parameters[i]).flatten()),
# x.unique(),#color': df.index.get_level_values(0),
'line': {'width': 0.5, 'color': 'white'},
},
# error_y=ErrorY(
# type='data',
# array=df['Error'],
# thickness=1.5,
# width=2,
# color='#B4E8FC'
# ),
)
layout = Layout(
height=450,
xaxis=dict(
range=[0, 200],
showgrid=False,
showline=False,
zeroline=False,
fixedrange=True,
tickvals=[0, 50, 100, 150, 200],
ticktext=['200', '150', '100', '50', '0'],
title=''
),
yaxis=dict(
range=[min(-5, min(self.df[y])),
max(0, max(self.df[y]))],
showline=False,
fixedrange=True,
zeroline=False,
# nticks=max(6, round(df['Speed'].iloc[-1]/10))
),
margin=Margin(
t=45,
l=50,
r=50
)
)
return Figure(data=[trace], layout=layout)
class self_shading:
def __init__(self):
'''GordonDing 1992 values for epsilon'''
self.ang = np.linspace(0, 90, 10)
self.eps_dir_LuZ = [2.17, 2.17, 2.23, 2.23, 2.29, 2.37, 2.41, 2.45, 2.45, 2.45]
self.eps_dir_EuZ = [3.14, 3.14, 3.05, 2.94, 2.80, 2.64, 2.47, 2.33, 2.33, 2.33]
self.eps_dif_LuZ = 4.61,
self.eps_dif_EuZ = 2.70
def epsilon(self, sza):
eps = interpolate.interp1d(self.ang, self.eps_dif_EuZ)(sza)
return eps
class calc:
def __init__(self):
pass
def PAR(self, wl, Ed):
'''
Compute instantaneous PAR from Ed spectrum.
PAR in mW m-2
PAR_quanta in µmol photon m-2 s-1
:param wl:
:param Ed:
:return:
'''
# ---------------------------------------------
# PARAMETERS
# Planck constant in J s or W s2
h = 6.6260695729e-3 # d-34
# light speed in m s-1
c = 2.99792458e0 # d8
# Avogadro Number in mol-1
Avogadro = 6.0221412927e0 # d23
hc = Avogadro * h * c
# ---------------------------------------------
idx_par = (wl >= 400) & (wl <= 700)
wl = wl[idx_par]
Ed = Ed[idx_par]
par = integrate.trapz(Ed, wl)
par_quanta = integrate.trapz(np.multiply(wl,Ed), wl) / hc
return par, par_quanta
def earth_sun_correction(self, dayofyear):
'''
Earth-Sun distance correction factor for adjustment of mean solar irradiance
:param dayofyear:
:return: correction factor
'''
theta = 2. * np.pi * dayofyear / 365
d2 = 1.00011 + 0.034221 * np.cos(theta) + 0.00128 * np.sin(theta) + \
0.000719 * np.cos(2 * theta) + 0.000077 * np.sin(2 * theta)
return d2
def bidir(self, sza, vza, azi):
bidir = 1
return bidir
def angle_w(self, angle_air, n=1.334):
'''
convert above surface angle (angle_air) into sub-surface angle
:param angle_air in deg
:param n: refractive index of water
:return: sub-surface angle in deg
'''
return np.degrees(np.arcsin(np.sin(np.radians(angle_air)) / n))
def spline_2d(self, gin, arr, gout):
'''
Interpolation of a 6D array (arr) with bicubic splines on a 2D grid
corresponding to the 5th and 6th dimensions of arr.
Return 4D array interpolated on gout.
:param gin: regular 2D grid of the tabulated data (tuple/array/list of arrays)
:param arr: tabulated data (N dimensions, interpolation on N-1 and N)
:param gout: new 2D grid on which data are interpolated (with dims 2 and 3 of the same length);
(tuple/array/list of arrays)
:return: Interpolated data (1D or 3D array depending on the dimension shapes of gout
'''
N = arr.shape
interp = np.zeros(N[:-2])
for i in range(N[0]):
for j in range(N[1]):
for k in range(N[2]):
for l in range(N[3]):
interp[i, j, k, l] = interpolate.RectBivariateSpline(gin[0], gin[1], arr[i, j, k, l, ...])(
gout[0], gout[1], grid=False)
return interp
def spline_4d(self, gin, lut, gout):
'''
Interpolation with two successive bicubic splines on a regular 4D grid.
Designed for interpolation in radiative transfer look-up tables with the two last dimensions
(i.e., wavelength and solar zenith angle) of the same length.
Those dimensions are then reduced/merged to a single one to get interpolated data on a 3D grid.
:param gin: regular 4D grid of the tabulated data (tuple/array/list of arrays)
:param lut: tabulated data
:param gout: new 4D grid on which data are interpolated (with dims 2 and 3 of the same length);
(tuple/array/list of arrays)
:return: Interpolated data (1D or 3D array depending on the dimension shapes of gout
'''
N = gin[0].__len__(), gin[1].__len__(), gin[2].__len__(), gin[3].__len__()
Nout = gout[0].__len__(), gout[1].__len__(), gout[2].__len__()
tmp = np.zeros([N[0], N[1], Nout[2]])
for i in range(N[0]):
for j in range(N[1]):
tmp[i, j, :] = interpolate.RectBivariateSpline(gin[2], gin[3], lut[i, j, :, :])(gout[2], gout[3], grid=False)
if Nout[0] == Nout[1] == 1:
interp = np.ndarray(Nout[2])
for iband in range(Nout[2]):
interp[iband] = interpolate.RectBivariateSpline(gin[0], gin[1], tmp[:, :, iband])(gout[0], gout[1], grid=False)
else:
interp = np.ndarray([Nout[0], Nout[1], Nout[2]])
for iband in range(Nout[2]):
interp[:, :, iband] = interpolate.RectBivariateSpline(gin[0], gin[1], tmp[:, :, iband])(gout[0], gout[1],
grid=True)
return interp
build/lib/process/process_compar_awr.py deleted 100644 → 0
View file @ c9a02a96
import base64
import pandas as pd
import numpy as np
import glob
import io
import os
from textwrap import dedent as d
import re
import matplotlib.pyplot as plt
import plotly
import plotly.graph_objs as go
from scipy.interpolate import interp1d
from utils.sunposition import sunpos
import utils.utils as u
import utils.auxdata as ua
from trios.process import *
coordf = glob.glob("/DATA/OBS2CO/data/info/mesures_in_situ.csv")[0]
coords = pd.read_csv(coordf, sep=';')
dirfig = os.path.abspath('/DATA/OBS2CO/data/trios/fig')
awrfiles = glob.glob("/DATA/OBS2CO/data/trios/raw/aw*idpr*.csv")
# awrfiles = glob.glob("/DATA/OBS2CO/data/trios/test_setup/raw/aw*idpr*.csv")
swrfiles = glob.glob("/DATA/OBS2CO/data/trios/raw/Lu0*idpr*.csv")
iopw = ua.iopw()
iopw.load_iopw()
def add_curve(ax, x, mean, std, c='red', label=''):
ax.plot(x, mean, linestyle='solid', c=c, lw=2.5,
alpha=0.8, label=label)
ax.fill_between(x,
mean - std,
mean + std, alpha=0.35, color=c)
idpr = '167'
# get idpr numbers
idprs = np.unique([re.findall(r'idpr(\d+)', x)[0] for x in swrfiles])
#idprs = np.array(['170'])
# loop over idpr
for idpr in idprs:
c = coords[coords.ID_prel == int(idpr)] # .values[0]
lat = c['Lat'].values[0]
lon = c['Lon'].values[0]
alt = 0 # c['Altitude']
name = c['ID_lac'].values[0]
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(10, 8))
fig.subplots_adjust(left=0.1, right=0.9, hspace=.5, wspace=0.65)
# -----------------------------------------------
# SWR processing
# -----------------------------------------------
uswr = u.swr_data(idpr, swrfiles)
if uswr.file:
df, wl_swr = uswr.reader(lat, lon, alt)
df['sza', ''] = np.nan
for index, row in df.iterrows():
# print index
sza = sunpos(index, lat, lon, alt)[1]
df.at[index, 'sza'] = sza
swr = swr_process(df, wl_swr)
Rrs_swr = swr.call_process()
add_curve(ax, wl_swr, Rrs_swr.transpose().mean(axis=1), Rrs_swr.transpose().std(axis=1), label='swr', c='black')
Rrs_swr = swr.call_process(shade_corr=True)
add_curve(ax, wl_swr, Rrs_swr.transpose().mean(axis=1), Rrs_swr.transpose().std(axis=1), label='swr', c='red')
# -----------------------------------------------
# AWR processing
# -----------------------------------------------
azi = 135
vza = 40
awr = u.awr_data(idpr, awrfiles)
if awr.Edf:
index_idx = [0]
d = u.data(index_idx)
Ed, wl_Ed = d.load_csv(awr.Edf)
Lsky, wl_Lsky = d.load_csv(awr.Lskyf)
Lt, wl_Lt = d.load_csv(awr.Ltf)
# ''' interpolate Ed and Lsky data upon Lt wavelength'''
wl = wl_Lt
Lt.columns = pd.MultiIndex.from_tuples(zip(['Lt'] * len(wl), wl), names=['param', 'wl'])
intEd = interp1d(wl_Ed, Ed.values, fill_value='extrapolate')(wl)
newEd = pd.DataFrame(index=Ed.index,
columns=pd.MultiIndex.from_tuples(zip(['Ed'] * len(wl), wl), names=['param', 'wl']),
data=intEd)
intLsky = interp1d(wl_Lsky, Lsky.values, fill_value='extrapolate')(wl)
newLsky = pd.DataFrame(index=Lsky.index, columns=pd.MultiIndex.from_tuples(zip(['Lsky'] * len(wl), wl),
names=['param', 'wl']), data=intLsky)
awr = awr_process()
ws = [2]
print(azi, vza)
Lsky = newLsky # .loc[(newLsky.index.get_level_values(1) == vza) & (newLsky.index.get_level_values(2) == azi)]
Ed = newEd # .loc[(newEd.index.get_level_values(1) == vza) & (newEd.index.get_level_values(2) == azi)]
# Lsky_idx = Lsky.index
# Ed_idx= Ed.index
# Lt_idx = Lt.index
# Lsky.reset_index(level=[1,2],inplace=True)
# Ed.reset_index(level=[1,2],inplace=True)
# Lt.reset_index(level=[1,2],inplace=True)
# merge sensor data on time
df = pd.merge_asof(Lt, Ed, left_index=True, right_index=True, tolerance=pd.Timedelta("2 seconds"),
direction="nearest")
df = pd.merge_asof(df, Lsky, left_index=True, right_index=True, tolerance=pd.Timedelta("2 seconds"),
direction="nearest")
# add solar angle data and idpr
# compute solar angle (mean between fisrt and last aqcuisition time
df['sza', ''] = np.nan
for index, row in df.iterrows():
# print index
sza = sunpos(index, lat, lon, alt)[1]
df.at[index, 'sza'] = sza
rho_h = awr.get_rho_values([df.sza.mean()], [vza], [azi], wl=wl)
rho15 = awr.get_rho_mobley(awr.rhoM2015, [df.sza.mean()], [vza], [azi], [ws])
rho99 = awr.get_rho_mobley(awr.rhoM1999, [df.sza.mean()], [vza], [azi], [ws])
Rrs_h = (df.loc[:, 'Lt'] - rho_h * df.loc[:, 'Lsky']) / df.loc[:, 'Ed']
Rrs15 = (df.loc[:, 'Lt'] - rho15 * df.loc[:, 'Lsky']) / df.loc[:, 'Ed']
Rrs99 = (df.loc[:, 'Lt'] - rho99 * df.loc[:, 'Lsky']) / df.loc[:, 'Ed']
# plt.figure()
add_curve(ax, wl, Rrs15.transpose().mean(axis=1), Rrs15.transpose().std(axis=1),
label='M2015 (' + str(rho15) + ')')
add_curve(ax, wl, Rrs99.transpose().mean(axis=1), Rrs99.transpose().std(axis=1), c='orange',
label='M1999(' + str(rho99) + ')')
add_curve(ax, wl, Rrs_h.transpose().mean(axis=1), Rrs_h.transpose().std(axis=1), c='grey',
label='h(' + str(rho_h.mean()) + ')')
ax.set_title('azi=' + str(azi) + ', vza=' + str(vza) + ', sza=' + str(sza))
ax.legend(loc='best', frameon=False)
ax.set_ylabel(r'$R_{rs}\ (sr^{-1})$')
ax.set_xlabel(r'Wavelength (nm)')
fig.savefig(os.path.join(dirfig, 'trios_awr_' + name + '_idpr' + idpr + '.png'))
plt.close()
build/lib/process/process_test_setup.py deleted 100644 → 0
View file @ c9a02a96
import base64
import pandas as pd
import numpy as np
import glob
import io
import os
from textwrap import dedent as d
import re
import matplotlib.pyplot as plt
import plotly
import plotly.graph_objs as go
from scipy.interpolate import interp1d
from utils.sunposition import sunpos
import utils.utils as u
from trios.process import *
coordf = glob.glob("/DATA/OBS2CO/data/info/mesures_in_situ.csv")[0]
coords = pd.read_csv(coordf, sep=';'