def test_xarray_with_coords():
pytest.importorskip('dask')
SA_chunk = SA.chunk(chunks={'y': 1, 't': 1})
CT_chunk = CT.chunk(chunks={'y': 1, 't': 1})
lat_chunk = lat.chunk(chunks={'y': 1})
# Dimensions and cordinates match:
expected = gsw.sigma0(SA_vals, CT_vals)
xarray = gsw.sigma0(SA, CT)
chunked = gsw.sigma0(SA_chunk, CT_chunk)
assert_allclose(xarray, expected)
assert_allclose(chunked, expected)
# Broadcasting along dimension required (dimensions known)
expected = gsw.alpha(SA_vals, CT_vals, p_vals[np.newaxis, :, np.newaxis])
xarray = gsw.alpha(SA, CT, p)
chunked = gsw.alpha(SA_chunk, CT_chunk, p)
assert_allclose(xarray, expected)
assert_allclose(chunked, expected)
# Broadcasting along dimension required (dimensions unknown/exclusive)
expected = gsw.z_from_p(p_vals[:, np.newaxis], lat_vals[np.newaxis, :])
xarray = gsw.z_from_p(p, lat)
chunked = gsw.z_from_p(p, lat_chunk)
assert_allclose(xarray, expected)
assert_allclose(chunked, expected)
def plot_TS(K, T, S, labels, tit, plotdir):
col = ['r', 'c', 'pink', 'g', 'b']
ss = np.linspace(32.5, 35.5, 16)
tt = np.linspace(-3, 3, 15)
ss2, tt2 = np.meshgrid(ss, tt)
s0 = gsw.sigma0(ss2, tt2)
vd = np.arange(23, 30, 0.3)
plt.figure(figsize=(15, 10))
for ii in range(5):
ax = plt.subplot(2, 3, ii + 1)
idx = np.where(labels == ii)[0][:]
ax.scatter(S[idx, :], T[idx, :], color=col[ii], alpha=0.5, s=10)
ax.set_xlim(32.5, 35.5)
ax.set_ylim(-2.2, 2)
cs = ax.contour(ss,
tt,
s0,
vd,
colors='k',
linestyles='dashed',
linewidths=0.5,
alpha=0.8)
plt.clabel(cs, inline=0, fontsize=10)
ax.set_xlabel('SA')
ax.set_ylabel('CT')
outfile = os.path.join(plotdir, 'gmm_TS_K%i_%s.png' % (K, tit))
plt.savefig(outfile, bbox_inches='tight', dpi=200)
plt.show()
def gambar_TS(self, ax, S, T, cores, labels, jumlah_garis_TS,
posisi_judul):
# T-S Diagram.
s = ma.masked_invalid(S).mean(axis=1)
t = ma.masked_invalid(T).mean(axis=1)
Te = np.linspace(t.min(), t.max(), jumlah_garis_TS)
Se = np.linspace(s.min(), s.max(), jumlah_garis_TS)
Tg, Sg = np.meshgrid(Te, Se)
sigma_theta = gsw.sigma0(Sg, Tg)
cnt = np.linspace(sigma_theta.min(), sigma_theta.max(),
jumlah_garis_TS)
divider = make_axes_locatable(ax)
axTS = divider.append_axes("right", 2, pad=1)
#axTS.set(xlim=(33.2,35), ylim=(6,33))
cs = axTS.contour(Sg,
Tg,
sigma_theta,
colors='grey',
levels=cnt,
zorder=1)
kw = dict(color='r', fontsize=14, fontweight='black')
for i in range(cores.shape[1]):
axTS.text(cores[1, i], cores[0, i], labels[i], **kw)
axTS.plot(s, t, 'k')
axTS.yaxis.set_label_position(posisi_judul)
axTS.yaxis.set_ticks_position(posisi_judul)
axTS.set_xlabel("Salinity [g kg$^{-1}$]")
axTS.set_ylabel("Temperature [$^\circ$C]", rotation=-90, labelpad=20)
axTS.set_title("T-S Diagram")
axTS.xaxis.set_major_locator(MaxNLocator(nbins=4))
def o2pl2pkg(p_col, t_col, sal_col, dopl_col, dopkg_col, lat_col, lon_col,
inMat):
"""o2pl2pkg convert ml/l dissolved oxygen to umol/kg
Input:
- t_col, temperature column header deg c.
- sal_col, salinity column header psu.
- dopl_col, dissolved column header ml/l.
- dopkg_col, dissolved column header umol/kg
- lat_col, latitude for entire cast deg.
- lon_col, longitude for entire cast deg.
- inMat, dtype ndarray processed ctd time data.
Output:
- Converted Oxygen column umol/kg
Example:
>>> # linear interpolation of NaNs
>>> outArray = o2pl2kg(inArr)
"""
pkg = np.ndarray(shape=len(inMat), dtype=[(dopkg_col, np.float)])
# Absolute sailinity from Practical salinity.
SA = gsw.SA_from_SP(inMat[sal_col], inMat[p_col], inMat[lat_col],
inMat[lon_col])
# Conservative temperature from insitu temperature.
CT = gsw.CT_from_t(SA, inMat[t_col], inMat[p_col])
s0 = gsw.sigma0(
SA, CT
) # Potential density from Absolute Salinity g/Kg Conservative temperature deg C.
# Convert DO ml/l to umol/kg
for i in range(0, len(inMat[dopl_col])):
pkg[i] = inMat[dopl_col][i] * 44660 / (s0[i] + 1000)
return pkg
def convert_ctddata(ctd_dir):
'''
Reads raw CTD profile data and converts it to xarray
'''
from epsilontools.tools import load_matfile
dat = load_matfile(ctd_dir)
time = pd.to_datetime(dat['UXT'], unit='s')
dat = xr.Dataset(
{
'T': ('time', dat['T']),
'S': ('time', dat['S']),
'p': ('time', dat['P'])
},
coords={
'time': time,
})
# TODO: need to check units when integrating!
dat['sigma'] = ('time', gsw.sigma0(dat['S'], dat['T']) + 1000)
dat['z'] = -dat.p
dat['w'] = dat.z.differentiate('time', datetime_unit='s')
temp = dat.swap_dims({'time': 'z'})
temp['N2'] = -9.81 * temp.sigma.differentiate('z') / 1025
temp['dTdz'] = temp.T.differentiate('z')
return temp.swap_dims({'z': 'time'})
def calc_mld(SA, CT, P, crit=.125, sd=5.):
psi = find_nearest(P, sd)[1]
rho = gsw.sigma0(SA, CT)
rho_surf = rho[:psi + 1].mean()
idx = np.where(rho >= rho_surf + crit)[0][0]
mld = P[idx]
return mld
def aaoptode_sternvolmer(foil_coef, optode_phase, tempc, salin, press):
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%
# %% AAOPTODE_STERNVOLMER: For Aanderaa optode 4XXX series, to interpret
# % calphase measurements based on the Stern Volmer equation. To be used in
# % combination with aaoptode_salpresscorr, which handles salinity and
# % pressure corrections.
#
# %% INPUTS
# % foil_coef: Struct of calibration coefficients
# % optode_phase: vector of optode phase measurements (calphase or dphase)
# % tempc: temperature in deg C
# % salin: Salinity
# % press: pressure (db) for pressure correction
#
# %% OUTPUTS
# % optode_uM: Oxygen concentration in uM
# % optode_umolkg: Oxygen concentration in umol/kg
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# % H. Palevsky, 8/6/2019, based on sg_aaoptode.m
# % Uchida et al. 2008 Stern-Volmer based calbration mode
C = foil_coef;
Ksv = C[0] + C[1]*tempc+C[2]*tempc**2;
P0 = C[3] + C[4]*tempc;
PC = C[5] + C[6]*optode_phase;
optode_uM = ((P0/PC)-1)/Ksv;
# % note - this uses SR, reference salinity
SA = 35.16504/35*salin;
CT = gsw.CT_from_t(SA,tempc,press);
optode_umolkg = 1000*optode_uM/(1000+ gsw.sigma0(SA,CT));
return optode_uM, optode_umolkg
def add_ctd_params(df_in: MutableMapping[str, Sequence],
cfg: Mapping[str, Any],
lon=16.7,
lat=55.2):
"""
Calculate all parameters from 'sigma0', 'depth', 'soundV', 'SA' that is specified in cfg['out']['data_columns']
:param df_in: DataFrame with columns:
'Pres', 'Temp90' or 'Temp', and may be others:
'Lat', 'Lon': to use instead cfg['in']['lat'] and lat and -//- lon
:param cfg: dict with fields:
['out']['data_columns'] - list of columns in output dataframe
['in'].['b_temp_on_its90'] - optional
:param lon: # 54.8707 # least priority values
:param lon: # 19.3212
:return: DataFrame with only columns specified in cfg['out']['data_columns']
"""
ctd = df_in
params_to_calc = set(cfg['out']['data_columns']).difference(ctd.columns)
params_coord_needed_for = params_to_calc.intersection(
('depth', 'sigma0', 'SA', 'soundV')) # need for all cols?
if any(params_coord_needed_for):
# todo: load from nav:
if np.any(ctd.get('Lat')):
lat = ctd['Lat']
lon = ctd['Lon']
else:
if 'lat' in cfg['in']:
lat = cfg['in']['lat']
lon = cfg['in']['lon']
else:
print(
'Calc', '/'.join(params_coord_needed_for),
f'using MANUAL INPUTTED coordinates: lat={lat}, lon={lon}')
if 'Temp90' not in ctd.columns:
if cfg['in'].get('b_temp_on_its90'):
ctd['Temp90'] = ctd['Temp']
else:
ctd['Temp90'] = gsw.conversions.t90_from_t68(df_in['Temp'])
ctd['SA'] = gsw.SA_from_SP(
ctd['Sal'], ctd['Pres'], lat=lat,
lon=lon) # or Sstar_from_SP() for Baltic where SA=S*
# Val['Sal'] = gsw.SP_from_C(Val['Cond'], Val['Temp'], Val['P'])
if 'soundV' in params_to_calc:
ctd['soundV'] = gsw.sound_speed_t_exact(ctd['SA'], ctd['Temp90'],
ctd['Pres'])
if 'depth' in params_to_calc:
ctd['depth'] = np.abs(gsw.z_from_p(np.abs(ctd['Pres']), lat))
if 'sigma0' in params_to_calc:
CT = gsw.CT_from_t(ctd['SA'], ctd['Temp90'], ctd['Pres'])
ctd['sigma0'] = gsw.sigma0(ctd['SA'], CT)
# ctd = pd.DataFrame(ctd, columns=cfg['out']['data_columns'], index=df_in.index)
if 'Lat' in params_to_calc and not 'Lat' in ctd.columns:
ctd['Lat'] = lat
ctd['Lon'] = lon
return ctd[cfg['out']['data_columns']]
def derive_csv(data):
density = gsw.z_from_p(cast[6].values,lat)
absolute_sal=gsw.SA_from_SP(cast[10].values,density,lon,lat)
reference_sal=gsw.SR_from_SP(absolute_sal)
conservative_temp=gsw.CT_from_t(absolute_sal,cast[8],density)
potential_density=gsw.sigma0(absolute_sal,conservative_temp)
return density,absolute_sal,reference_sal,conservative_temp,potential_density
def barrier_layer_thickness(SA, CT):
"""
Compute the thickness of water separating the mixed surface layer from the
thermocline. A more precise definition would be the difference between
mixed layer depth (MLD) calculated from temperature minus the mixed layer
depth calculated using density.
"""
import gsw
sigma_theta = gsw.sigma0(SA, CT)
mask = mixed_layer_depth(CT)
mld = np.where(mask)[0][-1]
sig_surface = sigma_theta[0]
sig_bottom_mld = gsw.sigma0(SA[0], CT[mld])
d_sig_t = sig_surface - sig_bottom_mld
d_sig = sigma_theta - sig_bottom_mld
mask = d_sig < d_sig_t # Barrier layer.
return Series(mask, index=SA.index, name='BLT')
def barrier_layer_thickness(SA, CT):
"""
Compute the thickness of water separating the mixed surface layer from the
thermocline. A more precise definition would be the difference between
mixed layer depth (MLD) calculated from temperature minus the mixed layer
depth calculated using density.
"""
import gsw
sigma_theta = gsw.sigma0(SA, CT)
mask = mixed_layer_depth(CT)
mld = np.where(mask)[0][-1]
sig_surface = sigma_theta[0]
sig_bottom_mld = gsw.sigma0(SA[0], CT[mld])
d_sig_t = sig_surface - sig_bottom_mld
d_sig = sigma_theta - sig_bottom_mld
mask = d_sig < d_sig_t # Barrier layer.
return Series(mask, index=SA.index, name="BLT")
def dens0(S, T, P):
# ctd file contain in situ temperature and practical salinity
# CT= conservative temperature
# SA= absolute salinity
# p is sea pressure (dbar)
SA = gsw.SA_from_SP(S, P, 6., 42.)
CT = gsw.CT_from_t(SA, T, P)
# sound speed
#C = gsw.sound_speed(SA, CT, P)
return gsw.sigma0(SA, CT) + 1000.
def sigma0(S, T, p, lat=None, lon=None):
ones = xr.ones_like(S)
p = ones * S['p']
if lat is None:
lat = ones * S['lat']
if lon is None:
lon = ones * S['lon']
SA = gsw.SA_from_SP(S, p, lon, lat)
CT = gsw.CT_from_t(SA, T, p)
rho = gsw.sigma0(SA, CT)
return rho
def oxy_to_umolkg(df_sal, df_pressure, df_lat, df_lon, df_temp, df_oxy):
'''Rewritten from Courtney's method to use array-likes (aka use dataframes and ndarrays).
'''
# Absolute salinity from Practical salinity.
SA = gsw.SA_from_SP(df_sal, df_pressure, df_lat, df_lon)
# Conservative temperature from insitu temperature.
CT = gsw.CT_from_t(SA, df_temp, df_pressure)
s0 = gsw.sigma0(
SA, CT
) # Potential density from Absolute Salinity g/Kg Conservative temperature deg C.
series = df_oxy * 44660 / (s0 + 1000)
return series
def derive_cnv(self):
"""Compute SP, SA, CT, z, and GP from a cnv pre-processed cast."""
import gsw
cast = self.copy()
p = cast.index.values.astype(float)
cast['SP'] = gsw.SP_from_C(cast['c0S/m'].values * 10.,
cast['t090C'].values, p)
cast['SA'] = gsw.SA_from_SP(cast['SP'].values, p, self.lon, self.lat)
cast['SR'] = gsw.SR_from_SP(cast['SP'].values)
cast['CT'] = gsw.CT_from_t(cast['SA'].values, cast['t090C'].values, p)
cast['z'] = -gsw.z_from_p(p, self.lat)
cast['sigma0_CT'] = gsw.sigma0(cast['SA'].values, cast['CT'].values)
return cast
def sbe43(volts, p, t, c, coefs, lat=0.0, lon=0.0):
# NOTE: lat/lon = 0 is not "acceptable" for GSW, come up with something else?
"""
SBE equation for converting SBE43 engineering units to oxygen (ml/l).
SensorID: 38
Parameters
----------
volts : array-like
Raw voltage
p : array-like
Converted pressure (dbar)
t : array-like
Converted temperature (Celsius)
c : array-like
Converted conductivity (mS/cm)
coefs : dict
Dictionary of calibration coefficients (Soc, Voffset, Tau20, A, B, C, E)
lat : array-like, optional
Latitude (decimal degrees north)
lon : array-like, optional
Longitude (decimal degrees)
Returns
-------
oxy_ml_l : array-like
Converted oxygen (mL/L)
"""
# TODO: is there any reason for this to output mL/L? if oxygen eq uses o2sol
# in umol/kg, result is in umol/kg... which is what we use at the end anyway?
t_Kelvin = t + 273.15
SP = gsw.SP_from_C(c, t, p)
SA = gsw.SA_from_SP(SP, p, lon, lat)
CT = gsw.CT_from_t(SA, t, p)
sigma0 = gsw.sigma0(SA, CT)
o2sol = gsw.O2sol(SA, CT, p, lon, lat) # umol/kg
o2sol_ml_l = oxy_umolkg_to_ml(o2sol,
sigma0) # equation expects mL/L (see TODO)
# NOTE: lat/lon always required to get o2sol (and need SA/CT for sigma0 anyway)
# the above is equivalent to:
# pt = gsw.pt0_from_t(SA, t, p)
# o2sol = gsw.O2sol_SP_pt(s, pt)
oxy_ml_l = (coefs["Soc"] * (volts + coefs["offset"]) *
(1.0 + coefs["A"] * t + coefs["B"] * np.power(t, 2) +
coefs["C"] * np.power(t, 3)) * o2sol_ml_l *
np.exp(coefs["E"] * p / t_Kelvin))
return np.around(oxy_ml_l, 4)
def sigma_from_CTD(sal, temp, press, lon, lat, ref=0):
"""
Calculates potential density from CTD parameters at various reference pressures
Parameters
----------
sal :array-like
Salinity in PSU (PSS-78)
temp :array_like
In-situ temperature in deg C
press :array_like
Pressure in dbar
lon :array_like
longitude in decimal degrees
lat :array_like
latitute in decimal degrees
ref :int
reference pressure point for caluclateing sigma0 (in ref * 1000 dBar ref[0-4])
Returns
-------
simga :array-like
Potential density calculated at a reference pressure of ref * 1000 dBar
"""
CT = gsw.CT_from_t(sal, temp, press)
SA = gsw.SA_from_SP(sal, press, lon, lat)
# Reference pressure in ref*1000 dBars
if ref == 0:
sigma = gsw.sigma0(SA, CT)
elif ref == 1:
sigma = gsw.sigma1(SA, CT)
elif ref == 2:
sigma = gsw.sigma2(SA, CT)
elif ref == 3:
sigma = gsw.sigma3(SA, CT)
elif ref == 4:
sigma = gsw.sigma4(SA, CT)
return sigma
def calc_teos10_columns(self, lat, lng):
# Practical Salinity
SP = gsw.SP_from_C(self.data['Cond'], self.data['Temp'], self.data['Pres'])
# Absolute Salinity
SA = gsw.SA_from_SP_Baltic(SP, lng, lat)
# Conservative Temperature
CT = gsw.CT_from_t(SA, self.data['Temp'], self.data['Pres'])
# Sigma(density) with reference pressure of 0 dbar
sigma = gsw.sigma0(SA, CT)
# Depth
depth = list(map(abs, gsw.z_from_p(self.data['Pres'], lat)))
return {'PracticalSalinity' : SP,
'AbsoluteSalinity' : SA,
'ConservativeTemperature' : CT,
'Sigma(density)' : sigma,
'Depth' : depth}
def add_SA_CT_PT(xray):
if 'PRES' in list(xray.data_vars):
PRES_out = xray['PRES']
else:
PRES_out = -gsw.p_from_z(xray['DEPTH'])
SA_out = gsw.SA_from_SP(xray['PSAL'], PRES_out, xray.LONGITUDE,
xray.LATITUDE)
if 'PTMP' in list(xray.data_vars):
PT_out = xray['PTMP']
else:
PT_out = gsw.pt0_from_t(SA_out, xray['TEMP'], PRES_out)
CT_out = gsw.CT_from_pt(SA_out, PT_out)
PD_out = gsw.sigma0(SA_out, CT_out)
xray['ASAL'] = (('TIME', 'DEPTH'), SA_out)
xray['PTMP'] = (('TIME', 'DEPTH'), PT_out)
xray['CTMP'] = (('TIME', 'DEPTH'), CT_out)
xray['PDEN'] = (('TIME', 'DEPTH'), PD_out)
def __Density(self):
temp = ArgoData(Type='Temperature', Month=self.Month)
temp.AllData()
sal = ArgoData(Type='Salinity', Month=self.Month)
sal.AllData()
self.lons = temp.lons
self.lats = temp.lats
self.press = temp.press
self.press_units = temp.press_units
self.t_units = 'kg/m^3'
self.t_title = temp.t_title
press = np.zeros(temp.t_all.shape)
for i in range(len(self.press)):
press[i].fill(self.press[i])
self.t_all = gsw.sigma0(
sal.t_all, temp.t_all) #potential density (rho for density)
def TSdiagram(df, salt='sal00', temp='t090C', figsize=(10,10)):
"""Plot a TS diagram with parametric isopycnals based on the limits given in the df
Parameters
----------
df : pandas.DataFrame
dataframe containing the T/S pair to plot
salt : str, optional
salt variable column name, by default 'sal00'
temp : str, optional
temp variable column name, by default 't090C'
"""
# create parametric isopycnals
T = np.linspace(df[temp].min() - 1,
df[temp].max() + 1,
100)
S = np.linspace(df[salt].min() - 0.1,
df[salt].max() + 0.1,
100)
T,S = np.meshgrid(T,S)
# compute density
rho = gsw.sigma0(S,T)
##-- dataviz --##
fig,ax = plt.subplots(figsize=figsize)
# plot isopycnals as background
cr_bground = ax.contour(S, T, rho, colors='grey',
zorder=1,
linewidths=(0.5),
linestyles=('dashed'))
# identification of some isopycnals
cl_bground = ax.clabel(cr_bground, fontsize=10, inline=True, fmt="%0.1f")
# adding TS pairs
ts_cr = ax.scatter(df[salt], df[temp], s=10, alpha=1, color='k')
ax.set_xlabel('Salinity [psu]', fontsize=14)
ax.set_ylabel(r'Temperature [$^o$C]', fontsize=14)
return fig,ax
def loadArgoRunsFromFile(partialUrl):
pressuresOut = []
densitiesOut = []
tempsOut = []
if downloadRun(partialUrl) != -1:
runId = runIdFromPartial(partialUrl)
dataset = Dataset("runs/" + runId + ".nc")
pressures = dataset.variables["pres_adjusted"][:][0]
salts = dataset.variables["psal"][:][0]
temps = dataset.variables["temp"][:][0]
for index in range(len(pressures)):
if pressures[index] != "_":
pres = pressures[index]
psal = salts[index]
temp = temps[index]
temp = gsw.conversions.CT_from_t(psal, temp, pres)
tempsOut.append(temp)
pressuresOut.append(float(pres))
densitiesOut.append(float(gsw.sigma0(psal, temp)))
return pressuresOut, densitiesOut, tempsOut
def buoyancy_freq(data):
#Get buoyancy frequency
dp = np.diff(data['c_pres'].values, axis=0)
data['dp'] = np.append(dp, dp[-1])
data['dp'] = data['dp'].mask(
((data['dp'] - data['dp'].mean()).abs() > data['dp'].std()))
data['dp'] = data['dp'].interpolate().rolling(5).mean()
CT = gsw.CT_from_t(data['c_sal'], data['c_temp'], data['c_pres'])
SA = gsw.SA_from_SP(data['c_sal'], data['c_pres'], 174, -43)
pdens = gsw.sigma0(SA, CT)
data['pdens'] = pdens
dpdens = np.diff(data['pdens'].values, axis=0)
data['dpdens'] = np.append(dpdens, dpdens[-1])
data['dpdens'] = data['dpdens'].mask(
((data['dpdens'] - data['dpdens'].mean()).abs() >
data['dpdens'].std()))
data['dpdens'] = data['dpdens'].interpolate().rolling(5).mean()
data['N2'] = (9.7963 * data['dpdens']) / (data['pdens'] * data['dp'])
#filter buoyancy frequency by removing outliers
#data['N2'] = data['N2'].mask(data['N2']< 0.000005)
data['N2'] = data["N2"].replace([np.inf, -np.inf], np.nan)
data['N2'] = data['N2'].mask(
((data['N2'] - data['N2'].mean()).abs() > data['N2'].std()))
data['N2'] = data['N2'].interpolate().rolling(10).mean()
#data['N2'] = data['N2'].mask(((data['N2']-data['N2'].mean()).abs() > 3*data['N2'].std()))
#data['N2'] = data['N2'].interpolate()
#Sorted
data['pdens_sort'] = np.sort(pdens)
dpdens_sort = np.diff(data['pdens_sort'].values, axis=0)
data['dpdens_sort'] = np.append(dpdens_sort, dpdens_sort[-1])
data['dpdens_sort'] = data['dpdens_sort'].mask(
((data['dpdens_sort'] - data['dpdens_sort'].mean()).abs() >
data['dpdens_sort'].std()))
data['dpdens_sort'] = data['dpdens_sort'].interpolate().rolling(5).mean()
data['N2_sort'] = (9.7963 * data['dpdens_sort']) / (data['pdens_sort'] *
data['dp'])
return data
def density_contours4TS(ax):
"""This function puts lines of constant density
into a given T-S-asxis"""
Tl = ax.get_ylim()
Sl = ax.get_xlim()
DS = (Sl[1] - Sl[0]) / 10
DT = (Tl[1] - Tl[0]) / 10
s = np.arange(Sl[0], Sl[1] + DS, DS)
t = np.arange(Tl[0], Tl[1] + DT, DT)
S, T = np.meshgrid(s, t)
R = gsw.sigma0(S, T)
minR = np.min(R)
maxR = np.max(R)
DR = maxR - minR
Rlevels = np.arange(minR, maxR, DR / 7)
conts = ax.contour(S, T, R, levels=Rlevels, colors='.7', Linewidth=1)
def gambar_utama(self, S, T, depth, latitude, hasil_mixing):
s = ma.masked_invalid(self.S).mean(axis=1)
t = ma.masked_invalid(self.T).mean(axis=1)
Te = np.linspace(t.min(), t.max(), 10)
Se = np.linspace(s.min(), s.max(), 10)
Tg, Sg = np.meshgrid(Te, Se)
sigma_theta = gsw.sigma0(Sg, Tg)
cnt = np.linspace(sigma_theta.min(), sigma_theta.max(), 15)
Reds = brewer2mpl.get_map('Reds', 'Sequential', 9).mpl_colormap
Blues = brewer2mpl.get_map('Blues', 'Sequential', 9).mpl_colormap
Greens = brewer2mpl.get_map('Greens', 'Sequential', 9).mpl_colormap
warna = [Reds, Blues, Greens]
# Grid for contouring.
zg, xg = np.meshgrid(self.depth, self.latitude)
self.fig, self.ax = plt.subplots(nrows=1,
ncols=1,
figsize=(14, 6),
facecolor='w')
self.ax.invert_yaxis()
kl = []
percent = [50, 60, 70, 80, 90, 100]
# m = np.zeros(hasil_mixing.shape)
for i in range(hasil_mixing.shape[2]):
k = self.ax.contourf(xg,
zg,
hasil_mixing[0:, 0:, i].transpose(),
percent,
cmap=warna[i],
zorder=3)
k.set_clim(percent[0], percent[-1])
kl.append(k)
return self.fig, kl, self.ax
def calc_preind_co2_AOU_method(arrowdate, obs_year, target_year, scen):
import numpy as np
import netCDF4 as nc
import gsw
test_LO = hm.load_nc(arrowdate)
tdate = arrowdate
yy = tdate.format('YYYY')
mm = tdate.format('MM')
dd = tdate.format('DD')
ymd = f'y{yy}m{mm}d{dd}'
#open dataset & retrieve relevant variables, calculate potential density
zlevels = (test_LO['deptht'][:])
sal = test_LO['vosaline'][0, :, 0, :]
temp = test_LO['votemper'][0, :, 0, :]
sigma0 = gsw.sigma0(sal, temp)
DIC = test_LO['DIC'][0, :, 0, :]
TA = test_LO['TA'][0, :, 0, :]
O2 = test_LO['OXY'][0, :, 0, :]
depth_this = np.zeros_like(TA)
zeros = np.zeros_like(TA)
#depth_this - array of depths of same shape as DIC
for i in range(0, 950):
depth_this[:, i] = zlevels
### GET AGE AND WATERMASS WITNESSED CO2
#calculate pycnal's last surfacing, according to exp function
#found using cfc ages
params0 = 0.1301889490932413
params1 = 3.8509914822057825
params2 = 8.301166081413104 #change to 2015 since model year is 2015
water_age = (params0 * np.exp(-params1 * (25.15 - sigma0)) + params2)
# year_watermass_at_surface = int(targetyear - age)
# watermass_witnessed_co2_obs = int(hm.co2_from_year(scen,year_watermass_at_surface))
#get witnessed co2 both of the present day water parcel and the target year water parcel
obs_year_ar = np.zeros_like(water_age)
obs_year_ar[:] = obs_year
target_year_ar = np.zeros_like(water_age)
target_year_ar[:] = target_year
year_watermass_at_surface = (obs_year_ar - water_age).astype(int)
watermass_witnessed_co2_obs = hm.co2_from_year(scen,
year_watermass_at_surface)
print(np.min(watermass_witnessed_co2_obs))
print(np.shape(watermass_witnessed_co2_obs))
if target_year < 1905:
watermass_witnessed_co2_target = 284
else:
watermass_witnessed_co2_target = \
hm.co2_from_year(scen,year_watermass_at_surface+(target_year_ar-obs_year_ar))
###GET AOU
#(1) estimate AOU on 26 (assoc with water parcel with DIC_{w,2019,26,jdf})
# = f(O2_{w,2019,26,jdf},S_{w,2019,26,jdf},T_{w,2019,26,jdf}, P_{w,2019,26,jdf})
#(P is there to determine T when last at surface - I'll call it preT next)
AOU_stoich = hm.get_AOU_stoich(sal, temp, O2, sigma0, water_age)
### GET PREFORMED DIC
obs_preformed_dic = DIC - AOU_stoich
#### get preformed pco2 and target year preformed pco2
pHr, OmAr, pco2r = hm.oned_moxy(sal, temp, obs_preformed_dic, TA, 1,
np.zeros_like(sal))
obsyear_pref_pco2 = pco2r
diseqPCO2 = obsyear_pref_pco2 - watermass_witnessed_co2_obs
targetyear_pref_pco2 = watermass_witnessed_co2_target + diseqPCO2
print('calculating target year preformed DIC')
target_preformed_dic = np.zeros_like(DIC)
target_preformed_dic_r = np.ravel(target_preformed_dic)
targetyear_pref_pco2_r = np.ravel(targetyear_pref_pco2)
depth_r = np.ravel(depth_this)
sal_r = np.ravel(sal)
temp_r = np.ravel(temp)
TA_r = np.ravel(TA)
zeros_r = np.zeros_like(TA_r)
sigma0_r = np.ravel(sigma0)
start = time.time()
for i in range(0, len(TA_r)):
if i % (950 * 5) == 0:
print(f'level: {i/(950*5)}')
### the surface needs better handling
if sigma0_r[i] < 25.0:
target_preformed_dic_r[i] = 9999
#### the bottom can be actually taken from the cell right above it, no need to do this painful calculation
if depth_r[i] > 330:
target_preformed_dic_r[i] = 6666
else:
t_dic = hm.find_DIC_corresp_to_pco2(sal_r[i], temp_r[i],
targetyear_pref_pco2_r[i],
TA_r[i], 1, 0)
target_preformed_dic_r[i] = t_dic
print('seconds taken at the hard part')
print(time.time() - start)
# deltaDIC = obs_preformed_dic - target_preformed_dic
# print('max deltaDIC: '+str(np.max(deltaDIC)) + ', min deltaDIC: '+ str(np.min(deltaDIC)))
# final_target_DIC = DIC - deltaDIC
## the top and bottom can be dealt with differently
DIC_r = np.ravel(DIC)
obs_preformed_dic_r = np.ravel(obs_preformed_dic)
deltaDIC_r = obs_preformed_dic_r - target_preformed_dic_r
final_target_DIC_r = DIC_r - deltaDIC_r
for i in range(0, len(TA_r)):
if sigma0_r[i] < 25.0:
deltaDIC_r[i] = 9999
obs_preformed_dic_r[i] = 9999
target_preformed_dic_r[i] = 9999
final_target_DIC_r[i] = 9999
if depth_r[i] > 330:
deltaDIC_r[i] = 6666
obs_preformed_dic_r[i] = 6666
target_preformed_dic_r[i] = 6666
final_target_DIC_r[i] = 6666
deltaDIC = deltaDIC_r.reshape(40, 950)
obs_preformed_dic = obs_preformed_dic_r.reshape(40, 950)
target_preformed_dic = target_preformed_dic_r.reshape(40, 950)
final_target_DIC = final_target_DIC_r.reshape(40, 950)
#target_preformed_dic = target_preformed_dic_r.reshape(40,950)
# target_year_ar = np.zeros_like(final_target_DIC)
# target_year_ar[:] = target_year
f = nc.Dataset(
f'./JdF_future_DIC/LO_TY_{target_year}_scen_{scen}_{ymd}_DIC_nosurfnodeep.nc',
'w',
format='NETCDF4') #'w' stands for write
g = f.createGroup('preindustrial_DIC')
g.createDimension('xval', 950)
g.createDimension('depth', 40)
g.createDimension('single', 1)
ts = g.createVariable('sigma0', 'f4', ('depth', 'xval'))
ts[:] = sigma0
ts2 = g.createVariable('water_age', 'f4', ('depth', 'xval'))
ts2[:] = water_age
ts2a = g.createVariable('target_year', 'f4', ('single'))
ts2a[:] = target_year
# ts3 = g.createVariable('watermass_witnessed_co2_obs','f4',('depth','xval'))
# ts3[:] = watermass_witnessed_co2_obs
# ts3a = g.createVariable('watermass_witnessed_co2_target','f4',('depth','xval'))
# ts3a[:] = watermass_witnessed_co2_target
ts4 = g.createVariable('AOU_stoich', 'f4', ('depth', 'xval'))
ts4[:] = AOU_stoich
ts5 = g.createVariable('obsyear_pref_pco2', 'f4', ('depth', 'xval'))
ts5[:] = obsyear_pref_pco2
ts5a = g.createVariable('targetyear_pref_pco2', 'f4', ('depth', 'xval'))
ts5a[:] = targetyear_pref_pco2
ts5b = g.createVariable('obsyear_pref_dic', 'f4', ('depth', 'xval'))
ts5b[:] = obs_preformed_dic
ts5c = g.createVariable('targetyear_pref_dic', 'f4', ('depth', 'xval'))
ts5c[:] = target_preformed_dic
ts6 = g.createVariable('final_target_DIC', 'f4', ('depth', 'xval'))
ts6[:] = final_target_DIC
f.close()
def save_as_xr(input, output):
'''Read float files, compose xarray dataset, convert variables,
and save as netcdf last updated: june 11, 2019
'''
a = load_matfile(str(input))
output = str(output)
# u = 0.5 * (a['A']['u1'].flatten()[0] + a['A']['u2'].flatten()[0])
# v = 0.5 * (a['A']['v1'].flatten()[0] + a['A']['v2'].flatten()[0])
# dudz = 0.5 * (a['A']['du1dz'].flatten()[0] + a['A']['du2dz'].flatten()[0])
# dvdz = 0.5 * (a['A']['dv1dz'].flatten()[0] + a['A']['dv2dz'].flatten()[0])
# eps = np.nanmedian(np.dstack((a['A']['eps1'].flatten()[0],
# a['A']['eps2'].flatten()[0])), axis=2)
# chi = np.nanmedian(np.dstack((a['A']['chi1'].flatten()[0],
# a['A']['chi2'].flatten()[0])), axis=2)
# compose dataset object
ds = xr.Dataset(
{ # define wanted variables here!
'sigma': (['z', 'time'], a['A']['Sigma'].flatten()[0]),
'u1': (['z', 'time'], a['A']['u1'].flatten()[0]),
'u2': (['z', 'time'], a['A']['u2'].flatten()[0]),
'v1': (['z', 'time'], a['A']['v1'].flatten()[0]),
'v2': (['z', 'time'], a['A']['v2'].flatten()[0]),
'du1dz': (['z', 'time'], a['A']['du1dz'].flatten()[0]),
'du2dz': (['z', 'time'], a['A']['du2dz'].flatten()[0]),
'dv1dz': (['z', 'time'], a['A']['dv1dz'].flatten()[0]),
'dv2dz': (['z', 'time'], a['A']['dv2dz'].flatten()[0]),
'eps1': (['z', 'time'], a['A']['eps1'].flatten()[0]),
'eps2': (['z', 'time'], a['A']['eps2'].flatten()[0]),
'chi1': (['z', 'time'], a['A']['chi1'].flatten()[0]),
'chi2': (['z', 'time'], a['A']['chi2'].flatten()[0]),
# variables needed for QC
'RotP': (['z', 'time'], a['A']['RotP'].flatten()[0]),
'W': (['z', 'time'], a['A']['W'].flatten()[0]),
'verr1': (['z', 'time'], a['A']['verr1'].flatten()[0]),
'verr2': (['z', 'time'], a['A']['verr2'].flatten()[0]),
'kT1': (['z', 'time'], a['A']['kT1'].flatten()[0]),
'kT2': (['z', 'time'], a['A']['kT2'].flatten()[0]),
'T': (['z', 'time'], a['A']['T'].flatten()[0]),
'S': (['z', 'time'], a['A']['S'].flatten()[0]),
'n2': (['z', 'time'], a['A']['N2'].flatten()[0])
},
coords={
'pressure': (['z'], a['A']['Pr'].flatten()[0].astype(float)),
'z': a['A']['Pr'].flatten()[0].astype(float),
'lat': (['time'], a['A']['lat'].flatten()[0]),
'lon': (['time'], a['A']['lon'].flatten()[0]),
'time': a['A']['Jday_gmt'].flatten()[0].astype(float)
},
attrs={'floatid': output.split('_')[1].split('.')[0]})
# remove nans
ds = ds.dropna(dim='time', how='all')
# convert to datetime
ds = ds.assign_coords(time=(dn2dt_vec(ds.time)))
# comvert pressure to depth
ds = ds.assign_coords(z=(gsw.z_from_p(ds.z, ds.lat.mean()).astype(float)))
# ds = ds.assign_coords(z=-ds.z)
_, index = np.unique(ds.time, return_index=True)
ds = ds.isel(time=index)
# convert variables
p, lon, lat = xr.broadcast(ds.pressure, ds.lon, ds.lat)
ds['S'] = xr.DataArray(gsw.SA_from_SP(ds.S, p, lon, lat),
dims=['z', 'time'])
ds['T'] = xr.DataArray(gsw.CT_from_t(ds.S, ds.T, p), dims=['z', 'time'])
ds['rho0'] = xr.DataArray(gsw.sigma0(ds.S, ds.T) + 1000,
dims=['z', 'time'])
# save as netcdf
ds.to_netcdf(str(output))
CT = gsw.CT_from_t(SA, temp_s, depth_s)
#CT_5mean=np.mean(CT)
#SA_5mean=np.mean(SA)
# plot T/S diagram - altered from example from https://medium.com@hafezahmad/making-#temperature-salinity-diagrams-called-the-t-s-diagram-with-python-and-r-#programming-5deec6378a29
mint = np.min(CT)
maxt = np.max(CT)
mins = np.min(SA)
maxs = np.max(SA)
tempL = np.linspace(mint - 1, maxt + 1, len(SA))
salL = np.linspace(mins - 1, maxs + 1, len(SA))
Tg, Sg = np.meshgrid(tempL, salL)
sigma_theta = gsw.sigma0(Sg, Tg)
cnt = np.linspace(sigma_theta.min(), sigma_theta.max(), len(SA))
fig, ax = plt.subplots(figsize=(10, 10))
cs = ax.contour(Sg, Tg, sigma_theta, colors='grey', zorder=1)
cl = plt.clabel(cs, fontsize=10)
#sc=plt.scatter(SA_5_day_mean,CT_5_day_mean,c=cnt)
sc = plt.scatter(SA, CT, c=cnt)
cb = plt.colorbar(sc)
cb.set_label('Density')
plt.xlabel('Salinity A')
plt.ylabel('Conservative Temperature')
plt.title('T-S at BATS at T= ' + str(year) + ' - ' + str(month) + ' - ' +
str(day) + '')
cb.set_label('Density')
plt.show()
for l in np.arange(len(new_dates_num)):
P_PD[:, l] = depth_range
SA = gsw.SA_from_SP(S_PD, P_PD, lon_array_pd, lat_array_pd)
CT = gsw.CT_from_t(SA, T_PD, P_PD)
oxy_eq = gsw.O2sol(SA, CT, P_PD, lon_array_pd, lat_array_pd)
OS_PD = O_PD / oxy_eq * 100
D_PD = np.zeros(T_PD.shape)
D_PD[:] = np.NaN
for r in np.arange(D_PD.shape[0]):
for c in np.arange(D_PD.shape[1]):
if np.isnan(SA[r, c]) == False and np.isnan(
CT[r, c]) == False:
D_PD[r, c] = gsw.sigma0(SA[r, c], CT[r, c])
plt.figure(figsize=(figx, figy))
plt.pcolormesh(X,
Y,
OS_PD,
vmin=minOsat,
vmax=maxOsat,
cmap=cmo.haline)
plt.gca().invert_yaxis()
plt.colorbar()
plt.xticks(rotation=45)
plt.title('Oxygen Saturation Float: ' + str(WMO))
plt.savefig(SectionFigDir + 'Pres_' + str(interp_pres) + '_' +
str(WMO) + '_Interp_OxygenSaturation.jpg')
plt.clf()
from ocean_tools import TKED
import gsw
directory = '../../Data/deployment_raw/'
outdir = '../../plots/ctd/LT_Lo_R/'
deployment_name = 'deploy1_'
measurement_type = 'ctd_'
file_type = 'raw_'
for i in range(58):
c_file = 'C' + ("%07d" % (i, ))
c_data = pd.read_pickle(directory + deployment_name + file_type + c_file)
CT = gsw.CT_from_t(c_data['c_sal'], c_data['c_temp'], c_data['c_pres'])
SA = gsw.SA_from_SP(c_data['c_sal'], c_data['c_pres'], 174, -43)
pdens = gsw.sigma0(SA, CT)
c_data["pdens"] = pdens
[LT, Td, Nsqu, Lo, R, x_sorted,
idxs] = TKED.thorpe_scales1(c_data["c_depth"].values * -1,
c_data['pdens'].values,
full_output=True)
#plt.show()
fig2, (ax2, ax3, ax4) = plt.subplots(1, 3, sharey=True)
# Temperature
ax2.plot(LT, c_data["c_depth"].values, c='k')
ax2.set_ylabel('Depth (m)')
#ax2.set_ylim(ax2.get_ylim()[::-1]) #this reverses the yaxis (i.e. deep at the bottom)
ax2.set_xlabel('LT (m)')
ax2.xaxis.set_label_position('top') # this moves the label to the top
ax2.xaxis.set_ticks_position('top') # this moves the ticks to the top
ppitch = sx_pitch.mean(axis=1) # <0: downcast | >0: upcast
print('Fill NaNs in matrices - SeaExplorer')
for var in list(ds.var()):
if var != 'profile_index':
exec('sx_' + var + '[ppitch<0] = sx_' + var + '[ppitch<0].fillna(method="ffill", limit=10, axis=1)')
exec('sx_' + var + '[ppitch>0] = sx_' + var + '[ppitch>0].fillna(method="bfill", limit=10, axis=1)')
exec('sx_' + var + ' = sx_' + var + '[~pd.isna(sx_' + var + '.iloc[:,0:50].mean(axis=1))]') # correction specific for this deployment
print(' Done!')
# TEOS-10 conversion SeaExplorer
P = sx_pressure.values
lon0, lat0 = ds['longitude'].values.mean(), ds['latitude'].values.mean()
SA = gsw.SA_from_SP(sx_salinity.values, P, lon0, lat0)
CT = gsw.CT_from_t(SA, sx_temperature.values, P)
sigma0 = gsw.sigma0(SA, CT)
SA_sort = np.array(list(map(lambda x, y: y[x], np.argsort(sigma0, axis=1), SA)))
CT_sort = np.array(list(map(lambda x, y: y[x], np.argsort(sigma0, axis=1), CT)))
P_sort = np.array(list(map(lambda x, y: y[x], np.argsort(sigma0, axis=1), P)))
N2, p_mid = gsw.Nsquared(SA_sort, CT_sort, P_sort, lat=lat0, axis=1)
# Oxygen conversion
Ofreq = sx_oxygen_frequency.values
Soc = float(dpl['calibration.SBE43F.soc'])
Foffset = float(dpl['calibration.SBE43F.foffset'])
A = float(dpl['calibration.SBE43F.a'])
B = float(dpl['calibration.SBE43F.b'])
C = float(dpl['calibration.SBE43F.c'])
E = float(dpl['calibration.SBE43F.e'])
K = CT + 273.15 # Temp in Kelvin