def stageData(self, m):
# Get the observational data
obs = Variable(filename=self.source,
variable_name=self.variable,
alternate_vars=self.alternate_vars)
# Reduce the sites
if self.map:
obs.lat = obs.lat[self.map]
obs.lon = obs.lon[self.map]
obs.depth = obs.depth[self.map]
obs.data = obs.data[:, self.map]
obs.ndata = len(self.map)
# Get the model result
force_emulation = self.keywords.get("force_emulation",
"False").lower() == "true"
never_emulation = self.keywords.get("never_emulation",
"False").lower() == "true"
no_co2 = False
mod = None
if not force_emulation:
try:
#print "Trying to get co2 from %s" % m.name
mod = m.extractTimeSeries(
self.variable,
alt_vars=self.alternate_vars,
initial_time=obs.time_bnds[0, 0],
final_time=obs.time_bnds[-1, 1],
lats=None if obs.spatial else obs.lat,
lons=None if obs.spatial else obs.lon)
except il.VarNotInModel:
#print "co2 not in %s" % m.name
no_co2 = True
if (((mod is None) or no_co2) and (not never_emulation)):
#print "Emulating co2 in %s" % m.name
mod = self.emulatedModelResult(m, obs)
if mod is None: raise il.VarNotInModel()
# get the right layering, closest to the layer elevation where all aren't masked.
if mod.layered:
ind = (np.abs(obs.depth[:, np.newaxis] - mod.depth)).argmin(axis=1)
for i in range(ind.size):
while (mod.data[:, ind[i], i].mask.sum() >
0.5 * mod.data.shape[0]):
ind[i] += 1
data = []
for i in range(ind.size):
data.append(mod.data[:, ind[i], i])
mod.data = np.ma.masked_array(data).T
mod.depth = None
mod.depth_bnds = None
mod.layered = False
obs, mod = il.MakeComparable(obs,
mod,
mask_ref=True,
clip_ref=True)
mod.data.mask += obs.data.mask
# Remove the trend via quadradic polynomial
obs = _detrend(obs)
mod = _detrend(mod)
return obs, mod
def getDiurnalDataForGivenYear(var, year):
"""
"""
# Get this year's data, make sure there is enough
spd = int(round(1 / np.diff(var.time_bnds, axis=1).mean()))
datum = cftime.date2num(cftime.datetime(year, 1, 1), "days since 1850-1-1")
ind = np.where(year == var.year)[0]
t = var.time[ind] - datum
tb = var.time_bnds[ind] - datum
data = var.data[ind, 0]
# Reshape the data
begin = np.argmin(tb[:(spd - 1), 0] % 1)
end = begin + int(t[begin:].size / float(spd) - 1) * spd
shift = int(round((var.tmax - 12) / (var.dt * 24)))
begin += shift
end += shift
shp = (-1, spd) + data.shape[1:]
data = data[begin:end].reshape(shp)
t = t[begin:end].reshape(shp).mean(axis=1)
# Diurnal magnitude
mag = Variable(name="mag%d" % year,
unit=var.unit,
time=t,
data=data.max(axis=1) - data.min(axis=1))
# Some of the tower data is 'intelligently' masked which leads to
# too much of the data being removed to use my change-detection
# algorithm to determine season begin/end.
mag.skip = False
if mag.data.mask.all(): raise NotEnoughDataInYear # if year is all masked
dmag = (mag.data.max() - mag.data.min())
if dmag < 1e-14:
raise NotEnoughDataInYear # if diurnal mag has no amplitude
# Some mask out off seasons, season is taken to be all the data
begin_day, end_day = mag.time[mag.data.mask == False][[
0, -1
]] # begin/end of the mask data
if ((begin_day < 2 and end_day < 363)
or (begin_day > 2 and end_day > 363)):
# this is likely a dataset which is a partial year
raise NotEnoughDataInYear
elif (begin_day > 2 and end_day < 363):
# this is likely a dataset that masks out off-seasons
season = np.asarray([begin_day, end_day])
else:
season = findSeasonalTiming(mag.time, mag.data)
centroid = findSeasonalCentroid(mag.time, mag.data)
mag.season = season
mag.centroid = centroid
# Mask out off season
mask = (t < season[0]) + (t > season[1])
data = np.ma.masked_array(data,
mask=mask[:, np.newaxis] *
np.ones(data.shape[1], dtype=bool))
# Mean seasonal diurnal cycle
uncert = np.zeros((data.shape[1], 2))
for i in range(data.shape[1]):
d = data[:, i].compressed()
if d.size == 0: continue
uncert[i, :] = np.percentile(d, [10, 90])
day = np.linspace(0, 1, spd + 1)
day = 0.5 * (day[:-1] + day[1:])
with np.errstate(under='ignore', over='ignore'):
cycle = Variable(name="cycle%d" % year,
unit=var.unit,
time=day,
data=data.mean(axis=0),
data_bnds=uncert)
# Mean seasonal uptake
uptake = Variable(unit=var.unit,
time=var.time[ind] - datum,
time_bnds=var.time_bnds[ind] - datum,
data=var.data[ind, 0])
uptake.data = np.ma.masked_array(uptake.data,
mask=((uptake.time < season[0]) +
(uptake.time > season[1])))
uptake = uptake.integrateInTime(mean=True)
cycle.uptake = uptake.data
# Timing of peak seasonal cycle, could be a maximum or minimum,
# check second derivative of a best-fit parabola to the daytime
# data.
begin = int(spd / 4)
end = int(spd * 3 / 4)
p = np.polyfit(cycle.time[begin:end], cycle.data[begin:end], 2)
if p[0] < 0:
cycle.peak = day[cycle.data.argmax()] * 24
else:
cycle.peak = day[cycle.data.argmin()] * 24
return mag, cycle
