def spc(station, flag_col, start, end, logfile, diagnostics = False, plots = False, doMonth = False):
'''
Run pressure cross checks on SLP and STNLP
:param object station: station object
:param array flag_col: which columns to fill in flag_array
:param datetime start: start of dataset
:param datetime end: end of dataset
:param file logfile: logfile to store outputs
:param bool plots: do plots or not
:param bool diagnostics: extra verbose information
:param bool doMonth: account for incomplete months
:returns:
'''
slp = getattr(station, 'slp')
stnlp = getattr(station, 'stnlp')
month_ranges = utils.month_starts_in_pairs(start, end)
station.qc_flags[:,flag_col[0]] = spc_diff(slp, stnlp, station.qc_flags[:,flag_col[0]], month_ranges, start, end, logfile, plots = plots, diagnostics = diagnostics, doMonth = doMonth)
station = utils.append_history(station, "Pressure Cross Check")
return # spc
def hcc(station, flag_col, start, end, logfile, diagnostics=False, plots=False):
"""
Run humidity cross checks on temperature and dewpoint temperature obs
:param object station: station object
:param array flag_col: which columns to fill in flag_array
:param datetime start: start of dataset
:param datetime end: end of dataset
:param file logfile: logfile to store outputs
:param bool plots: do plots or not
:param bool diagnostics: extra verbose information
:returns:
"""
temperatures = getattr(station, "temperatures")
dewpoints = getattr(station, "dewpoints")
month_ranges = utils.month_starts_in_pairs(start, end)
# Supersaturation
station.qc_flags[:, flag_col[0]] = hcc_sss(
temperatures.data, dewpoints.data, month_ranges, start, logfile, plots=plots, diagnostics=diagnostics
)
# Dew point depression
precip = getattr(station, "precip1_depth")
cloudbase = getattr(station, "cloud_base")
past_sigwx = getattr(station, "past_sigwx1")
times = station.time.data
station.qc_flags[:, flag_col[1]] = hcc_dpd(
times,
temperatures.data,
dewpoints.data,
precip.data,
cloudbase.data,
past_sigwx.data,
start,
logfile,
plots=plots,
diagnostics=diagnostics,
)
# Dew point cutoffs
station.qc_flags[:, flag_col[2]] = hcc_cutoffs(
temperatures.data, dewpoints.data, month_ranges, logfile, start, plots=plots, diagnostics=diagnostics
)
for col in range(3):
flag_locs = np.where(station.qc_flags[:, flag_col[col]] != 0)
station.dewpoints.flags[flag_locs] = 1
station = utils.append_history(station, "Temperature-Humidity Cross Check")
return # hcc
def hcc(station, flag_col, start, end, logfile, diagnostics = False, plots = False):
'''
Run humidity cross checks on temperature and dewpoint temperature obs
:param object station: station object
:param array flag_col: which columns to fill in flag_array
:param datetime start: start of dataset
:param datetime end: end of dataset
:param file logfile: logfile to store outputs
:param bool plots: do plots or not
:param bool diagnostics: extra verbose information
:returns:
'''
temperatures = getattr(station, 'temperatures')
dewpoints = getattr(station, 'dewpoints')
month_ranges = utils.month_starts_in_pairs(start, end)
# Supersaturation
station.qc_flags[:,flag_col[0]] = hcc_sss(temperatures.data, dewpoints.data, month_ranges, start, logfile, plots = plots, diagnostics = diagnostics)
# Dew point depression
precip1 = getattr(station, 'precip1_depth')
precip2 = getattr(station, 'precip2_depth')
precip3 = getattr(station, 'precip3_depth')
precip6 = getattr(station, 'precip6_depth')
precip9 = getattr(station, 'precip9_depth')
precip12 = getattr(station, 'precip12_depth')
precip15 = getattr(station, 'precip15_depth')
precip18 = getattr(station, 'precip18_depth')
precip24 = getattr(station, 'precip24_depth')
cloudbase = getattr(station, 'cloud_base')
past_sigwx = getattr(station, 'past_sigwx1')
times = station.time.data
# combine all the precips together
precips = np.array([precip1.data, precip2.data, precip3.data, precip6.data, precip9.data, precip12.data, precip15.data, precip18.data, precip24.data])
station.qc_flags[:,flag_col[1]] = hcc_dpd(times, temperatures.data, dewpoints.data, precips, cloudbase.data, past_sigwx.data, start, logfile, plots = plots, diagnostics = diagnostics)
# Dew point cutoffs
station.qc_flags[:,flag_col[2]] = hcc_cutoffs(temperatures.data, dewpoints.data, month_ranges, logfile, start, plots = plots, diagnostics = diagnostics)
for col in range(3):
flag_locs = np.where(station.qc_flags[:, flag_col[col]] != 0)
station.dewpoints.flags[flag_locs] = 1
station = utils.append_history(station, "Temperature-Humidity Cross Check")
return # hcc
def wind_rose_check(station, flag_col, start, end, logfile, plots=False, diagnostics=False):
"""
Checks for large differences in the year-to-year wind-rose shape.
Uses RMSE and fits Gaussian. Finds gap in distribution to flag beyond
:param MetStation station: station object
:param int flag_col: which column to store the flags in
:param datetime start: start of data
:param datetime end: end of data
:param bool plots: run the plots
:param bool diagnostics: run the diagnostics
"""
direction = station.winddirs.data
speed = station.windspeeds.data
flags = station.qc_flags[:, flag_col]
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges_years = month_ranges.reshape(-1, 12, 2)
# histogram of wind directions ( ~ unravelled wind-rose)
bw = 20
bins = range(0, 360 + bw, bw)
full_hist, binEdges = np.histogram(direction, bins=bins, normed=True)
# use rmse as this is known (Chi-sq remains just in case)
rmse, chisq = -np.ma.ones([month_ranges_years.shape[0]]), -np.ma.ones([month_ranges_years.shape[0]])
# run through each year to extract RMSE's
for y, year in enumerate(month_ranges_years):
if len(direction[year[0][0] : year[-1][0]].compressed()) > 0:
hist, binEdges = np.histogram(direction[year[0][0] : year[-1][0]], bins=bins, normed=True)
chisq[y] = np.sum((full_hist - hist) ** 2 / (full_hist + hist)) / 2.0
rmse[y] = np.sqrt(np.mean((full_hist - hist) ** 2))
else:
rmse.mask[y] = True
# now to bin up the differences and see what the fit is.
# need to have values spread so can bin!
if len(np.unique(rmse.compressed())) > 1:
binEdges, bincenters = wind_create_bins(rmse)
hist, binEdges = np.histogram(rmse, bins=binEdges) # , density=True)
norm = get_histogram_norm(rmse, binEdges)
# inputs for fit
mu = np.mean(rmse)
std = np.std(rmse)
# try to get decent fit to bulk of obs.
# initial_values = [np.max(hist), np.mean(rmse), np.std(rmse), stats.skew(rmse), stats.kurtosis(rmse)] # norm, mean, std, sk#ew, kurtosis
# fit = leastsq(utils.residualsGH, initial_values, [bincenters, hist, np.ones(len(hist))])
# res = utils.hermite2gauss(fit[0])
# plot_gaussian = utils.funcGH(fit[0], bincenters)
fit = stats.rice.fit(rmse.compressed(), loc=0, scale=np.ma.std(rmse))
dist_pdf = stats.rice.pdf(bincenters, fit[:-2], loc=fit[-2], scale=fit[-1]) * norm
gaussian = utils.fit_gaussian(bincenters, hist, max(hist), mu=mu, sig=std)
# invert Gaussian to find initial threshold, then hunt for first gap beyond
# threshold = utils.invert_gaussian(PROB_THRESHOLD, gaussian)
# invert Rician to find initial threshold, then hunt for first gap beyond
if dist_pdf[-1] < PROB_THRESHOLD:
# then curve has dropped below the threshold, so can find some updated ones.
threshold = -np.where(dist_pdf[::-1] > PROB_THRESHOLD)[0][0]
else:
threshold = bincenters[-1]
n = 0
center = np.argmax(hist)
gap = bincenters[-1] # nothing should be beyond this
while True:
if center + n + 1 == len(bincenters):
# gone beyond edge - nothing to flag, so just break
break
if bincenters[center + n] < threshold:
n += 1
# continue moving outwards
continue
if hist[center + n] == 0:
# found one
if center + n + 1 == len(bincenters):
# gone beyond edge - nothing to flag - escape
break
elif hist[center + n + 1] == 0:
# has to be two bins wide?
gap = bincenters[center + n]
break
n += 1
# run through each year to extract RMSE's
for y, year in enumerate(month_ranges_years):
if rmse[y] > gap:
# only flag where there are observations
good, = np.where(
np.logical_or(
direction.mask[year[0][0] : year[-1][0]] == False, speed.mask[year[0][0] : year[-1][0]] == False
)
)
flags[year[0][0] : year[-1][0]][good] = 1
if diagnostics or plots:
print "Flagging {} RMSE {} > {}".format(y + start.year, rmse[y], gap)
elif rmse.mask[y] == False:
if diagnostics or plots:
print "{}".format(y + start.year)
if plots:
import matplotlib.pyplot as plt
# plot underlying histogram
plt.clf()
plot_hist = np.array([float(x) if x != 0 else 1e-1 for x in hist])
plt.step(binEdges[1:], plot_hist, color="k")
# plot the Rician distribution on top
plt.plot(bincenters, dist_pdf, "r-", label="Rician")
# plot the gaussian on top
plt.plot(binEdges[1:], utils.gaussian(bincenters, gaussian), color="b", ls=":", label="Gaussian")
plt.yscale("log")
plt.ylim([0.001, 2 * max(plot_hist)])
# plot the thresholds
plt.axvline(threshold, color="g")
plt.axvline(gap, color="r")
# plot flagged values in different colour
if len(rmse[rmse > gap]) > 0:
plt.step(binEdges[1:][bincenters >= gap], plot_hist[bincenters >= gap], color="r")
# prettify
plt.xlabel("RMSE between complete record and each year")
plt.ylabel("Frequency")
plt.title(station.id + " annual wind rose differences")
plt.xlim([0, 1.1 * np.ma.max(rmse)])
plt.legend(loc="lower right", frameon=False)
plt.show()
# plot all the annual wind roses, flattened out.
plt.clf()
hist, binEdges = np.histogram(direction, bins=np.arange(0.0, 360.0 + DEGREEBINS, DEGREEBINS), normed=True)
bincenters = (binEdges[:-1] + binEdges[1:]) / 2.0
plt.plot(bincenters, hist, "k-", lw=2)
for y, year in enumerate(month_ranges_years):
if len(speed[year[0][0] : year[-1][0]].compressed() > 0):
hist, binEdges = np.histogram(direction[year[0][0] : year[-1][0]], bins=binEdges, normed=True)
plt.plot(bincenters, hist)
plt.xlabel("Direction (degrees)")
plt.show()
# plot wind roses as wind roses
plot_wind_rose(speed, direction, "{} - {}".format(station.id, "all years"))
for y, year in enumerate(month_ranges_years):
if len(speed[year[0][0] : year[-1][0]].compressed() > 0):
plot_wind_rose(
speed[year[0][0] : year[-1][0]],
direction[year[0][0] : year[-1][0]],
"{} - {}".format(station.id, start.year + y),
label="RMSE {:6.4f}\nThreshold {:6.4f}".format(rmse[y], gap),
)
# and apply the flags and output text
flag_locs, = np.where(flags != 0)
if plots or diagnostics:
utils.print_flagged_obs_number(logfile, "Wind Rose Check", "windspeeds/dirs", len(flag_locs), noWrite=True)
else:
utils.print_flagged_obs_number(logfile, "Wind Rose Check", "windspeeds/dirs", len(flag_locs))
station.qc_flags[:, flag_col] = flags
# and flag the variables
station.windspeeds.flags[flag_locs] = 1
station.winddirs.flags[flag_locs] = 1
return # wind_rose_check
def wind_rose_check(station, flag_col, start, end, logfile, plots = False, diagnostics = False, doMonth = False):
'''
Checks for large differences in the year-to-year wind-rose shape.
Uses RMSE and fits Gaussian. Finds gap in distribution to flag beyond
:param MetStation station: station object
:param int flag_col: which column to store the flags in
:param datetime start: start of data
:param datetime end: end of data
:param bool plots: run the plots
:param bool diagnostics: run the diagnostics
'''
st_var_spd = getattr(station, "windspeeds")
st_var_dir = getattr(station, "winddirs")
direction = st_var_dir.data
speed = st_var_spd.data
flags = station.qc_flags[:,flag_col]
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges_years = month_ranges.reshape(-1,12,2)
filtered_direction = utils.apply_filter_flags(st_var_dir, doMonth = doMonth, start = start, end = end)
filtered_speed = utils.apply_filter_flags(st_var_spd, doMonth = doMonth, start = start, end = end)
# histogram of wind directions ( ~ unravelled wind-rose)
dir_bins = range(0,360+DEGREEBINS,DEGREEBINS)
full_hist, full_binEdges = np.histogram(filtered_direction.compressed(), bins = dir_bins, normed = True)
if diagnostics:
print full_hist
# use rmse as this is known (Chi-sq remains just in case)
rmse, chisq = -np.ma.ones([month_ranges_years.shape[0]]), -np.ma.ones([month_ranges_years.shape[0]])
# run through each year to extract RMSE's
for y,year in enumerate(month_ranges_years):
if len(direction[year[0][0]:year[-1][0]].compressed()) > 0:
hist, dummy = np.histogram(direction[year[0][0]:year[-1][0]].compressed(), bins = dir_bins, normed = True)
chisq[y] = np.sum((full_hist-hist)**2/(full_hist+hist))/2.
rmse[y] = np.sqrt(np.mean((full_hist-hist)**2))
else:
rmse.mask[y] = True
# now to bin up the differences and see what the fit is.
# need to have values spread so can bin!
if len(np.unique(rmse.compressed())) > 1:
rmse_binEdges, rmse_bincenters = wind_create_bins(rmse)
hist, rmse_binEdges = np.histogram(rmse, bins = rmse_binEdges)#, density=True)
norm = get_histogram_norm(rmse, rmse_binEdges)
# inputs for fit
mu = np.mean(rmse)
std = np.std(rmse)
# try to get decent fit to bulk of obs.
# initial_values = [np.max(hist), np.mean(rmse), np.std(rmse), stats.skew(rmse), stats.kurtosis(rmse)] # norm, mean, std, sk#ew, kurtosis
# fit = leastsq(utils.residualsGH, initial_values, [bincenters, hist, np.ones(len(hist))])
# res = utils.hermite2gauss(fit[0])
# plot_gaussian = utils.funcGH(fit[0], bincenters)
fit = stats.rice.fit(rmse.compressed(), loc = 0, scale = np.ma.std(rmse))
dist_pdf = stats.rice.pdf(rmse_bincenters, fit[:-2], loc=fit[-2], scale=fit[-1]) * norm
gaussian = utils.fit_gaussian(rmse_bincenters, hist, max(hist), mu = mu, sig = std)
# invert Gaussian to find initial threshold, then hunt for first gap beyond
# threshold = utils.invert_gaussian(PROB_THRESHOLD, gaussian)
# invert Rician to find initial threshold, then hunt for first gap beyond
if dist_pdf[-1] < PROB_THRESHOLD:
# then curve has dropped below the threshold, so can find some updated ones.
threshold = -np.where(dist_pdf[::-1] > PROB_THRESHOLD)[0][0]
else:
threshold = rmse_bincenters[-1]
n = 0
center = np.argmax(hist)
gap = rmse_bincenters[-1] # nothing should be beyond this
while True:
if center + n + 1 == len(rmse_bincenters):
# gone beyond edge - nothing to flag, so just break
break
if rmse_bincenters[center + n] < threshold:
n += 1
# continue moving outwards
continue
if hist[center + n] == 0:
# found one
if center + n + 1 == len(rmse_bincenters):
# gone beyond edge - nothing to flag - escape
break
elif hist[center + n + 1] == 0:
# has to be two bins wide?
gap = rmse_bincenters[center + n]
break
n += 1
# run through each year to extract RMSE's
for y,year in enumerate(month_ranges_years):
if rmse[y] > gap:
# only flag where there are observations
good, = np.where(np.logical_or(direction.mask[year[0][0]:year[-1][0]] == False, speed.mask[year[0][0]:year[-1][0]] == False))
if len(good) > 100:
flags[year[0][0]:year[-1][0]][good] = 1
if diagnostics or plots:
print "Flagging {} RMSE {} > {}".format(y+start.year, rmse[y], gap)
else:
if diagnostics or plots:
print "{} beyond threshold (RMSE {} > {}) but retained as only {} observations\n".format(y+start.year, rmse[y], gap, len(good))
logfile.write("{} beyond threshold but retained as only {} observations\n".format(y+start.year, len(good)))
elif rmse.mask[y] == False:
if diagnostics or plots:
print "{}".format(y+start.year)
if plots:
import matplotlib.pyplot as plt
# plot underlying histogram
plt.clf()
plot_hist = np.array([float(x) if x != 0 else 1e-1 for x in hist])
plt.step(rmse_binEdges[1:], plot_hist, color = 'k')
# plot the Rician distribution on top
plt.plot(rmse_bincenters, dist_pdf, "r-", label = "Rician")
# plot the gaussian on top
plt.plot(rmse_binEdges[1:], utils.gaussian(rmse_bincenters, gaussian), color = 'b', ls = ":", label = "Gaussian")
plt.yscale("log")
plt.ylim([0.001, 2*max(plot_hist)])
# plot the thresholds
plt.axvline(threshold, color = 'g')
plt.axvline(gap, color = 'r')
# plot flagged values in different colour
if len(rmse[rmse > gap]) > 0:
plt.step(rmse_binEdges[1:][rmse_bincenters >= gap], plot_hist[rmse_bincenters >= gap], color = 'r')
# prettify
plt.xlabel("RMSE between complete record and each year")
plt.ylabel("Frequency")
plt.title(station.id + " annual wind rose differences")
plt.xlim([0, 1.1*np.ma.max(rmse)])
plt.legend(loc = "lower right", frameon = False)
plt.show()
# plot all the annual wind roses, flattened out.
plt.clf()
bincenters = (full_binEdges[:-1] + full_binEdges[1:])/2.
plt.plot(bincenters, full_hist, "k-", lw = 2)
for y,year in enumerate(month_ranges_years):
if len(speed[year[0][0]:year[-1][0]].compressed() > 0):
hist, binEdges = np.histogram(direction[year[0][0]:year[-1][0]].compressed(), bins = dir_bins, normed = True)
plt.plot(bincenters, hist)
plt.xlabel("Direction (degrees)")
plt.show()
# plot wind roses as wind roses
plot_wind_rose(speed, direction, "{} - {}".format(station.id, "all years"))
for y,year in enumerate(month_ranges_years):
if len(speed[year[0][0]:year[-1][0]].compressed() > 0):
plot_wind_rose(speed[year[0][0]:year[-1][0]], direction[year[0][0]:year[-1][0]], "{} - {}".format(station.id, start.year + y), label = "RMSE {:6.4f}\nThreshold {:6.4f}".format(rmse[y], gap))
else:
print "no data for {}".format(year)
# and apply the flags and output text
flag_locs, = np.where(flags != 0)
utils.print_flagged_obs_number(logfile, "Wind Rose Check", "windspeeds/dirs", len(flag_locs), noWrite=diagnostics)
station.qc_flags[:,flag_col] = flags
# and flag the variables
station.windspeeds.flags[flag_locs] = 1
station.winddirs.flags[flag_locs] = 1
return # wind_rose_check
def evc(station, variable_list, flag_col, start, end, logfile, diagnostics = False, plots = False, idl = False):
if plots or diagnostics:
import matplotlib.pyplot as plt
import calendar
# very similar to climatological check - ensure that not duplicating
for v, variable in enumerate(variable_list):
st_var = getattr(station, variable)
reporting_resolution = utils.reporting_accuracy(utils.apply_filter_flags(st_var))
reporting_freq = utils.reporting_frequency(utils.apply_filter_flags(st_var))
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges = month_ranges.reshape(-1,12,2)
month_data_count = np.zeros(month_ranges.shape[0:2])
# for each month
for month in range(12):
# set up hourly climatologies
hourly_clims = np.zeros(24)
hourly_clims.fill(st_var.data.fill_value)
this_month, year_ids, month_data_count[:,month] = utils.concatenate_months(month_ranges[:,month,:], st_var.data, hours = True)
# # extract each year and append together
# year_ids = [] # counter to determine which year each day corresponds to
# for year in range(month_ranges.shape[0]):
# this_year = st_var.data[month_ranges[year,month][0]:month_ranges[year,month][1]]
# if year == 0:
# # store so can access each hour of day separately
# this_month = this_year.reshape(-1,24)
# year_ids = [year for x in range(this_month.shape[0])]
# month_data_count[year,month] = len(this_year.compressed())
# else:
# this_year = this_year.reshape(-1,24)
# this_month = np.ma.concatenate((this_month, this_year), axis = 0)
# year_ids.extend([year for x in range(this_year.shape[0])])
# month_data_count[year,month] = len(this_year.compressed())
# winsorize and get hourly climatology
for h in range(24):
this_hour = this_month[:,h]
if len(this_hour.compressed()) > 100:
# winsorize & climatologies - done to match IDL
if idl:
this_hour_winsorized = utils.winsorize(np.append(this_hour.compressed(), -999999), 0.05, idl = idl)
hourly_clims[h] = np.ma.sum(this_hour_winsorized)/(len(this_hour_winsorized) - 1)
else:
this_hour_winsorized = utils.winsorize(this_hour.compressed(), 0.05, idl = idl)
hourly_clims[h] = np.ma.mean(this_hour_winsorized)
hourly_clims = np.ma.masked_where(hourly_clims == st_var.data.fill_value, hourly_clims)
anomalies = this_month - np.tile(hourly_clims, (this_month.shape[0], 1))
# extract IQR of anomalies (using 1/2 value to match IDL)
if len(anomalies.compressed()) >= 10:
iqr = utils.IQR(anomalies.compressed().reshape(-1)) / 2. # to match IDL
if iqr < 1.5: iqr = 1.5
else:
iqr = st_var.mdi
normed_anomalies = anomalies / iqr
variances = np.ma.zeros(month_ranges.shape[0])
variances.mask = [False for i in range(month_ranges.shape[0])]
rep_accuracies = np.zeros(month_ranges.shape[0])
rep_freqs = np.zeros(month_ranges.shape[0])
variances.fill(st_var.mdi)
rep_accuracies.fill(st_var.mdi)
rep_freqs.fill(st_var.mdi)
year_ids = np.array(year_ids)
# extract variance of normalised anomalies for each year
for y, year in enumerate(range(month_ranges.shape[0])):
year_locs = np.where(year_ids == y)
this_year = normed_anomalies[year_locs,:]
this_year = this_year.reshape(-1)
# end of similarity with Climatological check
if len(this_year.compressed()) >= 30:
variances[y] = utils.mean_absolute_deviation(this_year, median = True)
rep_accuracies[y] = utils.reporting_accuracy(this_year)
rep_freqs[y] = utils.reporting_frequency(this_year)
else:
variances.mask[y] = True
good = np.where(month_data_count[:,month] >= 100)
# get median and IQR of variance for all years for this month
if len(good[0]) >= 10:
median_variance = np.median(variances[good])
iqr_variance = utils.IQR(variances[good]) / 2. # to match IDL
if iqr_variance < 0.01: iqr_variance = 0.01
else:
median_variance = st_var.mdi
iqr_variance = st_var.mdi
# if SLP, then get median and MAD of SLP and windspeed for month
if variable in ["slp", "windspeeds"]:
winds = getattr(station, "windspeeds")
slp = getattr(station, "slp")
# refactor this as similar in style to how target data extracted
for y, year in enumerate(range(month_ranges.shape[0])):
if y == 0:
winds_year = winds.data[month_ranges[year,month][0]:month_ranges[year,month][1]]
winds_month = winds_year.reshape(-1,24)
slp_year = slp.data[month_ranges[year,month][0]:month_ranges[year,month][1]]
slp_month = slp_year.reshape(-1,24)
else:
winds_year = winds.data[month_ranges[year,month][0]:month_ranges[year,month][1]]
winds_year = winds_year.reshape(-1,24)
winds_month = np.ma.concatenate((winds_month, winds_year), axis = 0)
slp_year = slp.data[month_ranges[year,month][0]:month_ranges[year,month][1]]
slp_year = slp_year.reshape(-1,24)
slp_month = np.ma.concatenate((slp_month, slp_year), axis = 0)
median_wind = np.ma.median(winds_month)
median_slp = np.ma.median(slp_month)
wind_MAD = utils.mean_absolute_deviation(winds_month.compressed())
slp_MAD = utils.mean_absolute_deviation(slp_month.compressed())
if diagnostics:
print "median windspeed {} m/s, MAD = {}".format(median_wind, wind_MAD)
print "median slp {} hPa, MAD = {}".format(median_slp, slp_MAD)
# now test to see if variance exceeds expected range
for y, year in enumerate(range(month_ranges.shape[0])):
if (variances[y] != st_var.mdi) and (iqr_variance != st_var.mdi) and \
(median_variance != st_var.mdi) and (month_data_count[y,month] >= DATA_COUNT_THRESHOLD):
# if SLP, then need to test if deep low pressure ("hurricane/storm") present
# as this will increase the variance for this month + year
if variable in ["slp", "windspeeds"]:
iqr_threshold = 6.
# increase threshold if reporting frequency and resolution of this
# year doesn't match average
if (rep_accuracies[y] != reporting_resolution) and \
(rep_freqs[y] != reporting_freq):
iqr_threshold = 8.
if diagnostics:
print np.abs(variances[y] - median_variance) / iqr_variance, variances[y] , median_variance , iqr_variance , iqr_threshold, month+1, year+start.year
if np.abs((variances[y] - median_variance) / iqr_variance) > iqr_threshold:
# check for storms
winds_month = winds.data[month_ranges[year,month][0]:month_ranges[year,month][1]]
slp_month = slp.data[month_ranges[year,month][0]:month_ranges[year,month][1]]
storm = False
if (len(winds_month.compressed()) >= 1) and (len(slp_month.compressed()) >= 1):
# find max wind & min SLP
# max_wind_loc = np.where(winds_month == np.max(winds_month))[0][0]
# min_slp_loc = np.where(slp_month == np.min(slp_month))[0][0]
# if these are above thresholds and within one day of each other,
# then it likely was a storm
# print "fix this in case of multiple max/min locations"
# if (np.abs(max_wind_loc - min_slp_loc) <= 24) and \
# (((np.max(winds_month) - median_wind) / wind_MAD) > MAD_THRESHOLD) and \
# (((median_slp - np.min(slp_month)) / slp_MAD) > MAD_THRESHOLD):
# locations where winds greater than threshold
high_winds, = np.where((winds_month - median_wind)/wind_MAD > MAD_THRESHOLD)
# and where SLP less than threshold
low_slps, = np.where((median_slp - slp_month)/slp_MAD > MAD_THRESHOLD)
# if any locations match, then it's a storm
match_loc = high_winds[np.in1d(high_winds, low_slps)]
if len(match_loc) > 0:
storm = True
else:
print "write spurious"
# check the SLP first difference series
# to ensure a drop down and climb out of minimum SLP/or climb up and down from maximum wind speed
if variable == "slp":
diffs = np.diff(slp_month.compressed())
elif variable == "windspeeds":
diffs = np.diff(winds_month.compressed())
negs, poss = 0,0
biggest_neg, biggest_pos = 0,0
for diff in diffs:
if diff > 0:
if negs > biggest_neg: biggest_neg = negs
negs = 0
poss += 1
else:
if poss > biggest_pos: biggest_pos = poss
poss = 0
negs += 1
if (biggest_neg < 10) and (biggest_pos < 10) and not storm:
# not a hurricane, so mask
station.qc_flags[month_ranges[year,month,0]:month_ranges[year,month,1], flag_col[v]] = 1
if plots or diagnostics:
print "No Storm or Hurricane in %i %i - flagging\n" % (month+1, y+start.year)
else:
logfile.write("No Storm or Hurricane in %i %i - flagging\n" % (month+1, y+start.year))
else:
# hurricane
if plots or diagnostics:
print "Storm or Hurricane in %i %i - not flagging\n" % (month+1, y+start.year)
else:
logfile.write("Storm or Hurricane in %i %i - not flagging\n" % (month+1, y+start.year))
if plots:
# plot showing the pressure, pressure first differences and the wind speeds
plot_times = utils.times_hours_to_datetime(station.time.data[month_ranges[year,month][0]:month_ranges[year,month][1]], start)
evc_plot_slp_wind(plot_times, slp_month, diffs, median_slp, slp_MAD, winds_month, median_wind, wind_MAD)
else:
iqr_threshold = 8.
if (rep_accuracies[y] != reporting_resolution) and \
(rep_freqs[y] != reporting_freq):
iqr_threshold = 10.
if np.abs(variances[y] - median_variance) / iqr_variance > iqr_threshold:
if diagnostics:
print "flagging {} {}".format(year+start.year,calendar.month_name[month+1])
# remove the data
station.qc_flags[month_ranges[year,month,0]:month_ranges[year,month,1], flag_col[v]] = 1
if plots:
plot_variances = (variances - median_variance) / iqr_variance
plot_variances = np.ma.masked_where(month_data_count[:,month] < DATA_COUNT_THRESHOLD,plot_variances)
evc_plot_hist(plot_variances, iqr_threshold, "Variance Check - %s - %s" % (variable, calendar.month_name[month+1]))
flag_locs = np.where(station.qc_flags[:, flag_col[v]] != 0)
if plots or diagnostics:
utils.print_flagged_obs_number(logfile, "Variance", variable, len(flag_locs[0]), noWrite = True)
else:
utils.print_flagged_obs_number(logfile, "Variance", variable, len(flag_locs[0]))
# copy flags into attribute
st_var.flags[flag_locs] = 1
# matches 030660 for T, D and SLP 21/8/2014
station = utils.append_history(station, "Excess Variance Check")
return # evc
def dgc_all_obs(station,
variable,
flags,
start,
end,
logfile,
plots=False,
diagnostics=False,
idl=False,
windspeeds=False,
GH=False,
doMonth=False):
'''RJHD addition working on all observations'''
if plots:
import matplotlib.pyplot as plt
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges = month_ranges.reshape(-1, 12, 2)
# extract variable
st_var = getattr(station, variable)
# apply flags (and mask incomplete year if appropriate)
all_filtered = utils.apply_filter_flags(st_var,
doMonth=doMonth,
start=start,
end=end)
st_var_complete_year = copy.deepcopy(st_var)
if doMonth:
# restrict the incomplete year if appropriate - keep other flagged obs.
full_year_end = utils.get_first_hour_this_year(start, end)
st_var_complete_year.data.mask[full_year_end:] = True
for month in range(12):
# if requiring wind data, extract data and find monthly averages
if windspeeds == True:
st_var_wind = getattr(station, "windspeeds")
if doMonth:
# restrict the incomplete year if appropriate
st_var_wind.data.mask[full_year_end:] = True
# get monthly averages
windspeeds_month = np.empty([])
for y, year in enumerate(month_ranges[:, month, :]):
if y == 0:
windspeeds_month = np.ma.array(
st_var_wind.data[year[0]:year[1]])
else:
windspeeds_month = np.ma.concatenate(
[windspeeds_month, st_var_wind.data[year[0]:year[1]]])
windspeeds_month_average = dgc_get_monthly_averages(
windspeeds_month, OBS_LIMIT, st_var_wind.mdi, MEAN)
windspeeds_month_mad = utils.mean_absolute_deviation(
windspeeds_month, median=True)
# pull data from each calendar month together
this_month_data, dummy, dummy = utils.concatenate_months(
month_ranges[:, month, :], st_var.data, hours=False)
this_month_filtered, dummy, dummy = utils.concatenate_months(
month_ranges[:, month, :], all_filtered, hours=False)
this_month_complete, dummy, dummy = utils.concatenate_months(
month_ranges[:, month, :], st_var_complete_year.data, hours=False)
# if enough clean and complete data for this calendar month find the median and IQR
if len(this_month_filtered.compressed()) > OBS_LIMIT:
if idl:
monthly_median = utils.idl_median(
this_month_filtered.compressed().reshape(-1))
else:
monthly_median = np.ma.median(this_month_filtered)
iqr = utils.IQR(this_month_filtered.compressed())
if iqr == 0.0:
# to get some spread if IQR too small
iqr = utils.IQR(this_month_filtered.compressed(),
percentile=0.05)
print "Spurious_stations file not yet sorted"
# if have an IQR, anomalise using median and standardise using IQR
if iqr != 0.0:
monthly_values = np.ma.array(
(this_month_data.compressed() - monthly_median) / iqr)
complete_values = np.ma.array(
(this_month_complete.compressed() - monthly_median) / iqr)
# use complete years only for the histogram - aiming to find outliers.
bins, bincenters = utils.create_bins(complete_values, BIN_SIZE)
dummy, plot_bincenters = utils.create_bins(
complete_values, BIN_SIZE / 10.)
hist, binEdges = np.histogram(complete_values, bins=bins)
"""
Change to monthly updates Oct 2017
Thought about changing distribution to use filtered values
But this changes the test beyond just dealing with additional months
Commented out lines below would be alternative.
"""
# bins, bincenters = utils.create_bins(filtered_values, BIN_SIZE)
# dummy, plot_bincenters = utils.create_bins(filtered_values, BIN_SIZE/10.)
# hist, binEdges = np.histogram(filtered_values, bins = bins)
# used filtered (incl. incomplete year mask) to determine the distribution.
if GH:
# Use Gauss-Hermite polynomials to add skew and kurtosis to Gaussian fit - January 2015 ^RJHD
# Feb 2019 - if large amounts off centre, can affect initial values
# switched to median and MAD
initial_values = [
np.max(hist),
np.median(complete_values),
utils.mean_absolute_deviation(complete_values,
median=True),
stats.skew(complete_values),
stats.kurtosis(complete_values)
] # norm, mean, std, skew, kurtosis
fit = leastsq(utils.residualsGH, initial_values,
[bincenters, hist,
np.ones(len(hist))])
res = utils.hermite2gauss(fit[0], diagnostics=diagnostics)
plot_gaussian = utils.funcGH(fit[0], plot_bincenters)
# adjust to remove the rising bumps seen in some fits - artefacts of GH fitting?
mid_point = np.argmax(plot_gaussian)
bad, = np.where(
plot_gaussian[mid_point:] < FREQUENCY_THRESHOLD / 10.)
if len(bad) > 0:
plot_gaussian[mid_point:][
bad[0]:] = FREQUENCY_THRESHOLD / 10.
bad, = np.where(
plot_gaussian[:mid_point] < FREQUENCY_THRESHOLD / 10.)
if len(bad) > 0:
plot_gaussian[:mid_point][:bad[
-1]] = FREQUENCY_THRESHOLD / 10.
# extract threshold values
good_values = np.argwhere(
plot_gaussian > FREQUENCY_THRESHOLD)
l_minimum_threshold = round(
plot_bincenters[good_values[0]]) - 1
u_minimum_threshold = 1 + round(
plot_bincenters[good_values[-1]])
if diagnostics:
print hist
print res
print iqr, l_minimum_threshold, u_minimum_threshold
# or just a standard Gaussian
else:
gaussian = utils.fit_gaussian(
bincenters,
hist,
max(hist),
mu=np.median(complete_values),
sig=utils.mean_absolute_value(complete_values))
# assume the same threshold value
u_minimum_threshold = 1 + round(
utils.invert_gaussian(FREQUENCY_THRESHOLD, gaussian))
l_minimum_threshold = -u_minimum_threshold
plot_gaussian = utils.gaussian(plot_bincenters, gaussian)
if diagnostics:
print hist
print gaussian
print iqr, u_minimum_threshold, 1. + utils.invert_gaussian(
FREQUENCY_THRESHOLD, gaussian)
if plots:
dgc_set_up_plot(plot_gaussian,
complete_values,
variable,
threshold=(u_minimum_threshold,
l_minimum_threshold),
sub_par="observations",
GH=GH)
if GH:
plt.figtext(
0.15,
0.67,
'Mean %.2f, S.d. %.2f,\nSkew %.2f, Kurtosis %.2f' %
(res['mean'], res['dispersion'], res['skewness'],
res['kurtosis']),
color='k',
size='small')
# now trying to find gaps in the distribution
uppercount = len(
np.where(monthly_values > u_minimum_threshold)[0])
lowercount = len(
np.where(monthly_values < l_minimum_threshold)[0])
# this needs refactoring - but lots of variables to pass in
if plots or diagnostics: gap_plot_values = np.array([])
# do one side of distribution and then other
if uppercount > 0:
gap_start = dgc_find_gap(hist, binEdges,
u_minimum_threshold)
if gap_start != 0:
# if found a gap, then go through each year for this calendar month
# and flag observations further from middle
for y, year in enumerate(month_ranges[:, month, :]):
# not using filtered - checking all available data
this_year_data = np.ma.array(
st_var.data[year[0]:year[1]])
this_year_flags = np.array(flags[year[0]:year[1]])
gap_cleaned_locations = np.ma.where(
((this_year_data - monthly_median) /
iqr) > gap_start)
this_year_flags[gap_cleaned_locations] = 1
flags[year[0]:year[1]] = this_year_flags
if plots or diagnostics:
gap_plot_values = np.append(
gap_plot_values,
(this_year_data[gap_cleaned_locations].
compressed() - monthly_median) / iqr)
if len(gap_cleaned_locations[0]) > 0:
print "Upper {}-{} - {} obs flagged".format(
y + start.year, month,
len(gap_cleaned_locations[0]))
print gap_cleaned_locations, this_year_data[
gap_cleaned_locations]
if lowercount > 0:
gap_start = dgc_find_gap(hist, binEdges,
l_minimum_threshold)
if gap_start != 0:
# if found a gap, then go through each year for this calendar month
# and flag observations further from middle
for y, year in enumerate(month_ranges[:, month, :]):
this_year_data = np.ma.array(
st_var.data[year[0]:year[1]])
this_year_flags = np.array(flags[year[0]:year[1]])
gap_cleaned_locations = np.ma.where(
np.logical_and(
((this_year_data - monthly_median) / iqr) <
gap_start, this_year_data.mask != True))
# add flag requirement for low pressure bit if appropriate
this_year_flags[gap_cleaned_locations] = 1
flags[year[0]:year[1]] = this_year_flags
if plots or diagnostics:
gap_plot_values = np.append(
gap_plot_values,
(this_year_data[gap_cleaned_locations].
compressed() - monthly_median) / iqr)
if len(gap_cleaned_locations[0]) > 0:
print "Lower {}-{} - {} obs flagged".format(
y + start.year, month,
len(gap_cleaned_locations[0]))
print gap_cleaned_locations, this_year_data[
gap_cleaned_locations]
# if doing SLP then do extra checks for storms
if windspeeds:
windspeeds_year = np.ma.array(
st_var_wind.data[year[0]:year[1]])
this_year_flags[
gap_cleaned_locations] = 2 # tentative flags
slp_average = dgc_get_monthly_averages(
this_month_data, OBS_LIMIT, st_var.mdi,
MEAN)
slp_mad = utils.mean_absolute_deviation(
this_month_data, median=True)
# need to ensure that this_year_data is less than slp_average, hence order of test
storms, = np.ma.where((((windspeeds_year - windspeeds_month_average) / windspeeds_month_mad) > MAD_THRESHOLD) &\
(((slp_average - this_year_data) / slp_mad) > MAD_THRESHOLD))
# using IDL terminology
if len(storms) >= 2:
# use the first difference series to find when there are gaps in
# contiguous sequences of storm observations - want to split up into
# separate storm events
storm_1diffs = np.diff(storms)
separations, = np.where(storm_1diffs != 1)
# expand around storm signal so that all low SLP values covered, and unflagged
if len(separations) >= 1:
print " multiple storms in {} {}".format(
y + start.year, month)
# if more than one storm signal that month, then use intervals
# in the first difference series to expand around the first interval alone
storm_start = 0
storm_finish = separations[0] + 1
first_storm = dgc_expand_storms(
storms[storm_start:storm_finish],
len(this_year_data))
final_storms = copy.deepcopy(
first_storm)
for j in range(len(separations)):
# then do the rest in a loop
if j + 1 == len(separations):
# final one
this_storm = dgc_expand_storms(
storms[separations[j] +
1:],
len(this_year_data))
else:
this_storm = dgc_expand_storms(
storms[separations[j] +
1:separations[j +
1] +
1],
len(this_year_data))
final_storms = np.append(
final_storms, this_storm)
else:
# else just expand around the signal by 6 hours either way
final_storms = dgc_expand_storms(
storms, len(this_year_data))
else:
final_storms = storms
if len(storms) >= 1:
print "Tropical Storm signal in {} {}".format(
y + start.year, month)
this_year_flags[final_storms] = 0
# and write flags back into array
flags[year[0]:year[1]] = this_year_flags
if plots:
hist, binEdges = np.histogram(gap_plot_values, bins=bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters,
plot_hist,
'r-',
label='flagged',
where='mid')
import calendar
plt.text(0.1,
0.9,
calendar.month_name[month + 1],
transform=plt.gca().transAxes)
plt.legend(loc='lower center',
ncol=3,
bbox_to_anchor=(0.5, -0.2),
frameon=False,
prop={'size': 13})
plt.show()
#plt.savefig(IMAGELOCATION+'/'+station.id+'_DistributionalGap_'+str(month+1)+'.png')
nflags, = np.where(flags != 0)
utils.print_flagged_obs_number(logfile,
"Distributional Gap All",
variable,
len(nflags),
noWrite=diagnostics)
return flags # dgc_all_obs
def clean_up(st_var,
flags,
input_flag_cols,
out_flag_col,
start,
end,
times,
plots=False):
'''
Clean up the remaining observations if many flagged or few left in a month
:param MetVar st_var: input station object
:param array flags: QC flags array
:param array input_flag_cols: which columns to check over
:param int out_flag_col: in which column to set the flags
:param datetime start: start of dataset
:param datetime end: end of dataset
:param array times: hourly time stamps
:param bool plots: show plots
'''
month_ranges = utils.month_starts_in_pairs(start, end)
total_flags = np.sum(flags[:, input_flag_cols], axis=1)
filtered = utils.apply_filter_flags(st_var)
# test each month
for month in month_ranges:
this_month = filtered[month[0]:month[1]]
# if less than 20 obs, then flag remaining
if len(this_month.compressed()) < 20:
locs = np.where(this_month.mask == False)[0]
# only flag those observations that actually exist.
if len(locs) > 0:
month_range = np.arange(month[0], month[1], dtype=("int"))
flags[month_range[locs], out_flag_col] = 1
if plots:
cu_plots(times,
st_var.data,
month_range[0],
month_range[-1],
start,
st_var.name,
extra_text="few_obs")
# if 40% of obs flagged, then flag remainig
else:
good_locs = np.where(this_month.mask == False)[0]
flag_locs = np.where(total_flags[month[0]:month[1]] > 0)[0]
# good_locs - internal and neighbour flags already applied, so need to add
# these back in.
proportion = float(
len(flag_locs)) / float(len(good_locs) + len(flag_locs))
if proportion > 0.4:
month_range = np.arange(month[0], month[1], dtype=("int"))
flags[month_range[good_locs], out_flag_col] = 1
if plots:
cu_plots(times,
st_var.data,
month_range[0],
month_range[-1],
start,
st_var.name,
extra_text="lots flagged")
return # clean_up
def fvc(station,
variable_list,
flag_col,
start,
end,
logfile,
diagnostics=False,
plots=False,
doMonth=False):
'''
Check for certain values occurring more frequently than would be expected
:param object station: station object to process
:param list variable_list: list of variables to process
:param list flag_col: columns to fill in flag array
:param datetime start: datetime object of start of data
:param datetime end: datetime object of end of data
:param file logfile: logfile to store outputs
:param bool diagnostics: produce extra diagnostic output
:param bool plots: produce plots
:param bool month: ignore months after last complete year/season for distribution
'''
MIN_DATA_REQUIRED = 500 # to create histogram for complete record
MIN_DATA_REQUIRED_YEAR = 100 # to create histogram
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges_years = month_ranges.reshape(-1, 12, 2)
for v, variable in enumerate(variable_list):
st_var = getattr(station, variable)
reporting_accuracy = utils.reporting_accuracy(
utils.apply_filter_flags(st_var))
# apply flags - for detection only
filtered_data = utils.apply_filter_flags(st_var,
doMonth=doMonth,
start=start,
end=end)
for season in range(5): # Year,MAM,JJA,SON,JF+D
if season == 0:
# all year
season_data = np.ma.masked_values(filtered_data.compressed(),
st_var.fdi)
thresholds = [30, 20, 10]
else:
thresholds = [20, 15, 10]
season_data = np.ma.array([])
for y, year in enumerate(month_ranges_years):
# churn through months extracting data, accounting for fdi and concatenating together
if season == 1:
#mam
season_data = np.ma.concatenate([
season_data,
np.ma.masked_values(
filtered_data[year[2][0]:year[4][-1]],
st_var.fdi)
])
elif season == 2:
#jja
season_data = np.ma.concatenate([
season_data,
np.ma.masked_values(
filtered_data[year[5][0]:year[7][-1]],
st_var.fdi)
])
elif season == 3:
#son
season_data = np.ma.concatenate([
season_data,
np.ma.masked_values(
filtered_data[year[8][0]:year[10][-1]],
st_var.fdi)
])
elif season == 4:
#d+jf
season_data = np.ma.concatenate([
season_data,
np.ma.masked_values(
filtered_data[year[0][0]:year[1][-1]],
st_var.fdi)
])
season_data = np.ma.concatenate([
season_data,
np.ma.masked_values(
filtered_data[year[-1][0]:year[-1][-1]],
st_var.fdi)
])
season_data = season_data.compressed()
if len(season_data) > MIN_DATA_REQUIRED:
if 0 < reporting_accuracy <= 0.5: # -1 used as missing value
bins, bincenters = utils.create_bins(season_data, 0.5)
else:
bins, bincenters = utils.create_bins(season_data, 1.0)
hist, binEdges = np.histogram(season_data, bins=bins)
if plots:
plot_hist, bincenters = fvc_plot_setup(season_data,
hist,
binEdges,
st_var.name,
title="%s" %
(SEASONS[season]))
bad_bin = np.zeros(len(hist))
# scan through bin values and identify bad ones
for e, element in enumerate(hist):
if e > 3 and e <= (len(hist) - 3):
# don't bother with first three or last three bins
seven_bins = hist[e - 3:e + 3 + 1]
if (seven_bins[3]
== seven_bins.max()) and (seven_bins[3] != 0):
# is local maximum and != zero
if (seven_bins[3] / float(seven_bins.sum()) >=
0.5) and (seven_bins[3] >= thresholds[0]):
# contains >50% of data and is greater than threshold
bad_bin[e] = 1
# for plotting remove good bins
else:
if plots: plot_hist[e] = 1e-1
else:
if plots: plot_hist[e] = 1e-1
else:
if plots: plot_hist[e] = 1e-1
if plots:
import matplotlib.pyplot as plt
plt.step(bincenters, plot_hist, 'r-', where='mid')
plt.show()
# having identified possible bad bins, check each year in turn, on unfiltered data
for y, year in enumerate(month_ranges_years):
if season == 0:
# year
year_data = np.ma.masked_values(
st_var.data[year[0][0]:year[-1][-1]], st_var.fdi)
year_flags = station.qc_flags[year[0][0]:year[-1][-1],
flag_col[v]]
elif season == 1:
#mam
year_data = np.ma.masked_values(
st_var.data[year[2][0]:year[4][-1]], st_var.fdi)
year_flags = station.qc_flags[year[2][0]:year[4][-1],
flag_col[v]]
elif season == 2:
#jja
year_data = np.ma.masked_values(
st_var.data[year[5][0]:year[7][-1]], st_var.fdi)
year_flags = station.qc_flags[year[5][0]:year[7][-1],
flag_col[v]]
elif season == 3:
#son
year_data = np.ma.masked_values(
st_var.data[year[8][0]:year[10][-1]], st_var.fdi)
year_flags = station.qc_flags[year[8][0]:year[10][-1],
flag_col[v]]
elif season == 4:
#d+jf
year_data = np.ma.concatenate([np.ma.masked_values(st_var.data[year[0][0]:year[1][-1]], st_var.fdi),\
np.ma.masked_values(st_var.data[year[-1][0]:year[-1][-1]], st_var.fdi)])
year_flags = np.append(
station.qc_flags[year[0][0]:year[1][-1],
flag_col[v]],
station.qc_flags[year[-1][0]:year[-1][-1],
flag_col[v]])
if len(year_data.compressed()) > MIN_DATA_REQUIRED_YEAR:
hist, binEdges = np.histogram(year_data.compressed(),
bins=bins)
if plots:
plot_hist, bincenters = fvc_plot_setup(
year_data.compressed(),
hist,
binEdges,
st_var.name,
title="%s - %s" %
(y + start.year, SEASONS[season]))
for e, element in enumerate(hist):
if bad_bin[e] == 1:
# only look at pre-identified bins
if e >= 3 and e <= (len(hist) - 3):
# don't bother with first three or last three bins
seven_bins = hist[e - 3:e + 3 +
1].astype('float')
if (seven_bins[3] == seven_bins.max()
) and (seven_bins[3] != 0):
# is local maximum and != zero
if (seven_bins[3]/seven_bins.sum() >= 0.5 and seven_bins[3] >= thresholds[1]) \
or (seven_bins[3]/seven_bins.sum() >= 0.9 and seven_bins[3] >= thresholds[2]):
# contains >50% or >90% of data and is greater than appropriate threshold
# Flag these data
bad_points = np.where(
(year_data >= binEdges[e]) &
(year_data < binEdges[e + 1]))
year_flags[bad_points] = 1
# for plotting remove good bins
else:
if plots: plot_hist[e] = 1e-1
else:
if plots: plot_hist[e] = 1e-1
else:
if plots: plot_hist[e] = 1e-1
else:
if plots: plot_hist[e] = 1e-1
if diagnostics or plots:
nflags = len(np.where(year_flags != 0)[0])
print "{} {}".format(y + start.year, nflags)
if plots:
if nflags > 0:
plt.step(bincenters,
plot_hist,
'r-',
where='mid')
plt.show()
else:
plt.clf()
# copy flags back
if season == 0:
station.qc_flags[year[0][0]:year[-1][-1],
flag_col[v]] = year_flags
elif season == 1:
station.qc_flags[year[2][0]:year[4][-1],
flag_col[v]] = year_flags
elif season == 2:
station.qc_flags[year[5][0]:year[7][-1],
flag_col[v]] = year_flags
elif season == 3:
station.qc_flags[year[8][0]:year[10][-1],
flag_col[v]] = year_flags
elif season == 4:
split = len(station.qc_flags[year[0][0]:year[1][-1],
flag_col[v]])
station.qc_flags[year[0][0]:year[1][-1],
flag_col[v]] = year_flags[:split]
station.qc_flags[year[-1][0]:year[-1][-1],
flag_col[v]] = year_flags[split:]
flag_locs = np.where(station.qc_flags[:, flag_col[v]] != 0)
utils.print_flagged_obs_number(logfile,
"Frequent Value",
variable,
len(flag_locs[0]),
noWrite=diagnostics)
# copy flags into attribute
st_var.flags[flag_locs] = 1
station = utils.append_history(station, "Frequent Values Check")
return # fvc
def spc_diff(sfc, stn, flags, month_ranges, start, end, logfile, plots = False, diagnostics = False, doMonth = False):
'''
Pressure difference check, on individual obs. Remove very silly stnlp
:param array sfc: SLP
:param array stn: STNLP
:param array flags: flags_array
:param array month_ranges: array of month start and end times
:param datetime start: DATASTART
:param datetime end: DATAEND
:param file logfile: logfile to store outputs
:param bool plots: do plots or not
:param bool diagnostics: extra verbose output
:param bool doMonth: account for spare month
:returns: flags - locations where flags have been set
'''
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges = month_ranges.reshape(-1,12,2)
# apply flags (and mask incomplete year if appropriate)
sfc_filtered = utils.apply_filter_flags(sfc, doMonth = doMonth, start = start, end = end)
stn_filtered = utils.apply_filter_flags(stn, doMonth = doMonth, start = start, end = end)
# get the differences
diffs = sfc.data - stn.data
diffs_filtered = sfc_filtered - stn_filtered
# robust statistics
median_difference = np.ma.median(diffs)
mad_difference = utils.mean_absolute_deviation(diffs, median = True)
# where exceed
high, = np.ma.where(diffs > (median_difference + MAD_THRESHOLD*mad_difference))
low, = np.ma.where(diffs < (median_difference - MAD_THRESHOLD*mad_difference))
# set flags
if len(high) != 0:
if diagnostics: print "Number of high differences {}".format(len(high))
flags[high] = 1
if len(low) != 0:
if diagnostics: print "Number of low differences {}".format(len(low))
flags[low] = 1
if plots:
import matplotlib.pyplot as plt
plt.clf()
plt.hist(diffs.compressed(), bins = np.arange(np.round(median_difference)-10, np.round(median_difference)+10, 0.1))
plt.axvline(x = (median_difference + 4*mad_difference), ls = "--", c = "r")
plt.axvline(x = (median_difference - 4*mad_difference), ls = "--", c = "r")
plt.xlim([median_difference - 11, median_difference + 11])
plt.ylabel("Observations")
plt.xlabel("Difference (hPa)")
plt.show()
# How to set the range of allowable values.
nflags, = np.where(flags != 0)
utils.print_flagged_obs_number(logfile, "Station Level Pressure", "stnlp", len(nflags), noWrite=diagnostics)
return flags # spc_diff
def clean_up(st_var, flags, input_flag_cols, out_flag_col, start, end, times, plots=False):
"""
Clean up the remaining observations if many flagged or few left in a month
:param MetVar st_var: input station object
:param array flags: QC flags array
:param array input_flag_cols: which columns to check over
:param int out_flag_col: in which column to set the flags
:param datetime start: start of dataset
:param datetime end: end of dataset
:param array times: hourly time stamps
:param bool plots: show plots
"""
month_ranges = utils.month_starts_in_pairs(start, end)
total_flags = np.sum(flags[:, input_flag_cols], axis=1)
filtered = utils.apply_filter_flags(st_var)
# test each month
for month in month_ranges:
this_month = filtered[month[0] : month[1]]
# if less than 20 obs, then flag remaining
if len(this_month.compressed()) < 20:
locs = np.where(this_month.mask == False)[0]
# only flag those observations that actually exist.
if len(locs) > 0:
month_range = np.arange(month[0], month[1], dtype=("int"))
flags[month_range[locs], out_flag_col] = 1
if plots:
cu_plots(
times, st_var.data, month_range[0], month_range[-1], start, st_var.name, extra_text="few_obs"
)
# if 40% of obs flagged, then flag remainig
else:
good_locs = np.where(this_month.mask == False)[0]
flag_locs = np.where(total_flags[month[0] : month[1]] > 0)[0]
# good_locs - internal and neighbour flags already applied, so need to add
# these back in.
proportion = float(len(flag_locs)) / float(len(good_locs) + len(flag_locs))
if proportion > 0.4:
month_range = np.arange(month[0], month[1], dtype=("int"))
flags[month_range[good_locs], out_flag_col] = 1
if plots:
cu_plots(
times,
st_var.data,
month_range[0],
month_range[-1],
start,
st_var.name,
extra_text="lots flagged",
)
return # clean_up
def coc(station, variable_list, flag_col, start, end, logfile, diagnostics = False, plots = False, idl = False):
for v, variable in enumerate(variable_list):
st_var = getattr(station, variable)
all_filtered = utils.apply_filter_flags(st_var)
# is this needed 13th Nov 2014 RJHD
#reporting_resolution = utils.reporting_accuracy(utils.apply_filter_flags(st_var))
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges = month_ranges.reshape(-1,12,2)
for month in range(12):
hourly_climatologies = np.zeros(24)
hourly_climatologies.fill(st_var.mdi)
# append all e.g. Januaries together
this_month, year_ids, dummy = utils.concatenate_months(month_ranges[:,month,:], st_var.data, hours = True)
this_month_filtered, dummy, dummy = utils.concatenate_months(month_ranges[:,month,:], all_filtered, hours = True)
# if fixed climatology period, sort this here
# get as array of 24 hrs.
this_month = np.ma.array(this_month)
this_month = this_month.reshape(-1,24)
this_month_filtered = np.ma.array(this_month_filtered)
this_month_filtered = this_month_filtered.reshape(-1,24)
# get hourly climatology for each month
for hour in range(24):
this_hour = this_month[:,hour]
# need to have data if this is going to work!
if len(this_hour.compressed()) > 0:
# winsorize & climatologies - done to match IDL
if idl:
this_hour = utils.winsorize(np.append(this_hour.compressed(), -999999), 0.05, idl = idl)
hourly_climatologies[hour] = np.ma.sum(this_hour)/(len(this_hour) - 1)
else:
this_hour = utils.winsorize(this_hour.compressed(), 0.05, idl = idl)
hourly_climatologies[hour] = np.ma.mean(this_hour)
if len(this_month.compressed()) > 0:
# can get stations with few obs in a particular variable.
# anomalise each hour over month appropriately
anomalies = this_month - np.tile(hourly_climatologies, (this_month.shape[0],1))
anomalies_filtered = this_month_filtered - np.tile(hourly_climatologies, (this_month_filtered.shape[0],1))
if len(anomalies.compressed()) >= 10:
iqr = utils.IQR(anomalies.compressed().reshape(-1))/2. # to match IDL
if iqr < 1.5: iqr = 1.5
else:
iqr = st_var.mdi
normed_anomalies = anomalies / iqr
normed_anomalies_filtered = anomalies_filtered / iqr
# get average anomaly for year
year_ids = np.array(year_ids)
monthly_vqvs = np.ma.zeros(month_ranges.shape[0])
monthly_vqvs.mask = [False for x in range(month_ranges.shape[0])]
for year in range(month_ranges.shape[0]):
year_locs = np.where(year_ids == year)
this_year = normed_anomalies_filtered[year_locs,:]
if len(this_year.compressed()) > 0:
# need to have data for this to work!
if idl:
monthly_vqvs[year] = utils.idl_median(this_year.compressed().reshape(-1))
else:
monthly_vqvs[year] = np.ma.median(this_year)
else:
monthly_vqvs.mask[year] = True
# low pass filter
normed_anomalies = coc_low_pass_filter(normed_anomalies, year_ids, monthly_vqvs, month_ranges.shape[0])
# copy from distributional_gap.py - refactor!
# get the threshold value
bins, bincenters = utils.create_bins(normed_anomalies, 1.)
hist, binEdges = np.histogram(normed_anomalies, bins = bins)
gaussian = utils.fit_gaussian(bincenters, hist, max(hist), mu=np.mean(normed_anomalies), sig = np.std(normed_anomalies))
minimum_threshold = round(1. + utils.invert_gaussian(FREQUENCY_THRESHOLD, gaussian))
if diagnostics:
print iqr, minimum_threshold, 1. + utils.invert_gaussian(FREQUENCY_THRESHOLD, gaussian)
print gaussian
print hist
if plots:
coc_set_up_plot(bincenters, hist, gaussian, variable, threshold = minimum_threshold, sub_par = "observations")
uppercount = len(np.where(normed_anomalies > minimum_threshold)[0])
lowercount = len(np.where(normed_anomalies < -minimum_threshold)[0])
these_flags = station.qc_flags[:, flag_col[v]]
gap_plot_values, tentative_plot_values = [], []
# find the gaps and apply the flags
gap_start = dgc.dgc_find_gap(hist, binEdges, minimum_threshold, gap_size = 1) # in DGC it is 2.
these_flags, gap_plot_values, tentative_plot_values =\
coc_find_and_apply_flags(month_ranges[:,month,:],normed_anomalies, these_flags, year_ids, minimum_threshold, gap_start, \
upper = True, plots = plots, gpv = gap_plot_values, tpv = tentative_plot_values)
gap_start = dgc.dgc_find_gap(hist, binEdges, -minimum_threshold, gap_size = 1) # in DGC it is 2.
these_flags, gap_plot_values, tentative_plot_values =\
coc_find_and_apply_flags(month_ranges[:,month,:],normed_anomalies, these_flags, year_ids, minimum_threshold, gap_start, \
upper = False, plots = plots, gpv = gap_plot_values, tpv = tentative_plot_values)
station.qc_flags[:, flag_col[v]] = these_flags
if uppercount + lowercount > 1000:
#print "not sorted spurious stations yet"
pass
if plots:
import matplotlib.pyplot as plt
hist, binEdges = np.histogram(tentative_plot_values, bins = bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters, plot_hist, c='orange', ls='-', label = 'tentative', where='mid')
hist, binEdges = np.histogram(gap_plot_values, bins = bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters, plot_hist, 'r-', label = 'flagged', where='mid')
import calendar
plt.text(0.1,0.9,calendar.month_name[month+1], transform = plt.gca().transAxes)
leg=plt.legend(loc='lower center',ncol=4, bbox_to_anchor=(0.5,-0.2),frameon=False,prop={'size':13},labelspacing=0.15,columnspacing=0.5)
plt.setp(leg.get_title(), fontsize=14)
plt.show()
#plt.savefig(IMAGELOCATION+'/'+station.id+'_ClimatologicalGap_'+str(month+1)+'.png')
flag_locs = np.where(station.qc_flags[:, flag_col[v]] != 0)
# copy flags into attribute
st_var.flags[flag_locs] = 1
if plots or diagnostics:
utils.print_flagged_obs_number(logfile, "Climatological", variable, len(flag_locs[0]), noWrite = True)
print "where\n"
nflags = len(np.where(station.qc_flags[:, flag_col[v]] == 1)[0])
utils.print_flagged_obs_number(logfile, " Firm Clim", variable, nflags, noWrite = True)
nflags = len(np.where(station.qc_flags[:, flag_col[v]] == 2)[0])
utils.print_flagged_obs_number(logfile, " Tentative Clim", variable, nflags, noWrite = True)
else:
utils.print_flagged_obs_number(logfile, "Climatological", variable, len(flag_locs[0]))
logfile.write("where\n")
nflags = len(np.where(station.qc_flags[:, flag_col[v]] == 1)[0])
utils.print_flagged_obs_number(logfile, " Firm Clim", variable, nflags)
nflags = len(np.where(station.qc_flags[:, flag_col[v]] == 2)[0])
utils.print_flagged_obs_number(logfile, " Tentative Clim", variable, nflags)
# firm flags match 030220
station = utils.append_history(station, "Climatological Check")
return
def detect(station,
neighbour,
variable,
flags,
neighbour_count,
start,
end,
distance=0,
diagnostics=False,
plots=False):
'''
Detect which observations are outliers
:param MetVar station: station object (target)
:param MetVar neighbour: station object (neighbour)
:param string variable: which variable to process
:param array flags: array to store how many neighbours thing each obs is bad
:param array neighbour_count: how many neighbours present at each obs
:param datetime start: start of dataset
:param datetime end: end of dataset
:param int distance: separation of target and neighbour
:param bool diagnostics: extra output
:param bool plots: make figures
:returns: None
'''
FILTERING_FLAG_COL = {
"temperatures": [0, 1, 4, 5, 8, 12, 16, 20, 27, 41, 44, 58],
"dewpoints":
[0, 2, 4, 6, 8, 9, 13, 17, 21, 28, 30, 31, 32, 42, 45, 59],
"slp": [0, 3, 4, 7, 11, 15, 19, 23, 29, 43, 46, 60],
"windspeeds": [0, 4, 10, 14, 18, 22, 56, 62, 63, 64]
} # not used, but ready for it.
st_var = getattr(station, variable)
neigh_var = getattr(neighbour, variable)
# filter by flags - not all (no Climatological [24,25], or Odd cluster [54,55,56,57]), T record check not in D,
total_flags = np.sum(station.qc_flags[:, FILTERING_FLAG_COL[variable]],
axis=1)
st_filtered = np.ma.masked_where(total_flags == 1, st_var.data)
neigh_filtered = np.ma.masked_where(total_flags == 1, neigh_var.data)
# match the observation times
match = np.where(
np.logical_and((st_filtered.data != st_var.mdi),
(neigh_filtered.data != neigh_var.mdi)))
month_ranges = utils.month_starts_in_pairs(start, end).reshape(
-1, 12, 2) # in year-long sets of pairs.
if len(match[0]) >= 100:
neighbour_count[match] += 1 # number of neighbours with data present
differences = np.ma.zeros(len(st_filtered))
differences.fill(st_var.mdi)
differences.mask = True
differences[
match] = st_filtered.data[match] - neigh_filtered.data[match]
differences.mask[match] = False
all_iqrs = np.zeros(len(differences))
# get monthly IQR values
for month in range(12):
this_month, dummy1, dummy2 = utils.concatenate_months(
month_ranges[:, month, :], differences, hours=False)
if len(this_month.compressed()) > 4:
iqr = utils.IQR(this_month.compressed())
if iqr <= 2.: iqr = 2.
else:
iqr = 2.
# and copy back into the array
for year in month_ranges[:, month, :]:
all_iqrs[year[0]:year[1]] = iqr
if plots:
plot_target_neigh_diffs_dist(differences, min(all_iqrs))
dubious = np.ma.where(np.ma.abs(differences) > 5. * all_iqrs)
if len(dubious[0]) >= 1.:
if variable == "slp":
# check if they are storms
positive = np.ma.where(differences > 5. * iqr)
negative = np.ma.where(differences < -5. * iqr)
# if majority negative (2/3) and separation > 100
if (distance > 100.) and (
float(len(positive[0])) / len(dubious[0]) < 0.333):
if len(positive[0]) > 0:
flags[positive] += 1
if len(negative[0]) > 0:
neighbour_count[match] -= 1
else:
flags[dubious] += 1
else:
flags[dubious] += 1
return # detect
def dgc_all_obs(station, variable, flags, start, end, plots = False, diagnostics = False, idl = False, windspeeds = False, GH = False):
'''RJHD addition working on all observations'''
if plots:
import matplotlib.pyplot as plt
st_var = getattr(station, variable)
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges = month_ranges.reshape(-1,12,2)
all_filtered = utils.apply_filter_flags(st_var)
for month in range(12):
if windspeeds == True:
st_var_wind = getattr(station, "windspeeds")
# get monthly averages
windspeeds_month = np.empty([])
for y, year in enumerate(month_ranges[:,month,:]):
if y == 0:
windspeeds_month = np.ma.array(st_var_wind.data[year[0]:year[1]])
else:
windspeeds_month = np.ma.concatenate([windspeeds_month, st_var_wind.data[year[0]:year[1]]])
windspeeds_month_average = dgc_get_monthly_averages(windspeeds_month, OBS_LIMIT, st_var_wind.mdi, MEAN)
windspeeds_month_mad = utils.mean_absolute_deviation(windspeeds_month, median=True)
this_month_data = np.array([])
this_month_filtered = np.array([])
this_month_data, dummy, dummy = utils.concatenate_months(month_ranges[:,month,:], st_var.data, hours = False)
this_month_filtered, dummy, dummy = utils.concatenate_months(month_ranges[:,month,:], all_filtered, hours = False)
if len(this_month_filtered.compressed()) > OBS_LIMIT:
if idl:
monthly_median = utils.idl_median(this_month_filtered.compressed().reshape(-1))
else:
monthly_median = np.ma.median(this_month_filtered)
iqr = utils.IQR(this_month_filtered.compressed())
if iqr == 0.0:
# to get some spread if IQR too small
iqr = utils.IQR(this_month_filtered.compressed(), percentile = 0.05)
print "Spurious_stations file not yet sorted"
if iqr != 0.0:
monthly_values = np.ma.array((this_month_data.compressed() - monthly_median) / iqr)
bins, bincenters = utils.create_bins(monthly_values, BIN_SIZE)
dummy, plot_bincenters = utils.create_bins(monthly_values, BIN_SIZE/10.)
hist, binEdges = np.histogram(monthly_values, bins = bins)
if GH:
# Use Gauss-Hermite polynomials to add skew and kurtosis to Gaussian fit - January 2015 ^RJHD
initial_values = [np.max(hist), np.mean(monthly_values), np.std(monthly_values), stats.skew(monthly_values), stats.kurtosis(monthly_values)] # norm, mean, std, skew, kurtosis
fit = leastsq(utils.residualsGH, initial_values, [bincenters, hist, np.ones(len(hist))])
res = utils.hermite2gauss(fit[0], diagnostics = diagnostics)
plot_gaussian = utils.funcGH(fit[0], plot_bincenters)
# adjust to remove the rising bumps seen in some fits - artefacts of GH fitting?
mid_point = np.argmax(plot_gaussian)
bad, = np.where(plot_gaussian[mid_point:] < FREQUENCY_THRESHOLD/10.)
if len(bad) > 0: plot_gaussian[mid_point:][bad[0]:] = FREQUENCY_THRESHOLD/10.
bad, = np.where(plot_gaussian[:mid_point] < FREQUENCY_THRESHOLD/10.)
if len(bad) > 0: plot_gaussian[:mid_point][:bad[-1]] = FREQUENCY_THRESHOLD/10.
# extract threshold values
good_values = np.argwhere(plot_gaussian > FREQUENCY_THRESHOLD)
l_minimum_threshold = round(plot_bincenters[good_values[0]]) - 1
u_minimum_threshold = 1 + round(plot_bincenters[good_values[-1]])
else:
gaussian = utils.fit_gaussian(bincenters, hist, max(hist), mu = np.mean(monthly_values), sig = np.std(monthly_values))
# assume the same threshold value
u_minimum_threshold = 1 + round(utils.invert_gaussian(FREQUENCY_THRESHOLD, gaussian))
l_minimum_threshold = -u_minimum_threshold
plot_gaussian = utils.gaussian(plot_bincenters, gaussian)
if diagnostics:
if GH:
print hist
print res
print iqr, l_minimum_threshold, u_minimum_threshold
else:
print hist
print gaussian
print iqr, u_minimum_threshold, 1. + utils.invert_gaussian(FREQUENCY_THRESHOLD, gaussian)
if plots:
dgc_set_up_plot(plot_gaussian, monthly_values, variable, threshold = (u_minimum_threshold, l_minimum_threshold), sub_par = "observations", GH = GH)
if GH:
plt.figtext(0.15, 0.67, 'Mean %.2f, S.d. %.2f,\nSkew %.2f, Kurtosis %.2f' %(res['mean'], res['dispersion'], res['skewness'], res['kurtosis']), color='k', size='small')
uppercount = len(np.where(monthly_values > u_minimum_threshold)[0])
lowercount = len(np.where(monthly_values < l_minimum_threshold)[0])
# this needs refactoring - but lots of variables to pass in
if plots or diagnostics: gap_plot_values = np.array([])
if uppercount > 0:
gap_start = dgc_find_gap(hist, binEdges, u_minimum_threshold)
if gap_start != 0:
for y, year in enumerate(month_ranges[:,month,:]):
this_year_data = np.ma.array(all_filtered[year[0]:year[1]])
this_year_flags = np.array(flags[year[0]:year[1]])
gap_cleaned_locations = np.where(((this_year_data - monthly_median) / iqr) > gap_start)
this_year_flags[gap_cleaned_locations] = 1
flags[year[0]:year[1]] = this_year_flags
if plots or diagnostics: gap_plot_values = np.append(gap_plot_values, (this_year_data[gap_cleaned_locations].compressed() - monthly_median)/iqr)
if lowercount > 0:
gap_start = dgc_find_gap(hist, binEdges, l_minimum_threshold)
if gap_start != 0:
for y, year in enumerate(month_ranges[:,month,:]):
this_year_data = np.ma.array(all_filtered[year[0]:year[1]])
this_year_flags = np.array(flags[year[0]:year[1]])
gap_cleaned_locations = np.where(np.logical_and(((this_year_data - monthly_median) / iqr) < gap_start, this_year_data.mask != True))
this_year_flags[gap_cleaned_locations] = 1
flags[year[0]:year[1]] = this_year_flags
if plots or diagnostics: gap_plot_values = np.append(gap_plot_values, (this_year_data[gap_cleaned_locations].compressed() - monthly_median)/iqr)
if windspeeds:
this_year_flags[gap_cleaned_locations] = 2 # tentative flags
slp_average = dgc_get_monthly_averages(this_month_data, OBS_LIMIT, st_var.mdi, MEAN)
slp_mad = utils.mean_absolute_deviation(this_month_data, median=True)
storms = np.where((((windspeeds_month - windspeeds_month_average) / windspeeds_month_mad) > 4.5) &\
(((this_month_data - slp_average) / slp_mad) > 4.5))
if len(storms[0]) >= 2:
storm_1diffs = np.diff(storms)
separations = np.where(storm_1diffs != 1)
#for sep in separations:
if plots:
hist, binEdges = np.histogram(gap_plot_values, bins = bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters, plot_hist, 'r-', label = 'flagged', where='mid')
import calendar
plt.text(0.1,0.9,calendar.month_name[month+1], transform = plt.gca().transAxes)
plt.legend(loc='lower center',ncol=3, bbox_to_anchor=(0.5,-0.2),frameon=False,prop={'size':13})
plt.show()
#plt.savefig(IMAGELOCATION+'/'+station.id+'_DistributionalGap_'+str(month+1)+'.png')
if diagnostics:
utils.print_flagged_obs_number("", "Distributional Gap", variable, len(gap_plot_values), noWrite=True)
return flags # dgc_all_obs
def dgc_monthly(station, variable, flags, start, end, plots=False, diagnostics=False, idl = False):
'''
Original Distributional Gap Check
:param obj station: station object
:param str variable: variable to act on
:param array flags: flags array
:param datetime start: data start
:param datetime end: data end
:param bool plots: run plots
:param bool diagnostics: run diagnostics
:param bool idl: run IDL equivalent routines for median
:returns:
flags - updated flag array
'''
if plots:
import matplotlib.pyplot as plt
st_var = getattr(station, variable)
month_ranges = utils.month_starts_in_pairs(start, end)
# get monthly averages
month_average = np.empty(month_ranges.shape[0])
month_average.fill(st_var.mdi)
month_average_filtered = np.empty(month_ranges.shape[0])
month_average_filtered.fill(st_var.mdi)
all_filtered = utils.apply_filter_flags(st_var)
for m, month in enumerate(month_ranges):
data = st_var.data[month[0]:month[1]]
filtered = all_filtered[month[0]:month[1]]
month_average[m] = dgc_get_monthly_averages(data, OBS_LIMIT, st_var.mdi, MEAN)
month_average_filtered[m] = dgc_get_monthly_averages(filtered, OBS_LIMIT, st_var.mdi, MEAN)
# get overall monthly climatologies - use filtered data
month_average = month_average.reshape(-1,12)
month_average_filtered = month_average_filtered.reshape(-1,12)
standardised_months = np.empty(month_average.shape)
standardised_months.fill(st_var.mdi)
for m in range(12):
valid_filtered = np.where(month_average_filtered[:,m] != st_var.mdi)
if len(valid_filtered[0]) >= VALID_MONTHS:
valid_data = month_average_filtered[valid_filtered,m][0]
if MEAN:
clim = np.mean(valid_data)
spread = np.stdev(valid_data)
else:
if idl:
clim = utils.idl_median(valid_data.compressed().reshape(-1))
else:
clim = np.median(valid_data)
spread = utils.IQR(valid_data)
if spread <= SPREAD_LIMIT:
spread = SPREAD_LIMIT
standardised_months[valid_filtered,m] = (month_average[valid_filtered,m] - clim) / spread
standardised_months = standardised_months.reshape(month_ranges.shape[0])
good_months = np.where(standardised_months != st_var.mdi)
# must be able to do this with masked arrays
if plots:
bins, bincenters = utils.create_bins(standardised_months[good_months], BIN_SIZE)
dummy, plot_bincenters = utils.create_bins(standardised_months[good_months], BIN_SIZE/10.)
hist, binEdges = np.histogram(standardised_months[good_months], bins = bins)
fit = utils.fit_gaussian(bincenters, hist, max(hist), mu = np.mean(standardised_months[good_months]), sig = np.std(standardised_months[good_months]))
plot_gaussian = utils.gaussian(plot_bincenters, fit)
dgc_set_up_plot(plot_gaussian, standardised_months[good_months], variable, sub_par = "Months")
# remove all months with a large standardised offset
if len(good_months[0]) >= MONTH_LIMIT:
standardised_months = np.ma.masked_values(standardised_months, st_var.mdi)
large_offsets = np.where(standardised_months >= LARGE_LIMIT)
if len(large_offsets[0]) > 0:
for lo in large_offsets[0]:
flags[month_ranges[lo,0]:month_ranges[lo,1]] = 1
if plots:
hist, binEdges = np.histogram(standardised_months[large_offsets], bins = bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters, plot_hist, 'g-', label = '> %i' % LARGE_LIMIT, where = 'mid', zorder = 5)
plt.axvline(5,c='g')
plt.axvline(-5,c='g')
# walk distribution from centre and see if any assymetry
sort_order = standardised_months[good_months].argsort()
mid_point = len(good_months[0]) / 2
good = True
iter = 1
while good:
if standardised_months[good_months][sort_order][mid_point - iter] != standardised_months[good_months][sort_order][mid_point + iter]:
# using IDL notation
tempvals = [np.abs(standardised_months[good_months][sort_order][mid_point - iter]),np.abs(standardised_months[good_months][sort_order][mid_point + iter])]
if min(tempvals) != 0:
if max(tempvals)/min(tempvals) >= 2. and min(tempvals) >= 1.5:
# substantial asymmetry in distribution - at least 1.5 from centre and difference of 2.
if tempvals[0] == max(tempvals):
# LHS
bad = good_months[0][sort_order][:mid_point - iter]
if plots: badplot = standardised_months[good_months][sort_order][:mid_point - iter]
elif tempvals[1] == max(tempvals):
#RHS
bad = good_months[0][sort_order][mid_point + iter:]
if plots: badplot = standardised_months[good_months][sort_order][mid_point + iter:]
for b in bad:
flags[month_ranges[b,0]:month_ranges[b,1]] = 1
if plots:
hist, binEdges = np.histogram(badplot, bins = bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters, plot_hist, 'r-', label = 'Gap', where = 'mid', zorder = 4)
good = False
iter += 1
if iter == mid_point: break
if plots:
plt.legend(loc='lower center',ncol=4, bbox_to_anchor=(0.5,-0.2),frameon=False,prop={'size':13})
plt.show()
#plt.savefig(IMAGELOCATION+'/'+station.id+'_DistributionalGap.png')
return flags # dgc_monthly
def dmc(station, variable_list, full_variable_list, flag_col, start, end, logfile, diagnostics=False, plots=False):
'''
Method copied from check_duplicates.pro
:param obj station: station object with suitable attributes (see netcdf_procs.py)
:param list variable_list: list of netcdf variables to process
:param list full_variable_list: the variables for flags to be applied to
:param list flag_col: which column to set in flag array
:param datetime start: data start
:param datetime end: data end
:param file logfile: logfile to store outputs
:param bool diagnostics: extra verbosity
:param bool plots: do plots
'''
MIN_DATA_REQUIRED = 20 # obs per month
# get array of Nx2 start/end pairs
month_ranges = utils.month_starts_in_pairs(start, end)
for v, variable in enumerate(variable_list):
st_var = getattr(station, variable)
# double loop structure - not ideal
duplicated = np.zeros(len(month_ranges))
for sm, source_month in enumerate(month_ranges):
if diagnostics: print "Month %i of %i" % (sm + 1, len(month_ranges))
source_data = st_var.data[source_month[0]:source_month[1]]
if duplicated[sm] == 0:
# don't repeat if already a duplicated
for tm, target_month in enumerate(month_ranges[sm + 1:]):
target_data = st_var.data[target_month[0]:target_month[1]]
# match the data periods
overlap = np.min([len(source_data), len(target_data)])
s_data, t_data = source_data[:overlap], target_data[:overlap]
s_valid, t_valid = np.where(s_data.compressed() != st_var.fdi), \
np.where(t_data.compressed() != st_var.fdi)
# if enough of an overlap
if (len(s_valid[0]) >= MIN_DATA_REQUIRED) and \
(len(t_valid[0]) >= MIN_DATA_REQUIRED):
if len(s_valid[0]) < len(t_valid[0]):
duplicated = duplication_test(source_data, target_data, s_valid, sm, tm, source_month, target_month, duplicated, diagnostics, station.qc_flags, flag_col[v])
else:
# swap the list of valid points
duplicated = duplication_test(source_data, target_data, t_valid, sm, tm, source_month, target_month, duplicated, diagnostics, station.qc_flags, flag_col[v])
if plots:
dmc_plot(s_data, t_data, start, source_month[0], target_month[0], st_var.name)
# target month
# source month
# variable list
flag_locs = np.where(station.qc_flags[:, flag_col[v]] != 0)
utils.print_flagged_obs_number(logfile, "Duplicate Month", variable, len(flag_locs[0]), noWrite = diagnostics)
# copy flags into attribute
st_var.flags[flag_locs] = 1
utils.apply_flags_all_variables(station, full_variable_list, flag_col[variable_list == "temperatures"], logfile, "Duplicate Months", plots = plots, diagnostics = diagnostics)
station = utils.append_history(station, "Duplicate Months Check")
return # dmc
def fvc(station, variable_list, flag_col, start, end, logfile, diagnostics = False, plots = False):
'''
Check for certain values occurring more frequently than would be expected
:param object station: station object to process
:param list variable_list: list of variables to process
:param list flag_col: columns to fill in flag array
:param datetime start: datetime object of start of data
:param datetime end: datetime object of end of data
:param file logfile: logfile to store outputs
:param bool diagnostics: produce extra diagnostic output
:param bool plots: produce plots
'''
MIN_DATA_REQUIRED = 500 # to create histogram for complete record
MIN_DATA_REQUIRED_YEAR = 100 # to create histogram
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges_years = month_ranges.reshape(-1,12,2)
for v,variable in enumerate(variable_list):
st_var = getattr(station, variable)
reporting_accuracy = utils.reporting_accuracy(utils.apply_filter_flags(st_var))
# apply flags - for detection only
filtered_data = utils.apply_filter_flags(st_var)
for season in range(5): # Year,MAM,JJA,SON,JF+D
if season == 0:
# all year
season_data = np.ma.masked_values(filtered_data.compressed(), st_var.fdi)
thresholds = [30,20,10]
else:
thresholds = [20,15,10]
season_data = np.ma.array([])
for y,year in enumerate(month_ranges_years):
# churn through months extracting data, accounting for fdi and concatenating together
if season == 1:
#mam
season_data = np.ma.concatenate([season_data, np.ma.masked_values(filtered_data[year[2][0]:year[4][-1]], st_var.fdi)])
elif season == 2:
#jja
season_data = np.ma.concatenate([season_data, np.ma.masked_values(filtered_data[year[5][0]:year[7][-1]], st_var.fdi)])
elif season == 3:
#son
season_data = np.ma.concatenate([season_data, np.ma.masked_values(filtered_data[year[8][0]:year[10][-1]], st_var.fdi)])
elif season == 4:
#d+jf
season_data = np.ma.concatenate([season_data, np.ma.masked_values(filtered_data[year[0][0]:year[1][-1]], st_var.fdi)])
season_data = np.ma.concatenate([season_data, np.ma.masked_values(filtered_data[year[-1][0]:year[-1][-1]], st_var.fdi)])
season_data = season_data.compressed()
if len(season_data) > MIN_DATA_REQUIRED:
if 0 < reporting_accuracy <= 0.5: # -1 used as missing value
bins, bincenters = utils.create_bins(season_data, 0.5)
else:
bins, bincenters = utils.create_bins(season_data, 1.0)
hist, binEdges = np.histogram(season_data, bins = bins)
if plots:
plot_hist, bincenters = fvc_plot_setup(season_data, hist, binEdges, st_var.name, title = "%s" % (SEASONS[season]))
bad_bin = np.zeros(len(hist))
# scan through bin values and identify bad ones
for e, element in enumerate(hist):
if e > 3 and e <= (len(hist) - 3):
# don't bother with first three or last three bins
seven_bins = hist[e-3:e+3+1]
if (seven_bins[3] == seven_bins.max()) and (seven_bins[3] != 0):
# is local maximum and != zero
if (seven_bins[3]/float(seven_bins.sum()) >= 0.5) and (seven_bins[3] >= thresholds[0]):
# contains >50% of data and is greater than threshold
bad_bin[e] = 1
# for plotting remove good bins
else:
if plots: plot_hist[e]=1e-1
else:
if plots: plot_hist[e]=1e-1
else:
if plots: plot_hist[e]=1e-1
if plots:
plt.step(bincenters, plot_hist, 'r-', where='mid')
plt.show()
# having identified possible bad bins, check each year in turn
for y,year in enumerate(month_ranges_years):
if season == 0:
# year
year_data = np.ma.masked_values(st_var.data[year[0][0]:year[-1][-1]], st_var.fdi)
year_flags = station.qc_flags[year[0][0]:year[-1][-1],flag_col[v]]
elif season == 1:
#mam
year_data = np.ma.masked_values(st_var.data[year[2][0]:year[4][-1]], st_var.fdi)
year_flags = station.qc_flags[year[2][0]:year[4][-1],flag_col[v]]
elif season == 2:
#jja
year_data = np.ma.masked_values(st_var.data[year[5][0]:year[7][-1]], st_var.fdi)
year_flags = station.qc_flags[year[5][0]:year[7][-1],flag_col[v]]
elif season == 3:
#son
year_data = np.ma.masked_values(st_var.data[year[8][0]:year[10][-1]], st_var.fdi)
year_flags = station.qc_flags[year[8][0]:year[10][-1],flag_col[v]]
elif season == 4:
#d+jf
year_data = np.ma.concatenate([np.ma.masked_values(st_var.data[year[0][0]:year[1][-1]], st_var.fdi),\
np.ma.masked_values(st_var.data[year[-1][0]:year[-1][-1]], st_var.fdi)])
year_flags = np.append(station.qc_flags[year[0][0]:year[1][-1],flag_col[v]],station.qc_flags[year[-1][0]:year[-1][-1],flag_col[v]])
if len(year_data.compressed()) > MIN_DATA_REQUIRED_YEAR:
hist, binEdges = np.histogram(year_data.compressed(), bins = bins)
if plots:
plot_hist, bincenters = fvc_plot_setup(hist, binEdges, st_var.name, title = "%s - %s" % (y+start.year, SEASONS[season]))
for e, element in enumerate(hist):
if bad_bin[e] == 1:
# only look at pre-identified bins
if e >= 3 and e <= (len(hist) - 3):
# don't bother with first three or last three bins
seven_bins = hist[e-3:e+3+1].astype('float')
if (seven_bins[3] == seven_bins.max()) and (seven_bins[3] != 0):
# is local maximum and != zero
if (seven_bins[3]/seven_bins.sum() >= 0.5 and seven_bins[3] >= thresholds[1]) \
or (seven_bins[3]/seven_bins.sum() >= 0.9 and seven_bins[3] >= thresholds[2]):
# contains >50% or >90% of data and is greater than appropriate threshold
# Flag these data
bad_points = np.where((year_data >= binEdges[e]) & (year_data < binEdges[e+1]))
year_flags[bad_points] = 1
# for plotting remove good bins
else:
if plots: plot_hist[e]=1e-1
else:
if plots: plot_hist[e]=1e-1
else:
if plots: plot_hist[e]=1e-1
else:
if plots: plot_hist[e]=1e-1
if diagnostics or plots:
nflags = len(np.where(year_flags != 0)[0])
print "{} {}".format(y + start.year, nflags)
if plots:
if nflags > 0:
plt.step(bincenters, plot_hist, 'r-', where='mid')
plt.show()
else:
plt.clf()
# copy flags back
if season == 0:
station.qc_flags[year[0][0]:year[-1][-1], flag_col[v]] = year_flags
elif season == 1:
station.qc_flags[year[2][0]:year[4][-1], flag_col[v]] = year_flags
elif season == 2:
station.qc_flags[year[5][0]:year[7][-1], flag_col[v]] = year_flags
elif season == 3:
station.qc_flags[year[8][0]:year[10][-1], flag_col[v]] = year_flags
elif season == 4:
split = len(station.qc_flags[year[0][0]:year[1][-1], flag_col[v]])
station.qc_flags[year[0][0]:year[1][-1], flag_col[v]] = year_flags[:split]
station.qc_flags[year[-1][0]:year[-1][-1], flag_col[v]] = year_flags[split:]
flag_locs = np.where(station.qc_flags[:, flag_col[v]] != 0)
if plots or diagnostics:
utils.print_flagged_obs_number(logfile, "Frequent Value", variable, len(flag_locs[0]), noWrite = True)
else:
utils.print_flagged_obs_number(logfile, "Frequent Value", variable, len(flag_locs[0]))
# copy flags into attribute
st_var.flags[flag_locs] = 1
station = utils.append_history(station, "Frequent Values Check")
return # fvc
def sc(station, variable_list, flag_col, start, end, logfile, diagnostics = False, plots = False, second = False):
'''
Spike Check, looks for spikes up to 3 observations long, using thresholds
calculated from the data itself.
:param MetVar station: the station object
:param list variable_list: list of observational variables to process
:param list flag_col: the columns to set on the QC flag array
:param datetime start: dataset start time
:param datetime end: dataset end time
:param file logfile: logfile to store outputs
:param bool plots: do plots
:param bool second: run for second time
:returns:
'''
print "refactor"
for v, variable in enumerate(variable_list):
flags = station.qc_flags[:, flag_col[v]]
prev_flag_number = 0
if second:
# count currently existing flags:
prev_flag_number = len(flags[flags != 0])
st_var = getattr(station, variable)
all_filtered = utils.apply_filter_flags(st_var)
reporting_resolution = utils.reporting_accuracy(utils.apply_filter_flags(st_var))
# to match IDL system - should never be called as would mean no data
if reporting_resolution == -1: reporting_resolution = 1
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges = month_ranges.reshape(-1,12,2)
good = np.where(all_filtered.mask == False)
full_time_diffs = np.ma.zeros(len(all_filtered))
full_time_diffs.mask = all_filtered.mask
full_time_diffs[good] = station.time.data[good][1:] - station.time.data[good][:-1]
# develop critical values using clean values
# NOTE 4/7/14 - make sure that Missing and Flagged values treated appropriately
print "sort the differencing if values were flagged rather than missing"
full_filtered_diffs = np.ma.zeros(len(all_filtered))
full_filtered_diffs.mask = all_filtered.mask
full_filtered_diffs[good] = all_filtered.compressed()[1:] - all_filtered.compressed()[:-1]
# test all values
good_to_uncompress = np.where(st_var.data.mask == False)
full_value_diffs = np.ma.zeros(len(st_var.data))
full_value_diffs.mask = st_var.data.mask
full_value_diffs[good_to_uncompress] = st_var.data.compressed()[1:] - st_var.data.compressed()[:-1]
# convert to compressed time to match IDL
value_diffs = full_value_diffs.compressed()
time_diffs = full_time_diffs.compressed()
filtered_diffs = full_filtered_diffs.compressed()
flags = flags[good_to_uncompress]
critical_values = np.zeros([9,12])
critical_values.fill(st_var.mdi)
# link observation to calendar month
month_locs = np.zeros(full_time_diffs.shape)
for month in range(12):
for year in range(month_ranges.shape[0]):
if year == 0:
this_month_time_diff = full_time_diffs[month_ranges[year,month,0]:month_ranges[year,month,1]]
this_month_filtered_diff = full_filtered_diffs[month_ranges[year,month,0]:month_ranges[year,month,1]]
else:
this_month_time_diff = np.ma.concatenate([this_month_time_diff, full_time_diffs[month_ranges[year,month,0]:month_ranges[year,month,1]]])
this_month_filtered_diff = np.ma.concatenate([this_month_filtered_diff, full_filtered_diffs[month_ranges[year,month,0]:month_ranges[year,month,1]]])
month_locs[month_ranges[year,month,0]:month_ranges[year,month,1]] = month
for delta in range(1,9):
locs = np.ma.where(this_month_time_diff == delta)
if len(locs[0]) >= 100:
iqr = utils.IQR(this_month_filtered_diff[locs])
if iqr == 0. and delta == 1:
critical_values[delta-1,month] = 6.
elif iqr == 0:
critical_values[delta-1,month] = st_var.mdi
else:
critical_values[delta-1,month] = 6. * iqr
# January 2015 - changed to dynamically calculating the thresholds if less than IQR method ^RJHD
if plots:
import calendar
title = "{}, {}-hr differences".format(calendar.month_name[month+1], delta)
line_label = st_var.name
xlabel = "First Difference Magnitudes"
else:
title, line_label, xlabel = "","",""
threshold = utils.get_critical_values(this_month_filtered_diff[locs], binmin = 0, binwidth = 0.5, plots = plots, diagnostics = diagnostics, title = title, line_label = line_label, xlabel = xlabel, old_threshold = critical_values[delta-1,month])
if threshold < critical_values[delta-1,month]: critical_values[delta-1,month] = threshold
if plots or diagnostics:
print critical_values[delta-1,month] , iqr, 6 * iqr
month_locs = month_locs[good_to_uncompress]
if diagnostics:
print critical_values[0,:]
# not less than 5x reporting accuracy
good_critical_values = np.where(critical_values != st_var.mdi)
low_critical_values = np.where(critical_values[good_critical_values] <= 5.*reporting_resolution)
temporary = critical_values[good_critical_values]
temporary[low_critical_values] = 5.*reporting_resolution
critical_values[good_critical_values] = temporary
if diagnostics:
print critical_values[0,:], 5.*reporting_resolution
# check hourly against 2 hourly, if <2/3 the increase to avoid crazy rejection rate
for month in range(12):
if critical_values[0,month] != st_var.mdi and critical_values[1,month] != st_var.mdi:
if critical_values[0,month]/critical_values[1,month] <= 0.66:
critical_values[0,month] = 0.66 * critical_values[1,month]
if diagnostics:
print critical_values[0,:]
# get time differences for unfiltered data
full_time_diffs = np.ma.zeros(len(st_var.data))
full_time_diffs.mask = st_var.data.mask
full_time_diffs[good_to_uncompress] = station.time.data[good_to_uncompress][1:] - station.time.data[good_to_uncompress][:-1]
time_diffs = full_time_diffs.compressed()
# go through each difference, identify which month it is in if passes spike thresholds
# spikes at the beginning or ends of sections
for t in np.arange(len(time_diffs)):
if (np.abs(time_diffs[t - 1]) > 240) and (np.abs(time_diffs[t]) < 3):
# 10 days before but short gap thereafter
next_values = st_var.data[good_to_uncompress[0][t + 1:]]
good, = np.where(next_values.mask == False)
next_median = np.ma.median(next_values[good[:10]])
next_diff = np.abs(value_diffs[t]) # out of spike
median_diff = np.abs(next_median - st_var.data[good_to_uncompress[0][t]]) # are the remaining onees
if (critical_values[time_diffs[t] - 1, month_locs[t]] != st_var.mdi):
# jump from spike > critical but average after < critical / 2
if (np.abs(median_diff) < critical_values[time_diffs[t] - 1, month_locs[t]] / 2.) and\
(np.abs(next_diff) > critical_values[time_diffs[t] - 1, month_locs[t]]) :
flags[t] = 1
if plots or diagnostics:
sc_diagnostics_and_plots(station.time.data, st_var.data, good_to_uncompress[0][t], good_to_uncompress[0][t+1], start, variable, plots = plots)
elif (np.abs(time_diffs[t - 1]) < 3) and (np.abs(time_diffs[t]) > 240):
# 10 days after but short gap before
prev_values = st_var.data[good_to_uncompress[0][:t - 1]]
good, = np.where(prev_values.mask == False)
prev_median = np.ma.median(prev_values[good[-10:]])
prev_diff = np.abs(value_diffs[t - 1])
median_diff = np.abs(prev_median - st_var.data[good_to_uncompress[0][t]])
if (critical_values[time_diffs[t - 1] - 1, month_locs[t]] != st_var.mdi):
# jump into spike > critical but average before < critical / 2
if (np.abs(median_diff) < critical_values[time_diffs[t - 1] - 1, month_locs[t]] / 2.) and\
(np.abs(prev_diff) > critical_values[time_diffs[t - 1] - 1, month_locs[t]]) :
flags[t] = 1
if plots or diagnostics:
sc_diagnostics_and_plots(station.time.data, st_var.data, good_to_uncompress[0][t], good_to_uncompress[0][t+1], start, variable, plots = plots)
''' this isn't the nicest way, but a direct copy from IDL
masked arrays might help remove some of the lines
Also, this is relatively slow'''
for t in np.arange(len(time_diffs)):
for spk_len in [1,2,3]:
if t >= spk_len and t < len(time_diffs) - spk_len:
# check if time differences are appropriate, for multi-point spikes
if (np.abs(time_diffs[t - spk_len]) <= spk_len * 3) and\
(np.abs(time_diffs[t]) <= spk_len * 3) and\
(time_diffs[t - spk_len - 1] - 1 < spk_len * 3) and\
(time_diffs[t + 1] - 1 < spk_len * 3) and \
((spk_len == 1) or \
((spk_len == 2) and (np.abs(time_diffs[t - spk_len + 1]) <= spk_len * 3)) or \
((spk_len == 3) and (np.abs(time_diffs[t - spk_len + 1]) <= spk_len * 3) and (np.abs(time_diffs[t - spk_len + 2]) <= spk_len * 3))):
# check if differences are valid
if (value_diffs[t - spk_len] != st_var.mdi) and \
(value_diffs[t - spk_len] != st_var.fdi) and \
(critical_values[time_diffs[t - spk_len] - 1, month_locs[t]] != st_var.mdi):
# if exceed critical values
if (np.abs(value_diffs[t - spk_len]) >= critical_values[time_diffs[t - spk_len] - 1, month_locs[t]]):
# are signs of two differences different
if (math.copysign(1, value_diffs[t]) != math.copysign(1, value_diffs[t - spk_len])):
# are within spike differences small
if (spk_len == 1) or\
((spk_len == 2) and (np.abs(value_diffs[t - spk_len + 1]) < critical_values[time_diffs[t - spk_len + 1] -1, month_locs[t]] / 2.)) or \
((spk_len == 3) and (np.abs(value_diffs[t - spk_len + 1]) < critical_values[time_diffs[t - spk_len + 1] -1, month_locs[t]] / 2.) and\
(np.abs(value_diffs[t - spk_len + 2]) < critical_values[time_diffs[t - spk_len + 2] -1, month_locs[t]] / 2.)):
# check if following value is valid
if (value_diffs[t] != st_var.mdi) and (critical_values[time_diffs[t] - 1, month_locs[t]] != st_var.mdi) and\
(value_diffs[t] != st_var.fdi):
# and if at least critical value
if (np.abs(value_diffs[t]) >= critical_values[time_diffs[t] - 1, month_locs[t]]):
# test if surrounding differences below 1/2 critical value
if (np.abs(value_diffs[t - spk_len - 1]) <= critical_values[time_diffs[t - spk_len - 1] - 1, month_locs[t]] / 2.):
if (np.abs(value_diffs[t + 1]) <= critical_values[time_diffs[t + 1] - 1, month_locs[t]] / 2.):
# set the flags
flags[ t - spk_len + 1 : t +1] = 1
if plots or diagnostics:
sc_diagnostics_and_plots(station.time.data, st_var.data, good_to_uncompress[0][t-spk_len+1], good_to_uncompress[0][t+1], start, variable, plots = plots)
station.qc_flags[good_to_uncompress, flag_col[v]] = flags
flag_locs = np.where(station.qc_flags[:, flag_col[v]] != 0)
if plots or diagnostics:
utils.print_flagged_obs_number(logfile, "Spike", variable, len(flag_locs[0]) - prev_flag_number, noWrite = True) # additional flags
else:
utils.print_flagged_obs_number(logfile, "Spike", variable, len(flag_locs[0]) - prev_flag_number) # additional flags
# copy flags into attribute
st_var.flags[flag_locs] = 1
# matches 030660 - but with adapted IDL
# matches 030220 OK, but finds more but all are reasonable 1/9/14
do_interactive = False
if plots and do_interactive == True:
import matplotlib.pyplot as plt
plot_times = utils.times_hours_to_datetime(station.time.data, start)
plt.clf()
plt.plot(plot_times, all_filtered, 'bo', ls='-')
flg = np.where(flags[:, flag_col[v]] == 1)
plt.plot(plot_times[flg], all_filtered[flg], 'ro', markersize=10)
plt.show()
station = utils.append_history(station, "Spike Check")
return # sc
def dgc_monthly(station,
variable,
flags,
start,
end,
plots=False,
diagnostics=False,
idl=False):
'''
Original Distributional Gap Check
:param obj station: station object
:param str variable: variable to act on
:param array flags: flags array
:param datetime start: data start
:param datetime end: data end
:param bool plots: run plots
:param bool diagnostics: run diagnostics
:param bool idl: run IDL equivalent routines for median
:returns:
flags - updated flag array
'''
if plots:
import matplotlib.pyplot as plt
st_var = getattr(station, variable)
month_ranges = utils.month_starts_in_pairs(start, end)
# get monthly averages
month_average = np.empty(month_ranges.shape[0])
month_average.fill(st_var.mdi)
month_average_filtered = np.empty(month_ranges.shape[0])
month_average_filtered.fill(st_var.mdi)
all_filtered = utils.apply_filter_flags(st_var)
for m, month in enumerate(month_ranges):
data = st_var.data[month[0]:month[1]]
filtered = all_filtered[month[0]:month[1]]
month_average[m] = dgc_get_monthly_averages(data, OBS_LIMIT,
st_var.mdi, MEAN)
month_average_filtered[m] = dgc_get_monthly_averages(
filtered, OBS_LIMIT, st_var.mdi, MEAN)
# get overall monthly climatologies - use filtered data
month_average = month_average.reshape(-1, 12)
month_average_filtered = month_average_filtered.reshape(-1, 12)
standardised_months = np.empty(month_average.shape)
standardised_months.fill(st_var.mdi)
for m in range(12):
valid_filtered = np.where(month_average_filtered[:, m] != st_var.mdi)
if len(valid_filtered[0]) >= VALID_MONTHS:
valid_data = month_average_filtered[valid_filtered, m][0]
if MEAN:
clim = np.mean(valid_data)
spread = np.stdev(valid_data)
else:
if idl:
clim = utils.idl_median(
valid_data.compressed().reshape(-1))
else:
clim = np.median(valid_data)
spread = utils.IQR(valid_data)
if spread <= SPREAD_LIMIT:
spread = SPREAD_LIMIT
standardised_months[valid_filtered,
m] = (month_average[valid_filtered, m] -
clim) / spread
standardised_months = standardised_months.reshape(month_ranges.shape[0])
good_months = np.where(standardised_months != st_var.mdi)
# must be able to do this with masked arrays
if plots:
bins, bincenters = utils.create_bins(standardised_months[good_months],
BIN_SIZE)
dummy, plot_bincenters = utils.create_bins(
standardised_months[good_months], BIN_SIZE / 10.)
hist, binEdges = np.histogram(standardised_months[good_months],
bins=bins)
fit = utils.fit_gaussian(bincenters,
hist,
max(hist),
mu=np.mean(standardised_months[good_months]),
sig=np.std(standardised_months[good_months]))
plot_gaussian = utils.gaussian(plot_bincenters, fit)
dgc_set_up_plot(plot_gaussian,
standardised_months[good_months],
variable,
sub_par="Months")
# remove all months with a large standardised offset
if len(good_months[0]) >= MONTH_LIMIT:
standardised_months = np.ma.masked_values(standardised_months,
st_var.mdi)
large_offsets = np.where(standardised_months >= LARGE_LIMIT)
if len(large_offsets[0]) > 0:
for lo in large_offsets[0]:
flags[month_ranges[lo, 0]:month_ranges[lo, 1]] = 1
if plots:
hist, binEdges = np.histogram(
standardised_months[large_offsets], bins=bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters,
plot_hist,
'g-',
label='> %i' % LARGE_LIMIT,
where='mid',
zorder=5)
plt.axvline(5, c='g')
plt.axvline(-5, c='g')
# walk distribution from centre and see if any assymetry
sort_order = standardised_months[good_months].argsort()
mid_point = len(good_months[0]) / 2
good = True
iter = 1
while good:
if standardised_months[good_months][sort_order][
mid_point -
iter] != standardised_months[good_months][sort_order][
mid_point + iter]:
# using IDL notation
tempvals = [
np.abs(
standardised_months[good_months][sort_order][mid_point
- iter]),
np.abs(
standardised_months[good_months][sort_order][mid_point
+ iter])
]
if min(tempvals) != 0:
if max(tempvals) / min(tempvals) >= 2. and min(
tempvals) >= 1.5:
# substantial asymmetry in distribution - at least 1.5 from centre and difference of 2.
if tempvals[0] == max(tempvals):
# LHS
bad = good_months[0][sort_order][:mid_point - iter]
if plots:
badplot = standardised_months[good_months][
sort_order][:mid_point - iter]
elif tempvals[1] == max(tempvals):
#RHS
bad = good_months[0][sort_order][mid_point + iter:]
if plots:
badplot = standardised_months[good_months][
sort_order][mid_point + iter:]
for b in bad:
flags[month_ranges[b, 0]:month_ranges[b, 1]] = 1
if plots:
hist, binEdges = np.histogram(badplot, bins=bins)
plot_hist = np.array(
[0.01 if h == 0 else h for h in hist])
plt.step(bincenters,
plot_hist,
'r-',
label='Gap',
where='mid',
zorder=4)
good = False
iter += 1
if iter == mid_point: break
if plots:
plt.legend(loc='lower center',
ncol=4,
bbox_to_anchor=(0.5, -0.2),
frameon=False,
prop={'size': 13})
plt.show()
#plt.savefig(IMAGELOCATION+'/'+station.id+'_DistributionalGap.png')
return flags # dgc_monthly
def coc(station,
variable_list,
flag_col,
start,
end,
logfile,
diagnostics=False,
plots=False,
idl=False):
for v, variable in enumerate(variable_list):
st_var = getattr(station, variable)
all_filtered = utils.apply_filter_flags(st_var)
# is this needed 13th Nov 2014 RJHD
#reporting_resolution = utils.reporting_accuracy(utils.apply_filter_flags(st_var))
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges = month_ranges.reshape(-1, 12, 2)
for month in range(12):
hourly_climatologies = np.zeros(24)
hourly_climatologies.fill(st_var.mdi)
# append all e.g. Januaries together
this_month, year_ids, dummy = utils.concatenate_months(
month_ranges[:, month, :], st_var.data, hours=True)
this_month_filtered, dummy, dummy = utils.concatenate_months(
month_ranges[:, month, :], all_filtered, hours=True)
# if fixed climatology period, sort this here
# get as array of 24 hrs.
this_month = np.ma.array(this_month)
this_month = this_month.reshape(-1, 24)
this_month_filtered = np.ma.array(this_month_filtered)
this_month_filtered = this_month_filtered.reshape(-1, 24)
# get hourly climatology for each month
for hour in range(24):
this_hour = this_month[:, hour]
# need to have data if this is going to work!
if len(this_hour.compressed()) > 0:
# winsorize & climatologies - done to match IDL
if idl:
this_hour = utils.winsorize(np.append(
this_hour.compressed(), -999999),
0.05,
idl=idl)
hourly_climatologies[hour] = np.ma.sum(this_hour) / (
len(this_hour) - 1)
else:
this_hour = utils.winsorize(this_hour.compressed(),
0.05,
idl=idl)
hourly_climatologies[hour] = np.ma.mean(this_hour)
if len(this_month.compressed()) > 0:
# can get stations with few obs in a particular variable.
# anomalise each hour over month appropriately
anomalies = this_month - np.tile(hourly_climatologies,
(this_month.shape[0], 1))
anomalies_filtered = this_month_filtered - np.tile(
hourly_climatologies, (this_month_filtered.shape[0], 1))
if len(anomalies.compressed()) >= 10:
iqr = utils.IQR(anomalies.compressed().reshape(
-1)) / 2. # to match IDL
if iqr < 1.5: iqr = 1.5
else:
iqr = st_var.mdi
normed_anomalies = anomalies / iqr
normed_anomalies_filtered = anomalies_filtered / iqr
# get average anomaly for year
year_ids = np.array(year_ids)
monthly_vqvs = np.ma.zeros(month_ranges.shape[0])
monthly_vqvs.mask = [
False for x in range(month_ranges.shape[0])
]
for year in range(month_ranges.shape[0]):
year_locs = np.where(year_ids == year)
this_year = normed_anomalies_filtered[year_locs, :]
if len(this_year.compressed()) > 0:
# need to have data for this to work!
if idl:
monthly_vqvs[year] = utils.idl_median(
this_year.compressed().reshape(-1))
else:
monthly_vqvs[year] = np.ma.median(this_year)
else:
monthly_vqvs.mask[year] = True
# low pass filter
normed_anomalies = coc_low_pass_filter(normed_anomalies,
year_ids, monthly_vqvs,
month_ranges.shape[0])
# copy from distributional_gap.py - refactor!
# get the threshold value
bins, bincenters = utils.create_bins(normed_anomalies, 1.)
hist, binEdges = np.histogram(normed_anomalies, bins=bins)
gaussian = utils.fit_gaussian(bincenters,
hist,
max(hist),
mu=np.mean(normed_anomalies),
sig=np.std(normed_anomalies))
minimum_threshold = round(
1. + utils.invert_gaussian(FREQUENCY_THRESHOLD, gaussian))
if diagnostics:
print iqr, minimum_threshold, 1. + utils.invert_gaussian(
FREQUENCY_THRESHOLD, gaussian)
print gaussian
print hist
if plots:
coc_set_up_plot(bincenters,
hist,
gaussian,
variable,
threshold=minimum_threshold,
sub_par="observations")
uppercount = len(
np.where(normed_anomalies > minimum_threshold)[0])
lowercount = len(
np.where(normed_anomalies < -minimum_threshold)[0])
these_flags = station.qc_flags[:, flag_col[v]]
gap_plot_values, tentative_plot_values = [], []
# find the gaps and apply the flags
gap_start = dgc.dgc_find_gap(hist,
binEdges,
minimum_threshold,
gap_size=1) # in DGC it is 2.
these_flags, gap_plot_values, tentative_plot_values =\
coc_find_and_apply_flags(month_ranges[:,month,:],normed_anomalies, these_flags, year_ids, minimum_threshold, gap_start, \
upper = True, plots = plots, gpv = gap_plot_values, tpv = tentative_plot_values)
gap_start = dgc.dgc_find_gap(hist,
binEdges,
-minimum_threshold,
gap_size=1) # in DGC it is 2.
these_flags, gap_plot_values, tentative_plot_values =\
coc_find_and_apply_flags(month_ranges[:,month,:],normed_anomalies, these_flags, year_ids, minimum_threshold, gap_start, \
upper = False, plots = plots, gpv = gap_plot_values, tpv = tentative_plot_values)
station.qc_flags[:, flag_col[v]] = these_flags
if uppercount + lowercount > 1000:
#print "not sorted spurious stations yet"
pass
if plots:
import matplotlib.pyplot as plt
hist, binEdges = np.histogram(tentative_plot_values,
bins=bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters,
plot_hist,
c='orange',
ls='-',
label='tentative',
where='mid')
hist, binEdges = np.histogram(gap_plot_values, bins=bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters,
plot_hist,
'r-',
label='flagged',
where='mid')
import calendar
plt.text(0.1,
0.9,
calendar.month_name[month + 1],
transform=plt.gca().transAxes)
leg = plt.legend(loc='lower center',
ncol=4,
bbox_to_anchor=(0.5, -0.2),
frameon=False,
prop={'size': 13},
labelspacing=0.15,
columnspacing=0.5)
plt.setp(leg.get_title(), fontsize=14)
plt.show()
#plt.savefig(IMAGELOCATION+'/'+station.id+'_ClimatologicalGap_'+str(month+1)+'.png')
flag_locs = np.where(station.qc_flags[:, flag_col[v]] != 0)
# copy flags into attribute
st_var.flags[flag_locs] = 1
if plots or diagnostics:
utils.print_flagged_obs_number(logfile,
"Climatological",
variable,
len(flag_locs[0]),
noWrite=True)
print "where\n"
nflags = len(np.where(station.qc_flags[:, flag_col[v]] == 1)[0])
utils.print_flagged_obs_number(logfile,
" Firm Clim",
variable,
nflags,
noWrite=True)
nflags = len(np.where(station.qc_flags[:, flag_col[v]] == 2)[0])
utils.print_flagged_obs_number(logfile,
" Tentative Clim",
variable,
nflags,
noWrite=True)
else:
utils.print_flagged_obs_number(logfile, "Climatological", variable,
len(flag_locs[0]))
logfile.write("where\n")
nflags = len(np.where(station.qc_flags[:, flag_col[v]] == 1)[0])
utils.print_flagged_obs_number(logfile, " Firm Clim", variable,
nflags)
nflags = len(np.where(station.qc_flags[:, flag_col[v]] == 2)[0])
utils.print_flagged_obs_number(logfile, " Tentative Clim",
variable, nflags)
# firm flags match 030220
station = utils.append_history(station, "Climatological Check")
return
def dgc_all_obs(station,
variable,
flags,
start,
end,
plots=False,
diagnostics=False,
idl=False,
windspeeds=False,
GH=False):
'''RJHD addition working on all observations'''
if plots:
import matplotlib.pyplot as plt
st_var = getattr(station, variable)
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges = month_ranges.reshape(-1, 12, 2)
all_filtered = utils.apply_filter_flags(st_var)
for month in range(12):
if windspeeds == True:
st_var_wind = getattr(station, "windspeeds")
# get monthly averages
windspeeds_month = np.empty([])
for y, year in enumerate(month_ranges[:, month, :]):
if y == 0:
windspeeds_month = np.ma.array(
st_var_wind.data[year[0]:year[1]])
else:
windspeeds_month = np.ma.concatenate(
[windspeeds_month, st_var_wind.data[year[0]:year[1]]])
windspeeds_month_average = dgc_get_monthly_averages(
windspeeds_month, OBS_LIMIT, st_var_wind.mdi, MEAN)
windspeeds_month_mad = utils.mean_absolute_deviation(
windspeeds_month, median=True)
this_month_data = np.array([])
this_month_filtered = np.array([])
this_month_data, dummy, dummy = utils.concatenate_months(
month_ranges[:, month, :], st_var.data, hours=False)
this_month_filtered, dummy, dummy = utils.concatenate_months(
month_ranges[:, month, :], all_filtered, hours=False)
if len(this_month_filtered.compressed()) > OBS_LIMIT:
if idl:
monthly_median = utils.idl_median(
this_month_filtered.compressed().reshape(-1))
else:
monthly_median = np.ma.median(this_month_filtered)
iqr = utils.IQR(this_month_filtered.compressed())
if iqr == 0.0:
# to get some spread if IQR too small
iqr = utils.IQR(this_month_filtered.compressed(),
percentile=0.05)
print "Spurious_stations file not yet sorted"
if iqr != 0.0:
monthly_values = np.ma.array(
(this_month_data.compressed() - monthly_median) / iqr)
bins, bincenters = utils.create_bins(monthly_values, BIN_SIZE)
dummy, plot_bincenters = utils.create_bins(
monthly_values, BIN_SIZE / 10.)
hist, binEdges = np.histogram(monthly_values, bins=bins)
if GH:
# Use Gauss-Hermite polynomials to add skew and kurtosis to Gaussian fit - January 2015 ^RJHD
initial_values = [
np.max(hist),
np.mean(monthly_values),
np.std(monthly_values),
stats.skew(monthly_values),
stats.kurtosis(monthly_values)
] # norm, mean, std, skew, kurtosis
fit = leastsq(utils.residualsGH, initial_values,
[bincenters, hist,
np.ones(len(hist))])
res = utils.hermite2gauss(fit[0], diagnostics=diagnostics)
plot_gaussian = utils.funcGH(fit[0], plot_bincenters)
# adjust to remove the rising bumps seen in some fits - artefacts of GH fitting?
mid_point = np.argmax(plot_gaussian)
bad, = np.where(
plot_gaussian[mid_point:] < FREQUENCY_THRESHOLD / 10.)
if len(bad) > 0:
plot_gaussian[mid_point:][
bad[0]:] = FREQUENCY_THRESHOLD / 10.
bad, = np.where(
plot_gaussian[:mid_point] < FREQUENCY_THRESHOLD / 10.)
if len(bad) > 0:
plot_gaussian[:mid_point][:bad[
-1]] = FREQUENCY_THRESHOLD / 10.
# extract threshold values
good_values = np.argwhere(
plot_gaussian > FREQUENCY_THRESHOLD)
l_minimum_threshold = round(
plot_bincenters[good_values[0]]) - 1
u_minimum_threshold = 1 + round(
plot_bincenters[good_values[-1]])
else:
gaussian = utils.fit_gaussian(bincenters,
hist,
max(hist),
mu=np.mean(monthly_values),
sig=np.std(monthly_values))
# assume the same threshold value
u_minimum_threshold = 1 + round(
utils.invert_gaussian(FREQUENCY_THRESHOLD, gaussian))
l_minimum_threshold = -u_minimum_threshold
plot_gaussian = utils.gaussian(plot_bincenters, gaussian)
if diagnostics:
if GH:
print hist
print res
print iqr, l_minimum_threshold, u_minimum_threshold
else:
print hist
print gaussian
print iqr, u_minimum_threshold, 1. + utils.invert_gaussian(
FREQUENCY_THRESHOLD, gaussian)
if plots:
dgc_set_up_plot(plot_gaussian,
monthly_values,
variable,
threshold=(u_minimum_threshold,
l_minimum_threshold),
sub_par="observations",
GH=GH)
if GH:
plt.figtext(
0.15,
0.67,
'Mean %.2f, S.d. %.2f,\nSkew %.2f, Kurtosis %.2f' %
(res['mean'], res['dispersion'], res['skewness'],
res['kurtosis']),
color='k',
size='small')
uppercount = len(
np.where(monthly_values > u_minimum_threshold)[0])
lowercount = len(
np.where(monthly_values < l_minimum_threshold)[0])
# this needs refactoring - but lots of variables to pass in
if plots or diagnostics: gap_plot_values = np.array([])
if uppercount > 0:
gap_start = dgc_find_gap(hist, binEdges,
u_minimum_threshold)
if gap_start != 0:
for y, year in enumerate(month_ranges[:, month, :]):
this_year_data = np.ma.array(
all_filtered[year[0]:year[1]])
this_year_flags = np.array(flags[year[0]:year[1]])
gap_cleaned_locations = np.where(
((this_year_data - monthly_median) /
iqr) > gap_start)
this_year_flags[gap_cleaned_locations] = 1
flags[year[0]:year[1]] = this_year_flags
if plots or diagnostics:
gap_plot_values = np.append(
gap_plot_values,
(this_year_data[gap_cleaned_locations].
compressed() - monthly_median) / iqr)
if lowercount > 0:
gap_start = dgc_find_gap(hist, binEdges,
l_minimum_threshold)
if gap_start != 0:
for y, year in enumerate(month_ranges[:, month, :]):
this_year_data = np.ma.array(
all_filtered[year[0]:year[1]])
this_year_flags = np.array(flags[year[0]:year[1]])
gap_cleaned_locations = np.where(
np.logical_and(
((this_year_data - monthly_median) / iqr) <
gap_start, this_year_data.mask != True))
this_year_flags[gap_cleaned_locations] = 1
flags[year[0]:year[1]] = this_year_flags
if plots or diagnostics:
gap_plot_values = np.append(
gap_plot_values,
(this_year_data[gap_cleaned_locations].
compressed() - monthly_median) / iqr)
if windspeeds:
this_year_flags[
gap_cleaned_locations] = 2 # tentative flags
slp_average = dgc_get_monthly_averages(
this_month_data, OBS_LIMIT, st_var.mdi,
MEAN)
slp_mad = utils.mean_absolute_deviation(
this_month_data, median=True)
storms = np.where((((windspeeds_month - windspeeds_month_average) / windspeeds_month_mad) > 4.5) &\
(((this_month_data - slp_average) / slp_mad) > 4.5))
if len(storms[0]) >= 2:
storm_1diffs = np.diff(storms)
separations = np.where(storm_1diffs != 1)
#for sep in separations:
if plots:
hist, binEdges = np.histogram(gap_plot_values, bins=bins)
plot_hist = np.array([0.01 if h == 0 else h for h in hist])
plt.step(bincenters,
plot_hist,
'r-',
label='flagged',
where='mid')
import calendar
plt.text(0.1,
0.9,
calendar.month_name[month + 1],
transform=plt.gca().transAxes)
plt.legend(loc='lower center',
ncol=3,
bbox_to_anchor=(0.5, -0.2),
frameon=False,
prop={'size': 13})
plt.show()
#plt.savefig(IMAGELOCATION+'/'+station.id+'_DistributionalGap_'+str(month+1)+'.png')
if diagnostics:
utils.print_flagged_obs_number("",
"Distributional Gap",
variable,
len(gap_plot_values),
noWrite=True)
return flags # dgc_all_obs
def sc(station,
variable_list,
flag_col,
start,
end,
logfile,
diagnostics=False,
plots=False,
doMonth=False):
'''
Spike Check, looks for spikes up to 3 observations long, using thresholds
calculated from the data itself.
:param MetVar station: the station object
:param list variable_list: list of observational variables to process
:param list flag_col: the columns to set on the QC flag array
:param datetime start: dataset start time
:param datetime end: dataset end time
:param file logfile: logfile to store outputs
:param bool plots: do plots
:param bool doMonth: account for incomplete months
:returns:
'''
print "refactor"
for v, variable in enumerate(variable_list):
flags = station.qc_flags[:, flag_col[v]]
st_var = getattr(station, variable)
# if incomplete year, mask all obs for the incomplete bit
all_filtered = utils.apply_filter_flags(st_var,
doMonth=doMonth,
start=start,
end=end)
reporting_resolution = utils.reporting_accuracy(
utils.apply_filter_flags(st_var))
# to match IDL system - should never be called as would mean no data
if reporting_resolution == -1:
reporting_resolution = 1
month_ranges = utils.month_starts_in_pairs(start, end)
month_ranges = month_ranges.reshape(-1, 12, 2)
good, = np.where(all_filtered.mask == False)
full_time_diffs = np.ma.zeros(len(all_filtered), dtype=int)
full_time_diffs.mask = copy.deepcopy(all_filtered.mask[:])
full_time_diffs[good[:-1]] = station.time.data[
good[1:]] - station.time.data[good[:-1]]
# develop critical values using clean values
# NOTE 4/7/14 - make sure that Missing and Flagged values treated appropriately
print "sort the differencing if values were flagged rather than missing"
full_filtered_diffs = np.ma.zeros(len(all_filtered))
full_filtered_diffs.mask = copy.deepcopy(all_filtered.mask[:])
full_filtered_diffs[good[:-1]] = all_filtered.compressed(
)[1:] - all_filtered.compressed()[:-1]
# test all values
good_to_uncompress, = np.where(st_var.data.mask == False)
full_value_diffs = np.ma.zeros(len(st_var.data))
full_value_diffs.mask = copy.deepcopy(st_var.data.mask[:])
full_value_diffs[good_to_uncompress[:-1]] = st_var.data.compressed(
)[1:] - st_var.data.compressed()[:-1]
# convert to compressed time to match IDL
value_diffs = full_value_diffs.compressed()
time_diffs = full_time_diffs.compressed()
filtered_diffs = full_filtered_diffs.compressed()
flags = flags[good_to_uncompress]
critical_values = np.zeros([9, 12])
critical_values.fill(st_var.mdi)
# link observation to calendar month
month_locs = np.zeros(full_time_diffs.shape, dtype=int)
for month in range(12):
for year in range(month_ranges.shape[0]):
if year == 0:
this_month_time_diff = full_time_diffs[month_ranges[
year, month, 0]:month_ranges[year, month, 1]]
this_month_filtered_diff = full_filtered_diffs[
month_ranges[year, month, 0]:month_ranges[year, month,
1]]
else:
this_month_time_diff = np.ma.concatenate([
this_month_time_diff,
full_time_diffs[month_ranges[year, month,
0]:month_ranges[year,
month, 1]]
])
this_month_filtered_diff = np.ma.concatenate([
this_month_filtered_diff,
full_filtered_diffs[month_ranges[year, month,
0]:month_ranges[year,
month,
1]]
])
month_locs[month_ranges[year, month,
0]:month_ranges[year, month,
1]] = month
for delta in range(1, 9):
locs = np.ma.where(this_month_time_diff == delta)
if len(locs[0]) >= 100:
iqr = utils.IQR(this_month_filtered_diff[locs])
if iqr == 0. and delta == 1:
critical_values[delta - 1, month] = 6.
elif iqr == 0:
critical_values[delta - 1, month] = st_var.mdi
else:
critical_values[delta - 1, month] = 6. * iqr
# January 2015 - changed to dynamically calculating the thresholds if less than IQR method ^RJHD
if plots:
import calendar
title = "{}, {}-hr differences".format(
calendar.month_name[month + 1], delta)
line_label = st_var.name
xlabel = "First Difference Magnitudes"
else:
title, line_label, xlabel = "", "", ""
threshold = utils.get_critical_values(
this_month_filtered_diff[locs],
binmin=0,
binwidth=0.5,
plots=plots,
diagnostics=diagnostics,
title=title,
line_label=line_label,
xlabel=xlabel,
old_threshold=critical_values[delta - 1, month])
if threshold < critical_values[delta - 1, month]:
critical_values[delta - 1, month] = threshold
if plots or diagnostics:
print critical_values[delta - 1, month], iqr, 6 * iqr
month_locs = month_locs[good_to_uncompress]
if diagnostics:
print critical_values[0, :]
# not less than 5x reporting accuracy
good_critical_values = np.where(critical_values != st_var.mdi)
low_critical_values = np.where(
critical_values[good_critical_values] <= 5. * reporting_resolution)
temporary = critical_values[good_critical_values]
temporary[low_critical_values] = 5. * reporting_resolution
critical_values[good_critical_values] = temporary
if diagnostics:
print critical_values[0, :], 5. * reporting_resolution
# check hourly against 2 hourly, if <2/3 the increase to avoid crazy rejection rate
for month in range(12):
if critical_values[0, month] != st_var.mdi and critical_values[
1, month] != st_var.mdi:
if critical_values[0, month] / critical_values[1,
month] <= 0.66:
critical_values[0,
month] = 0.66 * critical_values[1, month]
if diagnostics:
print "critical values"
print critical_values[0, :]
# get time differences for unfiltered data
full_time_diffs = np.ma.zeros(len(st_var.data), dtype=int)
full_time_diffs.mask = copy.deepcopy(st_var.data.mask[:])
full_time_diffs[good_to_uncompress[:-1]] = station.time.data[
good_to_uncompress[1:]] - station.time.data[
good_to_uncompress[:-1]]
time_diffs = full_time_diffs.compressed()
# go through each difference, identify which month it is in if passes spike thresholds
# spikes at the beginning or ends of sections
for t in np.arange(len(time_diffs)):
if (np.abs(time_diffs[t - 1]) > 240) and (np.abs(time_diffs[t]) <
3):
# 10 days before but short gap thereafter
next_values = st_var.data[good_to_uncompress[t + 1:]]
good, = np.where(next_values.mask == False)
next_median = np.ma.median(next_values[good[:10]])
next_diff = np.abs(value_diffs[t]) # out of spike
median_diff = np.abs(next_median -
st_var.data[good_to_uncompress[t]]
) # are the remaining onees
if (critical_values[time_diffs[t] - 1, month_locs[t]] !=
st_var.mdi):
# jump from spike > critical but average after < critical / 2
if (np.abs(median_diff) < critical_values[time_diffs[t] - 1, month_locs[t]] / 2.) and\
(np.abs(next_diff) > critical_values[time_diffs[t] - 1, month_locs[t]]) :
flags[t] = 1
if plots or diagnostics:
sc_diagnostics_and_plots(station.time.data,
st_var.data,
good_to_uncompress[t],
good_to_uncompress[t + 1],
start,
variable,
plots=plots)
elif (np.abs(time_diffs[t - 1]) < 3) and (np.abs(time_diffs[t]) >
240):
# 10 days after but short gap before
prev_values = st_var.data[good_to_uncompress[:t - 1]]
good, = np.where(prev_values.mask == False)
prev_median = np.ma.median(prev_values[good[-10:]])
prev_diff = np.abs(value_diffs[t - 1])
median_diff = np.abs(prev_median -
st_var.data[good_to_uncompress[t]])
if (critical_values[time_diffs[t - 1] - 1, month_locs[t]] !=
st_var.mdi):
# jump into spike > critical but average before < critical / 2
if (np.abs(median_diff) < critical_values[time_diffs[t - 1] - 1, month_locs[t]] / 2.) and\
(np.abs(prev_diff) > critical_values[time_diffs[t - 1] - 1, month_locs[t]]) :
flags[t] = 1
if plots or diagnostics:
sc_diagnostics_and_plots(station.time.data,
st_var.data,
good_to_uncompress[t],
good_to_uncompress[t + 1],
start,
variable,
plots=plots)
''' this isn't the nicest way, but a direct copy from IDL
masked arrays might help remove some of the lines
Also, this is relatively slow'''
for t in np.arange(len(time_diffs)):
for spk_len in [1, 2, 3]:
if t >= spk_len and t < len(time_diffs) - spk_len:
# check if time differences are appropriate, for multi-point spikes
if (np.abs(time_diffs[t - spk_len]) <= spk_len * 3) and\
(np.abs(time_diffs[t]) <= spk_len * 3) and\
(time_diffs[t - spk_len - 1] - 1 < spk_len * 3) and\
(time_diffs[t + 1] - 1 < spk_len * 3) and \
((spk_len == 1) or \
((spk_len == 2) and (np.abs(time_diffs[t - spk_len + 1]) <= spk_len * 3)) or \
((spk_len == 3) and (np.abs(time_diffs[t - spk_len + 1]) <= spk_len * 3) and (np.abs(time_diffs[t - spk_len + 2]) <= spk_len * 3))):
# check if differences are valid
if (value_diffs[t - spk_len] != st_var.mdi) and \
(value_diffs[t - spk_len] != st_var.fdi) and \
(critical_values[time_diffs[t - spk_len] - 1, month_locs[t]] != st_var.mdi):
# if exceed critical values
if (np.abs(value_diffs[t - spk_len]) >=
critical_values[time_diffs[t - spk_len] -
1, month_locs[t]]):
# are signs of two differences different
if (math.copysign(1, value_diffs[t])
!= math.copysign(
1, value_diffs[t - spk_len])):
# are within spike differences small
if (spk_len == 1) or\
((spk_len == 2) and (np.abs(value_diffs[t - spk_len + 1]) < critical_values[time_diffs[t - spk_len + 1] -1, month_locs[t]] / 2.)) or \
((spk_len == 3) and (np.abs(value_diffs[t - spk_len + 1]) < critical_values[time_diffs[t - spk_len + 1] -1, month_locs[t]] / 2.) and\
(np.abs(value_diffs[t - spk_len + 2]) < critical_values[time_diffs[t - spk_len + 2] -1, month_locs[t]] / 2.)):
# check if following value is valid
if (value_diffs[t] != st_var.mdi) and (critical_values[time_diffs[t] - 1, month_locs[t]] != st_var.mdi) and\
(value_diffs[t] != st_var.fdi):
# and if at least critical value
if (np.abs(value_diffs[t]) >=
critical_values[
time_diffs[t] - 1,
month_locs[t]]):
# test if surrounding differences below 1/2 critical value
if (np.abs(
value_diffs[t - spk_len
- 1]
) <= critical_values[
time_diffs[t -
spk_len -
1] - 1,
month_locs[t]] / 2.):
if (np.abs(
value_diffs[t + 1]
) <= critical_values[
time_diffs[t + 1] -
1, month_locs[t]] /
2.):
# set the flags
flags[t - spk_len +
1:t + 1] = 1
if plots or diagnostics:
sc_diagnostics_and_plots(
station.time.
data,
st_var.data,
good_to_uncompress[
t -
spk_len +
1],
good_to_uncompress[
t + 1],
start,
variable,
plots=plots)
station.qc_flags[good_to_uncompress, flag_col[v]] = flags
flag_locs, = np.where(station.qc_flags[:, flag_col[v]] != 0)
utils.print_flagged_obs_number(logfile,
"Spike",
variable,
len(flag_locs),
noWrite=diagnostics) # additional flags
# copy flags into attribute
st_var.flags[flag_locs] = 1
# matches 030660 - but with adapted IDL
# matches 030220 OK, but finds more but all are reasonable 1/9/14
do_interactive = False
if plots and do_interactive == True:
import matplotlib.pyplot as plt
plot_times = utils.times_hours_to_datetime(station.time.data,
start)
plt.clf()
plt.plot(plot_times, all_filtered, 'bo', ls='-')
flg = np.where(flags[:, flag_col[v]] == 1)
plt.plot(plot_times[flg], all_filtered[flg], 'ro', markersize=10)
plt.show()
station = utils.append_history(station, "Spike Check")
return # sc
def detect(station, neighbour, variable, flags, neighbour_count, start, end, distance = 0, diagnostics = False, plots = False):
'''
Detect which observations are outliers
:param MetVar station: station object (target)
:param MetVar neighbour: station object (neighbour)
:param string variable: which variable to process
:param array flags: array to store how many neighbours thing each obs is bad
:param array neighbour_count: how many neighbours present at each obs
:param datetime start: start of dataset
:param datetime end: end of dataset
:param int distance: separation of target and neighbour
:param bool diagnostics: extra output
:param bool plots: make figures
:returns: None
'''
FILTERING_FLAG_COL = {"temperatures":[0,1,4,5,8,12,16,20,27,41,44,58],
"dewpoints":[0,2,4,6,8,9,13,17,21,28,30,31,32,42,45,59],
"slp":[0,3,4,7,11,15,19,23,29,43,46,60],
"windspeeds":[0,4,10,14,18,22,56,62,63,64]} # not used, but ready for it.
st_var = getattr(station, variable)
neigh_var = getattr(neighbour, variable)
# filter by flags - not all (no Climatological or Odd cluster), T record check not in D,
total_flags = np.sum(station.qc_flags[:,FILTERING_FLAG_COL[variable]], axis = 1)
st_filtered = np.ma.masked_where(total_flags == 1, st_var.data)
neigh_filtered = np.ma.masked_where(total_flags == 1, neigh_var.data)
# match the observation times
match = np.where(np.logical_and((st_filtered.data != st_var.mdi), (neigh_filtered.data != neigh_var.mdi)))
month_ranges = utils.month_starts_in_pairs(start, end).reshape(-1,12,2) # in year-long sets of pairs.
if len(match[0]) >= 100:
neighbour_count[match] += 1 # number of neighbours with data present
differences = np.ma.zeros(len(st_filtered))
differences.fill(st_var.mdi)
differences.mask = True
differences[match] = st_filtered.data[match] - neigh_filtered.data[match]
differences.mask[match] = False
all_iqrs = np.zeros(len(differences))
# get monthly IQR values
for month in range(12):
this_month, dummy1, dummy2 = utils.concatenate_months(month_ranges[:,month,:], differences, hours = False)
if len(this_month.compressed()) > 4:
iqr = utils.IQR(this_month.compressed())
if iqr <= 2.: iqr = 2.
else:
iqr = 2.
# and copy back into the array
for year in month_ranges[:,month,:]:
all_iqrs[year[0]:year[1]] = iqr
if plots:
plot_target_neigh_diffs_dist(differences, min(iqr))
dubious = np.ma.where(np.ma.abs(differences) > 5. * all_iqrs)
if len(dubious[0]) >= 1.:
if variable == "slp":
# check if they are storms
positive = np.ma.where(differences > 5. * iqr)
negative = np.ma.where(differences < -5. * iqr)
# if majority negative (2/3) and separation > 100
if (distance > 100.) and (float(len(positive[0]))/len(dubious[0]) < 0.333):
if len(positive[0]) > 0:
flags[positive] += 1
if len(negative[0]) > 0:
neighbour_count[match] -= 1
else:
flags[dubious] += 1
else:
flags[dubious] += 1
return # detect
