def main(sDir, url_list, start_time, end_time, preferred_only):
rd_list = []
for uu in url_list:
elements = uu.split('/')[-2].split('-')
rd = '-'.join((elements[1], elements[2], elements[3], elements[4]))
if rd not in rd_list:
rd_list.append(rd)
for r in rd_list:
print('\n{}'.format(r))
datasets = []
for u in url_list:
splitter = u.split('/')[-2].split('-')
rd_check = '-'.join(
(splitter[1], splitter[2], splitter[3], splitter[4]))
if rd_check == r:
udatasets = cf.get_nc_urls([u])
datasets.append(udatasets)
datasets = list(itertools.chain(*datasets))
fdatasets = []
if preferred_only == 'yes':
# get the preferred stream information
ps_df, n_streams = cf.get_preferred_stream_info(r)
for index, row in ps_df.iterrows():
for ii in range(n_streams):
try:
rms = '-'.join((r, row[ii]))
except TypeError:
continue
for dd in datasets:
spl = dd.split('/')[-2].split('-')
catalog_rms = '-'.join(
(spl[1], spl[2], spl[3], spl[4], spl[5], spl[6]))
fdeploy = dd.split('/')[-1].split('_')[0]
if rms == catalog_rms and fdeploy == row['deployment']:
fdatasets.append(dd)
else:
fdatasets = datasets
fdatasets = np.unique(fdatasets).tolist()
for fd in fdatasets:
ds = xr.open_dataset(fd, mask_and_scale=False)
ds = ds.swap_dims({'obs': 'time'})
if start_time is not None and end_time is not None:
ds = ds.sel(time=slice(start_time, end_time))
if len(ds['time'].values) == 0:
print(
'No data to plot for specified time range: ({} to {})'.
format(start_time, end_time))
continue
fname, subsite, refdes, method, stream, deployment = cf.nc_attributes(
fd)
sci_vars = cf.return_science_vars(stream)
print('\nPlotting {} {}'.format(r, deployment))
array = subsite[0:2]
filename = '_'.join(fname.split('_')[:-1])
save_dir = os.path.join(sDir, array, subsite, refdes,
'timeseries_plots')
cf.create_dir(save_dir)
tm = ds['time'].values
t0 = pd.to_datetime(tm.min()).strftime('%Y-%m-%dT%H:%M:%S')
t1 = pd.to_datetime(tm.max()).strftime('%Y-%m-%dT%H:%M:%S')
title = ' '.join((deployment, refdes, method))
# -------- plot entire deployment --------
for var in sci_vars:
print(var)
vv = ds[var]
fv = vv._FillValue
# need to round SPKIR values to 1 decimal place to match the global ranges. otherwise, values that
# round to zero (e.g. 1.55294e-05) will be excluded by the global range test
# v = np.round(vv.values.T, 1) # .T = transpose 2D array
v = vv.values.T
n_nan = np.sum(np.isnan(v))
# convert fill values to nans
v[v == fv] = np.nan
n_fv = np.sum(np.isnan(v)) - n_nan
# plot before global ranges are removed
fig, ax = pf.plot_spkir(tm, v, vv.name, vv.units)
ax.set_title((title + '\n' + t0 + ' - ' + t1), fontsize=9)
sfile = '-'.join((filename, var, t0[:10]))
pf.save_fig(save_dir, sfile)
# reject data outside of global ranges
[g_min, g_max] = cf.get_global_ranges(r, var)
if g_min is not None and g_max is not None:
v[v < g_min] = np.nan
v[v > g_max] = np.nan
n_grange = np.sum(np.isnan(v)) - n_fv - n_nan
else:
n_grange = 'no global ranges'
# plot after global ranges are removed
fig, ax = pf.plot_spkir(tm, v, vv.name, vv.units)
title2 = 'removed: {} global ranges [{}, {}]'.format(
n_grange, g_min, g_max)
ax.set_title((title + '\n' + t0 + ' - ' + t1 + '\n' + title2),
fontsize=9)
sfile = '-'.join((filename, var, t0[:10], 'rmgr'))
pf.save_fig(save_dir, sfile)
# -------- break the deployment into months and plot --------
save_dir = os.path.join(sDir, array, subsite, refdes,
'timeseries_plots', 'monthly')
cf.create_dir(save_dir)
# create list of start and end dates
dt_start = dt.datetime.strptime(t0, '%Y-%m-%dT%H:%M:%S')
dt_end = dt.datetime.strptime(t1, '%Y-%m-%dT%H:%M:%S')
start_dates = [dt_start.strftime('%m-%d-%YT00:00:00')]
end_dates = []
ts1 = dt_start
while ts1 <= dt_end:
ts2 = ts1 + dt.timedelta(days=1)
if ts2.month != ts1.month:
start_dates.append(ts2.strftime('%m-%d-%YT00:00:00'))
end_dates.append(ts1.strftime('%m-%d-%YT23:59:59'))
ts1 = ts2
end_dates.append(dt_end.strftime('%m-%d-%YT23:59:59'))
for sd, ed in zip(start_dates, end_dates):
sd_format = dt.datetime.strptime(sd, '%m-%d-%YT%H:%M:%S')
ed_format = dt.datetime.strptime(ed, '%m-%d-%YT%H:%M:%S')
ds_month = ds.sel(time=slice(sd_format, ed_format))
if len(ds_month['time'].values) == 0:
print(
'No data to plot for specified time range: ({} to {})'.
format(sd, ed))
continue
tm = ds_month['time'].values
t0 = pd.to_datetime(tm.min()).strftime('%Y-%m-%dT%H:%M:%S')
t1 = pd.to_datetime(tm.max()).strftime('%Y-%m-%dT%H:%M:%S')
for var in sci_vars:
print(var)
vv = ds_month[var]
fv = vv._FillValue
v = vv.values.T # transpose 2D array
n_nan = np.sum(np.isnan(v))
# convert fill values to nans
v[v == fv] = np.nan
n_fv = np.sum(np.isnan(v)) - n_nan
# reject data outside of global ranges
[g_min, g_max] = cf.get_global_ranges(r, var)
if g_min is not None and g_max is not None:
v[v < g_min] = np.nan
v[v > g_max] = np.nan
n_grange = np.sum(np.isnan(v)) - n_fv - n_nan
else:
n_grange = 'no global ranges'
# plot after global ranges are removed
fig, ax = pf.plot_spkir(tm, v, vv.name, vv.units)
title2 = 'removed: {} global ranges [{}, {}]'.format(
n_grange, g_min, g_max)
ax.set_title(
(title + '\n' + t0 + ' - ' + t1 + '\n' + title2),
fontsize=9)
sfile = '-'.join((filename, var, t0[:7], 'rmgr'))
pf.save_fig(save_dir, sfile)
def main(sDir, plotting_sDir, url_list, sd_calc):
dr = pd.read_csv('https://datareview.marine.rutgers.edu/notes/export')
drn = dr.loc[dr.type == 'exclusion']
rd_list = []
for uu in url_list:
elements = uu.split('/')[-2].split('-')
rd = '-'.join((elements[1], elements[2], elements[3], elements[4]))
if rd not in rd_list:
rd_list.append(rd)
for r in rd_list:
print('\n{}'.format(r))
datasets = []
for u in url_list:
splitter = u.split('/')[-2].split('-')
rd_check = '-'.join(
(splitter[1], splitter[2], splitter[3], splitter[4]))
if rd_check == r:
udatasets = cf.get_nc_urls([u])
datasets.append(udatasets)
datasets = list(itertools.chain(*datasets))
fdatasets = []
# get the preferred stream information
ps_df, n_streams = cf.get_preferred_stream_info(r)
pms = []
for index, row in ps_df.iterrows():
for ii in range(n_streams):
try:
rms = '-'.join((r, row[ii]))
pms.append(row[ii])
except TypeError:
continue
for dd in datasets:
spl = dd.split('/')[-2].split('-')
catalog_rms = '-'.join(
(spl[1], spl[2], spl[3], spl[4], spl[5], spl[6]))
fdeploy = dd.split('/')[-1].split('_')[0]
if rms == catalog_rms and fdeploy == row['deployment']:
fdatasets.append(dd)
main_sensor = r.split('-')[-1]
fdatasets_sel = cf.filter_collocated_instruments(
main_sensor, fdatasets)
# find time ranges to exclude from analysis for data review database
subsite = r.split('-')[0]
subsite_node = '-'.join((subsite, r.split('-')[1]))
drne = drn.loc[drn.reference_designator.isin(
[subsite, subsite_node, r])]
et = []
for i, row in drne.iterrows():
sdate = cf.format_dates(row.start_date)
edate = cf.format_dates(row.end_date)
et.append([sdate, edate])
# get science variable long names from the Data Review Database
stream_sci_vars = cd.sci_var_long_names(r)
# check if the science variable long names are the same for each stream
sci_vars_dict = cd.sci_var_long_names_check(stream_sci_vars)
# get the preferred stream information
ps_df, n_streams = cf.get_preferred_stream_info(r)
# build dictionary of science data from the preferred dataset for each deployment
print('\nAppending data from files')
sci_vars_dict, pressure_unit, pressure_name = cd.append_science_data(
ps_df, n_streams, r, fdatasets_sel, sci_vars_dict, et)
# analyze combined dataset
print('\nAnalyzing combined dataset and writing summary file')
array = subsite[0:2]
save_dir = os.path.join(sDir, array, subsite)
cf.create_dir(save_dir)
rows = []
if ('FLM' in r) and (
'CTDMO' in r
): # calculate Flanking Mooring CTDMO stats based on pressure
headers = [
'common_stream_name', 'preferred_methods_streams',
'deployments', 'long_name', 'units', 't0', 't1', 'fill_value',
'global_ranges', 'n_all', 'press_min_max',
'n_excluded_forpress', 'n_nans', 'n_fillvalues', 'n_grange',
'define_stdev', 'n_outliers', 'n_stats', 'mean', 'min', 'max',
'stdev', 'note'
]
else:
headers = [
'common_stream_name', 'preferred_methods_streams',
'deployments', 'long_name', 'units', 't0', 't1', 'fill_value',
'global_ranges', 'n_all', 'n_nans', 'n_fillvalues', 'n_grange',
'define_stdev', 'n_outliers', 'n_stats', 'mean', 'min', 'max',
'stdev'
]
for m, n in sci_vars_dict.items():
print('\nSTREAM: ', m)
if m == 'common_stream_placeholder':
m = 'science_data_stream'
if m == 'metbk_hourly': # don't calculate ranges for metbk_hourly
continue
if ('FLM' in r) and (
'CTDMO' in r
): # calculate Flanking Mooring CTDMO stats based on pressure
# index the pressure variable to filter and calculate stats on the rest of the variables
sv_press = 'Seawater Pressure'
vinfo_press = n['vars'][sv_press]
# first, index where data are nans, fill values, and outside of global ranges
fv_press = list(np.unique(vinfo_press['fv']))[0]
pdata = vinfo_press['values']
[pind, __, __, __, __,
__] = index_dataset(r, vinfo_press['var_name'], pdata,
fv_press)
pdata_filtered = pdata[pind]
[__, pmean, __, __, psd,
__] = cf.variable_statistics(pdata_filtered, None)
# index of pressure = average of all 'valid' pressure data +/- 1 SD
ipress_min = pmean - psd
ipress_max = pmean + psd
ind_press = (pdata >= ipress_min) & (pdata <= ipress_max)
# calculate stats for all variables
print('\nPARAMETERS:')
for sv, vinfo in n['vars'].items():
print(sv)
fv_lst = np.unique(vinfo['fv']).tolist()
if len(fv_lst) == 1:
fill_value = fv_lst[0]
else:
print('No unique fill value for {}'.format(sv))
lunits = np.unique(vinfo['units']).tolist()
n_all = len(vinfo['t'])
# filter data based on pressure index
t_filtered = vinfo['t'][ind_press]
data_filtered = vinfo['values'][ind_press]
deploy_filtered = vinfo['deployments'][ind_press]
n_excluded = n_all - len(t_filtered)
[dataind, g_min, g_max, n_nan, n_fv,
n_grange] = index_dataset(r, vinfo['var_name'],
data_filtered, fill_value)
t_final = t_filtered[dataind]
data_final = data_filtered[dataind]
deploy_final = deploy_filtered[dataind]
t0 = pd.to_datetime(
min(t_final)).strftime('%Y-%m-%dT%H:%M:%S')
t1 = pd.to_datetime(
max(t_final)).strftime('%Y-%m-%dT%H:%M:%S')
deploy = list(np.unique(deploy_final))
deployments = [int(dd) for dd in deploy]
if len(data_final) > 1:
[num_outliers, mean, vmin, vmax, sd, n_stats
] = cf.variable_statistics(data_final, sd_calc)
else:
mean = None
vmin = None
vmax = None
sd = None
n_stats = None
note = 'restricted stats calculation to data points where pressure is within defined ranges' \
' (average of all pressure data +/- 1 SD)'
rows.append([
m,
list(np.unique(pms)), deployments, sv, lunits, t0, t1,
fv_lst, [g_min, g_max], n_all,
[round(ipress_min, 2),
round(ipress_max,
2)], n_excluded, n_nan, n_fv, n_grange, sd_calc,
num_outliers, n_stats, mean, vmin, vmax, sd, note
])
# plot CTDMO data used for stats
psave_dir = os.path.join(plotting_sDir, array, subsite, r,
'timeseries_plots_stats')
cf.create_dir(psave_dir)
dr_data = cf.refdes_datareview_json(r)
deployments = []
end_times = []
for index, row in ps_df.iterrows():
deploy = row['deployment']
deploy_info = cf.get_deployment_information(
dr_data, int(deploy[-4:]))
deployments.append(int(deploy[-4:]))
end_times.append(
pd.to_datetime(deploy_info['stop_date']))
sname = '-'.join((r, sv))
fig, ax = pf.plot_timeseries_all(t_final,
data_final,
sv,
lunits[0],
stdev=None)
ax.set_title(
(r + '\nDeployments: ' + str(sorted(deployments)) +
'\n' + t0 + ' - ' + t1),
fontsize=8)
for etimes in end_times:
ax.axvline(x=etimes,
color='k',
linestyle='--',
linewidth=.6)
pf.save_fig(psave_dir, sname)
if sd_calc:
sname = '-'.join((r, sv, 'rmoutliers'))
fig, ax = pf.plot_timeseries_all(t_final,
data_final,
sv,
lunits[0],
stdev=sd_calc)
ax.set_title(
(r + '\nDeployments: ' + str(sorted(deployments)) +
'\n' + t0 + ' - ' + t1),
fontsize=8)
for etimes in end_times:
ax.axvline(x=etimes,
color='k',
linestyle='--',
linewidth=.6)
pf.save_fig(psave_dir, sname)
else:
if not sd_calc:
sdcalc = None
print('\nPARAMETERS: ')
for sv, vinfo in n['vars'].items():
print(sv)
fv_lst = np.unique(vinfo['fv']).tolist()
if len(fv_lst) == 1:
fill_value = fv_lst[0]
else:
print(fv_lst)
print('No unique fill value for {}'.format(sv))
lunits = np.unique(vinfo['units']).tolist()
t = vinfo['t']
if len(t) > 1:
data = vinfo['values']
n_all = len(t)
if 'SPKIR' in r or 'presf_abc_wave_burst' in m:
if 'SPKIR' in r:
[dd_data, g_min, g_max, n_nan, n_fv,
n_grange] = index_dataset_2d(
r, 'spkir_abj_cspp_downwelling_vector',
data, fill_value)
else:
[dd_data, g_min, g_max, n_nan, n_fv,
n_grange] = index_dataset_2d(
r, 'presf_wave_burst_pressure', data,
fill_value)
t_final = t
t0 = pd.to_datetime(
min(t_final)).strftime('%Y-%m-%dT%H:%M:%S')
t1 = pd.to_datetime(
max(t_final)).strftime('%Y-%m-%dT%H:%M:%S')
deploy_final = vinfo['deployments']
deploy = list(np.unique(deploy_final))
deployments = [int(dd) for dd in deploy]
num_outliers = []
mean = []
vmin = []
vmax = []
sd = []
n_stats = []
for i in range(len(dd_data)):
dd = data[i]
# drop nans before calculating stats
dd = dd[~np.isnan(dd)]
[
num_outliersi, meani, vmini, vmaxi, sdi,
n_statsi
] = cf.variable_statistics(dd, sd_calc)
num_outliers.append(num_outliersi)
mean.append(meani)
vmin.append(vmini)
vmax.append(vmaxi)
sd.append(sdi)
n_stats.append(n_statsi)
else:
[dataind, g_min, g_max, n_nan, n_fv,
n_grange] = index_dataset(r, vinfo['var_name'],
data, fill_value)
t_final = t[dataind]
if len(t_final) > 0:
t0 = pd.to_datetime(
min(t_final)).strftime('%Y-%m-%dT%H:%M:%S')
t1 = pd.to_datetime(
max(t_final)).strftime('%Y-%m-%dT%H:%M:%S')
data_final = data[dataind]
# if sv == 'Dissolved Oxygen Concentration':
# xx = (data_final > 0) & (data_final < 400)
# data_final = data_final[xx]
# t_final = t_final[xx]
# if sv == 'Seawater Conductivity':
# xx = (data_final > 1) & (data_final < 400)
# data_final = data_final[xx]
# t_final = t_final[xx]
deploy_final = vinfo['deployments'][dataind]
deploy = list(np.unique(deploy_final))
deployments = [int(dd) for dd in deploy]
if len(data_final) > 1:
[
num_outliers, mean, vmin, vmax, sd,
n_stats
] = cf.variable_statistics(
data_final, sd_calc)
else:
sdcalc = None
num_outliers = None
mean = None
vmin = None
vmax = None
sd = None
n_stats = None
else:
sdcalc = None
num_outliers = None
mean = None
vmin = None
vmax = None
sd = None
n_stats = None
deployments = None
t0 = None
t1 = None
else:
sdcalc = None
num_outliers = None
mean = None
vmin = None
vmax = None
sd = None
n_stats = None
deployments = None
t0 = None
t1 = None
t_final = []
if sd_calc:
print_sd = sd_calc
else:
print_sd = sdcalc
rows.append([
m,
list(np.unique(pms)), deployments, sv, lunits, t0, t1,
fv_lst, [g_min, g_max], n_all, n_nan, n_fv, n_grange,
print_sd, num_outliers, n_stats, mean, vmin, vmax, sd
])
if len(t_final) > 0:
# plot data used for stats
psave_dir = os.path.join(
plotting_sDir, array, subsite, r,
'timeseries_reviewed_datarange')
cf.create_dir(psave_dir)
dr_data = cf.refdes_datareview_json(r)
deployments = []
end_times = []
for index, row in ps_df.iterrows():
deploy = row['deployment']
deploy_info = cf.get_deployment_information(
dr_data, int(deploy[-4:]))
deployments.append(int(deploy[-4:]))
end_times.append(
pd.to_datetime(deploy_info['stop_date']))
sname = '-'.join((r, sv))
# plot hourly averages for streaming data
if 'streamed' in sci_vars_dict[list(
sci_vars_dict.keys())[0]]['ms'][0]:
sname = '-'.join((sname, 'hourlyavg'))
df = pd.DataFrame({
'dfx': t_final,
'dfy': data_final
})
dfr = df.resample('H', on='dfx').mean()
# Plot all data
fig, ax = pf.plot_timeseries_all(dfr.index,
dfr['dfy'],
sv,
lunits[0],
stdev=None)
ax.set_title((r + '\nDeployments: ' +
str(sorted(deployments)) + '\n' +
t0 + ' - ' + t1),
fontsize=8)
for etimes in end_times:
ax.axvline(x=etimes,
color='k',
linestyle='--',
linewidth=.6)
pf.save_fig(psave_dir, sname)
if sd_calc:
sname = '-'.join(
(sname, 'hourlyavg_rmoutliers'))
fig, ax = pf.plot_timeseries_all(dfr.index,
dfr['dfy'],
sv,
lunits[0],
stdev=sd_calc)
ax.set_title((r + '\nDeployments: ' +
str(sorted(deployments)) + '\n' +
t0 + ' - ' + t1),
fontsize=8)
for etimes in end_times:
ax.axvline(x=etimes,
color='k',
linestyle='--',
linewidth=.6)
pf.save_fig(psave_dir, sname)
elif 'SPKIR' in r:
fig, ax = pf.plot_spkir(t_final, dd_data, sv,
lunits[0])
ax.set_title((r + '\nDeployments: ' +
str(sorted(deployments)) + '\n' +
t0 + ' - ' + t1),
fontsize=8)
for etimes in end_times:
ax.axvline(x=etimes,
color='k',
linestyle='--',
linewidth=.6)
pf.save_fig(psave_dir, sname)
# plot each wavelength
wavelengths = [
'412nm', '443nm', '490nm', '510nm', '555nm',
'620nm', '683nm'
]
for wvi in range(len(dd_data)):
fig, ax = pf.plot_spkir_wv(
t_final, dd_data[wvi], sv, lunits[0], wvi)
ax.set_title((r + '\nDeployments: ' +
str(sorted(deployments)) + '\n' +
t0 + ' - ' + t1),
fontsize=8)
for etimes in end_times:
ax.axvline(x=etimes,
color='k',
linestyle='--',
linewidth=.6)
snamewvi = '-'.join((sname, wavelengths[wvi]))
pf.save_fig(psave_dir, snamewvi)
elif 'presf_abc_wave_burst' in m:
fig, ax = pf.plot_presf_2d(t_final, dd_data, sv,
lunits[0])
ax.set_title((r + '\nDeployments: ' +
str(sorted(deployments)) + '\n' +
t0 + ' - ' + t1),
fontsize=8)
for etimes in end_times:
ax.axvline(x=etimes,
color='k',
linestyle='--',
linewidth=.6)
snamewave = '-'.join((sname, m))
pf.save_fig(psave_dir, snamewave)
else: # plot all data if not streamed
fig, ax = pf.plot_timeseries_all(t_final,
data_final,
sv,
lunits[0],
stdev=None)
ax.set_title((r + '\nDeployments: ' +
str(sorted(deployments)) + '\n' +
t0 + ' - ' + t1),
fontsize=8)
for etimes in end_times:
ax.axvline(x=etimes,
color='k',
linestyle='--',
linewidth=.6)
pf.save_fig(psave_dir, sname)
if sd_calc:
sname = '-'.join((r, sv, 'rmoutliers'))
fig, ax = pf.plot_timeseries_all(t_final,
data_final,
sv,
lunits[0],
stdev=sd_calc)
ax.set_title((r + '\nDeployments: ' +
str(sorted(deployments)) + '\n' +
t0 + ' - ' + t1),
fontsize=8)
for etimes in end_times:
ax.axvline(x=etimes,
color='k',
linestyle='--',
linewidth=.6)
pf.save_fig(psave_dir, sname)
fsum = pd.DataFrame(rows, columns=headers)
fsum.to_csv('{}/{}_data_ranges.csv'.format(save_dir, r), index=False)
def main(sDir, url_list, start_time, end_time):
rd_list = []
for uu in url_list:
elements = uu.split('/')[-2].split('-')
rd = '-'.join((elements[1], elements[2], elements[3], elements[4]))
if rd not in rd_list:
rd_list.append(rd)
for r in rd_list:
print('\n{}'.format(r))
datasets = []
for u in url_list:
splitter = u.split('/')[-2].split('-')
rd_check = '-'.join((splitter[1], splitter[2], splitter[3], splitter[4]))
if rd_check == r:
udatasets = cf.get_nc_urls([u])
datasets.append(udatasets)
datasets = list(itertools.chain(*datasets))
fdatasets = []
# get the preferred stream information
ps_df, n_streams = cf.get_preferred_stream_info(r)
for index, row in ps_df.iterrows():
for ii in range(n_streams):
try:
rms = '-'.join((r, row[ii]))
except TypeError:
continue
for dd in datasets:
spl = dd.split('/')[-2].split('-')
catalog_rms = '-'.join((spl[1], spl[2], spl[3], spl[4], spl[5], spl[6]))
fdeploy = dd.split('/')[-1].split('_')[0]
if rms == catalog_rms and fdeploy == row['deployment']:
fdatasets.append(dd)
main_sensor = r.split('-')[-1]
fdatasets_sel = cf.filter_collocated_instruments(main_sensor, fdatasets)
# get science variable long names from the Data Review Database
#stream_sci_vars = cd.sci_var_long_names(r)
if 'SPKIR' in r or 'PRESF' in r: # only get the main science variable for SPKIR
stream_vars = cd.sci_var_long_names(r)
else:
stream_vars = var_long_names(r)
# check if the science variable long names are the same for each stream and initialize empty arrays
sci_vars_dict = cd.sci_var_long_names_check(stream_vars)
# get the preferred stream information
ps_df, n_streams = cf.get_preferred_stream_info(r)
# build dictionary of science data from the preferred dataset for each deployment
print('\nAppending data from files')
et = []
sci_vars_dict, __, __ = cd.append_science_data(ps_df, n_streams, r, fdatasets_sel, sci_vars_dict, et, start_time, end_time)
# get end times of deployments
dr_data = cf.refdes_datareview_json(r)
deployments = []
dend_times = []
for index, row in ps_df.iterrows():
deploy = row['deployment']
deploy_info = get_deployment_information(dr_data, int(deploy[-4:]))
deployments.append(int(deploy[-4:]))
dend_times.append(pd.to_datetime(deploy_info['stop_date']))
subsite = r.split('-')[0]
array = subsite[0:2]
save_dir = os.path.join(sDir, array, subsite, r, 'timeseries_plots_preferred_all')
cf.create_dir(save_dir)
print('\nPlotting data')
for m, n in sci_vars_dict.items():
for sv, vinfo in n['vars'].items():
print(sv)
if 'SPKIR' in r:
fv_lst = np.unique(vinfo['fv']).tolist()
if len(fv_lst) == 1:
fill_value = fv_lst[0]
else:
print(fv_lst)
print('No unique fill value for {}'.format(sv))
sv_units = np.unique(vinfo['units']).tolist()
t = vinfo['t']
if len(t) > 1:
data = vinfo['values']
[dd_data, g_min, g_max] = index_dataset_2d(r, 'spkir_abj_cspp_downwelling_vector', data, fill_value)
t0 = pd.to_datetime(min(t)).strftime('%Y-%m-%dT%H:%M:%S')
t1 = pd.to_datetime(max(t)).strftime('%Y-%m-%dT%H:%M:%S')
deploy_final = vinfo['deployments']
deploy = list(np.unique(deploy_final))
deployments = [int(dd) for dd in deploy]
sname = '-'.join((r, sv))
fig, ax = pf.plot_spkir(t, dd_data, sv, sv_units[0])
ax.set_title((r + '\nDeployments: ' + str(sorted(deployments)) + '\n' + t0 + ' - ' + t1 + '\n'
+ 'removed global ranges +/- [{} - {}]'.format(g_min, g_max)), fontsize=8)
for etimes in dend_times:
ax.axvline(x=etimes, color='k', linestyle='--', linewidth=.6)
pf.save_fig(save_dir, sname)
# plot each wavelength
wavelengths = ['412nm', '443nm', '490nm', '510nm', '555nm', '620nm', '683nm']
for wvi in range(len(dd_data)):
fig, ax = pf.plot_spkir_wv(t, dd_data[wvi], sv, sv_units[0], wvi)
ax.set_title(
(r + '\nDeployments: ' + str(sorted(deployments)) + '\n' + t0 + ' - ' + t1 + '\n'
+ 'removed global ranges +/- [{} - {}]'.format(g_min, g_max)), fontsize=8)
for etimes in dend_times:
ax.axvline(x=etimes, color='k', linestyle='--', linewidth=.6)
snamewvi = '-'.join((sname, wavelengths[wvi]))
pf.save_fig(save_dir, snamewvi)
elif 'presf_abc_wave_burst' in m:
fv_lst = np.unique(vinfo['fv']).tolist()
if len(fv_lst) == 1:
fill_value = fv_lst[0]
else:
print(fv_lst)
print('No unique fill value for {}'.format(sv))
sv_units = np.unique(vinfo['units']).tolist()
t = vinfo['t']
if len(t) > 1:
data = vinfo['values']
[dd_data, g_min, g_max] = index_dataset_2d(r, 'presf_wave_burst_pressure', data, fill_value)
t0 = pd.to_datetime(min(t)).strftime('%Y-%m-%dT%H:%M:%S')
t1 = pd.to_datetime(max(t)).strftime('%Y-%m-%dT%H:%M:%S')
deploy_final = vinfo['deployments']
deploy = list(np.unique(deploy_final))
deployments = [int(dd) for dd in deploy]
sname = '-'.join((r, sv))
fig, ax = pf.plot_presf_2d(t, dd_data, sv, sv_units[0])
ax.set_title((r + '\nDeployments: ' + str(sorted(deployments)) + '\n' + t0 + ' - ' + t1 + '\n'
+ 'removed global ranges +/- [{} - {}]'.format(g_min, g_max)), fontsize=8)
for etimes in dend_times:
ax.axvline(x=etimes, color='k', linestyle='--', linewidth=.6)
pf.save_fig(save_dir, sname)
else:
if type(vinfo['values']) != dict: # if the variable is not a 2D array
if 'Spectra' not in sv:
if len(vinfo['t']) < 1:
print('no variable data to plot')
else:
sv_units = vinfo['units'][0]
sv_name = vinfo['var_name']
t0 = pd.to_datetime(min(vinfo['t'])).strftime('%Y-%m-%dT%H:%M:%S')
t1 = pd.to_datetime(max(vinfo['t'])).strftime('%Y-%m-%dT%H:%M:%S')
x = vinfo['t']
y = vinfo['values']
# reject NaNs and values of 0.0
nan_ind = (~np.isnan(y)) & (y != 0.0)
x_nonan = x[nan_ind]
y_nonan = y[nan_ind]
# reject fill values
fv_ind = y_nonan != vinfo['fv'][0]
x_nonan_nofv = x_nonan[fv_ind]
y_nonan_nofv = y_nonan[fv_ind]
# reject extreme values
Ev_ind = cf.reject_extreme_values(y_nonan_nofv)
y_nonan_nofv_nE = y_nonan_nofv[Ev_ind]
x_nonan_nofv_nE = x_nonan_nofv[Ev_ind]
# reject values outside global ranges:
global_min, global_max = cf.get_global_ranges(r, sv_name)
if any(e is None for e in [global_min, global_max]):
y_nonan_nofv_nE_nogr = y_nonan_nofv_nE
x_nonan_nofv_nE_nogr = x_nonan_nofv_nE
else:
gr_ind = cf.reject_global_ranges(y_nonan_nofv_nE, global_min, global_max)
y_nonan_nofv_nE_nogr = y_nonan_nofv_nE[gr_ind]
x_nonan_nofv_nE_nogr = x_nonan_nofv_nE[gr_ind]
if len(y_nonan_nofv) > 0:
if m == 'common_stream_placeholder':
sname = '-'.join((r, sv))
else:
sname = '-'.join((r, m, sv))
plt_deploy = [int(x) for x in list(np.unique(vinfo['deployments']))]
# plot hourly averages for cabled and FDCHP data
if 'streamed' in sci_vars_dict[list(sci_vars_dict.keys())[0]]['ms'][0] or 'FDCHP' in r:
sname = '-'.join((sname, 'hourlyavg'))
df = pd.DataFrame({'dfx': x_nonan_nofv_nE_nogr, 'dfy': y_nonan_nofv_nE_nogr})
dfr = df.resample('H', on='dfx').mean()
# Plot all data
fig, ax = pf.plot_timeseries_all(dfr.index, dfr['dfy'], sv, sv_units, stdev=None)
ax.set_title((r + '\nDeployments: ' + str(plt_deploy) + '\n' + t0 + ' - ' + t1),
fontsize=8)
# if plotting a specific time range, plot deployment lines only for those deployments
if type(start_time) == dt.datetime:
for e in list(np.unique(vinfo['deployments'])):
etime = dend_times[int(e) - 1]
ax.axvline(x=etime, color='b', linestyle='--', linewidth=.6)
else:
for etime in dend_times:
ax.axvline(x=etime, color='b', linestyle='--', linewidth=.6)
pf.save_fig(save_dir, sname)
else:
# Plot all data
fig, ax = pf.plot_timeseries_all(x_nonan_nofv, y_nonan_nofv, sv, sv_units, stdev=None)
ax.set_title((r + '\nDeployments: ' + str(plt_deploy) + '\n' + t0 + ' - ' + t1),
fontsize=8)
# if plotting a specific time range, plot deployment lines only for those deployments
if type(start_time) == dt.datetime:
# for e in list(np.unique(vinfo['deployments'])):
# etime = dend_times[int(e) - 1]
# ax.axvline(x=etime, color='b', linestyle='--', linewidth=.6)
etime = dend_times[int(list(np.unique(vinfo['deployments']))[0]) - 1]
ax.axvline(x=etime, color='b', linestyle='--', linewidth=.6)
else:
for etime in dend_times:
ax.axvline(x=etime, color='b', linestyle='--', linewidth=.6)
# if not any(e is None for e in [global_min, global_max]):
# ax.axhline(y=global_min, color='r', linestyle='--', linewidth=.6)
# ax.axhline(y=global_max, color='r', linestyle='--', linewidth=.6)
# else:
# maxpoint = x[np.argmax(y_nonan_nofv)], max(y_nonan_nofv)
# ax.annotate('No Global Ranges', size=8,
# xy=maxpoint, xytext=(5, 5), textcoords='offset points')
pf.save_fig(save_dir, sname)
# Plot data with outliers removed
fig, ax = pf.plot_timeseries_all(x_nonan_nofv_nE_nogr, y_nonan_nofv_nE_nogr, sv, sv_units,
stdev=5)
ax.set_title((r + '\nDeployments: ' + str(plt_deploy) + '\n' + t0 + ' - ' + t1),
fontsize=8)
# if plotting a specific time range, plot deployment lines only for those deployments
if type(start_time) == dt.datetime:
# for e in list(np.unique(vinfo['deployments'])):
# etime = dend_times[int(e) - 1]
# ax.axvline(x=etime, color='b', linestyle='--', linewidth=.6)
etime = dend_times[int(list(np.unique(vinfo['deployments']))[0]) - 1]
ax.axvline(x=etime, color='b', linestyle='--', linewidth=.6)
else:
for etime in dend_times:
ax.axvline(x=etime, color='b', linestyle='--', linewidth=.6)
# if not any(e is None for e in [global_min, global_max]):
# ax.axhline(y=global_min, color='r', linestyle='--', linewidth=.6)
# ax.axhline(y=global_max, color='r', linestyle='--', linewidth=.6)
# else:
# maxpoint = x[np.argmax(y_nonan_nofv_nE_nogr)], max(y_nonan_nofv_nE_nogr)
# ax.annotate('No Global Ranges', size=8,
# xy=maxpoint, xytext=(5, 5), textcoords='offset points')
sfile = '_'.join((sname, 'rmoutliers'))
pf.save_fig(save_dir, sfile)