def get_vcm(self, mask):
# mask = 'cal333+cal05+cal20+cal80+csat' for instance
if '+' in mask:
names = mask.split('+')
to_read = [name for name in names if name not in self.data]
ds = da.read_nc(self.filename, to_read, axis='tai_time', verbose=self.verbose)
for name in to_read:
self.data[name] = ds[name].values
if 'csat' in names:
# negative data can happen e.g. for csat when there are no files.
# it does *not* happen when the are no colocated profile, as far as I know.
# need to do sthing better than that ?
self.data['csat'] = np.clip(self.data['csat'], 0, 3)
output = self.data[names[0]]
for name in names[1:]:
output += self.data[name]
else:
if mask not in self.data:
self.data[mask] = da.read_nc(self.filename, mask, axis='tai_time').values
if 'csat' in mask:
self.data[mask] = np.clip(self.data[mask], 0, 3)
output = self.data[mask]
output = np.clip(output, 0, 3)
return output
def test_format(dim_array, tmpdir):
fname = tmpdir.join("test.nc").strpath # have test.nc in some temporary directory
a = DimArray([1,2], dims=['xx0'])
b = DimArray([3.,4.,5.], dims=['xx1'])
a.write_nc(fname,"a", mode='w')
b.write_nc(fname,"b", mode='a')
# b.write_nc(fname.replace('.nc','netcdf3.nc'),name="b", mode='w', format='NETCDF3_CLASSIC')
ds = da.Dataset([('a',a),('b',b)])
# NETCDF3_CLASSIC
ds.write_nc(fname.replace('.nc','netcdf3.nc'), mode='w', format='NETCDF3_CLASSIC')
dscheck = da.read_nc(fname.replace('.nc','netcdf3.nc'))
assert_equal_datasets(ds, dscheck)
# # NETCDF3_64bit
# ds.write_nc(fname.replace('.nc','netcdf3_64b.nc'), mode='w', format='NETCDF3_64BIT')
# dscheck = da.read_nc(fname.replace('.nc','netcdf3_64b.nc'))
# assert_equal_datasets(ds, dscheck)
data = read_nc(fname)
assert(np.all(data['a'] == a))
assert(np.all(data['b'] == b))
ds = da.Dataset(a=a, b=b)
for k in ds:
assert(np.all(ds[k] == data[k]))
def my_read_vcm(f=f, verbose=False):
filename = f
lon = da.read_nc(filename, 'lon', verbose=verbose).values
lat = da.read_nc(filename, 'lat', verbose=verbose).values
data = da.Dataset()
data['cal333'] = da.read_nc(filename, 'cal333', verbose=verbose)
altitude = data['cal333'].altitude
def main(window):
window = int(window)
years = range(2006, 2015)
fullvcm = []
fullnprof = []
for year in years:
mask = 'out.{:02d}/{:04d}/*.nc4'.format(window, year)
print mask
try:
vcm = da.read_nc(mask, vcm_name, axis='file')
except ValueError:
print 'No monthlies for {:04d}, skipping'.format(year)
continue
# vcm.reset_axis(filename_to_datetime, 'file')
nprof = da.read_nc(mask, 'nprof', axis='file')
# nprof.reset_axis(filename_to_datetime, 'file')
fullvcm.append(vcm)
fullnprof.append(nprof)
vcm = da.concatenate(fullvcm, axis='file')
nprof = da.concatenate(fullnprof, axis='file')
print vcm, nprof
np.savez('series_%d.npz' % window,
vcm=vcm,
nprof=nprof,
altmin=vcm.labels[1],
time=vcm.labels[0],
lon=vcm.labels[2])
def my_read_vcm(f=f, verbose=False):
filename = f
lon = da.read_nc(filename, 'lon', verbose=verbose).values
lat = da.read_nc(filename, 'lat', verbose=verbose).values
data = da.Dataset()
data['cal333'] = da.read_nc(filename, 'cal333', verbose=verbose)
altitude = data['cal333'].altitude
def sum_arrays_from_files(filemask, array_names=None):
if array_names is None:
datasets = da.read_nc(filemask, axis='day')
else:
datasets = da.read_nc(filemask, array_names, axis='day')
datasets = datasets.sum(axis='day')
return datasets
def main(mask='out/200607/*nc4'):
dset = da.read_nc(mask, ['lat', 'cloudpts'], axis='tai_time')
npts = dset['cloudpts']
lat = dset['lat']
h_cprof, xx = np.histogram(lat, latbins, weights=1. * (npts > 0))
h_nprof, xx = np.histogram(lat, latbins)
fraction = h_cprof / (h_nprof)
plt.figure(figsize=[10,3])
plt.plot(latbins[:-1], 100. * fraction, lw=0.5)
plt.grid()
plt.xlabel('Latitude')
plt.ylabel('Percents')
plt.title('Fraction of cloudsat-only cloudy profiles')
npts, xx = np.histogram(lat, latbins, weights = npts)
npts_per_prof = 1. * npts / (h_cprof *3)
plt.figure(figsize=[10,3])
plt.plot(latbins[:-1], npts_per_prof, lw=0.5)
plt.grid()
plt.xlabel('Latitude')
plt.title('Number of cloudy points in cloudsat-only cloudy profiles')
plt.show()
def gather(mask):
import glob
flist = glob.glob(mask)
for f in flist:
print f
dset = da.read_nc(f, ["csat", "lat", "cloudpts"])
csat = dset["csat"].values
lat = dset["lat"].values
altitude = dset["csat"].altitude
idx = dset["cloudpts"].values > 0
del dset
cpts = dict()
nprof = dict()
for l in lats:
idx1 = np.where((lat >= lats[l][0]) & (lat < lats[l][1]))[0]
idx2 = np.where((lat >= -lats[l][1]) & (lat < -lats[l][0]))[0]
idx = np.concatenate([idx1, idx2])
if l in cpts:
nprof[l] = nprof[l] + idx.shape[0]
cpts[l] = cpts[l] + np.take(csat, idx, axis=0).sum(axis=0)
else:
nprof[l] = np.sum(idx)
cpts[l] = np.take(csat, idx, axis=0).sum(axis=0)
cprofl = dict()
for l in lats:
cprofl[l] = 100.0 * cpts[l] / nprof[l]
return cprofl, altitude
def gather(mask):
import glob
flist = glob.glob(mask)
for f in flist:
print f
dset = da.read_nc(f, ['csat', 'lat', 'cloudpts'])
csat = dset['csat'].values
lat = dset['lat'].values
altitude = dset['csat'].altitude
idx = (dset['cloudpts'].values > 0)
del dset
cpts = dict()
nprof = dict()
for l in lats:
idx1 = np.where((lat >= lats[l][0]) & (lat < lats[l][1]))[0]
idx2 = np.where((lat >= -lats[l][1]) & (lat < -lats[l][0]))[0]
idx = np.concatenate([idx1, idx2])
if l in cpts:
nprof[l] = nprof[l] + idx.shape[0]
cpts[l] = cpts[l] + np.take(csat, idx, axis=0).sum(axis=0)
else:
nprof[l] = np.sum(idx)
cpts[l] = np.take(csat, idx, axis=0).sum(axis=0)
cprofl = dict()
for l in lats:
cprofl[l] = 100. * cpts[l] / nprof[l]
return cprofl, altitude
def aggregate_arrays_from_files(files, array_name, summed_along=None):
aggregated = None
files.sort()
prevmax = 0
for f in files:
data = da.read_nc(f)
if array_name not in data:
continue
array = data[array_name]
if summed_along is not None:
array = array.sum(axis=summed_along)
if aggregated is None:
aggregated = 1. * array
else:
aggregated += array
if aggregated.max() < prevmax:
print 'PROBLEME !'
print 'Previous maximum = ', prevmax, ', current max = ', aggregated.max()
return aggregated
def show_file(filename, title):
data = da.read_nc(filename)
vcm05 = data['vcm_cal333']
vcm_lonlat = 1. * vcm05.sum(axis='altitude') / data['nprof']
pcolor_vcm(vcm_lonlat, title)
def compound_precip_temp_index(combinations, out_file):
"""
Not documented yet
"""
out = {}
for name, conditions in combinations.items():
conds = []
description = []
for condition in conditions:
nc = da.read_nc(condition[0])
conds.append(nc[condition[1]].squeeze())
description.append(nc[condition[1]].description)
compound_state = conds[0].copy()
compound_state[:] = False
for cond in conds:
compound_state += cond
compound_state /= len(conds)
out[name] = da.DimArray(np.array(compound_state.values, dtype=np.byte),
axes=compound_state.axes,
dims=compound_state.dims,
dtype=np.byte)
out[name].description = ' AND '.join(description)
da.Dataset(out).write_nc(out_file)
def main(mask='out/200607/*nc4'):
dset = da.read_nc(mask, ['lat', 'cloudpts'], axis='tai_time')
npts = dset['cloudpts']
lat = dset['lat']
h_cprof, xx = np.histogram(lat, latbins, weights=1. * (npts > 0))
h_nprof, xx = np.histogram(lat, latbins)
fraction = h_cprof / (h_nprof)
plt.figure(figsize=[10, 3])
plt.plot(latbins[:-1], 100. * fraction, lw=0.5)
plt.grid()
plt.xlabel('Latitude')
plt.ylabel('Percents')
plt.title('Fraction of cloudsat-only cloudy profiles')
npts, xx = np.histogram(lat, latbins, weights=npts)
npts_per_prof = 1. * npts / (h_cprof * 3)
plt.figure(figsize=[10, 3])
plt.plot(latbins[:-1], npts_per_prof, lw=0.5)
plt.grid()
plt.xlabel('Latitude')
plt.title('Number of cloudy points in cloudsat-only cloudy profiles')
plt.show()
def main(mask='out/200607/*nc4'):
dset = da.read_nc(mask, ['lon', 'lat', 'cloudpts'], axis='tai_time')
cloudy = 1 * (dset['cloudpts'] > 0)
h, xx, yy = np.histogram2d(dset['lon'].values, dset['lat'].values, bins=[lonbins, latbins], weights=cloudy)
nprof, xx, yy = np.histogram2d(dset['lon'].values, dset['lat'].values, bins=[lonbins, latbins])
map_show(lonbins, latbins, h, nprof)
def gather_info_track(self, overwrite=False):
out_file = self._working_dir + 'surrounding_info.nc'
if overwrite and os.path.isfile(out_file):
os.system('rm ' + out_file)
elif overwrite == False and os.path.isfile(out_file):
self._track_info = da.read_nc(out_file)
return self._track_info
track_info = {}
for id_, track in self._tcs.items():
track = track[np.isfinite(track[:, 't']), :]
info = np.zeros([
6, track.shape[0], self._win2 * 2 + 1, self._win2 * 2 + 1
]) * np.nan
for i, p in enumerate(track.values.tolist()):
box_2 = [
int(bb) for bb in self.get_box(p[1], p[2], self._win2)
]
info[0, i,
abs(p[1] - box_2[0] - 12):box_2[1] - p[1] + 12,
abs(p[2] - box_2[2] - 12):box_2[3] - p[2] +
12] = self._VO[int(p[0]), box_2[0]:box_2[1],
box_2[2]:box_2[3]]
info[1, i,
abs(p[1] - box_2[0] - 12):box_2[1] - p[1] + 12,
abs(p[2] - box_2[2] - 12):box_2[3] - p[2] +
12] = self._MSLP[int(p[0]), box_2[0]:box_2[1],
box_2[2]:box_2[3]]
info[2, i,
abs(p[1] - box_2[0] - 12):box_2[1] - p[1] + 12,
abs(p[2] - box_2[2] - 12):box_2[3] - p[2] +
12] = self._Wind10[int(p[0]), box_2[0]:box_2[1],
box_2[2]:box_2[3]]
if self._SST is not None:
info[3, i,
abs(p[1] - box_2[0] - 12):box_2[1] - p[1] + 12,
abs(p[2] - box_2[2] - 12):box_2[3] - p[2] +
12] = self._SST[int(p[0]), box_2[0]:box_2[1],
box_2[2]:box_2[3]]
if self._T is not None:
info[4, i,
abs(p[1] - box_2[0] - 12):box_2[1] - p[1] + 12,
abs(p[2] - box_2[2] - 12):box_2[3] - p[2] +
12] = self._T[int(p[0]), 0, box_2[0]:box_2[1],
box_2[2]:box_2[3]]
info[5, i,
abs(p[1] - box_2[0] - 12):box_2[1] - p[1] + 12,
abs(p[2] - box_2[2] - 12):box_2[3] - p[2] +
12] = self._T[int(p[0]), 1, box_2[0]:box_2[1],
box_2[2]:box_2[3]]
track_info[str(id_)] = da.DimArray(
info,
axes=[['VO', 'MSLP', 'Wind10', 'SST', 'T850', 'T500'],
range(len(track.time)),
range(self._win2 * 2 + 1),
range(self._win2 * 2 + 1)],
dims=['time_id', 'variable', 'lat', 'lon'])
self._track_info = da.Dataset(track_info)
self._track_info.write_nc(out_file, mode='w')
def precip_to_index(
in_file,
out_file,
var_name='pr',
unit_multiplier=1,
states={
'dry': {
'mod': 'below',
'threshold': 1
},
'wet': {
'mod': 'above',
'threshold': 1
},
'5mm': {
'mod': 'above',
'threshold': 5
},
'10mm': {
'mod': 'above',
'threshold': 10
}
}):
"""
Classifies daily precipitation into 'wet' and 'dry' days based on a `threshold`
Parameters
----------
anom_file: str
filepath of a daily precipitation file. The variable that is read in can be specified with `var_name`.
out_file: str
filepath of a state file
var_name: str
name of the variable read in `anom_file`
threshold: float,default=0.5
threshold used to differentiate between wet and dry days
unit_multiplier: float,default=1
factor to multiply daily precipiation with to get mm as units
overwrite: bool
overwrites existing files
"""
nc = da.read_nc(in_file)
pr = nc[var_name].squeeze() * unit_multiplier
out = {}
for name, state_dict in states.items():
state = nc[var_name].squeeze().copy()
state[:] = False
if state_dict['mod'] == 'above':
state[pr >= state_dict['threshold']] = True
if state_dict['mod'] == 'below':
state[pr <= state_dict['threshold']] = True
out[name] = da.DimArray(np.array(state.values, dtype=np.byte),
axes=state.axes,
dims=state.dims,
dtype=np.byte)
out[name].description = 'days with precipitation ' + state_dict[
'mod'] + ' ' + str(state_dict['threshold']) + 'mm'
da.Dataset(out).write_nc(out_file)
def dayfiles_to_windows(files, outfile):
window_sum = da.read_nc(files, axis='day', verbose=False)
window_sum.sum(axis='day')
#print 'Saving ' + outfile
#print ' cf = ', 100. * np.sum(window_sum['cal333+cal05+cal20+cal80+csat_cprof']) / np.sum(window_sum['nprof'])
cf = 100. * np.sum(window_sum['cal333+cal05+cal20+cal80+csat_cprof'])/np.sum(window_sum['nprof'])
if cf < 60:
print 'WARNING: cf < 60%'
window_sum.write_nc(outfile, 'w')
def test_redundant_axis(tmpdir):
# see test in test_dataset.py
ds = da.Dataset()
ds["myaxis"] = da.DimArray([10,20,30], da.Axis([10,20,30], 'myaxis'))
assert list(ds.keys()) == ["myaxis"]
assert ds.dims == ("myaxis",)
fname = tmpdir.join("test_redundant_axis.nc").strpath # have test.nc in some temporary directory
ds.write_nc(fname)
# read whole dataset: variable not counted as variable
ds = da.read_nc(fname)
assert list(ds.keys()) == []
assert ds.dims == ("myaxis",)
# specify dimension variable
ds = da.read_nc(fname, ["myaxis"])
assert list(ds.keys()) == ["myaxis"]
assert ds.dims == ("myaxis",)
def __init__(self, filename, verbose=True):
self.filename = filename
self.verbose = verbose
dimarrays = da.read_nc(filename, ['lon', 'lat', 'cal333'], axis='tai_time', verbose=verbose)
self.altitude = dimarrays['cal333'].altitude
self.lon = dimarrays['lon'].values
self.lat = dimarrays['lat'].values
self.data = {'cal333':dimarrays['cal333'].values}
self.time = dimarrays['cal333'].tai_time
def detect_dieng(self,
overwrite=False,
dis_VO_max=8,
min_number_cells=6,
thr_VO=1 * 10**(-5),
thr_RH=50):
out_file = self._working_dir + str(
self._identifier) + '_detected_positions.nc'
if overwrite and os.path.isfile(out_file):
os.system('rm ' + out_file)
elif overwrite == False and os.path.isfile(out_file):
self._detected = da.read_nc(out_file)['detected']
return self._detected
# convert distances from degrees into grid-cells
dis_VO_max = self.degree_to_step(dis_VO_max)
detect = np.array([[np.nan] * 6])
print('detecting\n10------50-------100')
for t, progress in zip(
self._time_i,
np.array([['-'] + [''] * (len(self._time_i) / 20 + 1)] *
20).flatten()[0:len(self._time_i)]):
sys.stdout.write(progress)
sys.stdout.flush()
coords = peak_local_max(self._VO[t, :, :],
min_distance=int(dis_VO_max))
#print(coords)
for y_, x_ in zip(coords[:, 0], coords[:, 1]):
if self._VO[t, y_, x_] > thr_VO:
yy, xx = self.find_group(field=self._VO[t, :, :],
y=y_,
x=x_,
thresh=thr_VO)
if len(yy) >= min_number_cells:
if self._RH[t, y_,
x_] >= thr_RH and self._lat[y_] < 35:
#y_,x_ = sum(yy) / len(yy), sum(xx) / len(yy)
tmp = [
t, y_, x_, self._VO[t, y_, x_], self._RH[t, y_,
x_],
len(yy)
]
detect = np.concatenate((detect, np.array([tmp])))
self._detected = da.DimArray(
np.array(detect[1:, :]),
axes=[
range(detect.shape[0] - 1),
['t', 'y', 'x', 'VO', 'RH', 'members']
],
dims=['ID', 'z'])
da.Dataset({'detected': self._detected}).write_nc(out_file, mode='w')
print('\ndone')
return self._detected
def window_cloud_ceiling(f):
dset = da.read_nc(f, ["cal333+cal05+cal20+cal80+csat", "cal333+cal05+cal20+cal80+csat_cprof", "nprof"])
vcm, cprof, nprof = (
dset["cal333+cal05+cal20+cal80+csat"],
dset["cal333+cal05+cal20+cal80+csat_cprof"],
dset["nprof"],
)
cf_lat, cf_lat2 = compute_cf(vcm, cprof, nprof)
ceiling = tropic_width.cloud_cover_top(vcm.altitude, cf_lat)
return ceiling, vcm.lat, cprof, nprof
def show_file(input, title):
data = da.read_nc(input)
vcm_prof = data['cal333+cal05+cal20+cal80+csat']
nprof = data['cal333+cal05+cal20+cal80+csat_cprof']
cf_lat = 1. * vcm_prof.values.T / nprof.values
cf_lat = cf_lat.T
cf_lat = np.ma.masked_invalid(cf_lat)
pcolor_zonal(vcm_prof.labels[0], vcm_prof.labels[1], cf_lat, 'Cloud fraction ' + title)
def window_cloud_ceiling(f):
dset = da.read_nc(f, [
'cal333+cal05+cal20+cal80+csat', 'cal333+cal05+cal20+cal80+csat_cprof',
'nprof'
])
vcm, cprof, nprof = dset['cal333+cal05+cal20+cal80+csat'], dset[
'cal333+cal05+cal20+cal80+csat_cprof'], dset['nprof']
cf_lat, cf_lat2 = compute_cf(vcm, cprof, nprof)
ceiling = tropic_width.cloud_cover_top(vcm.altitude, cf_lat)
return ceiling, vcm.lat, cprof, nprof
def main(mask='out/200607/*.nc4'):
print mask
files = glob.glob(mask)
print len(files)
for f in files:
d = da.read_nc(f)
print f
for n in 'cal333+cal05+cal20+cal80+csat_cprof', 'cal333+cal05+cal20+cal80_cprof':
cf = 100. * d[n].sum() / d['nprof'].sum()
print ' ', n, d['nprof'].sum(), d[n].sum(), cf
def dayfiles_to_windows(files, outfile):
window_sum = da.read_nc(files, axis='day', verbose=False)
window_sum.sum(axis='day')
#print 'Saving ' + outfile
#print ' cf = ', 100. * np.sum(window_sum['cal333+cal05+cal20+cal80+csat_cprof']) / np.sum(window_sum['nprof'])
cf = 100. * np.sum(
window_sum['cal333+cal05+cal20+cal80+csat_cprof']) / np.sum(
window_sum['nprof'])
if cf < 60:
print 'WARNING: cf < 60%'
window_sum.write_nc(outfile, 'w')
def main(mask='out/200607/*.nc4'):
print mask
files = glob.glob(mask)
print len(files)
for f in files:
d = da.read_nc(f)
print f
for n in 'cal333+cal05+cal20+cal80+csat_cprof', 'cal333+cal05+cal20+cal80_cprof':
cf = 100. * d[n].sum() / d['nprof'].sum()
print ' ', n, d['nprof'].sum(), d[n].sum(), cf
def test_standalone_axis(tmpdir):
# see test in test_dataset.py
ds = da.Dataset()
ds.axes.append(da.Axis([10,20,30], 'myaxis'))
assert list(ds.keys()) == []
assert ds.dims == ("myaxis",)
fname = tmpdir.join("test_standalone_axis.nc").strpath # have test.nc in some temporary directory
ds.write_nc(fname)
# read again
ds = da.read_nc(fname)
assert list(ds.keys()) == []
assert ds.dims == ("myaxis",)
def temp_anomaly_to_ind_old(anom_file,
out_file,
var_name='tas',
seasons={
'MAM': [3, 4, 5],
'JJA': [6, 7, 8],
'SON': [9, 10, 11],
'DJF': [12, 1, 2]
},
overwrite=True):
"""
Classifies daily temperature anomalies into 'cold' and 'warm' days using the season and grid-cell specific median as threshold
Parameters
----------
anom_file: str
filepath of a temperature anomalies file. The variable that is read in can be specified with `var_name`.
out_file: str
filepath of a state file
var_name: str
name of the variable read in `anom_file`
seasons: dict, default=`{'MAM':{'months':[3,4,5],'index':0}, 'JJA':{'months':[6,7,8],'index':1}, 'SON':{'months':[9,10,11],'index':2}, 'DJF':{'months':[12,1,2],'index':3}}``
dictionnary used to cluster detected periods into seasons. If no seasonal analysis is required use `seasons={'year':{'months':range(12),'index':0}}`
overwrite: bool
overwrites existing files
"""
nc = da.read_nc(anom_file)
if 'calendar' in nc['time'].attrs.keys():
datevar = num2date(nc['time'].values,
units=nc['time'].units,
calendar=nc['time'].calendar)
else:
datevar = num2date(nc['time'].values, units=nc['time'].units)
month = np.array([date.month for date in datevar])
anom = nc[var_name].squeeze()
state = nc[var_name].squeeze().copy() * np.nan
for season in seasons.keys():
days_in_season = np.where((month == seasons[season][0])
| (month == seasons[season][1])
| (month == seasons[season][2]))[0]
seasonal_median = np.nanmedian(anom.ix[days_in_season, :, :], axis=0)
anom.ix[days_in_season, :, :] -= seasonal_median
state[anom >= 0] = 1
state[anom < 0] = -1
if overwrite: os.system('rm ' + out_file)
state.description = 'daily anomalies - seasonal medain of daily anomalies at grid cell level. positive anomalies -> 1 negative anomalies -> -1'
da.Dataset({'state': state}).write_nc(out_file)
def main(mask='out/200607/*nc4'):
dset = da.read_nc(mask, ['cloudpts'], axis='tai_time')
cpts = dset['cloudpts']
cpts = cpts/3.
print 'Range of cloudy points in cloudsat-only cloudy profiles : ', np.min(cpts.values), np.max(cpts.values)
plt.figure()
cpts.plot(lw=0.5)
plt.figure()
plt.hist(cpts[cpts>0].values, 20)
plt.show()
def main(window):
window = int(window)
years = range(2006,2015)
fullvcm = []
fullnprof = []
for year in years:
mask = 'out.{:02d}/{:04d}/*.nc4'.format(window, year)
print mask
try:
vcm = da.read_nc(mask, vcm_name, axis='file')
except ValueError:
print 'No monthlies for {:04d}, skipping'.format(year)
continue
# vcm.reset_axis(filename_to_datetime, 'file')
nprof = da.read_nc(mask, 'nprof', axis='file')
# nprof.reset_axis(filename_to_datetime, 'file')
fullvcm.append(vcm)
fullnprof.append(nprof)
vcm = da.concatenate(fullvcm, axis='file')
nprof = da.concatenate(fullnprof, axis='file')
print vcm, nprof
np.savez('series_%d.npz' % window, vcm=vcm, nprof=nprof, altmin=vcm.labels[1], time=vcm.labels[0], lon=vcm.labels[2])
def month_tropic_width(f):
dset = da.read_nc(["cal333+cal05+cal20+cal80+csat", "cal333+cal05+cal20+cal80+csat_cprof"])
vcm = dset["cal333+cal05+cal20+cal80+csat"]
nprof = dset["nprof"]
cf_lat = np.ma.masked_invalid(1.0 * vcm.values.T / nprof.values)
cf_lat = cf_lat.T
tropic_range = dict()
for vcm_min in vcm_mins:
tropic_range[vcm_min] = tropic_width.tropic_width3(vcm.lat, vcm.altitude, cf_lat, vcm_min)
return tropic_range
def cf_zonal(filename):
data = da.read_nc(filename)
try:
vcm_prof = data['cal333+cal05+cal20+cal80+csat']
nprof = data['cal333+cal05+cal20+cal80+csat_cprof']
except KeyError:
return None, None, None
cf_lat = 1. * vcm_prof.values.T / nprof.values
cf_lat = cf_lat.T
cf_lat = np.ma.masked_invalid(cf_lat)
return vcm_prof.labels[0], vcm_prof.labels[1], cf_lat
def cf_zonal(filename):
data = da.read_nc(filename)
try:
vcm_prof = data['cal333+cal05+cal20+cal80+csat']
nprof = data['cal333+cal05+cal20+cal80+csat_cprof']
except KeyError:
return None, None, None
cf_lat = 1. * vcm_prof.values.T / nprof.values
cf_lat = cf_lat.T
cf_lat = np.ma.masked_invalid(cf_lat)
return vcm_prof.labels[0], vcm_prof.labels[1], cf_lat
def main(mask='out/200607/*nc4'):
dset = da.read_nc(mask, ['cloudpts'], axis='tai_time')
cpts = dset['cloudpts']
cpts = cpts / 3.
print 'Range of cloudy points in cloudsat-only cloudy profiles : ', np.min(
cpts.values), np.max(cpts.values)
plt.figure()
cpts.plot(lw=0.5)
plt.figure()
plt.hist(cpts[cpts > 0].values, 20)
plt.show()
def ttest_roundtrip_datetime(axis, tmpdir):
a = da.DimArray(np.arange(axis.size), axes=[axis])
# write
fname = tmpdir.join("test_datetime.nc").strpath # have test.nc in some temporary directory
a.write_nc(fname, 'myarray') # write
# read-back
actual = da.read_nc(fname, 'myarray')
if axis.dtype.kind == "M":
pass
# TODO: convert axis to datetime
else:
assert_equal_dimarrays(actual, expected=a)
def month_tropic_width(f):
dset = da.read_nc([
'cal333+cal05+cal20+cal80+csat', 'cal333+cal05+cal20+cal80+csat_cprof'
])
vcm = dset['cal333+cal05+cal20+cal80+csat']
nprof = dset['nprof']
cf_lat = np.ma.masked_invalid(1. * vcm.values.T / nprof.values)
cf_lat = cf_lat.T
tropic_range = dict()
for vcm_min in vcm_mins:
tropic_range[vcm_min] = tropic_width.tropic_width3(
vcm.lat, vcm.altitude, cf_lat, vcm_min)
return tropic_range
def setUp(self):
ncfile = da.get_ncfile('greenland_velocity.nc')
try:
self.grl = da.read_nc(ncfile)
except:
self.grl = None
warnings.warn('could not read netCDF: no test_coords')
return
grl = self.grl
self.vmag = grl['surfvelmag']
self.vx = grl['surfvelx']
self.vy = grl['surfvely']
self.lon = grl['lon']
self.lat = grl['lat']
self.mapping = grl['mapping']._metadata()
def get_atl_tcs(file='/Users/peterpfleiderer/Projects/tropical_cyclones/data/Allstorms.ibtracs_all.v03r10.nc'):
TC=da.read_nc(file)
# select north atlantic basin
tc_sel=TC.ix[TC['basin'][:,0]==0]
# select time period
tc_sel=tc_sel.ix[tc_sel['season']>=1900,:]
# select main tracks
tc_sel=tc_sel.ix[tc_sel['track_type']==0,:]
tc_lat=tc_sel['lat_for_mapping']
tc_lon=tc_sel['lon_for_mapping']
# tc_sel=tc_sel.ix[np.where(tc_sel_cat>0)]
tmp_time=tc_sel['source_time']
tc_year,tc_month,tc_yrmn,tc_yrFr=tmp_time.copy(),tmp_time.copy(),tmp_time.copy(),tmp_time.copy()
for storm in tmp_time.storm:
for tt in tmp_time.time:
if np.isfinite(tmp_time[storm,tt]):
datevar=num2date(tmp_time[storm,tt],units = tmp_time.units)
tc_year[storm,tt]=datevar.year
tc_month[storm,tt]=datevar.month
tc_yrmn[storm,tt]=datevar.year+float(datevar.month-1)/12.
tc_yrFr[storm,tt]=toYearFraction(datevar)
# remove extratropical time steps (and distrubances)
tc_wind=tc_sel['source_wind'].ix[:,:,0]
tc_wind.ix[tc_sel['nature_for_mapping']!=2]==np.nan
tc_wind.ix[tc_sel['nature_for_mapping']!=3]==np.nan
tc_pres=tc_sel['source_pres'].ix[:,:,0]
tc_pres.ix[tc_sel['nature_for_mapping']!=2]==np.nan
tc_pres.ix[tc_sel['nature_for_mapping']!=3]==np.nan
ds=da.Dataset({
'wind':tc_wind,
'mslp':tc_pres,
'lat':tc_lat,
'lon':tc_lon,
'time':tc_sel['source_time'],
'year':tc_year,
'month':tc_month,
'yrmn':tc_yrmn,
'yrFr':tc_yrFr,
})
return(ds)
def integrate(self, years, out_dir=None, **kwargs):
"""Run the model as it were from command-line
years : float
years of simulation
out_dir : str, optional
provide an output directory for the simulation
(otherwise a new directory will be created)
**kwargs : passed to run_model
This includes 'dt' (time step etc...)
"""
if out_dir:
self.out_dir = out_dir
else:
self.out_dir = self._get_out_dir(create=True) # new out directory
self._instance_directories.append(self.out_dir)
self._class_directories.append(self.out_dir)
# write glacier state to disk
in_file = self._get_in_file()
self.to_dataset().write_nc(in_file)
# and use it both as a restart and file and reference geometry file
res = run_model(years,
params=self.params,
out_dir=self.out_dir,
in_file=in_file,
rst_file=in_file,
**kwargs)
if res != 0:
warnings.warn("result value is not 0. Problem during integration?")
return None
# read results from restart file
ds = da.read_nc(os.path.join(self.out_dir, 'restart.nc'))
gl = self.from_dataset(ds)
# read results from output file, whose geometry extends further
# ds = self.read_output(os.path.join(self.out_dir, 'output.nc'))
gl.params = self.params # copy params
return gl
def month_tropic_width(monthfile):
try:
data = da.read_nc(monthfile)
except:
return None
try:
vcm = 1. * data['cal333+cal05+cal20+cal80+csat']
nprof = 1. * data['cal333+cal05+cal20+cal80+csat_cprof']
except KeyError:
return None
cf_lat = vcm.values.T / nprof.values
cf_lat = cf_lat.T
cf_lat = np.ma.masked_invalid(cf_lat)
tropic_range = dict()
for vcm_min in vcm_mins:
tropic_range[vcm_min] = tropic_width3(vcm.labels[0], vcm.labels[1], cf_lat, vcm_min=vcm_min)
return tropic_range
def aggregate_arrays_from_files(files, array_name, summed_along=None, bounds=None):
aggregated = None
files.sort()
for f in files:
data = da.read_nc(f)
if array_name not in data:
continue
array = data[array_name]
if summed_along is not None:
array = array.sum(axis=summed_along)
if aggregated is None:
aggregated = 1. * array
else:
aggregated += array
print aggregated.max()
return aggregated
def month_tropic_width(monthfile):
try:
data = da.read_nc(monthfile)
except:
return None
try:
vcm = 1. * data['cal333+cal05+cal20+cal80+csat']
nprof = 1. * data['cal333+cal05+cal20+cal80+csat_cprof']
except KeyError:
return None
cf_lat = vcm.values.T / nprof.values
cf_lat = cf_lat.T
cf_lat = np.ma.masked_invalid(cf_lat)
tropic_range = dict()
for vcm_min in vcm_mins:
tropic_range[vcm_min] = tropic_width3(vcm.labels[0],
vcm.labels[1],
cf_lat,
vcm_min=vcm_min)
return tropic_range
import os,sys,glob,time,collections,gc,itertools,timeit
import numpy as np
from netCDF4 import Dataset,netcdftime,num2date
import dimarray as da
sys.path.append('/Users/peterpfleiderer/Documents/Projects/HAPPI_persistence/persistence_in_models/')
import cython_function
sys.path.append('/global/homes/p/pepflei/weather_persistence/')
sys.path.append('/Users/peterpfleiderer/Documents/Projects/weather_persistence/')
from persistence_functions import *
period=da.read_nc('data/tests/tas_Aday_ECHAM6-3-LR_Plus20-Future_CMIP5-MMM-est1_v2-0_run010_period.nc')
tas=da.read_nc('data/tests/tas_Aday_ECHAM6-3-LR_Plus20-Future_CMIP5-MMM-est1_v2-0_run010.nc')['tas']
mask=da.read_nc('data/tests/landmask_96x192_NA-1.nc')['landmask']
mask[mask!=1]=0
mask=np.asarray(mask,np.int32)
# land_yx=[(period.lat[np.argmin(abs(lat-period.lat))],period.lon[np.argmin(abs(lon-period.lon))]) for lat,lon in itertools.product(mask.lat,mask.lon) if mask[lat,lon]==1]
# coord=np.array([(np.argmin(abs(lat-period.lat)),np.argmin(abs(lon-period.lon))) for lat,lon in itertools.product(mask.lat,mask.lon) if mask[lat,lon]==1],np.int32)
# Ni=len(period.period_id)
# Ny=len(period.lat)
# Nx=len(period.lon)
# periods_of_interest=np.array([[i,y,x] for i,y,x in itertools.product(range(Ni),range(Ny),range(Nx)) if period['period_season'].ix[i,y,x]==1])
def period_analysis_py(ids,lats_lons):
for i,y,x in itertools.product(range(Ni),range(Ny),range(Nx)):
ll=period['period_length'][per_id,lat_lon[0],lat_lon[1]]
if ll>0 & period['period_season'][per_id,lat_lon[0],lat_lon[1]]==1:
'/p/projects/ikiimp/HAPPI/HAPPI_Peter/persistence_in_HAPPI/')
os.chdir('/p/projects/ikiimp/HAPPI/HAPPI_Peter/')
in_path = '/p/tmp/pepflei/HAPPI/raw_data/EKE/' + model + '/'
out_path = '/p/tmp/pepflei/HAPPI/raw_data/reg_merge/' + model + '/'
home_path = '/p/projects/ikiimp/HAPPI/HAPPI_Peter/persistence_in_HAPPI/'
except:
sys.path.append('/global/homes/p/pepflei/persistence_in_models/')
os.chdir('/global/homes/p/pepflei/')
working_path = '/global/cscratch1/sd/pepflei/EKE/' + model + '/'
working_path = '/global/cscratch1/sd/pepflei/EKE/' + model + '/'
home_path = '/global/homes/p/pepflei/persistence_in_models/'
import __settings
model_dict = __settings.model_dict
masks = da.read_nc('masks/srex_mask_' + model_dict[model]['grid'] + '.nc')
all_files = sorted(
glob.glob(in_path + scenario + '/monEKE*_' + scenario + '*.nc'))
big_merge = {}
big_merge['eke'] = da.read_nc(all_files[0])['eke'][:, 0:, :]
big_merge['run_id'] = da.read_nc(all_files[0])['eke'][:, 0:, :].copy()
big_merge['run_id'].values = 0
for i_run, file_name in enumerate(all_files[1:]):
print(file_name)
big_merge['eke'] = da.concatenate(
(big_merge['eke'], da.read_nc(file_name)['eke'][:, 0:, :]))
tmp = da.read_nc(file_name)['eke'][:, 0:, :].copy()
tmp.values = i_run + 1
import os, sys, glob, time, collections, gc
import numpy as np
from netCDF4 import Dataset, netcdftime, num2date
import matplotlib.pylab as plt
import dimarray as da
import itertools
import matplotlib
import pandas as pd
import seaborn as sns
sns.set()
plt.rc('font', family='Calibri')
os.chdir(
'/Users/peterpfleiderer/Documents/Projects/gmt/gmt_method_sensitivities')
gmt_cowtan = da.read_nc('../data/gmt_all_cowtan.nc')['gmt']
gmt_all = da.read_nc('data/gmt_reproducedErrors.nc')['gmt']
# select special runs
all_model_runs=[u'ACCESS1-0_r1i1p1',u'ACCESS1-3_r1i1p1',u'CCSM4_r1i1p1',u'CESM1-BGC_r1i1p1',u'CESM1-CAM5_r1i1p1',u'CMCC-CMS_r1i1p1',u'CMCC-CM_r1i1p1',u'CNRM-CM5_r1i1p1',\
u'CSIRO-Mk3-6-0_r1i1p1',u'CanESM2_r1i1p1',u'EC-EARTH_r1i1p1',u'GFDL-CM3_r1i1p1',u'GFDL-ESM2G_r1i1p1',u'GFDL-ESM2M_r1i1p1',u'GISS-E2-H-CC_r1i1p1',u'GISS-E2-H_r1i1p1',\
u'GISS-E2-R-CC_r1i1p1',u'GISS-E2-R_r1i1p1',u'HadGEM2-AO_r1i1p1',u'HadGEM2-CC_r1i1p1',u'HadGEM2-ES_r1i1p1',u'IPSL-CM5A-LR_r1i1p1',u'IPSL-CM5A-MR_r1i1p1',u'IPSL-CM5B-LR_r1i1p1',\
u'MIROC-ESM-CHEM_r1i1p1',u'MIROC-ESM_r1i1p1',u'MIROC5_r1i1p1',u'MPI-ESM-LR_r1i1p1',u'MPI-ESM-MR_r1i1p1',u'MRI-CGCM3_r1i1p1',u'MRI-ESM1_r1i1p1',u'NorESM1-ME_r1i1p1',u'NorESM1-M_r1i1p1']
# tos issue models
tos_issues = [
u'EC-EARTH_r1i1p1',
u'MIROC5_r1i1p1',
u'MRI-CGCM3_r1i1p1',
u'MRI-ESM1_r1i1p1',
import matplotlib.pyplot as plt
import seaborn as sns
import scipy.ndimage as ndimage
from shapely.geometry.polygon import Polygon
from shapely.geometry import Point
import matplotlib.ticker as mticker
import cartopy
import cartopy.crs as ccrs
os.chdir('/Users/peterpfleiderer/Projects/tropical_cyclones/')
sys.path.append('/Users/peterpfleiderer/Projects/tropical_cyclones/TC_scripts')
import TC_support ; TC_support = reload(TC_support)
if 'TC' not in globals():
TC=da.read_nc('data/Allstorms.ibtracs_all.v03r10.nc')
tc_sel=TC.ix[np.where(TC['basin'][:,0]==0)[0]]
tc_sel=tc_sel.ix[tc_sel['season']>=1979]
tc_sel=tc_sel.ix[tc_sel['season']>=1979]
tc_lat=tc_sel['lat_for_mapping']
tc_lon=tc_sel['lon_for_mapping']
tc_lon[tc_lon<0]+=360
tc_wind=tc_sel['source_wind']
tc_wind[np.isnan(tc_wind)]=-999
tc_sel_cat=np.array(TC_support.tc_cat(np.nanmin(tc_sel['source_pres'],axis=(1,2)),'pressure'))
tc_sel=tc_sel.ix[np.where(tc_sel_cat>0)]
nc=da.read_nc('data/CAR25/item16222_6hrly_inst/item16222_6hrly_inst_p014_2017-06_2017-10.nc')
lats = nc['global_latitude1'].values
lons = nc['global_longitude1'].values
'-o',
help="overwrite output files",
action="store_true")
args = parser.parse_args()
if args.overwrite:
overwrite = True
else:
overwrite = False
identifiers = [
nn.split('_')[-3]
for nn in glob.glob('../data/WAH/batch_755/region/item16222_6hrly_inst/*')
]
for style in ['contours']:
if os.path.isfile('detection/ATL/ATL_all_tracks_' + style +
'.nc') == False or overwrite:
# check for duplicates
all_tracks = {}
for identifier in identifiers:
tmp = da.read_nc('detection/ATL/' + str(identifier) +
'/track_info_' + style + '.nc')
for id_, track in tmp.items():
if id_ not in ['z', 'time']:
all_tracks[id_] = track
all_tracks = da.Dataset({'all_tracks': all_tracks})
all_tracks.write_nc('detection/ATL/ATL_all_tracks_' + style + '.nc',
mode='w')
def ncload(ncfile, variables=None, bbox=None, maxshape=None, map_var_names=None, map_dim_names=None, time_idx=None, time_dim='time', inverted_y_axis=False, dataroot=None, x=None, y=None, xdim='x', ydim='y'):
"""Standard ncload for netCDF files
Parameters
----------
map_var_name : None or dict-like : make standard variables and actual file variables names match
map_dim_name : None or dict-like : make standard dimensions and actual file dimensions names match
inverted_y_axis : deal with the case where y axis is inverted (Rignot and Mouginot, Morlighem...)
time_idx, time_dim : can be provided to extract a time slice
dataroot : provide an alternative root path for datasets
x, y : array-like : provide coordinates directly, when not present in file.
"""
ncfile = get_datafile(ncfile, dataroot)
variables, _variable = check_variables(variables)
# determine the variables to load
if map_var_names is not None:
map_var_names = map_var_names.copy() # becaause of pop
ncvariables = [map_var_names.pop(nm,nm) for nm in variables]
else:
ncvariables = variables
if map_dim_names is not None:
xnm = map_dim_names[xdim]
ynm = map_dim_names[ydim]
else:
xnm = xdim
ynm = ydim
# open the netCDF dataset
nc_ds = nc.Dataset(ncfile)
external_axes = x is not None or y is not None
if x is None:
x = nc_ds.variables[xnm]
if y is None:
y = nc_ds.variables[ynm]
# determine the indices to extract
slice_x, slice_y = get_slices_xy(xy=(x, y), bbox=bbox, maxshape=maxshape, inverted_y_axis=inverted_y_axis)
indices = {xnm:slice_x,ynm:slice_y}
if time_idx is not None:
indices[time_dim] = time_idx
# load the data using dimarray (which also copy attributes etc...)
data = da.read_nc(nc_ds, ncvariables, indices=indices, indexing='position')
# close dataset
nc_ds.close()
# in case axes were provided externally, just replace the values
if external_axes:
data.axes[xnm][:] = x[slice_x]
data.axes[ynm][:] = y[slice_y]
# rename dimensions appropriately and set metadata
if map_dim_names is not None:
if data.dims == (xnm, ynm):
data.dims = (xdim, ydim)
elif data.dims == (ynm, xnm):
data.dims = (ydim, xdim)
# unknown case? do nothing
# rename variable names
if map_var_names is not None:
data.rename_keys({ncvar:var for var, ncvar in zip(variables, ncvariables)}, inplace=True)
# only one variable
if _variable is not None:
data = data[_variable]
return data
def setup_class(cls):
cls.ds = da.read_nc(cls.ncfile)
#encoding:utf-8
# Created by V. Noel [LMD/CNRS] on 2014-07-09
import glob
import numpy as np
from datetime import datetime
import dimarray as da
d = datetime(2008,9,2)
mask = 'out/%04d%02d/vcm_%04d-%02d-%02d*.nc4' % (d.year, d.month, d.year, d.month, d.day)
print mask
files = glob.glob(mask)
for f in files:
print 'Looking in', f
d = da.read_nc(f)
lat = d['lat']
idxlat = lat.values < -60
# idxlat = (lat.values > -30) & (lat.values < 30)
alt = d['cal333'].altitude
idxalt = alt > 15
for var in 'cal333', 'cal05', 'cal20', 'cal80', 'csat':
cm = d[var].values
cm = cm[idxlat,:]
cm = cm[:,idxalt]
if np.sum(cm) > 0:
print 'high polar clouds found in ', var, np.sum(cm)
# use tmpdir fixture
#def test_ncio():
def test_ncio(tmpdir):
fname = tmpdir.join("test.nc").strpath # have test.nc in some temporary directory
a = DimArray([1,2], dims='xx0')
b = DimArray([3,4,5], dims='xx1')
a.write_nc(fname,"a", mode='w')
b.write_nc(fname,"b", mode='a')
try:
b.write_nc(fname.replace('.nc','netcdf3.nc'),"b", mode='w', format='NETCDF3_CLASSIC')
except Exception, msg:
warn("writing as NETCDF3_CLASSIC failed (known bug on 64bits systems): {msg}".format(msg=repr(msg)))
data = read_nc(fname)
assert(np.all(data['a'] == a))
assert(np.all(data['b'] == b))
ds = da.Dataset(a=a, b=b)
for k in ds:
assert(np.all(ds[k] == data[k]))
def main(**kw):
try:
test_ncio()
except RuntimeError, msg:
warn("NetCDF test failed: {}".format(msg))
if __name__ == "__main__":
main()
def main(input="test.out/200801/vcm_2008-01-01T01-30-23ZN.nc4"):
fig = plt.figure(figsize=[12, 12])
vcm = da.read_nc(input)
plot_vcms(vcm)
plt.show()
def test_debug_doc():
direc = da.get_datadir()
temp = da.read_nc(direc+'/cmip5.*.nc', 'temp', align=True, axis='model')
