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delepoullea
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Create intermediate netcdf file
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6 files changed

+352
-209
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6 files changed

+352
-209
lines changed

‎global_tracking.py‎

Lines changed: 161 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -2,65 +2,194 @@
22

33
from netCDF4 import Dataset
44
import numpy as np
5+
import logging
56

67

78
class GlobalTracking(object):
89
"""
910
1011
"""
12+
13+
VAR_DESCR = dict(
14+
time=dict(
15+
attr_name='new_time_tmp',
16+
nc_name='j1',
17+
nc_type='int32',
18+
nc_dims=('Nobs',),
19+
nc_attr=dict(
20+
long_name='Julian date',
21+
units='days',
22+
description='date of this observation',
23+
reference=2448623,
24+
reference_description="Julian date on Jan 1, 1992",
25+
)
26+
),
27+
type_cyc=dict(
28+
attr_name=None,
29+
nc_name='cyc',
30+
nc_type='byte',
31+
nc_dims=('Nobs',),
32+
nc_attr=dict(
33+
long_name='cyclonic',
34+
units='boolean',
35+
description='cyclonic -1; anti-cyclonic +1',
36+
)
37+
),
38+
lon=dict(
39+
attr_name='new_lon_tmp',
40+
nc_name='lon',
41+
nc_type='float32',
42+
nc_dims=('Nobs',),
43+
nc_attr=dict(
44+
units='deg. longitude',
45+
)
46+
),
47+
lat=dict(
48+
attr_name='new_lat_tmp',
49+
nc_name='lat',
50+
nc_type='float32',
51+
nc_dims=('Nobs',),
52+
nc_attr=dict(
53+
units='deg. latitude',
54+
)
55+
),
56+
amplitude=dict(
57+
attr_name='new_amp_tmp',
58+
nc_name='A',
59+
nc_type='float32',
60+
nc_dims=('Nobs',),
61+
nc_attr=dict(
62+
long_name='amplitude',
63+
units='cm',
64+
description='magnitude of the height difference between the '
65+
'extremum of SSH within the eddy and the SSH '
66+
'around the contour defining the eddy perimeter',
67+
)
68+
),
69+
rayon=dict(
70+
attr_name=None,
71+
nc_name='L',
72+
nc_type='float32',
73+
nc_dims=('Nobs',),
74+
nc_attr=dict(
75+
long_name='speed radius scale',
76+
units='km',
77+
description='radius of a circle whose area is equal to that '
78+
'enclosed by the contour of maximum circum-average'
79+
' speed',
80+
)
81+
),
82+
speed_radius=dict(
83+
attr_name='new_uavg_tmp',
84+
nc_name='U',
85+
nc_type='float32',
86+
nc_dims=('Nobs',),
87+
nc_attr=dict(
88+
long_name='maximum circum-averaged speed',
89+
units='cm/sec',
90+
description='average speed of the contour defining the radius '
91+
'scale L',
92+
)
93+
),
94+
eke=dict(
95+
attr_name='new_teke_tmp',
96+
nc_name='Teke',
97+
nc_type='float32',
98+
nc_dims=('Nobs',),
99+
nc_attr=dict(
100+
long_name='sum EKE within contour Ceff',
101+
units='m^2/sec^2',
102+
description='sum of eddy kinetic energy within contour '
103+
'defining the effective radius',
104+
)
105+
),
106+
radius_e=dict(
107+
attr_name='new_radii_e_tmp',
108+
nc_name='radius_e',
109+
nc_type='float32',
110+
nc_dims=('Nobs',),
111+
nc_attr=dict(
112+
long_name='effective radius scale',
113+
units='km',
114+
description='effective eddy radius',
115+
)
116+
),
117+
)
118+
11119
def __init__(self, eddy, ymd_str):
12120
"""
13121
"""
14-
self.tracklist = eddy.tracklist
15-
self.sign_type = eddy.SIGN_TYPE
16122
self.ymd_str = ymd_str
17-
self.num_tracks = np.sum([i.alive for i in self.tracklist])
123+
self.eddy = eddy
124+
125+
@property
126+
def sign_type(self):
127+
return self.eddy.SIGN_TYPE
18128

19129
def create_netcdf(self):
20130
"""
21131
"""
22-
with Dataset('%s_%s.nc' % (self.sign_type, self.ymd_str),
23-
'w', format='NETCDF4') as nc:
132+
eddy_size = None
133+
for key in self.VAR_DESCR:
134+
attr_name = self.VAR_DESCR[key]['attr_name']
135+
if attr_name is not None and hasattr(self.eddy, attr_name):
136+
eddy_size = len(getattr(self.eddy, attr_name))
137+
break
24138

139+
filename = '%s_%s.nc' % (self.sign_type, self.ymd_str)
140+
with Dataset(filename, 'w', format='NETCDF4') as h_nc:
141+
logging.info('Create intermediary file %s', filename)
25142
# Create dimensions
26-
nc.createDimension('tracks', self.num_tracks)
27-
nc.createDimension('properties', None)
28-
# Create variables
29-
t = 0
30-
for track in self.tracklist:
31-
# if track.alive:
32-
varname = 'track_%s' % np.str(t).zfill(4)
33-
nc.createVariable(varname, np.float64, ('properties'))
34-
t += 1
35-
nc.createVariable('track_lengths', np.int, ('tracks'))
143+
logging.debug('Create Dimensions "Nobs"')
144+
h_nc.createDimension('Nobs', eddy_size)
145+
# Iter on variables to create:
146+
for key, value in self.VAR_DESCR.iteritems():
147+
attr_name = value['attr_name']
148+
if attr_name is None or not hasattr(self.eddy, attr_name):
149+
continue
150+
logging.debug('Create Variable %s',
151+
value['nc_name'])
152+
var = h_nc.createVariable(
153+
varname=value['nc_name'],
154+
datatype=value['nc_type'],
155+
dimensions=value['nc_dims'],
156+
zlib=True,
157+
complevel=1,
158+
)
159+
for attr, attr_value in value['nc_attr'].iteritems():
160+
var.setncattr(attr, attr_value)
161+
162+
var[:] = getattr(self.eddy, attr_name)
36163

37164
def write_tracks(self):
38165
"""
39166
"""
40-
t = 0
41-
for track in self.tracklist:
42-
tracklen = len(track.lon)
43-
if track.alive:
44-
properties = np.hstack((
45-
track.dayzero, track.saved2nc,
46-
track.save_extras, track.lon, track.lat,
47-
track.amplitude, track.radius_s,
48-
track.radius_e, track.uavg,
49-
track.teke, track.ocean_time))
50-
51-
with Dataset('%s_%s.nc' % (self.sign_type, self.ymd_str), 'a') as nc:
52-
varname = 'track_%s' % np.str(t).zfill(4)
53-
nc.variables[varname][:] = properties
54-
nc.variables['track_lengths'][t] = tracklen
55-
t += 1
167+
# t = 0
168+
# print self.old_lon
169+
# for track in self.tracklist:
170+
# tracklen = len(track.lon)
171+
# if track.alive:
172+
# properties = np.hstack((
173+
# track.dayzero, track.saved2nc,
174+
# track.save_extras, track.lon, track.lat,
175+
# track.amplitude, track.radius_s,
176+
# track.radius_e, track.uavg,
177+
# track.teke, track.ocean_time))
178+
#
179+
# with Dataset('%s_%s.nc' % (self.sign_type,
180+
# self.ymd_str), 'a') as nc:
181+
# varname = 'track_%s' % np.str(t).zfill(4)
182+
# nc.variables[varname][:] = properties
183+
# nc.variables['track_lengths'][t] = tracklen
184+
# t += 1
56185

57186
def read_tracks(self):
58187
"""
59188
Read and sort the property data for returning to the
60189
Eddy object
61190
"""
62191
with Dataset('Anticyclonic_20140312.nc') as nc:
63-
tracklens = nc.variables['track_lengths'][:]
192+
tracklengths = nc.variables['track_lengths'][:]
64193
for t, tracklen in enumerate(tracklengths):
65194

66195
varname = 'track_%s' % np.str(t).zfill(4)

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