-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathproc_cr10x_wq_v2.py
376 lines (331 loc) · 12.5 KB
/
proc_cr10x_wq_v2.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
#!/usr/bin/env python
# Last modified: Time-stamp: <2010-12-09 16:14:11 haines>
"""
how to parse data, and assert what data and info goes into
creating and updating monthly netcdf files
parse data water quality data from ysi 6600 V2
collected on Campbell Scientific DataLogger (loggernet) (csi)
parser : sample date and time,
water temperature, conductivity, pH, dissolved oxygen, turbidity, and system battery
creator : lat, lon, z, time, wtemp, cond, ph, turb, do_sat, do_mg, battvolts
updator : time, wtemp, cond, ph, turb, do_sat, do_mg, battvolts
Examples
--------
>> (parse, create, update) = load_processors('proc_csi_wq_v2')
or
>> si = get_config(cn+'.sensor_info')
>> (parse, create, update) = load_processors(si['adcp']['proc_module'])
>> lines = load_data(filename)
>> data = parse(platform_info, sensor_info, lines)
>> create(platform_info, sensor_info, data) or
>> update(platform_info, sensor_info, data)
"""
from raw2proc import *
from procutil import *
from ncutil import *
now_dt = datetime.utcnow()
now_dt.replace(microsecond=0)
def parser(platform_info, sensor_info, lines):
"""
From FSL (CSI datalogger program files):
15 Output_Table 15.00 Min
1 15 L
2 Year_RTM L
3 Day_RTM L
4 Hour_Minute_RTM L
5 Rain15sec_TOT L
6 SonLevlft L
7 SonFlow L
8 PrDepthft L
9 PrFlowcfs L
1 Output_Table 60.00 Min
1 1 L
2 Year_RTM L
3 Day_RTM L
4 Hour_Minute_RTM L
5 H2OTempC L
6 SpCond L
7 DOSat L
8 DOmg L
9 PH L
10 Turb L
11 BattVolts L
Example data:
1,2005,83,1600,16.47,0,.4,.04,8.14,115.5,14.25
15,2005,83,1615,0,4.551,-.547,.897,.885
15,2005,83,1630,0,4.541,.727,.908,1.005
15,2005,83,1645,0,4.537,6.731,.878,.676
15,2005,83,1700,0,4.537,6.731,.83,.167
1,2005,83,1700,16.57,0,.4,.03,8.03,145.7,13.08
15,2005,83,1715,0,4.547,5.29,.847,.347
15,2005,83,1730,0,4.541,.908,.842,.287
15,2005,83,1745,0,4.547,7.3,.853,.407
15,2005,83,1800,0,4.551,6.939,.855,.437
1,2005,83,1800,15.65,0,.2,.02,7.91,111.3,12.98
"""
import numpy
from datetime import datetime
from time import strptime
import math
# get sample datetime from filename
fn = sensor_info['fn']
sample_dt_start = filt_datetime(fn)
# how many samples
nsamp = 0
for line in lines:
m=re.search("^1,", line)
if m:
nsamp=nsamp+1
N = nsamp
data = {
'dt' : numpy.array(numpy.ones((N,), dtype=object)*numpy.nan),
'time' : numpy.array(numpy.ones((N,), dtype=long)*numpy.nan),
'wtemp' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
'cond' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
'do_sat' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
'do_mg' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
'ph' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
'turb' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
'battvolts' : numpy.array(numpy.ones((N,), dtype=float)*numpy.nan),
}
# sample count
i = 0
for line in lines:
csi = []
# split line and parse float and integers
m=re.search("^1,", line)
if m:
sw = re.split(',', line)
else:
continue
for s in sw:
m = re.search(REAL_RE_STR, s)
if m:
csi.append(float(m.groups()[0]))
if len(csi)==11:
# get sample datetime from data
yyyy = csi[1]
yday = csi[2]
(MM, HH) = math.modf(csi[3]/100.)
MM = math.ceil(MM*100.)
if (HH == 24):
yday=yday+1
HH = 0.
sample_str = '%04d-%03d %02d:%02d' % (yyyy, yday, HH, MM)
# if sensor_info['utc_offset']:
# sample_dt = scanf_datetime(sample_str, fmt='%m-%d-%Y %H:%M:%S') + \
# timedelta(hours=sensor_info['utc_offset'])
# else:
sample_dt = scanf_datetime(sample_str, fmt='%Y-%j %H:%M')
data['dt'][i] = sample_dt # sample datetime
data['time'][i] = dt2es(sample_dt) # sample time in epoch seconds
#
data['wtemp'][i] = csi[4] # water temperature (C)
data['cond'][i] = csi[5] # specific conductivity (mS/cm)
data['do_sat'][i] = csi[6] # saturated dissolved oxygen (% air sat)
data['do_mg'][i] = csi[7] # dissolved oxygen (mg/l)
data['ph'][i] = csi[8] # ph
data['turb'][i] = csi[9] # turbidity (NTU)
data['battvolts'][i] = csi[10] # battery (volts)
i=i+1
# if-elif
# for line
# check that no data[dt] is set to Nan or anything but datetime
# keep only data that has a resolved datetime
keep = numpy.array([type(datetime(1970,1,1)) == type(dt) for dt in data['dt'][:]])
if keep.any():
for param in data.keys():
data[param] = data[param][keep]
return data
def creator(platform_info, sensor_info, data):
#
#
title_str = sensor_info['description']+' at '+ platform_info['location']
global_atts = {
'title' : title_str,
'institution' : 'Unversity of North Carolina at Chapel Hill (UNC-CH)',
'institution_url' : 'http://nccoos.unc.edu',
'institution_dods_url' : 'http://nccoos.unc.edu',
'metadata_url' : 'http://nccoos.unc.edu',
'references' : 'http://ehs.unc.edu',
'contact' : 'Sara Haines ([email protected])',
'station_owner' : 'Environment, Health, and Safety Office',
'station_contact' : 'Sharon Myers ([email protected])',
#
'source' : 'fixed-point observation',
'history' : 'raw2proc using ' + sensor_info['process_module'],
'comment' : 'File created using pycdf'+pycdfVersion()+' and numpy '+pycdfArrayPkg(),
# conventions
'Conventions' : 'CF-1.0; SEACOOS-CDL-v2.0',
# SEACOOS CDL codes
'format_category_code' : 'fixed-point',
'institution_code' : platform_info['institution'],
'platform_code' : platform_info['id'],
'package_code' : sensor_info['id'],
# institution specific
'project' : 'Environment, Health, and Safety (EHS)',
'project_url' : 'http://ehs.unc.edu/environment/water_quality',
# timeframe of data contained in file yyyy-mm-dd HH:MM:SS
# first date in monthly file
'start_date' : data['dt'][0].strftime("%Y-%m-%d %H:%M:%S"),
# last date in monthly file
'end_date' : data['dt'][-1].strftime("%Y-%m-%d %H:%M:%S"),
'release_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
#
'creation_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
'modification_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
'process_level' : 'level1',
#
# must type match to data (e.g. fillvalue is real if data is real)
'_FillValue' : -99999.,
}
var_atts = {
# coordinate variables
'time' : {'short_name': 'time',
'long_name': 'Time',
'standard_name': 'time',
'units': 'seconds since 1970-1-1 00:00:00 -0', # UTC
'axis': 'T',
},
'lat' : {'short_name': 'lat',
'long_name': 'Latitude',
'standard_name': 'latitude',
'reference':'geographic coordinates',
'units': 'degrees_north',
'valid_range':(-90.,90.),
'axis': 'Y',
},
'lon' : {'short_name': 'lon',
'long_name': 'Longitude',
'standard_name': 'longitude',
'reference':'geographic coordinates',
'units': 'degrees_east',
'valid_range':(-180.,180.),
'axis': 'Y',
},
'z' : {'short_name': 'z',
'long_name': 'Height',
'standard_name': 'height',
'reference':'zero at sea-surface',
'positive' : 'up',
'units': 'm',
'axis': 'Z',
},
# data variables
'wtemp': {'short_name': 'wtemp',
'long_name': 'Water Temperature',
'standard_name': 'water_temperature',
'units': 'degrees_Celsius',
},
'cond': {'short_name': 'cond',
'long_name': 'Conductivity',
'standard_name': 'conductivity',
'units': 'mS cm-1',
},
'turb': {'short_name': 'turb',
'long_name': 'Turbidity',
'standard_name': 'turbidity',
'units': 'NTU',
},
'ph': {'short_name': 'ph',
'long_name': 'pH',
'standard_name': 'ph',
'units': '',
},
'do_mg': {'short_name': 'do_mg',
'long_name': 'ROX Optical Dissolved Oxygen, Derived Concentration',
'standard_name': 'dissolved_oxygen_concentration',
'units': 'mg l-1',
},
'do_sat': {'short_name': 'do_sat',
'long_name': 'ROX Optical Dissolved Oxygen, Percent of Air Saturation',
'standard_name': 'dissolved_oxygen_relative_to_air_saturation',
'units': '%',
},
'battvolts': {'short_name': 'battery',
'long_name': 'Battery Voltage of the Station',
'standard_name': 'battery_voltage',
'units': 'volts',
},
}
# dimension names use tuple so order of initialization is maintained
dim_inits = (
('ntime', NC.UNLIMITED),
('nlat', 1),
('nlon', 1),
('nz', 1),
)
# using tuple of tuples so order of initialization is maintained
# using dict for attributes order of init not important
# use dimension names not values
# (varName, varType, (dimName1, [dimName2], ...))
var_inits = (
# coordinate variables
('time', NC.INT, ('ntime',)),
('lat', NC.FLOAT, ('nlat',)),
('lon', NC.FLOAT, ('nlon',)),
('z', NC.FLOAT, ('nz',)),
# data variables
('wtemp', NC.FLOAT, ('ntime',)),
('cond', NC.FLOAT, ('ntime',)),
('turb', NC.FLOAT, ('ntime',)),
('ph', NC.FLOAT, ('ntime',)),
('do_mg', NC.FLOAT, ('ntime',)),
('do_sat', NC.FLOAT, ('ntime',)),
('battvolts', NC.FLOAT, ('ntime',)),
)
# subset data only to month being processed (see raw2proc.process())
i = data['in']
# var data
var_data = (
('lat', platform_info['lat']),
('lon', platform_info['lon']),
('z', platform_info['altitude']),
#
('time', data['time'][i]),
#
('wtemp', data['wtemp'][i]),
('cond', data['cond'][i]),
('turb', data['turb'][i]),
('ph', data['ph'][i]),
('do_mg', data['do_mg'][i]),
('do_sat', data['do_sat'][i]),
('battvolts', data['battvolts'][i]),
)
return (global_atts, var_atts, dim_inits, var_inits, var_data)
def updater(platform_info, sensor_info, data):
#
global_atts = {
# update times of data contained in file (yyyy-mm-dd HH:MM:SS)
# last date in monthly file
'end_date' : data['dt'][-1].strftime("%Y-%m-%d %H:%M:%S"),
'release_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
#
'modification_date' : now_dt.strftime("%Y-%m-%d %H:%M:%S"),
}
# data variables
# update any variable attributes like range, min, max
var_atts = {}
# var_atts = {
# 'wtemp': {'max': max(data.u),
# 'min': min(data.v),
# },
# 'cond': {'max': max(data.u),
# 'min': min(data.v),
# },
# }
# subset data only to month being processed (see raw2proc.process())
i = data['in']
# data
var_data = (
('time', data['time'][i]),
('wtemp', data['wtemp'][i]),
('cond', data['cond'][i]),
('turb', data['turb'][i]),
('ph', data['ph'][i]),
('do_mg', data['do_mg'][i]),
('do_sat', data['do_sat'][i]),
('battvolts', data['battvolts'][i]),
)
return (global_atts, var_atts, var_data)
#