def get(self, fn, x):
try:
dbd = dbdreader.DBD(fn)
v = dbd.get(x)
except Exception as e:
raise e
return v
def test_G3S_data_file(self):
print(
"Reading a G3S data file for which the byte order needs to be swapped."
)
dbd = dbdreader.DBD("../data/unit_887-2021-321-3-0.sbd",
cacheDir='../data/cac')
tm, depth = dbd.get("m_depth")
self.assertAlmostEqual(depth.max(), 34.5, delta=0.1)
def test_non_standard_cache_dir_generate_cachefile(self):
print("non_standard_cache_dir_generated_cachefile")
# this should create a cache file. Remove it if already present.
try:
os.unlink('../data/cac/(813b137d.cac')
except FileNotFoundError:
pass
dbd = dbdreader.DBD("../data/ammonite-2008-028-01-000.mbd",
cacheDir='../data/cac')
depth = dbd.get("m_depth")
self.assertEqual(len(depth), 2)
def get_method(self, method, fn, x, *y):
dbd = dbdreader.DBD(fn)
try:
if method == 'sync':
v = dbd.get_sync(x, *y)
elif method == 'xy':
v = dbd.get_xy(x, *y)
elif method == 'list':
v = dbd.get_list(*y)
except Exception as e:
raise e
return v
def get(self, fn, x):
try:
dbd = dbdreader.DBD(fn)
v = dbd.get(x)
except Exception as e:
raise e
finally:
try:
dbd.close()
except:
pass
return v
def updateParameterList(self):
# loop trough all files until one has a working parameterlist
for fid in self.fileList:
dbd = dbdreader.DBD(fid)
if len(dbd.parameterNames) > 0:
break # if there are parameters in the list break loop and use those
if not dbd.parameterNames: # if no file contained proper parameter info
print('------------------')
print(
'!!!! None of the provided files has sufficient parameter information'
)
print('------------------')
self.parameterList = dbd.parameterNames
def get_method(self, method, fn, x, y):
dbd = dbdreader.DBD(fn)
try:
if method == 'sync':
v = dbd.get_sync(x, y)
elif method == 'xy':
v = dbd.get_xy(x, y)
elif method == 'list':
v = dbd.get_list(y)
except Exception as e:
raise e
finally:
try:
dbd.close()
except:
pass
return v
def loadData(self):
# initialize data structure
self.Data = []
for i in range(len(self.varList) + 1): # +1 is for time dimension
self.Data.append(np.array([]))
# load data
for f in range(len(self.fileList)):
tmpdbd = dbdreader.DBD(self.fileList[f]) # just file name
# check if variables are in the file:
inorout = np.zeros((len(self.varList)))
loadingList = []
for i in range(len(self.varList)):
if self.varList[i] in tmpdbd.parameterNames:
inorout[i] = 1
loadingList.append(self.varList[i])
#tmpdata = tmpdbd.get_sync( *self.varList )
tmpdata = tmpdbd.get_sync(*loadingList)
cnt = 1 # index 0 is or the time vector
self.Data[0] = np.concatenate(
(self.Data[0], tmpdata[0])) # time vector
for i in range(len(inorout)):
if inorout[i] == 1:
self.Data[i + 1] = np.concatenate(
(self.Data[i + 1], tmpdata[cnt]))
cnt += 1
else: # if the variable was not in the file fill with nans
if self.varList[i] in ['file_no']:
self.Data[i + 1] = np.concatenate(
(self.Data[i + 1], np.ones(tmpdata[0].shape) * f))
else:
self.Data[i + 1] = np.concatenate(
(self.Data[i + 1],
np.ones(tmpdata[0].shape) * np.nan))
# convert time data
self.Data[0] = np.asarray(
[dt.datetime.utcfromtimestamp(t) for t in self.Data[0]])
def test_missing_cache_file(self):
print("Throw an error when cache file is missing...")
with self.assertRaises(dbdreader.DbdError) as e:
dbd = dbdreader.DBD("../data/unit_887-2021-321-3-0.sbd")
import numpy as np
import gsw
import dbdreader
import ndf
dbd = dbdreader.DBD(
"/home/lucas/gliderdata/toulon_201504/hd/comet-2015-098-03-000.ebd")
tmp = dbd.get_sync("sci_ctd41cp_timestamp",
["sci_water_temp", "sci_water_cond", "sci_water_pressure"])
t, tctd, T, C, P = np.compress(tmp[2] > 0, tmp, axis=1)
SP = gsw.SP_from_C(C * 10, T, P * 10)
SA = gsw.SA_from_SP(SP, P * 10, 43.1, 4.8)
CT = gsw.CT_from_t(SA, T, P * 10)
rho = gsw.rho(SA, CT, P * 10)
i = np.argsort(rho)
z_s = P[i] * 10
rho_is = rho[i]
zi = np.arange(0, P.max() * 10, 2)
rhoi = np.interp(zi, z_s, rho_is)
data = ndf.NDF()
data.add_parameter("rho", "kg/m^3", (zi, rhoi), "in situ density toulon exp.")
data.save("toulon/density_profile_toulon.ndf")
#!/bin/python3
import os
import sys
import dbdreader
if len(sys.argv)==1:
raise ValueError("Supply one or more dbd/ebd files.")
for fn in sys.argv[1:]:
if not os.path.isfile(fn):
print("Skipping %s..."%(fn))
continue
try:
dbd = dbdreader.DBD(fn)
except:
print("Skipping %s..."%(fn))
else:
fileopen_time = dbd.get_fileopen_time()
os.utime(fn, times=(fileopen_time, fileopen_time))
def test_non_standard_cache_dir(self):
print("non_standard_cache_dir")
dbd = dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd",
cacheDir='../data/cac')
depth = dbd.get("m_depth")
self.assertEqual(len(depth), 2)
def test_get_mission_name(self):
print("get_mission_name")
dbd = dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd")
t = dbd.get_mission_name()
self.assertEqual(t, "micro.mi")
def test_file_open_time(self):
print("file_open_time")
dbd = dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd")
t = dbd.get_fileopen_time()
self.assertEqual(t, 1406221414)
def test_get_list(self):
print("get_list")
dbd = dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd")
x, y = dbd.get_list("m_lat", "m_lon")
def test_get_sync_obselete(self):
print("get_sync_obselete")
dbd = dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd")
x = dbd.get_sync("m_depth", ['m_lat', 'm_lon'])
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
import numpy as np
import dbdreader
# open a given file
dbd = dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd")
# print what parameters are available:
for i, p in enumerate(dbd.parameterNames):
print("%2d: %s" % (i, p))
# get the measured depth
tm, depth = dbd.get("m_depth")
max_depth = depth.max()
print("\nmax depth %f m" % (max_depth))
# get lat lon
lat, lon = dbd.get_xy("m_lat", "m_lon")
# interpolate roll speed on depth time
tm, depth, roll, speed = dbd.get_sync("m_depth", ["m_roll", "m_speed"])
import numpy as np
import dbdreader
# open a given file
# Note that the default location for cache files ($HOME/.dbdreader) is
# overriden.
dbd = dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd",
cacheDir='../data/cac')
# print what parameters are available:
for i, p in enumerate(dbd.parameterNames):
print("%2d: %s" % (i, p))
# get the measured depth
tm, depth = dbd.get("m_depth")
max_depth = depth.max()
print("\nmax depth %f m" % (max_depth))
# get lat lon
lat, lon = dbd.get_xy("m_lat", "m_lon")
# interpolate roll speed on depth time
tm, depth, roll, speed = dbd.get_sync("m_depth", "m_roll", "m_speed")
print("\nmax speed %f m/s" % (np.nanmax(speed)))
# close the file again.
dbd.close()
import dbdreader
dbd = dbdreader.DBD(
"/home/lucas/gliderdata/helgoland201407/hd/sebastian-2014-227-00-160.dbd")
depth = dbd.get("m_depth")
print(depth[0].shape)
print(depth[0].mean())
