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Merged
ctroupin merged 9 commits into from
Jan 9, 2019
Merged

Opendap #1

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fc687d3
SLA file
ctroupin Jan 9, 2019
d13bf4a
opendap paths
ctroupin Jan 9, 2019
c90455b
download SST if needed
ctroupin Jan 9, 2019
696757e
download SST if needed
ctroupin Jan 9, 2019
a1280f2
unused file
ctroupin Jan 9, 2019
ff79761
config
ctroupin Jan 9, 2019
f6aede9
methods
ctroupin Jan 9, 2019
ba0ec84
rm
ctroupin Jan 9, 2019
d85890b
read files from opendap
ctroupin Jan 9, 2019
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Binary file added data/alborex_mean_sla.nc
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63 changes: 43 additions & 20 deletions python/alborexconfig.json
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Original file line number Diff line number Diff line change
@@ -1,28 +1,51 @@
{
"datafiles":{
"adcp": "/home/ctroupin/Data/Alborex/ADCP/dep0023_socib-rv_scb-rdi001_L1_2014-05.nc",
"ctd": "/home/ctroupin/Data/Alborex/CTD/dep0007_socib-rv_scb-sbe9002_L1_2014-05-25.nc",
"ctdlegs": ["/home/ctroupin/Data/Alborex/CTD/ctd_positions_Leg1.txt",
"/home/ctroupin/Data/Alborex/CTD/ctd_positions_Leg2.txt"],
"coast": "/home/ctroupin/Data/Alborex/Coastline/coastline_f.dat",
"altimetry": "../data/alborex_mean_sla.nc",
"ctdlegs": ["../data/ctd_positions_Leg1.txt",
"../data/ctd_positions_Leg2.txt"],
"sst": ["../data/A2014145125000.L2_LAC_SST.nc",
"../data/A2014150020500.L2_LAC_SST.nc"],
"front": "../data/front_coordinates.dat",
"adcp": "http://thredds.socib.es/thredds/dodsC/research_vessel/current_profiler/socib_rv-scb_rdi001/L1/2014/dep0023_socib-rv_scb-rdi001_L1_2014-05.nc",
"ctd": "http://thredds.socib.es/thredds/dodsC/research_vessel/ctd/socib_rv-scb_sbe9002/L1_corr/2014/dep0007_socib-rv_scb-sbe9002_L1_corr_2014-05-25.nc",
"gliders": ["http://thredds.socib.es/thredds/dodsC/auv/glider/icoast00-ime_slcost000/L1/2014/dep0005_icoast00_ime-slcost000_L1_2014-05-25_data_dt.nc",
"http://thredds.socib.es/thredds/dodsC/auv/glider/ideep00-ime_sldeep000/L1/2014/dep0012_ideep00_ime-sldeep000_L1_2014-05-25_data_dt.nc"],
"profilers": ["/home/ctroupin/Data/Alborex/Profilers/dep0001_profiler-drifter-arvora3001_ogs-arvora3001_L1_2014-05-25.nc",
"/home/ctroupin/Data/Alborex/Profilers/dep0001_profiler-drifter-provbioll001_ogs-provbioll001_L1_2014-05-25.nc"],
"coast": "/home/ctroupin/Data/Alborex/Coastline/coastline_cartex_f3.txt",
"rv": "/home/ctroupin/Data/Alborex/RV/dep0015_socib-rv_scb-pos001_L1_2014-05-25.nc",
"altimetry": "/home/ctroupin/Data/Alborex/Altimetry/mean.nc",
"coast": "/home/ctroupin/Data/Alborex/Coastline/coastline_f.dat",
"thermosal": "/home/ctroupin/Data/Alborex/RV/dep0015_socib-rv_scb-tsl001_L1_2014-05-25_HR.nc"
},
"datadirs":{
"sst": "/home/ctroupin/Data/Alborex/SST/",
"drifters": "/home/ctroupin/Data/Alborex/Drifters",
"profilers": "/home/ctroupin/Data/Alborex/Profilers",
"adcp": "/home/ctroupin/Data/Alborex/ADCP",
"gliders": "/home/ctroupin/Data/Alborex/Gliders"
"profilers": ["http://thredds.socib.es/thredds/dodsC/drifter/profiler_drifter/profiler_drifter_arvora3001-ogs_arvora3001/L1/2014/dep0001_profiler-drifter-arvora3001_ogs-arvora3001_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/profiler_drifter/profiler_drifter_provbioll001-ogs_provbioll001/L1/2014/dep0001_profiler-drifter-provbioll001_ogs-provbioll001_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/profiler_drifter/profiler_drifter_arvorc001-ime_arvorc001/L1/2014/dep0001_profiler-drifter-arvorc001_ime-arvorc001_L1_2014-05-25.nc"],
"drifters": ["http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp018-scb_svp013/L1/2014/dep0001_drifter-svp018_scb-svp013_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp019-scb_svp014/L1/2014/dep0001_drifter-svp019_scb-svp014_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp020-scb_svp015/L1/2014/dep0001_drifter-svp020_scb-svp015_L1_2014-05-28.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp021-scb_svp016/L1/2014/dep0001_drifter-svp021_scb-svp016_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp022-scb_svp017/L1/2014/dep0001_drifter-svp022_scb-svp017_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp024-scb_svp019/L1/2014/dep0001_drifter-svp024_scb-svp019_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp025-scb_svp020/L1/2014/dep0001_drifter-svp025_scb-svp020_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp027-scb_svp022/L1/2014/dep0001_drifter-svp027_scb-svp022_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp036-ime_svp007/L1/2014/dep0001_drifter-svp036_ime-svp007_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp037-ime_svp008/L1/2014/dep0001_drifter-svp037_ime-svp008_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp038-ime_svp009/L1/2014/dep0001_drifter-svp038_ime-svp009_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp039-ime_svp010/L1/2014/dep0001_drifter-svp039_ime-svp010_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp040-ime_svp011/L1/2014/dep0001_drifter-svp040_ime-svp011_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp041-ime_svp012/L1/2014/dep0001_drifter-svp041_ime-svp012_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp042-ime_svp006/L1/2014/dep0001_drifter-svp042_ime-svp006_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp043-ogs_svp001/L1/2014/dep0001_drifter-svp043_ogs-svp001_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp044-ogs_svp002/L1/2014/dep0001_drifter-svp044_ogs-svp002_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp045-ogs_svp003/L1/2014/dep0001_drifter-svp045_ogs-svp003_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp046-ogs_svp004/L1/2014/dep0001_drifter-svp046_ogs-svp004_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp047-ogs_svp005/L1/2014/dep0001_drifter-svp047_ogs-svp005_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp048-ime_svp013/L1/2014/dep0001_drifter-svp048_ime-svp013_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp049-ime_svp014/L1/2014/dep0001_drifter-svp049_ime-svp014_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp051-ime_svp016/L1/2014/dep0001_drifter-svp051_ime-svp016_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp052-ime_svp017/L1/2014/dep0001_drifter-svp052_ime-svp017_L1_2014-05-25.nc",
"http://thredds.socib.es/thredds/dodsC/drifter/surface_drifter/drifter_svp054-ime_svp019/L1/2014/dep0001_drifter-svp054_ime-svp019_L1_2014-05-25.nc"],
"rv": "http://thredds.socib.es/thredds/dodsC/research_vessel/gps/socib_rv-scb_pos001/L1/2014/05/dep0015_socib-rv_scb-pos001_L1_2014-05-25.nc",
"thermosal": "http://thredds.socib.es/thredds/dodsC/research_vessel/thermosalinometer/socib_rv-scb_tsl001/L1/2014/05/dep0015_socib-rv_scb-tsl001_L1_2014-05-25.nc",
"sstremote": ["https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/A2014145125000.L2_LAC_SST.nc",
"https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/A2014150020500.L2_LAC_SST.nc"]
},
"figdir": "/home/ctroupin/Publis/201703_AlborexData/figures",
"figdirleaflet": "/home/ctroupin/Publis/201703_AlborexData/leaflet/images/",
"figdir": "../figures",
"figdirleaflet": "../leaflet/images/",
"domain":{
"coordinates1": [-6.75, 3.001, 34.75, 40.0],
"coordinates2": [-1.0, -0.25, 36.65, 37.25],
Expand Down
55 changes: 27 additions & 28 deletions python/alborexdata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -179,27 +179,27 @@ def get_from_netcdf(self, datafile):
"""
Read the coordinates and the temperature from existing data file
"""
if os.path.exists(datafile):
with netCDF4.Dataset(datafile, 'r') as nc:
self.lon = nc.get_variables_by_attributes(standard_name='longitude')[0][:]
self.lat = nc.get_variables_by_attributes(standard_name='latitude')[0][:]
self.time = nc.get_variables_by_attributes(standard_name='time')[0][:]
self.timeunits = nc.get_variables_by_attributes(standard_name='time')[0].units
self.dates = netCDF4.num2date(self.time, self.timeunits)

try:
self.qclat = nc.get_variables_by_attributes(standard_name='latitude status_flag')[0][:]
except IndexError:
self.qclat = None
with netCDF4.Dataset(datafile, 'r') as nc:
self.lon = nc.get_variables_by_attributes(standard_name='longitude')[0][:]
self.lat = nc.get_variables_by_attributes(standard_name='latitude')[0][:]
self.time = nc.get_variables_by_attributes(standard_name='time')[0][:]
self.timeunits = nc.get_variables_by_attributes(standard_name='time')[0].units
self.dates = netCDF4.num2date(self.time, self.timeunits)

try:
self.qclon = nc.get_variables_by_attributes(standard_name='longitude status_flag')[0][:]
except IndexError:
self.qclon = None
try:
self.temperature = nc.get_variables_by_attributes(standard_name='sea_water_temperature')[0][:]
except IndexError:
self.temperature = None
try:
self.qclat = nc.get_variables_by_attributes(standard_name='latitude status_flag')[0][:]
except IndexError:
self.qclat = None

try:
self.qclon = nc.get_variables_by_attributes(standard_name='longitude status_flag')[0][:]
except IndexError:
self.qclon = None
try:
self.temperature = nc.get_variables_by_attributes(standard_name='sea_water_temperature')[0][:]
except IndexError:
self.temperature = None

def apply_qc_latlon(self, QC=[1]):
"""
Expand Down Expand Up @@ -304,15 +304,14 @@ def get_from_netcdf(self, datafile):
"""
Read the coordinates and the field values from a netCDF file
"""
if os.path.exists(datafile):
with netCDF4.Dataset(datafile, 'r') as nc:
self.lon = nc.get_variables_by_attributes(standard_name='longitude')[0][:]
self.lat = nc.get_variables_by_attributes(standard_name='latitude')[0][:]
self.time = nc.get_variables_by_attributes(standard_name='time')[0][:]
timeunits = nc.get_variables_by_attributes(standard_name='time')[0].units
self.dates = netCDF4.num2date(self.time, timeunits)
self.salinity = nc.get_variables_by_attributes(standard_name='sea_water_salinity')[0][:]
self.temperature = nc.get_variables_by_attributes(standard_name='sea_water_temperature')[0][:]
with netCDF4.Dataset(datafile, 'r') as nc:
self.lon = nc.get_variables_by_attributes(standard_name='longitude')[0][:]
self.lat = nc.get_variables_by_attributes(standard_name='latitude')[0][:]
self.time = nc.get_variables_by_attributes(standard_name='time')[0][:]
timeunits = nc.get_variables_by_attributes(standard_name='time')[0].units
self.dates = netCDF4.num2date(self.time, timeunits)
self.salinity = nc.get_variables_by_attributes(standard_name='sea_water_salinity')[0][:]
self.temperature = nc.get_variables_by_attributes(standard_name='sea_water_temperature')[0][:]

class CTD():

Expand Down
527 changes: 0 additions & 527 deletions python/figure1_AlborexData.ipynb
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