def getprofile(time,lon,lat):
lon = float(lon)
lat = float(lat)
R=Rectangle(lon,lon,lat,lat)
Profilelist=bio_float.FloatSelector(None,TimeInterval.fromdatetimes(time, time),R)
profile=Profilelist[0]
return profile
def MooringSelector(var, T, region):
LOC = "/gss/gss_work/DRES_OGS_BiGe/Observations/TIME_RAW_DATA/ONLINE/COPERNICUS/mooring/"
INTEREST_VARLIST=['PHOS','SLCA','CPHL','NTRA','PHPH','DOX1']
ALLVARLIST=['PHOS','SLCA','AMON','DOX1','DOX2','CPHL','NTRZ','NTRA','NTRI','PHPH']
A = INDEX_FILE
nFiles=A.size
selected = []
for i in range(nFiles):
filename=os.path.basename(A['file_name'][i])
parameters = A['parameters'][i]
ti = TimeInterval(A[i]['time_coverage_start'],A[i]['time_coverage_end'],'%Y-%m-%dT%H:%M:%S' )
lon = A[i]['geospatial_lon_min']
lat = A[i]['geospatial_lat_min']
if var is None:
VarCondition = False
for thevar in ALLVARLIST:
if thevar in parameters: VarCondition = True
else:
VarCondition = var in parameters
Filecondition = VarCondition & (filename[:2]=='MO') & ("mooring" in A['file_name'][i])
if Filecondition & (ti.isInWindow(T)) & region.is_inside(lon, lat):
filepath = LOC + os.path.basename(A[i]['file_name'])
ncIN = NC.netcdf_file(filepath,'r')
timesInFile = ncIN.variables['TIME'].data.copy() # days since 1950-01-01T00:00:00Z
ncIN.close()
available_params = A['parameters'][i]
M = Mooring(lon,lat,filepath,available_params)
for t in timesInFile:
dateprofile = basetime + datetime.timedelta(days = t)
if T.contains(dateprofile):
mp = MooringProfile(dateprofile,lon,lat,M,available_params)
selected.append(mp)
return selected
matplotlib.use('Agg')
from commons.time_interval import TimeInterval
from commons.Timelist import TimeList
from instruments.matchup_manager import Matchup_Manager
import basins.OGS as OGS
from instruments import lovbio_float as bio_float
from commons.mask import Mask
from commons.utils import addsep
from datetime import timedelta
starttime=args.starttime
end__time=args.endtime
INPUTDIR=addsep(args.inputdir)
BASEDIR=addsep(args.basedir)
TI=TimeInterval(starttime,end__time,'%Y%m%d')
TI.end_time = TI.end_time + timedelta(1)
TheMask=Mask(args.maskfile)
Profilelist=bio_float.FloatSelector(None,TI,OGS.med)
TL = TimeList.fromfilenames(TI, INPUTDIR,"ave*.nc")
M = Matchup_Manager(Profilelist,TL,BASEDIR)
profilerscript = BASEDIR + 'jobProfiler.sh'
M.writefiles_for_profiling('VarDescriptor_valid_online.xml', profilerscript) # preparation of data for aveScan
M.dumpModelProfiles(profilerscript) # sequential launch of aveScan
M.getFloatMatchups(Profilelist,TheMask.zlevels,args.outdir)