def add_data(self):
""" """
ekcl = ekc.EpicKeyCodes()
for k in self.data.columns.values:
try:
kname = self.epicvars[k]
if kname is None: #dave K designated variables which aren't in epic.key of form -4084 for key 84
kname = ekcl.epic_dic_call( self.sbe2epic[k][-2:] )
temp = ('_'.join((kname[0].strip().strip('\\'), self.sbe2epic[k].split('-')[-1])))
elif (kname[0].strip().lower()) is not '': #no variables without Epic Keys
temp = ('_'.join((kname[0].strip().strip('\\'), self.sbe2epic[k])))
else:
continue
except:
continue
di = self.rec_vars.index(temp)
self.var_class[di][:] = self.data[k].values
def variable_init(self):
"""data.columns.values is a list of all parameters in seabird file.
We need to match these to EPIC key codes. These can be found in the EPICNetCDF folder
Usage:
------
from EPICnetCDF import SBE_Epiclibrary
from EPICnetCDF import epic_key_codes as ekc
ekcl = ekc.EpicKeyCodes()
ekcl.epic_dic_call(SBE_Epiclibrary.SBE_EPIC['sal00'])
#will return
#['S ', 'SALINITY (PSU) ', 'sal', 'PSU', ' ', 'Practical Salinity Units']
DataFrame.columns.values[0]
"""
ekcl = ekc.EpicKeyCodes()
self.epicvars = {}
self.sbe2epic = {}
# get list of only epic variables in sbe file
for pname in self.data.columns.values:
try:
self.epicvars[pname] = ekcl.epic_dic_call(SBE_Epiclibrary.SBE_EPIC[pname])
self.sbe2epic[pname] = SBE_Epiclibrary.SBE_EPIC[pname]
except KeyError:
print "%s is not in the SBE_Epiclibrary and will not be added to the .nc file" % pname
#build record variable attributes
rec_vars, rec_var_name, rec_var_longname = [], [], []
rec_var_generic_name, rec_var_missing, rec_var_units, rec_epic_code = [], [], [], []
# for each epic variable, build required metainformation from epic.key file
for i, k in enumerate(self.epicvars.keys()):
kname = self.epicvars[k]
if kname is None: # variables not in epic.key but given epic like codes
# these are often secondary instruments
kname = ekcl.epic_dic_call(self.sbe2epic[k][-2:])
print "Variables in .cnv file %s listed as secondary" % ( k )
rec_vars.append( k.replace('/','per') )
rec_var_name.append( kname[0].strip() )
rec_var_longname.append( kname[1].strip() )
rec_var_generic_name.append( kname[2].strip() )
rec_var_units.append( kname[3].strip() )
rec_epic_code.append( self.sbe2epic[k] )
else:
print "Variables in .cnv file %s" % ( k )
rec_vars.append( k.replace('/','per') )
rec_var_name.append( kname[0].strip() )
rec_var_longname.append( kname[1].strip() )
rec_var_generic_name.append( kname[2].strip() )
rec_var_units.append( kname[3].strip() )
rec_epic_code.append( self.sbe2epic[k] )
#hard coded variables are expected coordinate variables
rec_vars = ['time','dep','lat','lon'] + rec_vars
rec_var_name = ['', '', '', ''] + rec_var_name
rec_var_longname = ['', '', '', ''] + rec_var_longname
rec_var_generic_name = ['', '', '', ''] + rec_var_generic_name
rec_var_units = ['Days Since 01 01 0001 00:00:00','dbar','degrees_north','degrees_east'] + rec_var_units
rec_var_type= ['f8'] + ['f4' for spot in rec_vars[1:]]
rec_epic_code = ['','1','500','501'] + rec_epic_code
rec_var_missing = [-9999. for spot in rec_vars]
var_class = []
var_class.append(self.rootgrpID.createVariable(rec_vars[0], rec_var_type[0], self.dim_vars[0]))#time1
var_class.append(self.rootgrpID.createVariable(rec_vars[1], rec_var_type[1], self.dim_vars[1]))#depth
var_class.append(self.rootgrpID.createVariable(rec_vars[2], rec_var_type[2], self.dim_vars[2]))#lat
var_class.append(self.rootgrpID.createVariable(rec_vars[3], rec_var_type[3], self.dim_vars[3]))#lon
for i, v in enumerate(rec_vars[4:]): #1D coordinate variables
var_class.append(self.rootgrpID.createVariable(rec_vars[i+4], rec_var_type[i+4], self.dim_vars))
### add variable attributes
for i, v in enumerate(var_class): #4dimensional for all vars
print ("Adding Variable {0}").format(v)#
v.setncattr('name',rec_var_name[i])
v.long_name = rec_var_longname[i]
v.generic_name = rec_var_generic_name[i]
v.units = rec_var_units[i]
v.historic_epic_code = rec_epic_code[i]
v.missing_value = rec_var_missing[i]
self.var_class = var_class
self.rec_vars = rec_vars
def variable_init(self):
"""data.columns.values is a list of all parameters in seabird file.
We need to match these to EPIC key codes. These can be found in the EPICNetCDF folder
Usage:
------
from EPICnetCDF import SBE_Epiclibrary
from EPICnetCDF import epic_key_codes as ekc
ekcl = ekc.EpicKeyCodes()
ekcl.epic_dic_call(SBE_Epiclibrary.SBE_EPIC['sal00'])
#will return
#['S ', 'SALINITY (PSU) ', 'sal', 'PSU', ' ', 'Practical Salinity Units']
DataFrame.columns.values[0]
"""
ekcl = ekc.EpicKeyCodes()
self.epicvars = {}
self.sbe2epic = {}
# get list of only epic variables in sbe file
for pname in self.data.columns.values:
try:
self.epicvars[pname] = ekcl.epic_dic_call(SBE_Epiclibrary.SBE_EPIC[pname])
self.sbe2epic[pname] = SBE_Epiclibrary.SBE_EPIC[pname]
print pname
except KeyError:
print "%s is not in the SBE_Epiclibrary and will not be added to the .nc file" % pname
#build record variable attributes
rec_vars, rec_var_name, rec_var_longname = [], [], []
rec_var_generic_name, rec_var_FORTRAN, rec_var_units, rec_var_epic = [], [], [], []
# for each epic variable, build required metainformation from epic.key file
# temperatures should always be first
for i, k in enumerate(sorted(self.epicvars.keys())):
kname = self.epicvars[k]
if kname is None: #dave K designated variables which aren't in epic.key of form -4084 for key 84
print "Variables in .cnv file %s using identifier %s" % (k, self.sbe2epic[k].split('_')[-1])
kname = ekcl.epic_dic_call( self.sbe2epic[k][-2:] )
rec_vars.append('_'.join((kname[0].strip().strip('\\'), self.sbe2epic[k].split('-')[-1])))
elif (kname[0].strip().lower()) is not '': #no variables without Epic Keys
print "Variables in .cnv file %s" % ('_'.join((kname[0].strip().strip('\\'), self.sbe2epic[k])))
rec_vars.append('_'.join((kname[0].strip().strip('\\'), self.sbe2epic[k])))
else:
print "No EPICkey. Variables in .cnv file %s - %s skipped" % (k, self.sbe2epic[k].split('_')[-1])
continue
rec_var_name.append( kname[0].strip() )
rec_var_longname.append( kname[1].strip() )
rec_var_generic_name.append( kname[2].strip() )
rec_var_units.append( kname[3].strip() )
rec_var_FORTRAN.append( kname[4].strip() )
rec_var_epic.append( int(self.sbe2epic[k].split('_')[-1]) )
rec_vars = ['time','time2','dep','lat','lon'] + rec_vars
rec_var_name = ['', '', '', '', ''] + rec_var_name
rec_var_longname = ['', '', '', '', ''] + rec_var_longname
rec_var_generic_name = ['', '', '', '', ''] + rec_var_generic_name
rec_var_FORTRAN = ['', '', '', '', ''] + rec_var_FORTRAN
rec_var_units = ['True Julian Day', 'msec since 0:00 GMT','dbar','degree_north','degree_west'] + rec_var_units
rec_var_type= ['i4', 'i4'] + ['f4' for spot in rec_vars[2:]]
rec_var_strtype= ['EVEN', 'EVEN', 'EVEN', 'EVEN', 'EVEN']
rec_epic_code = [624,624,1,500,501] + rec_var_epic
var_class = []
var_class.append(self.rootgrpID.createVariable(rec_vars[0], rec_var_type[0], self.dim_vars[0]))#time1
var_class.append(self.rootgrpID.createVariable(rec_vars[1], rec_var_type[1], self.dim_vars[0]))#time2
var_class.append(self.rootgrpID.createVariable(rec_vars[2], rec_var_type[2], self.dim_vars[1]))#depth
var_class.append(self.rootgrpID.createVariable(rec_vars[3], rec_var_type[3], self.dim_vars[2]))#lat
var_class.append(self.rootgrpID.createVariable(rec_vars[4], rec_var_type[4], self.dim_vars[3]))#lon
for i, v in enumerate(rec_vars[5:]): #1D coordinate variables
var_class.append(self.rootgrpID.createVariable(rec_vars[i+5], rec_var_type[i+5], self.dim_vars))
### add variable attributes
for i, v in enumerate(var_class): #4dimensional for all vars
print ("Adding Variable {0}").format(v)#
v.setncattr('name',rec_var_name[i])
v.long_name = rec_var_longname[i]
v.generic_name = rec_var_generic_name[i]
v.FORTRAN_format = rec_var_FORTRAN[i]
v.units = rec_var_units[i]
if (i <= 4) :
#no type indicator for non dimensional variables
v.type = rec_var_strtype[i]
v.epic_code = rec_epic_code[i]
self.var_class = var_class
self.rec_vars = rec_vars