def get_geocoords(infile, lat='lat', lon='lon'):
df = EcoFOCI_netCDF(infile)
nchandle = df._getnchandle_()
data = {}
for j, v in enumerate([lat, lon]):
data[v] = nchandle.variables[v][:]
df.close()
return (data)
def from_netcdf_1dsplice(infile, height_ind, lat_ind, lon_ind):
""" Uses ncreadfile_dic which returns a dictionary of all data from netcdf"""
###nc readin/out
df = EcoFOCI_netCDF(infile)
nchandle = df._getnchandle_()
params = df.get_vars() #gets all of them
print "Parameters available: "
#print params
ncdata = ncreadfile_dic_slice(nchandle, params, height_ind=height_ind, lat_ind=lat_ind, lon_ind=lon_ind)
df.close()
return ncdata
def load(self):
self.data = {}
for ind, ncfile in enumerate(self.files_path):
print("Working on {0}").format(ncfile)
df = EcoFOCI_netCDF(ncfile)
df.get_global_atts()
vars_dic = df.get_vars()
if self.plot_var in vars_dic:
ncdata = df.ncreadfile_dic()
df.close()
ncdata[self.plot_var][np.where(
ncdata[self.plot_var] > 1e34)] = np.nan
else:
continue
self.ncdata = ncdata #only save last file
self.data[self.pointer_dic['nominal_depth'][ind]] = {
'data': ncdata[self.plot_var][:, 0, 0, 0],
'time': EPIC2Datetime(ncdata['time'], ncdata['time2'])
}
parser.add_argument('-m360',
'--m360',
action="store_true",
help='make range 0-360')
args = parser.parse_args()
###nc readin
ncfile = args.sourcefile
df = EcoFOCI_netCDF(ncfile)
global_atts = df.get_global_atts()
vars_dic = df.get_vars()
data = df.ncreadfile_dic()
if 'lon' in df.variables.keys():
if args.m360:
df.variables['lon'][:] = -1. * df.variables['lon'][:] + 360
else:
df.variables['lon'][:] = -1. * df.variables['lon'][:]
vars_dic['lon'].units = 'degree_east'
elif 'longitude' in df.variables.keys():
if args.m360:
df.variables['longitude'][:] = -1. * df.variables['longitude'][:] + 360
else:
df.variables['longitude'][:] = -1. * df.variables['longitude'][:]
vars_dic['longitude'].units = 'degree_east'
else:
print("Longitude variable not found")
df.close()
### cycle through all files, retrieve data and plot
print files_path
writer = pd.ExcelWriter('data/' + MooringID + '_' + plot_var + '.xlsx',
engine='xlsxwriter',
datetime_format='YYYY-MM-DD HH:MM:SS')
label_thin = []
for ind, ncfile in enumerate(files_path):
print "Working on {activefile}".format(activefile=ncfile)
#open/read netcdf files
df = EcoFOCI_netCDF(ncfile)
global_atts = df.get_global_atts()
vars_dic = df.get_vars()
ncdata = df.ncreadfile_dic()
df.close()
nctime = EPIC2Datetime(ncdata['time'], ncdata['time2'])
#find and replace missing values with nans so they don't plot
try:
ncdata[plot_var][np.where(ncdata[plot_var] > 1e30)] = np.nan
try:
label_thin = label_thin + [label[ind]]
except TypeError:
label_thin = label_thin + ['']
except KeyError:
pass
try:
help='fixed temperature scale (min max)')
parser.add_argument(
'-timebounds',
'--timebounds',
nargs=3,
type=str,
help='fixed timebounds start: yyyy-mm-dd end: yyyy-mm-dd "month"')
args = parser.parse_args()
print "Working on file %s " % args.DataPath
nc = EcoFOCI_netCDF(args.DataPath)
ncdata = nc.ncreadfile_dic()
g_atts = nc.get_global_atts()
nc.close()
cast_time = EPIC2Datetime(ncdata['time'], ncdata['time2'])
doy = np.array([x.timetuple().tm_yday for x in cast_time])
p1 = TimeseriesPorpertyPropertyPlot()
try:
t1 = p1.add_title(mooringid=global_atts['MOORING'],
lat=ncdata['lat'][0],
lon=ncdata['lon'][0],
depth=ncdata['depth'][0],
instrument=args.instname)
except KeyError:
t1 = p1.add_title(mooringid=global_atts['MOORING'],
lat=ncdata['latitude'][0],
lon=ncdata['longitude'][0],