def _append_spectrum(self):
"""Append spectra after ensuring same spectral basis."""
self.spec_list.append(
interp_spec(inspec=self.spec_data,
infreq=self.freqs,
indir=self.dirs,
outfreq=self.interp_freq,
outdir=self.interp_dir))
self.time_list.append(self.header.get('time'))
def read_swans(fileglob, ndays=None, int_freq=True, int_dir=False, dirorder=True, ntimes=None):
"""Read multiple swan files into single Dataset.
Args:
- fileglob (str, list): glob pattern specifying files to read.
- ndays (float): number of days to keep from each file, choose None to
keep entire period.
- int_freq (ndarray, bool): frequency array for interpolating onto:
- ndarray: 1d array specifying frequencies to interpolate onto.
- True: logarithm array is constructed such that fmin=0.0418 Hz,
fmax=0.71856 Hz, df=0.1f.
- False: No interpolation performed in frequency space.
- int_dir (ndarray, bool): direction array for interpolating onto:
- ndarray: 1d array specifying directions to interpolate onto.
- True: circular array is constructed such that dd=10 degrees.
- False: No interpolation performed in direction space.
- dirorder (bool): if True ensures directions are sorted.
- ntimes (int): use it to read only specific number of times, useful
for checking headers only.
Returns:
- dset (SpecDataset): spectra dataset object read from file with
different sites and cycles concatenated along the 'site' and 'time'
dimensions.
Note:
- If multiple cycles are provided, 'time' coordinate is replaced by
'cycletime' multi-index coordinate.
- If more than one cycle is prescribed from fileglob, each cycle must
have same number of sites.
- Either all or none of the spectra in fileglob must have tabfile
associated to provide wind/depth data.
- Concatenation is done with numpy arrays for efficiency.
"""
swans = sorted(fileglob) if isinstance(fileglob, list) else sorted(glob.glob(fileglob))
assert swans, 'No SWAN file identified with fileglob %s' % (fileglob)
# Default spectral basis for interpolating
if int_freq == True:
int_freq = [0.04118 * 1.1**n for n in range(31)]
elif int_freq == False:
int_freq = None
if int_dir == True:
int_dir = np.arange(0, 360, 10)
elif int_dir == False:
int_dir = None
cycles = list()
dsets = SortedDict()
tabs = SortedDict()
all_times = list()
all_sites = SortedDict()
all_lons = SortedDict()
all_lats = SortedDict()
deps = SortedDict()
wspds = SortedDict()
wdirs = SortedDict()
for filename in swans:
swanfile = SwanSpecFile(filename, dirorder=dirorder)
times = swanfile.times
lons = list(swanfile.x)
lats = list(swanfile.y)
sites = [os.path.splitext(os.path.basename(filename))[0]] if len(lons)==1 else np.arange(len(lons))+1
freqs = swanfile.freqs
dirs = swanfile.dirs
if ntimes is None:
spec_list = [s for s in swanfile.readall()]
else:
spec_list = [swanfile.read() for itime in range(ntimes)]
# Read tab files for winds / depth
if swanfile.is_tab:
try:
tab = read_tab(swanfile.tabfile).rename(columns={'dep': attrs.DEPNAME})
if len(swanfile.times) == tab.index.size:
if 'X-wsp' in tab and 'Y-wsp' in tab:
tab[attrs.WSPDNAME], tab[attrs.WDIRNAME] = uv_to_spddir(tab['X-wsp'], tab['Y-wsp'], coming_from=True)
else:
warnings.warn(
"Times in {} and {} not consistent, not appending winds and depth"
.format(swanfile.filename, swanfile.tabfile)
)
tab = pd.DataFrame()
tab = tab[list(set(tab.columns).intersection((attrs.DEPNAME, attrs.WSPDNAME, attrs.WDIRNAME)))]
except Exception as exc:
warnings.warn(
"Cannot parse depth and winds from {}:\n{}".format(swanfile.tabfile, exc)
)
else:
tab = pd.DataFrame()
# Shrinking times
if ndays is not None:
tend = times[0] + datetime.timedelta(days=ndays)
if tend > times[-1]:
raise IOError('Times in %s does not extend for %0.2f days' % (filename, ndays))
iend = times.index(min(times, key=lambda d: abs(d - tend)))
times = times[0:iend+1]
spec_list = spec_list[0:iend+1]
tab = tab.loc[times[0]:tend] if tab is not None else tab
spec_list = flatten_list(spec_list, [])
# Interpolate spectra
if int_freq is not None or int_dir is not None:
spec_list = [interp_spec(spec, freqs, dirs, int_freq, int_dir) for spec in spec_list]
freqs = int_freq if int_freq is not None else freqs
dirs = int_dir if int_dir is not None else dirs
# Appending
try:
arr = np.array(spec_list).reshape(len(times), len(sites), len(freqs), len(dirs))
cycle = times[0]
if cycle not in dsets:
dsets[cycle] = [arr]
tabs[cycle] = [tab]
all_sites[cycle] = sites
all_lons[cycle] = lons
all_lats[cycle] = lats
all_times.append(times)
nsites = 1
else:
dsets[cycle].append(arr)
tabs[cycle].append(tab)
all_sites[cycle].extend(sites)
all_lons[cycle].extend(lons)
all_lats[cycle].extend(lats)
nsites += 1
except:
if len(spec_list) != arr.shape[0]:
raise IOError('Time length in %s (%i) does not match previous files (%i), cannot concatenate',
(filename, len(spec_list), arr.shape[0]))
else:
raise
swanfile.close()
cycles = dsets.keys()
# Ensuring sites are consistent across cycles
sites = all_sites[cycle]
lons = all_lons[cycle]
lats = all_lats[cycle]
for site, lon, lat in zip(all_sites.values(), all_lons.values(), all_lats.values()):
if (list(site) != list(sites)) or (list(lon) != list(lons)) or (list(lat) != list(lats)):
raise IOError('Inconsistent sites across cycles in glob pattern provided')
# Ensuring consistent tabs
cols = set([frozenset(tabs[cycle][n].columns) for cycle in cycles for n in range(len(tabs[cycle]))])
if len(cols) > 1:
raise IOError('Inconsistent tab files, ensure either all or none of the spectra have associated tabfiles and columns are consistent')
# Concat sites
for cycle in cycles:
dsets[cycle] = np.concatenate(dsets[cycle], axis=1)
deps[cycle] = np.vstack([tab[attrs.DEPNAME].values for tab in tabs[cycle]]).T if attrs.DEPNAME in tabs[cycle][0] else None
wspds[cycle] = np.vstack([tab[attrs.WSPDNAME].values for tab in tabs[cycle]]).T if attrs.WSPDNAME in tabs[cycle][0] else None
wdirs[cycle] = np.vstack([tab[attrs.WDIRNAME].values for tab in tabs[cycle]]).T if attrs.WDIRNAME in tabs[cycle][0] else None
time_sizes = [dsets[cycle].shape[0] for cycle in cycles]
# Concat cycles
if len(dsets) > 1:
dsets = np.concatenate(dsets.values(), axis=0)
deps = np.concatenate(deps.values(), axis=0) if attrs.DEPNAME in tabs[cycle][0] else None
wspds = np.concatenate(wspds.values(), axis=0) if attrs.WSPDNAME in tabs[cycle][0] else None
wdirs = np.concatenate(wdirs.values(), axis=0) if attrs.WDIRNAME in tabs[cycle][0] else None
else:
dsets = dsets[cycle]
deps = deps[cycle] if attrs.DEPNAME in tabs[cycle][0] else None
wspds = wspds[cycle] if attrs.WSPDNAME in tabs[cycle][0] else None
wdirs = wdirs[cycle] if attrs.WDIRNAME in tabs[cycle][0] else None
# Creating dataset
times = flatten_list(all_times, [])
dsets = xr.DataArray(
data=dsets,
coords=OrderedDict(((attrs.TIMENAME, times), (attrs.SITENAME, sites), (attrs.FREQNAME, freqs), (attrs.DIRNAME, dirs))),
dims=(attrs.TIMENAME, attrs.SITENAME, attrs.FREQNAME, attrs.DIRNAME),
name=attrs.SPECNAME,
).to_dataset()
dsets[attrs.LATNAME] = xr.DataArray(data=lats, coords={attrs.SITENAME: sites}, dims=[attrs.SITENAME])
dsets[attrs.LONNAME] = xr.DataArray(data=lons, coords={attrs.SITENAME: sites}, dims=[attrs.SITENAME])
if wspds is not None:
dsets[attrs.WSPDNAME] = xr.DataArray(data=wspds, dims=[attrs.TIMENAME, attrs.SITENAME],
coords=OrderedDict(((attrs.TIMENAME, times), (attrs.SITENAME, sites))))
dsets[attrs.WDIRNAME] = xr.DataArray(data=wdirs, dims=[attrs.TIMENAME, attrs.SITENAME],
coords=OrderedDict(((attrs.TIMENAME, times), (attrs.SITENAME, sites))))
if deps is not None:
dsets[attrs.DEPNAME] = xr.DataArray(data=deps, dims=[attrs.TIMENAME, attrs.SITENAME],
coords=OrderedDict(((attrs.TIMENAME, times), (attrs.SITENAME, sites))))
# Setting multi-index
if len(cycles) > 1:
dsets = dsets.rename({attrs.TIMENAME: 'cycletime'})
cycletime = zip(
[item for sublist in [[c]*t for c,t in zip(cycles, time_sizes)] for item in sublist],
dsets.cycletime.values
)
dsets['cycletime'] = pd.MultiIndex.from_tuples(cycletime, names=[attrs.CYCLENAME, attrs.TIMENAME])
dsets['cycletime'].attrs = attrs.ATTRS[attrs.TIMENAME]
set_spec_attributes(dsets)
if 'dir' in dsets and len(dsets.dir)>1:
dsets[attrs.SPECNAME].attrs.update({'_units': 'm^{2}.s.degree^{-1}', '_variable_name': 'VaDens'})
else:
dsets[attrs.SPECNAME].attrs.update({'units': 'm^{2}.s', '_units': 'm^{2}.s', '_variable_name': 'VaDens'})
return dsets