wavespectra 4.2.0__tar.gz → 4.3.0__tar.gz

{wavespectra-4.2.0/wavespectra.egg-info → wavespectra-4.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wavespectra
-Version: 4.2.0
+Version: 4.3.0
 Summary: Library for ocean wave spectra
 Author-email: Wavespectra Developers <r.guedes@oceanum.science>
 Maintainer-email: Rafael Guedes <r.guedes@oceanum.science>, Tom Durrant <t.durrant@oceanum.science>

{wavespectra-4.2.0 → wavespectra-4.3.0}/tests/test_cli.py

@@ -1,4 +1,5 @@
 """Test model wrapper."""
+
 from pathlib import Path
 import pytest
 import xarray as xr

{wavespectra-4.2.0 → wavespectra-4.3.0}/tests/test_specarray.py

@@ -1,4 +1,5 @@
 """Testing the SpecArray accessor."""
+
 import os
 import numpy as np
 import xarray as xr

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/__init__.py

@@ -4,6 +4,7 @@
 - Making reading functions available at module level
 
 """
+
 import warnings
 
 try:
@@ -13,7 +14,7 @@ except ImportError:
     warnings.warn("Cannot import accessors at the main module level")
 
 
-__version__ = "4.2.0"
+__version__ = "4.3.0"
 
 
 def _import_functions(pkgname="input", prefix="read"):

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/cli.py

@@ -1,4 +1,5 @@
 """Console script for wavespectra."""
+
 from pathlib import Path
 import click
 import yaml

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/construct/__init__.py

@@ -23,6 +23,7 @@ References:
   geophysical research 69: 5181-5190.
 
 """
+
 import xarray as xr
 import wavespectra
 from wavespectra.core.attributes import attrs, set_spec_attributes

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/construct/frequency.py

@@ -1,4 +1,5 @@
 """Frequency spectral shapes."""
+
 import numpy as np
 import xarray as xr
 from scipy.constants import g, pi
@@ -32,9 +33,7 @@ def pierson_moskowitz(freq, fp, alpha=0.0081, hs=None, **kwargs):
     if not isinstance(freq, xr.DataArray):
         freq = to_coords(freq, "freq")
 
-    dsout = (
-        alpha * g**2 / (2 * pi) ** 4 / freq**5 * np.exp(-1.25 * (freq / fp) ** -4)
-    )
+    dsout = alpha * g**2 / (2 * pi) ** 4 / freq**5 * np.exp(-1.25 * (freq / fp) ** -4)
 
     if hs is not None:
         dsout = scaled(dsout, hs)

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/core/attributes.py

@@ -2,6 +2,7 @@
 
 attrs (dict): standarised names for spectral variables, standard_names and units
 """
+
 import os
 import yaml
 import xarray as xr

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/core/npstats.py

@@ -1,4 +1,5 @@
 """Wave spectra stats on numpy arrays sourced by apply_ufuncs."""
+
 import numpy as np
 from scipy.constants import g, pi
 

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/core/swan.py

@@ -1,4 +1,5 @@
 """Read and write swan spectra files"""
+
 from pathlib import Path
 import re
 import gzip

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/core/utils.py

@@ -1,4 +1,5 @@
 """Utility functions."""
+
 import copy
 import itertools
 import numpy as np

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/core/xrstats.py

@@ -1,4 +1,5 @@
 """Peak based wave stats ufuncs."""
+
 import xarray as xr
 
 from wavespectra.core.attributes import attrs

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/__init__.py

@@ -9,6 +9,7 @@ All functions defined with these conventions will be dynamically
 imported at the module level
 
 """
+
 import xarray as xr
 
 from wavespectra.core.attributes import attrs

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/dataset.py

@@ -1,4 +1,5 @@
 """Construct the SpecArray accessor from existing dataset from known format."""
+
 import logging
 
 from wavespectra.input.ww3 import from_ww3

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/era5.py

@@ -1,4 +1,5 @@
 """Read ERA5 2D Wave Spectra NetCDF files"""
+
 import numpy as np
 from xarray.backends import BackendEntrypoint
 

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/funwave.py

@@ -1,4 +1,5 @@
 """Read Funwave 2D Wave Maker files"""
+
 from xarray.backends import BackendEntrypoint
 import numpy as np
 import xarray as xr

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/json.py

@@ -1,4 +1,5 @@
 """Read ERA5 2D Wave Spectra NetCDF files"""
+
 from xarray.backends import BackendEntrypoint
 import json
 import datetime

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/ncswan.py

@@ -1,4 +1,5 @@
 """Read Native SWAN netCDF spectra files."""
+
 from xarray.backends import BackendEntrypoint
 import numpy as np
 

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/ndbc.py

@@ -3,6 +3,7 @@
 https://dods.ndbc.noaa.gov/
 
 """
+
 import logging
 from xarray.backends import BackendEntrypoint
 import xarray as xr
@@ -26,7 +27,7 @@ MAPPING = {
 }
 
 
-def read_ndbc(url, directional=True, dd=10.0, chunks={}):
+def read_ndbc(url, directional=True, dd=10.0, chunks={}, weight_coeff: bool = False):
     """Read Spectra from NDBC netCDF format.
 
     Args:
@@ -35,6 +36,8 @@ def read_ndbc(url, directional=True, dd=10.0, chunks={}):
         - dd (float): Directional resolution for 2D spectra (deg).
         - chunks (dict): Chunk sizes for dimensions in dataset. By default
           dataset is loaded using single chunk for all dimensions.
+        - weight_coef (bool): Weight the coefficient to avoid negative value
+          in spectrum.
 
     Returns:
         - dset (SpecDataset): spectra dataset object read from NDBC file.
@@ -48,22 +51,35 @@ def read_ndbc(url, directional=True, dd=10.0, chunks={}):
 
     """
     dset = xr.open_dataset(url).chunk(chunks)
-    return from_ndbc(dset, directional=directional, dd=dd)
+    return from_ndbc(dset, directional=directional, dd=dd, weight_coeff=weight_coeff)
 
 
-def _construct_spectra(ef, swd1, swd2, swr1, swr2, dir):
+def _construct_spectra(ef, swd1, swd2, swr1, swr2, dir, weight_coeff: bool = False):
     """Construct 2D spectra."""
-    d = 0.5 + swr1 * np.cos(D2R * (dir - swd1)) + swr2 * np.cos(2 * D2R * (dir - swd2))
+    if weight_coeff:
+        d = (
+            0.5
+            + 2 / 3 * swr1 * np.cos(D2R * (dir - swd1))
+            + 1 / 6 * swr2 * np.cos(2 * D2R * (dir - swd2))
+        )
+    else:
+        d = (
+            0.5
+            + swr1 * np.cos(D2R * (dir - swd1))
+            + swr2 * np.cos(2 * D2R * (dir - swd2))
+        )
     return ef * d * D2R / np.pi
 
 
-def from_ndbc(dset, directional=True, dd=10.0):
+def from_ndbc(dset, directional=True, dd=10.0, weight_coeff: bool = False):
     """Format NDBC netcdf dataset to implement the wavespectra accessor.
 
     Args:
         - dset (xr.Dataset): Dataset created from a NDBC netcdf file.
         - directional (bool): Constructs 2D spectra if True, returns 1D if False.
         - dd (float): Directional resolution for 2D spectra (deg).
+        - weight_coef (bool): Weight the coefficient to avoid negative value
+          in spectrum.
 
     Returns:
         - Formated dataset with the SpecDataset accessor in the `spec` namespace.
@@ -103,6 +119,7 @@ def from_ndbc(dset, directional=True, dd=10.0):
             swr1=dset.wave_spectrum_r1,
             swr2=dset.wave_spectrum_r2,
             dir=xr.DataArray(dirs, dims=(attrs.DIRNAME,), coords={attrs.DIRNAME: dirs}),
+            weight_coeff=weight_coeff,
         )
     else:
         dset = dset.spectral_wave_density

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/ndbc_ascii.py

@@ -57,22 +57,35 @@ def read_file(filename):
     return df
 
 
-def construct_spectra(spden, swdir1, swdir2, swr1, swr2, dirs):
+def construct_spectra(
+    spden, swdir1, swdir2, swr1, swr2, dirs, weight_coeff: bool = False
+):
     dirmat = dirs.reshape((1, 1, -1))
-    D_fd = (
-        IPI
-        * (
-            0.5
-            + swr1 * np.cos(D2R * (dirmat - swdir1))
-            + swr2 * np.cos(2 * D2R * (dirmat - swdir2))
+    if weight_coeff:
+        D_fd = (
+            IPI
+            * (
+                0.5
+                + 2 / 3 * swr1 * np.cos(D2R * (dirmat - swdir1))
+                + 1 / 6 * swr2 * np.cos(2 * D2R * (dirmat - swdir2))
+            )
+            * D2R
+        )
+    else:
+        D_fd = (
+            IPI
+            * (
+                0.5
+                + swr1 * np.cos(D2R * (dirmat - swdir1))
+                + swr2 * np.cos(2 * D2R * (dirmat - swdir2))
+            )
+            * D2R
         )
-        * D2R
-    )
     S = spden * D_fd
     return S
 
 
-def read_ndbc_ascii(filename, dirs=np.arange(0, 360, 10)):
+def read_ndbc_ascii(filename, dirs=np.arange(0, 360, 10), weight_coeff: bool = False):
     """Read spectra from NDBC wave buoy ASCII files.
 
     Both the history and realtime formats are supported. Realtime formats are decribed
@@ -87,6 +100,8 @@ def read_ndbc_ascii(filename, dirs=np.arange(0, 360, 10)):
           automatically detected.
         - dirs (array): vector of directional bins for spectral reconstruction.
         - attrs (dict): additional global attributes.
+        - weight_coef (bool): Weight the coefficient to avoid negative value
+          in spectrum.
 
     Returns:
         - dset (SpecDataset): spectra dataset object read from NDBC buoy file(s).
@@ -133,6 +148,7 @@ def read_ndbc_ascii(filename, dirs=np.arange(0, 360, 10)):
             df_swr1.values.reshape(spshape),
             df_swr2.values.reshape(spshape),
             dirs,
+            weight_coeff=weight_coeff,
         )
     coords = OrderedDict(
         ((attrs.TIMENAME, times), (attrs.FREQNAME, freqs), (attrs.DIRNAME, dirs))
@@ -148,9 +164,9 @@ def read_ndbc_ascii(filename, dirs=np.arange(0, 360, 10)):
             dims=(attrs.TIMENAME),
             name=attrs.SPECNAME,
         )
-        dset[
-            "Sep_Freq"
-        ] = sfreq  # Add the NDBC defined separation frequency for realtime diagnostics
+        dset["Sep_Freq"] = (
+            sfreq  # Add the NDBC defined separation frequency for realtime diagnostics
+        )
     dset = dset.sortby(
         "time", ascending=True
     )  # Realtime data is in reversed time order

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/netcdf.py

@@ -1,4 +1,5 @@
 """Read generic netCDF spectra files."""
+
 from xarray.backends import BackendEntrypoint
 
 from wavespectra.specdataset import SpecDataset

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/octopus.py

@@ -1,4 +1,5 @@
 """Read Octopus spectra files."""
+
 from xarray.backends import BackendEntrypoint
 import gzip
 import datetime

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/swan.py

@@ -7,6 +7,7 @@ Functions:
     read_swanow: Read SWAN nowcast from fileglob, keep overlapping dates
         from most recent files.
 """
+
 from xarray.backends import BackendEntrypoint
 from pathlib import Path
 import os

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/wavespectra.py

@@ -1,4 +1,5 @@
 """Read netCDF or ZARR formatted with wavespectra conventions."""
+
 from xarray.backends import BackendEntrypoint
 
 from wavespectra.specdataset import SpecDataset

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/ww3.py

@@ -1,4 +1,5 @@
 """Read Native WW3 spectra files."""
+
 from xarray.backends import BackendEntrypoint
 
 from wavespectra.specdataset import SpecDataset

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/ww3_station.py

@@ -1,4 +1,5 @@
 """Read directional spectra from WW3 station output file."""
+
 from xarray.backends import BackendEntrypoint
 from collections import OrderedDict
 import re

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/wwm.py

@@ -1,4 +1,5 @@
 """Read Native WWM netCDF spectra files."""
+
 from xarray.backends import BackendEntrypoint
 import numpy as np
 

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/input/xwaves.py

@@ -1,4 +1,5 @@
 """Read XWaves MAT files"""
+
 from xarray.backends import BackendEntrypoint
 import datetime
 import xarray as xr

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/output/funwave.py

@@ -1,4 +1,5 @@
 """FUNWAVE output plugin."""
+
 import os
 from zipfile import ZipFile, ZIP_DEFLATED
 from io import StringIO

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/output/json.py

@@ -1,4 +1,5 @@
 """Json output plugin."""
+
 import json
 
 

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/output/netcdf.py

@@ -1,4 +1,5 @@
 """Generic netCDF output plugin."""
+
 from wavespectra.core.attributes import attrs
 
 

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/output/octopus.py

@@ -1,4 +1,5 @@
 """OCTOPUS output plugin."""
+
 import gzip
 import numpy as np
 import xarray as xr

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/output/orcaflex.py

@@ -1,4 +1,5 @@
 """Orcaflex output plugin - using orcaflex API."""
+
 import numpy as np
 
 

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/output/swan.py

@@ -1,4 +1,5 @@
 """SWAN ASCII output plugin."""
+
 import numpy as np
 from wavespectra.core.attributes import attrs
 from wavespectra.core.swan import SwanSpecFile
@@ -41,7 +42,8 @@ def to_swan(
     """
     # If grid reshape into site, otherwise ensure there is site dim to iterate over
     dset = self._check_and_stack_dims()
-    ntime = min(ntime or dset.time.size, dset.time.size)
+    time_size = dset.time.size if "time" in dset.dims else 1
+    ntime = min(ntime or time_size, time_size)
 
     # Handle datasets with missing lon/lat
     for arr, name in zip((lons, lats), (attrs.LONNAME, attrs.LATNAME)):
@@ -55,7 +57,9 @@ def to_swan(
     # Ensure time dimension exists
     is_time = attrs.TIMENAME in dset[attrs.SPECNAME].dims
     if not is_time:
-        dset = dset.expand_dims({attrs.TIMENAME: [None]})
+        dset[attrs.SPECNAME] = dset[attrs.SPECNAME].expand_dims(
+            {attrs.TIMENAME: [None]}
+        )
         times = dset[attrs.TIMENAME].values
     else:
         times = dset[attrs.TIMENAME].to_index().to_pydatetime()

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/output/ww3.py

@@ -1,4 +1,5 @@
 """Native WAVEWATCH3 output plugin."""
+
 import os
 import yaml
 import numpy as np

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/partition/partition.py

@@ -1,4 +1,5 @@
 """Partitioning interface."""
+
 from itertools import combinations
 import numpy as np
 import xarray as xr

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/specarray.py

@@ -23,6 +23,7 @@ Reference:
     - Phillips (1957). On the generation of waves by turbulent wind, Journal of Fluid Mechanics, 2, pp 426-434.
 
 """
+
 import re
 import numpy as np
 import xarray as xr

{wavespectra-4.2.0 → wavespectra-4.3.0}/wavespectra/specdataset.py

@@ -1,4 +1,5 @@
 """Wrapper around the xarray dataset."""
+
 import types
 import os
 import re

{wavespectra-4.2.0 → wavespectra-4.3.0/wavespectra.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wavespectra
-Version: 4.2.0
+Version: 4.3.0
 Summary: Library for ocean wave spectra
 Author-email: Wavespectra Developers <r.guedes@oceanum.science>
 Maintainer-email: Rafael Guedes <r.guedes@oceanum.science>, Tom Durrant <t.durrant@oceanum.science>