roms-tools 1.6.2__py3-none-any.whl → 2.0.0__py3-none-any.whl

roms_tools/setup/surface_forcing.py

@@ -1,8 +1,6 @@
 import xarray as xr
-import pandas as pd
-import yaml
 import importlib.metadata
-from dataclasses import dataclass, field, asdict
+from dataclasses import dataclass, field
 from roms_tools.setup.grid import Grid
 from datetime import datetime
 import numpy as np
@@ -14,14 +12,17 @@ from roms_tools.setup.datasets import (
     CESMBGCSurfaceForcingDataset,
 )
 from roms_tools.setup.utils import (
+    get_target_coords,
     nan_check,
     substitute_nans_by_fillvalue,
     interpolate_from_climatology,
     get_variable_metadata,
     group_dataset,
     save_datasets,
-    get_target_coords,
     rotate_velocities,
+    convert_to_roms_time,
+    _to_yaml,
+    _from_yaml,
 )
 from roms_tools.setup.plot import _plot
 import matplotlib.pyplot as plt
@@ -104,8 +105,8 @@ class SurfaceForcing:
 
         data.apply_lateral_fill()
 
-        variable_info = self._set_variable_info(data)
-        var_names = variable_info.keys()
+        self._set_variable_info(data)
+        var_names = self.variable_info.keys()
 
         processed_fields = {}
         # lateral regridding
@@ -117,7 +118,7 @@ class SurfaceForcing:
                 )
 
         # rotation of velocities and interpolation to u/v points
-        if "uwnd" in variable_info and "vwnd" in variable_info:
+        if "uwnd" in self.variable_info and "vwnd" in self.variable_info:
             processed_fields["uwnd"], processed_fields["vwnd"] = rotate_velocities(
                 processed_fields["uwnd"],
                 processed_fields["vwnd"],
@@ -133,7 +134,7 @@ class SurfaceForcing:
 
         ds = self._write_into_dataset(processed_fields, data, d_meta)
 
-        self._validate(ds, target_coords["mask"], variable_info)
+        self._validate(ds)
 
         # substitute NaNs over land by a fill value to avoid blow-up of ROMS
         for var_name in ds.data_vars:
@@ -212,9 +213,8 @@ class SurfaceForcing:
 
         Returns
         -------
-        dict
-            A dictionary where the keys are variable names and the values are dictionaries of metadata
-            about each variable, including 'location', 'is_vector', 'vector_pair', and 'is_3d'.
+        None
+            This method updates the instance attribute `variable_info` with the metadata dictionary for the variables.
         """
         default_info = {
             "location": "rho",
@@ -255,7 +255,7 @@ class SurfaceForcing:
                 else:
                     variable_info[var_name] = {**default_info, "validate": False}
 
-        return variable_info
+        object.__setattr__(self, "variable_info", variable_info)
 
     def _apply_correction(self, processed_fields, data):
 
@@ -302,38 +302,9 @@ class SurfaceForcing:
         ds = self._add_global_metadata(ds)
 
         # Convert the time coordinate to the format expected by ROMS
-        if data.climatology:
-            ds.attrs["climatology"] = str(True)
-            # Preserve absolute time coordinate for readability
-            ds = ds.assign_coords(
-                {"abs_time": np.datetime64(self.model_reference_date) + ds["time"]}
-            )
-            # Convert to pandas TimedeltaIndex
-            timedelta_index = pd.to_timedelta(ds["time"].values)
-
-            # Determine the start of the year for the base_datetime
-            start_of_year = datetime(self.model_reference_date.year, 1, 1)
-
-            # Calculate the offset from midnight of the new year
-            offset = self.model_reference_date - start_of_year
-
-            # Convert the timedelta to nanoseconds first, then to days
-            sfc_time = xr.DataArray(
-                (timedelta_index - offset).view("int64") / 3600 / 24 * 1e-9,
-                dims="time",
-            )
-        else:
-            # Preserve absolute time coordinate for readability
-            ds = ds.assign_coords({"abs_time": ds["time"]})
-
-            sfc_time = (
-                (ds["time"] - np.datetime64(self.model_reference_date)).astype(
-                    "float64"
-                )
-                / 3600
-                / 24
-                * 1e-9
-            )
+        ds, sfc_time = convert_to_roms_time(
+            ds, self.model_reference_date, data.climatology
+        )
 
         if self.type == "physics":
             time_coords = ["time"]
@@ -347,14 +318,6 @@ class SurfaceForcing:
             ]
         for time_coord in time_coords:
             ds = ds.assign_coords({time_coord: sfc_time})
-            ds[time_coord].attrs[
-                "long_name"
-            ] = f"days since {str(self.model_reference_date)}"
-            ds[time_coord].encoding["units"] = "days"
-            ds[time_coord].attrs["units"] = "days"
-            if data.climatology:
-                ds[time_coord].attrs["cycle_length"] = 365.25
-        ds.encoding["unlimited_dims"] = "time"
 
         if self.type == "bgc":
             ds = ds.drop_vars(["time"])
@@ -365,7 +328,7 @@ class SurfaceForcing:
 
         return ds
 
-    def _validate(self, ds, mask, variable_info):
+    def _validate(self, ds):
         """Validates the dataset by checking for NaN values at wet points, which would
         indicate missing raw data coverage over the target domain.
 
@@ -373,12 +336,6 @@ class SurfaceForcing:
         ----------
         ds : xarray.Dataset
             The dataset to validate.
-        mask : xarray.DataArray
-            Land mask (1=ocean, 0=land) to determine wet points in the domain.
-        variable_info : dict
-            A dictionary containing metadata about each variable (e.g., location,
-            whether it's a 3D variable, etc.). Used to retrieve information for
-            validating each variable.
 
         Raises
         ------
@@ -393,8 +350,8 @@ class SurfaceForcing:
 
         for var_name in ds.data_vars:
             # Only validate variables based on "validate" flag if use_dask is False
-            if not self.use_dask or variable_info[var_name]["validate"]:
-                nan_check(ds[var_name].isel(time=0), mask)
+            if not self.use_dask or self.variable_info[var_name]["validate"]:
+                nan_check(ds[var_name].isel(time=0), self.target_coords["mask"])
 
     def _add_global_metadata(self, ds=None):
 
@@ -579,49 +536,8 @@ class SurfaceForcing:
         filepath : Union[str, Path]
             The path to the YAML file where the parameters will be saved.
         """
-        filepath = Path(filepath)
-
-        # Serialize Grid data
-        grid_data = asdict(self.grid)
-        grid_data.pop("ds", None)  # Exclude non-serializable fields
-        grid_data.pop("straddle", None)
-
-        # Include the version of roms-tools
-        try:
-            roms_tools_version = importlib.metadata.version("roms-tools")
-        except importlib.metadata.PackageNotFoundError:
-            roms_tools_version = "unknown"
-
-        # Create header
-        header = f"---\nroms_tools_version: {roms_tools_version}\n---\n"
-
-        # Create YAML data for Grid and optional attributes
-        grid_yaml_data = {"Grid": grid_data}
-
-        # Combine all sections
-        surface_forcing_data = {
-            "SurfaceForcing": {
-                "start_time": self.start_time.isoformat(),
-                "end_time": self.end_time.isoformat(),
-                "source": self.source,
-                "type": self.type,
-                "correct_radiation": self.correct_radiation,
-                "use_coarse_grid": self.use_coarse_grid,
-                "model_reference_date": self.model_reference_date.isoformat(),
-            }
-        }
 
-        # Merge YAML data while excluding empty sections
-        yaml_data = {
-            **grid_yaml_data,
-            **surface_forcing_data,
-        }
-
-        with filepath.open("w") as file:
-            # Write header
-            file.write(header)
-            # Write YAML data
-            yaml.dump(yaml_data, file, default_flow_style=False, sort_keys=False)
+        _to_yaml(self, filepath)
 
     @classmethod
     def from_yaml(
@@ -642,33 +558,8 @@ class SurfaceForcing:
             An instance of the SurfaceForcing class.
         """
         filepath = Path(filepath)
-        # Read the entire file content
-        with filepath.open("r") as file:
-            file_content = file.read()
-
-        # Split the content into YAML documents
-        documents = list(yaml.safe_load_all(file_content))
-
-        surface_forcing_data = None
-
-        # Process the YAML documents
-        for doc in documents:
-            if doc is None:
-                continue
-            if "SurfaceForcing" in doc:
-                surface_forcing_data = doc["SurfaceForcing"]
-
-        if surface_forcing_data is None:
-            raise ValueError("No SurfaceForcing configuration found in the YAML file.")
-
-        # Convert from string to datetime
-        for date_string in ["model_reference_date", "start_time", "end_time"]:
-            surface_forcing_data[date_string] = datetime.fromisoformat(
-                surface_forcing_data[date_string]
-            )
 
-        # Create Grid instance from the YAML file
         grid = Grid.from_yaml(filepath)
+        params = _from_yaml(cls, filepath)
 
-        # Create and return an instance of SurfaceForcing
-        return cls(grid=grid, **surface_forcing_data, use_dask=use_dask)
+        return cls(grid=grid, **params, use_dask=use_dask)

roms_tools/setup/tides.py

@@ -1,11 +1,9 @@
 from datetime import datetime
 import xarray as xr
 import numpy as np
-import yaml
-import importlib.metadata
 from typing import Dict, Union, List
-
-from dataclasses import dataclass, field, asdict
+import importlib.metadata
+from dataclasses import dataclass, field
 from roms_tools.setup.grid import Grid
 from roms_tools.setup.plot import _plot
 from roms_tools.setup.datasets import TPXODataset
@@ -19,6 +17,8 @@ from roms_tools.setup.utils import (
     get_target_coords,
     rotate_velocities,
     get_vector_pairs,
+    _to_yaml,
+    _from_yaml,
 )
 from roms_tools.setup.regrid import LateralRegrid
 import matplotlib.pyplot as plt
@@ -85,8 +85,8 @@ class TidalForcing:
 
         data.apply_lateral_fill()
 
-        variable_info = self._set_variable_info()
-        var_names = variable_info.keys()
+        self._set_variable_info()
+        var_names = self.variable_info.keys()
 
         processed_fields = {}
         # lateral regridding
@@ -98,7 +98,7 @@ class TidalForcing:
                 )
 
         # rotation of velocities and interpolation to u/v points
-        vector_pairs = get_vector_pairs(variable_info)
+        vector_pairs = get_vector_pairs(self.variable_info)
         for pair in vector_pairs:
             u_component = pair[0]
             v_component = pair[1]
@@ -129,7 +129,7 @@ class TidalForcing:
 
         ds = self._add_global_metadata(ds)
 
-        self._validate(ds, variable_info)
+        self._validate(ds)
 
         # substitute NaNs over land by a fill value to avoid blow-up of ROMS
         for var_name in ds.data_vars:
@@ -163,9 +163,8 @@ class TidalForcing:
 
         Returns
         -------
-        dict
-            A dictionary where the keys are variable names and the values are dictionaries of metadata
-            about each variable, including 'location', 'is_vector', 'vector_pair', and 'is_3d'.
+        None
+            This method updates the instance attribute `variable_info` with the metadata dictionary for the variables.
         """
         default_info = {
             "location": "rho",
@@ -210,7 +209,7 @@ class TidalForcing:
             },
         }
 
-        return variable_info
+        object.__setattr__(self, "variable_info", variable_info)
 
     def _write_into_dataset(self, processed_fields, d_meta):
 
@@ -243,7 +242,7 @@ class TidalForcing:
 
         return ds
 
-    def _validate(self, ds, variable_info):
+    def _validate(self, ds):
         """Validates the dataset by checking for NaN values at wet points for specified
         variables, which would indicate missing raw data coverage over the target
         domain.
@@ -252,8 +251,6 @@ class TidalForcing:
         ----------
         ds : xarray.Dataset
             The dataset to validate, containing tidal variables and a mask for wet points.
-        variable_info : dict
-            A dictionary containing metadata about the variables, including whether to validate them.
 
         Raises
         ------
@@ -268,7 +265,7 @@ class TidalForcing:
         """
         for var_name in ds.data_vars:
             # only validate variables based on "validate" flag if use_dask is false
-            if not self.use_dask or variable_info[var_name]["validate"]:
+            if not self.use_dask or self.variable_info[var_name]["validate"]:
                 nan_check(ds[var_name].isel(ntides=0), self.grid.ds.mask_rho)
 
     def plot(self, var_name, ntides=0) -> None:
@@ -418,42 +415,8 @@ class TidalForcing:
         filepath : Union[str, Path]
             The path to the YAML file where the parameters will be saved.
         """
-        filepath = Path(filepath)
 
-        grid_data = asdict(self.grid)
-        grid_data.pop("ds", None)  # Exclude non-serializable fields
-        grid_data.pop("straddle", None)
-
-        # Include the version of roms-tools
-        try:
-            roms_tools_version = importlib.metadata.version("roms-tools")
-        except importlib.metadata.PackageNotFoundError:
-            roms_tools_version = "unknown"
-
-        # Create header
-        header = f"---\nroms_tools_version: {roms_tools_version}\n---\n"
-
-        # Extract grid data
-        grid_yaml_data = {"Grid": grid_data}
-
-        # Extract tidal forcing data
-        tidal_forcing_data = {
-            "TidalForcing": {
-                "source": self.source,
-                "ntides": self.ntides,
-                "allan_factor": self.allan_factor,
-                "model_reference_date": self.model_reference_date.isoformat(),
-            }
-        }
-
-        # Combine both sections
-        yaml_data = {**grid_yaml_data, **tidal_forcing_data}
-
-        with filepath.open("w") as file:
-            # Write header
-            file.write(header)
-            # Write YAML data
-            yaml.dump(yaml_data, file, default_flow_style=False, sort_keys=False)
+        _to_yaml(self, filepath)
 
     @classmethod
     def from_yaml(
@@ -474,36 +437,9 @@ class TidalForcing:
             An instance of the TidalForcing class.
         """
         filepath = Path(filepath)
-        # Read the entire file content
-        with filepath.open("r") as file:
-            file_content = file.read()
-
-        # Split the content into YAML documents
-        documents = list(yaml.safe_load_all(file_content))
-
-        tidal_forcing_data = None
-
-        # Process the YAML documents
-        for doc in documents:
-            if doc is None:
-                continue
-            if "TidalForcing" in doc:
-                tidal_forcing_data = doc["TidalForcing"]
-                break
-
-        if tidal_forcing_data is None:
-            raise ValueError("No TidalForcing configuration found in the YAML file.")
-
-        # Convert the model_reference_date from string to datetime
-        tidal_forcing_params = tidal_forcing_data
-        tidal_forcing_params["model_reference_date"] = datetime.fromisoformat(
-            tidal_forcing_params["model_reference_date"]
-        )
 
-        # Create Grid instance from the YAML file
         grid = Grid.from_yaml(filepath)
-
-        # Create and return an instance of TidalForcing
+        tidal_forcing_params = _from_yaml(cls, filepath)
         return cls(grid=grid, **tidal_forcing_params, use_dask=use_dask)
 
     def _correct_tides(self, data):