eo-tides 0.3.0__py3-none-any.whl → 0.4.0__py3-none-any.whl

eo_tides/utils.py

@@ -6,6 +6,7 @@ import os
 import pathlib
 import textwrap
 import warnings
+from collections import Counter
 from typing import List, Union
 
 import numpy as np
@@ -23,6 +24,14 @@ from tqdm import tqdm
 DatetimeLike = Union[np.ndarray, pd.DatetimeIndex, pd.Timestamp, datetime.datetime, str, List[str]]
 
 
+def _get_duplicates(array):
+    """
+    Return any duplicates in a list or array.
+    """
+    c = Counter(array)
+    return [k for k in c if c[k] > 1]
+
+
 def _set_directory(
     directory: str | os.PathLike | None = None,
 ) -> os.PathLike:
@@ -68,6 +77,99 @@ def _standardise_time(
     return np.atleast_1d(time)
 
 
+def _standardise_models(
+    model: str | list[str],
+    directory: str | os.PathLike,
+    ensemble_models: list[str] | None = None,
+) -> tuple[list[str], list[str], list[str] | None]:
+    """
+    Take an input model name or list of names, and return a list
+    of models to process, requested models, and ensemble models,
+    as required by the `model_tides` function.
+
+    Handles two special values passed to `model`: "all", which
+    will model tides for all models available in `directory`, and
+    "ensemble", which will model tides for all models in a list
+    of custom ensemble models.
+    """
+
+    # Turn inputs into arrays for consistent handling
+    models_requested = list(np.atleast_1d(model))
+
+    # Raise error if list contains duplications
+    duplicates = _get_duplicates(models_requested)
+    if len(duplicates) > 0:
+        raise ValueError(f"The model parameter contains duplicate values: {duplicates}")
+
+    # Get full list of supported models from pyTMD database
+    available_models, valid_models = list_models(
+        directory, show_available=False, show_supported=False, raise_error=True
+    )
+    custom_options = ["ensemble", "all"]
+
+    # Error if any models are not supported
+    if not all(m in valid_models + custom_options for m in models_requested):
+        error_text = (
+            f"One or more of the requested models are not valid:\n"
+            f"{models_requested}\n\n"
+            "The following models are supported:\n"
+            f"{valid_models}"
+        )
+        raise ValueError(error_text)
+
+    # Error if any models are not available in `directory`
+    if not all(m in available_models + custom_options for m in models_requested):
+        error_text = (
+            f"One or more of the requested models are valid, but not available in `{directory}`:\n"
+            f"{models_requested}\n\n"
+            f"The following models are available in `{directory}`:\n"
+            f"{available_models}"
+        )
+        raise ValueError(error_text)
+
+    # If "all" models are requested, update requested list to include available models
+    if "all" in models_requested:
+        models_requested = available_models + [m for m in models_requested if m != "all"]
+
+    # If "ensemble" modeling is requested, use custom list of ensemble models
+    if "ensemble" in models_requested:
+        print("Running ensemble tide modelling")
+        ensemble_models = (
+            ensemble_models
+            if ensemble_models is not None
+            else [
+                "EOT20",
+                "FES2012",
+                "FES2014_extrapolated",
+                "FES2022_extrapolated",
+                "GOT4.10",
+                "GOT5.6_extrapolated",
+                "TPXO10-atlas-v2-nc",
+                "TPXO8-atlas-nc",
+                "TPXO9-atlas-v5-nc",
+            ]
+        )
+
+        # Error if any ensemble models are not available in `directory`
+        if not all(m in available_models for m in ensemble_models):
+            error_text = (
+                f"One or more of the requested ensemble models are not available in `{directory}`:\n"
+                f"{ensemble_models}\n\n"
+                f"The following models are available in `{directory}`:\n"
+                f"{available_models}"
+            )
+            raise ValueError(error_text)
+
+        # Return set of all ensemble plus any other requested models
+        models_to_process = sorted(list(set(ensemble_models + [m for m in models_requested if m != "ensemble"])))
+
+    # Otherwise, models to process are the same as those requested
+    else:
+        models_to_process = models_requested
+
+    return models_to_process, models_requested, ensemble_models
+
+
 def _clip_model_file(
     nc: xr.Dataset,
     bbox: BoundingBox,
@@ -178,7 +280,7 @@ def clip_models(
     output_directory: str | os.PathLike,
     bbox: tuple[float, float, float, float],
     model: list | None = None,
-    buffer: float = 1,
+    buffer: float = 5,
     overwrite: bool = False,
 ):
     """
@@ -211,7 +313,7 @@ def clip_models(
         in the input directly.
     buffer : float, optional
         Buffer distance (in degrees) added to the bounding box to provide
-        sufficient data on edges of study area. Defaults to 1 degree.
+        sufficient data on edges of study area. Defaults to 5 degrees.
     overwrite : bool, optional
         If True, overwrite existing files in the output directory.
         Defaults to False.
@@ -393,7 +495,14 @@ def list_models(
     expected_paths = {}
     for m in supported_models:
         model_file = model_database[m]["model_file"]
-        model_file = model_file[0] if isinstance(model_file, list) else model_file
+
+        # Handle GOT5.6 differently to ensure we test for presence of GOT5.6 constituents
+        if m in ("GOT5.6", "GOT5.6_extrapolated"):
+            model_file = [file for file in model_file if "GOT5.6" in file][0]
+        else:
+            model_file = model_file[0] if isinstance(model_file, list) else model_file
+
+        # Add path to dict
         expected_paths[m] = str(directory / pathlib.Path(model_file).expanduser().parent)
 
     # Define column widths

eo_tides/validation.py

@@ -5,6 +5,7 @@ from numbers import Number
 
 import geopandas as gpd
 import pandas as pd
+import tqdm
 from odc.geo.geom import BoundingBox
 from pandas.tseries.offsets import MonthBegin, MonthEnd, YearBegin, YearEnd
 from scipy import stats
@@ -152,21 +153,24 @@ def _load_gauge_metadata(metadata_path):
 
 
 def _load_gesla_dataset(site, path, na_value):
-    with warnings.catch_warnings():
-        warnings.simplefilter("ignore", FutureWarning)
-        gesla_df = (
-            pd.read_csv(
-                path,
-                skiprows=41,
-                names=["date", "time", "sea_level", "qc_flag", "use_flag"],
-                sep=r"\s+",  # sep="\s+",
-                parse_dates=[[0, 1]],
-                index_col=0,
-                na_values=na_value,
-            )
-            .rename_axis("time")
-            .assign(site_code=site)
+    # Read dataset
+    gesla_df = pd.read_csv(
+        path,
+        skiprows=41,
+        names=["date", "time", "sea_level", "qc_flag", "use_flag"],
+        sep=r"\s+",
+        na_values=na_value,
+    )
+
+    # Combine two date fields
+    gesla_df = (
+        gesla_df.assign(
+            time=pd.to_datetime(gesla_df["date"] + " " + gesla_df["time"]),
+            site_code=site,
         )
+        .drop(columns=["date"])
+        .set_index("time")
+    )
 
     return gesla_df
 
@@ -301,13 +305,11 @@ def load_gauge_gesla(
     paths_na = metadata_df.loc[site_code, ["file_name", "null_value"]]
 
     # Load and combine into a single dataframe
-    data_df = (
-        pd.concat([_load_gesla_dataset(s, p, na_value=na) for s, p, na in paths_na.itertuples()])
-        .sort_index()
-        .loc[slice(start_time, end_time)]
-        .reset_index()
-        .set_index("site_code")
-    )
+    gauge_list = [
+        _load_gesla_dataset(s, p, na_value=na)
+        for s, p, na in tqdm.tqdm(paths_na.itertuples(), total=len(paths_na), desc="Loading GESLA gauges")
+    ]
+    data_df = pd.concat(gauge_list).sort_index().loc[slice(start_time, end_time)].reset_index().set_index("site_code")
 
     # Optionally filter by use flag column
     if filter_use_flag:

{eo_tides-0.3.0.dist-info → eo_tides-0.4.0.dist-info}/METADATA

@@ -1,9 +1,9 @@
 Metadata-Version: 2.1
 Name: eo-tides
-Version: 0.3.0
+Version: 0.4.0
 Summary: Tide modelling tools for large-scale satellite earth observation analysis
-Author: Stephen Sagar, Claire Phillips, Vanessa Newey
-Author-email: Robbi Bishop-Taylor <Robbi.BishopTaylor@ga.gov.au>
+Author: Robbi Bishop-Taylor, Stephen Sagar, Claire Phillips, Vanessa Newey
+Author-email: Robbi.BishopTaylor@ga.gov.au
 Project-URL: Homepage, https://GeoscienceAustralia.github.io/eo-tides/
 Project-URL: Repository, https://github.com/GeoscienceAustralia/eo-tides
 Project-URL: Documentation, https://GeoscienceAustralia.github.io/eo-tides/
@@ -24,26 +24,27 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: <4.0,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: colorama >=0.4.3
-Requires-Dist: geopandas >=0.10.0
-Requires-Dist: matplotlib >=3.8.0
-Requires-Dist: numpy >=1.26.0
-Requires-Dist: odc-geo >=0.4.7
-Requires-Dist: pandas >=2.2.0
-Requires-Dist: psutil >=5.8.0
-Requires-Dist: pyproj >=3.6.1
-Requires-Dist: pyTMD ==2.1.8
-Requires-Dist: scikit-learn >=1.4.0
-Requires-Dist: scipy >=1.11.2
-Requires-Dist: shapely >=2.0.6
-Requires-Dist: tqdm >=4.55.0
-Requires-Dist: xarray >=2022.3.0
+Requires-Dist: colorama>=0.4.3
+Requires-Dist: geopandas>=0.10.0
+Requires-Dist: matplotlib>=3.8.0
+Requires-Dist: numpy>=1.26.0
+Requires-Dist: odc-geo>=0.4.7
+Requires-Dist: pandas>=2.2.0
+Requires-Dist: psutil>=5.8.0
+Requires-Dist: pyogrio>=0.7.0
+Requires-Dist: pyproj>=3.6.1
+Requires-Dist: pyTMD==2.2.0
+Requires-Dist: scikit-learn>=1.4.0
+Requires-Dist: scipy>=1.11.2
+Requires-Dist: shapely>=2.0.6
+Requires-Dist: tqdm>=4.55.0
+Requires-Dist: xarray>=2022.3.0
 Provides-Extra: notebooks
-Requires-Dist: odc-stac >=0.3.10 ; extra == 'notebooks'
-Requires-Dist: odc-geo[tiff,warp] >=0.4.7 ; extra == 'notebooks'
-Requires-Dist: pystac-client >=0.8.3 ; extra == 'notebooks'
-Requires-Dist: folium >=0.16.0 ; extra == 'notebooks'
-Requires-Dist: planetary-computer >=1.0.0 ; extra == 'notebooks'
+Requires-Dist: odc-stac>=0.3.10; extra == "notebooks"
+Requires-Dist: odc-geo[tiff,warp]>=0.4.7; extra == "notebooks"
+Requires-Dist: pystac-client>=0.8.3; extra == "notebooks"
+Requires-Dist: folium>=0.16.0; extra == "notebooks"
+Requires-Dist: planetary_computer>=1.0.0; extra == "notebooks"
 
 # `eo-tides`: Tide modelling tools for large-scale satellite earth observation analysis
 

eo_tides-0.4.0.dist-info/RECORD

@@ -0,0 +1,11 @@
+eo_tides/__init__.py,sha256=pGvVlxMKiYjm_273G-oYcOgVuPra7uEdNZv0oN1i69c,1693
+eo_tides/eo.py,sha256=d4zFs_uhuTekJDDqiX7oIzvS1iP6nEr0rG2Yy4xbsEU,22746
+eo_tides/model.py,sha256=X_nuYkBbzq3cLgJc0dUknlL6w_90O9rz_2BOqX5uxsg,34585
+eo_tides/stats.py,sha256=-nL6Ay6TvA5GSdnglHoLMu5JZf6-YjQKERBGLjAZs34,22993
+eo_tides/utils.py,sha256=9xJ1q-b-TVHg5zFyLy6AT_srrPQDvmFdWJmlGSPaJF0,26563
+eo_tides/validation.py,sha256=KP8WLT5z7KLFjQ9oDla7VJOyLQAK4SVbcz2ySAbsbwI,11882
+eo_tides-0.4.0.dist-info/LICENSE,sha256=owxWsXViCL2J6Ks3XYhot7t4Y93nstmXAT95Zf030Cc,11350
+eo_tides-0.4.0.dist-info/METADATA,sha256=cqO3zJGPj-l5Xzi-cfPtkd7pzUUTt5ENVvCRM16HXFQ,8045
+eo_tides-0.4.0.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+eo_tides-0.4.0.dist-info/top_level.txt,sha256=lXZDUUM1DlLdKWHRn8zdmtW8Rx-eQOIWVvt0b8VGiyQ,9
+eo_tides-0.4.0.dist-info/RECORD,,

{eo_tides-0.3.0.dist-info → eo_tides-0.4.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

eo_tides-0.3.0.dist-info/RECORD

@@ -1,11 +0,0 @@
-eo_tides/__init__.py,sha256=rn6slQP0bAhqM9cL2W8omiEM8f0b7libt6WsQ5DvYTE,1655
-eo_tides/eo.py,sha256=Vc_AHqT0_IDqdwbOpNcONjHhiCtbCe8Osk2gvzUeNmU,22377
-eo_tides/model.py,sha256=T0IFvSiXjiTvlY-Vi7-jneHPfaCLt95pmcRd8CZxOjE,34478
-eo_tides/stats.py,sha256=lchWWJ5gBDuZWvaD8TF-12Xlo2qCWiNI2IcgAaKWy2U,22668
-eo_tides/utils.py,sha256=tqXAkLk_Dm8s3yuXPxBBkHW3PZ42ayV8VCQjNw3wDZw,22433
-eo_tides/validation.py,sha256=UREsc0yWRO4x0PJXvyoIx8gYiBZiRSim4z6TmAz_VDM,11857
-eo_tides-0.3.0.dist-info/LICENSE,sha256=owxWsXViCL2J6Ks3XYhot7t4Y93nstmXAT95Zf030Cc,11350
-eo_tides-0.3.0.dist-info/METADATA,sha256=lajVK9XoAA2fJqA9R3HHYJ7iUJFMtmxh3U07uGTs4_4,8040
-eo_tides-0.3.0.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-eo_tides-0.3.0.dist-info/top_level.txt,sha256=lXZDUUM1DlLdKWHRn8zdmtW8Rx-eQOIWVvt0b8VGiyQ,9
-eo_tides-0.3.0.dist-info/RECORD,,