## dea_coastaltools.py
"""
Coastal analysis and tide modelling tools.
License: The code in this notebook is licensed under the Apache License,
Version 2.0 (https://www.apache.org/licenses/LICENSE-2.0). Digital Earth
Australia data is licensed under the Creative Commons by Attribution 4.0
license (https://creativecommons.org/licenses/by/4.0/).
Contact: If you need assistance, post a question on the Open Data Cube
Slack channel (http://slack.opendatacube.org/) or the GIS Stack Exchange
(https://gis.stackexchange.com/questions/ask?tags=open-data-cube) using
the `open-data-cube` tag (you can view previously asked questions here:
https://gis.stackexchange.com/questions/tagged/open-data-cube).
If you would like to report an issue with this script, you can file one
on GitHub (https://github.com/GeoscienceAustralia/dea-notebooks/issues/new).
Last modified: November 2023
"""
# Import required packages
import os
import pyproj
import pathlib
import warnings
import scipy.interpolate
import numpy as np
import xarray as xr
import pandas as pd
import geopandas as gpd
import matplotlib.pyplot as plt
import matplotlib.colors as colors
from scipy import stats
from warnings import warn
from functools import partial
from shapely.geometry import box, shape
from owslib.wfs import WebFeatureService
from datacube.utils.geometry import CRS
from dea_tools.datahandling import parallel_apply
# Fix converters for tidal plot
from pandas.plotting import register_matplotlib_converters
register_matplotlib_converters()
WFS_ADDRESS = "https://geoserver.dea.ga.gov.au/geoserver/wfs"
[docs]
def transect_distances(transects_gdf, lines_gdf, mode="distance"):
"""
Take a set of transects (e.g. shore-normal beach survey lines), and
determine the distance along the transect to each object in a set of
lines (e.g. shorelines). Distances are measured in the CRS of the
input datasets.
For coastal applications, transects should be drawn from land to
water (with the first point being on land so that it can be used
as a consistent location from which to measure distances.
The distance calculation can be performed using two modes:
- 'distance': Distances are measured from the start of the
transect to where it intersects with each line. Any transect
that intersects a line more than once is ignored. This mode is
useful for measuring e.g. the distance to the shoreline over
time from a consistent starting location.
- 'width' Distances are measured between the first and last
intersection between a transect and each line. Any transect
that intersects a line only once is ignored. This is useful
for e.g. measuring the width of a narrow area of coastline over
time, e.g. the neck of a spit or tombolo.
Parameters
----------
transects_gdf : geopandas.GeoDataFrame
A GeoDataFrame containing one or multiple vector profile lines.
The GeoDataFrame's index column will be used to name the rows in
the output distance table.
lines_gdf : geopandas.GeoDataFrame
A GeoDataFrame containing one or multiple vector line features
that intersect the profile lines supplied to `transects_gdf`.
The GeoDataFrame's index column will be used to name the columns
in the output distance table.
mode : string, optional
Whether to use 'distance' (for measuring distances from the
start of a profile) or 'width' mode (for measuring the width
between two profile intersections). See docstring above for more
info; defaults to 'distance'.
Returns
-------
distance_df : pandas.DataFrame
A DataFrame containing distance measurements for each profile
line (rows) and line feature (columns).
"""
import warnings
from shapely.errors import ShapelyDeprecationWarning
from shapely.geometry import Point
def _intersect_dist(transect_gdf, lines_gdf, mode=mode):
"""
Take an individual transect, and determine the distance along
the transect to each object in a set of lines (e.g. shorelines).
"""
# Identify intersections between transects and lines
intersect_points = lines_gdf.apply(
lambda x: x.geometry.intersection(transect_gdf.geometry), axis=1
)
# In distance mode, identify transects with one intersection only,
# and use this as the end point and the start of the transect as the
# start point when measuring distances
if mode == "distance":
start_point = Point(transect_gdf.geometry.coords[0])
point_df = intersect_points.apply(
lambda x: pd.Series({"start": start_point, "end": x})
if x.type == "Point"
else pd.Series({"start": None, "end": None})
)
# In width mode, identify transects with multiple intersections, and
# use the first intersection as the start point and the second
# intersection for the end point when measuring distances
if mode == "width":
point_df = intersect_points.apply(
lambda x: pd.Series({"start": x.geoms[0], "end": x.geoms[-1]})
if x.type == "MultiPoint"
else pd.Series({"start": None, "end": None})
)
# Calculate distances between valid start and end points
distance_df = point_df.apply(
lambda x: x.start.distance(x.end) if x.start else None, axis=1
)
return distance_df
# Run code after ignoring Shapely pre-v2.0 warnings
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=ShapelyDeprecationWarning)
# Assert that both datasets use the same CRS
assert transects_gdf.crs == lines_gdf.crs, (
"Please ensure both " "input datasets use the same CRS."
)
# Run distance calculations
distance_df = transects_gdf.apply(
lambda x: _intersect_dist(x, lines_gdf), axis=1
)
return pd.DataFrame(distance_df)
[docs]
def get_coastlines(
bbox: tuple, crs="EPSG:4326", layer="shorelines_annual", drop_wms=True
) -> gpd.GeoDataFrame:
"""
Load DEA Coastlines annual shorelines or rates of change points data
for a provided bounding box using WFS.
For a full description of the DEA Coastlines dataset, refer to the
official Geoscience Australia product description:
/data/product/dea-coastlines
Parameters
----------
bbox : (xmin, ymin, xmax, ymax), or geopandas object
Bounding box expressed as a tutple. Alternatively, a bounding
box can be automatically extracted by suppling a
geopandas.GeoDataFrame or geopandas.GeoSeries.
crs : str, optional
Optional CRS for the bounding box. This is ignored if `bbox`
is provided as a geopandas object.
layer : str, optional
Which DEA Coastlines layer to load. Options include the annual
shoreline vectors ("shorelines_annual") and the rates of change
points ("rates_of_change"). Defaults to "shorelines_annual".
drop_wms : bool, optional
Whether to drop WMS-specific attribute columns from the data.
These columns are used for visualising the dataset on DEA Maps,
and are unlikely to be useful for scientific analysis. Defaults
to True.
Returns
-------
gpd.GeoDataFrame
A GeoDataFrame containing shoreline or point features and
associated metadata.
"""
# If bbox is a geopandas object, convert to bbox
try:
crs = str(bbox.crs)
bbox = bbox.total_bounds
except:
pass
# Query WFS
wfs = WebFeatureService(url=WFS_ADDRESS, version="1.1.0")
layer_name = f"dea:{layer}"
response = wfs.getfeature(
typename=layer_name,
bbox=tuple(bbox) + (crs,),
outputFormat="json",
)
# Load data as a geopandas.GeoDataFrame
coastlines_gdf = gpd.read_file(response)
# Clip to extent of bounding box
extent = gpd.GeoSeries(box(*bbox), crs=crs).to_crs(coastlines_gdf.crs)
coastlines_gdf = coastlines_gdf.clip(extent)
# Optionally drop WMS-specific columns
if drop_wms:
coastlines_gdf = coastlines_gdf.loc[
:, ~coastlines_gdf.columns.str.contains("wms_")
]
return coastlines_gdf
def _model_tides(
model,
x,
y,
time,
directory,
crs,
method,
extrapolate,
cutoff,
output_units,
mode,
):
"""
Worker function applied in parallel by `model_tides`. Handles the
extraction of tide modelling constituents and tide modelling using
`pyTMD`.
"""
import pyTMD.constants
import pyTMD.eop
import pyTMD.io
import pyTMD.time
import pyTMD.io.model
import pyTMD.predict
import pyTMD.spatial
import pyTMD.utilities
# Get parameters for tide model; use custom definition file for
# FES2012 (leave this as an undocumented feature for now)
if model == "FES2012":
pytmd_model = pyTMD.io.model(directory).from_file(
directory / "model_FES2012.def"
)
elif model == "TPXO8-atlas-v1":
pytmd_model = pyTMD.io.model(directory).from_file(directory / "model_TPXO8.def")
else:
pytmd_model = pyTMD.io.model(
directory, format="netcdf", compressed=False
).elevation(model)
# Convert x, y to latitude/longitude
transformer = pyproj.Transformer.from_crs(crs, "EPSG:4326", always_xy=True)
lon, lat = transformer.transform(x.flatten(), y.flatten())
# Convert datetime
timescale = pyTMD.time.timescale().from_datetime(time.flatten())
# Read tidal constants and interpolate to grid points
if pytmd_model.format in ("OTIS", "ATLAS", "ESR"):
amp, ph, D, c = pyTMD.io.OTIS.extract_constants(
lon,
lat,
pytmd_model.grid_file,
pytmd_model.model_file,
pytmd_model.projection,
type=pytmd_model.type,
method=method,
extrapolate=extrapolate,
cutoff=cutoff,
grid=pytmd_model.format,
)
# Use delta time at 2000.0 to match TMD outputs
deltat = np.zeros((len(timescale)), dtype=np.float64)
elif pytmd_model.format == "netcdf":
amp, ph, D, c = pyTMD.io.ATLAS.extract_constants(
lon,
lat,
pytmd_model.grid_file,
pytmd_model.model_file,
type=pytmd_model.type,
method=method,
extrapolate=extrapolate,
cutoff=cutoff,
scale=pytmd_model.scale,
compressed=pytmd_model.compressed,
)
# Use delta time at 2000.0 to match TMD outputs
deltat = np.zeros((len(timescale)), dtype=np.float64)
elif pytmd_model.format == "GOT":
amp, ph, c = pyTMD.io.GOT.extract_constants(
lon,
lat,
pytmd_model.model_file,
method=method,
extrapolate=extrapolate,
cutoff=cutoff,
scale=pytmd_model.scale,
compressed=pytmd_model.compressed,
)
# Delta time (TT - UT1)
deltat = timescale.tt_ut1
elif pytmd_model.format == "FES":
amp, ph = pyTMD.io.FES.extract_constants(
lon,
lat,
pytmd_model.model_file,
type=pytmd_model.type,
version=pytmd_model.version,
method=method,
extrapolate=extrapolate,
cutoff=cutoff,
scale=pytmd_model.scale,
compressed=pytmd_model.compressed,
)
# Available model constituents
c = pytmd_model.constituents
# Delta time (TT - UT1)
deltat = timescale.tt_ut1
# Calculate complex phase in radians for Euler's
cph = -1j * ph * np.pi / 180.0
# Calculate constituent oscillation
hc = amp * np.exp(cph)
# Determine the number of points and times to process. If in
# "one-to-many" mode, these counts are used to repeat our extracted
# constituents and timesteps so we can extract tides for all
# combinations of our input times and tide modelling points.
# If in "one-to-one" mode, we avoid this step by setting counts to 1
# (e.g. "repeat 1 times")
points_repeat = len(x) if mode == "one-to-many" else 1
time_repeat = len(time) if mode == "one-to-many" else 1
# If in "one-to-many" mode, repeat constituents to length of time
# and number of input coords before passing to `predict_tide_drift`
t, hc, deltat = (
np.tile(timescale.tide, points_repeat),
hc.repeat(time_repeat, axis=0),
np.tile(deltat, points_repeat),
)
# Predict tidal elevations at time and infer minor corrections
npts = len(t)
tide = np.ma.zeros((npts), fill_value=np.nan)
tide.mask = np.any(hc.mask, axis=1)
# Predict tides
tide.data[:] = pyTMD.predict.drift(
t, hc, c, deltat=deltat, corrections=pytmd_model.format
)
minor = pyTMD.predict.infer_minor(
t, hc, c, deltat=deltat, corrections=pytmd_model.format
)
tide.data[:] += minor.data[:]
# Replace invalid values with fill value
tide.data[tide.mask] = tide.fill_value
# Convert data to pandas.DataFrame, and set index to our input
# time/x/y values
tide_df = pd.DataFrame(
{
"time": np.tile(time, points_repeat),
"x": np.repeat(x, time_repeat),
"y": np.repeat(y, time_repeat),
"tide_model": model,
"tide_m": tide,
}
).set_index(["time", "x", "y"])
# Optionally convert outputs to integer units (can save memory)
if output_units == "m":
tide_df["tide_m"] = tide_df.tide_m.astype(np.float32)
elif output_units == "cm":
tide_df["tide_m"] = (tide_df.tide_m * 100).astype(np.int16)
elif output_units == "mm":
tide_df["tide_m"] = (tide_df.tide_m * 1000).astype(np.int16)
return tide_df
[docs]
def model_tides(
x,
y,
time,
model="FES2014",
directory=None,
crs="EPSG:4326",
method="spline",
extrapolate=True,
cutoff=None,
mode="one-to-many",
parallel=True,
parallel_splits=5,
output_units="m",
output_format="long",
epsg=None,
):
"""
Compute tides at multiple points and times using tidal harmonics.
This function supports any tidal model supported by
`pyTMD`, including the FES2014 Finite Element Solution
tide model, and the TPXO8-atlas and TPXO9-atlas-v5
TOPEX/POSEIDON global tide models.
This function requires access to tide model data files.
These should be placed in a folder with subfolders matching
the formats specified by `pyTMD`:
https://pytmd.readthedocs.io/en/latest/getting_started/Getting-Started.html#directories
For FES2014 (https://www.aviso.altimetry.fr/es/data/products/auxiliary-products/global-tide-fes/description-fes2014.html):
- {directory}/fes2014/ocean_tide/
- {directory}/fes2014/load_tide/
For TPXO8-atlas (https://www.tpxo.net/tpxo-products-and-registration):
- {directory}/tpxo8_atlas/
For TPXO9-atlas-v5 (https://www.tpxo.net/tpxo-products-and-registration):
- {directory}/TPXO9_atlas_v5/
For EOT20 (https://www.seanoe.org/data/00683/79489/):
- {directory}/EOT20/ocean_tides/
- {directory}/EOT20/load_tides/
For GOT4.10c (https://earth.gsfc.nasa.gov/geo/data/ocean-tide-models):
- {directory}/GOT4.10c/grids_oceantide_netcdf/
For HAMTIDE (https://www.cen.uni-hamburg.de/en/icdc/data/ocean/hamtide.html):
- {directory}/hamtide/
This function is a modification of the `pyTMD` package's
`compute_tide_corrections` function. For more info:
https://pytmd.readthedocs.io/en/stable/user_guide/compute_tide_corrections.html
Parameters:
-----------
x, y : float or list of floats
One or more x and y coordinates used to define
the location at which to model tides. By default these
coordinates should be lat/lon; use "crs" if they
are in a custom coordinate reference system.
time : A datetime array or pandas.DatetimeIndex
An array containing `datetime64[ns]` values or a
`pandas.DatetimeIndex` providing the times at which to
model tides in UTC time.
model : string, optional
The tide model used to model tides. Options include:
- "FES2014" (only pre-configured option on DEA Sandbox)
- "TPXO9-atlas-v5"
- "TPXO8-atlas"
- "EOT20"
- "HAMTIDE11"
- "GOT4.10"
directory : string, optional
The directory containing tide model data files. If no path is
provided, this will default to the environment variable
"DEA_TOOLS_TIDE_MODELS" if set, otherwise "/var/share/tide_models".
Tide modelling files should be stored in sub-folders for each
model that match the structure provided by `pyTMD`:
https://pytmd.readthedocs.io/en/latest/getting_started/Getting-Started.html#directories
For example:
- {directory}/fes2014/ocean_tide/
{directory}/fes2014/load_tide/
- {directory}/tpxo8_atlas/
- {directory}/TPXO9_atlas_v5/
crs : str, optional
Input coordinate reference system for x and y coordinates.
Defaults to "EPSG:4326" (WGS84; degrees latitude, longitude).
method : string, optional
Method used to interpolate tidal contsituents
from model files. Options include:
- "spline": scipy bivariate spline interpolation (default)
- "bilinear": quick bilinear interpolation
- "linear", "nearest": scipy regular grid interpolations
extrapolate : bool, optional
Whether to extrapolate tides for x and y coordinates outside of
the valid tide modelling domain using nearest-neighbor.
cutoff : int or float, optional
Extrapolation cutoff in kilometers. The default is None, which
will extrapolate for all points regardless of distance from the
valid tide modelling domain.
mode : string, optional
The analysis mode to use for tide modelling. Supports two options:
- "one-to-many": Models tides for every timestep in "time" at
every input x and y coordinate point. This is useful if you
want to model tides for a specific list of timesteps across
multiple spatial points (e.g. for the same set of satellite
acquisition times at various locations across your study area).
- "one-to-one": Model tides using a different timestep for each
x and y coordinate point. In this mode, the number of x and
y points must equal the number of timesteps provided in "time".
parallel : boolean, optional
Whether to parallelise tide modelling using `concurrent.futures`.
If multiple tide models are requested, these will be run in
parallel. Optionally, tide modelling can also be run in parallel
across input x and y coordinates (see "parallel_splits" below).
Default is True.
parallel_splits : int, optional
Whether to split the input x and y coordinates into smaller,
evenly-sized chunks that are processed in parallel. This can
provide a large performance boost when processing large numbers
of coordinates. The default is 5 chunks, which will split
coordinates into 5 parallelised chunks.
output_units : str, optional
Whether to return modelled tides in floating point metre units,
or integer centimetre units (i.e. scaled by 100) or integer
millimetre units (i.e. scaled by 1000. Returning outputs in
integer units can be useful for reducing memory usage.
Defaults to "m" for metres; set to "cm" for centimetres or "mm"
for millimetres.
output_format : str, optional
Whether to return the output dataframe in long format (with
results stacked vertically along "tide_model" and "tide_m"
columns), or wide format (with a column for each tide model).
Defaults to "long".
epsg : int, DEPRECATED
Deprecated; use "crs" instead.
Returns
-------
A pandas.DataFrame containing tide heights for every
combination of time and point coordinates.
"""
# Deprecate `epsg` param
if epsg is not None:
warn(
"The `epsg` parameter is deprecated; please use `crs` to "
"provide CRS information in the form 'EPSG:XXXX'",
DeprecationWarning,
stacklevel=2,
)
# Set tide modelling files directory. If no custom path is provided,
# first try global environmental var, then "/var/share/tide_models"
if directory is None:
if "DEA_TOOLS_TIDE_MODELS" in os.environ:
directory = os.environ["DEA_TOOLS_TIDE_MODELS"]
else:
directory = "/var/share/tide_models"
# Verify path exists
directory = pathlib.Path(directory).expanduser()
if not directory.exists():
raise FileNotFoundError("Invalid tide directory")
# If time passed as a single Timestamp, convert to datetime64
if isinstance(time, pd.Timestamp):
time = time.to_datetime64()
# Turn inputs into arrays for consistent handling
model = np.atleast_1d(model)
x = np.atleast_1d(x)
y = np.atleast_1d(y)
time = np.atleast_1d(time)
# Validate input arguments
assert method in ("bilinear", "spline", "linear", "nearest")
assert output_units in (
"m",
"cm",
"mm",
), "Output units must be either 'm', 'cm', or 'mm'."
assert output_format in (
"long",
"wide",
), "Output format must be either 'long' or 'wide'."
assert len(x) == len(y), "x and y must be the same length."
if mode == "one-to-one":
assert len(x) == len(time), (
"The number of supplied x and y points and times must be "
"identical in 'one-to-one' mode. Use 'one-to-many' mode if "
"you intended to model multiple timesteps at each point."
)
# Verify that all provided models are in list of supported models
valid_models = [
"FES2014",
"TPXO9-atlas-v5",
"TPXO8-atlas",
"EOT20",
"HAMTIDE11",
"GOT4.10",
"FES2012", # Requires custom tide model definition file
"TPXO8-atlas-v1", # Requires custom tide model definition file
]
if not all(m in valid_models for m in model):
raise ValueError(
f"One or more of the models requested {model} is not valid. "
f"The following models are currently supported: {valid_models}"
)
# Update tide modelling func to add default keyword arguments that
# are used for every iteration during parallel processing
iter_func = partial(
_model_tides,
directory=directory,
crs=crs,
method=method,
extrapolate=extrapolate,
cutoff=np.inf if cutoff is None else cutoff,
output_units=output_units,
mode=mode,
)
# Ensure requested parallel splits is not smaller than number of points
parallel_splits = min(parallel_splits, len(x))
# Parallelise if either multiple models or multiple splits requested
if parallel & ((len(model) > 1) | (parallel_splits > 1)):
from concurrent.futures import ProcessPoolExecutor
from tqdm import tqdm
with ProcessPoolExecutor() as executor:
print(f"Modelling tides using {', '.join(model)} in parallel")
# Optionally split lon/lat points into `splits_n` chunks
# that will be applied in parallel
x_split = np.array_split(x, parallel_splits)
y_split = np.array_split(y, parallel_splits)
# Get every combination of models and lat/lon points, and
# extract as iterables that can be passed to `executor.map()`
# In "one-to-many" mode, pass entire set of timesteps to each
# parallel iteration by repeating timesteps by number of total
# parallel iterations. In "one-to-one" mode, split up
# timesteps into smaller parallel chunks too.
if mode == "one-to-many":
model_iters, x_iters, y_iters = zip(
*[
(m, x_split[i], y_split[i])
for m in model
for i in range(parallel_splits)
]
)
time_iters = [time] * len(model_iters)
elif mode == "one-to-one":
time_split = np.array_split(time, parallel_splits)
model_iters, x_iters, y_iters, time_iters = zip(
*[
(m, x_split[i], y_split[i], time_split[i])
for m in model
for i in range(parallel_splits)
]
)
# Apply func in parallel, iterating through each input param
model_outputs = list(
tqdm(
executor.map(iter_func, model_iters, x_iters, y_iters, time_iters),
total=len(model_iters),
)
)
# Model tides in series if parallelisation is off
else:
model_outputs = []
for model_i in model:
print(f"Modelling tides using {model_i}")
tide_df = iter_func(model_i, x, y, time)
model_outputs.append(tide_df)
# Combine outputs into a single dataframe
tide_df = pd.concat(model_outputs, axis=0)
# Optionally convert to a wide format dataframe with a tide model in
# each dataframe column
if output_format == "wide":
# Pivot into wide format with each time model as a column
print("Converting to a wide format dataframe")
tide_df = tide_df.pivot(columns="tide_model", values="tide_m")
# If in 'one-to-one' mode, reindex using our input time/x/y
# values to ensure the output is sorted the same as our inputs
if mode == "one-to-one":
output_indices = pd.MultiIndex.from_arrays(
[time, x, y], names=["time", "x", "y"]
)
tide_df = tide_df.reindex(output_indices)
return tide_df
def _pixel_tides_resample(
tides_lowres,
ds,
resample_method="bilinear",
dask_chunks="auto",
dask_compute=True,
):
"""
Resamples low resolution tides modelled by `pixel_tides` into the
geobox (e.g. spatial resolution and extent) of the original higher
resolution satellite dataset.
Parameters:
-----------
tides_lowres : xarray.DataArray
The low resolution tide modelling data array to be resampled.
ds : xarray.Dataset
The dataset whose geobox will be used as the template for the
resampling operation. This is typically the same satellite
dataset originally passed to `pixel_tides`.
resample_method : string, optional
The resampling method to use. Defaults to "bilinear"; valid
options include "nearest", "cubic", "min", "max", "average" etc.
dask_chunks : str or tuple, optional
Can be used to configure custom Dask chunking for the final
resampling step. The default of "auto" will automatically set
x/y chunks to match those in `ds` if they exist, otherwise will
set x/y chunks that cover the entire extent of the dataset.
For custom chunks, provide a tuple in the form `(y, x)`, e.g.
`(2048, 2048)`.
dask_compute : bool, optional
Whether to compute results of the resampling step using Dask.
If False, this will return `tides_highres` as a Dask array.
Returns:
--------
tides_highres, tides_lowres : tuple of xr.DataArrays
In addition to `tides_lowres` (see above), a high resolution
array of tide heights will be generated matching the
exact spatial resolution and extent of `ds`.
"""
# Determine spatial dimensions
y_dim, x_dim = ds.odc.spatial_dims
# Convert array to Dask, using no chunking along y and x dims,
# and a single chunk for each timestep/quantile and tide model
tides_lowres_dask = tides_lowres.chunk(
{d: None if d in [y_dim, x_dim] else 1 for d in tides_lowres.dims}
)
# Automatically set Dask chunks for reprojection if set to "auto".
# This will either use x/y chunks if they exist in `ds`, else
# will cover the entire x and y dims) so we don't end up with
# hundreds of tiny x and y chunks due to the small size of
# `tides_lowres` (possible odc.geo bug?)
if dask_chunks == "auto":
if ds.chunks is not None:
if (y_dim in ds.chunks) & (x_dim in ds.chunks):
dask_chunks = (ds.chunks[y_dim], ds.chunks[x_dim])
else:
dask_chunks = ds.odc.geobox.shape
else:
dask_chunks = ds.odc.geobox.shape
# Reproject into the GeoBox of `ds` using odc.geo and Dask
tides_highres = tides_lowres_dask.odc.reproject(
how=ds.odc.geobox,
chunks=dask_chunks,
resampling=resample_method,
).rename("tide_m")
# Optionally process and load into memory with Dask
if dask_compute:
tides_highres.load()
return tides_highres, tides_lowres
[docs]
def pixel_tides(
ds,
times=None,
resample=True,
calculate_quantiles=None,
resolution=None,
buffer=None,
resample_method="bilinear",
model="FES2014",
dask_chunks="auto",
dask_compute=True,
**model_tides_kwargs,
):
"""
Obtain tide heights for each pixel in a dataset by modelling
tides into a low-resolution grid surrounding the dataset,
then (optionally) spatially resample this low-res data back
into the original higher resolution dataset extent and resolution.
Parameters:
-----------
ds : xarray.Dataset
A dataset whose geobox (`ds.odc.geobox`) will be used to define
the spatial extent of the low resolution tide modelling grid.
times : pandas.DatetimeIndex or list of pandas.Timestamps, optional
By default, the function will model tides using the times
contained in the `time` dimension of `ds`. Alternatively, this
param can be used to model tides for a custom set of times
instead. For example:
`times=pd.date_range(start="2000", end="2001", freq="5h")`
resample : bool, optional
Whether to resample low resolution tides back into `ds`'s original
higher resolution grid. Set this to `False` if you do not want
low resolution tides to be re-projected back to higher resolution.
calculate_quantiles : list or np.array, optional
Rather than returning all individual tides, low-resolution tides
can be first aggregated using a quantile calculation by passing in
a list or array of quantiles to compute. For example, this could
be used to calculate the min/max tide across all times:
`calculate_quantiles=[0.0, 1.0]`.
resolution: int, optional
The desired resolution of the low-resolution grid used for tide
modelling. The default None will create a 5000 m resolution grid
if `ds` has a projected CRS (i.e. metre units), or a 0.05 degree
resolution grid if `ds` has a geographic CRS (e.g. degree units).
Note: higher resolutions do not necessarily provide better
tide modelling performance, as results will be limited by the
resolution of the underlying global tide model (e.g. 1/16th
degree / ~5 km resolution grid for FES2014).
buffer : int, optional
The amount by which to buffer the higher resolution grid extent
when creating the new low resolution grid. This buffering is
important as it ensures that ensure pixel-based tides are seamless
across dataset boundaries. This buffer will eventually be clipped
away when the low-resolution data is re-projected back to the
resolution and extent of the higher resolution dataset. To
ensure that at least two pixels occur outside of the dataset
bounds, the default None applies a 12000 m buffer if `ds` has a
projected CRS (i.e. metre units), or a 0.12 degree buffer if
`ds` has a geographic CRS (e.g. degree units).
resample_method : string, optional
If resampling is requested (see `resample` above), use this
resampling method when converting from low resolution to high
resolution pixels. Defaults to "bilinear"; valid options include
"nearest", "cubic", "min", "max", "average" etc.
model : string or list of strings
The tide model or a list of models used to model tides, as
supported by the `pyTMD` Python package. Options include:
- "FES2014" (default; pre-configured on DEA Sandbox)
- "TPXO8-atlas"
- "TPXO9-atlas-v5"
- "EOT20"
- "HAMTIDE11"
- "GOT4.10"
dask_chunks : str or tuple, optional
Can be used to configure custom Dask chunking for the final
resampling step. The default of "auto" will automatically set
x/y chunks to match those in `ds` if they exist, otherwise will
set x/y chunks that cover the entire extent of the dataset.
For custom chunks, provide a tuple in the form `(y, x)`, e.g.
`(2048, 2048)`.
dask_compute : bool, optional
Whether to compute results of the resampling step using Dask.
If False, this will return `tides_highres` as a Dask array.
**model_tides_kwargs :
Optional parameters passed to the `dea_tools.coastal.model_tides`
function. Important parameters include "directory" (used to
specify the location of input tide modelling files) and "cutoff"
(used to extrapolate modelled tides away from the coast; if not
specified here, cutoff defaults to `np.inf`).
Returns:
--------
If `resample` is False:
tides_lowres : xr.DataArray
A low resolution data array giving either tide heights every
timestep in `ds` (if `times` is None), tide heights at every
time in `times` (if `times` is not None), or tide height quantiles
for every quantile provided by `calculate_quantiles`.
If `resample` is True:
tides_highres, tides_lowres : tuple of xr.DataArrays
In addition to `tides_lowres` (see above), a high resolution
array of tide heights will be generated that matches the
exact spatial resolution and extent of `ds`. This will contain
either tide heights every timestep in `ds` (if `times` is None),
tide heights at every time in `times` (if `times` is not None),
or tide height quantiles for every quantile provided by
`calculate_quantiles`.
"""
import odc.geo.xr
from odc.geo.geobox import GeoBox
# First test if no time dimension and nothing passed to `times`
if ("time" not in ds.dims) & (times is None):
raise ValueError(
"`ds` does not contain a 'time' dimension. Times are required "
"for modelling tides: please pass in a set of custom tides "
"using the `times` parameter. For example: "
"`times=pd.date_range(start='2000', end='2001', freq='5h')`"
)
# If custom times are provided, convert them to a consistent
# pandas.DatatimeIndex format
if times is not None:
if isinstance(times, list):
time_coords = pd.DatetimeIndex(times)
elif isinstance(times, pd.Timestamp):
time_coords = pd.DatetimeIndex([times])
else:
time_coords = times
# Otherwise, use times from `ds` directly
else:
time_coords = ds.coords["time"]
# Set defaults passed to `model_tides`
model_tides_kwargs.setdefault("cutoff", np.inf)
# Standardise model into a list for easy handling
model = [model] if isinstance(model, str) else model
# Test if no time dimension and nothing passed to `times`
if ("time" not in ds.dims) & (times is None):
raise ValueError(
"`ds` does not contain a 'time' dimension. Times are required "
"for modelling tides: please pass in a set of custom tides "
"using the `times` parameter. For example: "
"`times=pd.date_range(start='2000', end='2001', freq='5h')`"
)
# If custom times are provided, convert them to a consistent
# pandas.DatatimeIndex format
if times is not None:
if isinstance(times, list):
time_coords = pd.DatetimeIndex(times)
elif isinstance(times, pd.Timestamp):
time_coords = pd.DatetimeIndex([times])
else:
time_coords = times
# Otherwise, use times from `ds` directly
else:
time_coords = ds.coords["time"]
# Determine spatial dimensions
y_dim, x_dim = ds.odc.spatial_dims
# Determine resolution and buffer, using different defaults for
# geographic (i.e. degrees) and projected (i.e. metres) CRSs:
crs_units = ds.odc.geobox.crs.units[0][0:6]
if ds.odc.geobox.crs.geographic:
if resolution is None:
resolution = 0.05
elif resolution > 360:
raise ValueError(
f"A resolution of greater than 360 was "
f"provided, but `ds` has a geographic CRS "
f"in {crs_units} units. Did you accidently "
f"provide a resolution in projected "
f"(i.e. metre) units?"
)
if buffer is None:
buffer = 0.12
else:
if resolution is None:
resolution = 5000
elif resolution < 1:
raise ValueError(
f"A resolution of less than 1 was provided, "
f"but `ds` has a projected CRS in "
f"{crs_units} units. Did you accidently "
f"provide a resolution in geographic "
f"(degree) units?"
)
if buffer is None:
buffer = 12000
# Raise error if resolution is less than dataset resolution
dataset_res = ds.odc.geobox.resolution.x
if resolution < dataset_res:
raise ValueError(
f"The resolution of the low-resolution tide "
f"modelling grid ({resolution:.2f}) is less "
f"than `ds`'s pixel resolution ({dataset_res:.2f}). "
f"This can cause extremely slow tide modelling "
f"performance. Please select provide a resolution "
f"greater than {dataset_res:.2f} using "
f"`pixel_tides`'s 'resolution' parameter."
)
# Create a new reduced resolution tide modelling grid after
# first buffering the grid
print(
f"Creating reduced resolution {resolution} x {resolution} "
f"{crs_units} tide modelling array"
)
buffered_geobox = ds.odc.geobox.buffered(buffer)
rescaled_geobox = GeoBox.from_bbox(
bbox=buffered_geobox.boundingbox, resolution=resolution
)
rescaled_ds = odc.geo.xr.xr_zeros(rescaled_geobox)
# Flatten grid to 1D, then add time dimension
flattened_ds = rescaled_ds.stack(z=(x_dim, y_dim))
flattened_ds = flattened_ds.expand_dims(dim={"time": time_coords.values})
# Model tides in parallel, returning a pandas.DataFrame
tide_df = model_tides(
x=flattened_ds[x_dim],
y=flattened_ds[y_dim],
time=flattened_ds.time,
crs=f"EPSG:{ds.odc.geobox.crs.epsg}",
model=model,
**model_tides_kwargs,
)
# Convert our pandas.DataFrame tide modelling outputs to xarray
tides_lowres = (
# Rename x and y dataframe indexes to match x and y xarray dims
tide_df.rename_axis(["time", x_dim, y_dim])
# Add tide model column to dataframe indexes so we can convert
# our dataframe to a multidimensional xarray
.set_index("tide_model", append=True)
# Convert to xarray and select our tide modelling xr.DataArray
.to_xarray()
.tide_m
# Re-index and transpose into our input coordinates and dim order
.reindex_like(rescaled_ds)
.transpose("tide_model", "time", y_dim, x_dim)
)
# Optionally calculate and return quantiles rather than raw data.
# Set dtype to dtype of the input data as quantile always returns
# float64 (memory intensive)
if calculate_quantiles is not None:
print("Computing tide quantiles")
tides_lowres = tides_lowres.quantile(q=calculate_quantiles, dim="time").astype(
tides_lowres.dtype
)
# If only one tidal model exists, squeeze out "tide_model" dim
if len(tides_lowres.tide_model) == 1:
tides_lowres = tides_lowres.squeeze("tide_model")
# Ensure CRS is present before we apply any resampling
tides_lowres = tides_lowres.odc.assign_crs(ds.odc.geobox.crs)
# Reproject into original high resolution grid
if resample:
print("Reprojecting tides into original array")
tides_highres, tides_lowres = _pixel_tides_resample(
tides_lowres, ds, resample_method, dask_chunks, dask_compute
)
return tides_highres, tides_lowres
else:
print("Returning low resolution tide array")
return tides_lowres
[docs]
def tidal_tag(
ds,
ebb_flow=False,
swap_dims=False,
tidepost_lat=None,
tidepost_lon=None,
return_tideposts=False,
**model_tides_kwargs,
):
"""
Takes an xarray.Dataset and returns the same dataset with a new
`tide_m` variable giving the height of the tide at the exact
moment of each satellite acquisition.
The function models tides at the centroid of the dataset by default,
but a custom tidal modelling location can be specified using
`tidepost_lat` and `tidepost_lon`.
The default settings use the FES2014 global tidal model, implemented
using the pyTMD Python package. FES2014 was produced by NOVELTIS,
LEGOS, CLS Space Oceanography Division and CNES. It is distributed
by AVISO, with support from CNES (http://www.aviso.altimetry.fr/).
Parameters
----------
ds : xarray.Dataset
An xarray.Dataset object with x, y and time dimensions
ebb_flow : bool, optional
An optional boolean indicating whether to compute if the
tide phase was ebbing (falling) or flowing (rising) for each
observation. The default is False; if set to True, a new
`ebb_flow` variable will be added to the dataset with each
observation labelled with 'Ebb' or 'Flow'.
swap_dims : bool, optional
An optional boolean indicating whether to swap the `time`
dimension in the original xarray.Dataset to the new
`tide_m` variable. Defaults to False.
tidepost_lat, tidepost_lon : float or int, optional
Optional coordinates used to model tides. The default is None,
which uses the centroid of the dataset as the tide modelling
location.
return_tideposts : bool, optional
An optional boolean indicating whether to return the `tidepost_lat`
and `tidepost_lon` location used to model tides in addition to the
xarray.Dataset. Defaults to False.
**model_tides_kwargs :
Optional parameters passed to the `dea_tools.coastal.model_tides`
function. Important parameters include "model" and "directory",
used to specify the tide model to use and the location of its files.
Returns
-------
The original xarray.Dataset with a new `tide_m` variable giving
the height of the tide (and optionally, its ebb-flow phase) at the
exact moment of each satellite acquisition (if `return_tideposts=True`,
the function will also return the `tidepost_lon` and `tidepost_lat`
location used in the analysis).
"""
import odc.geo.xr
# If custom tide modelling locations are not provided, use the
# dataset centroid
if not tidepost_lat or not tidepost_lon:
tidepost_lon, tidepost_lat = ds.odc.geobox.geographic_extent.centroid.coords[0]
print(
f"Setting tide modelling location from dataset centroid: "
f"{tidepost_lon:.2f}, {tidepost_lat:.2f}"
)
else:
print(
f"Using user-supplied tide modelling location: "
f"{tidepost_lon:.2f}, {tidepost_lat:.2f}"
)
# Use tidal model to compute tide heights for each observation:
# model = (
# "FES2014" if "model" not in model_tides_kwargs else model_tides_kwargs["model"]
# )
tide_df = model_tides(
x=tidepost_lon,
y=tidepost_lat,
time=ds.time,
crs="EPSG:4326",
**model_tides_kwargs,
)
# If tides cannot be successfully modeled (e.g. if the centre of the
# xarray dataset is located is over land), raise an exception
if tide_df.tide_m.isnull().all():
raise ValueError(
f"Tides could not be modelled for dataset centroid located "
f"at {tidepost_lon:.2f}, {tidepost_lat:.2f}. This can occur if "
f"this coordinate occurs over land. Please manually specify "
f"a tide modelling location located over water using the "
f"`tidepost_lat` and `tidepost_lon` parameters."
)
# Assign tide heights to the dataset as a new variable
ds["tide_m"] = xr.DataArray(tide_df.tide_m, coords=[ds.time])
# Optionally calculate the tide phase for each observation
if ebb_flow:
# Model tides for a time 15 minutes prior to each previously
# modelled satellite acquisition time. This allows us to compare
# tide heights to see if they are rising or falling.
print("Modelling tidal phase (e.g. ebb or flow)")
tide_pre_df = model_tides(
x=tidepost_lon,
y=tidepost_lat,
time=(ds.time - pd.Timedelta("15 min")),
crs="EPSG:4326",
**model_tides_kwargs,
)
# Compare tides computed for each timestep. If the previous tide
# was higher than the current tide, the tide is 'ebbing'. If the
# previous tide was lower, the tide is 'flowing'
tidal_phase = [
"Ebb" if i else "Flow"
for i in tide_pre_df.tide_m.values > tide_df.tide_m.values
]
# Assign tide phase to the dataset as a new variable
ds["ebb_flow"] = xr.DataArray(tidal_phase, coords=[ds.time])
# If swap_dims = True, make tide height the primary dimension
# instead of time
if swap_dims:
# Swap dimensions and sort by tide height
ds = ds.swap_dims({"time": "tide_m"})
ds = ds.sortby("tide_m")
ds = ds.drop_vars("time")
if return_tideposts:
return ds, tidepost_lon, tidepost_lat
else:
return ds
[docs]
def tidal_stats(
ds,
tidepost_lat=None,
tidepost_lon=None,
plain_english=True,
plot=True,
modelled_freq="2h",
linear_reg=False,
round_stats=3,
**model_tides_kwargs,
):
"""
Takes an xarray.Dataset and statistically compares the tides
modelled for each satellite observation against the full modelled
tidal range. This comparison can be used to evaluate whether the
tides observed by satellites (e.g. Landsat) are biased compared to
the natural tidal range (e.g. fail to observe either the highest or
lowest tides etc).
For more information about the tidal statistics computed by this
function, refer to Figure 8 in Bishop-Taylor et al. 2018:
https://www.sciencedirect.com/science/article/pii/S0272771418308783#fig8
The function models tides at the centroid of the dataset by default,
but a custom tidal modelling location can be specified using
`tidepost_lat` and `tidepost_lon`.
The default settings use the FES2014 global tidal model, implemented
using the pyTMD Python package. FES2014 was produced by NOVELTIS,
LEGOS, CLS Space Oceanography Division and CNES. It is distributed
by AVISO, with support from CNES (http://www.aviso.altimetry.fr/).
Parameters
----------
ds : xarray.Dataset
An xarray.Dataset object with x, y and time dimensions
tidepost_lat, tidepost_lon : float or int, optional
Optional coordinates used to model tides. The default is None,
which uses the centroid of the dataset as the tide modelling
location.
plain_english : bool, optional
An optional boolean indicating whether to print a plain english
version of the tidal statistics to the screen. Defaults to True.
plot : bool, optional
An optional boolean indicating whether to plot how satellite-
observed tide heights compare against the full tidal range.
Defaults to True.
modelled_freq : str, optional
An optional string giving the frequency at which to model tides
when computing the full modelled tidal range. Defaults to '2h',
which computes a tide height for every two hours across the
temporal extent of `ds`.
linear_reg: bool, optional
Experimental: whether to return linear regression stats that
assess whether dstellite-observed and all available tides show
any decreasing or increasing trends over time. Not currently
recommended as all observed regressions always return as
significant due to far larger sample size.
round_stats : int, optional
The number of decimal places used to round the output statistics.
Defaults to 3.
**model_tides_kwargs :
Optional parameters passed to the `dea_tools.coastal.model_tides`
function. Important parameters include "model" and "directory",
used to specify the tide model to use and the location of its files.
Returns
-------
A pandas.Series object containing the following statistics:
tidepost_lat: latitude used for modelling tide heights
tidepost_lon: longitude used for modelling tide heights
observed_min_m: minimum tide height observed by the satellite
all_min_m: minimum tide height from all available tides
observed_max_m: maximum tide height observed by the satellite
all_max_m: maximum tide height from all available tides
observed_range_m: tidal range observed by the satellite
all_range_m: full astronomical tidal range based on all
available tides
spread_m: proportion of the full astronomical tidal range observed
by the satellite (see Bishop-Taylor et al. 2018)
low_tide_offset: proportion of the lowest tides never observed
by the satellite (see Bishop-Taylor et al. 2018)
high_tide_offset: proportion of the highest tides never observed
by the satellite (see Bishop-Taylor et al. 2018)
If `linear_reg = True`, the output will also contain:
observed_slope: slope of any relationship between observed tide
heights and time
all_slope: slope of any relationship between all available tide
heights and time
observed_pval: significance/p-value of any relationship between
observed tide heights and time
all_pval: significance/p-value of any relationship between
all available tide heights and time
"""
# Model tides for each observation in the supplied xarray object
ds_tides, tidepost_lon, tidepost_lat = tidal_tag(
ds,
tidepost_lat=tidepost_lat,
tidepost_lon=tidepost_lon,
return_tideposts=True,
**model_tides_kwargs,
)
# Drop spatial ref for nicer plotting
if "spatial_ref" in ds_tides:
ds_tides = ds_tides.drop_vars("spatial_ref")
# Generate range of times covering entire period of satellite record
all_timerange = pd.date_range(
start=ds_tides.time.min().item(),
end=ds_tides.time.max().item(),
freq=modelled_freq,
)
# Model tides for each timestep
all_tides_df = model_tides(
x=tidepost_lon,
y=tidepost_lat,
time=all_timerange,
crs="EPSG:4326",
**model_tides_kwargs,
)
# Get coarse statistics on all and observed tidal ranges
obs_mean = ds_tides.tide_m.mean().item()
all_mean = all_tides_df.tide_m.mean()
obs_min, obs_max = ds_tides.tide_m.quantile([0.0, 1.0]).values
all_min, all_max = all_tides_df.tide_m.quantile([0.0, 1.0]).values
# Calculate tidal range
obs_range = obs_max - obs_min
all_range = all_max - all_min
# Calculate Bishop-Taylor et al. 2018 tidal metrics
spread = obs_range / all_range
low_tide_offset = abs(all_min - obs_min) / all_range
high_tide_offset = abs(all_max - obs_max) / all_range
print(all_tides_df)
# Extract x (time in decimal years) and y (distance) values
all_times = all_tides_df.index.get_level_values("time")
all_x = (
all_times.year + ((all_times.dayofyear - 1) / 365) + ((all_times.hour - 1) / 24)
)
all_y = all_tides_df.tide_m.values.astype(np.float32)
time_period = all_x.max() - all_x.min()
# Extract x (time in decimal years) and y (distance) values
obs_x = (
ds_tides.time.dt.year
+ ((ds_tides.time.dt.dayofyear - 1) / 365)
+ ((ds_tides.time.dt.hour - 1) / 24)
)
obs_y = ds_tides.tide_m.values.astype(np.float32)
# Compute linear regression
obs_linreg = stats.linregress(x=obs_x, y=obs_y)
all_linreg = stats.linregress(x=all_x, y=all_y)
if plain_english:
print(
f"\n{spread:.0%} of the {all_range:.2f} m modelled astronomical "
f"tidal range is observed at this location.\nThe lowest "
f"{low_tide_offset:.0%} and highest {high_tide_offset:.0%} "
f"of astronomical tides are never observed.\n"
)
if linear_reg:
if obs_linreg.pvalue > 0.05:
print(
f"Observed tides show no significant trends "
f"over the ~{time_period:.0f} year period."
)
else:
obs_slope_desc = "decrease" if obs_linreg.slope < 0 else "increase"
print(
f"Observed tides {obs_slope_desc} significantly "
f"(p={obs_linreg.pvalue:.3f}) over time by "
f"{obs_linreg.slope:.03f} m per year (i.e. a "
f"~{time_period * obs_linreg.slope:.2f} m "
f"{obs_slope_desc} over the ~{time_period:.0f} year period)."
)
if all_linreg.pvalue > 0.05:
print(
f"All tides show no significant trends "
f"over the ~{time_period:.0f} year period."
)
else:
all_slope_desc = "decrease" if all_linreg.slope < 0 else "increase"
print(
f"All tides {all_slope_desc} significantly "
f"(p={all_linreg.pvalue:.3f}) over time by "
f"{all_linreg.slope:.03f} m per year (i.e. a "
f"~{time_period * all_linreg.slope:.2f} m "
f"{all_slope_desc} over the ~{time_period:.0f} year period)."
)
if plot:
# Create plot and add all time and observed tide data
fig, ax = plt.subplots(figsize=(10, 5))
all_tides_df.reset_index(["x", "y"]).tide_m.plot(ax=ax, alpha=0.4)
ds_tides.tide_m.plot.line(
ax=ax, marker="o", linewidth=0.0, color="black", markersize=2
)
# Add horizontal lines for spread/offsets
ax.axhline(obs_min, color="black", linestyle=":", linewidth=1)
ax.axhline(obs_max, color="black", linestyle=":", linewidth=1)
ax.axhline(all_min, color="black", linestyle=":", linewidth=1)
ax.axhline(all_max, color="black", linestyle=":", linewidth=1)
# Add text annotations for spread/offsets
ax.annotate(
f" High tide\n offset ({high_tide_offset:.0%})",
xy=(all_timerange.max(), np.mean([all_max, obs_max])),
va="center",
)
ax.annotate(
f" Spread\n ({spread:.0%})",
xy=(all_timerange.max(), np.mean([obs_min, obs_max])),
va="center",
)
ax.annotate(
f" Low tide\n offset ({low_tide_offset:.0%})",
xy=(all_timerange.max(), np.mean([all_min, obs_min])),
)
# Remove top right axes and add labels
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
ax.set_ylabel("Tide height (m)")
ax.set_xlabel("")
ax.margins(x=0.015)
# Export pandas.Series containing tidal stats
output_stats = {
"tidepost_lat": tidepost_lat,
"tidepost_lon": tidepost_lon,
"observed_mean_m": obs_mean,
"all_mean_m": all_mean,
"observed_min_m": obs_min,
"all_min_m": all_min,
"observed_max_m": obs_max,
"all_max_m": all_max,
"observed_range_m": obs_range,
"all_range_m": all_range,
"spread": spread,
"low_tide_offset": low_tide_offset,
"high_tide_offset": high_tide_offset,
}
if linear_reg:
output_stats.update(
{
"observed_slope": obs_linreg.slope,
"all_slope": all_linreg.slope,
"observed_pval": obs_linreg.pvalue,
"all_pval": all_linreg.pvalue,
}
)
return pd.Series(output_stats).round(round_stats)
[docs]
def tidal_tag_otps(
ds,
tidepost_lat=None,
tidepost_lon=None,
ebb_flow=False,
swap_dims=False,
return_tideposts=False,
):
"""
Takes an xarray.Dataset and returns the same dataset with a new
`tide_m` variable giving the height of the tide at the exact
moment of each satellite acquisition.
By default, the function models tides for the centroid of the
dataset, but a custom tidal modelling location can be specified
using `tidepost_lat` and `tidepost_lon`.
Tides are modelled using the OTPS tidal modelling software based on
the TPXO8 tidal model: http://volkov.oce.orst.edu/tides/tpxo8_atlas.html
Parameters
----------
ds : xarray.Dataset
An xarray.Dataset object with x, y and time dimensions
tidepost_lat, tidepost_lon : float or int, optional
Optional coordinates used to model tides. The default is None,
which uses the centroid of the dataset as the tide modelling
location.
ebb_flow : bool, optional
An optional boolean indicating whether to compute if the
tide phase was ebbing (falling) or flowing (rising) for each
observation. The default is False; if set to True, a new
`ebb_flow` variable will be added to the dataset with each
observation labelled with 'Ebb' or 'Flow'.
swap_dims : bool, optional
An optional boolean indicating whether to swap the `time`
dimension in the original xarray.Dataset to the new
`tide_m` variable. Defaults to False.
return_tideposts : bool, optional
An optional boolean indicating whether to return the `tidepost_lat`
and `tidepost_lon` location used to model tides in addition to the
xarray.Dataset. Defaults to False.
Returns
-------
The original xarray.Dataset with a new `tide_m` variable giving
the height of the tide (and optionally, its ebb-flow phase) at the
exact moment of each satellite acquisition (if `return_tideposts=True`,
the function will also return the `tidepost_lon` and `tidepost_lat`
location used in the analysis).
"""
# Load tide modelling functions from either OTPS for pyfes
try:
from otps import TimePoint
from otps import predict_tide
except ImportError:
from dea_tools.pyfes_model import TimePoint, predict_tide
# If custom tide modelling locations are not provided, use the
# dataset centroid
if not tidepost_lat or not tidepost_lon:
tidepost_lon, tidepost_lat = ds.extent.centroid.to_crs(
crs=CRS("EPSG:4326")
).coords[0]
print(
f"Setting tide modelling location from dataset centroid: "
f"{tidepost_lon:.2f}, {tidepost_lat:.2f}"
)
else:
print(
f"Using user-supplied tide modelling location: "
f"{tidepost_lon:.2f}, {tidepost_lat:.2f}"
)
# Use the tidal model to compute tide heights for each observation:
print(f"Modelling tides using OTPS and the TPXO8 tidal model")
obs_datetimes = ds.time.data.astype("M8[s]").astype("O").tolist()
obs_timepoints = [TimePoint(tidepost_lon, tidepost_lat, dt) for dt in obs_datetimes]
obs_predictedtides = predict_tide(obs_timepoints)
# If tides cannot be successfully modeled (e.g. if the centre of the
# xarray dataset is located is over land), raise an exception
if len(obs_predictedtides) > 0:
# Extract tide heights
obs_tideheights = [predictedtide.tide_m for predictedtide in obs_predictedtides]
# Assign tide heights to the dataset as a new variable
ds["tide_m"] = xr.DataArray(obs_tideheights, coords=[ds.time])
# Optionally calculate the tide phase for each observation
if ebb_flow:
# Model tides for a time 15 minutes prior to each previously
# modelled satellite acquisition time. This allows us to compare
# tide heights to see if they are rising or falling.
print("Modelling tidal phase (e.g. ebb or flow)")
pre_times = ds.time - pd.Timedelta("15 min")
pre_datetimes = pre_times.data.astype("M8[s]").astype("O").tolist()
pre_timepoints = [
TimePoint(tidepost_lon, tidepost_lat, dt) for dt in pre_datetimes
]
pre_predictedtides = predict_tide(pre_timepoints)
# Compare tides computed for each timestep. If the previous tide
# was higher than the current tide, the tide is 'ebbing'. If the
# previous tide was lower, the tide is 'flowing'
tidal_phase = [
"Ebb" if pre.tide_m > obs.tide_m else "Flow"
for pre, obs in zip(pre_predictedtides, obs_predictedtides)
]
# Assign tide phase to the dataset as a new variable
ds["ebb_flow"] = xr.DataArray(tidal_phase, coords=[ds.time])
# If swap_dims = True, make tide height the primary dimension
# instead of time
if swap_dims:
# Swap dimensions and sort by tide height
ds = ds.swap_dims({"time": "tide_m"})
ds = ds.sortby("tide_m")
ds = ds.drop_vars("time")
if return_tideposts:
return ds, tidepost_lon, tidepost_lat
else:
return ds
else:
raise ValueError(
f"Tides could not be modelled for dataset centroid located "
f"at {tidepost_lon:.2f}, {tidepost_lat:.2f}. This can occur if "
f"this coordinate occurs over land. Please manually specify "
f"a tide modelling location located over water using the "
f"`tidepost_lat` and `tidepost_lon` parameters."
)
[docs]
def tidal_stats_otps(
ds,
tidepost_lat=None,
tidepost_lon=None,
plain_english=True,
plot=True,
modelled_freq="2h",
linear_reg=False,
round_stats=3,
):
"""
Takes an xarray.Dataset and statistically compares the tides
modelled for each satellite observation against the full modelled
tidal range. This comparison can be used to evaluate whether the
tides observed by satellites (e.g. Landsat) are biased compared to
the natural tidal range (e.g. fail to observe either the highest or
lowest tides etc).
By default, the function models tides for the centroid of the
dataset, but a custom tidal modelling location can be specified
using `tidepost_lat` and `tidepost_lon`.
For more information about the tidal statistics computed by this
function, refer to Figure 8 in Bishop-Taylor et al. 2018:
https://www.sciencedirect.com/science/article/pii/S0272771418308783#fig8
Tides are modelled using the OTPS tidal modelling software based on
the TPXO8 tidal model: http://volkov.oce.orst.edu/tides/tpxo8_atlas.html
Parameters
----------
ds : xarray.Dataset
An xarray.Dataset object with x, y and time dimensions
tidepost_lat, tidepost_lon : float or int, optional
Optional coordinates used to model tides. The default is None,
which uses the centroid of the dataset as the tide modelling
location.
plain_english : bool, optional
An optional boolean indicating whether to print a plain english
version of the tidal statistics to the screen. Defaults to True.
plot : bool, optional
An optional boolean indicating whether to plot how satellite-
observed tide heights compare against the full tidal range.
Defaults to True.
modelled_freq : str, optional
An optional string giving the frequency at which to model tides
when computing the full modelled tidal range. Defaults to '2h',
which computes a tide height for every two hours across the
temporal extent of `ds`.
linear_reg: bool, optional
Experimental: whether to return linear regression stats that
assess whether dstellite-observed and all available tides show
any decreasing or increasing trends over time. Not currently
recommended as all observed regressions always return as
significant due to far larger sample size.
round_stats : int, optional
The number of decimal places used to round the output statistics.
Defaults to 3.
Returns
-------
A pandas.Series object containing the following statistics:
tidepost_lat: latitude used for modelling tide heights
tidepost_lon: longitude used for modelling tide heights
observed_min_m: minimum tide height observed by the satellite
all_min_m: minimum tide height from all available tides
observed_max_m: maximum tide height observed by the satellite
all_max_m: maximum tide height from all available tides
observed_range_m: tidal range observed by the satellite
all_range_m: full astronomical tidal range based on all
available tides
spread_m: proportion of the full astronomical tidal range observed
by the satellite (see Bishop-Taylor et al. 2018)
low_tide_offset: proportion of the lowest tides never observed
by the satellite (see Bishop-Taylor et al. 2018)
high_tide_offset: proportion of the highest tides never observed
by the satellite (see Bishop-Taylor et al. 2018)
If `linear_reg = True`, the output will also contain:
observed_slope: slope of any relationship between observed tide
heights and time
all_slope: slope of any relationship between all available tide
heights and time
observed_pval: significance/p-value of any relationship between
observed tide heights and time
all_pval: significance/p-value of any relationship between
all available tide heights and time
"""
# Load tide modelling functions from either OTPS for pyfes
try:
from otps import TimePoint
from otps import predict_tide
except ImportError:
from dea_tools.pyfes_model import TimePoint, predict_tide
# Model tides for each observation in the supplied xarray object
ds_tides, tidepost_lon, tidepost_lat = tidal_tag_otps(
ds, tidepost_lat=tidepost_lat, tidepost_lon=tidepost_lon, return_tideposts=True
)
# Drop spatial ref for nicer plotting
if "spatial_ref" in ds_tides:
ds_tides = ds_tides.drop_vars("spatial_ref")
# Generate range of times covering entire period of satellite record
all_timerange = pd.date_range(
start=ds_tides.time.min().item(),
end=ds_tides.time.max().item(),
freq=modelled_freq,
)
all_datetimes = all_timerange.values.astype("M8[s]").astype("O").tolist()
# Use the tidal model to compute tide heights for each observation:
all_timepoints = [TimePoint(tidepost_lon, tidepost_lat, dt) for dt in all_datetimes]
all_predictedtides = predict_tide(all_timepoints)
all_tideheights = [predictedtide.tide_m for predictedtide in all_predictedtides]
# Get coarse statistics on all and observed tidal ranges
obs_mean = ds_tides.tide_m.mean().item()
all_mean = np.mean(all_tideheights)
obs_min, obs_max = ds_tides.tide_m.quantile([0.0, 1.0]).values
all_min, all_max = np.quantile(all_tideheights, [0.0, 1.0])
# Calculate tidal range
obs_range = obs_max - obs_min
all_range = all_max - all_min
# Calculate Bishop-Taylor et al. 2018 tidal metrics
spread = obs_range / all_range
low_tide_offset = abs(all_min - obs_min) / all_range
high_tide_offset = abs(all_max - obs_max) / all_range
# Extract x (time in decimal years) and y (distance) values
all_x = (
all_timerange.year
+ ((all_timerange.dayofyear - 1) / 365)
+ ((all_timerange.hour - 1) / 24)
)
all_y = all_tideheights
time_period = all_x.max() - all_x.min()
# Extract x (time in decimal years) and y (distance) values
obs_x = (
ds_tides.time.dt.year
+ ((ds_tides.time.dt.dayofyear - 1) / 365)
+ ((ds_tides.time.dt.hour - 1) / 24)
)
obs_y = ds_tides.tide_m.values.astype(np.float32)
# Compute linear regression
obs_linreg = stats.linregress(x=obs_x, y=obs_y)
all_linreg = stats.linregress(x=all_x, y=all_y)
if plain_english:
print(
f"\n{spread:.0%} of the {all_range:.2f} m modelled astronomical "
f"tidal range is observed at this location.\nThe lowest "
f"{low_tide_offset:.0%} and highest {high_tide_offset:.0%} "
f"of astronomical tides are never observed.\n"
)
if linear_reg:
# Plain english
if obs_linreg.pvalue > 0.05:
print(
f"Observed tides show no significant trends "
f"over the ~{time_period:.0f} year period."
)
else:
obs_slope_desc = "decrease" if obs_linreg.slope < 0 else "increase"
print(
f"Observed tides {obs_slope_desc} significantly "
f"(p={obs_linreg.pvalue:.3f}) over time by "
f"{obs_linreg.slope:.03f} m per year (i.e. a "
f"~{time_period * obs_linreg.slope:.2f} m "
f"{obs_slope_desc} over the ~{time_period:.0f} year period)."
)
if all_linreg.pvalue > 0.05:
print(
f"All tides show no significant trends "
f"over the ~{time_period:.0f} year period."
)
else:
all_slope_desc = "decrease" if all_linreg.slope < 0 else "increase"
print(
f"All tides {all_slope_desc} significantly "
f"(p={all_linreg.pvalue:.3f}) over time by "
f"{all_linreg.slope:.03f} m per year (i.e. a "
f"~{time_period * all_linreg.slope:.2f} m "
f"{all_slope_desc} over the ~{time_period:.0f} year period)."
)
if plot:
# Create plot and add all time and observed tide data
fig, ax = plt.subplots(figsize=(10, 5))
ax.plot(all_timerange, all_tideheights, alpha=0.4)
ds_tides.tide_m.plot.line(
ax=ax, marker="o", linewidth=0.0, color="black", markersize=2
)
# Add horizontal lines for spread/offsets
ax.axhline(obs_min, color="black", linestyle=":", linewidth=1)
ax.axhline(obs_max, color="black", linestyle=":", linewidth=1)
ax.axhline(all_min, color="black", linestyle=":", linewidth=1)
ax.axhline(all_max, color="black", linestyle=":", linewidth=1)
# Add text annotations for spread/offsets
ax.annotate(
f" High tide\n offset ({high_tide_offset:.0%})",
xy=(all_timerange.max(), np.mean([all_max, obs_max])),
va="center",
)
ax.annotate(
f" Spread\n ({spread:.0%})",
xy=(all_timerange.max(), np.mean([obs_min, obs_max])),
va="center",
)
ax.annotate(
f" Low tide\n offset ({low_tide_offset:.0%})",
xy=(all_timerange.max(), np.mean([all_min, obs_min])),
)
# Remove top right axes and add labels
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
ax.set_ylabel("Tide height (m)")
ax.set_xlabel("")
ax.margins(x=0.015)
# Export pandas.Series containing tidal stats
output_stats = {
"tidepost_lat": tidepost_lat,
"tidepost_lon": tidepost_lon,
"observed_mean_m": obs_mean,
"all_mean_m": all_mean,
"observed_min_m": obs_min,
"all_min_m": all_min,
"observed_max_m": obs_max,
"all_max_m": all_max,
"observed_range_m": obs_range,
"all_range_m": all_range,
"spread": spread,
"low_tide_offset": low_tide_offset,
"high_tide_offset": high_tide_offset,
}
if linear_reg:
output_stats.update(
{
"observed_slope": obs_linreg.slope,
"all_slope": all_linreg.slope,
"observed_pval": obs_linreg.pvalue,
"all_pval": all_linreg.pvalue,
}
)
return pd.Series(output_stats).round(round_stats)
[docs]
def glint_angle(solar_azimuth, solar_zenith, view_azimuth, view_zenith):
"""
Calculates glint angles for each pixel in a satellite image based
on the relationship between the solar and sensor zenith and azimuth
viewing angles at the moment the image was acquired.
Glint angle is considered a predictor of sunglint over water; small
glint angles (e.g. < 20 degrees) are associated with a high
probability of sunglint due to the viewing angle of the sensor
being aligned with specular reflectance of the sun from the water's
surface.
Based on code from https://towardsdatascience.com/how-to-implement-
sunglint-detection-for-sentinel-2-images-in-python-using-metadata-
info-155e683d50
Parameters
----------
solar_azimuth : array-like
Array of solar azimuth angles in degrees. In DEA Collection 3,
this is contained in the "oa_solar_azimuth" band.
solar_zenith : array-like
Array of solar zenith angles in degrees. In DEA Collection 3,
this is contained in the "oa_solar_zenith" band.
view_azimuth : array-like
Array of sensor/viewing azimuth angles in degrees. In DEA
Collection 3, this is contained in the "oa_satellite_azimuth"
band.
view_zenith : array-like
Array of sensor/viewing zenith angles in degrees. In DEA
Collection 3, this is contained in the "oa_satellite_view" band.
Returns
-------
glint_array : numpy.ndarray
Array of glint angles in degrees. Small values indicate higher
probabilities of sunglint.
"""
# Convert angle arrays to radians
solar_zenith_rad = np.deg2rad(solar_zenith)
solar_azimuth_rad = np.deg2rad(solar_azimuth)
view_zenith_rad = np.deg2rad(view_zenith)
view_azimuth_rad = np.deg2rad(view_azimuth)
# Calculate sunglint angle
phi = solar_azimuth_rad - view_azimuth_rad
glint_angle = np.cos(view_zenith_rad) * np.cos(solar_zenith_rad) - np.sin(
view_zenith_rad
) * np.sin(solar_zenith_rad) * np.cos(phi)
# Convert to degrees
glint_array = np.degrees(np.arccos(glint_angle))
return glint_array
