From 270a06b80d9aa3ea91d646d40730da7efacc2a64 Mon Sep 17 00:00:00 2001 From: Michael Chin Date: Mon, 14 Sep 2026 14:50:49 +1000 Subject: [PATCH 01/25] Port simple_paleobathymetry Steps 1, 3 and 4 into gplately (#444) Adds gplately.paleobathymetry with age_to_basement_depth() (Step 1: four published thermal-subsidence models), dutkiewicz_2017_sediment_thickness() (Step 3: the Dutkiewicz et al. 2017 age/distance-to-margin polynomial fit), and sediment_isostatic_correction()/paleobathymetry() (Step 4: Sykes 1996 isostatic sediment-load correction), ported from and numerically verified against EarthByte's simple_paleobathymetry workflow. Ships the RHCW18 age-depth lookup table used by the 'rhcw18' model. Step 2 (lifetime-mean distance to the nearest passive continental margin) and Step 5 (pyBacktrack merge) are deliberately not included here: Step 2 needs the proximity/obstacle-routing engine tracked in gplately#445, and Step 5 is tracked in gplately#447. See the module docstring and the #444 comment thread for the reasoning. Co-Authored-By: Claude Sonnet 5 --- gplately/__init__.py | 8 + gplately/data/RHCW18_age_depth.dat | 3001 +++++++++++++++++ gplately/paleobathymetry.py | 355 ++ .../pytestcases/test_9_paleobathymetry.py | 95 + 4 files changed, 3459 insertions(+) create mode 100644 gplately/data/RHCW18_age_depth.dat create mode 100644 gplately/paleobathymetry.py create mode 100644 tests-dir/pytestcases/test_9_paleobathymetry.py diff --git a/gplately/__init__.py b/gplately/__init__.py index f2b442e9..2715e1ec 100644 --- a/gplately/__init__.py +++ b/gplately/__init__.py @@ -52,6 +52,14 @@ from .auxiliary import get_plate_reconstruction, get_gplot from .data_server import DataServer from .raster import Raster +from .paleobathymetry import ( + AGE_DEPTH_MODELS, + DUTKIEWICZ_2017_SEDIMENT_THICKNESS, + age_to_basement_depth, + dutkiewicz_2017_sediment_thickness, + sediment_isostatic_correction, + paleobathymetry, +) from .grids import ( read_netcdf_grid, write_netcdf_grid, diff --git 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See the GNU General Public License +# for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +# + +"""Paleobathymetry of oceanic crust, reconstructed from seafloor age and sediment loading. + +This is a port of the physics in EarthByte's `simple_paleobathymetry +`__ workflow (see its README for the +full derivation and references). Paleobathymetry is computed as:: + + paleobathymetry = basement_depth + sediment_thickness - isostatic_correction + +* :func:`age_to_basement_depth` -- seafloor age -> depth to igneous basement (thermal + subsidence; the *simple_paleobathymetry* workflow's Step 1). +* :func:`dutkiewicz_2017_sediment_thickness` -- seafloor age + distance to the nearest + passive continental margin -> predicted compacted sediment thickness (Dutkiewicz et al., + 2017; Step 3). +* :func:`sediment_isostatic_correction` / :func:`paleobathymetry` -- combine basement depth + and sediment thickness into paleobathymetry, correcting for sediment loading (Sykes, 1996; + Step 4). + +**Not yet included here** (see `gplately#444 `__ +for status): the *simple_paleobathymetry* workflow's Step 2, which computes each ocean point's +lifetime-mean distance to the nearest passive continental margin by reconstructing it backward +through time -- this needs the proximity/obstacle-routing engine tracked in +`gplately#445 `__. Nor Step 5, which merges +this module's output with pyBacktrack's present-day paleobathymetry to also cover submerged +continental crust and long-subducted ocean crust -- tracked in +`gplately#447 `__. Callers must supply their +own distance-to-passive-margin array/grid to :func:`dutkiewicz_2017_sediment_thickness` until +Step 2 lands. +""" + +import math +from importlib.resources import files + +import numpy as np + +__all__ = [ + "AGE_DEPTH_MODELS", + "DUTKIEWICZ_2017_SEDIMENT_THICKNESS", + "age_to_basement_depth", + "dutkiewicz_2017_sediment_thickness", + "sediment_isostatic_correction", + "paleobathymetry", +] + + +# Four published thermal-subsidence (age -> basement depth) models, keyed by their canonical +# name plus the alternative spellings accepted by `age_to_basement_depth`'s `model` argument. +AGE_DEPTH_MODELS = ("gdh1", "rhcw18", "parsons_sclater", "crosby09") + +_AGE_DEPTH_MODEL_ALIASES = { + "gdh1": "gdh1", + "ghd1": "gdh1", + "stein_stein": "gdh1", + "steinstein": "gdh1", + "rhcw18": "rhcw18", + "rchw18": "rhcw18", + "richards": "rhcw18", + "richards18": "rhcw18", + "r18": "rhcw18", + "parsons_sclater": "parsons_sclater", + "ps": "parsons_sclater", + "ps_tbl": "parsons_sclater", + "parsons": "parsons_sclater", + "crosby09": "crosby09", + "crosby": "crosby09", + "crosby_2009": "crosby09", + "cmk09": "crosby09", +} + +# The Richards, Hoggard, Cowton & White (2018) age-depth relationship has no closed-form +# expression, so it ships as a lookup table (age in Ma, depth in m) that we interpolate. +_DEFAULT_RICHARDS_TABLE_FILENAME = str( + files("gplately").joinpath("data", "RHCW18_age_depth.dat") +) +_richards_table_cache = {} + + +def _load_richards_table(richards_table_filename=None): + path = str(richards_table_filename or _DEFAULT_RICHARDS_TABLE_FILENAME) + if path not in _richards_table_cache: + table = np.loadtxt(path) + order = np.argsort(table[:, 0]) + _richards_table_cache[path] = (table[order, 0], table[order, 1]) + return _richards_table_cache[path] + + +def age_to_basement_depth(age, model="gdh1", richards_table_filename=None): + """Convert seafloor age to depth-to-basement using a thermal subsidence model. + + Depth to basement is the seafloor depth *before* any sediment is added on top: as oceanic + lithosphere moves away from a mid-ocean ridge it cools, the mantle lithosphere thickens and + becomes denser, and the column subsides isostatically. + + Parameters + ---------- + age : array_like + Seafloor age in Ma. NaN (no age, e.g. continental crust) stays NaN in the output. + model : str, default: "gdh1" + One of ``"gdh1"`` (Stein & Stein, 1992), ``"rhcw18"`` (Richards, Hoggard, Cowton & + White, 2018), ``"parsons_sclater"`` (Parsons & Sclater, 1977) or ``"crosby09"`` + (Crosby, McKenzie & Sclater, 2009); see :data:`AGE_DEPTH_MODELS`. Common alternative + spellings are also accepted. + richards_table_filename : str, optional + Path to the two-column (age Ma, depth m) age-depth lookup table used by the + ``"rhcw18"`` model. Defaults to the table shipped with GPlately (the RHCW18 preferred + parameters from the `RHCW18_Plate_Model + `__ repository). + + Returns + ------- + numpy.ndarray + Depth to basement in metres, negative downwards, NaN where ``age`` is NaN. + + References + ---------- + * Stein, C.A. & Stein, S. (1992). A model for the global variation in oceanic depth and + heat flow with lithospheric age. *Nature*, 359, 123-129. + * Parsons, B. & Sclater, J.G. (1977). An analysis of the variation of ocean floor + bathymetry and heat flow with age. *JGR*, 82, 803-827. + * Crosby, A.G., McKenzie, D. & Sclater, J.G. (2006); Crosby, A.G. & McKenzie, D. (2009). + The relationship between depth, age and gravity in the oceans; and an analysis of young + ocean depth, gravity and global residual topography. *GJI*. + * Richards, F.D., Hoggard, M.J., Cowton, L.R. & White, N.J. (2018). Reassessing the + thermal structure of oceanic lithosphere with revised global inventories of basement + depths and heat flow measurements. *JGR: Solid Earth*, 123, 9136-9161. + """ + age = np.asarray(age, dtype="float64") + depth = np.full(age.shape, np.nan, dtype="float64") + valid = ~np.isnan(age) + + key = _AGE_DEPTH_MODEL_ALIASES.get(str(model).strip().lower()) + if key is None: + raise ValueError( + f"Unknown age-depth model {model!r}. Choose one of: " + + ", ".join(AGE_DEPTH_MODELS) + ) + + if key == "gdh1": + neg = valid & (age < 0) + young = valid & (age >= 0) & (age <= 20) + old = valid & (age > 20) + depth[neg] = -2600.0 + depth[young] = -(2600.0 + 365.0 * np.sqrt(age[young])) + depth[old] = -(5651.0 - 2473.0 * np.exp(-0.0278 * age[old])) + + elif key == "rhcw18": + ages_tbl, depths_tbl = _load_richards_table(richards_table_filename) + # Ages older than the table's range are held at its deepest value (np.interp's + # default `right`); depths are negated to match this module's sign convention. + depth[valid] = -1.0 * np.interp(age[valid], ages_tbl, depths_tbl, left=0.0) + + elif key == "parsons_sclater": + neg = valid & (age < 0) + young = valid & (age >= 0) & (age < 70) + old = valid & (age >= 70) + depth[neg] = -2500.0 + depth[young] = -(2500.0 + 350.0 * np.sqrt(age[young])) + depth[old] = -(6400.0 - 3200.0 * np.exp(-age[old] / 62.8)) + + else: # crosby09 + young = valid & (age >= 0) & (age <= 75) + mid = valid & (age > 75) & (age <= 160) + old = valid & (age > 160) + depth[young] = -(2652.0 + 324.0 * np.sqrt(age[young])) + depth[mid] = -( + 5028.0 + 5.26 * age[mid] - 250.0 * np.sin((age[mid] - 75.0) / 30.0) + ) + depth[old] = -5750.0 + + return depth + + +# Dutkiewicz, A., Muller, R.D., Wang, X., O'Callaghan, S., Cannon, J. & Wright, N.M. (2017). +# Predicting sediment thickness on vanished ocean crust since 200 Ma. Geochemistry, +# Geophysics, Geosystems, 18, 4586-4603. +# +# The fitted degree-3 polynomial relates the *logarithm* of compacted sediment thickness to +# standardised seafloor age and standardised distance to the nearest passive continental +# margin. These are the published constants (also the gplately Zahirovic2022 defaults used by +# EarthByte's predicting-sediment-thickness and simple_paleobathymetry workflows); distances +# are in **kilometres**, matching the 0-3000 km calibrated range these constants were fitted +# over (simple_paleobathymetry's README describes the same constants as metres, which appears +# to be a documentation error -- see the discussion on gplately#444). +DUTKIEWICZ_2017_SEDIMENT_THICKNESS = { + "mean_age": 61.18406823, + "mean_distance_km": 1835.28118479, + "variance_age": 1934.6999014, + "variance_distance_km2": 1207521.8995806, + "max_age": 191.87276, + "max_distance_km": 3000.0, + "polynomial_coefficients": ( + 5.441401190368497, + 0.46893096, + -0.07320928, + -0.24077496, + -0.10840657, + 0.00381672, + 0.06831728, + 0.01179914, + 0.01158149, + -0.39880562, + ), +} + + +def dutkiewicz_2017_sediment_thickness( + age, + distance_to_margin_km, + mean_age=DUTKIEWICZ_2017_SEDIMENT_THICKNESS["mean_age"], + mean_distance_km=DUTKIEWICZ_2017_SEDIMENT_THICKNESS["mean_distance_km"], + variance_age=DUTKIEWICZ_2017_SEDIMENT_THICKNESS["variance_age"], + variance_distance_km2=DUTKIEWICZ_2017_SEDIMENT_THICKNESS["variance_distance_km2"], + polynomial_coefficients=DUTKIEWICZ_2017_SEDIMENT_THICKNESS[ + "polynomial_coefficients" + ], + max_age=DUTKIEWICZ_2017_SEDIMENT_THICKNESS["max_age"], + max_distance_km=DUTKIEWICZ_2017_SEDIMENT_THICKNESS["max_distance_km"], +): + """Predict compacted sediment thickness from seafloor age and distance to a passive margin. + + Implements the Dutkiewicz et al. (2017) relationship: a degree-3 polynomial, fitted to a + global compilation of sediment-thickness measurements, relating the logarithm of compacted + sediment thickness to standardised seafloor age and standardised distance to the nearest + passive continental margin (older, nearer-margin crust has thicker sediment cover). + + Parameters + ---------- + age : array_like + Seafloor age in Ma. + distance_to_margin_km : array_like + Distance to the nearest passive continental margin, in kilometres -- typically the + *lifetime-mean* distance of each point of ocean floor to the nearest passive margin, + as it drifted from the ridge to its current position (this module does not compute + that distance grid; see the module docstring). + mean_age, mean_distance_km, variance_age, variance_distance_km2, polynomial_coefficients : float or sequence + Standardisation and polynomial-fit constants. Default to the published Dutkiewicz et + al. (2017) values (:data:`DUTKIEWICZ_2017_SEDIMENT_THICKNESS`); override to use a + relationship retrained on a different present-day age grid or sediment-thickness + dataset. + max_age, max_distance_km : float or None + Values above these are clamped before standardising, since the fit is only meaningful + within its calibrated range. ``None`` disables clamping for that predictor. + + Returns + ------- + numpy.ndarray + Predicted compacted sediment thickness in metres (positive). NaN in, NaN out. + + References + ---------- + Dutkiewicz, A., Muller, R.D., Wang, X., O'Callaghan, S., Cannon, J. & Wright, N.M. (2017). + Predicting sediment thickness on vanished ocean crust since 200 Ma. *Geochemistry, + Geophysics, Geosystems*, 18, 4586-4603. + """ + age = np.asarray(age, dtype="float64") + distance_km = np.asarray(distance_to_margin_km, dtype="float64") + + if max_age is not None: + age = np.where(age > max_age, max_age, age) + if max_distance_km is not None: + distance_km = np.where( + distance_km > max_distance_km, max_distance_km, distance_km + ) + + a = (age - mean_age) / math.sqrt(variance_age) + d = (distance_km - mean_distance_km) / math.sqrt(variance_distance_km2) + + c = polynomial_coefficients + log_sediment_thickness = ( + c[0] * 1.0 + + c[1] * a + + c[2] * d + + c[3] * a * a + + c[4] * a * d + + c[5] * d * d + + c[6] * a * a * a + + c[7] * a * a * d + + c[8] * a * d * d + + c[9] * d * d * d + ) + return np.exp(log_sediment_thickness) + + +def sediment_isostatic_correction(sediment_thickness_m): + """Isostatic correction (Sykes, 1996) for the seafloor depression caused by sediment load. + + Adding a sediment pile on top of basement does not raise the seafloor by the full pile + thickness, because the added weight pushes the crust down. This is the correction to + subtract. + + Parameters + ---------- + sediment_thickness_m : array_like + Sediment thickness in metres (positive). + + Returns + ------- + numpy.ndarray + Isostatic correction in metres (positive; clamped to >= 0), NaN where + ``sediment_thickness_m`` is NaN. + + References + ---------- + Sykes, T.J.S. (1996). A correction for sediment load upon the ocean floor: uniform versus + varying sediment density estimations. *Marine Geology*, 133, 35-49. + """ + h_km = np.asarray(sediment_thickness_m, dtype="float64") / 1000.0 + correction_m = (0.43422 * h_km - 0.010395 * h_km * h_km) * 1000.0 + # np.clip (unlike `np.where(correction_m >= 0, ...)`) propagates NaN rather than silently + # turning masked (non-ocean) NaN cells into 0. + return np.clip(correction_m, 0.0, None) + + +def paleobathymetry(basement_depth_m, sediment_thickness_m): + """Combine basement depth and sediment thickness into isostatically-compensated paleobathymetry. + + ``paleobathymetry = basement_depth + sediment_thickness - isostatic_correction`` (see + :func:`sediment_isostatic_correction`). This describes oceanic crust only -- crust whose + age is defined in the seafloor-age grid that ``basement_depth_m`` was derived from (see + :func:`age_to_basement_depth`); it does not cover submerged continental crust or crust that + has since subducted (see the module docstring re: Step 5 / pyBacktrack). + + Parameters + ---------- + basement_depth_m : array_like + Depth to igneous basement in metres, negative downwards (:func:`age_to_basement_depth`). + sediment_thickness_m : array_like + Sediment thickness in metres, positive (e.g. :func:`dutkiewicz_2017_sediment_thickness`). + + Returns + ------- + numpy.ndarray + Paleobathymetry (depth of the sediment-covered ocean floor) in metres, negative + downwards. + """ + basement_depth_m = np.asarray(basement_depth_m, dtype="float64") + sediment_thickness_m = np.asarray(sediment_thickness_m, dtype="float64") + correction_m = sediment_isostatic_correction(sediment_thickness_m) + return basement_depth_m + sediment_thickness_m - correction_m diff --git a/tests-dir/pytestcases/test_9_paleobathymetry.py b/tests-dir/pytestcases/test_9_paleobathymetry.py new file mode 100644 index 00000000..701ab5a9 --- /dev/null +++ b/tests-dir/pytestcases/test_9_paleobathymetry.py @@ -0,0 +1,95 @@ +import numpy as np +import pytest +from conftest import logger + +import gplately +from gplately.paleobathymetry import ( + AGE_DEPTH_MODELS, + age_to_basement_depth, + dutkiewicz_2017_sediment_thickness, + paleobathymetry, + sediment_isostatic_correction, +) + +logger.info(__name__) + + +@pytest.mark.parametrize("model", AGE_DEPTH_MODELS) +def test_age_to_basement_depth_shape_and_sign(model): + age = np.array([np.nan, 0.0, 5.0, 50.0, 150.0]) + depth = age_to_basement_depth(age, model=model) + + assert depth.shape == age.shape + assert np.isnan(depth[0]) + # basement depth is negative (below sea level) everywhere age is defined + assert np.all(depth[1:] < 0) + # older crust is deeper (more negative) than younger crust + assert np.all(np.diff(depth[1:]) < 0) + + +def test_age_to_basement_depth_unknown_model(): + with pytest.raises(ValueError): + age_to_basement_depth(np.array([10.0]), model="not-a-model") + + +def test_age_to_basement_depth_gdh1_reference_values(): + # Stein & Stein (1992) GDH1, checked against the published formula by hand. + age = np.array([0.0, 20.0, 100.0]) + depth = age_to_basement_depth(age, model="gdh1") + expected = np.array( + [ + -2600.0, + -(2600.0 + 365.0 * np.sqrt(20.0)), + -(5651.0 - 2473.0 * np.exp(-0.0278 * 100.0)), + ] + ) + np.testing.assert_allclose(depth, expected) + + +def test_dutkiewicz_sediment_thickness_positive_and_masked(): + age = np.array([np.nan, 0.0, 100.0, 100.0]) + distance_km = np.array( + [np.nan, 500.0, 500.0, 3500.0] + ) # last value exceeds the clamp + + thickness = dutkiewicz_2017_sediment_thickness(age, distance_km) + + assert np.isnan(thickness[0]) + assert np.all(thickness[1:] > 0) + # clamped distance (3500 -> 3000 km) must match evaluating at exactly the clamp. + clamped = dutkiewicz_2017_sediment_thickness(np.array([100.0]), np.array([3000.0])) + np.testing.assert_allclose(thickness[3], clamped[0]) + + +def test_sediment_isostatic_correction_nan_propagates_and_nonnegative(): + sediment_thickness_m = np.array([np.nan, 0.0, 500.0, 5000.0]) + correction = sediment_isostatic_correction(sediment_thickness_m) + + assert np.isnan(correction[0]) + assert np.all(correction[1:] >= 0.0) + + +def test_paleobathymetry_combines_basement_and_sediment(): + basement_depth_m = np.array([-3000.0, -4000.0]) + sediment_thickness_m = np.array([0.0, 500.0]) + + result = paleobathymetry(basement_depth_m, sediment_thickness_m) + correction = sediment_isostatic_correction(sediment_thickness_m) + + np.testing.assert_allclose( + result, basement_depth_m + sediment_thickness_m - correction + ) + # zero sediment thickness means paleobathymetry equals basement depth exactly. + assert result[0] == basement_depth_m[0] + + +def test_public_api_exports(): + for name in ( + "AGE_DEPTH_MODELS", + "DUTKIEWICZ_2017_SEDIMENT_THICKNESS", + "age_to_basement_depth", + "dutkiewicz_2017_sediment_thickness", + "sediment_isostatic_correction", + "paleobathymetry", + ): + assert hasattr(gplately, name) From 7e7ee961b664963b3321630a9226cf37f428c0ec Mon Sep 17 00:00:00 2001 From: Michael Chin Date: Mon, 14 Sep 2026 15:19:46 +1000 Subject: [PATCH 02/25] Port distance-to-margin/sediment-thickness engine into gplately (#445); wire into #444 Adds gplately.sediment_thickness, a port of EarthByte's predicting-sediment-thickness ocean_basin_proximity.py engine: - generate_distance_grids(): for each ocean point in an age grid, reconstruct it backward through time (topological reconstruction via pygplates.TopologicalModel, distance queries via gplately's own ptt.utils.proximity_query) and accumulate its lifetime-mean distance to the nearest proximity feature (e.g. passive-margin COB line segments). - generate_sediment_thickness_grids(): combines an age grid with the distance grid above via gplately.paleobathymetry.dutkiewicz_2017_sediment_thickness. Exposed on the CLI as 'gplately generate-distance-grids'/'generate-sediment-grids' (aliases gdg/gsg), per #445's stated scope. Not ported: continent-obstacle shortest-path routing (ocean_basin_proximity.py's shortest_path.py) - distances are currently always great-circle; and topological (as opposed to static) proximity features. Both are documented gaps in the module docstring. Validated end-to-end against a real plate model (rotations/topologies/COBs) with a downloaded age grid: produces physically sensible distance (0-3000 km) and paleobathymetry (-2 to -5.5 km) values. Added unit tests using the existing Muller2019 test fixtures plus a synthetic age grid. Also adds gplately.paleobathymetry.simple_paleobathymetry(), the Steps 1-4 orchestrator for #444, which now calls generate_distance_grids() for Step 2 instead of requiring the caller to supply a distance grid. Co-Authored-By: Claude Sonnet 5 --- gplately/__init__.py | 6 + gplately/__main__.py | 4 + gplately/commands/sediment_thickness.py | 283 +++++++++++ gplately/paleobathymetry.py | 155 +++++- gplately/sediment_thickness.py | 440 ++++++++++++++++++ .../pytestcases/test_10_sediment_thickness.py | 152 ++++++ 6 files changed, 1031 insertions(+), 9 deletions(-) create mode 100644 gplately/commands/sediment_thickness.py create mode 100644 gplately/sediment_thickness.py create mode 100644 tests-dir/pytestcases/test_10_sediment_thickness.py diff --git a/gplately/__init__.py b/gplately/__init__.py index 2715e1ec..e4e32e1a 100644 --- a/gplately/__init__.py +++ b/gplately/__init__.py @@ -59,6 +59,12 @@ dutkiewicz_2017_sediment_thickness, sediment_isostatic_correction, paleobathymetry, + simple_paleobathymetry, +) +from .sediment_thickness import ( + generate_input_points_grid, + generate_distance_grids, + generate_sediment_thickness_grids, ) from .grids import ( read_netcdf_grid, diff --git a/gplately/__main__.py b/gplately/__main__.py index 95450fe6..588c8a26 100644 --- a/gplately/__main__.py +++ b/gplately/__main__.py @@ -31,6 +31,7 @@ regrid, reset_feature_type, rotate_grid, + sediment_thickness, ) from .ptt import ( cleanup_topologies, @@ -121,6 +122,9 @@ def main(): # add "rotate_grid" sub-command rotate_grid.add_parser(subparser) + # add "generate-distance-grids"/"generate-sediment-grids" sub-commands + sediment_thickness.add_parser(subparser) + # add "fix crossovers" sub-command fix_crossovers_cmd = subparser.add_parser( "fix_crossovers", diff --git a/gplately/commands/sediment_thickness.py b/gplately/commands/sediment_thickness.py new file mode 100644 index 00000000..1734a9f9 --- /dev/null +++ b/gplately/commands/sediment_thickness.py @@ -0,0 +1,283 @@ +# +# Copyright (C) 2026 The University of Sydney, Australia +# +# This program is free software; you can redistribute it and/or modify it under +# the terms of the GNU General Public License, version 2, as published by +# the Free Software Foundation. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +# for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +# + +import argparse +import logging +import os + +from plate_model_manager import PlateModelManager + +from ..grids import read_netcdf_grid +from ..sediment_thickness import ( + generate_distance_grids, + generate_sediment_thickness_grids, +) + +_logger = logging.getLogger("gplately") + + +def _resolve_age_grid_filenames_and_times(args): + times = list(range(int(args.min_time), int(args.max_time) + 1, int(args.time_step))) + if args.model_name: + plate_model = PlateModelManager().get_model( + args.model_name, data_dir=args.plate_model_repo + ) + if not plate_model: + raise Exception( + f"Unable to create PlateModel object for model {args.model_name}." + ) + age_grid_filenames_and_times = [ + (plate_model.get_age_grid(t), float(t)) for t in times + ] + elif args.age_grid_template: + age_grid_filenames_and_times = [ + (args.age_grid_template.format(time=t), float(t)) for t in times + ] + else: + raise Exception( + "No age grid source given: use -m/--model or --age-grid-template." + ) + return age_grid_filenames_and_times, plate_model if args.model_name else None + + +def _run_generate_distance_grids(args): + age_grid_filenames_and_times, plate_model = _resolve_age_grid_filenames_and_times( + args + ) + + rotation_files = args.rotation_filenames or ( + plate_model.get_rotation_model() if plate_model else None + ) + topology_files = args.topology_filenames or ( + plate_model.get_layer("Topologies") if plate_model else None + ) + proximity_files = args.proximity_filenames or ( + plate_model.get_layer("COBs", return_none_if_not_exist=True) + if plate_model + else None + ) + if not rotation_files or not topology_files: + raise Exception( + "No rotation/topology files found: use -m/--model, or --rotations/--topologies." + ) + if not proximity_files: + raise Exception( + "No proximity feature files found: use --proximity-features to supply " + "passive-margin continent-ocean-boundary line segments (the Plate Model " + "Manager does not deliver these for most models)." + ) + + _logger.info(f"Using rotation files: {rotation_files}") + _logger.info(f"Using topology files: {topology_files}") + _logger.info(f"Using proximity feature files: {proximity_files}") + + generate_distance_grids( + rotation_model=rotation_files, + proximity_features=proximity_files, + topological_features=topology_files, + age_grid_filenames_and_times=age_grid_filenames_and_times, + grid_spacing=args.grid_spacing, + time_increment=args.time_step, + max_reconstruction_time=args.max_reconstruction_time, + anchor_plate_id=args.anchor_plate_id or 0, + clamp_distance_km=args.clamp_distance_km, + output_directory=args.output_dir, + ) + _logger.info(f"Distance grids written to {args.output_dir}") + + +def _run_generate_sediment_grids(args): + age_grid_filenames_and_times, _ = _resolve_age_grid_filenames_and_times(args) + + distance_grids = {} + for _, t in age_grid_filenames_and_times: + distance_path = os.path.join( + args.distance_grids_dir, + "mean_distance_{:.1f}d_{:.1f}.nc".format(args.grid_spacing, t), + ) + grid, lon, lat = read_netcdf_grid(distance_path, return_grids=True) + distance_grids[t] = (lon, lat, grid) + + generate_sediment_thickness_grids( + age_grid_filenames_and_times, + distance_grids, + output_directory=args.output_dir, + ) + _logger.info(f"Sediment thickness grids written to {args.output_dir}") + + +def _add_common_arguments(cmd): + cmd.add_argument( + metavar="output_dir", + help="(required) output directory", + dest="output_dir", + ) + cmd.add_argument( + "-m", + "--model", + metavar="model_name", + dest="model_name", + default=None, + help="reconstruction model name (fetched via the Plate Model Manager); " + "supplies rotations/topologies/age-grids unless overridden below", + ) + cmd.add_argument( + "-f", + "--plate-model-repo", + metavar="plate_model_repo", + dest="plate_model_repo", + default="plate-model-repo", + help="local cache directory for -m/--model", + ) + cmd.add_argument( + "--age-grid-template", + metavar="age_grid_template", + dest="age_grid_template", + default=None, + help="alternative to -m/--model: a filename template for local age grids, " + "using '{time}' for the reconstruction age in Ma, e.g. 'agegrids/age_{time:.0f}Ma.nc'", + ) + cmd.add_argument( + "-e", + "--min-time", + metavar="min_time", + type=float, + default=0, + dest="min_time", + help="minimum time (Ma); default: 0", + ) + cmd.add_argument( + "-s", + "--max-time", + metavar="max_time", + type=float, + default=100, + dest="max_time", + help="maximum time (Ma); default: 100", + ) + cmd.add_argument( + "--time-step", + metavar="time_step", + type=float, + default=1, + dest="time_step", + help="time increment (Myr); default: 1", + ) + cmd.add_argument( + "-r", + "--grid-spacing", + metavar="grid_spacing", + type=float, + default=0.5, + dest="grid_spacing", + help="grid spacing (degrees); default: 0.5", + ) + cmd.add_argument( + "-a", + "--anchor-plate-id", + metavar="anchor_plate_id", + type=int, + default=None, + dest="anchor_plate_id", + help="anchor plate ID; default: 0", + ) + + +def add_parser(parser): + """add command line argument parsers for 'generate-distance-grids' and 'generate-sediment-grids'""" + + distance_cmd = parser.add_parser( + "generate-distance-grids", + aliases=("gdg",), + help="Generate distance-to-passive-margin grids (for predicting sediment thickness).", + add_help=True, + description=( + "For each ocean point in a seafloor-age grid, reconstruct it backward through " + "time and compute its lifetime-mean distance to the nearest passive-margin " + "continent-ocean-boundary line segment.\n\n" + "Example usage:\n" + " gplately gdg output_dir -m muller2025 --proximity-features cobs.gpml -e 0 -s 10\n" + ), + formatter_class=argparse.RawDescriptionHelpFormatter, + ) + _add_common_arguments(distance_cmd) + distance_cmd.add_argument( + "--proximity-features", + metavar="proximity_filenames", + nargs="+", + dest="proximity_filenames", + default=[], + help="passive-margin continent-ocean-boundary line-segment file(s); " + "required unless -m/--model's plate model provides a COBs layer", + ) + distance_cmd.add_argument( + "--rotations", + metavar="rotation_filenames", + nargs="+", + dest="rotation_filenames", + default=[], + help="alternative to -m/--model", + ) + distance_cmd.add_argument( + "--topologies", + metavar="topology_filenames", + nargs="+", + dest="topology_filenames", + default=[], + help="alternative to -m/--model", + ) + distance_cmd.add_argument( + "--max-reconstruction-time", + metavar="max_reconstruction_time", + type=float, + default=None, + dest="max_reconstruction_time", + help="do not reconstruct ocean points older than this (Ma); default: unlimited", + ) + distance_cmd.add_argument( + "--clamp-distance-km", + metavar="clamp_distance_km", + type=float, + default=3000.0, + dest="clamp_distance_km", + help="clamp mean distances above this (km); default: 3000", + ) + distance_cmd.set_defaults(func=_run_generate_distance_grids) + + sediment_cmd = parser.add_parser( + "generate-sediment-grids", + aliases=("gsg",), + help="Predict sediment-thickness grids from seafloor age and distance-to-margin grids.", + add_help=True, + description=( + "Combine a seafloor-age grid with the distance-to-passive-margin grids from " + "'generate-distance-grids' into predicted compacted sediment-thickness grids " + "(Dutkiewicz et al., 2017).\n\n" + "Example usage:\n" + " gplately gsg output_dir -m muller2025 --distance-grids-dir distances/ -e 0 -s 10\n" + ), + formatter_class=argparse.RawDescriptionHelpFormatter, + ) + _add_common_arguments(sediment_cmd) + sediment_cmd.add_argument( + "--distance-grids-dir", + metavar="distance_grids_dir", + required=True, + dest="distance_grids_dir", + help="directory of mean_distance_d_