gtrack 0.3.0__tar.gz

gtrack-0.3.0/PKG-INFO

@@ -0,0 +1,66 @@
+Metadata-Version: 2.4
+Name: gtrack
+Version: 0.3.0
+Summary: GPlates-based Tracking of Lithosphere and Kinematics
+Author: S. Ghelichkhani
+License: MIT
+Project-URL: Homepage, https://github.com/sghelichkhani/gtrack
+Project-URL: Documentation, https://gtrack.gadopt.org
+Project-URL: Repository, https://github.com/sghelichkhani/gtrack
+Keywords: plate tectonics,seafloor age,geodynamics,pygplates,lithosphere,kinematics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Requires-Dist: pygplates
+Provides-Extra: visualization
+Requires-Dist: matplotlib>=3.5; extra == "visualization"
+Requires-Dist: cartopy>=0.21; extra == "visualization"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=3.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.5; extra == "docs"
+Requires-Dist: mkdocs-material>=9.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.24; extra == "docs"
+Requires-Dist: mkdocs-jupyter>=0.24; extra == "docs"
+Provides-Extra: demos
+Requires-Dist: jupytext>=1.15; extra == "demos"
+Requires-Dist: nbconvert>=7.0; extra == "demos"
+Requires-Dist: ipykernel>=6.0; extra == "demos"
+Requires-Dist: matplotlib>=3.5; extra == "demos"
+Requires-Dist: cartopy>=0.21; extra == "demos"
+Requires-Dist: h5py>=3.0; extra == "demos"
+Provides-Extra: all
+Requires-Dist: gtrack[demos,dev,docs,visualization]; extra == "all"
+
+# gtrack
+
+**GPlates-based Tracking of Lithosphere and Kinematics**
+
+A Python package for computing lithospheric structure through geological time using plate tectonic reconstructions.
+
+## Installation
+
+```bash
+pip install gtrack
+```
+
+## Documentation
+
+For full documentation, examples, and API reference, visit:
+
+**[https://gtrack.gadopt.org](https://gtrack.gadopt.org)**
+
+## License
+
+MIT License

gtrack-0.3.0/README.md

@@ -0,0 +1,21 @@
+# gtrack
+
+**GPlates-based Tracking of Lithosphere and Kinematics**
+
+A Python package for computing lithospheric structure through geological time using plate tectonic reconstructions.
+
+## Installation
+
+```bash
+pip install gtrack
+```
+
+## Documentation
+
+For full documentation, examples, and API reference, visit:
+
+**[https://gtrack.gadopt.org](https://gtrack.gadopt.org)**
+
+## License
+
+MIT License

gtrack-0.3.0/gtrack/__init__.py

@@ -0,0 +1,137 @@
+"""
+gtrack: High-performance seafloor age tracking and point rotation.
+
+This package provides tools for:
+- Computing seafloor ages from plate tectonic reconstructions using Lagrangian
+  particle tracking with pygplates' C++ backend (GPlately-compatible)
+- Rotating user-provided points through geological time
+- Filtering points by polygon containment (e.g., continental regions)
+
+The main entry point is SeafloorAgeTracker, which provides both a stepwise
+interface and a one-shot compute_ages() method.
+
+Logging
+-------
+gtrack uses Python's logging module. Control verbosity via environment variable:
+
+    export GTRACK_LOGLEVEL=INFO    # Progress messages
+    export GTRACK_LOGLEVEL=DEBUG   # Detailed debug output
+    export GTRACK_LOGLEVEL=WARNING # Quiet (default)
+
+Or programmatically:
+
+>>> from gtrack import enable_verbose, enable_debug
+>>> enable_verbose()  # Show progress messages
+
+Example
+-------
+>>> from gtrack import SeafloorAgeTracker, TracerConfig
+>>>
+>>> # Simple one-shot computation
+>>> cloud = SeafloorAgeTracker.compute_ages(
+...     target_age=100,
+...     starting_age=200,
+...     rotation_files=['rotations.rot'],
+...     topology_files=['topologies.gpmlz']
+... )
+>>> ages = cloud.get_property('age')
+>>>
+>>> # Or stepwise for intermediate states
+>>> tracker = SeafloorAgeTracker(
+...     rotation_files=['rotations.rot'],
+...     topology_files=['topologies.gpmlz']
+... )
+>>> tracker.initialize(starting_age=200)
+>>> for age in range(199, -1, -1):
+...     cloud = tracker.step_to(age)
+"""
+
+__version__ = "0.2.0"
+
+# Logging configuration (import first to configure before other modules)
+from .logging import (
+    configure_logging,
+    set_log_level,
+    enable_verbose,
+    enable_debug,
+    disable_logging,
+    get_logger,
+)
+
+# Core seafloor age functionality
+from .config import TracerConfig
+from .hpc_integration import SeafloorAgeTracker
+
+# Point rotation API
+from .point_rotation import PointCloud, PointRotator
+from .polygon_filter import PolygonFilter
+from .io_formats import (
+    load_points_numpy,
+    load_points_latlon,
+    load_points_gpml,
+    save_points_numpy,
+    save_points_latlon,
+    save_points_gpml,
+    PointCloudCheckpoint,
+)
+
+# Utility modules (for advanced users)
+from .mesh import (
+    create_sphere_mesh_xyz,
+    create_sphere_mesh_latlon,
+)
+from .mor_seeds import (
+    generate_mor_seeds,
+    generate_mor_seeds_with_plate_ids,
+    get_ridge_geometries,
+)
+from .initial_conditions import (
+    compute_initial_ages,
+    default_age_distance_law,
+)
+from .boundaries import (
+    ContinentalPolygonCache,
+    ResolvedTopologyCache,
+    extract_ridge_geometries,
+    extract_ridge_points_latlon,
+)
+
+__all__ = [
+    # Main API
+    "SeafloorAgeTracker",
+    "TracerConfig",
+    # Logging
+    "configure_logging",
+    "set_log_level",
+    "enable_verbose",
+    "enable_debug",
+    "disable_logging",
+    "get_logger",
+    # Point rotation
+    "PointCloud",
+    "PointRotator",
+    "PolygonFilter",
+    # IO utilities
+    "load_points_numpy",
+    "load_points_latlon",
+    "load_points_gpml",
+    "save_points_numpy",
+    "save_points_latlon",
+    "save_points_gpml",
+    "PointCloudCheckpoint",
+    # Mesh generation (advanced)
+    "create_sphere_mesh_xyz",
+    "create_sphere_mesh_latlon",
+    # MOR seeds (advanced)
+    "generate_mor_seeds",
+    "generate_mor_seeds_with_plate_ids",
+    "get_ridge_geometries",
+    # Initial conditions (advanced)
+    "compute_initial_ages",
+    "default_age_distance_law",
+    # Caching (advanced)
+    "ContinentalPolygonCache",
+    "ResolvedTopologyCache",
+    "extract_ridge_geometries",
+    "extract_ridge_points_latlon",
+]

gtrack-0.3.0/gtrack/boundaries.py

@@ -0,0 +1,396 @@
+"""
+Plate boundary caching and extraction utilities.
+
+This module provides caching for resolved topologies and utility functions
+for extracting plate boundary information. The main reconstruction is handled
+by pygplates' C++ backend (TopologicalModel.reconstruct_geometry).
+"""
+
+import numpy as np
+import pygplates
+from collections import OrderedDict
+from typing import Dict, List, Optional, Tuple
+
+from .spatial import find_polygons
+
+
+class ResolvedTopologyCache:
+    """
+    LRU cache for resolved topologies at different timesteps.
+
+    Parameters
+    ----------
+    topology_features : pygplates.FeatureCollection or list
+        Topology features for resolving.
+    rotation_model : pygplates.RotationModel
+        Rotation model for reconstruction.
+    max_cache_size : int, default=10
+        Maximum number of timesteps to cache.
+    """
+
+    def __init__(
+        self,
+        topology_features,
+        rotation_model: pygplates.RotationModel,
+        max_cache_size: int = 10,
+    ):
+        self.topology_features = topology_features
+        self.rotation_model = rotation_model
+        self.max_cache_size = max_cache_size
+
+        # LRU cache: {time: (resolved_topologies, shared_boundary_sections)}
+        self._cache: OrderedDict = OrderedDict()
+
+    def get(self, time: float) -> Tuple[List, List]:
+        """
+        Get resolved topologies and shared boundary sections for a time.
+
+        Parameters
+        ----------
+        time : float
+            Geological time (Ma).
+
+        Returns
+        -------
+        resolved_topologies : list
+            List of resolved topology polygons.
+        shared_boundary_sections : list
+            List of shared boundary sections.
+        """
+        if time in self._cache:
+            # Move to end (most recently used)
+            self._cache.move_to_end(time)
+            return self._cache[time]
+
+        # Resolve topologies
+        resolved_topologies = []
+        shared_boundary_sections = []
+        pygplates.resolve_topologies(
+            self.topology_features,
+            self.rotation_model,
+            resolved_topologies,
+            time,
+            shared_boundary_sections,
+        )
+
+        # Add to cache
+        self._cache[time] = (resolved_topologies, shared_boundary_sections)
+
+        # Evict oldest if over capacity
+        while len(self._cache) > self.max_cache_size:
+            self._cache.popitem(last=False)
+
+        return resolved_topologies, shared_boundary_sections
+
+    def clear(self):
+        """Clear the cache."""
+        self._cache.clear()
+
+    def get_memory_usage(self) -> Dict[str, float]:
+        """Get approximate memory usage information."""
+        return {
+            'cached_timesteps': len(self._cache),
+            'max_cache_size': self.max_cache_size,
+        }
+
+
+class ContinentalPolygonCache:
+    """
+    Cache for reconstructed continental polygons with efficient point-in-polygon queries.
+
+    Parameters
+    ----------
+    continental_polygons : str or pygplates.FeatureCollection
+        Continental polygon features.
+    rotation_model : pygplates.RotationModel
+        Rotation model for reconstruction.
+    max_cache_size : int, default=10
+        Maximum number of timesteps to cache.
+    """
+
+    def __init__(
+        self,
+        continental_polygons,
+        rotation_model: pygplates.RotationModel,
+        max_cache_size: int = 10,
+    ):
+        # Load continental polygons
+        if isinstance(continental_polygons, str):
+            self._polygon_features = pygplates.FeatureCollection(continental_polygons)
+        else:
+            self._polygon_features = continental_polygons
+
+        self.rotation_model = rotation_model
+        self.max_cache_size = max_cache_size
+
+        # LRU cache: {time: list of reconstructed polygon geometries}
+        self._cache: OrderedDict = OrderedDict()
+
+    def get_polygons(self, time: float) -> List[pygplates.PolygonOnSphere]:
+        """
+        Get reconstructed continental polygons at a time.
+
+        Parameters
+        ----------
+        time : float
+            Geological time (Ma).
+
+        Returns
+        -------
+        list of pygplates.PolygonOnSphere
+            Reconstructed continental polygon geometries.
+        """
+        if time in self._cache:
+            self._cache.move_to_end(time)
+            return self._cache[time]
+
+        # Reconstruct polygons
+        reconstructed = []
+        pygplates.reconstruct(
+            self._polygon_features,
+            self.rotation_model,
+            reconstructed,
+            time,
+        )
+
+        # Extract polygon geometries
+        polygon_geometries = []
+        for rfg in reconstructed:
+            geom = rfg.get_reconstructed_geometry()
+            if isinstance(geom, pygplates.PolygonOnSphere):
+                polygon_geometries.append(geom)
+
+        # Cache
+        self._cache[time] = polygon_geometries
+
+        # Evict oldest if over capacity
+        while len(self._cache) > self.max_cache_size:
+            self._cache.popitem(last=False)
+
+        return polygon_geometries
+
+    def get_continental_mask(
+        self,
+        lats: np.ndarray,
+        lons: np.ndarray,
+        time: float,
+    ) -> np.ndarray:
+        """
+        Get boolean mask indicating which points are inside continental polygons.
+
+        Uses ptt.utils.points_in_polygons.find_polygons for efficient vectorized
+        point-in-polygon testing with spatial tree acceleration.
+
+        Parameters
+        ----------
+        lats : np.ndarray
+            Point latitudes in degrees.
+        lons : np.ndarray
+            Point longitudes in degrees.
+        time : float
+            Geological time (Ma).
+
+        Returns
+        -------
+        np.ndarray
+            Boolean array, True for points inside continental polygons.
+        """
+        polygons = self.get_polygons(time)
+
+        if len(polygons) == 0:
+            return np.zeros(len(lats), dtype=bool)
+
+        # Create all points in single C++ call using MultiPointOnSphere
+        points = pygplates.MultiPointOnSphere(zip(lats, lons)).get_points()
+
+        # Use vectorized point-in-polygon with spatial tree
+        containing_polygons = find_polygons(
+            points, polygons, all_polygons=False
+        )
+
+        # Convert to boolean mask: True if point is in any polygon
+        mask = np.array([p is not None for p in containing_polygons], dtype=bool)
+
+        return mask
+
+    def clear(self):
+        """Clear the cache."""
+        self._cache.clear()
+
+
+def extract_ridge_geometries(
+    time: float,
+    topology_features,
+    rotation_model: pygplates.RotationModel,
+) -> List[pygplates.PolylineOnSphere]:
+    """
+    Extract mid-ocean ridge geometries at a given time.
+
+    Parameters
+    ----------
+    time : float
+        Geological time (Ma).
+    topology_features : pygplates.FeatureCollection or list
+        Topology features.
+    rotation_model : pygplates.RotationModel
+        Rotation model.
+
+    Returns
+    -------
+    list of pygplates.PolylineOnSphere
+        Ridge geometries at the specified time.
+    """
+    resolved_topologies = []
+    shared_boundary_sections = []
+    pygplates.resolve_topologies(
+        topology_features,
+        rotation_model,
+        resolved_topologies,
+        time,
+        shared_boundary_sections,
+    )
+
+    ridge_geometries = []
+    for shared_boundary_section in shared_boundary_sections:
+        if (
+            shared_boundary_section.get_feature().get_feature_type()
+            == pygplates.FeatureType.create_gpml("MidOceanRidge")
+        ):
+            for shared_sub_segment in shared_boundary_section.get_shared_sub_segments():
+                ridge_geometries.append(shared_sub_segment.get_resolved_geometry())
+
+    return ridge_geometries
+
+
+def extract_ridge_points_latlon(
+    time: float,
+    topology_features,
+    rotation_model: pygplates.RotationModel,
+    tessellate_degrees: float = 0.5,
+) -> Tuple[np.ndarray, np.ndarray]:
+    """
+    Extract mid-ocean ridge points as lat/lon arrays.
+
+    Parameters
+    ----------
+    time : float
+        Geological time (Ma).
+    topology_features : pygplates.FeatureCollection or list
+        Topology features.
+    rotation_model : pygplates.RotationModel
+        Rotation model.
+    tessellate_degrees : float, default=0.5
+        Tessellation resolution in degrees.
+
+    Returns
+    -------
+    lats : np.ndarray
+        Ridge point latitudes in degrees.
+    lons : np.ndarray
+        Ridge point longitudes in degrees.
+    """
+    ridge_geometries = extract_ridge_geometries(time, topology_features, rotation_model)
+
+    if len(ridge_geometries) == 0:
+        return np.array([]), np.array([])
+
+    all_lats = []
+    all_lons = []
+
+    for geom in ridge_geometries:
+        tessellated = geom.to_tessellated(np.radians(tessellate_degrees))
+        for point in tessellated:
+            lat, lon = point.to_lat_lon()
+            all_lats.append(lat)
+            all_lons.append(lon)
+
+    return np.array(all_lats), np.array(all_lons)
+
+
+def extract_subduction_geometries(
+    time: float,
+    topology_features,
+    rotation_model: pygplates.RotationModel,
+) -> List[pygplates.PolylineOnSphere]:
+    """
+    Extract subduction zone geometries at a given time.
+
+    Parameters
+    ----------
+    time : float
+        Geological time (Ma).
+    topology_features : pygplates.FeatureCollection or list
+        Topology features.
+    rotation_model : pygplates.RotationModel
+        Rotation model.
+
+    Returns
+    -------
+    list of pygplates.PolylineOnSphere
+        Subduction zone geometries at the specified time.
+    """
+    resolved_topologies = []
+    shared_boundary_sections = []
+    pygplates.resolve_topologies(
+        topology_features,
+        rotation_model,
+        resolved_topologies,
+        time,
+        shared_boundary_sections,
+    )
+
+    subduction_geometries = []
+    for shared_boundary_section in shared_boundary_sections:
+        feature_type = shared_boundary_section.get_feature().get_feature_type()
+        if feature_type == pygplates.FeatureType.create_gpml("SubductionZone"):
+            for shared_sub_segment in shared_boundary_section.get_shared_sub_segments():
+                subduction_geometries.append(shared_sub_segment.get_resolved_geometry())
+
+    return subduction_geometries
+
+
+def extract_subduction_points_latlon(
+    time: float,
+    topology_features,
+    rotation_model: pygplates.RotationModel,
+    tessellate_degrees: float = 0.5,
+) -> Tuple[np.ndarray, np.ndarray]:
+    """
+    Extract subduction zone points as lat/lon arrays.
+
+    Parameters
+    ----------
+    time : float
+        Geological time (Ma).
+    topology_features : pygplates.FeatureCollection or list
+        Topology features.
+    rotation_model : pygplates.RotationModel
+        Rotation model.
+    tessellate_degrees : float, default=0.5
+        Tessellation resolution in degrees.
+
+    Returns
+    -------
+    lats : np.ndarray
+        Subduction zone point latitudes in degrees.
+    lons : np.ndarray
+        Subduction zone point longitudes in degrees.
+    """
+    subduction_geometries = extract_subduction_geometries(
+        time, topology_features, rotation_model
+    )
+
+    if len(subduction_geometries) == 0:
+        return np.array([]), np.array([])
+
+    all_lats = []
+    all_lons = []
+
+    for geom in subduction_geometries:
+        tessellated = geom.to_tessellated(np.radians(tessellate_degrees))
+        for point in tessellated:
+            lat, lon = point.to_lat_lon()
+            all_lats.append(lat)
+            all_lons.append(lon)
+
+    return np.array(all_lats), np.array(all_lons)