Source code for geoh5py.objects.points

#  Copyright (c) 2024 Mira Geoscience Ltd.
#  This file is part of geoh5py.
#  geoh5py is free software: you can redistribute it and/or modify
#  it under the terms of the GNU Lesser General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#  geoh5py is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  GNU Lesser General Public License for more details.
#  You should have received a copy of the GNU Lesser General Public License
#  along with geoh5py.  If not, see <>.

from __future__ import annotations

import uuid
import warnings

import numpy as np

from ..shared.utils import box_intersect, mask_by_extent
from .object_base import ObjectBase, ObjectType

[docs] class Points(ObjectBase): """ Points object made up of vertices. """ __TYPE_UID = uuid.UUID("{202C5DB1-A56D-4004-9CAD-BAAFD8899406}") def __init__(self, object_type: ObjectType, name="Points", **kwargs): self._vertices: np.ndarray | None = None super().__init__(object_type, name=name, **kwargs)
[docs] @classmethod def default_type_uid(cls) -> uuid.UUID: return cls.__TYPE_UID
@property def extent(self) -> np.ndarray | None: """ Geography bounding box of the object. :return: shape(2, 3) Bounding box defined by the bottom South-West and top North-East coordinates. """ if self.vertices is not None: return np.c_[self.vertices.min(axis=0), self.vertices.max(axis=0)].T return None
[docs] def mask_by_extent( self, extent: np.ndarray, inverse: bool = False ) -> np.ndarray | None: """ Sub-class extension of :func:`~geoh5py.shared.entity.Entity.mask_by_extent`. """ if self.extent is None or not box_intersect(self.extent, extent): return None return mask_by_extent(self.vertices, extent, inverse=inverse)
@property def vertices(self) -> np.ndarray | None: """ :obj:`~geoh5py.objects.object_base.ObjectBase.vertices` """ if self._vertices is None and self.on_file: self._vertices = self.workspace.fetch_array_attribute(self, "vertices") if self._vertices is not None: return self._vertices.view("<f8").reshape((-1, 3)) return None @vertices.setter def vertices(self, xyz: np.ndarray): if xyz.ndim != 2 or xyz.shape[1] != 3: raise ValueError( f"Array of vertices must be of shape (*, 3). Array of shape {xyz.shape} provided." ) if self._vertices is not None and xyz.shape[0] < self._vertices.shape[0]: raise ValueError( "Attempting to assign 'vertices' with fewer values. " "Use the `remove_vertices` method instead." ) self._vertices = np.asarray( np.core.records.fromarrays( xyz.T.tolist(), dtype=[("x", "<f8"), ("y", "<f8"), ("z", "<f8")], ) ) self.workspace.update_attribute(self, "vertices")
[docs] def remove_vertices( self, indices: list[int] | np.ndarray, clear_cache: bool = False ): """ Safely remove vertices and corresponding data entries. :param indices: Indices of vertices to remove. :param clear_cache: Clear cached data and attributes. """ if self.vertices is None: warnings.warn("No vertices to be removed.", UserWarning) return if isinstance(indices, list): indices = np.array(indices) if not isinstance(indices, np.ndarray): raise TypeError("Indices must be a list or numpy array.") if ( isinstance(self.vertices, np.ndarray) and np.max(indices) > self.vertices.shape[0] - 1 ): raise ValueError("Found indices larger than the number of vertices.") vertices = np.delete(self.vertices, indices, axis=0) self._vertices = None self.vertices = vertices self.remove_children_values(indices, "VERTEX", clear_cache=clear_cache)
[docs] def copy( self, parent=None, copy_children: bool = True, clear_cache: bool = False, mask: np.ndarray | None = None, **kwargs, ): """ Sub-class extension of :func:`~geoh5py.shared.entity.Entity.copy`. """ if mask is not None and self.vertices is not None: if not isinstance(mask, np.ndarray) or mask.shape != ( self.vertices.shape[0], ): raise ValueError("Mask must be an array of shape (n_vertices,).") kwargs.update({"vertices": self.vertices[mask]}) new_entity = super().copy( parent=parent, copy_children=copy_children, clear_cache=clear_cache, mask=mask, **kwargs, ) return new_entity