Source code for geoh5py.objects.object_base

#  Copyright (c) 2022 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 <>.

# pylint: disable=R0904

from __future__ import annotations

import uuid
import warnings
from abc import abstractmethod
from datetime import datetime
from typing import TYPE_CHECKING

import numpy as np

from import CommentsData, Data
from import DataAssociationEnum
from import PrimitiveTypeEnum
from ..groups import PropertyGroup
from ..shared import Entity
from ..shared.concatenation import Concatenated, ConcatenatedPropertyGroup
from ..shared.utils import mask_by_extent
from .object_type import ObjectType

    from .. import workspace

[docs]class ObjectBase(Entity): """ Object base class. """ _attribute_map: dict = Entity._attribute_map.copy() _attribute_map.update( {"Last focus": "last_focus", "PropertyGroups": "property_groups"} ) def __init__(self, object_type: ObjectType, **kwargs): assert object_type is not None self._comments = None self._entity_type = object_type self._extent = None self._last_focus = "None" self._property_groups: list[PropertyGroup] | None = None # self._clipping_ids: list[uuid.UUID] = [] if not any(key for key in kwargs if key in ["name", "Name"]): kwargs["name"] = type(self).__name__ super().__init__(**kwargs) if == "Entity": = type(self).__name__
[docs] def add_comment(self, comment: str, author: str = None): """ Add text comment to an object. :param comment: Text to be added as comment. :param author: Name of author or defaults to :obj:`~geoh5py.workspace.workspace.Workspace.contributors`. """ date ="%Y-%m-%dT%H:%M:%S") if author is None: author = ",".join(self.workspace.contributors) comment_dict = {"Author": author, "Date": date, "Text": comment} if self.comments is None: self.add_data( { "UserComments": { "values": [comment_dict], "association": "OBJECT", "entity_type": {"primitive_type": "TEXT"}, } } ) else: self.comments.values = self.comments.values + [comment_dict]
[docs] def add_data( self, data: dict, property_group: str | PropertyGroup | None = None ) -> Data | list[Data]: """ Create :obj:`` from dictionary of name and arguments. The provided arguments can be any property of the target Data class. :param data: Dictionary of data to be added to the object, e.g. .. code-block:: python data = { "data_A": { 'values': [v_1, v_2, ...], 'association': 'VERTEX' }, "data_B": { 'values': [v_1, v_2, ...], 'association': 'CELLS' }, } :return: List of new Data objects. """ data_objects = [] for name, attr in data.items(): assert isinstance(attr, dict), ( f"Given value to data {name} should of type {dict}. " f"Type {type(attr)} given instead." ) attr["name"] = name self.validate_data_association(attr) entity_type = self.validate_data_type(attr) kwargs = {"parent": self, "association": attr["association"]} for key, val in attr.items(): if key in ["parent", "association", "entity_type", "type"]: continue kwargs[key] = val data_object = self.workspace.create_entity( Data, entity=kwargs, entity_type=entity_type ) if not isinstance(data_object, Data): continue if property_group is not None: self.add_data_to_group(data_object, property_group) data_objects.append(data_object) if len(data_objects) == 1: return data_objects[0] return data_objects
[docs] def add_data_to_group( self, data: list | Data | uuid.UUID, property_group: str | PropertyGroup ) -> PropertyGroup: """ Append data children to a :obj:`~geoh5py.groups.property_group.PropertyGroup` All given data must be children of the parent object. :param data: :obj:`` object, :obj:`~geoh5py.shared.entity.Entity.uid` or :obj:`` of data. :param property_group: Name or :obj:`~geoh5py.groups.property_group.PropertyGroup`. A new group is created if none exist with the given name. :return: The target property group. """ if isinstance(data, list): uids = [] for datum in data: uids += self.reference_to_uid(datum) else: uids = self.reference_to_uid(data) association = None template = self.workspace.get_entity(uids[0])[0] if isinstance(template, Data): association = template.association if isinstance(property_group, str): property_group = self.find_or_create_property_group( name=property_group, association=association, ) for uid in uids: assert uid in [ child.uid for child in self.children ], f"Given data with uuid {uid} does not match any known children" if uid not in self.workspace.update_attribute(self, "property_groups") return property_group
@property def cells(self): """ :obj:`numpy.array` of :obj:`int`: Array of indices defining the connection between :obj:`~geoh5py.objects.object_base.ObjectBase.vertices`. """ @property def comments(self): """ Fetch a :obj:`` entity from children. """ for child in self.children: if isinstance(child, CommentsData): return child return None
[docs] @classmethod @abstractmethod def default_type_uid(cls) -> uuid.UUID: ...
[docs] def copy_from_extent( self, bounds: np.ndarray, parent=None, copy_children: bool = True ) -> ObjectBase | None: """ Find indices of vertices within a rectangular bounds. :param bounds: shape(2, 2) Bounding box defined by the South-West and North-East coordinates. Extents can also be provided as 3D coordinates with shape(2, 3) defining the top and bottom limits. :param attributes: Dictionary of attributes to clip by extent. """ if not any(mask_by_extent(bounds, self.extent)) and not any( mask_by_extent(self.extent, bounds) ): return None new_entity = self.copy(parent=parent, copy_children=copy_children) return new_entity.clip_by_extent(bounds)
[docs] def clip_by_extent(self, bounds: np.ndarray) -> ObjectBase | None: """ Find indices of cells within a rectangular bounds. :param bounds: shape(2, 2) Bounding box defined by the South-West and North-East coordinates. Extents can also be provided as 3D coordinates with shape(2, 3) defining the top and bottom limits. :param attributes: Dictionary of attributes to clip by extent. """ # TODO Clip entity within bounds. warnings.warn( f"Method 'clip_by_extent' for entity {type(self)} not fully implemented. " f"Bounds {bounds} ignored." ) return self
@property def entity_type(self) -> ObjectType: """ :obj:`~geoh5py.shared.entity_type.EntityType`: Object type. """ return self._entity_type @property def extent(self): if self._extent is None: locations = getattr(self, "vertices", None) if locations is None: locations = getattr(self, "centroids", None) if locations is not None: self._extent = np.c_[locations.min(axis=0), locations.max(axis=0)].T return self._extent @property def faces(self): ...
[docs] @classmethod def find_or_create_type( cls, workspace: workspace.Workspace, **kwargs ) -> ObjectType: """ Find or create a type instance for a given object class. :param workspace: Target :obj:`~geoh5py.workspace.workspace.Workspace`. :return: The ObjectType instance for the given object class. """ return ObjectType.find_or_create(workspace, cls, **kwargs)
[docs] def find_or_create_property_group(self, **kwargs) -> PropertyGroup: """ Find or create :obj:`~geoh5py.groups.property_group.PropertyGroup` from given name and properties. :param kwargs: Any arguments taken by the :obj:`~geoh5py.groups.property_group.PropertyGroup` class. :return: A new or existing :obj:`~geoh5py.groups.property_group.PropertyGroup` """ property_groups = [] if self._property_groups is not None: property_groups = self._property_groups if "name" in kwargs and any( == kwargs["name"] for pg in property_groups ): prop_group = [pg for pg in property_groups if == kwargs["name"]][0] else: kwargs["parent"] = self if ( "property_group_type" not in kwargs and "Property Group Type" not in kwargs ): if isinstance(self, Concatenated): kwargs["property_group_type"] = "Interval table" else: kwargs["property_group_type"] = "Multi-element" if isinstance(self, Concatenated): prop_group = ConcatenatedPropertyGroup(**kwargs) else: prop_group = PropertyGroup(**kwargs) property_groups += [prop_group] self._property_groups = property_groups return prop_group
[docs] def get_data(self, name: str | uuid.UUID) -> list[Data]: """ Get a child :obj:`` by name. :param name: Name of the target child data :return: A list of children Data objects """ entity_list = [] for child in self.children: if isinstance(child, Data): if ( isinstance(name, uuid.UUID) and child.uid == name ) or == name: entity_list.append(child) return entity_list
[docs] def get_data_list(self, attribute="name") -> list[str]: """ Get a list of names of all children :obj:``. :return: List of names of data associated with the object. """ name_list = [] for child in self.children: if isinstance(child, Data): name_list.append(getattr(child, attribute)) return sorted(name_list)
@property def last_focus(self) -> str: """ :obj:`bool`: Object visible in camera on start. """ return self._last_focus @last_focus.setter def last_focus(self, value: str): self._last_focus = value @property def n_cells(self) -> int | None: """ :obj:`int`: Number of cells. """ if self.cells is not None: return self.cells.shape[0] return None @property def n_vertices(self) -> int | None: """ :obj:`int`: Number of vertices. """ if self.vertices is not None: return self.vertices.shape[0] return None @property def property_groups(self) -> list[PropertyGroup] | None: """ :obj:`list` of :obj:`~geoh5py.groups.property_group.PropertyGroup`. """ return self._property_groups @property_groups.setter def property_groups(self, prop_groups: list[PropertyGroup]): if prop_groups is None: property_groups = None else: property_groups = self._property_groups if property_groups is None: property_groups = [] for prop_group in prop_groups: if not any( pg.uid == prop_group.uid for pg in property_groups ) and not any( == for pg in property_groups): prop_group.parent = self property_groups += [prop_group] self._property_groups = property_groups self.workspace.update_attribute(self, "property_groups")
[docs] def remove_children_values(self, indices: list[int], association: str): for child in self.children: if ( getattr(child, "values", None) is not None and isinstance(child.association, DataAssociationEnum) and == association ): child.values = np.delete(child.values, indices, axis=0)
@property def vertices(self): r""" :obj:`numpy.array` of :obj:`float`, shape (\*, 3): Array of x, y, z coordinates defining the position of points in 3D space. """
[docs] def validate_data_association(self, attribute_dict): """ Get a dictionary of attributes and validate the data 'association' keyword. """ if attribute_dict.get("association") is not None: return if ( getattr(self, "n_cells", None) is not None and attribute_dict["values"].ravel().shape[0] == self.n_cells ): attribute_dict["association"] = "CELL" elif ( getattr(self, "n_vertices", None) is not None and attribute_dict["values"].ravel().shape[0] == self.n_vertices ): attribute_dict["association"] = "VERTEX" else: attribute_dict["association"] = "OBJECT"
[docs] @staticmethod def validate_data_type(attribute_dict): """ Get a dictionary of attributes and validate the type of data. """ entity_type = attribute_dict.get("entity_type") if entity_type is None: primitive_type = attribute_dict.get("type") if primitive_type is not None: assert ( primitive_type.upper() in PrimitiveTypeEnum.__members__ ), f"Data 'type' should be one of {PrimitiveTypeEnum.__members__}" entity_type = {"primitive_type": primitive_type.upper()} else: values = attribute_dict.get("values") if values is None or ( isinstance(values, np.ndarray) and (values.dtype in [np.float32, np.float64]) ): entity_type = {"primitive_type": "FLOAT"} elif isinstance(values, np.ndarray) and ( values.dtype in [np.uint32, np.int32] ): entity_type = {"primitive_type": "INTEGER"} elif isinstance(values, str): entity_type = {"primitive_type": "TEXT"} else: raise NotImplementedError( "Only add_data values of type FLOAT, INTEGER and TEXT have been implemented" ) return entity_type