Source code for geoh5py.workspace.workspace

#  Copyright (c) 2023 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=too-many-lines, too-many-public-methods, too-many-arguments, too-many-locals

from __future__ import annotations

import inspect
import shutil
import subprocess
import tempfile
import uuid
import warnings
import weakref
from contextlib import AbstractContextManager, contextmanager
from gc import collect
from getpass import getuser
from io import BytesIO
from pathlib import Path
from subprocess import CalledProcessError
from typing import TYPE_CHECKING, ClassVar, cast
from weakref import ReferenceType

import h5py
import numpy as np

from .. import data, groups, objects
from import CommentsData, Data, DataType
from import TextData
from import VisualParameters
from ..groups import (
from import H5Reader, H5Writer
from ..objects import Drillhole, ObjectBase
from ..shared import weakref_utils
from ..shared.concatenation import (
from ..shared.entity import Entity
from ..shared.exceptions import Geoh5FileClosedError
from ..shared.utils import (

    from ..groups import group
    from ..objects import object_base
    from ..shared import EntityType

# pylint: disable=too-many-instance-attributes
[docs] class Workspace(AbstractContextManager): """ The Workspace class manages all Entities created or imported from the *geoh5* structure. The basic requirements needed to create a Workspace are: :param h5file: Path to the *geoh5* file or :obj:`oi.BytesIO` representation of a geoh5 structure. :param contributors: List of contributors to the project. :param distance_unit: Distance unit used in the project. :param ga_version: Version of the *geoh5* file format. :param mode: Mode in which the *geoh5* file is opened. :param name: Name of the project. :param repack: Repack the *geoh5* file after closing. :param version: Version of the project. """ _active_ref: ClassVar[ReferenceType[Workspace]] | type(None) = type(None) # type: ignore _attribute_map = { "Contributors": "contributors", "Distance unit": "distance_unit", "GA Version": "ga_version", "Version": "version", } def __init__( self, h5file: str | Path | BytesIO | None = None, contributors: tuple[str] = (getuser(),), distance_unit: str = "meter", ga_version: str = "1", mode="r+", name: str = "GEOSCIENCE", repack: bool = False, version: float = 2.1, ): self._data: dict[uuid.UUID, ReferenceType[data.Data]] = {} self._distance_unit: str = distance_unit self._contributors: np.ndarray = np.asarray( contributors, dtype=h5py.special_dtype(vlen=str) ) self._ga_version: str = ga_version self._geoh5: h5py.File | bool = False self._groups: dict[uuid.UUID, ReferenceType[Group]] = {} self._property_groups: dict[uuid.UUID, ReferenceType[PropertyGroup]] = {} self._h5file: str | Path | BytesIO | None = None self._mode: str = mode self._name: str = name self._objects: dict[uuid.UUID, ReferenceType[ObjectBase]] = {} self._repack: bool = repack self._root: Entity | PropertyGroup | None = None self._types: dict[uuid.UUID, ReferenceType[EntityType]] = {} self._version: float = version self.h5file = h5file
[docs] def activate(self): """Makes this workspace the active one. In case the workspace gets deleted, safely returns None. """ if Workspace._active_ref() is not self: Workspace._active_ref = weakref.ref(self)
[docs] @staticmethod def active() -> Workspace: """Get the active workspace.""" active_one = Workspace._active_ref() if active_one is None: raise RuntimeError("No active workspace.") # so that type check does not complain of possible returned None return cast(Workspace, active_one)
def _all_data(self) -> list[data.Data]: """Get all active Data entities registered in the workspace.""" self.remove_none_referents(self._data, "Data") return [cast("Data", v()) for v in self._data.values()] def _all_groups(self) -> list[groups.Group]: """Get all active Group entities registered in the workspace.""" self.remove_none_referents(self._groups, "Groups") return [cast("Group", v()) for v in self._groups.values()] def _all_property_groups(self) -> list[PropertyGroup]: """Get all active PropertyGroup entities registered in the workspace.""" self.remove_none_referents(self._property_groups, "PropertyGroups") return [cast("PropertyGroup", v()) for v in self._property_groups.values()] def _all_objects(self) -> list[objects.ObjectBase]: """Get all active Object entities registered in the workspace.""" self.remove_none_referents(self._objects, "Objects") return [cast("ObjectBase", v()) for v in self._objects.values()] def _all_types(self) -> list[EntityType]: """Get all active entity types registered in the workspace.""" self.remove_none_referents(self._types, "Types") return [cast("EntityType", v()) for v in self._types.values()] @property def attribute_map(self) -> dict: """ Mapping between names used in the geoh5 database. """ return self._attribute_map
[docs] def close(self): """ Close the file and clear properties for future open. """ if not self._geoh5: return if self.geoh5.mode in ["r+", "a"]: for entity in self.groups: if isinstance(entity, Concatenator) and self.repack: self.update_attribute(entity, "concatenated_attributes") self._io_call(H5Writer.save_entity, self.root, add_children=True, mode="r+") self.geoh5.close() self._data = {} if ( self.repack and not isinstance(self._h5file, BytesIO) and self._h5file is not None ): temp_file = Path(tempfile.gettempdir()) / Path(self._h5file).name try: f'h5repack --native "{self._h5file}" "{temp_file}"', check=True, shell=True, stdout=subprocess.DEVNULL, ) Path(self._h5file).unlink() shutil.move(temp_file, self._h5file) except CalledProcessError: pass self.repack = False
@property def contributors(self) -> np.ndarray: """ :obj:`numpy.array` of :obj:`str` List of contributors name. """ return self._contributors @contributors.setter def contributors(self, value: list[str]): self._contributors = np.asarray(value, dtype=h5py.special_dtype(vlen=str))
[docs] def copy_to_parent( self, entity, parent, omit_list: tuple = (), clear_cache: bool = False, **kwargs, ): """ Copy an entity to a different parent with copies of children. :param entity: Entity to be copied. :param parent: Target parent to copy the entity under. :param omit_list: List of property names to omit on copy :param clear_cache: Clear array attributes after copy. :param kwargs: Additional keyword arguments passed to the copy constructor. :return: The Entity registered to the workspace. """ entity_kwargs = get_attributes( entity, omit_list=[ "_uid", "_entity_type", "_on_file", "_centroids", "_extent", "_visual_parameters", ] + list(omit_list), attributes={"uid": None, "parent": None}, ) if entity_kwargs is None: return None entity_type_kwargs = get_attributes( entity.entity_type, omit_list=["_workspace", "_on_file"] + list(omit_list), ) # overwrite kwargs entity_kwargs.update( (k, kwargs[k]) for k in entity_kwargs.keys() & kwargs.keys() ) entity_type_kwargs.update( (k, kwargs[k]) for k in entity_type_kwargs.keys() & kwargs.keys() ) if not isinstance(parent, (ObjectBase, Group, Workspace)): raise ValueError( "Input 'parent' should be of type (ObjectBase, Group, Workspace)" ) if isinstance(parent, Workspace): parent = parent.root # Assign the same uid if possible if parent.workspace.get_entity(entity.uid)[0] is None: entity_kwargs["uid"] = entity.uid entity_kwargs["parent"] = parent entity_type = type(entity) if isinstance(entity, Data): entity_type = Data entity_kwargs.pop("property_groups", None) new_object = parent.workspace.create_entity( entity_type, **{"entity": entity_kwargs, "entity_type": entity_type_kwargs} ) if clear_cache: clear_array_attributes(entity) clear_array_attributes(new_object) return new_object
[docs] @classmethod def copy_property_groups( cls, entity: ObjectBase, propery_groups: list[PropertyGroup], data_map: dict ): for prop_group in propery_groups: properties = None if is not None: properties = [data_map[uid] for uid in] entity.find_or_create_property_group( **{ "association": prop_group.association, "name":, "property_group_type": prop_group.property_group_type, "properties": properties, } )
[docs] @classmethod def create(cls, path: str | Path, **kwargs) -> Workspace: """Create a named blank workspace and save to disk.""" return cls(**kwargs).save_as(path)
[docs] def create_from_concatenation(self, attributes): if "Name" in attributes: attributes["Name"] = attributes["Name"].replace("\u2044", "/") if "Object Type ID" in attributes: recovered_entity = self.create_entity( ObjectBase, save_on_creation=False, **{ "entity": attributes, "entity_type": {"uid": attributes["Object Type ID"]}, }, ) else: recovered_entity = self.create_entity( Data, save_on_creation=False, **{ "entity": attributes, "entity_type": self.fetch_type( uuid.UUID(attributes["Type ID"]), "Data" ), }, ) if recovered_entity is not None: recovered_entity.on_file = True recovered_entity.entity_type.on_file = True return recovered_entity
[docs] def create_data( self, entity_class, entity_kwargs: dict, entity_type_kwargs: dict | DataType, ) -> Data | None: """ Create a new Data entity with attributes. :param entity_class: :obj:`` class. :param entity_kwargs: Properties of the entity. :param entity_type_kwargs: Properties of the entity_type. :return: The newly created entity. """ if isinstance(entity_type_kwargs, DataType): data_type = entity_type_kwargs else: data_type = data.data_type.DataType.find_or_create( self, **entity_type_kwargs ) for name, member in inspect.getmembers(data): if ( inspect.isclass(member) and issubclass(member, entity_class) and member is not entity_class and hasattr(member, "primitive_type") and inspect.ismethod(member.primitive_type) and data_type.primitive_type is member.primitive_type() ): if member is CommentsData and not any( isinstance(val, str) and val == "UserComments" for val in entity_kwargs.values() ): continue if self.version > 1.0 and isinstance( entity_kwargs["parent"], ConcatenatedObject ): member = type(name + "Concatenated", (ConcatenatedData, member), {}) if member is TextData and any( isinstance(val, str) and "Visual Parameters" == val for val in entity_kwargs.values() ): member = VisualParameters created_entity = member(data_type, **entity_kwargs) return created_entity return None
[docs] def create_entity( self, entity_class, save_on_creation: bool = True, compression: int = 5, **kwargs, ) -> Entity | None: """ Function to create and register a new entity and its entity_type. :param entity_class: Type of entity to be created :param save_on_creation: Save the entity to geoh5 immediately :param compression: Compression level for data. :return entity: Newly created entity registered to the workspace """ entity_kwargs: dict = kwargs.get("entity", {}) entity_type_kwargs: dict = kwargs.get("entity_type", {}) if entity_class is not RootGroup and ( "parent" not in entity_kwargs or entity_kwargs["parent"] is None ): entity_kwargs["parent"] = self.root created_entity: Data | Group | ObjectBase | None = None if entity_class is None or issubclass(entity_class, Data): created_entity = self.create_data(Data, entity_kwargs, entity_type_kwargs) if isinstance(created_entity, VisualParameters): entity_kwargs["parent"].visual_parameters = created_entity elif entity_class is RootGroup: created_entity = RootGroup( RootGroup.find_or_create_type(self, **entity_type_kwargs), **entity_kwargs, ) elif issubclass(entity_class, (Group, ObjectBase)): created_entity = self.create_object_or_group( entity_class, entity_kwargs, entity_type_kwargs ) if created_entity is not None and save_on_creation and self.h5file is not None: self.save_entity(created_entity, compression=compression) return created_entity
[docs] def register_property_group(self, property_group: PropertyGroup) -> PropertyGroup: """ Create a new PropertyGroup entity with attributes. :param property_group: :obj:`` class. return the newly created entity. """ if not isinstance(property_group, PropertyGroup): raise TypeError("property_group must be a PropertyGroup instance") self._register_property_group(property_group) if not property_group.on_file: self.add_or_update_property_group(property_group) return property_group
[docs] def add_or_update_property_group( self, property_group: PropertyGroup, remove: bool = False ): """ Add or update a property group to the workspace. """ if isinstance(property_group, ConcatenatedPropertyGroup): parent = property_group.parent parent.concatenator.update_attributes(parent, "property_groups") else: self._io_call( H5Writer.add_or_update_property_group, property_group, remove=remove, mode="r+", )
[docs] def create_object_or_group( self, entity_class, entity_kwargs: dict, entity_type_kwargs: dict ) -> Group | ObjectBase | None: """ Create an object or a group with attributes. :param entity_class: :obj:`~geoh5py.objects.object_base.ObjectBase` or :obj:`` class. :param entity_kwargs: Attributes of the entity. :param entity_type_kwargs: Attributes of the entity_type. :return: A new Object or Group. """ entity_type_uid = None for key, val in entity_type_kwargs.items(): if key.lower() in ["id", "uid"]: entity_type_uid = uuid.UUID(str(val)) if entity_type_uid is None: if hasattr(entity_class, "default_type_uid"): entity_type_uid = entity_class.default_type_uid() else: entity_type_uid = uuid.uuid4() for name, member in inspect.getmembers(groups) + inspect.getmembers(objects): if ( inspect.isclass(member) and issubclass(member, entity_class.__bases__) and member is not entity_class.__bases__ and hasattr(member, "default_type_uid") and not member == CustomGroup and member.default_type_uid() == entity_type_uid ): if self.version > 1.0: if member in (DrillholeGroup, IntegratorDrillholeGroup): member = type(name + "Concatenator", (Concatenator, member), {}) elif member is Drillhole and isinstance( entity_kwargs.get("parent"), (DrillholeGroup, IntegratorDrillholeGroup), ): member = type( name + "Concatenated", (ConcatenatedDrillhole, member), {} ) entity_type = member.find_or_create_type(self, **entity_type_kwargs) created_entity = member(entity_type, **entity_kwargs) return created_entity # Special case for CustomGroup without uuid if entity_class == Group: entity_type = groups.custom_group.CustomGroup.find_or_create_type( self, **entity_type_kwargs ) created_entity = groups.custom_group.CustomGroup( entity_type, **entity_kwargs ) return created_entity return None
@property def data(self) -> list[data.Data]: """Get all active Data entities registered in the workspace.""" return self._all_data()
[docs] def fetch_or_create_root(self): root = self.load_entity(uuid.uuid4(), "root") if root is not None and not isinstance(root, PropertyGroup): self._root = root self._root.on_file = True self._root.entity_type.on_file = True self.fetch_children(self._root, recursively=True) else: self._root = self.create_entity(RootGroup, save_on_creation=False) for entity_type in ["group", "object"]: uuids = self._io_call(H5Reader.fetch_uuids, entity_type, mode="r") for uid in uuids: if isinstance(self.get_entity(uid)[0], Entity): continue recovered_object = self.load_entity(uid, entity_type) if isinstance(recovered_object, (Group, ObjectBase)): self.fetch_children(recovered_object, recursively=True)
[docs] def remove_children(self, parent, children: list): """ Remove a list of entities from a parent. The target entities remain present on file. """ for child in children: if isinstance(child, PropertyGroup): self._io_call( H5Writer.add_or_update_property_group, child, remove=True, mode="r+" ) else: ref_type = self.str_from_type(child) self._io_call( H5Writer.remove_child, child.uid, ref_type, parent, mode="r+" )
[docs] def remove_entity(self, entity: Entity): """ Function to remove an entity and its children from the workspace. """ if not entity.allow_delete: raise UserWarning( f"The 'allow_delete' property of entity {entity} prevents it from " "being removed. Please revise." ) if not isinstance(entity, Concatenated): self.workspace.remove_recursively(entity) if isinstance(entity, Concatenated): entity.concatenator.remove_entity(entity) else: ref_type = self.str_from_type(entity) self._io_call( H5Writer.remove_entity, entity.uid, ref_type, mode="r+", ) del entity collect() self.remove_none_referents(self._types, "Types")
[docs] def remove_none_referents( self, referents: dict[uuid.UUID, ReferenceType], rtype: str, ): """ Search and remove deleted entities """ rem_list: list = [] for key, value in referents.items(): if value() is None: rem_list += [key] self._io_call( H5Writer.remove_entity, key, rtype, parent=self, mode="r+" ) for key in rem_list: del referents[key]
[docs] def remove_recursively(self, entity: Entity): """Delete an entity and its children from the workspace and geoh5 recursively""" parent = entity.parent if hasattr(entity, "children"): for child in entity.children: self.remove_entity(child) parent.remove_children(entity)
[docs] def deactivate(self): """Deactivate this workspace if it was the active one, else does nothing.""" if Workspace._active_ref() is self: Workspace._active_ref = type(None)
@property def distance_unit(self) -> str: """ :obj:`str` Distance unit used in the project. """ return self._distance_unit @distance_unit.setter def distance_unit(self, value: str): self._distance_unit = value
[docs] def fetch_array_attribute(self, entity: Entity, key: str = "cells") -> np.ndarray: """ Fetch attribute stored as structured array from the source geoh5. :param entity: Unique identifier of target entity. :param key: Field array name :return: Structured array. """ if isinstance(entity, Concatenated): return entity.concatenator.fetch_values(entity, key) return self._io_call( H5Reader.fetch_array_attribute, entity.uid, "Objects" if isinstance(entity, ObjectBase) else "Groups", key, mode="r", )
[docs] def fetch_children( self, entity: Entity | PropertyGroup | None, recursively: bool = False, ) -> list: """ Recover and register children entities from the geoh5. :param entity: Parental entity. :param recursively: Recover all children down the project tree. :return list: List of children entities. """ if entity is None or isinstance(entity, ConcatenatedData): return [] entity_type = "data" if isinstance(entity, Group): entity_type = "group" elif isinstance(entity, ObjectBase): entity_type = "object" if isinstance(entity, RootGroup) and not entity.on_file: children_list = {child.uid: "" for child in entity.children} else: children_list = self._io_call( H5Reader.fetch_children, entity.uid, entity_type, mode="r" ) if isinstance(entity, Concatenator): if any(entity.children): return entity.children cat_children = entity.fetch_concatenated_objects() children_list.update( { str2uuid(as_str_if_utf8_bytes(uid)): attr for uid, attr in cat_children.items() } ) family_tree = [] for uid, child_type in children_list.items(): recovered_object = self.get_entity(uid)[0] if recovered_object is None and not isinstance(entity, PropertyGroup): recovered_object = self.load_entity(uid, child_type, parent=entity) if not ( recovered_object is None or isinstance(recovered_object, PropertyGroup) ): recovered_object.on_file = True recovered_object.entity_type.on_file = True family_tree += [recovered_object] if recursively and isinstance(recovered_object, (Group, ObjectBase)): family_tree += self.fetch_children( recovered_object, recursively=True ) if getattr(recovered_object, "property_groups", None) is not None: family_tree += getattr(recovered_object, "property_groups") if getattr(entity, "property_groups", None) is not None: family_tree += getattr(entity, "property_groups") return family_tree
[docs] def fetch_concatenated_attributes( self, entity: Concatenator | ConcatenatedObject ) -> dict | None: """ Fetch attributes of Concatenated entity. :param entity: Concatenator group or ConcatenateObject. :return: Dictionary of attributes. """ if isinstance(entity, Group): entity_type = "Group" else: raise NotImplementedError( "Method 'fetch_concatenated_attributes' currently only implemented " "for 'Group' entities." ) return self._io_call( H5Reader.fetch_concatenated_attributes, entity.uid, entity_type, entity.concat_attr_str, mode="r", )
[docs] def fetch_concatenated_list( self, entity: Group | ObjectBase, label: str ) -> list | None: """ Fetch list of data or indices of ConcatenatedData entities. :param entity: Concatenator group. :param label: Label name of the h5py.Group. :return: List of concatenated Data names. """ if isinstance(entity, Group): entity_type = "Group" else: raise NotImplementedError( "Method 'fetch_concatenated_list' currently only implemented " "for 'Group' entities." ) return self._io_call( H5Reader.fetch_concatenated_attributes, entity.uid, entity_type, label, mode="r", )
[docs] def fetch_concatenated_values( self, entity: Group | ObjectBase, label: str ) -> tuple | None: """ Fetch data under the ConcatenatedData Data group of an entity. :param entity: Concatenator group. :param label: Name of the target data. :return: Index array and data values for the target label. """ if isinstance(entity, Group): entity_type = "Group" else: raise NotImplementedError( "Method 'fetch_concatenated_values' currently only implemented " "for 'Group' entities." ) return self._io_call( H5Reader.fetch_concatenated_values, entity.uid, entity_type, label, mode="r", )
[docs] def fetch_metadata(self, uid: uuid.UUID, argument="Metadata") -> dict | None: """ Fetch the metadata of an entity from the source geoh5. :param uid: Entity uid containing the metadata. :param argument: Optional argument for other json-like attributes. :return: Dictionary of values. """ return self._io_call( H5Reader.fetch_metadata, uid, argument=argument, entity_type="Groups" if isinstance(self.get_entity(uid)[0], Group) else "Objects", mode="r", )
[docs] def fetch_property_groups(self, entity: Entity) -> list[PropertyGroup]: """ Fetch all property_groups on an object from the source geoh5 :param entity: Target object :return: List of PropertyGroups """ raise DeprecationWarning( f"Method 'fetch_property_groups' of {self} as been removed. " "Use `entity.property_groups` instead." )
[docs] def fetch_type(self, uid: uuid.UUID, entity_type: str) -> dict: """ Fetch attributes of a specific entity type. :param uid: Unique identifier of the entity type. :param entity_type: One of 'Data', 'Object' or 'Group' """ return self._io_call(H5Reader.fetch_type, uid, entity_type)
[docs] def fetch_values(self, entity: Entity) -> np.ndarray | str | float | None: """ Fetch the data values from the source geoh5. :param entity: Entity with 'values'. :return: Array of values. """ if isinstance(entity, ConcatenatedData): return entity.concatenator.fetch_values(entity, return self._io_call(H5Reader.fetch_values, entity.uid)
[docs] def fetch_file_object(self, uid: uuid.UUID, file_name: str) -> bytes | None: """ Fetch an image from file name. :param uid: Unique identifier of target data object. :param file_name: Name of the file to fetch. :return: Array of values. """ return self._io_call(H5Reader.fetch_file_object, uid, file_name)
[docs] def finalize(self) -> None: """ Deprecate method finalize. """ warnings.warn( "The 'finalize' method will be deprecated in future versions of geoh5py in" " favor of `workspace.close()`. " "Please update your code to suppress this warning.", DeprecationWarning, ) self.close()
[docs] def find_data(self, data_uid: uuid.UUID) -> Entity | None: """ Find an existing and active Data entity. """ return weakref_utils.get_clean_ref(self._data, data_uid)
[docs] def find_entity(self, entity_uid: uuid.UUID) -> Entity | PropertyGroup | None: """Get all active entities registered in the workspace.""" return ( self.find_group(entity_uid) or self.find_data(entity_uid) or self.find_object(entity_uid) or self.find_property_group(entity_uid) )
[docs] def find_group(self, group_uid: uuid.UUID) -> group.Group | None: """ Find an existing and active Group object. """ return weakref_utils.get_clean_ref(self._groups, group_uid)
[docs] def find_property_group( self, property_group_uid: uuid.UUID ) -> PropertyGroup | None: """ Find an existing and active PropertyGroup object. """ return weakref_utils.get_clean_ref(self._property_groups, property_group_uid)
[docs] def find_object(self, object_uid: uuid.UUID) -> object_base.ObjectBase | None: """ Find an existing and active Object. """ return weakref_utils.get_clean_ref(self._objects, object_uid)
[docs] def find_type( self, type_uid: uuid.UUID, type_class: type[EntityType] ) -> EntityType | None: """ Find an existing and active EntityType. :param type_uid: Unique identifier of target type. :param type_class: The type of entity to find. """ found_type = weakref_utils.get_clean_ref(self._types, type_uid) return found_type if isinstance(found_type, type_class) else None
@property def ga_version(self) -> str: """ :obj:`str` Version of Geoscience Analyst software. """ return self._ga_version @ga_version.setter def ga_version(self, value: str): self._ga_version = value
[docs] def get_entity(self, name: str | uuid.UUID) -> list[Entity | PropertyGroup | None]: """ Retrieve an entity from one of its identifier, either by name or :obj:`uuid.UUID`. :param name: Object identifier, either name or uuid. :return: List of entities with the same given name. """ if isinstance(name, uuid.UUID): list_entity_uid = [name] else: # Extract all objects uuid with matching name list_entity_uid = [ key for key, val in self.list_entities_name.items() if val == name ] if not list_entity_uid: return [None] entity_list: list[Entity | None | PropertyGroup] = [] for uid in list_entity_uid: entity_list.append(self.find_entity(uid)) return entity_list
@property def groups(self) -> list[groups.Group]: """Get all active Group entities registered in the workspace.""" return self._all_groups() @property def property_groups(self) -> list[PropertyGroup]: """Get all active PropertyGroup entities registered in the workspace.""" return self._all_property_groups() @property def geoh5(self) -> h5py.File: """ Instance of h5py.File. """ if not self._geoh5: raise Geoh5FileClosedError return self._geoh5 @property def h5file(self) -> str | Path | BytesIO | None: """ Target *geoh5* file name with path or BytesIO object representation. On :func:``, the BytesIO representation gets replaced by a Path to a file on disk. """ return self._h5file @h5file.setter def h5file(self, file: str | Path | BytesIO | None): if self._h5file is not None: raise ValueError( "The 'h5file' attribute cannot be changed once it has been set." ) if not isinstance(file, (str, Path, BytesIO, type(None))): raise ValueError( "The 'h5file' attribute must be a str, " "pathlib.Path to the target geoh5 file or BytesIO. " f"Provided {file} of type({type(file)})" ) if isinstance(file, type(None)) or ( isinstance(file, (str, Path)) and not Path(file).is_file() ): self._h5file = BytesIO() self._geoh5 = h5py.File(self.h5file, "a") with self._geoh5: self._root = self.create_entity(RootGroup, save_on_creation=False) H5Writer.init_geoh5(self.geoh5, self) elif isinstance(file, BytesIO): self._h5file = file if isinstance(file, (str, Path)): if Path(file).suffix != ".geoh5": raise ValueError("Input 'h5file' file must have a 'geoh5' extension.") if not Path(file).is_file(): warnings.warn( "From version 0.8.0, the 'h5file' attribute must be a string " "or path to an existing file, or user must call the 'create' " "method. We will attempt to `save` the file for you, but this " "behaviour will be removed in future releases.", ) self.save_as(file) self.close() else: self._h5file = Path(file) @property def list_data_name(self) -> dict[uuid.UUID, str]: """ :obj:`dict` of :obj:`uuid.UUID` keys and name values for all registered Data. """ data_name = {} for key, val in self._data.items(): entity = val() if entity is not None: data_name[key] = return data_name @property def list_entities_name(self) -> dict[uuid.UUID, str]: """ :return: :obj:`dict` of :obj:`uuid.UUID` keys and name values for all registered Entities. """ entities_name = self.list_groups_name entities_name.update(self.list_objects_name) entities_name.update(self.list_data_name) entities_name.update(self.list_property_groups_name) return entities_name @property def list_groups_name(self) -> dict[uuid.UUID, str]: """ :obj:`dict` of :obj:`uuid.UUID` keys and name values for all registered Groups. """ groups_name = {} for key, val in self._groups.items(): entity = val() if entity is not None: groups_name[key] = return groups_name @property def list_property_groups_name(self) -> dict[uuid.UUID, str]: """ :obj:`dict` of :obj:`uuid.UUID` keys and name values for all registered Groups. """ property_groups_name = {} for key, val in self._property_groups.items(): entity = val() if entity is not None: property_groups_name[key] = return property_groups_name @property def list_objects_name(self) -> dict[uuid.UUID, str]: """ :obj:`dict` of :obj:`uuid.UUID` keys and name values for all registered Objects. """ objects_name = {} for key, val in self._objects.items(): entity = val() if entity is not None: objects_name[key] = return objects_name
[docs] def load_entity( self, uid: uuid.UUID, entity_type: str, parent: Entity | None = None, ) -> Entity | PropertyGroup | None: """ Recover an entity from geoh5. :param uid: Unique identifier of entity :param entity_type: One of entity type 'group', 'object', 'data' or 'root' :param parent: Parent entity. :return entity: Entity loaded from geoh5 """ child = self.get_entity(uid)[0] if isinstance(child, (Entity, PropertyGroup)): return child base_classes = { "group": Group, "object": ObjectBase, "data": Data, "root": RootGroup, } attributes = self._io_call( H5Reader.fetch_attributes, uid, entity_type, mode="r" ) if attributes is None: return None if parent is not None: attributes[0]["entity"]["parent"] = parent entity = self.create_entity( base_classes[entity_type], save_on_creation=False, **{**attributes[0], **attributes[1]}, ) # Get property groups (key 2) from object attributes if isinstance(entity, ObjectBase) and len(attributes[2]) > 0: for kwargs in attributes[2].values(): entity.create_property_group(on_file=True, **kwargs) return entity
@property def name(self) -> str: """ :obj:`str` Name of the project. """ return self._name @property def objects(self) -> list[objects.ObjectBase]: """Get all active Object entities registered in the workspace.""" return self._all_objects()
[docs] def open(self, mode: str | None = None) -> Workspace: """ Open a geoh5 file and load the tree structure. :param mode: Optional mode of h5py.File. Defaults to 'r+'. :return: `self` """ if isinstance(self._geoh5, h5py.File) and self._geoh5: warnings.warn(f"Workspace already opened in mode {self._geoh5.mode}.") return self if mode is None: mode = self._mode try: self._geoh5 = h5py.File(self.h5file, mode) except OSError: self._geoh5 = h5py.File(self.h5file, "r") self._data = {} self._objects = {} self._groups = {} self._types = {} self._property_groups = {} proj_attributes = self._io_call(H5Reader.fetch_project_attributes, mode="r") for key, attr in proj_attributes.items(): setattr(self, self._attribute_map[key], attr) self.fetch_or_create_root() return self
def _register_type(self, entity_type: EntityType): weakref_utils.insert_once(self._types, entity_type.uid, entity_type) def _register_group(self, group: Group): weakref_utils.insert_once(self._groups, group.uid, group) def _register_data(self, data_obj: Entity): weakref_utils.insert_once(self._data, data_obj.uid, data_obj) def _register_object(self, obj: ObjectBase): weakref_utils.insert_once(self._objects, obj.uid, obj) def _register_property_group(self, property_group: PropertyGroup): weakref_utils.insert_once( self._property_groups, property_group.uid, property_group ) @property def root(self) -> Entity | PropertyGroup | None: """ :obj:`~geoh5py.groups.root_group.RootGroup` entity. """ return self._root @property def repack(self) -> bool: """ Flag to repack the file after data deletion. """ return self._repack @repack.setter def repack(self, value: bool): """ :type value: bool. """ self._repack = value
[docs] def save(self, filepath: str | Path) -> Workspace: warnings.warn( " is deprecated and will be remove in future versions," "use Workspace.save_as instead.", DeprecationWarning, ) return self.save_as(filepath)
[docs] def save_as(self, filepath: str | Path) -> Workspace: """ Save the workspace to disk. """ if self._geoh5 is not None: self.close() filepath = Path(filepath) if filepath.suffix == "": filepath = filepath.with_suffix(".geoh5") if filepath.suffix != ".geoh5": raise ValueError("Input 'h5file' file must have a 'geoh5' extension.") if filepath.exists(): raise FileExistsError(f"File {filepath} already exists.") if isinstance(self.h5file, BytesIO): with open(filepath, "wb") as file: file.write(self.h5file.getbuffer()) elif self.h5file is None: raise ValueError("Input 'h5file' file must be specified.") else: shutil.copy(self.h5file, filepath) self._h5file = filepath return self
[docs] def save_entity( self, entity: Entity, add_children: bool = True, compression: int = 5, ) -> None: """ Save or update an entity to geoh5. :param entity: Entity to be written to geoh5. :param add_children: Add children entities to geoh5. :param compression: Compression level for data. """ if isinstance(entity, Concatenated): entity.concatenator.add_save_concatenated(entity) if hasattr(entity, "entity_type"): self.save_entity_type(entity.entity_type) else: self._io_call( H5Writer.save_entity, entity, add_children=add_children, mode="r+", compression=compression, )
[docs] def save_entity_type(self, entity_type: EntityType) -> None: """ Save or update an entity_type to geoh5. :param entity_type: Entity to be written to geoh5. """ self._io_call(H5Writer.write_entity_type, entity_type, mode="r+")
[docs] @staticmethod def str_from_type(entity) -> str | None: if isinstance(entity, Data): return "Data" if isinstance(entity, Group): return "Groups" if isinstance(entity, ObjectBase): return "Objects" return None
@property def types(self) -> list[EntityType]: """Get all active entity types registered in the workspace.""" return self._all_types()
[docs] def update_attribute( self, entity: Entity | EntityType, attribute: str, channel: str | None = None, **kwargs, ) -> None: """ Save or update an entity to geoh5. :param entity: Entity to be written to geoh5. :param attribute: Name of the attribute to get updated to geoh5. :param channel: Optional channel argument for concatenated data and index. """ if entity.on_file: if isinstance(entity, Concatenated): entity.concatenator.update_attributes(entity, attribute) elif channel is not None: self._io_call( H5Writer.update_concatenated_field, entity, attribute, channel, mode="r+", ) else: self._io_call( H5Writer.update_field, entity, attribute, mode="r+", **kwargs ) self._io_call(H5Writer.clear_stats_cache, entity, mode="r+")
@property def version(self) -> float: """ :obj:`float` Version of the geoh5 file format. """ return self._version @version.setter def version(self, value: float): self._version = value @property def workspace(self) -> Workspace: """ This workspace instance itself. """ return self def _io_call(self, fun, *args, mode="r", **kwargs): """ Run a H5Writer or H5Reader function with validation of target geoh5 """ try: if self._geoh5 is None: return None if mode in ["r+", "a"] and self.geoh5.mode == "r": raise UserWarning( f"Error performing {fun}. " "Attempting to write to a geoh5 file in read-only mode. " "Consider closing the workspace (Geoscience ANALYST) and " "re-opening in mode='r+'." ) return fun(self.geoh5, *args, **kwargs) except Geoh5FileClosedError as error: if not Path(str(self.h5file)).is_file() and not isinstance( self.h5file, BytesIO ): raise FileNotFoundError( f"Error performing {fun}. " "The geoh5 file does not exist." r"Consider creating the geoh5 with Workspace().save('PATH\*.geoh5)'" ) from error raise Geoh5FileClosedError( f"Error executing {fun}. " + "Consider re-opening with `' " "or used within a context manager." ) from error def __exit__(self, exc_type, exc_value, traceback): self.close()
[docs] @contextmanager def active_workspace(workspace: Workspace): previous_active_ref = Workspace._active_ref # pylint: disable=protected-access workspace.activate() yield workspace workspace.deactivate() # restore previous active workspace when leaving the context previous_active = previous_active_ref() if previous_active is not None: previous_active.activate() # pylint: disable=no-member