geoh5py.workspace¶

geoh5py.workspace.workspace¶

class geoh5py.workspace.workspace.Workspace(h5file: str | Path | io.BytesIO = 'Analyst.geoh5', mode='a', **kwargs)[source]¶

Bases: AbstractContextManager

The Workspace class manages all Entities created or imported from the geoh5 structure.

The basic requirements needed to create a Workspace are:

Parameters: geoh5 – File name of the target geoh5 file. A new project is created if the target file cannot by found on disk.

activate()[source]¶

Makes this workspace the active one.

In case the workspace gets deleted, Workspace.active() safely returns None.

static active() → Workspace[source]¶: Get the active workspace.

property attribute_map: dict¶: Mapping between names used in the geoh5 database.

close()[source]¶: Close the file and clear properties for future open.

property contributors: ndarray¶: numpy.array of str List of contributors name.

classmethod copy_property_groups(entity: ObjectBase, propery_groups: list[PropertyGroup], data_map: dict)[source]¶

copy_to_parent(entity, parent, copy_children: bool = True, omit_list: tuple = (), extent: np.ndarray | None = None, **kwargs)[source]¶

Copy an entity to a different parent with copies of children.

Parameters

entity – Entity to be copied.
parent – Target parent to copy the entity under.
copy_children – Copy all children of the entity.
omit_list – List of property names to omit on copy
extent – Clip object’s copy by extent defined by a South-West and North-East corners.
kwargs – Additional keyword arguments passed to the copy constructor.

Returns

The Entity registered to the workspace.

create_data(entity_class, entity_kwargs: dict, entity_type_kwargs: dict | DataType) → Data | None[source]¶

Create a new Data entity with attributes.

Parameters

entity_class – Data class.
entity_kwargs – Properties of the entity.
entity_type_kwargs – Properties of the entity_type.

Returns

The newly created entity.

create_entity(entity_class, save_on_creation: bool = True, **kwargs) → Entity | None[source]¶

Function to create and register a new entity and its entity_type.

Parameters

entity_class – Type of entity to be created
save_on_creation – Save the entity to geoh5 immediately

Return entity

Newly created entity registered to the workspace

create_from_concatenation(attributes)[source]¶

create_object_or_group(entity_class, entity_kwargs: dict, entity_type_kwargs: dict) → Group | ObjectBase | None[source]¶

Create an object or a group with attributes.

Parameters

entity_class – ObjectBase or Group class.
entity_kwargs – Attributes of the entity.
entity_type_kwargs – Attributes of the entity_type.

Returns

A new Object or Group.

property data: list[data.Data]¶: Get all active Data entities registered in the workspace.

deactivate()[source]¶: Deactivate this workspace if it was the active one, else does nothing.

property distance_unit: str¶: str Distance unit used in the project.

fetch_array_attribute(entity: Entity, key: str = 'cells') → ndarray[source]¶

Fetch attribute stored as structured array from the source geoh5.

Parameters

entity – Unique identifier of target entity.
file – h5py.File or name of the target geoh5 file
key – Field array name

Returns

Structured array.

fetch_children(entity: Entity | None, recursively: bool = False) → list[source]¶

Recover and register children entities from the geoh5.

Parameters

entity – Parental entity.
recursively – Recover all children down the project tree.
file – h5py.File or name of the target geoh5 file.

Return list

List of children entities.

fetch_concatenated_attributes(entity: Concatenator | ConcatenatedObject) → dict | None[source]¶

Fetch attributes of Concatenated entity.

Parameters: entity – Concatenator group or ConcatenateObject.
Returns: Dictionary of attributes.

fetch_concatenated_list(entity: Group | ObjectBase, label: str) → list | None[source]¶

Fetch list of data or indices of ConcatenatedData entities.

Parameters

entity – Concatenator group.
label – Label name of the h5py.Group

Returns

List of concatenated Data names.

fetch_concatenated_values(entity: Group | ObjectBase, label: str) → tuple | None[source]¶

Fetch data under the ConcatenatedData Data group of an entity.

Parameters

entity – Concatenator group.
label – Name of the target data.

Returns

Index array and data values for the target label.

fetch_file_object(uid: uuid.UUID, file_name: str) → bytes | None[source]¶

Fetch an image from file name.

Parameters: uid – Unique identifier of target data object.
Returns: Array of values.

fetch_metadata(uid: uuid.UUID, argument='Metadata') → dict | None[source]¶

Fetch the metadata of an entity from the source geoh5.

Parameters

uid – Entity uid containing the metadata.
argument – Optional argument for other json-like attributes.

Returns

Dictionary of values.

fetch_or_create_root()[source]¶

fetch_property_groups(entity: Entity) → list[PropertyGroup][source]¶

Fetch all property_groups on an object from the source geoh5

Parameters: entity – Target object
Returns: List of PropertyGroups

fetch_type(uid: UUID, entity_type: str) → dict[source]¶: Fetch attributes of a specific entity type. :param uid: Unique identifier of the entity type. :param entity_type: One of ‘Data’, ‘Object’ or ‘Group’

fetch_values(entity: Entity) → np.ndarray | str | float | None[source]¶

Fetch the data values from the source geoh5.

Parameters: entity – Entity with ‘values’.
Returns: Array of values.

finalize() → None[source]¶

Deprecate method finalize

Parameters: file – h5py.File or name of the target geoh5 file

find_data(data_uid: uuid.UUID) → Entity | None[source]¶: Find an existing and active Data entity.

find_entity(entity_uid: uuid.UUID) → Entity | None[source]¶: Get all active entities registered in the workspace.

find_group(group_uid: uuid.UUID) → group.Group | None[source]¶: Find an existing and active Group object.

find_object(object_uid: uuid.UUID) → object_base.ObjectBase | None[source]¶: Find an existing and active Object.

find_type(type_uid: uuid.UUID, type_class: type[EntityType]) → EntityType | None[source]¶

Find an existing and active EntityType

Parameters: type_uid – Unique identifier of target type

property ga_version: str¶: str Version of Geoscience Analyst software.

property geoh5: File¶: Instance of h5py.File.

get_entity(name: str | uuid.UUID) → list[Entity | None][source]¶

Retrieve an entity from one of its identifier, either by name or uuid.UUID.

Parameters: name – Object identifier, either name or uuid.
Returns: List of entities with the same given name.

property groups: list[groups.Group]¶: Get all active Group entities registered in the workspace.

property h5file: str | Path | io.BytesIO¶

Str: Target geoh5 file name with path.

property list_data_name: dict[uuid.UUID, str]¶: dict of uuid.UUID keys and name values for all registered Data.

property list_entities_name: dict[uuid.UUID, str]¶

Returns: dict of uuid.UUID keys and name values for all registered Entities.

property list_groups_name: dict[uuid.UUID, str]¶: dict of uuid.UUID keys and name values for all registered Groups.

property list_objects_name: dict[uuid.UUID, str]¶: dict of uuid.UUID keys and name values for all registered Objects.

load_entity(uid: uuid.UUID, entity_type: str, parent: Entity | None = None) → Entity | None[source]¶

Recover an entity from geoh5.

Parameters

uid – Unique identifier of entity
entity_type – One of entity type ‘group’, ‘object’, ‘data’ or ‘root’

Return entity

Entity loaded from geoh5

property name: str¶: str Name of the project.

property objects: list[objects.ObjectBase]¶: Get all active Object entities registered in the workspace.

open(mode: str | None = None) → Workspace[source]¶

Open a geoh5 file and load the tree structure.

Parameters: mode – Optional mode of h5py.File. Defaults to ‘r+’.
Returns: self

remove_children(parent, children: list)[source]¶: Remove a list of entities from a parent. The target entities remain present on file.

remove_entity(entity: Entity)[source]¶: Function to remove an entity and its children from the workspace.

remove_none_referents(referents: dict[uuid.UUID, ReferenceType], rtype: str)[source]¶: Search and remove deleted entities

remove_recursively(entity: Entity)[source]¶: Delete an entity and its children from the workspace and geoh5 recursively

property repack: bool¶: Flag to repack the file after data deletion

property root: Entity | None¶: RootGroup entity.

save_entity(entity: Entity, add_children: bool = True) → None[source]¶

Save or update an entity to geoh5.

Parameters

entity – Entity to be written to geoh5.
add_children – Add children entities to geoh5.
file – h5py.File or name of the target geoh5

save_entity_type(entity_type: EntityType) → None[source]¶

Save or update an entity_type to geoh5.

Parameters: entity_type – Entity to be written to geoh5.

static str_from_type(entity) → str | None[source]¶

property types: list[EntityType]¶: Get all active entity types registered in the workspace.

update_attribute(entity: Entity | EntityType, attribute: str, channel: str | None = None, **kwargs) → None[source]¶

Save or update an entity to geoh5.

Parameters

entity – Entity to be written to geoh5.
attribute – Name of the attribute to get updated to geoh5.
channel – Optional channel argument for concatenated data and index.

property version: float¶: float Version of the geoh5 file format.

property workspace: Workspace¶: This workspace instance itself.

geoh5py.workspace.workspace.active_workspace(workspace: Workspace)[source]¶