VolumeFigureApi

class VolumeFigureApi[source]

Bases: supervisely.api.entity_annotation.figure_api.FigureApi

VolumeFigure for a single volume.

Methods

append_bulk

Add VolumeFigures to given Volume by ID.

create

Create new VolumeFigure for given slice in given volume ID.

download

Method returns a dictionary with pairs of image ID and list of FigureInfo for the given dataset ID.

download_geometries_batch

Download figure geometries with given IDs from storage.

download_geometry

Download figure geometry with given ID from storage.

download_sf_geometries

Download spatial figure geometries for the specified figure IDs and save them to the specified paths.

download_stl_meshes

Download STL meshes for the specified figure IDs and saves them to the specified paths.

exists

Checks if an entity with the given parent_id and name exists

get_by_ids

Get Figures information by IDs from given dataset ID.

get_free_name

Generates a free name for an entity with the given parent_id and name.

get_info_by_id

Get Figure information by ID.

get_info_by_name

Get information about an entity by its name from the Supervisely server.

get_list

Get list of entities in parent entity with given parent ID.

get_list_all_pages

Get list of all or limited quantity entities from the Supervisely server.

get_list_all_pages_generator

This generator function retrieves a list of all or a limited quantity of entities from the Supervisely server, yielding batches of entities as they are retrieved

info_sequence

NamedTuple FigureInfo information about Figure.

info_tuple_name

Get string name of NamedTuple for class.

interpolate

Interpolate a spatial figure with a ClosedSurfaceMesh geometry.

load_sf_geometry

Download geometry of an existing in Supervisely figure and load this data into the VolumeFigure object to complete this figure representation.

remove

Remove an entity with the specified ID from the Supervisely server.

remove_batch

Remove entities in batches from the Supervisely server.

upload_geometries_batch

Upload figure geometries with given figure IDs to storage.

upload_geometry

Upload figure geometry with given figure ID to storage.

upload_sf_geometries

Upload geometries as bytes into spatial figures in the project using their UUID keys.

upload_sf_geometry

Upload spatial figures geometry as bytes to storage by given ID.

upload_stl_meshes

Upload existing interpolations or create on the fly and and add them to empty mesh figures.

Attributes

MAX_WAIT_ATTEMPTS

Maximum number of attempts that will be made to wait for a certain condition to be met.

WAIT_ATTEMPT_TIMEOUT_SEC

Number of seconds for intervals between attempts.

InfoType

alias of supervisely.api.module_api.FigureInfo

append_bulk(volume_id, figures, key_id_map)[source]

Add VolumeFigures to given Volume by ID.

Parameters
volume_id : int

Volume ID in Supervisely.

key_id_map : KeyIdMap

KeyIdMap object.

figures : List[VolumeFigure]

List of VolumeFigure objects.

Returns

None

Return type

NoneType

Usage example
import supervisely as sly

from supervisely.volume_annotation.plane import Plane

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

project_id = 19370
volume_id = 19617444

key_id_map = sly.KeyIdMap()

project_meta_json = api.project.get_meta(project_id)
project_meta = sly.ProjectMeta.from_json(project_meta_json)

vol_ann_json = api.volume.annotation.download(volume_id)
vol_ann = sly.VolumeAnnotation.from_json(vol_ann_json, project_meta, key_id_map)
volume_obj_collection = vol_ann.objects.to_json()
vol_obj = sly.VolumeObject.from_json(volume_obj_collection[1], project_meta)

figure = sly.VolumeFigure(
    vol_obj,
    sly.Rectangle(20, 20, 129, 200),
    sly.Plane.AXIAL,
    45,
)

api.volume.figure.append_bulk(volume_id, [figure], key_id_map)
create(volume_id, object_id, plane_name, slice_index, geometry_json, geometry_type)[source]

Create new VolumeFigure for given slice in given volume ID.

Parameters
volume_id : int

Volume ID in Supervisely.

object_id : int

ID of the object to which the VolumeFigure belongs.

plane_name : str

Plane of the slice in volume.

slice_index : int

Number of the slice to add VolumeFigure.

geometry_json : dict

Parameters of geometry for VolumeFigure.

geometry_type : str

Type of VolumeFigure geometry.

Returns

New figure ID

Return type

int

Usage example
import supervisely as sly

from supervisely.volume_annotation.plane import Plane

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

volume_id = 19581134
object_id = 5565016
slice_index = 0
plane_name = Plane.AXIAL
geometry_json = {'points': {'exterior': [[500, 500], [1555, 1500]], 'interior': []}}
geometry_type = 'rectangle'

figure_id = api.volume.figure.create(
    volume_id,
    object_id,
    plane_name,
    slice_index,
    geometry_json,
    geometry_type
) # 87821207
download(dataset_id, image_ids=None, skip_geometry=False)

Method returns a dictionary with pairs of image ID and list of FigureInfo for the given dataset ID. Can be filtered by image IDs.

Parameters
dataset_id : int

Dataset ID in Supervisely.

image_ids : List[int], optional

Specify the list of image IDs within the given dataset ID. If image_ids is None, the method returns all possible pairs of images with figures. Note: Consider using sly.batched() to ensure that no figures are lost in the response.

skip_geometry : bool

Skip the download of figure geometry. May be useful for a significant api requets speed increase in the large datasets.

Returns

A dictionary where keys are image IDs and values are lists of figures.

Return type

class

Dict[int, List[FigureInfo]]

download_geometries_batch(ids)

Download figure geometries with given IDs from storage.

Parameters
ids : List[int]

List of figure IDs in Supervisely.

Returns

List of figure geometries in Supervisely JSON format.

Return type

List[dict]

download_geometry(figure_id)

Download figure geometry with given ID from storage.

Parameters
figure_id : int

Figure ID in Supervisely.

Returns

Figure geometry in Supervisely JSON format.

Return type

dict

download_sf_geometries(ids, paths)[source]

Download spatial figure geometries for the specified figure IDs and save them to the specified paths.

Parameters
ids : List[int]

List of VolumeFigure IDs in Supervisely.

paths : List[str]

List of paths to save the downloaded geometries.

Returns

None

Return type

NoneType

Usage example
import supervisely as sly

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

STORAGE_DIR = sly.app.get_data_dir()

volume_id = 19371414
project_id = 17215

volume = api.volume.get_info_by_id(volume_id)

key_id_map = sly.KeyIdMap()
project_meta_json = api.project.get_meta(project_id)
project_meta = sly.ProjectMeta.from_json(project_meta_json)

vol_ann_json = api.volume.annotation.download(volume_id)
id_to_paths = {}
vol_ann = sly.VolumeAnnotation.from_json(vol_ann_json, project_meta, key_id_map)

for sp_figure in vol_ann.spatial_figures:
    figure_id = key_id_map.get_figure_id(sp_figure.key())
    id_to_paths[figure_id] = f"{STORAGE_DIR}/{sp_figure.key().hex}.stl"
if id_to_paths:
    api.volume.figure.download_sf_geometries(*zip(*id_to_paths.items()))
download_stl_meshes(ids, paths)[source]

Download STL meshes for the specified figure IDs and saves them to the specified paths.

Parameters
ids : int

VolumeFigure ID in Supervisely.

paths : List[str]

List of paths to download.

Returns

None

Return type

NoneType

Usage example
import supervisely as sly

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

STORAGE_DIR = sly.app.get_data_dir()

volume_id = 19371414
project_id = 17215

volume = api.volume.get_info_by_id(volume_id)

key_id_map = sly.KeyIdMap()
project_meta_json = api.project.get_meta(project_id)
project_meta = sly.ProjectMeta.from_json(project_meta_json)

vol_ann_json = api.volume.annotation.download(volume_id)
id_to_paths = {}
vol_ann = sly.VolumeAnnotation.from_json(vol_ann_json, project_meta, key_id_map)

for sp_figure in vol_ann.spatial_figures:
    figure_id = key_id_map.get_figure_id(sp_figure.key())
    id_to_paths[figure_id] = f"{STORAGE_DIR}/{sp_figure.key().hex}.stl"
if id_to_paths:
    api.volume.figure.download_stl_meshes(*zip(*id_to_paths.items()))
exists(parent_id, name)

Checks if an entity with the given parent_id and name exists

Parameters
parent_id : int

ID of the parent entity.

name : str

Name of the entity.

Returns

Returns True if entity exists, and False if not

Return type

bool

Usage example
import supervisely as sly

# You can connect to API directly
address = 'https://app.supervise.ly/'
token = 'Your Supervisely API Token'
api = sly.Api(address, token)

# Or you can use API from environment
os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()


name = "IMG_0315.jpeg"
dataset_id = 55832
exists = api.image.exists(dataset_id, name)
print(exists) # True
get_by_ids(dataset_id, ids)

Get Figures information by IDs from given dataset ID.

Parameters
dataset_id : int

Dataset ID in Supervisely.

ids : List[int]

List of Figures IDs.

Returns

List of information about Figures. See info_sequence

Return type

List[NamedTuple]

Usage example
import supervisely as sly

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

dataset_id = 466642
figures_ids = [642155547, 642155548, 642155549]
figures_infos = api.video.figure.get_by_ids(dataset_id, figures_ids)
print(figures_infos)
# Output: [
#     [
#         642155547,
#         "2021-03-23T13:25:34.705Z",
#         "2021-03-23T13:25:34.705Z",
#         198703211,
#         152118,
#         124976,
#         466642,
#         0,
#         "rectangle",
#         {
#             "points": {
#                 "exterior": [
#                     [
#                         2240,
#                         1041
#                     ],
#                     [
#                         2463,
#                         1187
#                     ]
#                 ],
#                 "interior": []
#             }
#         }
#     ],
#     [
#         642155548,
#         "2021-03-23T13:25:34.705Z",
#         "2021-03-23T13:25:34.705Z",
#         198703211,
#         152118,
#         124976,
#         466642,
#         1,
#         "rectangle",
#         {
#             "points": {
#                 "exterior": [
#                     [
#                         2248,
#                         1048
#                     ],
#                     [
#                         2455,
#                         1176
#                     ]
#                 ],
#                 "interior": []
#             }
#         }
#     ],
#     [
#         642155549,
#         "2021-03-23T13:25:34.705Z",
#         "2021-03-23T13:25:34.705Z",
#         198703211,
#         152118,
#         124976,
#         466642,
#         2,
#         "rectangle",
#         {
#             "points": {
#                 "exterior": [
#                     [
#                         2237,
#                         1046
#                     ],
#                     [
#                         2464,
#                         1179
#                     ]
#                 ],
#                 "interior": []
#             }
#         }
#     ]
# ]
get_free_name(parent_id, name)

Generates a free name for an entity with the given parent_id and name. Adds an increasing suffix to original name until a unique name is found.

Parameters
parent_id : int

ID of the parent entity.

name : str

Name of the entity.

Returns

Returns free name.

Return type

str

Usage example
import supervisely as sly

# You can connect to API directly
address = 'https://app.supervise.ly/'
token = 'Your Supervisely API Token'
api = sly.Api(address, token)

# Or you can use API from environment
os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()


name = "IMG_0315.jpeg"
dataset_id = 55832
free_name = api.image.get_free_name(dataset_id, name)
print(free_name) # IMG_0315_001.jpeg
get_info_by_id(id)

Get Figure information by ID.

Parameters
id : int

Figure ID in Supervisely.

Returns

Information about Figure. See info_sequence

Return type

NamedTuple

Usage example
import supervisely as sly

figure_id = 588801373

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

figure_info = api.video.figure.get_info_by_id(figure_id)
print(figure_info)
# Output: [
#     588801373,
#     "2020-12-22T06:37:13.183Z",
#     "2020-12-22T06:37:13.183Z",
#     186648101,
#     112482,
#     110366,
#     419886,
#     0,
#     "bitmap",
#     {
#         "bitmap": {
#             "data": "eJw...Cgj4=",
#             "origin": [
#                 335,
#                 205
#             ]
#         }
#     }
# ]
get_info_by_name(parent_id, name, fields=[])

Get information about an entity by its name from the Supervisely server.

Parameters
parent_id : int

ID of the parent entity.

name : str

Name of the entity for which the information is being retrieved.

fields : List[str]

The list of api fields which will be returned with the response.

Usage example
import supervisely as sly

# You can connect to API directly
address = 'https://app.supervise.ly/'
token = 'Your Supervisely API Token'
api = sly.Api(address, token)

# Or you can use API from environment
os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()


dataset_id = 55832
name = "IMG_0315.jpeg"
info = api.image.get_info_by_name(dataset_id, name)
print(info)
# Output: ImageInfo(id=19369643, name='IMG_0315.jpeg', ...)
get_list(parent_id, filters=None)

Get list of entities in parent entity with given parent ID.

Parameters
parent_id : int

parent ID in Supervisely.

filters : List[Dict[str, str]], optional

List of parameters to sort output entities.

Usage example
import supervisely as sly

# You can connect to API directly
address = 'https://app.supervise.ly/'
token = 'Your Supervisely API Token'
api = sly.Api(address, token)

# Or you can use API from environment
os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()


dataset_id = 55832
images = api.image.get_list(dataset_id)
print(images)
# Output: [
    ImageInfo(id=19369642, ...)
    ImageInfo(id=19369643, ...)
    ImageInfo(id=19369644, ...)
]
get_list_all_pages(method, data, progress_cb=None, convert_json_info_cb=None, limit=None, return_first_response=False)

Get list of all or limited quantity entities from the Supervisely server.

Parameters
method : str

Request method name

data : dict

Dictionary with request body info

progress_cb : Progress, optional

Function for tracking download progress.

convert_json_info_cb : Callable, optional

Function for convert json info

limit : int, optional

Number of entity to retrieve

return_first_response : bool, optional

Specify if return first response

get_list_all_pages_generator(method, data, progress_cb=None, convert_json_info_cb=None, limit=None, return_first_response=False)

This generator function retrieves a list of all or a limited quantity of entities from the Supervisely server, yielding batches of entities as they are retrieved

Parameters
method : str

Request method name

data : dict

Dictionary with request body info

progress_cb : Progress, optional

Function for tracking download progress.

convert_json_info_cb : Callable, optional

Function for convert json info

limit : int, optional

Number of entity to retrieve

return_first_response : bool, optional

Specify if return first response

static info_sequence()

NamedTuple FigureInfo information about Figure.

Example
FigureInfo(id=588801373,
           updated_at='2020-12-22T06:37:13.183Z',
           created_at='2020-12-22T06:37:13.183Z',
           entity_id=186648101,
           object_id=112482,
           project_id=110366,
           dataset_id=419886,
           frame_index=0,
           geometry_type='bitmap',
           geometry={'bitmap': {'data': 'eJwdlns8...Cgj4=', 'origin': [335, 205]}})
static info_tuple_name()

Get string name of NamedTuple for class.

Returns

NamedTuple name.

Return type

str

Usage example
import supervisely as sly

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

tuple_name = api.video.figure.info_tuple_name()
print(tuple_name) # FigureInfo
interpolate(volume_id, spatial_figure, key_id_map)[source]

Interpolate a spatial figure with a ClosedSurfaceMesh geometry.

Parameters
volume_id : int

VolumeFigure ID in Supervisely.

spatial_figure : VolumeFigure

Spatial figure to interpolate.

key_id_map : KeyIdMap

KeyIdMap object.

Returns

None

Return type

NoneType

Usage example
import supervisely as sly

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

volume_id = 19371414
project_id = 17215

volume = api.volume.get_info_by_id(volume_id)

key_id_map = sly.KeyIdMap()
project_meta_json = api.project.get_meta(project_id)
project_meta = sly.ProjectMeta.from_json(project_meta_json)

vol_ann_json = api.volume.annotation.download(volume_id)
id_to_paths = {}
vol_ann = sly.VolumeAnnotation.from_json(vol_ann_json, project_meta, key_id_map)

for sp_figure in vol_ann.spatial_figures:
    res = volume_figure_api.interpolate(volume_id, sp_figure, key_id_map)
load_sf_geometry(spatial_figure, key_id_map)[source]

Download geometry of an existing in Supervisely figure and load this data into the VolumeFigure object to complete this figure representation.

Parameters
spatial_figure : VolumeFigure

The spatial figure object from VolumeAnnotation.

key_id_map : KeyIdMap object

The mapped keys and IDs.

remove(id)

Remove an entity with the specified ID from the Supervisely server.

Parameters
id : int

Entity ID in Supervisely.

Usage example
import supervisely as sly

# You can connect to API directly
address = 'https://app.supervise.ly/'
token = 'Your Supervisely API Token'
api = sly.Api(address, token)

# Or you can use API from environment
os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()


image_id = 19369643
api.image.remove(image_id)
remove_batch(ids, progress_cb=None, batch_size=50)

Remove entities in batches from the Supervisely server. All entity IDs must belong to the same nesting (for example team, or workspace, or project, or dataset). Therefore, it is necessary to sort IDs before calling this method.

Parameters
ids : List[int]

IDs of entities in Supervisely.

progress_cb : Callable

Function for control remove progress.

Usage example
import supervisely as sly

# You can connect to API directly
address = 'https://app.supervise.ly/'
token = 'Your Supervisely API Token'
api = sly.Api(address, token)

# Or you can use API from environment
os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()


image_ids = [19369645, 19369646, 19369647]
api.image.remove_batch(image_ids)
upload_geometries_batch(figure_ids, geometries)

Upload figure geometries with given figure IDs to storage.

Parameters
figure_ids : List[int]

List of figure IDs in Supervisely.

geometries : List[dict]

List of figure geometries in Supervisely JSON format.

Returns

None

Return type

None

upload_geometry(figure_id, geometry)

Upload figure geometry with given figure ID to storage.

Parameters
figure_id : int

Figure ID in Supervisely.

geometry : dict

Figure geometry in Supervisely JSON format.

Returns

None

Return type

None

upload_sf_geometries(spatial_figures, geometries, key_id_map)[source]

Upload geometries as bytes into spatial figures in the project using their UUID keys.

Parameters
spatial_figures : List[UUID]

List of UUID keys representing spatial figures.

geometries : Dict[UUID, bytes]

Dictionary where keys are UUIDs of spatial figures, and values are geometries represented as NRRD files in byte format.

key_id_map : KeyIdMap

The KeyIdMap object (a dictionary with bidict values).

Returns

None

Return type

NoneType

Usage example

import numpy as np
import supervisely as sly
from supervisely.volume.nrrd_encoder import encode

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

volume_id = 23772225
project_id = 28159
geometries = {}
key_id_map = sly.KeyIdMap()
geometry_bytes = encode(np.random.randint(2, size=(20, 20, 20), dtype=np.uint8))

vol_ann_json = api.volume.annotation.download(volume_id)
project_meta = sly.ProjectMeta.from_json(api.project.get_meta(project_id))
ann = sly.VolumeAnnotation.from_json(vol_ann_json, project_meta, key_id_map)
spatial_figures = [sp_figure.key() for sp_figure in ann.spatial_figures]
for figure in spatial_figures:
    geometries[figure] = geometry_bytes
api.volume.figure.upload_sf_geometries(spatial_figures, geometries, key_id_map)
upload_sf_geometry(spatial_figures, geometries, key_id_map)[source]

Upload spatial figures geometry as bytes to storage by given ID.

Parameters
spatial_figures : dict

Dictionary with figure IDs.

geometries : list

Dictionary with geometries, which represented as content of NRRD files in byte format.

key_id_map : KeyIdMap

KeyIdMap object (dict with bidict values)

Return type

NoneType

Usage example

upload_stl_meshes(volume_id, spatial_figures, key_id_map, interpolation_dir=None)[source]

Upload existing interpolations or create on the fly and and add them to empty mesh figures.

Parameters
volume_id : int

VolumeFigure ID in Supervisely.

spatial_figures : List[VolumeFigure]

List of spatial figures to upload.

key_id_map : KeyIdMap

KeyIdMap object.

Returns

None

Return type

NoneType

Usage example
import supervisely as sly

os.environ['SERVER_ADDRESS'] = 'https://app.supervise.ly'
os.environ['API_TOKEN'] = 'Your Supervisely API Token'
api = sly.Api.from_env()

volume_id = 19371414
project_id = 17215

volume = api.volume.get_info_by_id(volume_id)

key_id_map = sly.KeyIdMap()
project_meta_json = api.project.get_meta(project_id)
project_meta = sly.ProjectMeta.from_json(project_meta_json)

vol_ann_json = api.volume.annotation.download(volume_id)
id_to_paths = {}
vol_ann = sly.VolumeAnnotation.from_json(vol_ann_json, project_meta, key_id_map)
sp_figures = vol_ann.spatial_figures

res = volume_figure_api.upload_stl_meshes(volume_id, sp_figures, key_id_map)