VolumeApi¶

class VolumeApi(api)[source]¶

Bases: RemoveableBulkModuleApi

API for working with volumes.

Parameters:

api¶: Api object to use for API connection.

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

volume_id = 19581134
volume_info = api.volume.get_info_by_id(volume_id) # api usage example

Methods

`convert_info_to_json`	Convert information about an entity to a dictionary.
`download_path`	Download volume with given ID to local directory.
`download_path_async`	Downloads Volume with given ID to local path.
`download_paths_async`	Download Volumes with given IDs and saves them to given local paths asynchronously.
`download_slice_np`	Download slice as NumPy from Supervisely by ID.
`exists`	Checks if an entity with the given parent_id and name exists
`get_free_name`	Generates a free name for an entity with the given parent_id and name.
`get_free_names`	Returns list of free names for given dataset.
`get_info_by_id`	Get Volume information by ID in `VolumeInfo` format.
`get_info_by_name`	Get information about an entity by its name from the Supervisely server.
`get_list`	Get list of information about all volumes for a given dataset 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
`get_list_idx_page_async`	Get the list of items for a given page number.
`get_list_page_generator_async`	Yields list of images in dataset asynchronously page by page.
`info_sequence`	Get list of all `VolumeInfo` field names.
`info_tuple_name`	Get string name of `VolumeInfo` NamedTuple.
`raise_name_intersections_if_exist`	Raises error if volumes with given names already exist in dataset.
`remove`	Remove an entity with the specified ID from the Supervisely server.
`remove_batch`	Remove entities in batches from the Supervisely server.
`rename`	Renames Volume with given ID to a new name.
`upload_dicom_serie_paths`	Upload given DICOM series from given paths to Dataset.
`upload_dir`	Upload all volumes from given directory to Dataset recursively.
`upload_dirs`	Upload all volumes from given directories to Dataset recursively.
`upload_hash`	Upload Volume from given hash to Dataset.
`upload_hashes`	Upload Volumes from given hashes to Dataset.
`upload_np`	Upload given Volume in numpy format with given name to Dataset.
`upload_nrrd_serie_path`	Upload NRRD format volume from given path to Dataset.
`upload_nrrd_series_paths`	Upload NRRD format volumes from given paths to Dataset.

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 VolumeInfo

classmethod convert_info_to_json(info)¶

Convert information about an entity to a dictionary.

Parameters:

info : NamedTuple¶: Information about the entity.

Returns:

Dictionary with information about the entity.

Return type:

dict

static info_sequence()[source]¶

Get list of all VolumeInfo field names.

Returns:: List of VolumeInfo field names.
Return type:: List[str]

static info_tuple_name()[source]¶

Get string name of VolumeInfo NamedTuple.

Returns:: NamedTuple name.
Return type:: str

download_path(id, path, progress_cb=None)[source]¶

Download volume with given ID to local directory.

Parameters:

id : int¶: Volume ID in Supervisely.
path : str¶: Local path to save volume.
progress_cb : tqdm or callable, optional¶: Function for tracking download progress.

Returns:

Information about Volume.

Return type:

VolumeInfo

Usage Example:

import os
from tqdm import tqdm
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

src_dataset_id = 61229
volume_infos = api.volume.get_list(src_dataset_id)
volume_id = volume_infos[0].id
volume_info = api.volume.get_info_by_id(id=volume_id)

download_dir_name = "src/download/"
path = os.path.join(download_dir_name, volume_info.name)
if os.path.exists(path):
    os.remove(path)

p = tqdm_sly(desc="Volumes upload: ", total=volume_info.sizeb, is_size=True)
api.volume.download_path(volume_info.id, path, progress_cb=p)

if os.path.exists(path):
    print(f"Volume (ID {volume_info.id}) successfully downloaded.")

# Output:
# Volume (ID 18630603) successfully downloaded.

async download_path_async(id, path, semaphore=None, range_start=None, range_end=None, headers=None, chunk_size=1048576, check_hash=True, progress_cb=None, progress_cb_type='number')[source]¶

Downloads Volume with given ID to local path.

Parameters:

id : int¶: Volume ID in Supervisely.
path : str¶: Local save path for Volume.
semaphore=None¶: Semaphore for limiting the number of simultaneous downloads.
range_start : int, optional¶: Start byte of range for partial download.
range_end : int, optional¶: End byte of range for partial download.
headers : dict, optional¶: Headers for request.
chunk_size : int, optional¶: Size of chunk for downloading. Default is 1MB.
check_hash : bool, optional¶: If True, checks hash of downloaded file. Check is not supported for partial downloads. When range is set, hash check is disabled.
progress_cb : tqdm or callable, optional¶: Function for tracking download progress.
progress_cb_type : str, optional¶: Type of progress callback. Can be “number” or “size”. Default is “number”.

Returns:

None

Return type:

None

Usage Example:

import os
import asyncio
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

volume_info = api.volume.get_info_by_id(770918)
save_path = os.path.join("/path/to/save/", volume_info.name)

semaphore = asyncio.Semaphore(100)
loop = sly.utils.get_or_create_event_loop()
loop.run_until_complete(
    api.volume.download_path_async(volume_info.id, save_path, semaphore)
)

async download_paths_async(ids, paths, semaphore=None, headers=None, chunk_size=1048576, check_hash=True, progress_cb=None, progress_cb_type='number')[source]¶

Download Volumes with given IDs and saves them to given local paths asynchronously.

Parameters:

ids¶: List of Volume IDs in Supervisely.
paths¶: Local save paths for Volumes.
semaphore=None¶: Semaphore for limiting the number of simultaneous downloads.
headers : dict, optional¶: Headers for request.
chunk_size : int, optional¶: Size of chunk for downloading. Default is 1MB.
check_hash : bool, optional¶: If True, checks hash of downloaded file.
progress_cb : tqdm or callable, optional¶: Function for tracking download progress.
progress_cb_type : str, optional¶: Type of progress callback. Can be “number” or “size”. Default is “number”.

Raises:

ValueError – if len(ids) != len(paths)

Returns:

None

Return type:

None

Usage Example:

import os
import asyncio
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

ids = [770914, 770915]
paths = ["/path/to/save/volume1.nrrd", "/path/to/save/volume2.nrrd"]
loop = sly.utils.get_or_create_event_loop()
loop.run_until_complete(api.volume.download_paths_async(ids, paths))

download_slice_np(volume_id, slice_index, plane, window_center=None, window_width=None)[source]¶

Download slice as NumPy from Supervisely by ID.

Parameters:

volume_id : int¶: Volume ID in Supervisely.
slice_index : int¶: Slice index.
plane : str¶: Plane of the slice in volume.
window_center : float¶: Window center.
window_width : int¶: Window width.

Returns:

Information about Volume.

Return type:

VolumeInfo

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

volume_id = 19402023
slice_index = 60

image_np = api.volume.download_slice_np(
    volume_id=volume_id,
    slice_index=slice_index,
    plane=sly.Plane.SAGITTAL,
)

print(f"Image downloaded as NumPy array. Image shape: {image_np.shape}")

# Output:
# Image downloaded as NumPy array. Image shape: (256, 256, 3)

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 os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

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

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 os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

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_free_names(dataset_id, names)[source]¶

Returns list of free names for given dataset.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
names : List[str]¶: List of names to check.

Returns:

List of free names.

Return type:

List[str]

get_info_by_id(id)[source]¶

Get Volume information by ID in VolumeInfo format.

Parameters:

id : int¶: Volume ID in Supervisely.

Returns:

Information about Volume.

Return type:

VolumeInfo

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

volume_id = 19581134
volume_info = api.volume.get_info_by_id(volume_id)
print(volume_info)
# Output:
# VolumeInfo(
#     id=19581134,
#     name='CTChest.nrrd',
#     link=None,
#     hash='+0K2oFHpqA5dwRKQlhkvhXEh52cs=',
#     mime=None,
#     ext=None,
#     sizeb=46073411,
#     created_at='2023-03-29T12:30:37.078Z',
#     updated_at='2023-03-29T12:30:37.078Z',
#     meta={
#         'ACS': 'RAS',
#         'intensity': {'max': 3071, 'min': -3024},
#         'windowWidth': 6095,
#         'rescaleSlope': 1,
#         'windowCenter': 23.5,
#         'channelsCount': 1,
#         'dimensionsIJK': {'x': 512, 'y': 512, 'z': 139},
#         'IJK2WorldMatrix': [0.7617189884185793, 0, 0, -194.238403081894, 0, 0.7617189884185793, 0, -217.5384061336518, 0, 0, 2.5, -347.7500000000001, 0, 0, 0, 1],
#         'rescaleIntercept': 0
#     },
#     path_original='/h5af-public/images/original/M/e/7R/vs0p.nrrd',
#     full_storage_url='https://app.supervisely.com/.../original/M/e/7R/zX0p.nrrd',
#     tags=[],
#     team_id=435,
#     workspace_id=685,
#     project_id=18949,
#     dataset_id=61803,
#     file_meta={
#             'mime': 'image/nrrd',
#             'size': 46073411,
#             'type': 'int32',
#             'extra': {'stride': [1, 512, 262144],
#             'comments': []
#         }
#         'sizes': [512, 512, 139]
#         'space': 'right-anterior-superior'
#         'endian': 'little'
#         'encoding': 'gzip'
#         'dimension': 3
#         'space origin': [-194.238403081894, -217.5384061336518, -347.7500000000001]
#         'space dimension': 3
#         'space directions': [[0.7617189884185793, 0, 0], [0, 0.7617189884185793, 0], [0, 0, 2.5]]
#     }
#     figures_count=None,
#     objects_count=None,
#     processing_path='1/1560071'
# )

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 os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

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(dataset_id, filters=None, sort='id', sort_order='asc')[source]¶

Get list of information about all volumes for a given dataset ID.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
filters : List[Dict[str, str]], optional¶: List of parameters to sort output Volumes. See: https://api.docs.supervisely.com/#tag/Volumes/paths/~1volumes.list/get
sort : str¶: Attribute to sort the list by. The default is “id”. Valid values are “id”, “name”, “description”, “createdAt”, “updatedAt”.
sort_order : str¶: Order in which to sort the list. The default is “asc”. Valid values are “asc” (ascending) and “desc” (descending).

Returns:

List of information about volumes in given dataset.

Return type:

List[VolumeInfo]

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

dataset_id = 61803

volume_infos = api.volume.get_list(dataset_id)
print(volume_infos)
# Output: [VolumeInfo(id=19581134, ...), VolumeInfo(id=19581135, ...), VolumeInfo(id=19581136, ...)]

sorted_volume_infos = api.volume.get_list(dataset_id, sort="id", sort_order="desc")
# Output: [VolumeInfo(id=19581136, ...), VolumeInfo(id=19581135, ...), VolumeInfo(id=19581134, ...)]

filtered_volume_infos = api.volume.get_list(dataset_id, filters=[{'field': 'id', 'operator': '=', 'value': '19581135'}])
print(filtered_volume_infos)
# Output: [VolumeInfo(id=19581135, ...)]

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

Returns:

List of entities.

Return type:

List[dict]

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

async get_list_idx_page_async(method, data)¶

Get the list of items for a given page number. Page number is specified in the data dictionary.

Parameters:

method : str¶: Method to call for listing items.
data : dict¶: Data to pass to the API method.

Returns:

List of items.

Return type:

Tuple[int, List[NamedTuple]]

async get_list_page_generator_async(method, data, pages_count=None, semaphore=None)¶

Yields list of images in dataset asynchronously page by page.

Parameters:

method : str¶: Method to call for listing items.
data : dict¶: Data to pass to the API method.
pages_count : int, optional¶: Preferred number of pages to retrieve if used with a per_page limit. Will be automatically adjusted if the pagesCount differs from the requested number.
semaphore=None¶: Semaphore for limiting the number of simultaneous requests.

Returns:

List of images in dataset.

Return type:

AsyncGenerator[List[ImageInfo]]

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

method = 'images.list'
data = {'datasetId': 123456}

loop = sly.utils.get_or_create_event_loop()
images = loop.run_until_complete(api.image.get_list_generator_async(method, data))

raise_name_intersections_if_exist(dataset_id, names, message=None)[source]¶: Raises error if volumes with given names already exist in dataset. Default error message: “Volumes with the following names already exist in dataset [ID={dataset_id}]: {name_intersections}. Please, rename volumes and try again or set change_name_if_conflict=True to rename automatically on upload.” :param dataset_id: Dataset ID in Supervisely. :type dataset_id: int :param names: List of names to check. :type names: List[str] :param message: Error message. :type message: str, optional :returns: None :rtype: None

remove(id)¶

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

Parameters:

id : int¶: Entity ID in Supervisely.

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

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 os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

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

rename(id, name)[source]¶

Renames Volume with given ID to a new name.

Parameters:

id : int¶: Volume ID in Supervisely.
name : str¶: New Volume name.

Returns:

Information about updated Volume.

Return type:

VolumeInfo

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

volume_id = 123456
new_volume_name = "3333_new.nrrd"

api.volume.rename(id=volume_id, name=new_volume_name)

upload_dicom_serie_paths(dataset_id, name, paths, log_progress=True, anonymize=True)[source]¶

Upload given DICOM series from given paths to Dataset.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
name : str¶: Volume name with extension.
paths : List[str]¶: Local volumes paths.
log_progress : bool, optional¶: Determine if additional technical logs are displaying.
anonymize : bool, optional¶: Determine whether to hide PatientID and PatientName fields.

Returns:

Information about Volume.

Return type:

VolumeInfo

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

dicom_dir_name = "src/upload/MRHead_dicom/"
series_infos = sly.volume.inspect_dicom_series(root_dir=dicom_dir_name)

for serie_id, files in series_infos.items():
    item_path = files[0]
    name = f"{sly.fs.get_file_name(path=item_path)}.nrrd"
    dicom_info = api.volume.upload_dicom_serie_paths(
        dataset_id=dataset.id,
        name=name,
        paths=files,
        anonymize=True,
    )
    print(f"DICOM volume has been uploaded to Supervisely with ID: {dicom_info.id}")

# Output:
# DICOM volume has been uploaded to Supervisely with ID: 18630608

upload_dir(dataset_id, dir_path, progress_cb=None, log_progress=False, change_name_if_conflict=True)[source]¶

Upload all volumes from given directory to Dataset recursively.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
dir_path : str¶: Local directory path.
progress_cb : tqdm or callable, optional¶: Function for tracking download progress.
log_progress : bool¶: Determine if additional technical logs are displaying.
change_name_if_conflict : bool, optional¶: Determine if names are changing if conflict.

Returns:

List with information about Volumes.

Return type:

List[VolumeInfo]

Usage Example:

import os
from tqdm import tqdm
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

dataset_id = 61958
dir_path = "src/upload/volumes/"
volume_infos = api.volume.upload_dir(dataset_id, dir_path)
print(f"All volumes has been uploaded with IDs: {[x.id for x in volume_infos]}")

# Output:
# All volumes has been uploaded with IDs: [18630605, 18630606, 18630607]

upload_dirs(dataset_id, dir_paths, progress_cb=None, log_progress=False, change_name_if_conflict=True)[source]¶

Upload all volumes from given directories to Dataset recursively.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
dir_paths : List[str]¶: List of local directory paths.
progress_cb : tqdm or callable, optional¶: Function for tracking download progress.
log_progress : bool¶: Determine if additional technical logs are displaying.
change_name_if_conflict : bool, optional¶: Determine if names are changing if conflict.

Returns:

List with information about Volumes.

Return type:

List[VolumeInfo]

Usage Example:

import os
from tqdm import tqdm
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

dataset_id = 61958
dir_paths = ["src/upload/volumes1/", "src/upload/volumes2/"]
volume_infos = api.volume.upload_dirs(dataset_id, dir_paths)
print(f"All volumes has been uploaded with IDs: {[x.id for x in volume_infos]}")

# Output:
# All volumes has been uploaded with IDs: [18630605, 18630606, 18630607]

upload_hash(dataset_id, name, hash, meta=None)[source]¶

Upload Volume from given hash to Dataset.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
name : str¶: Volume name with extension.
hash : str¶: Volume hash.
meta : dict¶: A dictionary containing data associated with the volume.

Returns:

Information about Volume.

Return type:

VolumeInfo

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

dst_dataset_id = 61958
src_volume_id = 19581134
volume_info = api.volume.get_info_by_id(src_volume_id)
hash = volume_info.hash
# It is necessary to upload volume with the same extention as in src dataset
name = volume_info.name
meta = volume_info.meta
new_volume_info = api.volume.upload_hash(dst_dataset_id, name, hash, meta)
print(new_volume_info)
# Output:
# VolumeInfo(
#     id=19613940,
#     name='CTACardio.nrrd',
#     link=None,
#     hash='+0K2oFHpqA5dwRKQlh5bDUA0jkPsEE52cs=',
#     mime=None,
#     ext=None,
#     sizeb=67614735,
#     created_at='2023-03-29T12:30:37.078Z',
#     updated_at='2023-03-29T12:30:37.078Z',
#     meta={
#         'ACS': 'RAS',
#         'intensity': {'max': 3532, 'min': -1024},
#         'windowWidth': 4556,
#         'rescaleSlope': 1,
#         'windowCenter': 1254,
#         'channelsCount': 1,
#         'dimensionsIJK': {'x': 512, 'y': 512, 'z': 321}
#         'IJK2WorldMatrix': [0.9335939999999999, 0, 0, -238.53326699999997, 0, 0.9335939999999999, 0, -238.53326699999994, 0, 0, 1.25, -200.0000000000001, 0, 0, 0, 1],
#         'rescaleIntercept': 0
#     },
#     path_original='/h5af-public/images/original/M/e/7R/zfsfX0p.nrrd',
#     full_storage_url='https://app.supervisely.com/h5un-public/images/original/M/e/7R/zXdd0p.nrrd',
#     tags=[],
#     team_id=435,
#     workspace_id=685,
#     project_id=18949,
#     dataset_id=61958,
#     file_meta={
#             'mime': 'image/nrrd',
#             'size': 46073411,
#             'type': 'int32',
#             'extra': {'stride': [1, 512, 262144],
#             'comments': []
#         }
#         'sizes': [512, 512, 139]
#         'space': 'right-anterior-superior'
#         'endian': 'little'
#         'encoding': 'gzip'
#         'dimension': 3
#         'space origin': [-194.238403081894, -217.5384061336518, -347.7500000000001]
#         'space dimension': 3
#         'space directions': [[0.7617189884185793, 0, 0], [0, 0.7617189884185793, 0], [0, 0, 2.5]]
#     }
#     figures_count=None,
#     objects_count=None,
#     processing_path='1/1560071'
# )

upload_hashes(dataset_id, names, hashes, progress_cb=None, metas=None)[source]¶

Upload Volumes from given hashes to Dataset.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
names : List[str]¶: Volumes names with extension.
hashes : List[str]¶: Volumes hashes.
progress_cb : tqdm or callable, optional¶: Function for tracking download progress.
metas : List[dict], optional¶: Volumes metadata.

Returns:

List with information about Volumes.

Return type:

List[VolumeInfo]

Usage Example:

import os
from tqdm import tqdm

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

src_dataset_id = 61958
dst_dataset_id = 55853

hashes = []
names = []
metas = []
volume_infos = api.volume.get_list(src_dataset_id)

# Create lists of hashes, volumes names and meta information for each volume
for volume_info in volume_infos:
    hashes.append(volume_info.hash)
    # It is necessary to upload volumes with the same names(extentions) as in src dataset
    names.append(volume_info.name)
    metas.append(volume_info.meta)

p = tqdm(desc="api.volume.upload_hashes", total=len(hashes))
new_volumes_info = api.volume.upload_hashes(
    dataset_id=dst_dataset_id,
    names=names,
    hashes=hashes,
    progress_cb=p,
    metas=metas,
)

# Output:
# {"message": "progress", "event_type": "EventType.PROGRESS", "subtask": "Volumes upload: ", "current": 0, "total": 2, "timestamp": "2023-04-04T07:47:11.506Z", "level": "info"}
# {"message": "progress", "event_type": "EventType.PROGRESS", "subtask": "Volumes upload: ", "current": 2, "total": 2, "timestamp": "2023-04-04T07:47:11.563Z", "level": "info"}

upload_np(dataset_id, name, np_data, meta, progress_cb=None, batch_size=30)[source]¶

Upload given Volume in numpy format with given name to Dataset.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
name : str¶: Volume name with extension.
np_data : np.ndarray¶: image in RGB format(numpy matrix)
meta : dict, optional¶: Volume metadata.
progress_cb : tqdm or callable, optional¶: Function for tracking download progress.

Returns:

Information about Volume.

Return type:

VolumeInfo

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

np_volume, meta = sly.volume.read_nrrd_serie_volume_np(local_path)
nrrd_info_np = api.volume.upload_np(
    dataset.id,
    "MRHead_np.nrrd",
    np_volume,
    meta,
)
print(f"Volume uploaded as NumPy array to Supervisely with ID:{nrrd_info_np.id}")

# Output:
# Volume uploaded as NumPy array to Supervisely with ID:18562982

upload_nrrd_serie_path(dataset_id, name, path, log_progress=True, progress_cb=None)[source]¶

Upload NRRD format volume from given path to Dataset.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
name : str¶: Volume name with extension.
path : str¶: Local volume path.
log_progress : bool, optional¶: Determine if additional technical logs are displaying.

Returns:

Information about Volume.

Return type:

VolumeInfo

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

local_path = "src/upload/nrrd/MRHead.nrrd"

nrrd_info = api.volume.upload_nrrd_serie_path(
    dataset.id,
    "MRHead.nrrd",
    local_path,
)
print(f'"{nrrd_info.name}" volume uploaded to Supervisely with ID:{nrrd_info.id}')

# Output:
# "NRRD_1.nrrd" volume uploaded to Supervisely with ID:18562981

upload_nrrd_series_paths(dataset_id, names, paths, progress_cb=None, log_progress=True)[source]¶

Upload NRRD format volumes from given paths to Dataset.

Parameters:

dataset_id : int¶: Dataset ID in Supervisely.
names : List[str]¶: Volumes names with extensions.
paths : List[str]¶: Local volumes paths.
log_progress : bool¶: Determine if additional technical logs are displaying.
progress_cb : tqdm or callable, optional¶: Function for tracking download progress.

Returns:

Information about Volume.

Return type:

VolumeInfo

Usage Example:

import os
from dotenv import load_dotenv

import supervisely as sly

# Load secrets and create API object from .env file (recommended)
# Learn more here: https://developer.supervisely.com/getting-started/basics-of-authentication
if sly.is_development():
    load_dotenv(os.path.expanduser("~/supervisely.env"))

api = sly.Api.from_env()

local_dir_name = "src/upload/nrrd/"
all_nrrd_names = os.listdir(local_dir_name)
names = [f"1_{name}" for name in all_nrrd_names]
paths = [os.path.join(local_dir_name, name) for name in all_nrrd_names]

volume_infos = api.volume.upload_nrrd_series_paths(dataset.id, names, paths)
print(f"All volumes has been uploaded with IDs: {[x.id for x in volume_infos]}")

# Output:
# All volumes has been uploaded with IDs: [18630605, 18630606, 18630607]