monailabel.datastore.dicom module¶

class monailabel.datastore.dicom.DICOMWebDatastore(client, search_filter, cache_path=None, fetch_by_frame=False, convert_to_nifti=True)[source]¶

Bases: monailabel.datastore.local.LocalDatastore

Creates a LocalDataset object

Parameters:

datastore_path: str: a string to the directory tree of the desired dataset
datastore_config: str: optional file name of the dataset configuration file (by default dataset.json)

datalist(full_path=True)[source]¶

Return a dictionary of image and label pairs corresponding to the ‘image’ and ‘label’ keys respectively

Return type: List[Dict[str, Any]]
Returns: the {‘label’: image, ‘label’: label} pairs for training

get_image_uri(image_id)[source]¶

Retrieve image uri based on image id

Parameters: image_id (str) – the desired image’s id
Return type: str
Returns: return the image uri

get_label_uri(label_id, label_tag, image_id='')[source]¶

Retrieve label uri based on image id

Parameters

label_id (str) – the desired label’s id
label_tag (str) – the matching label’s tag

Return type

str

Returns

return the label uri

get_labeled_images(label_tag=None, labels=None)[source]¶

Get all images that have a corresponding label

Return type: List[str]
Returns: list of image ids List[str]

get_unlabeled_images(label_tag=None, labels=None)[source]¶

Get all images that have no corresponding label

Return type: List[str]
Returns: list of image ids List[str]

list_images()[source]¶

Return list of image ids available in the datastore

Return type: List[str]
Returns: list of image ids List[str]

name()[source]¶

Dataset name (if one is assigned)

Returns: Dataset name as string
Return type: name (str)

save_label(image_id, label_filename, label_tag, label_info, label_id='')[source]¶

Save a label for the given image id and return the newly saved label’s id

Parameters

image_id (str) – the image id for the label
label_filename (str) – the path to the label file
label_tag (str) – the tag for the label
label_info (Dict[str, Any]) – additional info for the label

Return type

str

Returns

the label id for the given label filename

class monailabel.datastore.dicom.DICOMwebClientX(url, session=None, qido_url_prefix=None, wado_url_prefix=None, stow_url_prefix=None, delete_url_prefix=None, proxies=None, headers=None, callback=None, chunk_size=1000000)[source]¶

Bases: dicomweb_client.web.DICOMwebClient

Instatiate client.

Parameters

url (str) – Unique resource locator of the DICOMweb service consisting of protocol, hostname (IP address or DNS name) of the machine that hosts the service and optionally port number and path prefix
session (Union[requests.Session, None], optional) – Session required to make connections to the DICOMweb service (see dicomweb_client.session_utils module to create a valid session if necessary)
qido_url_prefix (Union[str, None], optional) – URL path prefix for QIDO RESTful services
wado_url_prefix (Union[str, None], optional) – URL path prefix for WADO RESTful services
stow_url_prefix (Union[str, None], optional) – URL path prefix for STOW RESTful services
delete_url_prefix (Union[str, None], optional) – URL path prefix for DELETE RESTful services
proxies (Union[Dict[str, str], None], optional) – Mapping of protocol or protocol + host to the URL of a proxy server
headers (Union[Dict[str, str], None], optional) – Custom headers that should be included in request messages, e.g., authentication tokens
callback (Union[Callable[[requests.Response, ...], requests.Response], None], optional) – Callback function to manipulate responses generated from requests (see requests event hooks)
chunk_size (int, optional) – Maximum number of bytes that should be transferred per data chunk when streaming data from the server using chunked transfer encoding (used by iter_*() methods as well as the store_instances() method); defaults to 10**6 bytes (1MB)

Warning

Modifies the passed session (in particular header fields), so be careful when reusing the session outside the scope of an instance.

Warning

Choose the value of chunk_size carefully. A small value may cause significant network communication and message parsing overhead.

monailabel.datastore.cvat module

monailabel.datastore.dsa module