nbiatoolkit.nbia_cli

Attributes

`__version__`
`done_event`
`query`
`output`

Classes

`NBIAClient`	A client for interacting with the NBIA API.
`DICOMSorter`

Functions

`version`()
`_initialize_parser`(→ argparse.ArgumentParser)
`_add_extra_args`(→ argparse.Namespace)
`getResults_cli`(→ None)	Executes the given function with the provided keyword arguments and prints the results.
`writeResultsToFile`(→ None)	Writes the results of a query to a file.
`cli_wrapper`(→ List[str] \| None)	Wraps a function call with a loading animation.
`getPatients_cli`(→ None)
`getCollections_cli`(→ None)
`getNewPatients_cli`(→ None)
`getBodyPartCounts_cli`(→ None)
`getStudies_cli`(→ None)
`getSeries_cli`(→ None)
`getNewSeries_cli`(→ None)
`downloadSingleSeries_cli`(→ None)
`DICOMSorter_cli`()

Module Contents

class nbiatoolkit.nbia_cli.NBIAClient(username: str = 'nbia_guest', password: str = '', log_level: str = 'INFO', logger: logging.Logger | None = None, return_type: nbiatoolkit.utils.ReturnType | str = ReturnType.LIST)[source]

A client for interacting with the NBIA API.

The NBIAClient class provides a high-level interface for querying the NBIA API and downloading DICOM series.

Parameters:

username (str, optional) – The username for authentication. Defaults to “nbia_guest”.
password (str, optional) – The password for authentication. Defaults to an empty string.
log_level (str, optional) – The log level for the logger. Defaults to “INFO”.
return_type (Union[ReturnType, str], optional) – The return type for API responses. Defaults to ReturnType.LIST

OAuth_client

The OAuth2 client used for authentication.

Type:: OAuth2

headers

The API headers.

Type:: dict[str, str]

base_url

The base URL for API requests.

Type:: NBIA_ENDPOINTS

logger

The logger for logging client events.

Type:: Logger

return_type

The current return type for API responses.

Type:: str

__enter__()[source]

__exit__(exc_type, exc_value, traceback) → None[source]

property OAuth_client: nbiatoolkit.auth.OAuth2

property headers

property base_url: nbiatoolkit.utils.NBIA_BASE_URLS

property logger: logging.Logger

property return_type: str

_get_return(return_type: nbiatoolkit.utils.ReturnType | str | None) → nbiatoolkit.utils.ReturnType[source]

helper function to replace the following code: returnType: ReturnType = (

ReturnType(return_type) if return_type is not None else self._return_type

)

query_api(endpoint: nbiatoolkit.utils.NBIA_ENDPOINTS, params: dict = {}) → List[dict[Any, Any]][source]

getCollections(prefix: str = '', return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

Retrieves the collections from the NBIA server.

Parameters:

prefix (str, optional) – Prefix to filter the collections by. Defaults to “”.
return_type (Optional[Union[ReturnType, str]], optional) – Return type of the response. Defaults to None which uses the default return type.

Returns:

List of collections or DataFrame containing the collections.

Return type:

List[dict[Any, Any]] | pd.DataFrame

getCollectionDescriptions(collectionName: str, return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

Retrieves the description of a collection from the NBIA server.

Parameters:

collectionName (str) – The name of the collection.
return_type (Optional[Union[ReturnType, str]], optional) – Return type of the response. Defaults to None.

Returns:

List of collection descriptions or DataFrame containing the collection descriptions.

Return type:

List[dict[Any, Any]] | pd.DataFrame

getCollectionPatientCount(prefix: str = '', return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

Retrieves the patient count for collections.

Parameters:

prefix (str, optional) – Prefix to filter the collections by. Defaults to “”.
return_type (Optional[Union[ReturnType, str]], optional) – Return type of the response. Defaults to None which uses the default return type.

Returns:

List of collections and their patient counts or DataFrame containing the collections and their patient counts.

Return type:

List[dict[Any, Any]] | pd.DataFrame

getModalityValues(Collection: str = '', BodyPartExamined: str = '', Counts: bool = False, return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

Retrieves possible modality values from the NBIA database.

Parameters:

Collection (str, optional) – Collection name to filter by. Defaults to “”.
BodyPartExamined (str, optional) – BodyPart name to filter by. Defaults to “”.
Counts (bool, optional) – Flag to indicate whether to return patient counts. Defaults to False.
return_type (Optional[Union[ReturnType, str]], optional) – Return type of the response. Defaults to None which uses the default return type.

Returns:

List of modality values or DataFrame containing the modality values.

Return type:

List[dict[Any, Any]] | pd.DataFrame

getPatients(Collection: str = '', return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

Retrieves a list of patients from the NBIA API.

Parameters:

Collection (str, optional) – The name of the collection to filter the patients. Defaults to “”.
return_type (Optional[Union[ReturnType, str]], optional) – The desired return type. Defaults to None.

Returns:

A list of patient dictionaries or a pandas DataFrame, depending on the return type.

Return type:

List[dict[Any, Any]] | pd.DataFrame

getNewPatients(Collection: str, Date: str | datetime.datetime, return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

Retrieves new patients from the NBIA API based on the specified collection and date.

Parameters:

Collection (str) – The name of the collection to retrieve new patients from.
Date (Union[str, datetime]) – The date to filter the new patients. Can be a string in the format “YYYY/MM/DD” or a datetime object.
return_type (Optional[Union[ReturnType, str]]) – The desired return type. Defaults to None.

Returns:

A list of dictionaries or a pandas DataFrame containing the new patients.

Return type:

List[dict[Any, Any]] | pd.DataFrame

Raises:

AssertionError – If the Date argument is None.

getPatientsByCollectionAndModality(Collection: str, Modality: str, return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

Retrieves patients by collection and modality.

Parameters:

Collection (str) – The collection name.
Modality (str) – The modality name.
return_type (Optional[Union[ReturnType, str]], optional) – The desired return type. Defaults to None.

Returns:

The list of patients or a pandas DataFrame, depending on the return type.

Return type:

List[dict[Any, Any]] | pd.DataFrame

Raises:

AssertionError – If Collection or Modality is None.

getBodyPartCounts(Collection: str = '', Modality: str = '', return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

getStudies(Collection: str, PatientID: str = '', StudyInstanceUID: str = '', return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

Retrieves studies from the NBIA API based on the specified parameters.

Parameters:

Collection (str) – The name of the collection to retrieve studies from.
PatientID (str, optional) – The patient ID to filter the studies by. Defaults to “”.
StudyInstanceUID (str, optional) – The study instance UID to filter the studies by. Defaults to “”.
return_type (Optional[Union[ReturnType, str]], optional) – The desired return type. Defaults to None.

Returns:

A list of dictionaries or a pandas DataFrame containing the retrieved studies.

Return type:

List[dict[Any, Any]] | pd.DataFrame

getSeries(Collection: str = '', PatientID: str = '', StudyInstanceUID: str = '', Modality: str = '', SeriesInstanceUID: str = '', BodyPartExamined: str = '', ManufacturerModelName: str = '', Manufacturer: str = '', return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

getSeriesMetadata(SeriesInstanceUID: str | list[str], return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

getNewSeries(Date: str | datetime.datetime, return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

getDICOMTags(SeriesInstanceUID: str, return_type: nbiatoolkit.utils.ReturnType | str | None = None) → List[dict[Any, Any]] | pandas.DataFrame[source]

getRefSeriesUIDs(SeriesInstanceUID: str) → List[str][source]

generateFilePathFromDICOMTags(SeriesInstanceUID: str, filePattern: str = '%PatientName/%Modality-%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm') → str[source]

Generates a file path from DICOM tags.

Parameters:

SeriesInstanceUID (str) – The Series Instance UID of the DICOM series.
filePattern (str, optional) – The file pattern to use for generating the file path. Defaults to “%PatientName/%Modality-%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm”.

Returns:

The generated file path.

Return type:

str

Note

This only considers the first instance of the series. Meant to be used to determine the dirname of the series files.

downloadSeries(SeriesInstanceUID: str | list, downloadDir: str = './NBIA-Download', filePattern: str = '%PatientName/%Modality-%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm', overwrite: bool = False, nParallel: int = 1, Progressbar: bool = False) → bool[source]

parsePARAMS(params: dict) → dict[source]

nbiatoolkit.nbia_cli.__version__ = '1.3.1'

class nbiatoolkit.nbia_cli.DICOMSorter(sourceDir: str, destinationDir: str, targetPattern: str = '%PatientName/%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm', truncateUID: bool = True, sanitizeFilename: bool = True)[source]

sortDICOMFiles(shutil_option: str = 'copy', overwrite: bool = False, n_parallel: int = 1, progressbar=True) → bool[source]

nbiatoolkit.nbia_cli.done_event

nbiatoolkit.nbia_cli.query: str

nbiatoolkit.nbia_cli.output: io.TextIOWrapper | None = None

nbiatoolkit.nbia_cli.version()[source]

nbiatoolkit.nbia_cli._initialize_parser(description: str) → argparse.ArgumentParser[source]

nbiatoolkit.nbia_cli._add_extra_args(parser: argparse.ArgumentParser) → argparse.Namespace[source]

nbiatoolkit.nbia_cli.getResults_cli(func, **kwargs) → None[source]

Executes the given function with the provided keyword arguments and prints the results.

Parameters:

func – The function to be executed.
**kwargs – Keyword arguments to be passed to the function.

Returns:

None

nbiatoolkit.nbia_cli.writeResultsToFile(results: List, output: io.TextIOWrapper) → None[source]

Writes the results of a query to a file.

Parameters:

results – The results of the query.
output – The path to the output file.

Returns:

None

nbiatoolkit.nbia_cli.cli_wrapper(func, **kwargs) → List[str] | None[source]

Wraps a function call with a loading animation.

Parameters:

func – The function to be called.
**kwargs – Keyword arguments to be passed to the function.

Returns:

The result of the function call.

nbiatoolkit.nbia_cli.getPatients_cli() → None[source]

nbiatoolkit.nbia_cli.getCollections_cli() → None[source]

nbiatoolkit.nbia_cli.getNewPatients_cli() → None[source]

nbiatoolkit.nbia_cli.getBodyPartCounts_cli() → None[source]

nbiatoolkit.nbia_cli.getStudies_cli() → None[source]

nbiatoolkit.nbia_cli.getSeries_cli() → None[source]

nbiatoolkit.nbia_cli.getNewSeries_cli() → None[source]

nbiatoolkit.nbia_cli.downloadSingleSeries_cli() → None[source]

nbiatoolkit.nbia_cli.DICOMSorter_cli()[source]