nbiatoolkit.utils

Submodules

• nbiatoolkit.utils.conv_response_list
• nbiatoolkit.utils.md5
• nbiatoolkit.utils.nbia_endpoints
• nbiatoolkit.utils.parsers

Package Contents

Classes

NBIA_ENDPOINTS	This enum class defines the NBIA endpoints used in the NBIA toolkit.
NBIA_BASE_URLS	This enum class defines the NBIA base URLs used in the NBIA toolkit.
ReturnType	Generic enumeration.

Functions

validateMD5(→ bool)
convertMillis(→ str)	Convert milliseconds to a formatted date string.
clean_html(→ str)	Cleans the given HTML string by removing HTML tags and replacing special characters.
convertDateFormat(→ str)	Converts the input date to the desired format.
parse_response(→ List[dict[Any, Any]])	Response will be either JSON or bytes
conv_response_list(→ List[dict[Any, ...)	Function that takes in a list of dictionaries and returns either a list or a dataframe.

class nbiatoolkit.utils.NBIA_ENDPOINTS

Bases: enum.Enum

This enum class defines the NBIA endpoints used in the NBIA toolkit.

GET_COLLECTIONS = 'v2/getCollectionValues'

GET_COLLECTION_PATIENT_COUNT = 'getCollectionValuesAndCounts'

GET_COLLECTION_DESCRIPTIONS = 'getCollectionDescriptions'

GET_MODALITY_VALUES = 'v2/getModalityValues'

GET_MODALITY_PATIENT_COUNT = 'getModalityValuesAndCounts'

GET_PATIENTS = 'v2/getPatient'

GET_NEW_PATIENTS_IN_COLLECTION = 'v2/NewPatientsInCollection'

GET_PATIENT_BY_COLLECTION_AND_MODALITY = 'v2/getPatientByCollectionAndModality'

GET_BODY_PART_PATIENT_COUNT = 'getBodyPartValuesAndCounts'

GET_STUDIES = 'v2/getPatientStudy'

GET_SERIES = 'v2/getSeries'

GET_UPDATED_SERIES = 'v2/getUpdatedSeries'

GET_SERIES_METADATA = 'v1/getSeriesMetaData'

DOWNLOAD_SERIES = 'v2/getImageWithMD5Hash'

GET_DICOM_TAGS = 'getDicomTags'

__str__()

Return str(self).

_format()

class nbiatoolkit.utils.NBIA_BASE_URLS

Bases: enum.Enum

This enum class defines the NBIA base URLs used in the NBIA toolkit.

NBIA = 'https://services.cancerimagingarchive.net/nbia-api/services/'

NLST = 'https://nlst.cancerimagingarchive.net/nbia-api/services/'

LOGOUT_URL = 'https://services.cancerimagingarchive.net/nbia-api/logout'

__str__()

Return str(self).

_format()

class nbiatoolkit.utils.ReturnType

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

LIST = 'list'

DATAFRAME = 'dataframe'

nbiatoolkit.utils.validateMD5(seriesDir: str) → bool

nbiatoolkit.utils.convertMillis(millis: int) → str

Convert milliseconds to a formatted date string.

Parameters:

millis (int) – The number of milliseconds to convert.

Returns:

The formatted date string in the format ‘YYYY-MM-DD’.

Return type:

str

Raises:

AssertionError – If the input is not an integer.

nbiatoolkit.utils.clean_html(html_string: str) → str

Cleans the given HTML string by removing HTML tags and replacing special characters.

Parameters:

html_string (str) – The input HTML string to be cleaned.

Returns:

The cleaned text content without HTML tags and special characters.

Return type:

str

nbiatoolkit.utils.convertDateFormat(input_date: str | datetime.datetime, format: str = '%Y/%m/%d') → str

Converts the input date to the desired format.

Parameters:

input_date (str) – The date to be converted.

Returns:

The converted date in the format “YYYY/MM/DD”.

Return type:

str

Raises:

ValueError – If the input date has an invalid format.

nbiatoolkit.utils.parse_response(response: requests.Response) → List[dict[Any, Any]]

Response will be either JSON or bytes

nbiatoolkit.utils.conv_response_list(response_json: List[dict[Any, Any]], return_type: nbiatoolkit.utils.nbia_endpoints.ReturnType) → List[dict[Any, Any]] | pandas.DataFrame

Function that takes in a list of dictionaries and returns either a list or a dataframe.

Parameters:

• response_json (List[dict[Any, Any]]) – A response from the API in the form of a list of dictionaries.

• return_type (ReturnType) – The desired return type for the response.

Returns:

Either a list of dictionaries or a DataFrame.

Return type:

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