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utils

pacsanini.utils #

Simple utilities to facilitate the ingestion of resource values

into the application.

default_config_path() #

Returns the configuration file that should be used by default.

The choosing order is as such: 1. If set and if exists, use the PACSANINI_CONF_ENVVAR 2. If exists, use the DEFAULT_CONFIG_NAME 3. If exists, use the DEFAULT_SETTINGS_PATH 4. Otherwise, return None

Source code in pacsanini/utils.py 
def default_config_path() -> Optional[str]:
    """Returns the configuration file that should be used by default.
    The choosing order is as such:
    1. If set and if exists, use the PACSANINI_CONF_ENVVAR
    2. If exists, use the DEFAULT_CONFIG_NAME
    3. If exists, use the DEFAULT_SETTINGS_PATH
    4. Otherwise, return None
    """
    env_var = os.environ.get(PACSANINI_CONF_ENVVAR, "")
    if env_var and os.path.exists(env_var):
        return env_var
    if os.path.exists(DEFAULT_CONFIG_NAME):
        return DEFAULT_CONFIG_NAME
    if os.path.exists(DEFAULT_SETTINGS_PATH):
        return DEFAULT_SETTINGS_PATH
    return None

is_db_uri(uri) #

Return true if the URI is for a known database. False

otherwise (eg: it is a file path).

Source code in pacsanini/utils.py 
def is_db_uri(uri: str) -> bool:
    """Return true if the URI is for a known database. False
    otherwise (eg: it is a file path).
    """
    uri_lower = uri.lower()
    for dialect in SUPPORTED_DB_DIALECTS:
        if dialect.match(uri_lower):
            return True
    return False

read_resources(resources_path, query_level) #

Read a list of DICOM resources.

Parameters:

Name Type Description Default
resources_path str

The file path of the DICOM resources file to read.

 required
query_level QueryLevel

A way of indicating which field to read in the file. If PATIENT, the PatientID column will be read. If STUDY, the StudyInstanceUID column will be read.

 required

Exceptions:

Type Description
InvalidResourceFile

An InvalidResourceFile error is raised if the input CSV file does not contain a "PatientID" column if the query level is PATIENT or a "StudyInstanceUID" column if the query level is STUDY.

Returns:

Type Description
List[str]

A list of unique UIDS found in the given file.
Source code in pacsanini/utils.py 
def read_resources(resources_path: str, query_level: QueryLevel) -> List[str]:
    """Read a list of DICOM resources.

    Parameters
    ----------
    resources_path : str
        The file path of the DICOM resources file to read.
    query_level : QueryLevel
        A way of indicating which field to read in the file. If PATIENT,
        the PatientID column will be read. If STUDY, the StudyInstanceUID
        column will be read.

    Returns
    -------
    List[str]
        A list of unique UIDS found in the given file.

    Raises
    ------
    InvalidResourceFile
        An InvalidResourceFile error is raised if the input CSV file
        does not contain a "PatientID" column if the query level is
        PATIENT or a "StudyInstanceUID" column if the query level is
        STUDY.
    """
    resources = pd.read_csv(resources_path)
    if resources.shape[1] == 1:
        resources = resources[resources.columns[0]].unique().tolist()
    else:
        if QueryLevel.PATIENT == query_level:
            if not "PatientID" in resources.columns:
                raise InvalidResourceFile(
                    f"Expected to find a column named PatientID in {resources_path}"
                )
            resources = resources["PatientID"].unique().tolist()
        else:
            if not "StudyInstanceUID" in resources.columns:
                raise InvalidResourceFile(
                    f"Expected to find a column named StudyInstaceUID in {resources_path}"
                )
            resources = resources["StudyInstanceUID"].unique().tolist()

    return resources