Python.DICOM.elements

Complexity

Total Complexity

9

Size/Duplication

Total Lines	78
Duplicated Lines	0 %

Importance

Changes

0

4 Functions

Rating	Name	Duplication	Size	Complexity
A	DICOM_retrieveMRN()	0	12	2
A	DICOM_computeScanAge()	0	17	2
A	DICOM_updateElement()	0	22	3
A	DICOM_retrieveElements()	0	15	2

import logging

This module should have a docstring.

from DICOM.validate import DICOM_validator

Unable to import 'DICOM.validate'

def DICOM_retrieveElements(file_path, data_element):

The name DICOM_retrieveElements does not conform to the function naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    """
    A low level function used to retrieve elements from DICOM and return a LIST of matching element. ACCEPT PARTIAL MATCH

This line is too long as per the coding-style (121/100).

    :param file_path:
    :param data_element:
    :return: LIST of all data elements that match the pattern provided in the data_element and their value.  NO Regular EXPRESSION.

This line is too long as per the coding-style (131/100).

    """
    success, DICOM = DICOM_validator(file_path)

The name DICOM does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    if not success:
        return False, None, None

    # Get a list of all data elements that can have element label.
    element_values = DICOM.data_element(data_element).value

    return True, element_values


def DICOM_updateElement(file_path, data_element, element_value, out_path):

The name DICOM_updateElement does not conform to the function naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    """
    Update a particular data_element to the desired value, then write back to the SOURCE FILE!
    :param file_path:
    :param data_element:
    :param element_value:
    :return: bool on operation success, and string on reason.
    """

    """BE AWARE that if the key does not exist, it will not be created currently!"""

This string statement has no effect and could be removed.

    logger = logging.getLogger(__name__)
    success, DICOM = DICOM_validator(file_path)

The name DICOM does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    if not success:
        return False, "DICOM not valid."

    try:
        DICOM.data_element(data_element).value = element_value
    except KeyError:
        logger.info("Key " + data_element + " does not exist, creating the key.")
        return False, "DICOM key field does not exist. Not sure how to create one yet. "
    DICOM.save_as(out_path)
    return True, "Data element update completed."


def DICOM_retrieveMRN(file_path):

The name DICOM_retrieveMRN does not conform to the function naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    """
    Read the PatientID field which normally used as MRN number.
    :param file_path:
    :return: MRN number, as a STRING
    """
    success, value = DICOM_retrieveElements(file_path, "PatientID")

    if not success:

Unnecessary "else" after "return"

        return False, None
    else:
        return True, value


def DICOM_computeScanAge(file_path):

The name DICOM_computeScanAge does not conform to the function naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    """
    Read the PatientID field which normally used as MRN number.
    :param file_path:
    :return: Age as a relative delta time object.
    """

    from dateutil.relativedelta import relativedelta

    success, DICOM = DICOM_validator(file_path)

The name DICOM does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    if not success:
        return False, None
    from datetime import datetime
    scan_date = datetime.strptime(DICOM.SeriesDate, "%Y%m%d")
    birthday = datetime.strptime(DICOM.PatientBirthDate, "%Y%m%d")
    age = relativedelta(scan_date, birthday)
    return True, age

Final newline missing