Python.DICOM.validate

Complexity

Total Complexity

16

Size/Duplication

Total Lines	102
Duplicated Lines	0 %

Importance

Changes

0

3 Methods

Rating	Name	Duplication	Size	Complexity
A	DICOM_validate.file()	0	20	2
A	DICOM_validate.MRN()	0	13	4
C	DICOM_validate.path()	0	57	10

import sys

This module should have a docstring.

import logging
import os
from tqdm import tqdm

logging.basicConfig(stream=sys.stdout, level=logging.INFO)

class DICOM_validate:

The name DICOM_validate does not conform to the class naming conventions ([A-Z_][a-zA-Z0-9]+$).

This class should have a docstring.

The variable __class__ seems to be unused.

    @staticmethod
    def MRN(input_string):

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

This method should have a docstring.

        string=str(input_string)

Exactly one space required around assignment

        if not string.isdigit():
            return False
        try:
            MRN = int(string)

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

            if 0 < MRN < 9999999:

The if statement can be replaced with 'return bool(test)'

Unnecessary "else" after "return"

                return True
            else:
                return False
        except ValueError:
            return False

    @staticmethod
    def file(file_path):
        """
        validate to check if the DICOM file is an actual DICOM file.
        :param file_path:
        :return:
        """
        logger = logging.getLogger(__name__)

        global dicom

The name dicom does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

Global variable 'dicom' undefined at the module level

        dicom = None

        from pydicom.filereader import InvalidDicomError
        from pydicom.filereader import read_file
        try:
            dicom = read_file(file_path)
        except InvalidDicomError:
            logger.info(file_path + " is not a DICOM file. Skipping")
            return False, None
        return True, dicom

    @staticmethod
    def path(dir_path):
        """
        Some basic information of the participants must be consistent across the files, such as the SCAN DATE (assuming they are not scanning across MIDNIGHT POINT)

This line is too long as per the coding-style (164/100).

        Birthday date, subject name, etc MUST BE CONSISTENT across a SINGLE subject's folder, RIGHT!

        :param dir_path:
        :return:
        """
        logger = logging.getLogger(__name__)


        # Input check
        if not os.path.exists(dir_path) or not os.path.isdir(dir_path):
            logger.info("Bad data folder path")
            return False

        files = os.listdir(dir_path)

        # Used to record the first encountered patientID and name, and will check against subsequent folder for same matching information.

This line is too long as per the coding-style (138/100).

        global PatientID, PatientName

The name PatientID does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

The name PatientName does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

Global variable 'PatientID' undefined at the module level

Global variable 'PatientName' undefined at the module level

        validated_DICOM_files = []

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

        from DICOM.elements import DICOM_elements

Unable to import 'DICOM.elements'

        logger.info("Checking individual dicom files for patient info consistencies")

        # Check individual DICOM file for consistencies.
        for file in tqdm(files):

            # Skip current file if they are not DICOM files.
            isDICOM, _ = DICOM_validate.file(file)

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

            if not isDICOM:
                continue

            # Record first instance of patient ID and patient name.
            if PatientID is None and PatientName is None:

The variable PatientID was used before it was assigned.

The variable PatientName was used before it was assigned.

                Success, PatientID = DICOM_elements.retrieve(files[0], "PatientID")

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

                Success, PatientName = DICOM_elements.retrieve(files[0], "PatientName")

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

                # raise issue if not successful
                if not Success:
                    logger.info("DICOME meta data retrieval failure.")
                    return False
                continue

            # Check consistencies across folders in terms of patient ID, NAME.
            CurrentPatientID = DICOM_elements.retrieve(file, "PatientID")

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

            CurrentPatientName = DICOM_elements.retrieve(file, "PatientName")

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

            if not (PatientID == CurrentPatientID) or not (PatientName == CurrentPatientName):

There is an unnecessary parenthesis after not.

                logger.info("PatientID or Name mismatch from the dicom archive. .")
                return False

            validated_DICOM_files.append(file)

        return True, validated_DICOM_files

    #if __name__ == '__main__':