Python.DICOM.convert

Complexity

Total Complexity

11

Size/Duplication

Total Lines	67
Duplicated Lines	0 %

Importance

Changes

0

4 Methods

Rating	Name	Duplication	Size	Complexity
A	DICOM_convert.to_minc()	0	3	1
B	DICOM_convert.to_nii()	0	35	5
A	DICOM_convert.to_BIDS()	0	3	1
A	DICOM_convert.fix_series()	0	8	4

import sys

This module should have a docstring.

import logging
import os
import subprocess
import re

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

class DICOM_convert:

The name DICOM_convert 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 to_nii(input_folder, output_folder):
        """

        :param input_folder: Input_folder can be a root folder or flat.
        :return:
        """
        logger = logging.getLogger("DICOM to NII conversion")
        if not os.path.exists(input_folder) or not os.path.exists(output_folder):
            return False, "Argument input or output folder does not exist"

        try:

            # SUPER IMPORTANT! MAKE SURE dcm2niix by Chris Roden is in the system path!
            subprocess.check_output(['dcm2niix',
                                     '-b', 'y',
                                     '-z', 'y',
                                     '-v', 'y',
                                     '-f', "%s_%p",
                                     '-o', output_folder,
                                    input_folder])

Wrong continued indentation (add 1 space).

        # When dcmdjpeg has errors
        except subprocess.CalledProcessError as e:

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

            logger.info(e)
            ErrorMessage = "File type not compatible"

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

            logger.info(ErrorMessage)
            return False, ErrorMessage
        except Exception as e:

Catching very general exceptions such as Exception is usually not recommended.

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

            logger.info(e)
            ErrorMessage = "dcm2niix decompression call failed! Make sure dcm2niix is in your SYSTEM OS PATH and then check your input file:"

This line is too long as per the coding-style (141/100).

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

            logger.info(ErrorMessage)
            return False, ErrorMessage

        return True, "All conversion successfully finished."

    @staticmethod
    def fix_series(input_folder):

This method should have a docstring.

        os.chdir(input_folder)
        for file in os.listdir(input_folder):
            if re.match(r'^[0-9]_', file):
                os.rename(file, '00'+ file)
            elif re.match(r'^[0-9][0-9]_', file):
                os.rename(file, '0'+ file)

    @staticmethod
    def to_minc(input_folder, output_folder):

This method should have a docstring.

        raise NotImplementedError

    @staticmethod
    def to_BIDS(input_folder, output_folder):

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

This method should have a docstring.

        raise NotImplementedError


if __name__ == "__main__":
    DICOM_convert.fix_series(r"C:\FullyAnonymizedSubjects\Wed3ConvertResult\raw_sorted")
    #DICOM_convert.to_nii(r"C:\FullyAnonymizedSubjects\2018-08-15_TestSubject2\Wed2-Decompressed", r"C:\FullyAnonymizedSubjects\2018-08-15_TestSubject2\Test")

This line is too long as per the coding-style (158/100).