Python.DICOM.sort

Complexity

Total Complexity

6

Size/Duplication

Total Lines	80
Duplicated Lines	0 %

Importance

Changes

0

1 Method

Rating	Name	Duplication	Size	Complexity
B	DICOM_sort.into_folder()	0	63	6

import sys

This module should have a docstring.

import logging
import os
import shutil
from DICOM.elements import DICOM_elements

Unable to import 'DICOM.elements'

from DICOM.validate import DICOM_validate

Unable to import 'DICOM.validate'

from tqdm import tqdm

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

class DICOM_sort:

The name DICOM_sort 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 into_folder(input_folder, output_folder):

This function exceeds the maximum number of variables (16/15).

        """
        This function sort a input folder with or without sub layers and automaticlly flatten everything into a folder before then MOVING them into protocol based folder sorted by acquisition series.

This line is too long as per the coding-style (199/100).

        :param input_folder: Input_folder can be a root folder or flat.
        :return:
        """
        logger = logging.getLogger("DICOM sorting operation")

        #Element to check: Series number.

        from PythonUtils.file import flatcopy

Unable to import 'PythonUtils.file'

        from PythonUtils.folder import recursive_list

Unable to import 'PythonUtils.folder'

        # Get files
        file_list = recursive_list(input_folder)

        if not os.path.isdir(output_folder):
            os.mkdir(output_folder)


        # copy them to a flat structure to the output folder.
        flatcopy(file_list, output_folder, DICOM_validate.file)

        # decompress them if necessary.
        # oshelper_files.decompress_folder(output_folder)

        # Get files list again.
        file_list = recursive_list(output_folder)

        exception_encountered = 0

        logger.info("Sorting files into folders:")

        # File here should be the FULL path.
        for file in tqdm(file_list):

            success1, SeriesNumber = DICOM_elements.retrieve(file, "SeriesNumber")

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

            success2, SeriesDescription = DICOM_elements.retrieve(file, "SeriesDescription")

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

            if not success1 or not success2:
                logger.info("Skipped file with no acquisition series information: " + file)
                exception_encountered = exception_encountered + 1
                continue

            # Check MRI Series folder exists
            DestinationFolder = str(SeriesNumber) + '_' + SeriesDescription

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

            DestinationFolder = DestinationFolder.replace(' ', '_')

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

            DestinationFolder = DestinationFolder.replace(':', '_')

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

            DestinationFolder = DestinationFolder.replace(r'/', '_')

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

            DestinationFolder = DestinationFolder.replace(r'\\', '_')

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

            # Make destination folder if not exist.
            os.chdir(output_folder)
            if not os.path.exists(DestinationFolder):
                os.mkdir(DestinationFolder)

            # Get file name.
            _, filename = os.path.split(file)

            shutil.move(file, os.path.join(DestinationFolder, filename))
        logger.info("Total error encoutnered: " + str(exception_encountered))


if __name__ == "__main__":
    DICOM_sort.into_folder("C:\FullyAnonymizedSubjects\StreamLineTest", "C:\FullyAnonymizedSubjects\StreamLineTest\Test")

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

A suspicious escape sequence \F was found. Did you maybe forget to add an r prefix?

A suspicious escape sequence \S was found. Did you maybe forget to add an r prefix?

A suspicious escape sequence \T was found. Did you maybe forget to add an r prefix?