Python.DICOM.decompress

Complexity

Total Complexity

19

Size/Duplication

Total Lines	100
Duplicated Lines	0 %

Importance

Changes

0

4 Functions

Rating	Name	Duplication	Size	Complexity
B	DICOM_decompress()	0	43	6
A	DICOM_QuickTransferSyntaxCheck()	0	12	3
A	DICOM_TransferSyntax()	0	17	2
B	DICOM_RequireDecompression()	0	15	8

import logging

This module should have a docstring.

import os
import pydicom, subprocess

Multiple imports on one line (pydicom, subprocess)

standard import "import pydicom, subprocess" should be placed before "import pydicom, subprocess"

from DICOM.validate import DICOM_validator

Unable to import 'DICOM.validate'

from pydicom.filereader import read_file_meta_info

Imports from package pydicom are not grouped

def DICOM_decompress(input_file, out_put):

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

    """
    A wrapper for DCMDJPEG for decompression
    :param input_file:
    :param out_put:
    :return:
    """
    logger = logging.getLogger(__name__)

    if os.path.exists(out_put):
        return False, "Output_exist already."

    try:
        subprocess.check_output(['dcmdjpeg', input_file, out_put])

    # 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.output)
        ErrorMessage = "File type not compatible for " + input_file

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.output)

The Instance of Exception does not seem to have a member named output.

        ErrorMessage = "Unknown exception detected. Contact the author about " + input_file

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

    # Ensure that data is actually written out.
    if not os.path.exists(out_put):
        ErrorMessage = "Cannot write out final file for some reason " + input_file

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

    # Test read the data after writing.
    try:
        pydicom.read_file(out_put)
    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_]*))$).

        ErrorMessage = "Exception encountered while verifying the proper writing out of the DICOM data. Contact author to investigate, attach " + input_file

This line is too long as per the coding-style (156/100).

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

    logger.info("Success written " + input_file + " to " + out_put)
    return True, "All good"

def DICOM_RequireDecompression(transfer_syntax):

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

    """
    Determine if the transfer syntax symbolize LEE or JPEG compressed!
    :param transfer_syntax:
    :return: whether the DICOM files are compressed.
    """

    if not ("1.2.840.10008.1.2" in transfer_syntax):

There is an unnecessary parenthesis after not.

        raise ValueError
    elif transfer_syntax == "1.2.840.10008.1.2" or transfer_syntax[18] == '1' or transfer_syntax[18] == '2':

This line is too long as per the coding-style (108/100).

        return False
    elif transfer_syntax[18] == '4' or transfer_syntax[18] == '5' or transfer_syntax[18] == '6':
        return True
    else:
        raise ValueError


def DICOM_TransferSyntax(file_path):

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

    """
    Used to find if a file is compressed
    :param file_path:
    :return:
    """

    # Validity check:
    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_]*))$).

The variable DICOM seems to be unused.

    if not success:
        raise IOError

    # Now read the meta information.
    dicom_file = read_file_meta_info(file_path)
    transfer_syntax = dicom_file.TransferSyntaxUID

    return transfer_syntax

def DICOM_QuickTransferSyntaxCheck(file_path):

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

This function should have a docstring.

    # Validity check:
    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:
        raise IOError
    import dicom

    # Now read the meta information.
    if DICOM.file_meta.TransferSyntaxUID in dicom.dataset.NotCompressedPixelTransferSyntaxes:

Unnecessary "else" after "return"

The Module dicom does not seem to have a member named dataset.

        return False
    else:
        return True

Final newline missing