Python.DICOM.decompress.DICOM_TransferSyntax() - Code Metrics - Inspection of "Dicom Anonymization" - CNBP/DICOMTransit - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#2)

by Yang

created 2018-08-01 16:22 UTC

Python.DICOM.decompress.DICOM_TransferSyntax() A

↳ Parent: Python.DICOM.decompress

Complexity

Conditions

Size

Total Lines	17
Code Lines	7

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	7
dl	0
loc	17
rs	10
c	0
b	0
f	0
cc	2
nop	1

import logging
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
import os
import pydicom, subprocess


from DICOM.validate import DICOM_validator

from pydicom.filereader import read_file_meta_info



def DICOM_decompress(input_file, out_put):

    """
    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:

        logger.info(e.output)
        ErrorMessage = "File type not compatible for " + input_file

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

        logger.info(e.output)

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

        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

        logger.info(ErrorMessage)
        return False, ErrorMessage

    # Test read the data after writing.
    try:
        pydicom.read_file(out_put)
    except Exception as e:

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

        logger.info(ErrorMessage)
        return False, ErrorMessage

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

def DICOM_RequireDecompression(transfer_syntax):

    """
    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):

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

        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):

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

    # Validity check:
    success, DICOM = DICOM_validator(file_path)

    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):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    # Validity check:
    success, DICOM = DICOM_validator(file_path)

    if not success:
        raise IOError
    import dicom

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

        return False
    else:
        return True


1			import logging
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This module should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
2			import os
3			import pydicom, subprocess
			0 ignored issues – show introduced 2018-08-01 16:25 UTC by Report Bug Copy Issue Report Multiple imports on one line (pydicom, subprocess) Loading history... introduced 2018-08-01 16:25 UTC by Report Bug Copy Issue Report standard import "import pydicom, subprocess" should be placed before "import pydicom, subprocess" Loading history...
4
5			from DICOM.validate import DICOM_validator
			0 ignored issues – show introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unable to import 'DICOM.validate' Loading history...
6			from pydicom.filereader import read_file_meta_info
			0 ignored issues – show introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Imports from package pydicom are not grouped Loading history...
7
8
9			def DICOM_decompress(input_file, out_put):
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DICOM_decompress` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
10			"""
11			A wrapper for DCMDJPEG for decompression
12			:param input_file:
13			:param out_put:
14			:return:
15			"""
16			logger = logging.getLogger(__name__)
17
18			if os.path.exists(out_put):
19			return False, "Output_exist already."
20
21			try:
22			subprocess.check_output(['dcmdjpeg', input_file, out_put])
23
24			# When dcmdjpeg has errors
25			except subprocess.CalledProcessError as e:
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `e` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
26			logger.info(e.output)
27			ErrorMessage = "File type not compatible for " + input_file
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `ErrorMessage` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
28			logger.info(ErrorMessage)
29			return False, ErrorMessage
30			except Exception as e:
			0 ignored issues – show Best Practice introduced 2018-08-01 16:25 UTC by Report Bug Copy Issue Report Catching very general exceptions such as `Exception` is usually not recommended. Generally, you would want to handle very specific errors in the exception handler. This ensure that you do not hide other types of errors which should be fixed. So, unless you specifically plan to handle any error, consider adding a more specific exception. Loading history... Coding Style Naming introduced 2018-08-01 16:25 UTC by Report Bug Copy Issue Report The name `e` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
31			logger.info(e.output)
			0 ignored issues – show Bug introduced 2018-08-01 16:25 UTC by Report Bug Copy Issue Report The Instance of `Exception` does not seem to have a member named `output`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
32			ErrorMessage = "Unknown exception detected. Contact the author about " + input_file
			0 ignored issues – show Coding Style Naming introduced 2018-08-01 16:25 UTC by Report Bug Copy Issue Report The name `ErrorMessage` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
33			logger.info(ErrorMessage)
34			return False, ErrorMessage
35
36			# Ensure that data is actually written out.
37			if not os.path.exists(out_put):
38			ErrorMessage = "Cannot write out final file for some reason " + input_file
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `ErrorMessage` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
39			logger.info(ErrorMessage)
40			return False, ErrorMessage
41
42			# Test read the data after writing.
43			try:
44			pydicom.read_file(out_put)
45			except Exception as e:
			0 ignored issues – show Best Practice introduced 2018-08-01 16:25 UTC by Report Bug Copy Issue Report Catching very general exceptions such as `Exception` is usually not recommended. Generally, you would want to handle very specific errors in the exception handler. This ensure that you do not hide other types of errors which should be fixed. So, unless you specifically plan to handle any error, consider adding a more specific exception. Loading history... Coding Style Naming introduced 2018-08-01 16:25 UTC by Report Bug Copy Issue Report The name `e` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
46			ErrorMessage = "Exception encountered while verifying the proper writing out of the DICOM data. Contact author to investigate, attach " + input_file
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (156/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history... Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `ErrorMessage` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
47			logger.info(ErrorMessage)
48			return False, ErrorMessage
49
50			logger.info("Success written " + input_file + " to " + out_put)
51			return True, "All good"
52
53			def DICOM_RequireDecompression(transfer_syntax):
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DICOM_RequireDecompression` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
54			"""
55			Determine if the transfer syntax symbolize LEE or JPEG compressed!
56			:param transfer_syntax:
57			:return: whether the DICOM files are compressed.
58			"""
59
60			if not ("1.2.840.10008.1.2" in transfer_syntax):
			0 ignored issues – show Unused Code Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report There is an unnecessary parenthesis after `not`. Loading history...
61			raise ValueError
62			elif transfer_syntax == "1.2.840.10008.1.2" or transfer_syntax[18] == '1' or transfer_syntax[18] == '2':
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (108/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
63			return False
64			elif transfer_syntax[18] == '4' or transfer_syntax[18] == '5' or transfer_syntax[18] == '6':
65			return True
66			else:
67			raise ValueError
68
69
70			def DICOM_TransferSyntax(file_path):
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DICOM_TransferSyntax` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
71			"""
72			Used to find if a file is compressed
73			:param file_path:
74			:return:
75			"""
76
77			# Validity check:
78			success, DICOM = DICOM_validator(file_path)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DICOM` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Unused Code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The variable `DICOM` seems to be unused. Loading history...
79			if not success:
80			raise IOError
81
82			# Now read the meta information.
83			dicom_file = read_file_meta_info(file_path)
84			transfer_syntax = dicom_file.TransferSyntaxUID
85
86			return transfer_syntax
87
88			def DICOM_QuickTransferSyntaxCheck(file_path):
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DICOM_QuickTransferSyntaxCheck` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This function should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
89			# Validity check:
90			success, DICOM = DICOM_validator(file_path)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DICOM` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
91			if not success:
92			raise IOError
93			import dicom
94
95			# Now read the meta information.
96			if DICOM.file_meta.TransferSyntaxUID in dicom.dataset.NotCompressedPixelTransferSyntaxes:
			0 ignored issues – show unused-code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unnecessary "else" after "return" Loading history... Bug introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The Module `dicom` does not seem to have a member named `dataset`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
97			return False
98			else:
99			return True
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Final newline missing Loading history...

CNBP / DICOMTransit

Pull Request — master (#2)

Python.DICOM.decompress.DICOM_TransferSyntax() A

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