Python.DICOM.decompress.DICOM_decompress() - Code Metrics - Inspection of "Major update" - CNBP/DICOMTransit - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#3)

by Yang

created 2018-09-12 21:13 UTC

Python.DICOM.decompress.DICOM_decompress() B

↳ Parent: Python.DICOM.decompress

Complexity

Conditions

Size

Total Lines	43
Code Lines	28

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	28
dl	0
loc	43
rs	8.2746
c	0
b	0
f	0
cc	6
nop	2

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

from PythonUtils.folder import recursive_list

from tqdm import tqdm


from pydicom.filereader import read_file_meta_info


from DICOM.validate import DICOM_validate


class DICOM_decompress:
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    @staticmethod
    def save_as(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:
            # SUPER IMPORTANT! MAKE SURE DCMDJPEG is in the system path!
            subprocess.check_output(['dcmdjpeg', input_file, out_put])

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

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

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

            logger.info(e)
            ErrorMessage = "DCMDJPEG decompression call failed! Make sure DCMDJPEG is in your SYSTEMOS PATH and then check your input file:" + 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(e)
            logger.info(ErrorMessage)
            return False, ErrorMessage

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

    @staticmethod
    def check_decompression(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

    @staticmethod
    def get_transferSyntax(file_path):

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

        # Validity check:
        success, DICOM = DICOM_validate.file(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

    @staticmethod
    def check_decompression_quick(file_path):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        # Validity check:
        success, DICOM = DICOM_validate.file(file_path)

        if not success:
            raise IOError
        import pydicom.uid
param = 5

class Foo:
    def __init__(self, param):   # "param" would be flagged here
        self.param = param

        # Now read the meta information.
        if DICOM.file_meta.TransferSyntaxUID in pydicom.uid.UncompressedPixelTransferSyntaxes:

            return True
        else:
            return False

    @staticmethod
    def filelist(file_list):
        """
        Decompress all compressed files in the list OVERWRITE the files.
        :param file_list:
        :return:
        """
        logger = logging.getLogger("Decompressing files")

        for file in tqdm(file_list):

            logger.info("Decompressing: " + file)

            # find if the file is DICOM, if not, skip this file.
            is_DICOM_file, _ = DICOM_validate.file(file)

            if not is_DICOM_file:
                continue

            # check if the file is compressed.
            TransferSyntax = DICOM_decompress.get_transferSyntax(file)

            try:
                RequireDecompression = DICOM_decompress.check_decompression(TransferSyntax)

                if RequireDecompression:
                    DICOM_decompress.save_as(file, file)

            except ValueError:
                logger.info("Unknwonw DICOM syntax. You sure it is DICOM?")
                continue

    @staticmethod
    def decompress_folder(input_folder):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        files_list = recursive_list(input_folder)
        DICOM_decompress.filelist(files_list)


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 2018-09-12 21:17 UTC by Report Bug Copy Issue Report Multiple imports on one line (pydicom, subprocess) Loading history... introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report standard import "import pydicom, subprocess" should be placed before "import pydicom, subprocess" Loading history...
4			from PythonUtils.folder import recursive_list
			0 ignored issues – show introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report Unable to import 'PythonUtils.folder' Loading history...
5			from tqdm import tqdm
6
7
8			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...
9
10			from DICOM.validate import DICOM_validate
			0 ignored issues – show introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report Unable to import 'DICOM.validate' Loading history...
11
12			class DICOM_decompress:
			0 ignored issues – show Coding Style Naming introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report The name `DICOM_decompress` does not conform to the class naming conventions (`[A-Z_][a-zA-Z0-9]+$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report This class should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history... Unused Code introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report The variable `__class__` seems to be unused. Loading history...
13
14			@staticmethod
15			def save_as(input_file, out_put):
16			"""
17			A wrapper for DCMDJPEG for decompression
18			:param input_file:
19			:param out_put:
20			:return:
21			"""
22			logger = logging.getLogger(__name__)
23
24			if os.path.exists(out_put):
25			return False, "Output_exist already."
26
27			try:
28			# SUPER IMPORTANT! MAKE SURE DCMDJPEG is in the system path!
29			subprocess.check_output(['dcmdjpeg', input_file, out_put])
30
31			# When dcmdjpeg has errors
32			except subprocess.CalledProcessError as e:
			0 ignored issues – show Coding Style Naming introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report The name `e` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). 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...
33			logger.info(e)
34			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_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
35			logger.info(ErrorMessage)
36			return False, ErrorMessage
37			except Exception as e:
			0 ignored issues – show Best Practice introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report Catching very general exceptions such as `Exception` is usually not recommended. Generally, you would want to handle very specific errors in the exception handler. This ensure that you do not hide other types of errors which should be fixed. So, unless you specifically plan to handle any error, consider adding a more specific exception. Loading history... Coding Style Naming introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report The name `e` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). 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...
38			logger.info(e)
39			ErrorMessage = "DCMDJPEG decompression call failed! Make sure DCMDJPEG is in your SYSTEMOS PATH and then check your input file:" + input_file
			0 ignored issues – show Coding Style introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (153/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history... Coding Style Naming introduced 2018-09-12 21:17 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_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
40			logger.info(ErrorMessage)
41			return False, ErrorMessage
42
43			# Ensure that data is actually written out.
44			if not os.path.exists(out_put):
45			ErrorMessage = "Cannot write out final file for some reason " + input_file
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `ErrorMessage` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). 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...
46			logger.info(ErrorMessage)
47			return False, ErrorMessage
48
49			# Test read the data after writing.
50			try:
51			pydicom.read_file(out_put)
52			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_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
53			ErrorMessage = "Exception encountered while verifying the proper writing out of the DICOM data. Contact author to investigate, attach " + input_file
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (160/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history... Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `ErrorMessage` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). 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...
54			logger.info(e)
55			logger.info(ErrorMessage)
56			return False, ErrorMessage
57
58			logger.info("Success written " + input_file + " to " + out_put)
59			return True, "All good"
60
61			@staticmethod
62			def check_decompression(transfer_syntax):
63			"""
64			Determine if the transfer syntax symbolize LEE or JPEG compressed!
65			:param transfer_syntax:
66			:return: whether the DICOM files are compressed.
67			"""
68
69			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...
70			raise ValueError
71			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 (112/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
72			return False
73			elif transfer_syntax[18] == '4' or transfer_syntax[18] == '5' or transfer_syntax[18] == '6':
74			return True
75			else:
76			raise ValueError
77
78			@staticmethod
79			def get_transferSyntax(file_path):
			0 ignored issues – show Coding Style Naming introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report The name `get_transferSyntax` does not conform to the method naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
80			"""
81			Used to find if a file is compressed
82			:param file_path:
83			:return:
84			"""
85
86			# Validity check:
87			success, DICOM = DICOM_validate.file(file_path)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DICOM` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). 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...
88			if not success:
89			raise IOError
90
91			# Now read the meta information.
92			dicom_file = read_file_meta_info(file_path)
93			transfer_syntax = dicom_file.TransferSyntaxUID
94
95			return transfer_syntax
96
97			@staticmethod
98			def check_decompression_quick(file_path):
			0 ignored issues – show Coding Style introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report This method 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...
99			# Validity check:
100			success, DICOM = DICOM_validate.file(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...
101			if not success:
102			raise IOError
103			import pydicom.uid
			0 ignored issues – show Comprehensibility Bug introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report `pydicom` is re-defining a name which is already available in the outer-scope (previously defined on line `3`). It is generally a bad practice to shadow variables from the outer-scope. In most cases, this is done unintentionally and might lead to unexpected behavior: param = 5 class Foo: def __init__(self, param): # "param" would be flagged here self.param = param Loading history...
104
105			# Now read the meta information.
106			if DICOM.file_meta.TransferSyntaxUID in pydicom.uid.UncompressedPixelTransferSyntaxes:
			0 ignored issues – show Unused Code introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report The if statement can be replaced with 'return bool(test)' Loading history... unused-code introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report Unnecessary "else" after "return" Loading history...
107			return True
108			else:
109			return False
110
111			@staticmethod
112			def filelist(file_list):
113			"""
114			Decompress all compressed files in the list OVERWRITE the files.
115			:param file_list:
116			:return:
117			"""
118			logger = logging.getLogger("Decompressing files")
119
120			for file in tqdm(file_list):
121
122			logger.info("Decompressing: " + file)
123
124			# find if the file is DICOM, if not, skip this file.
125			is_DICOM_file, _ = DICOM_validate.file(file)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `is_DICOM_file` 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...
126			if not is_DICOM_file:
127			continue
128
129			# check if the file is compressed.
130			TransferSyntax = DICOM_decompress.get_transferSyntax(file)
			0 ignored issues – show Coding Style Naming introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report The name `TransferSyntax` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
131			try:
132			RequireDecompression = DICOM_decompress.check_decompression(TransferSyntax)
			0 ignored issues – show Coding Style Naming introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report The name `RequireDecompression` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). 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...
133			if RequireDecompression:
134			DICOM_decompress.save_as(file, file)
135
136			except ValueError:
137			logger.info("Unknwonw DICOM syntax. You sure it is DICOM?")
138			continue
139
140			@staticmethod
141			def decompress_folder(input_folder):
			0 ignored issues – show Coding Style introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report This method 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...
142			files_list = recursive_list(input_folder)
143			DICOM_decompress.filelist(files_list)
			0 ignored issues – show Coding Style introduced 2018-09-12 21:17 UTC by Report Bug Copy Issue Report Final newline missing Loading history...

CNBP / DICOMTransit

Pull Request — master (#3)

Python.DICOM.decompress.DICOM_decompress() B

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

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