Python.DICOM.test_DICOM.test_DICOM_RequireDecompression() - 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

test_DICOM_RequireDecompression() B

↳ Parent: Python.DICOM.test_DICOM

Complexity

Conditions

Size

Total Lines	6
Code Lines	6

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	6
dl	0
loc	6
rs	8.6666
c	0
b	0
f	0
cc	6
nop	0

import os
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
import sys
import logging
import unittest

from DICOM.validate import DICOM_validator

from DICOM.decompress import DICOM_RequireDecompression, DICOM_decompress

from DICOM.anonymize import DICOM_anonymizer

from DICOM.elements import DICOM_retrieveElements, DICOM_updateElement, DICOM_retrieveMRN, DICOM_computeScanAge

from pydicom.data import get_testdata_files


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

def get_test_DICOM_path():
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    filename = get_testdata_files("rtplan.dcm")[0]
    return filename

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

    logger = logging.getLogger(__name__)

    # Get all test files with "JPEG" in them.
    file_names = get_testdata_files("[Jj][Pp][Ee][Gg]")

    logger.info("List of files to try to decompress:")
    logger.info(file_names)

    success_counter = 0
    fail_counter = 0

    for file in file_names:
        logger.info("Processing: " + file)

        decompressed_file = file+"DECOM"

        success, reason = DICOM_decompress(file, decompressed_file)

        logger.info(reason)

        if success:
            success_counter += 1
            os.remove(decompressed_file) # restore the test environment to its former state.
            logger.info("Successful.")
        else:
            fail_counter += 1
            logger.info("Failed. Reason:" + reason)
    assert success_counter == 7 # within the test data folder, there should be SEVEN files with JPEG in their name that CAN be successfully loaded.

    assert fail_counter == 4 # within the test data folder, there should be FOUR files with JPEG in their name that CANNOT be successfully loaded.


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

    file_name = get_test_DICOM_path()
    success, data = DICOM_validator(file_name)

    assert success

    file_name = get_testdata_files("README.txt")[0]
    success, data = DICOM_validator(file_name)
    assert not success

def test_DICOM_RequireDecompression():
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    assert not (DICOM_RequireDecompression('1.2.840.10008.1.2'))

    assert not (DICOM_RequireDecompression('1.2.840.10008.1.2.1'))

    assert not (DICOM_RequireDecompression('1.2.840.10008.1.2.2'))

    assert (DICOM_RequireDecompression('1.2.840.10008.1.2.4'))

    assert (DICOM_RequireDecompression('1.2.840.10008.1.2.4.57'))



class MyTestCase(unittest.TestCase):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    def test_wrong_syntax(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        self.assertRaises(ValueError, DICOM_RequireDecompression, 'FakeTest')


def test_DICOM_anonymizer():
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    file_names = get_testdata_files("emri")
    for file_name in file_names:
        success = DICOM_anonymizer(file_name, "CNBP0010001")
        assert success
    for file_name in file_names:
        success, value = DICOM_retrieveElements(file_name, "PatientID")
        assert success
        assert (value == "CNBP0010001")



def test_DICOM_retrieveMRN():
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    path = get_testdata_files("emri_small_big_endian")[0]
    success, MRN = DICOM_retrieveMRN(path)

    assert success
    assert (MRN == 'CNBP0010001')



def test_DICOM_update():
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    path = get_testdata_files("emri")
    for file in path:
        success, _ = DICOM_updateElement(file, "PatientBirthDate", "19950101", file)
        assert success

    for file in path:
        success, value = DICOM_retrieveElements(file, "PatientBirthDate")
        assert success
        assert(value == "19950101")


def test_DICOM_computerScanAge():
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    logger = logging.getLogger("DICOM compute age")
    path = get_testdata_files("emri_small_RLE")[0]
    success, Age = DICOM_computeScanAge(path)

    assert success
    logger.info(Age.day)


if __name__ == '__main__':
    test_DICOM_decompress()


1			import os
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `test_DICOM` does not conform to the module naming conventions (`(([a-z_][a-z0-9_]*)\|([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 2018-07-31 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 sys
3			import logging
4			import unittest
5
6			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...
7			from DICOM.decompress import DICOM_RequireDecompression, DICOM_decompress
			0 ignored issues – show introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unable to import 'DICOM.decompress' Loading history...
8			from DICOM.anonymize import DICOM_anonymizer
			0 ignored issues – show introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unable to import 'DICOM.anonymize' Loading history...
9			from DICOM.elements import DICOM_retrieveElements, DICOM_updateElement, DICOM_retrieveMRN, DICOM_computeScanAge
			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 (111/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history... introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unable to import 'DICOM.elements' Loading history...
10			from pydicom.data import get_testdata_files
11
12
13			logging.basicConfig(stream=sys.stdout, level=logging.INFO)
14
15			def get_test_DICOM_path():
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `get_test_DICOM_path` 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...
16			filename = get_testdata_files("rtplan.dcm")[0]
17			return filename
18
19			def test_DICOM_decompress():
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `test_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... 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...
20
21			logger = logging.getLogger(__name__)
22
23			# Get all test files with "JPEG" in them.
24			file_names = get_testdata_files("[Jj][Pp][Ee][Gg]")
25
26			logger.info("List of files to try to decompress:")
27			logger.info(file_names)
28
29			success_counter = 0
30			fail_counter = 0
31
32			for file in file_names:
33			logger.info("Processing: " + file)
34
35			decompressed_file = file+"DECOM"
36
37			success, reason = DICOM_decompress(file, decompressed_file)
38
39			logger.info(reason)
40
41			if success:
42			success_counter += 1
43			os.remove(decompressed_file) # restore the test environment to its former state.
44			logger.info("Successful.")
45			else:
46			fail_counter += 1
47			logger.info("Failed. Reason:" + reason)
48			assert success_counter == 7 # within the test data folder, there should be SEVEN files with JPEG in their name that CAN be successfully loaded.
			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 (147/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
49			assert fail_counter == 4 # within the test data folder, there should be FOUR files with JPEG in their name that CANNOT be successfully loaded.
			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 (146/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
50
51			def test_DICOM_validator():
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `test_DICOM_validator` 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...
52
53			file_name = get_test_DICOM_path()
54			success, data = DICOM_validator(file_name)
			0 ignored issues – show Unused Code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The variable `data` seems to be unused. Loading history...
55			assert success
56
57			file_name = get_testdata_files("README.txt")[0]
58			success, data = DICOM_validator(file_name)
59			assert not success
60
61			def test_DICOM_RequireDecompression():
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `test_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... 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...
62			assert not (DICOM_RequireDecompression('1.2.840.10008.1.2'))
			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...
63			assert not (DICOM_RequireDecompression('1.2.840.10008.1.2.1'))
			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...
64			assert not (DICOM_RequireDecompression('1.2.840.10008.1.2.2'))
			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...
65			assert (DICOM_RequireDecompression('1.2.840.10008.1.2.4'))
			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 `assert`. Loading history...
66			assert (DICOM_RequireDecompression('1.2.840.10008.1.2.4.57'))
			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 `assert`. Loading history...
67
68
69			class MyTestCase(unittest.TestCase):
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 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 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The variable `__class__` seems to be unused. Loading history...
70			def test_wrong_syntax(self):
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 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...
71			self.assertRaises(ValueError, DICOM_RequireDecompression, 'FakeTest')
72
73
74			def test_DICOM_anonymizer():
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `test_DICOM_anonymizer` 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...
75			file_names = get_testdata_files("emri")
76			for file_name in file_names:
77			success = DICOM_anonymizer(file_name, "CNBP0010001")
78			assert success
79			for file_name in file_names:
80			success, value = DICOM_retrieveElements(file_name, "PatientID")
81			assert success
82			assert (value == "CNBP0010001")
			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 `assert`. Loading history...
83
84
85			def test_DICOM_retrieveMRN():
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `test_DICOM_retrieveMRN` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This function should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
86			path = get_testdata_files("emri_small_big_endian")[0]
87			success, MRN = DICOM_retrieveMRN(path)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `MRN` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). 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...
88			assert success
89			assert (MRN == 'CNBP0010001')
			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 `assert`. Loading history...
90
91
92			def test_DICOM_update():
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `test_DICOM_update` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This function should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
93			path = get_testdata_files("emri")
94			for file in path:
95			success, _ = DICOM_updateElement(file, "PatientBirthDate", "19950101", file)
96			assert success
97
98			for file in path:
99			success, value = DICOM_retrieveElements(file, "PatientBirthDate")
100			assert success
101			assert(value == "19950101")
			0 ignored issues – show Unused Code Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report There is an unnecessary parenthesis after `assert`. Loading history...
102
103			def test_DICOM_computerScanAge():
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `test_DICOM_computerScanAge` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). 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...
104			logger = logging.getLogger("DICOM compute age")
105			path = get_testdata_files("emri_small_RLE")[0]
106			success, Age = DICOM_computeScanAge(path)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `Age` 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...
107			assert success
108			logger.info(Age.day)
109
110
111			if __name__ == '__main__':
112			test_DICOM_decompress()
			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)

test_DICOM_RequireDecompression() B

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