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Similar blocks of code found in 2 locations. Consider refactoring.
Open

    def test_remove_stripe_based_interpolation(self):
        mat = np.random.rand(self.size, self.size)
        lis_off = np.linspace(0, 1, self.size)
        mat[:, self.b:self.e] = 6.0
        mat_corr = srm.remove_stripe_based_interpolation(
Severity: Major
Found in test/test_tomopy/test_prep/test_stripe.py and 1 other location - About 1 day to fix
test/test_tomopy/test_prep/test_stripe.py on lines 121..128

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 144.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    def test_remove_dead_stripe(self):
        mat = np.random.rand(self.size, self.size)
        lis_off = np.linspace(0, 1, self.size)
        mat[:, self.b:self.e] = 6.0
        mat_corr = srm.remove_dead_stripe(
Severity: Major
Found in test/test_tomopy/test_prep/test_stripe.py and 1 other location - About 1 day to fix
test/test_tomopy/test_prep/test_stripe.py on lines 140..147

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 144.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

File corr.py has 572 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# #########################################################################
# Copyright (c) 2015-2019, UChicago Argonne, LLC. All rights reserved.    #
Severity: Major
Found in source/tomopy/misc/corr.py - About 1 day to fix

    File rotation.py has 469 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    #!/usr/bin/env python
# -*- coding: utf-8 -*-

# #########################################################################
# Copyright (c) 2015-2019, UChicago Argonne, LLC. All rights reserved.    #
    Severity: Minor
    Found in source/tomopy/recon/rotation.py - About 7 hrs to fix

      File recon.py has 443 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      #!/usr/bin/env python
# -*- coding: utf-8 -*-

# #########################################################################
# Copyright (c) 2015-2019, UChicago Argonne, LLC. All rights reserved.    #
      Severity: Minor
      Found in source/tomopy/util/extern/recon.py - About 6 hrs to fix

        Function distribute_jobs has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.
        Open

        def distribute_jobs(arr,
                    func,
                    axis,
                    args=None,
                    kwargs=None,
        Severity: Minor
        Found in source/tomopy/util/mproc.py - About 5 hrs to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Function recon has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
        Open

        def recon(
        tomo, theta, center=None, sinogram_order=False, algorithm=None,
        init_recon=None, ncore=None, nchunk=None, **kwargs):
    """
    Reconstruct object from projection data.
        Severity: Minor
        Found in source/tomopy/recon/algorithm.py - About 4 hrs to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        File project.py has 360 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        #!/usr/bin/env python
# -*- coding: utf-8 -*-

# #########################################################################
# Copyright (c) 2015-2019, UChicago Argonne, LLC. All rights reserved.    #
        Severity: Minor
        Found in source/tomopy/sim/project.py - About 4 hrs to fix

          Similar blocks of code found in 7 locations. Consider refactoring.
          Open

              def test_peppers(self):
        assert_equals(peppers().dtype, 'float32')
        assert_equals(peppers().shape, (1, 512, 512))
        assert_equals(peppers(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(peppers(size=64).shape, (1, 64, 64))
          Severity: Major
          Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
          test/test_tomopy/test_misc/test_phantom.py on lines 63..67
          test/test_tomopy/test_misc/test_phantom.py on lines 69..73
          test/test_tomopy/test_misc/test_phantom.py on lines 75..79
          test/test_tomopy/test_misc/test_phantom.py on lines 81..85
          test/test_tomopy/test_misc/test_phantom.py on lines 87..91
          test/test_tomopy/test_misc/test_phantom.py on lines 99..103

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 77.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          Similar blocks of code found in 7 locations. Consider refactoring.
          Open

              def test_shepp2d(self):
        assert_equals(shepp2d().dtype, 'float32')
        assert_equals(shepp2d().shape, (1, 512, 512))
        assert_equals(shepp2d(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(shepp2d(size=64).shape, (1, 64, 64))
          Severity: Major
          Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
          test/test_tomopy/test_misc/test_phantom.py on lines 63..67
          test/test_tomopy/test_misc/test_phantom.py on lines 69..73
          test/test_tomopy/test_misc/test_phantom.py on lines 75..79
          test/test_tomopy/test_misc/test_phantom.py on lines 81..85
          test/test_tomopy/test_misc/test_phantom.py on lines 87..91
          test/test_tomopy/test_misc/test_phantom.py on lines 93..97

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 77.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          Similar blocks of code found in 7 locations. Consider refactoring.
          Open

              def test_checkerboard(self):
        assert_equals(checkerboard().dtype, 'float32')
        assert_equals(checkerboard().shape, (1, 512, 512))
        assert_equals(checkerboard(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(checkerboard(size=64).shape, (1, 64, 64))
          Severity: Major
          Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
          test/test_tomopy/test_misc/test_phantom.py on lines 63..67
          test/test_tomopy/test_misc/test_phantom.py on lines 69..73
          test/test_tomopy/test_misc/test_phantom.py on lines 75..79
          test/test_tomopy/test_misc/test_phantom.py on lines 87..91
          test/test_tomopy/test_misc/test_phantom.py on lines 93..97
          test/test_tomopy/test_misc/test_phantom.py on lines 99..103

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 77.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          Similar blocks of code found in 7 locations. Consider refactoring.
          Open

              def test_cameraman(self):
        assert_equals(cameraman().dtype, 'float32')
        assert_equals(cameraman().shape, (1, 512, 512))
        assert_equals(cameraman(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(cameraman(size=64).shape, (1, 64, 64))
          Severity: Major
          Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
          test/test_tomopy/test_misc/test_phantom.py on lines 63..67
          test/test_tomopy/test_misc/test_phantom.py on lines 69..73
          test/test_tomopy/test_misc/test_phantom.py on lines 81..85
          test/test_tomopy/test_misc/test_phantom.py on lines 87..91
          test/test_tomopy/test_misc/test_phantom.py on lines 93..97
          test/test_tomopy/test_misc/test_phantom.py on lines 99..103

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 77.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          Similar blocks of code found in 7 locations. Consider refactoring.
          Open

              def test_lena(self):
        assert_equals(lena().dtype, 'float32')
        assert_equals(lena().shape, (1, 512, 512))
        assert_equals(lena(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(lena(size=64).shape, (1, 64, 64))
          Severity: Major
          Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
          test/test_tomopy/test_misc/test_phantom.py on lines 63..67
          test/test_tomopy/test_misc/test_phantom.py on lines 69..73
          test/test_tomopy/test_misc/test_phantom.py on lines 75..79
          test/test_tomopy/test_misc/test_phantom.py on lines 81..85
          test/test_tomopy/test_misc/test_phantom.py on lines 93..97
          test/test_tomopy/test_misc/test_phantom.py on lines 99..103

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 77.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          Similar blocks of code found in 7 locations. Consider refactoring.
          Open

              def test_baboon(self):
        assert_equals(baboon().dtype, 'float32')
        assert_equals(baboon().shape, (1, 512, 512))
        assert_equals(baboon(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(baboon(size=64).shape, (1, 64, 64))
          Severity: Major
          Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
          test/test_tomopy/test_misc/test_phantom.py on lines 69..73
          test/test_tomopy/test_misc/test_phantom.py on lines 75..79
          test/test_tomopy/test_misc/test_phantom.py on lines 81..85
          test/test_tomopy/test_misc/test_phantom.py on lines 87..91
          test/test_tomopy/test_misc/test_phantom.py on lines 93..97
          test/test_tomopy/test_misc/test_phantom.py on lines 99..103

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 77.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          Similar blocks of code found in 7 locations. Consider refactoring.
          Open

              def test_barbara(self):
        assert_equals(barbara().dtype, 'float32')
        assert_equals(barbara().shape, (1, 512, 512))
        assert_equals(barbara(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(barbara(size=64).shape, (1, 64, 64))
          Severity: Major
          Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
          test/test_tomopy/test_misc/test_phantom.py on lines 63..67
          test/test_tomopy/test_misc/test_phantom.py on lines 75..79
          test/test_tomopy/test_misc/test_phantom.py on lines 81..85
          test/test_tomopy/test_misc/test_phantom.py on lines 87..91
          test/test_tomopy/test_misc/test_phantom.py on lines 93..97
          test/test_tomopy/test_misc/test_phantom.py on lines 99..103

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 77.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          File phantom.py has 337 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          #!/usr/bin/env python
# -*- coding: utf-8 -*-

# #########################################################################
# Copyright (c) 2015-2019, UChicago Argonne, LLC. All rights reserved.    #
          Severity: Minor
          Found in source/tomopy/misc/phantom.py - About 4 hrs to fix

            File wrappers.py has 335 lines of code (exceeds 250 allowed). Consider refactoring.
            Open

            #!/usr/bin/env python
# -*- coding: utf-8 -*-

# #########################################################################
# Copyright (c) 2015-2019, UChicago Argonne, LLC. All rights reserved.    #
            Severity: Minor
            Found in source/tomopy/recon/wrappers.py - About 4 hrs to fix

              Similar blocks of code found in 2 locations. Consider refactoring.
              Open

                  @unittest.skipUnless("CUDA_VERSION" in os.environ, "CUDA_VERSION not set.")
    def test_sirt_gpu(self):
        result = recon(self.prj, self.ang, algorithm='sirt', num_iter=4,
                       accelerated=True, device='gpu', ncore=1, pool_size=3)
        assert_allclose(result, read_file('sirt_accel_gpu.npy'), rtol=1e-2)
              Severity: Major
              Found in test/test_tomopy/test_recon/test_algorithm.py and 1 other location - About 3 hrs to fix
              test/test_tomopy/test_recon/test_algorithm.py on lines 143..147

              Duplicated Code

              Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

              Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

              When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

              Tuning

              This issue has a mass of 72.

              We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

              The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

              If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

              See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

              Refactorings

              Further Reading

              Similar blocks of code found in 2 locations. Consider refactoring.
              Open

                  @unittest.skipUnless("CUDA_VERSION" in os.environ, "CUDA_VERSION not set.")
    def test_mlem_gpu(self):
        result = recon(self.prj, self.ang, algorithm='mlem', num_iter=4,
                       accelerated=True, device='gpu', ncore=1, pool_size=3)
        assert_allclose(result, read_file('mlem_accel_gpu.npy'), rtol=1e-2)
              Severity: Major
              Found in test/test_tomopy/test_recon/test_algorithm.py and 1 other location - About 3 hrs to fix
              test/test_tomopy/test_recon/test_algorithm.py on lines 184..188

              Duplicated Code

              Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

              Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

              When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

              Tuning

              This issue has a mass of 72.

              We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

              The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

              If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

              See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

              Refactorings

              Further Reading

              Function configure has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
              Open

              def configure():
    # set site if set in environ
    if os.environ.get("CTEST_SITE") is not None:
        pyctest.CTEST_SITE = os.environ.get("CTEST_SITE")
              Severity: Minor
              Found in pyctest_tomopy.py - About 3 hrs to fix

              Cognitive Complexity

              Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

              A method's cognitive complexity is based on a few simple rules:

              • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
              • Code is considered more complex for each "break in the linear flow of the code"
              • Code is considered more complex when "flow breaking structures are nested"

              Further reading

              Severity
              Category
              Status
              Source
              Language