tomopy/tomopy

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Function remove_ring has 12 arguments (exceeds 4 allowed). Consider refactoring.
Open

def remove_ring(rec,
Severity: Major
Found in source/tomopy/misc/corr.py - About 1 hr to fix

    Function write_center has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
    Open

    def write_center(
            tomo, theta, dpath='tmp/center', cen_range=None, ind=None,
            mask=False, ratio=1., sinogram_order=False, algorithm='gridrec', filter_name='parzen'):
        """
        Save images reconstructed with a range of rotation centers.
    Severity: Minor
    Found in source/tomopy/recon/rotation.py - About 1 hr 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 _init_recon has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
    Open

    def _init_recon(shape, init_recon, val=1e-6, sharedmem=True, empty=False):
        if init_recon is None:
            if sharedmem:
                recon = dtype.empty_shared_array(shape)
                recon[:] = val
    Severity: Minor
    Found in source/tomopy/recon/algorithm.py - About 1 hr 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 find_slits_corners_aps_1id has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
    Open

    def find_slits_corners_aps_1id(img,
                                   method='quadrant+',
                                   medfilt2_kernel_size=3,
                                   medfilt_kernel_size=23,
                                   ):
    Severity: Minor
    Found in source/tomopy/prep/alignment.py - About 1 hr 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

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

        M0 = np.array([p['x0'], p['y0'], p['z0']], dtype=_dt).reshape(_shape)
    Severity: Major
    Found in source/tomopy/misc/phantom.py and 1 other location - About 1 hr to fix
    source/tomopy/misc/phantom.py on lines 415..415

    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 43.

    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_sirt(self):
            result = recon(self.prj, self.ang, algorithm='sirt', num_iter=4)
            assert_allclose(result, read_file('sirt.npy'), rtol=1e-2)
    Severity: Major
    Found in test/test_tomopy/test_recon/test_algorithm.py and 1 other location - About 1 hr to fix
    test/test_tomopy/test_recon/test_algorithm.py on lines 172..174

    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 43.

    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

        sc = np.array([p['a'], p['b'], p['c']], dtype=_dt).reshape(_shape)
    Severity: Major
    Found in source/tomopy/misc/phantom.py and 1 other location - About 1 hr to fix
    source/tomopy/misc/phantom.py on lines 414..414

    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 43.

    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_mlem(self):
            result = recon(self.prj, self.ang, algorithm='mlem', num_iter=4)
            assert_allclose(result, read_file('mlem.npy'), rtol=1e-2)
    Severity: Major
    Found in test/test_tomopy/test_recon/test_algorithm.py and 1 other location - About 1 hr to fix
    test/test_tomopy/test_recon/test_algorithm.py on lines 268..270

    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 43.

    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 project3 has 11 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def project3(
    Severity: Major
    Found in source/tomopy/sim/project.py - About 1 hr to fix

      Function ufo_dfi has 34 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

      def ufo_dfi(tomo, center, recon, theta, **kwargs):
          """
          Reconstruct object using UFO's Direct Fourier pipeline
          """
          import gi
      Severity: Minor
      Found in source/tomopy/recon/wrappers.py - About 1 hr to fix

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

            npad = ((0, 0), (pad[1], pad[1]), (pad[0], pad[0]))
        Severity: Major
        Found in source/tomopy/prep/alignment.py and 1 other location - About 1 hr to fix
        source/tomopy/prep/alignment.py on lines 293..293

        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 42.

        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

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

            npad = ((0, 0), (pad[1], pad[1]), (pad[0], pad[0]))
        Severity: Major
        Found in source/tomopy/prep/alignment.py and 1 other location - About 1 hr to fix
        source/tomopy/prep/alignment.py on lines 166..166

        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 42.

        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 main has 32 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

        def main(arg):
        
            import multiprocessing as mp
            default_ncores = mp.cpu_count()
            default_type = "partial"
        Severity: Minor
        Found in benchmarking/rec.py - About 1 hr to fix

          Function recon_accelerated has 10 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def recon_accelerated(
          Severity: Major
          Found in source/tomopy/recon/acceleration.py - About 1 hr to fix

            Function astra has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
            Open

            def astra(tomo, center, recon, theta, **kwargs):
                """
                Reconstruct object using the ASTRA toolbox
            
                Extra options
            Severity: Minor
            Found in source/tomopy/recon/wrappers.py - About 1 hr 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 write_center has 10 arguments (exceeds 4 allowed). Consider refactoring.
            Open

            def write_center(
            Severity: Major
            Found in source/tomopy/recon/rotation.py - About 1 hr to fix

              Function project2 has 10 arguments (exceeds 4 allowed). Consider refactoring.
              Open

              def project2(
              Severity: Major
              Found in source/tomopy/sim/project.py - About 1 hr to fix

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

                                coeff, _ = curve_fit(gauss1d, tmpx, tmpy,
                                                     p0=[tmpy[0], tmpx[0], 5.0],
                                                     maxfev=int(1e6),
                Severity: Major
                Found in source/tomopy/prep/alignment.py and 1 other location - About 1 hr to fix
                source/tomopy/prep/alignment.py on lines 666..668

                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 41.

                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

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

                                coeff, _ = curve_fit(gauss1d, tmpx, tmpy,
                                                     p0=[tmpy[0], tmpx[0], 5.0],
                                                     maxfev=int(1e6),
                Severity: Major
                Found in source/tomopy/prep/alignment.py and 1 other location - About 1 hr to fix
                source/tomopy/prep/alignment.py on lines 682..684

                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 41.

                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 run_pyctest has 31 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                def run_pyctest():
                    '''
                    Configure PyCTest and execute
                    '''
                    # run argparse, checkout source, copy over files
                Severity: Minor
                Found in pyctest_tomopy.py - About 1 hr to fix
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