tomopy/tomopy

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File rec.py has 308 lines of code (exceeds 250 allowed). Consider refactoring.
Open

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

"""
TomoPy script to reconstruct a TomoBank file
Severity: Minor
Found in benchmarking/rec.py - About 3 hrs to fix

    File algorithm.py has 307 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/algorithm.py - About 3 hrs to fix

      Function astra_rec has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
      Open

      def astra_rec(tomo, center, recon, theta, vol_geom, niter, proj_type, gpu_index, opts):
          # Lazy import ASTRA
          import astra as astra_mod
          nslices, nang, ndet = tomo.shape
          cfg = astra_mod.astra_dict(opts['method'])
      Severity: Minor
      Found in source/tomopy/recon/wrappers.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

      Identical blocks of code found in 3 locations. Consider refactoring.
      Open

          if pad is True:
              dx = _round_to_even(np.sqrt(ox * ox + oz * oz) + 2)
          elif pad is False:
              dx = ox
      Severity: Major
      Found in source/tomopy/sim/project.py and 2 other locations - About 3 hrs to fix
      source/tomopy/sim/project.py on lines 218..221
      source/tomopy/sim/project.py on lines 288..291

      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 65.

      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 3 locations. Consider refactoring.
      Open

          if pad is True:
              dx = _round_to_even(np.sqrt(ox * ox + oz * oz) + 2)
          elif pad is False:
              dx = ox
      Severity: Major
      Found in source/tomopy/sim/project.py and 2 other locations - About 3 hrs to fix
      source/tomopy/sim/project.py on lines 288..291
      source/tomopy/sim/project.py on lines 355..358

      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 65.

      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 3 locations. Consider refactoring.
      Open

          if pad is True:
              dx = _round_to_even(np.sqrt(ox * ox + oz * oz) + 2)
          elif pad is False:
              dx = ox
      Severity: Major
      Found in source/tomopy/sim/project.py and 2 other locations - About 3 hrs to fix
      source/tomopy/sim/project.py on lines 218..221
      source/tomopy/sim/project.py on lines 355..358

      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 65.

      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(found_opencv, "CPU acceleration requires OpenCV.")
          def test_mlem_accel(self):
              result = recon(self.prj, self.ang, algorithm='mlem', num_iter=4,
                             accelerated=True, device='cpu', ncore=1, pool_size=3)
              assert_allclose(result, read_file('mlem_accel.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 178..182

      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 64.

      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(found_opencv, "CPU acceleration requires OpenCV.")
          def test_sirt_accel(self):
              result = recon(self.prj, self.ang, algorithm='sirt', num_iter=4,
                             accelerated=True, device='cpu', ncore=1, pool_size=3)
              assert_allclose(result, read_file('sirt_accel.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 137..141

      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 64.

      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 mproc.py has 292 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/mproc.py - About 3 hrs to fix

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

        def remove_neg(arr, val=0., ncore=None):
            """
            Replace negative values in array with a given value.
        
            Parameters
        Severity: Major
        Found in source/tomopy/misc/corr.py and 1 other location - About 3 hrs to fix
        source/tomopy/misc/corr.py on lines 302..326

        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 62.

        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

            if size is None:
                if tomo.shape[2] > 2000:
                    size = 21
                else:
                    size = max(5, int(0.01 * tomo.shape[2]))
        Severity: Major
        Found in source/tomopy/prep/stripe.py and 1 other location - About 3 hrs to fix
        source/tomopy/prep/stripe.py on lines 418..422

        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 62.

        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 remove_nan(arr, val=0., ncore=None):
            """
            Replace NaN values in array with a given value.
        
            Parameters
        Severity: Major
        Found in source/tomopy/misc/corr.py and 1 other location - About 3 hrs to fix
        source/tomopy/misc/corr.py on lines 329..352

        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 62.

        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

            if size is None:
                if tomo.shape[2] > 2000:
                    size = 21
                else:
                    size = max(5, int(0.01 * tomo.shape[2]))
        Severity: Major
        Found in source/tomopy/prep/stripe.py and 1 other location - About 3 hrs to fix
        source/tomopy/prep/stripe.py on lines 498..502

        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 62.

        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 find_python_coverage():
            """
            Find the python coverage script
            """
            pypath = os.path.dirname(pyctest.PYTHON_EXECUTABLE)
        Severity: Major
        Found in benchmarking/__init__.py and 1 other location - About 2 hrs to fix
        benchmarking/__init__.py on lines 115..123

        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 61.

        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 find_python_nosetest():
            """
            Find the python nosetests script
            """
            pypath = os.path.dirname(pyctest.PYTHON_EXECUTABLE)
        Severity: Major
        Found in benchmarking/__init__.py and 1 other location - About 2 hrs to fix
        benchmarking/__init__.py on lines 126..134

        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 61.

        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

                if debug:
                    print('iter=' + str(n) + ', err=' + str(np.linalg.norm(err)))
                    conv[n] = np.linalg.norm(err)
        Severity: Major
        Found in source/tomopy/prep/alignment.py and 1 other location - About 2 hrs to fix
        source/tomopy/prep/alignment.py on lines 202..204

        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 60.

        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

                if debug:
                    print('iter=' + str(n) + ', err=' + str(np.linalg.norm(err)))
                    conv[n] = np.linalg.norm(err)
        Severity: Major
        Found in source/tomopy/prep/alignment.py and 1 other location - About 2 hrs to fix
        source/tomopy/prep/alignment.py on lines 341..343

        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 60.

        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 pad has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
        Open

        def pad(arr, axis, npad=None, mode='constant', ncore=None, **kwargs):
            """
            Pad an array along specified axis.
        
            Parameters
        Severity: Minor
        Found in source/tomopy/misc/morph.py - About 2 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

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

            for m in range(tomo.shape[1]):
                sino = tomo[:, m, :]
                tomo[:, m, :] = _rs_filter(
                    sino, window, listsign, size, dim, pad)
        Severity: Major
        Found in source/tomopy/prep/stripe.py and 1 other location - About 2 hrs to fix
        source/tomopy/prep/stripe.py on lines 740..742

        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 57.

        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 remove_large_stripe(tomo, snr=3, size=51, drop_ratio=0.1, norm=True,
                                ncore=None, nchunk=None):
            """
            Remove large stripe artifacts from sinogram using Nghia Vo's
            approach :cite:`Vo:18` (algorithm 5).
        Severity: Major
        Found in source/tomopy/prep/stripe.py and 1 other location - About 2 hrs to fix
        source/tomopy/prep/stripe.py on lines 865..901

        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 57.

        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

        Severity
        Category
        Status
        Source
        Language