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

    def ifft2(x, s=None, axes=(-2,-1), overwrite_input=False, extra_info=None):
        return np.fft.ifft2(x, s=s, axes=axes)
Severity: Minor
Found in source/tomopy/util/misc.py and 1 other location - About 50 mins to fix
source/tomopy/util/misc.py on lines 148..149

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 36.

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 not sinogram_order:
        # rotate to radiograph order
        tomo = np.swapaxes(tomo, 0, 1)  # doesn't copy data
        # copy data to sharedmem
        tomo = dtype.as_sharedmem(tomo, copy=True)
Severity: Major
Found in source/tomopy/sim/project.py and 2 other locations - About 50 mins to fix
source/tomopy/sim/project.py on lines 331..335
source/tomopy/sim/project.py on lines 396..400

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 36.

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 not sinogram_order:
        # rotate to radiograph order
        tomo = np.swapaxes(tomo, 0, 1)  # doesn't copy data
        # copy data to sharedmem
        tomo = dtype.as_sharedmem(tomo, copy=True)
Severity: Major
Found in source/tomopy/sim/project.py and 2 other locations - About 50 mins to fix
source/tomopy/sim/project.py on lines 396..400
source/tomopy/sim/project.py on lines 464..468

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 36.

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 fft2(x, s=None, axes=(-2,-1), overwrite_input=False, extra_info=None):
        return np.fft.fft2(x, s=s, axes=axes)
Severity: Minor
Found in source/tomopy/util/misc.py and 1 other location - About 50 mins to fix
source/tomopy/util/misc.py on lines 152..153

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 36.

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 remove_dead_stripe has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

def remove_dead_stripe(tomo,
Severity: Minor
Found in source/tomopy/prep/stripe.py - About 45 mins to fix

    Function _calc_proj_cnrs has 6 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def _calc_proj_cnrs(imgs,
    Severity: Minor
    Found in source/tomopy/prep/alignment.py - About 45 mins to fix

      Function _ellipsoid has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
      Open

      def _ellipsoid(params, shape=None, out=None, coords=None):
    """
    Generate a cube containing an ellipsoid defined by its parameters.
    If out is given, fills the given cube instead of creating a new one.
    """
      Severity: Minor
      Found in source/tomopy/misc/phantom.py - About 45 mins 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__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(self, ncompare, nslice, nrows, ncols, solution=None, dtype=float):
      Severity: Minor
      Found in source/tomopy/misc/benchmark.py - About 45 mins to fix

        Function _search_coarse has 6 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def _search_coarse(sino, smin, smax, ratio, drop, ncore=None):
        Severity: Minor
        Found in source/tomopy/recon/rotation.py - About 45 mins to fix

          Function distortion_correction_proj has 6 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def distortion_correction_proj(tomo, xcenter, ycenter, list_fact,
          Severity: Minor
          Found in source/tomopy/prep/alignment.py - About 45 mins to fix

            Function find_center_vo has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
            Open

            def find_center_vo(tomo, ind=None, smin=-50, smax=50, srad=6, step=0.25,
                   ratio=0.5, drop=20, ncore=None):
    """
    Find rotation axis location using Nghia Vo's method. :cite:`Vo:14`.
            Severity: Minor
            Found in source/tomopy/recon/rotation.py - About 45 mins 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 get_ncore_nchunk has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
            Open

            def get_ncore_nchunk(axis_size, ncore=None, nchunk=None):
    # limit chunk size to size of array along axis
    if nchunk and nchunk > axis_size:
        nchunk = axis_size
    # default ncore to max and limit number of cores to max number
            Severity: Minor
            Found in source/tomopy/util/mproc.py - About 45 mins 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 c_vector has 6 arguments (exceeds 4 allowed). Consider refactoring.
            Open

            def c_vector(tomo, center, recon1, recon2, theta, **kwargs):
            Severity: Minor
            Found in source/tomopy/util/extern/recon.py - About 45 mins to fix

              Function recon_accelerated has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
              Open

              def recon_accelerated(
        tomo, theta, center=None, emission=True, algorithm=None, hardware=None,
        implementation=None, acc_option=None, init_recon=None, **kwargs):
    """
    Reconstruct object from projection data using hardware acceleration.
              Severity: Minor
              Found in source/tomopy/recon/acceleration.py - About 45 mins 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 get_worker_ncore_slices has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
              Open

              def get_worker_ncore_slices(axis_size, ncore=None, nchunk=None):
    # default ncore to max (also defaults ncore == 0)
    if not ncore:
        ncore = mp.cpu_count()
    if nchunk is None:
              Severity: Minor
              Found in source/tomopy/util/mproc.py - About 45 mins 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 remove_outlier_cuda has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
              Open

              def remove_outlier_cuda(arr, dif, size=3, axis=0):
    """
    Remove high intensity bright spots from a 3D array along axis 0
    dimension using GPU.
              Severity: Minor
              Found in source/tomopy/misc/corr.py - About 45 mins 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 remove_outlier1d has 6 arguments (exceeds 4 allowed). Consider refactoring.
              Open

              def remove_outlier1d(arr, dif, size=3, axis=0, ncore=None, out=None):
              Severity: Minor
              Found in source/tomopy/misc/corr.py - About 45 mins to fix

                Function _calculate_metric has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
                Open

                def _calculate_metric(shift_col, sino1, sino2, sino3, mask):
    """
    Metric calculation.
    """
    shift_col = 1.0 * np.squeeze(shift_col)
                Severity: Minor
                Found in source/tomopy/recon/rotation.py - About 45 mins 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

                Avoid deeply nested control flow statements.
                Open

                                        if any(proc.exitcode for proc in proclist):
                            p.terminate()
                            raise RuntimeError(
                                "Child process terminated before finishing")
                        res.wait(timeout=1)
                Severity: Major
                Found in source/tomopy/util/mproc.py - About 45 mins to fix

                  Function _rs_large has 6 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                  def _rs_large(sinogram, snr, size, matindex, drop_ratio=0.1, norm=True):
                  Severity: Minor
                  Found in source/tomopy/prep/stripe.py - About 45 mins to fix
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