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Showing 176 of 354 total issues

Function _search_fine has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

def _search_fine(sino, srad, step, init_cen, ratio, drop, ncore=None):
Severity: Major
Found in source/tomopy/recon/rotation.py - About 50 mins to fix

    Function stripes_mask3d has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def stripes_mask3d(weights,
    Severity: Major
    Found in source/tomopy/prep/stripe.py - About 50 mins to fix

      Function c_project3 has 7 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def c_project3(objx, objy, objz, center, tomo, theta, axis):
      Severity: Major
      Found in source/tomopy/util/extern/recon.py - About 50 mins to fix

        Function normalize has 7 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def normalize(
        Severity: Major
        Found in source/tomopy/prep/normalize.py - About 50 mins to fix

          Function remove_stripe_fw has 7 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def remove_stripe_fw(tomo,
          Severity: Major
          Found in source/tomopy/prep/stripe.py - About 50 mins to fix

            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
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