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"

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

Open

def c_inpainter(

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

Open

def recon_accelerated(

Function remove_outlier3d has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

def remove_outlier3d(arr, dif, size=3, ncore=None):
    """
    Selectively applies 3D median filter to a 3D array to remove outliers. Also
    called a dezinger.

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

Open

def write_center(

Function median_filter3d has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

def median_filter3d(arr, size=3, ncore=None):
    """
    Apply 3D median filter to a 3D array.

    .. versionadded:: 1.13

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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

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

Open

def project2(

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

Function ufo_fbp has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def ufo_fbp(tomo, center, recon, theta, **kwargs):
    """
    Reconstruct object using UFO's FBP pipeline
    """
    import gi

Function vector2 has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

def vector2(tomo1, tomo2, theta1, theta2, center1=None, center2=None, num_iter=1, axis1=1, axis2=2):

Function astra_rec has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

def astra_rec(tomo, center, recon, theta, vol_geom, niter, proj_type, gpu_index, opts):

Function find_center_vo has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

def find_center_vo(tomo, ind=None, smin=-50, smax=50, srad=6, step=0.25,

Function lpmultigpu has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

def lpmultigpu(lp, lpmethod, recon, tomo, num_iter, reg_par, gpu_list, lock, ids):

Function recon has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

def recon(tomo,

Function reconstruct has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def reconstruct(h5fname, sino, rot_center, args, blocked_views=None):

    # not setting this will cause issues on supercomputers
    # allow user to override though
    os.environ.setdefault("OMP_NUM_THREADS", "1")

Function stripes_detect3d has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

def stripes_detect3d(tomo, size=10, radius=3, ncore=None):
    """
    Detect stripes in a 3D array. Usually applied to normalized projection
    data. The algorithm is presented in the paper :cite:`Kazantsev:23`.

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Function output_images has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

def output_images(rec, fpath, format="jpeg", scale=1, ncol=1):
    """Save an image stack as a series of concatenated images.

    Each set of ncol images are concatenated horizontally and saved together
    into files named {fpath}_0_{ncol}.{img_format},

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Function align_seq has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

def align_seq(
        prj, ang, fdir='.', iters=10, pad=(0, 0),
        blur=True, center=None, algorithm='sirt',
        upsample_factor=10, rin=0.5, rout=0.8,
        save=False, debug=True):

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Function build_name_append has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

def build_name_append(item, separate=True, prefix="[", suffix="]", check=True, reset=False):
    if reset:
        pyctest.BUILD_NAME = ""
    # if not list, check if is None
    if item is None or not item:

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