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Showing 44 of 78 total issues

Function batch_submit has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

def batch_submit(bucket, path, jobdir, credentials=None, state='session',
Severity: Major
Found in ndmg/scripts/ndmg_cloud.py - About 1 hr to fix

    Function group_level has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

    def group_level(inDir, outDir, dataset=None, atlas=None, minimal=False,
                log=False, hemispheres=False, dwi=True):
    """
    Crawls the output directory from ndmg and computes qc metrics on the
    derivatives produced
    Severity: Minor
    Found in ndmg/scripts/ndmg_bids.py - About 55 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 crawl_bucket has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

    def crawl_bucket(bucket, path, group=False):
    """
    Gets subject list for a given S3 bucket and path
    """
    if group:
    Severity: Minor
    Found in ndmg/scripts/ndmg_cloud.py - About 55 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 ndmg_dwi_pipeline has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

    def ndmg_dwi_pipeline(dwi, bvals, bvecs, mprage, atlas, mask, labels, outdir,
                  clean=False, fmt='edgelist'):
    """
    Creates a brain graph from MRI data
    """
    Severity: Minor
    Found in ndmg/scripts/ndmg_dwi_pipeline.py - About 55 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 loadGraphs has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

    def loadGraphs(filenames, verb=False):
    """
    Given a list of files, returns a dictionary of graphs

    Required parameters:
    Severity: Minor
    Found in ndmg/utils/loadGraphs.py - About 55 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 session_level has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def session_level(inDir, outDir, subjs, sesh=None, debug=False,
    Severity: Major
    Found in ndmg/scripts/ndmg_bids.py - About 50 mins to fix

      Function dwi2atlas has 7 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def dwi2atlas(self, dwi, gtab, t1w, atlas,
      Severity: Major
      Found in ndmg/register/register.py - About 50 mins to fix

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

        def make_panel_plot(basepath, outf, dataset=None, atlas=None, minimal=True,
        Severity: Major
        Found in ndmg/stats/qa_graphs_plotting.py - About 50 mins to fix

          Avoid deeply nested control flow statements.
          Open

                              if verbose:
                        print "Saving slice:", slices
                    imsave(dirname + '/%04d.png' % slices,
          Severity: Major
          Found in ndmg/utils/nifti_to_png.py - About 45 mins to fix

            Avoid deeply nested control flow statements.
            Open

                                if sesh is not None:
                        tpath = op.join(remo, 'sub-{}'.format(sub), 'ses-{}'.format(sesh))
                        tindir = op.join(inDir, 'sub-{}'.format(sub), 'ses-{}'.format(sesh))
                    else:
                        tpath = op.join(remo, 'sub-{}'.format(sub))
            Severity: Major
            Found in ndmg/scripts/ndmg_bids.py - About 45 mins to fix

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

                  def apply_warp(self, inp, out, ref, warp, xfm=None, mask=None):
              Severity: Minor
              Found in ndmg/register/register.py - About 45 mins to fix

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

                def visualize_fibs(fibs, fibfile, atlasfile, outdir, opacity, num_samples):
                Severity: Minor
                Found in ndmg/stats/qa_fibers.py - About 45 mins to fix

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

                  def reg_mri_pngs(mri, atlas, outdir, loc=0, mean=False, dim=4):
                  Severity: Minor
                  Found in ndmg/stats/qa_reg.py - About 45 mins to fix

                    Function align_nonlinear has 5 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                        def align_nonlinear(self, inp, ref, xfm, warp, mask=None):
                    Severity: Minor
                    Found in ndmg/register/register.py - About 35 mins to fix

                      Function plot_degrees has 5 arguments (exceeds 4 allowed). Consider refactoring.
                      Open

                      def plot_degrees(dats, name=None, ylab=None, xlab=None, hemi=True):
                      Severity: Minor
                      Found in ndmg/stats/plotly_helper.py - About 35 mins to fix

                        Function s3_push_data has 5 arguments (exceeds 4 allowed). Consider refactoring.
                        Open

                        def s3_push_data(bucket, remote, outDir, modifier, creds=True):
                        Severity: Minor
                        Found in ndmg/utils/bids.py - About 35 mins to fix

                          Function plot_density has 5 arguments (exceeds 4 allowed). Consider refactoring.
                          Open

                          def plot_density(xs, ys, name=None, ylab=None, xlab=None):
                          Severity: Minor
                          Found in ndmg/stats/plotly_helper.py - About 35 mins to fix

                            Function plot_series has 5 arguments (exceeds 4 allowed). Consider refactoring.
                            Open

                            def plot_series(dats, name=None, ylab=None, xlab=None, sort=False):
                            Severity: Minor
                            Found in ndmg/stats/plotly_helper.py - About 35 mins to fix

                              Function tensor2fa has 5 arguments (exceeds 4 allowed). Consider refactoring.
                              Open

                              def tensor2fa(tensors, tensor_name, dwi, derivdir, qcdir):
                              Severity: Minor
                              Found in ndmg/stats/qa_tensor.py - About 35 mins to fix

                                Function setup has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                Open

                                def setup(inDir, dwiListFile, bvalListFile, bvecListFile, mprageListFile):
                                Severity: Minor
                                Found in ndmg/scripts/ndmg_setup.py - About 35 mins to fix
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