Function create_json has a Cognitive Complexity of 47 (exceeds 5 allowed). Consider refactoring.

Open

def create_json(bucket, path, threads, jobdir, group=False, credentials=None,
                debug=False, dataset=None, log=False):
    """
    Takes parameters to make jsons
    """

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Function make_panel_plot has a Cognitive Complexity of 43 (exceeds 5 allowed). Consider refactoring.

Open

def make_panel_plot(basepath, outf, dataset=None, atlas=None, minimal=True,
                    log=True, hemispheres=True):
    fnames = [name for name in os.listdir(basepath)
              if os.path.splitext(name)[1] == '.pkl']
    fnames = sorted(fnames)

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Function main has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

def main():
    parser = ArgumentParser(description="This is an end-to-end connectome \
                            estimation pipeline from sMRI and DTI images")

    parser.add_argument('bids_dir', help='The directory with the input dataset'

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Function convert has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.

Open

def convert(indir, outdir,  verbose=False):
    """
    Takes in nifti images, creates directory structure desired by ndstore
    ingest, and then converts niftis to png stacks. This script should be
    called prior to ingesting MR data into ndstore.

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File register.py has 278 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/usr/bin/env python

# Copyright 2016 NeuroData (http://neurodata.io)
#
# Licensed under the Apache License, Version 2.0 (the "License");

File ndmg_cloud.py has 263 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/usr/bin/env python

# Copyright 2016 NeuroData (http://neurodata.io)
#
# Licensed under the Apache License, Version 2.0 (the "License");

Function compute_metrics has 46 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def compute_metrics(fs, outdir, atlas, verb=False):
    """
    Given a set of files and a directory to put things, loads graphs and
    performs set of analyses on them, storing derivatives in a pickle format
    in the desired output location.

Function make_graph has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def make_graph(self, streamlines, attr=None):
        """
        Takes streamlines and produces a graph

        **Positional Arguments:**

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Function plot_overlays has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

def plot_overlays(atlas, b0, cmaps):
    plt.rcParams.update({'axes.labelsize': 'x-large',
                         'axes.titlesize': 'x-large'})

    if b0.shape == (182, 218, 182):

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Function plot_rgb has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

def plot_rgb(im):
    plt.rcParams.update({'axes.labelsize': 'x-large',
                         'axes.titlesize': 'x-large'})

    if im.shape == (182, 218, 182):

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Function crawl_bids_directory has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

def crawl_bids_directory(inDir, subjs, sesh):
    """
    Given a BIDS directory and optionally list of sessions and subjects,
    crawls the path and returns pointers to all relevant files for analysis.
    """

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Function main has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def main():
    parser = ArgumentParser(description="This is an end-to-end connectome \
                            estimation pipeline from sMRI and DTI images")

    parser.add_argument('bids_dir', help='The directory with the input dataset'

Function ndmg_dwi_pipeline has 33 lines of code (exceeds 25 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
    """

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

Open

def ndmg_dwi_pipeline(dwi, bvals, bvecs, mprage, atlas, mask, labels, outdir,

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

Open

def main():

    ni = NI.NDIngest()

    """

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

Open

def create_json(bucket, path, threads, jobdir, group=False, credentials=None,

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

Open

    def align(self, inp, ref, xfm=None, out=None, dof=12, searchrad=True,

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

Open

def main():
    parser = ArgumentParser(description="This is an end-to-end connectome \
                            estimation pipeline from sMRI and DTI images")

    parser.add_argument('state', choices=['session',

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

Open

def batch_submit(bucket, path, jobdir, credentials=None, state='session',

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

Open

def group_level(inDir, outDir, dataset=None, atlas=None, minimal=False,