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ndmg/register/register.py

Summary

Maintainability
C
1 day
Test Coverage

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");
Severity: Minor
Found in ndmg/register/register.py - About 2 hrs to fix

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

        def align(self, inp, ref, xfm=None, out=None, dof=12, searchrad=True,
    Severity: Major
    Found in ndmg/register/register.py - About 1 hr to fix

      Function func2atlas has 8 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def func2atlas(self, func, t1w, atlas, atlas_brain, atlas_mask,
      Severity: Major
      Found in ndmg/register/register.py - About 1 hr 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 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 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 align has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
              Open

                  def align(self, inp, ref, xfm=None, out=None, dof=12, searchrad=True,
              bins=256, interp=None, cost="mutualinfo"):
        """
        Aligns two images and stores the transform between them
              Severity: Minor
              Found in ndmg/register/register.py - About 35 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

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

                  def align_epi(self, epi, t1, brain, out):
        """
        Algins EPI images to T1w image
        """
        cmd = 'epi_reg --epi={} --t1={} --t1brain={} --out={}'
              Severity: Major
              Found in ndmg/register/register.py and 1 other location - About 1 hr to fix
              ndmg/register/register.py on lines 116..133

              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 45.

              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 applyxfm(self, inp, ref, xfm, aligned):
        """
        Aligns two images with a given transform

        **Positional Arguments:**
              Severity: Major
              Found in ndmg/register/register.py and 1 other location - About 1 hr to fix
              ndmg/register/register.py on lines 83..89

              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 45.

              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

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