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tomography/xdesign

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src/xdesign/plot.py

Summary

Maintainability
F
3 days
Test Coverage

Function plot_phantom has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
Open

def plot_phantom(
    phantom,
    axis=None,
    labels=None,
    c_props=[],
Severity: Minor
Found in src/xdesign/plot.py - About 2 hrs 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 combine_grid has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

def combine_grid(Amin, A, Bmin, B):
    """Add grid B to grid A by aligning min corners and clipping B

    Parameters
    ----------
Severity: Minor
Found in src/xdesign/plot.py - About 1 hr 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 plot_histograms has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def plot_histograms(images, masks=None, thresh=0.025):
    """Plot the normalized histograms for the pixel intensity under each
    mask.

    Parameters
Severity: Minor
Found in src/xdesign/plot.py - About 1 hr 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_pie_glyphs has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

def get_pie_glyphs(xy, values, color='coverage', trace_normal=1, **kwargs):
    """Returns a list of pie glyphs at coordinates xy representing values

    The areas of the pie sectors are proportional to the elements of the
    vector that the glyph represents. The default color of the
Severity: Minor
Found in src/xdesign/plot.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

Function plot_geometry has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def plot_geometry(geometry, axis=None, alpha=None, c=None, z=0.0, t=0.0001):
    """Plot a :class:`.Entity` on the given axis.

    Parameters
    ----------
Severity: Minor
Found in src/xdesign/plot.py - About 25 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 discrete_geometry has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def discrete_geometry(geometry, psize, ratio=9):
    """Draw the geometry onto a patch the size of its bounding box.

    Parameters
    ----------
Severity: Minor
Found in src/xdesign/plot.py - About 25 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 plot_polygon(polygon, axis=None, alpha=None, c=None):
    """Plot a :class:`.Polygon` to the given axis.

    Parameters
    ----------
Severity: Major
Found in src/xdesign/plot.py and 1 other location - About 1 day to fix
src/xdesign/plot.py on lines 518..546

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 149.

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 plot_curve(curve, axis=None, alpha=None, c=None):
    """Plot a :class:`.Curve` to the given axis.

    Parameters
    ----------
Severity: Major
Found in src/xdesign/plot.py and 1 other location - About 1 day to fix
src/xdesign/plot.py on lines 487..515

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 149.

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

Line too long (80 > 79 characters)
Open

    assert color.shape == (M, 4), "color is wrong shape, {}".format(color.shape)
Severity: Minor
Found in src/xdesign/plot.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (102 > 79 characters)
Open

    `Warren Weckesser <http://stackoverflow.com/questions/30639656/numpy-roll-in-several-dimensions>`_
Severity: Minor
Found in src/xdesign/plot.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

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