File utilities.py
has 491 lines of code (exceeds 250 allowed). Consider refactoring. Open
"""
General utils used for this collection of scripts
Copyright (C) 2014-2019 Jiri Borovec <jiri.borovec@fel.cvut.cz>
"""
Function figure_pair_images_landmarks
has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring. Open
def figure_pair_images_landmarks(pair_landmarks, pair_images, names=None,
max_fig_size=FIGURE_SIZE):
""" create a figure with image pair and connect related landmarks by line
:param (ndarray) pair_landmarks: set of landmark coordinates
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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 create_consensus_landmarks
has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring. Open
def create_consensus_landmarks(path_annots, min_size=False, method='mean'):
""" create a consensus on set of landmarks and return normalised to 100%
:param [str] path_annots: path to CSV landmarks
:param bool min_size: use only max number of common points, 56 & 65 -> 56
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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 collect_triple_dir
has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring. Open
def collect_triple_dir(paths_landmarks, path_dataset, path_out, coll_dirs=None,
scales=None, with_user=False):
""" collect all subdir up to level of scales with user annotations
expected annotation structure is <tissue>/<user>_scale-<number>pc/<csv-file>
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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 collect_triple_dir
has 6 arguments (exceeds 4 allowed). Consider refactoring. Open
def collect_triple_dir(paths_landmarks, path_dataset, path_out, coll_dirs=None,
Function figure_image_landmarks
has 5 arguments (exceeds 4 allowed). Consider refactoring. Open
def figure_image_landmarks(landmarks, image, landmarks2=None, lnds2_name='',
Function figure_image_landmarks
has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def figure_image_landmarks(landmarks, image, landmarks2=None, lnds2_name='',
max_fig_size=FIGURE_SIZE):
""" create a figure with images and landmarks
:param ndarray landmarks: landmark coordinates
- Read upRead up
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 compute_landmarks_statistic
has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def compute_landmarks_statistic(landmarks_ref, landmarks_in, use_affine=False, im_size=None):
""" compute statistic on errors between reference and sensed landmarks
:param ndarray landmarks_ref: reference landmarks of shape (N, 2)
:param ndarray landmarks_in: input landmarks of shape (N, 2)
- Read upRead up
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
Identical blocks of code found in 2 locations. Consider refactoring. Open
for i, lnd in enumerate(pair_landmarks[0]):
ax.text(lnd[0] + 5, lnd[1] + 5, str(i + 1), fontsize=11, color='black')
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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 52.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Identical blocks of code found in 2 locations. Consider refactoring. Open
for i, lnd in enumerate(landmarks):
ax.text(lnd[0] + 5, lnd[1] + 5, str(i + 1), fontsize=11, color='black')
- Read upRead up
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 52.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76