Showing 17 of 22 total issues
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 export_visual_set_scale
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def export_visual_set_scale(d_paths):
""" export, visualise given set in particular scale
:param {str: str} d_paths: dictionary with path patterns
:return int: number of processed items
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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 visual_coannotation
has 6 arguments (exceeds 4 allowed). Consider refactoring. Open
def visual_coannotation(lnds_user, lnds_refs, path_dataset, path_user,
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 main
has 6 arguments (exceeds 4 allowed). Consider refactoring. Open
def main(path_annots, path_dataset, path_output, consensus='mean', visual=False,
Function evaluate_user
has 6 arguments (exceeds 4 allowed). Consider refactoring. Open
def evaluate_user(user_name, path_annots, path_out, path_dataset=None,
Function evaluate_user
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def evaluate_user(user_name, path_annots, path_out, path_dataset=None,
tp_consensus='mean', visual=False):
""" evaluate single user statistic against consensus
:param str user_name: annotator name
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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 main
has 5 arguments (exceeds 4 allowed). Consider refactoring. Open
def main(path_annots, path_dataset, scales, consensus='mean', nb_jobs=NB_THREADS):
Function compute_statistic
has 5 arguments (exceeds 4 allowed). Consider refactoring. Open
def compute_statistic(path_user, path_refs, tp_consensus='mean', path_dataset=None,
Function main
has 5 arguments (exceeds 4 allowed). Consider refactoring. Open
def main(path_landmarks, path_dataset, path_output, scales, nb_jobs=NB_THREADS):
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
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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 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)
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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 compute_statistic
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def compute_statistic(path_user, path_refs, tp_consensus='mean', path_dataset=None,
path_visu=None):
""" aggregate statistics over all his annotations
:param str path_user: path to user annotation
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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"