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Borda/dataset-histology-landmarks

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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>
"""
Severity: Minor
Found in handlers/utilities.py - About 7 hrs to fix

    Identical blocks of code found in 3 locations. Consider refactoring.
    Open

    if __name__ == '__main__':
    logging.basicConfig(level=logging.INFO)
    logging.info('running...')

    params = parse_args(create_arg_parser())
    Severity: Major
    Found in handlers/run_evaluate_landmarks.py and 2 other locations - About 2 hrs to fix
    handlers/run_generate_landmarks.py on lines 160..167
    handlers/run_visualise_landmarks.py on lines 224..231

    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 59.

    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

    Identical blocks of code found in 3 locations. Consider refactoring.
    Open

    if __name__ == '__main__':
    logging.basicConfig(level=logging.INFO)
    logging.info('running...')

    params = parse_args(create_arg_parser())
    Severity: Major
    Found in handlers/run_visualise_landmarks.py and 2 other locations - About 2 hrs to fix
    handlers/run_evaluate_landmarks.py on lines 217..224
    handlers/run_generate_landmarks.py on lines 160..167

    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 59.

    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

    Identical blocks of code found in 3 locations. Consider refactoring.
    Open

    if __name__ == '__main__':
    logging.basicConfig(level=logging.INFO)
    logging.info('running...')

    params = parse_args(create_arg_parser())
    Severity: Major
    Found in handlers/run_generate_landmarks.py and 2 other locations - About 2 hrs to fix
    handlers/run_evaluate_landmarks.py on lines 217..224
    handlers/run_visualise_landmarks.py on lines 224..231

    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 59.

    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

    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')
    Severity: Major
    Found in handlers/utilities.py and 1 other location - About 2 hrs to fix
    handlers/utilities.py on lines 520..521

    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

    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')
    Severity: Major
    Found in handlers/utilities.py and 1 other location - About 2 hrs to fix
    handlers/utilities.py on lines 452..453

    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

    Further Reading

    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
    Severity: Minor
    Found in handlers/utilities.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 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
    Severity: Minor
    Found in handlers/utilities.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 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>
    Severity: Minor
    Found in handlers/utilities.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 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
    Severity: Minor
    Found in handlers/run_visualise_landmarks.py - About 55 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 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,
    Severity: Minor
    Found in handlers/utilities.py - About 45 mins to fix

      Function main has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def main(path_annots, path_dataset, path_output, consensus='mean', visual=False,
      Severity: Minor
      Found in handlers/run_evaluate_landmarks.py - About 45 mins to fix

        Function visual_coannotation has 6 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def visual_coannotation(lnds_user, lnds_refs, path_dataset, path_user,
        Severity: Minor
        Found in handlers/run_evaluate_landmarks.py - About 45 mins to fix

          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
          Severity: Minor
          Found in handlers/run_evaluate_landmarks.py - About 45 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 evaluate_user has 6 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def evaluate_user(user_name, path_annots, path_out, path_dataset=None,
          Severity: Minor
          Found in handlers/run_evaluate_landmarks.py - About 45 mins to fix

            Function figure_image_landmarks has 5 arguments (exceeds 4 allowed). Consider refactoring.
            Open

            def figure_image_landmarks(landmarks, image, landmarks2=None, lnds2_name='',
            Severity: Minor
            Found in handlers/utilities.py - About 35 mins to fix

              Function main has 5 arguments (exceeds 4 allowed). Consider refactoring.
              Open

              def main(path_landmarks, path_dataset, path_output, scales, nb_jobs=NB_THREADS):
              Severity: Minor
              Found in handlers/run_visualise_landmarks.py - About 35 mins to fix

                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,
                Severity: Minor
                Found in handlers/run_evaluate_landmarks.py - About 35 mins to fix

                  Function main has 5 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                  def main(path_annots, path_dataset, scales, consensus='mean', nb_jobs=NB_THREADS):
                  Severity: Minor
                  Found in handlers/run_generate_landmarks.py - About 35 mins to fix

                    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
                    Severity: Minor
                    Found in handlers/utilities.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

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