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

def batch_mask2rws(mask_dir, rws_dir, **kwargs):
    """ Convert mask format annotation to rws format.

    Args:
        mask_dir (str): mask files directory.
Severity: Major
Found in medvision/annotation/mask2rws.py and 1 other location - About 7 hrs to fix
medvision/annotation/rws2mask.py on lines 58..76

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 111.

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 batch_rws2mask(rws_dir, mask_dir, **kwargs):
    """ Convert rws format annotation to mask format.

    Args:
        rws_dir (str): rws annotation files directory.
Severity: Major
Found in medvision/annotation/rws2mask.py and 1 other location - About 7 hrs to fix
medvision/annotation/mask2rws.py on lines 62..80

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 111.

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

    ih = np.minimum(np.expand_dims(a[:, 3], axis=1), b[:, 3]) - \
        np.maximum(np.expand_dims(a[:, 1], axis=1), b[:, 1]) + 1
Severity: Major
Found in medvision/evaluation/compute_overlap.py and 1 other location - About 5 hrs to fix
medvision/evaluation/compute_overlap.py on lines 8..9

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 87.

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

    iw = np.minimum(np.expand_dims(a[:, 2], axis=1), b[:, 2]) - \
        np.maximum(np.expand_dims(a[:, 0], axis=1), b[:, 0]) + 1
Severity: Major
Found in medvision/evaluation/compute_overlap.py and 1 other location - About 5 hrs to fix
medvision/evaluation/compute_overlap.py on lines 10..11

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 87.

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 eval_det has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
Open

def eval_det(dts, gts, num_classes=1, iou_thr=0.5):
    """ Evaluate a given dataset by comparing DT with GT.

    Args:
        dts (dict or list[list[ndarray]]): detected bounding boxes for
Severity: Minor
Found in medvision/evaluation/eval_det.py - About 3 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

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

    area = (b[:, 2] - b[:, 0] + 1) * (b[:, 3] - b[:, 1] + 1)
Severity: Major
Found in medvision/evaluation/compute_overlap.py and 1 other location - About 3 hrs to fix
medvision/evaluation/compute_overlap.py on lines 21..21

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 67.

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

    ua = np.expand_dims((a[:, 2] - a[:, 0] + 1) * (a[:, 3] - a[:, 1] + 1),
Severity: Major
Found in medvision/evaluation/compute_overlap.py and 1 other location - About 3 hrs to fix
medvision/evaluation/compute_overlap.py on lines 7..7

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 67.

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 imshow_bboxes has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
Open

def imshow_bboxes(
    img,
    bboxes,
    score_thr=0,
    colors=Color.green,
Severity: Minor
Found in medvision/visualization/image.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 dsmd2rws_bbox has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
Open

def dsmd2rws_bbox(
    rws_dir,
    dsmd,
    class2label,
    suffix='.json_A1',
Severity: Minor
Found in medvision/annotation/rws2dsmd.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 rws2dsmd_bbox has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

def rws2dsmd_bbox(
    filepaths,
    class2label,
    suffix='.json',
    num_classes=None
Severity: Minor
Found in medvision/annotation/rws2dsmd.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 eval_det4binarycls has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

def eval_det4binarycls(dts, gts, score_thrs):
    """ Evaluate a detector's classification capability.

    Only support 1-class detection. If (at least) 1 target is detected in
    an image, the image is considered to be 'positive'. Otherwise, the image
Severity: Minor
Found in medvision/evaluation/eval_det.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

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

        draw.ellipse([cx - r, cy - r, cx + r, cy + r], outline=1, fill=1)
Severity: Major
Found in medvision/annotation/rws2mask.py and 1 other location - About 1 hr to fix
medvision/annotation/rws2mask.py on lines 21..21

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

        draw.ellipse([cx - d, cy - d, cx + d, cy + d], outline=1, fill=1)
Severity: Major
Found in medvision/annotation/rws2mask.py and 1 other location - About 1 hr to fix
medvision/annotation/rws2mask.py on lines 34..34

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

Function dcmread_dr has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

def dcmread_dr(
    path: Union[str, Path],
    mode: DrReadMode = DrReadMode.MONOCHROME2,
    read_header: bool = False,
    itk_handler_enabled: bool = True
Severity: Minor
Found in medvision/dicom/dr_io.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 imshow_bboxes has 12 arguments (exceeds 4 allowed). Consider refactoring.
Open

def imshow_bboxes(
Severity: Major
Found in medvision/visualization/image.py - About 1 hr to fix

    Function download_url has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
    Open

    def download_url(
    url: str,
    dst_dir: str,
    *,
    filename: Optional[str] = None,
    Severity: Minor
    Found in medvision/network/download.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 save_det_dsmd has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    Open

    def save_det_dsmd(
    dsmd_path: Union[str, Path],
    data: Dict[str, List[np.ndarray]],
    class2label: Union[str, Dict[str, int]],
    auto_mkdirs: bool = True
    Severity: Minor
    Found in medvision/dataset/detection.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 shape_to_mask has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

    def shape_to_mask(img_shape, points, shape_type=None,
                  line_width=10, point_size=5):
    mask = np.zeros(img_shape[:2], dtype=np.uint8)
    mask = PIL.Image.fromarray(mask)
    draw = PIL.ImageDraw.Draw(mask)
    Severity: Minor
    Found in medvision/annotation/rws2mask.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 download_tree has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

        def download_tree(self, local_dir, remote_dir):
        logging.info('remote_dir, %s', remote_dir)
        if not os.path.exists(local_dir):
            os.makedirs(local_dir)
        self.ftp.cwd(remote_dir)
    Severity: Minor
    Found in medvision/util/ftputil.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 save_rws_bbox has 6 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def save_rws_bbox(
    Severity: Minor
    Found in medvision/annotation/rws.py - About 45 mins to fix
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