Sign upLogin

CellProfiler/centrosome

View on GitHub
Star

Showing 257 of 380 total issues

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

    if len(count_t) > 0:
        last_n = np.max(count_t)
        diff_i_t = diff_i[mask]
        diff_j_t = diff_j[mask]
        remainder = diff_i_t * 2 - diff_j_t
Severity: Major
Found in centrosome/cpmorphology.py and 1 other location - About 3 days to fix
centrosome/cpmorphology.py on lines 1121..1157

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 355.

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

    if len(count_t) > 0:
        last_n = np.max(count_t)
        diff_i_t = diff_i[mask]
        diff_j_t = diff_j[mask]
        remainder = diff_j_t * 2 - diff_i_t
Severity: Major
Found in centrosome/cpmorphology.py and 1 other location - About 3 days to fix
centrosome/cpmorphology.py on lines 1165..1201

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 355.

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 enhance_dark_holes(image, min_radius, max_radius, mask=None):
    """Enhance dark holes using a rolling ball filter

    image - grayscale 2-d image
    radii - a vector of radii: we enhance holes at each given radius
Severity: Major
Found in centrosome/filter.py and 1 other location - About 1 day to fix
centrosome/filter.py on lines 739..766

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 166.

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 granulometry_filter(image, min_radius, max_radius, mask=None):
    """Enhances bright structures within a min and max radius using a rolling ball filter

    image - grayscale 2-d image
    radii - a vector of radii: we enhance holes at each given radius
Severity: Major
Found in centrosome/filter.py and 1 other location - About 1 day to fix
centrosome/filter.py on lines 710..736

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 166.

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

            x = (
                np.sum(ss0 ** 2, 1) * (ss1[:, Y] - vv[:, Y])
                + np.sum(ss1 ** 2, 1) * (vv[:, Y] - ss0[:, Y])
                + np.sum(vv ** 2, 1) * (ss0[:, Y] - ss1[:, Y])
Severity: Major
Found in centrosome/cpmorphology.py and 1 other location - About 1 day to fix
centrosome/cpmorphology.py on lines 1675..1678

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 152.

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

            y = (
                np.sum(ss0 ** 2, 1) * (vv[:, X] - ss1[:, X])
                + np.sum(ss1 ** 2, 1) * (ss0[:, X] - vv[:, X])
                + np.sum(vv ** 2, 1) * (ss1[:, X] - ss0[:, X])
Severity: Major
Found in centrosome/cpmorphology.py and 1 other location - About 1 day to fix
centrosome/cpmorphology.py on lines 1670..1673

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 152.

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 4 locations. Consider refactoring.
Open

def hprewitt(image, mask=None):
    """Find the horizontal edges of an image using the Prewitt transform

    image - image to process
    mask  - mask of relevant points
Severity: Major
Found in centrosome/filter.py and 3 other locations - About 1 day to fix
centrosome/filter.py on lines 544..565
centrosome/filter.py on lines 568..589
centrosome/filter.py on lines 628..649

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 125.

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 4 locations. Consider refactoring.
Open

def vprewitt(image, mask=None):
    """Find the vertical edges of an image using the Prewitt transform

    image - image to process
    mask  - mask of relevant points
Severity: Major
Found in centrosome/filter.py and 3 other locations - About 1 day to fix
centrosome/filter.py on lines 544..565
centrosome/filter.py on lines 568..589
centrosome/filter.py on lines 604..625

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 125.

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 4 locations. Consider refactoring.
Open

def vsobel(image, mask=None):
    """Find the vertical edges of an image using the Sobel transform

    image - image to process
    mask  - mask of relevant points
Severity: Major
Found in centrosome/filter.py and 3 other locations - About 1 day to fix
centrosome/filter.py on lines 544..565
centrosome/filter.py on lines 604..625
centrosome/filter.py on lines 628..649

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 125.

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 4 locations. Consider refactoring.
Open

def hsobel(image, mask=None):
    """Find the horizontal edges of an image using the Sobel transform

    image - image to process
    mask  - mask of relevant points
Severity: Major
Found in centrosome/filter.py and 3 other locations - About 1 day to fix
centrosome/filter.py on lines 568..589
centrosome/filter.py on lines 604..625
centrosome/filter.py on lines 628..649

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 125.

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 4 locations. Consider refactoring.
Open

        binary_shrink_urb_table = erode_table | (
            make_table(
                False,
                np.array([[0, 1, 0], [0, 1, 0], [0, 0, 0]], bool),
                np.array([[0, 1, 0], [0, 1, 0], [0, 1, 0]], bool),
Severity: Major
Found in centrosome/cpmorphology.py and 3 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 356..365
centrosome/cpmorphology.py on lines 380..389
centrosome/cpmorphology.py on lines 392..401

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 121.

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 4 locations. Consider refactoring.
Open

        binary_shrink_lrl_table = erode_table | (
            make_table(
                False,
                np.array([[0, 0, 0], [0, 1, 1], [0, 0, 0]], bool),
                np.array([[0, 0, 0], [1, 1, 1], [0, 0, 0]], bool),
Severity: Major
Found in centrosome/cpmorphology.py and 3 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 356..365
centrosome/cpmorphology.py on lines 368..377
centrosome/cpmorphology.py on lines 392..401

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 121.

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 4 locations. Consider refactoring.
Open

        binary_shrink_llt_table = erode_table | (
            make_table(
                False,
                np.array([[0, 0, 0], [0, 1, 0], [0, 1, 0]], bool),
                np.array([[0, 1, 0], [0, 1, 0], [0, 1, 0]], bool),
Severity: Major
Found in centrosome/cpmorphology.py and 3 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 356..365
centrosome/cpmorphology.py on lines 368..377
centrosome/cpmorphology.py on lines 380..389

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 121.

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 4 locations. Consider refactoring.
Open

        binary_shrink_ulr_table = erode_table | (
            make_table(
                False,
                np.array([[0, 0, 0], [1, 1, 0], [0, 0, 0]], bool),
                np.array([[0, 0, 0], [1, 1, 1], [0, 0, 0]], bool),
Severity: Major
Found in centrosome/cpmorphology.py and 3 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 368..377
centrosome/cpmorphology.py on lines 380..389
centrosome/cpmorphology.py on lines 392..401

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 121.

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 7 locations. Consider refactoring.
Open

def majority(image, mask=None, iterations=1):
    """A pixel takes the value of the majority of its neighbors
    
    """
    global majority_table
Severity: Major
Found in centrosome/cpmorphology.py and 6 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 3468..3484
centrosome/cpmorphology.py on lines 3495..3514
centrosome/cpmorphology.py on lines 3548..3565
centrosome/cpmorphology.py on lines 3606..3622
centrosome/cpmorphology.py on lines 3637..3653
centrosome/cpmorphology.py on lines 3848..3868

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 116.

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 7 locations. Consider refactoring.
Open

def thicken(image, mask=None, iterations=1):
    """Thicken the objects in an image where doing so does not connect them
    
    0 0 0    ? ? ?
    0 0 0 -> ? 1 ?
Severity: Major
Found in centrosome/cpmorphology.py and 6 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 3468..3484
centrosome/cpmorphology.py on lines 3495..3514
centrosome/cpmorphology.py on lines 3548..3565
centrosome/cpmorphology.py on lines 3606..3622
centrosome/cpmorphology.py on lines 3637..3653
centrosome/cpmorphology.py on lines 3732..3745

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 116.

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 7 locations. Consider refactoring.
Open

def fill4(image, mask=None, iterations=1):
    """Fill 4-connected black pixels
    
    x 1 x     x 1 x
    1 0 1 ->  1 1 1
Severity: Major
Found in centrosome/cpmorphology.py and 6 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 3468..3484
centrosome/cpmorphology.py on lines 3495..3514
centrosome/cpmorphology.py on lines 3548..3565
centrosome/cpmorphology.py on lines 3606..3622
centrosome/cpmorphology.py on lines 3732..3745
centrosome/cpmorphology.py on lines 3848..3868

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 116.

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 7 locations. Consider refactoring.
Open

def fill(image, mask=None, iterations=1):
    """Fill isolated black pixels
    
    1 1 1     1 1 1
    1 0 1 ->  1 1 1
Severity: Major
Found in centrosome/cpmorphology.py and 6 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 3468..3484
centrosome/cpmorphology.py on lines 3495..3514
centrosome/cpmorphology.py on lines 3548..3565
centrosome/cpmorphology.py on lines 3637..3653
centrosome/cpmorphology.py on lines 3732..3745
centrosome/cpmorphology.py on lines 3848..3868

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 116.

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 7 locations. Consider refactoring.
Open

def clean(image, mask=None, iterations=1):
    """Remove isolated pixels
    
    0 0 0     0 0 0
    0 1 0 ->  0 0 0
Severity: Major
Found in centrosome/cpmorphology.py and 6 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 3468..3484
centrosome/cpmorphology.py on lines 3548..3565
centrosome/cpmorphology.py on lines 3606..3622
centrosome/cpmorphology.py on lines 3637..3653
centrosome/cpmorphology.py on lines 3732..3745
centrosome/cpmorphology.py on lines 3848..3868

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 116.

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 7 locations. Consider refactoring.
Open

def bridge(image, mask=None, iterations=1):
    """Fill in pixels that bridge gaps.
    
    1 0 0    1 0 0
    0 0 0 -> 0 1 0
Severity: Major
Found in centrosome/cpmorphology.py and 6 other locations - About 7 hrs to fix
centrosome/cpmorphology.py on lines 3495..3514
centrosome/cpmorphology.py on lines 3548..3565
centrosome/cpmorphology.py on lines 3606..3622
centrosome/cpmorphology.py on lines 3637..3653
centrosome/cpmorphology.py on lines 3732..3745
centrosome/cpmorphology.py on lines 3848..3868

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 116.

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

Severity
Category
Status
Source
Language