tomopy/tomopy

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Showing 147 of 306 total issues

Similar blocks of code found in 7 locations. Consider refactoring.
Open

    def test_baboon(self):
        assert_equals(baboon().dtype, 'float32')
        assert_equals(baboon().shape, (1, 512, 512))
        assert_equals(baboon(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(baboon(size=64).shape, (1, 64, 64))
Severity: Major
Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
test/test_tomopy/test_misc/test_phantom.py on lines 69..73
test/test_tomopy/test_misc/test_phantom.py on lines 75..79
test/test_tomopy/test_misc/test_phantom.py on lines 81..85
test/test_tomopy/test_misc/test_phantom.py on lines 87..91
test/test_tomopy/test_misc/test_phantom.py on lines 93..97
test/test_tomopy/test_misc/test_phantom.py on lines 99..103

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 77.

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 test_checkerboard(self):
        assert_equals(checkerboard().dtype, 'float32')
        assert_equals(checkerboard().shape, (1, 512, 512))
        assert_equals(checkerboard(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(checkerboard(size=64).shape, (1, 64, 64))
Severity: Major
Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
test/test_tomopy/test_misc/test_phantom.py on lines 63..67
test/test_tomopy/test_misc/test_phantom.py on lines 69..73
test/test_tomopy/test_misc/test_phantom.py on lines 75..79
test/test_tomopy/test_misc/test_phantom.py on lines 87..91
test/test_tomopy/test_misc/test_phantom.py on lines 93..97
test/test_tomopy/test_misc/test_phantom.py on lines 99..103

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 77.

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 test_shepp2d(self):
        assert_equals(shepp2d().dtype, 'float32')
        assert_equals(shepp2d().shape, (1, 512, 512))
        assert_equals(shepp2d(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(shepp2d(size=64).shape, (1, 64, 64))
Severity: Major
Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
test/test_tomopy/test_misc/test_phantom.py on lines 63..67
test/test_tomopy/test_misc/test_phantom.py on lines 69..73
test/test_tomopy/test_misc/test_phantom.py on lines 75..79
test/test_tomopy/test_misc/test_phantom.py on lines 81..85
test/test_tomopy/test_misc/test_phantom.py on lines 87..91
test/test_tomopy/test_misc/test_phantom.py on lines 93..97

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 77.

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 test_peppers(self):
        assert_equals(peppers().dtype, 'float32')
        assert_equals(peppers().shape, (1, 512, 512))
        assert_equals(peppers(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(peppers(size=64).shape, (1, 64, 64))
Severity: Major
Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
test/test_tomopy/test_misc/test_phantom.py on lines 63..67
test/test_tomopy/test_misc/test_phantom.py on lines 69..73
test/test_tomopy/test_misc/test_phantom.py on lines 75..79
test/test_tomopy/test_misc/test_phantom.py on lines 81..85
test/test_tomopy/test_misc/test_phantom.py on lines 87..91
test/test_tomopy/test_misc/test_phantom.py on lines 99..103

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 77.

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 test_lena(self):
        assert_equals(lena().dtype, 'float32')
        assert_equals(lena().shape, (1, 512, 512))
        assert_equals(lena(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(lena(size=64).shape, (1, 64, 64))
Severity: Major
Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
test/test_tomopy/test_misc/test_phantom.py on lines 63..67
test/test_tomopy/test_misc/test_phantom.py on lines 69..73
test/test_tomopy/test_misc/test_phantom.py on lines 75..79
test/test_tomopy/test_misc/test_phantom.py on lines 81..85
test/test_tomopy/test_misc/test_phantom.py on lines 93..97
test/test_tomopy/test_misc/test_phantom.py on lines 99..103

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 77.

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 test_barbara(self):
        assert_equals(barbara().dtype, 'float32')
        assert_equals(barbara().shape, (1, 512, 512))
        assert_equals(barbara(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(barbara(size=64).shape, (1, 64, 64))
Severity: Major
Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
test/test_tomopy/test_misc/test_phantom.py on lines 63..67
test/test_tomopy/test_misc/test_phantom.py on lines 75..79
test/test_tomopy/test_misc/test_phantom.py on lines 81..85
test/test_tomopy/test_misc/test_phantom.py on lines 87..91
test/test_tomopy/test_misc/test_phantom.py on lines 93..97
test/test_tomopy/test_misc/test_phantom.py on lines 99..103

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 77.

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 test_cameraman(self):
        assert_equals(cameraman().dtype, 'float32')
        assert_equals(cameraman().shape, (1, 512, 512))
        assert_equals(cameraman(size=(128, 256)).shape, (1, 128, 256))
        assert_equals(cameraman(size=64).shape, (1, 64, 64))
Severity: Major
Found in test/test_tomopy/test_misc/test_phantom.py and 6 other locations - About 4 hrs to fix
test/test_tomopy/test_misc/test_phantom.py on lines 63..67
test/test_tomopy/test_misc/test_phantom.py on lines 69..73
test/test_tomopy/test_misc/test_phantom.py on lines 81..85
test/test_tomopy/test_misc/test_phantom.py on lines 87..91
test/test_tomopy/test_misc/test_phantom.py on lines 93..97
test/test_tomopy/test_misc/test_phantom.py on lines 99..103

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 77.

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

    @unittest.skipUnless("CUDA_VERSION" in os.environ, "CUDA_VERSION not set.")
    def test_mlem_gpu(self):
        result = recon(self.prj, self.ang, algorithm='mlem', num_iter=4,
                       accelerated=True, device='gpu', ncore=1, pool_size=3)
        assert_allclose(result, read_file('mlem_accel_gpu.npy'), rtol=1e-2)
Severity: Major
Found in test/test_tomopy/test_recon/test_algorithm.py and 1 other location - About 3 hrs to fix
test/test_tomopy/test_recon/test_algorithm.py on lines 184..188

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 72.

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

    @unittest.skipUnless("CUDA_VERSION" in os.environ, "CUDA_VERSION not set.")
    def test_sirt_gpu(self):
        result = recon(self.prj, self.ang, algorithm='sirt', num_iter=4,
                       accelerated=True, device='gpu', ncore=1, pool_size=3)
        assert_allclose(result, read_file('sirt_accel_gpu.npy'), rtol=1e-2)
Severity: Major
Found in test/test_tomopy/test_recon/test_algorithm.py and 1 other location - About 3 hrs to fix
test/test_tomopy/test_recon/test_algorithm.py on lines 143..147

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 72.

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 pad is True:
        dx = _round_to_even(np.sqrt(ox * ox + oz * oz) + 2)
    elif pad is False:
        dx = ox
Severity: Major
Found in source/tomopy/sim/project.py and 2 other locations - About 3 hrs to fix
source/tomopy/sim/project.py on lines 218..221
source/tomopy/sim/project.py on lines 288..291

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 65.

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 pad is True:
        dx = _round_to_even(np.sqrt(ox * ox + oz * oz) + 2)
    elif pad is False:
        dx = ox
Severity: Major
Found in source/tomopy/sim/project.py and 2 other locations - About 3 hrs to fix
source/tomopy/sim/project.py on lines 288..291
source/tomopy/sim/project.py on lines 355..358

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 65.

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 pad is True:
        dx = _round_to_even(np.sqrt(ox * ox + oz * oz) + 2)
    elif pad is False:
        dx = ox
Severity: Major
Found in source/tomopy/sim/project.py and 2 other locations - About 3 hrs to fix
source/tomopy/sim/project.py on lines 218..221
source/tomopy/sim/project.py on lines 355..358

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 65.

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

    @unittest.skipUnless(found_opencv, "CPU acceleration requires OpenCV.")
    def test_mlem_accel(self):
        result = recon(self.prj, self.ang, algorithm='mlem', num_iter=4,
                       accelerated=True, device='cpu', ncore=1, pool_size=3)
        assert_allclose(result, read_file('mlem_accel.npy'), rtol=1e-2)
Severity: Major
Found in test/test_tomopy/test_recon/test_algorithm.py and 1 other location - About 3 hrs to fix
test/test_tomopy/test_recon/test_algorithm.py on lines 178..182

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 64.

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

    @unittest.skipUnless(found_opencv, "CPU acceleration requires OpenCV.")
    def test_sirt_accel(self):
        result = recon(self.prj, self.ang, algorithm='sirt', num_iter=4,
                       accelerated=True, device='cpu', ncore=1, pool_size=3)
        assert_allclose(result, read_file('sirt_accel.npy'), rtol=1e-2)
Severity: Major
Found in test/test_tomopy/test_recon/test_algorithm.py and 1 other location - About 3 hrs to fix
test/test_tomopy/test_recon/test_algorithm.py on lines 137..141

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 64.

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 remove_neg(arr, val=0., ncore=None):
    """
    Replace negative values in array with a given value.

    Parameters
Severity: Major
Found in source/tomopy/misc/corr.py and 1 other location - About 3 hrs to fix
source/tomopy/misc/corr.py on lines 302..326

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 62.

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

    if size is None:
        if tomo.shape[2] > 2000:
            size = 21
        else:
            size = max(5, int(0.01 * tomo.shape[2]))
Severity: Major
Found in source/tomopy/prep/stripe.py and 1 other location - About 3 hrs to fix
source/tomopy/prep/stripe.py on lines 418..422

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 62.

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 remove_nan(arr, val=0., ncore=None):
    """
    Replace NaN values in array with a given value.

    Parameters
Severity: Major
Found in source/tomopy/misc/corr.py and 1 other location - About 3 hrs to fix
source/tomopy/misc/corr.py on lines 329..352

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 62.

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

    if size is None:
        if tomo.shape[2] > 2000:
            size = 21
        else:
            size = max(5, int(0.01 * tomo.shape[2]))
Severity: Major
Found in source/tomopy/prep/stripe.py and 1 other location - About 3 hrs to fix
source/tomopy/prep/stripe.py on lines 498..502

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 62.

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 find_python_coverage():
    """
    Find the python coverage script
    """
    pypath = os.path.dirname(pyctest.PYTHON_EXECUTABLE)
Severity: Major
Found in benchmarking/__init__.py and 1 other location - About 2 hrs to fix
benchmarking/__init__.py on lines 115..123

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 61.

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 find_python_nosetest():
    """
    Find the python nosetests script
    """
    pypath = os.path.dirname(pyctest.PYTHON_EXECUTABLE)
Severity: Major
Found in benchmarking/__init__.py and 1 other location - About 2 hrs to fix
benchmarking/__init__.py on lines 126..134

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 61.

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

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