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Fixed test_centerline crashing due to bump in Python library #2754
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597dfa4
Removed nurbs dummy centerline (was not used)
jcohenadad 111289a
Changed output formatting for results
jcohenadad a456fa5
Changed ().I for np.linalg.pinv to address Singular mat error
jcohenadad c86fa84
Display default parameters
jcohenadad 9187c4b
Replaced polyfit by Polynomial.fit
jcohenadad e61ce56
Improved clarity of saved files for debugging
jcohenadad a6819d6
Excluded irrelevant or buggy tests
jcohenadad cbc18e9
Replaced polyfit by bspline in dummy centerline creation
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Original file line number | Diff line number | Diff line change |
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@@ -14,16 +14,15 @@ | |
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def polyfit_1d(x, y, xref, deg=5): | ||
""" | ||
1d Polynomial fitting using np.polyfit | ||
1d Polynomial fitting using numpy's Polynomial.fit | ||
:param x: | ||
:param y: | ||
:param deg: | ||
:param xref: np.array: vector of abscissa on which to project the fitted curve. Example: np.linspace(0, 50, 51) | ||
:return: p(xref): Fitted polynomial for each xref point | ||
:return: p.deriv(xref): Derivatives for each xref point | ||
""" | ||
from numpy import poly1d, polyfit | ||
p = poly1d(polyfit(x, y, deg=deg)) | ||
p = np.polynomial.Polynomial.fit(x, y, deg) | ||
Comment on lines
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There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. There is actually specified in np.polyfit documentation: Makes sense :-) |
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return p(xref), p.deriv(1)(xref) | ||
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@@ -69,8 +68,7 @@ def linear(x, y, xref, smooth=0, pz=1): | |
:param pz: float: dimension of pixel along superior-inferior direction (z, assuming RPI orientation) | ||
:return: | ||
""" | ||
from numpy import interp | ||
y_fit = interp(xref, x, y, left=None, right=None, period=None) | ||
y_fit = np.interp(xref, x, y, left=None, right=None, period=None) | ||
window_len = round_up_to_odd(smooth / float(pz)) | ||
logger.debug('Smoothing window: {}'.format(window_len)) | ||
y_fit = smooth1d(y_fit, window_len) | ||
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Would it be relevant to display the default value by default in order to reduce maintenance etc?
eg https://stackoverflow.com/a/12151325/13306686
If so, I will open a new issue
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Yes that would be awesome!