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Make PeaksAndMetrics pickle-able #1195

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merged 14 commits into from Mar 22, 2017
Merged

Make PeaksAndMetrics pickle-able #1195

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7d53841
Add get_state, set_state methods to PeaksAndMetrics.
arokem Mar 20, 2017
399ac2e
Don't implement set_state.
arokem Mar 20, 2017
2de6ca7
Test pickling of PAM objects.
arokem Mar 20, 2017
bcbdeac
Implement pickling of PAM objects as a reduce operation instead.
arokem Mar 20, 2017
d4bed65
Documentation and a bit more testing.
arokem Mar 20, 2017
9743fdb
Rename to `_pam_from_attrs`, use to reduce boilerplate.
arokem Mar 21, 2017
cec60bc
Implement `from_attrs` as an alternative constructor classmethod.
arokem Mar 21, 2017
0cef31f
Reimplement _pam_from_attrs as a free-standing function.
arokem Mar 22, 2017
116cd0e
Add optional argument to use other classes (e.g., when subclassing).
arokem Mar 22, 2017
a2d49bc
Make the klass input obligatory.
arokem Mar 22, 2017
8f221a0
Whitespace.
arokem Mar 22, 2017
f47076a
Correct docstring: this is not optional!
arokem Mar 22, 2017
ec3ac55
Whitespace.
arokem Mar 22, 2017
02c4ee7
Prettify the if statements.
arokem Mar 22, 2017
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32 changes: 17 additions & 15 deletions dipy/direction/peaks.py
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Expand Up @@ -157,8 +157,20 @@ def peak_directions(odf, sphere, relative_peak_threshold=.5,
return directions, values, indices


class PeaksAndMetrics(PeaksAndMetricsDirectionGetter):
def __reduce__(self): return _pam_from_attrs, (self.sphere,
self.peak_indices,
self.peak_values,
self.peak_dirs,
self.gfa,
self.qa,
self.shm_coeff,
self.B,
self.odf)
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Add self.__class__ as argument to allow sub-classing? Maybe, it would be better as first argument.



def _pam_from_attrs(sphere, peak_indices, peak_values, peak_dirs,
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Consider adding class as first argument? Or as optional argument at end? In case we need to sub-class?

Sorry to ask, but why do we need this otherwise empty sub-class?

class PeaksAndMetrics(PeaksAndMetricsDirectionGetter): pass

Why not use PeaksAndMetricsDirectionGetter directly?

gfa, qa, shm_coeff, B, odf):
gfa, qa, shm_coeff, B, odf, klass=PeaksAndMetrics):
"""
Construct a PeaksAndMetrics object from its attributes.

Expand Down Expand Up @@ -187,12 +199,14 @@ def _pam_from_attrs(sphere, peak_indices, peak_values, peak_dirs,
coefficients.
odf : ndarray
The orientation distribution function on the sphere in each voxel.
klass : class, optional
The class of object to be created. Default: PeaksAndMetrics

Returns
-------
PeaksAndMetrics class instance.
pam : Instance of the class `klass`.
"""
this_pam = PeaksAndMetrics()
this_pam = klass()
this_pam.sphere = sphere
this_pam.peak_dirs = peak_dirs
this_pam.peak_values = peak_values
Expand All @@ -205,18 +219,6 @@ def _pam_from_attrs(sphere, peak_indices, peak_values, peak_dirs,
return this_pam


class PeaksAndMetrics(PeaksAndMetricsDirectionGetter):
def __reduce__(self): return _pam_from_attrs, (self.sphere,
self.peak_indices,
self.peak_values,
self.peak_dirs,
self.gfa,
self.qa,
self.shm_coeff,
self.B,
self.odf)


def _peaks_from_model_parallel(model, data, sphere, relative_peak_threshold,
min_separation_angle, mask, return_odf,
return_sh, gfa_thr, normalize_peaks, sh_order,
Expand Down