Merge pull request dipy#1195 from arokem/pickle-pam-3.6

Make PeaksAndMetrics pickle-able

dipy/direction/peaks.py

@@ -157,8 +157,68 @@ def peak_directions(odf, sphere, relative_peak_threshold=.5,
     return directions, values, indices
 
 
+def _pam_from_attrs(klass, sphere, peak_indices, peak_values, peak_dirs,
+                    gfa, qa, shm_coeff, B, odf):
+    """
+    Construct a PeaksAndMetrics object (or object of a subclass) from its
+    attributes.
+
+    This is also useful for pickling/unpickling of these objects (see also
+    :func:`__reduce__` below).
+
+    Parameters
+    ----------
+    klass : class
+        The class of object to be created.
+    sphere : `Sphere` class instance.
+        Sphere for discretization.
+    peak_indices : ndarray
+        Indices (in sphere vertices) of the peaks in each voxel.
+    peak_values : ndarray
+        The value of the peaks.
+    peak_dirs : ndarray
+        The direction of each peak.
+    gfa : ndarray
+        The Generalized Fractional Anisotropy in each voxel.
+    qa : ndarray
+        Quantitative Anisotropy in each voxel.
+    shm_coeff : ndarray
+        The coefficients of the spherical harmonic basis for the ODF in
+        each voxel.
+    B : ndarray
+        The spherical harmonic matrix, for multiplication with the
+        coefficients.
+    odf : ndarray
+        The orientation distribution function on the sphere in each voxel.
+
+    Returns
+    -------
+    pam : Instance of the class `klass`.
+    """
+    this_pam = klass()
+    this_pam.sphere = sphere
+    this_pam.peak_dirs = peak_dirs
+    this_pam.peak_values = peak_values
+    this_pam.peak_indices = peak_indices
+    this_pam.gfa = gfa
+    this_pam.qa = qa
+    this_pam.shm_coeff = shm_coeff
+    this_pam.B = B
+    this_pam.odf = odf
+    return this_pam
+
+
 class PeaksAndMetrics(PeaksAndMetricsDirectionGetter):
-    pass
+    def __reduce__(self): return _pam_from_attrs, (self.__class__,
+                                                   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,
@@ -480,27 +540,16 @@ def peaks_from_model(model, data, sphere, relative_peak_threshold,
 
     qa_array /= global_max
 
-    pam = PeaksAndMetrics()
-    pam.sphere = sphere
-    pam.peak_dirs = peak_dirs
-    pam.peak_values = peak_values
-    pam.peak_indices = peak_indices
-    pam.gfa = gfa_array
-    pam.qa = qa_array
-
-    if return_sh:
-        pam.shm_coeff = shm_coeff
-        pam.B = B
-    else:
-        pam.shm_coeff = None
-        pam.B = None
-
-    if return_odf:
-        pam.odf = odf_array
-    else:
-        pam.odf = None
-
-    return pam
+    return _pam_from_attrs(PeaksAndMetrics,
+                           sphere,
+                           peak_indices,
+                           peak_values,
+                           peak_dirs,
+                           gfa_array,
+                           qa_array,
+                           shm_coeff if return_sh else None,
+                           B if return_sh else None,
+                           odf_array if return_odf else None)
 
 
 def gfa(samples):

dipy/direction/tests/test_peaks.py

@@ -1,4 +1,8 @@
 import numpy as np
+
+import pickle
+from io import BytesIO
+
 from numpy.testing import (assert_array_equal, assert_array_almost_equal,
                            assert_almost_equal, run_module_suite,
                            assert_equal, assert_)
@@ -485,6 +489,28 @@ def test_peaksFromModel():
     assert_array_equal(pam.peak_indices[mask, 0], odf_argmax)
     assert_array_equal(pam.peak_indices[mask, 1:], -1)
 
+    # Test serialization and deserialization:
+    for normalize_peaks in [True, False]:
+        for return_odf in [True, False]:
+            for return_sh in [True, False]:
+                pam = peaks_from_model(model, data, _sphere, .5, 45,
+                                       normalize_peaks=normalize_peaks,
+                                       return_odf=return_odf,
+                                       return_sh=return_sh)
+
+                b = BytesIO()
+                pickle.dump(pam, b)
+                b.seek(0)
+                new_pam = pickle.load(b)
+                b.close()
+
+                for attr in ['peak_dirs', 'peak_values', 'peak_indices',
+                             'gfa', 'qa', 'shm_coeff', 'B', 'odf']:
+                    assert_array_equal(getattr(pam, attr),
+                                       getattr(new_pam, attr))
+                    assert_array_equal(pam.sphere.vertices,
+                                       new_pam.sphere.vertices)
+
 
 def test_peaksFromModelParallel():
     SNR = 100

dipy/reconst/peak_direction_getter.pyx

@@ -125,4 +125,3 @@ cdef class PeaksAndMetricsDirectionGetter(DirectionGetter):
             return 0
         else:
             return 1
-