Merge pull request #1384 from gabknight/NF_cmc_pft_merged

NF - Particle Filtering Tractography (merge)

dipy/direction/pmf.pyx

@@ -29,7 +29,11 @@ cdef class SimplePmfGen(PmfGen):
         self.out = np.empty(pmf_array.shape[3])
 
     cdef double[:] get_pmf_c(self, double* point) nogil:
-        trilinear_interpolate4d_c(self.pmf_array, point, self.out)
+        cdef:
+            size_t len_pmf = self.out.shape[0]
+        if trilinear_interpolate4d_c(self.pmf_array, point, self.out):
+            for i in range(len_pmf):
+                self.out[i] = 0.0
         return self.out
 
 
@@ -62,13 +66,16 @@ cdef class SHCoeffPmfGen(PmfGen):
             size_t len_B = self.B.shape[1]
             double _sum
 
-        trilinear_interpolate4d_c(self.shcoeff, point, self.coeff)
-        for i in range(len_pmf):
-            _sum = 0
-            for j in range(len_B):
-                _sum += self.B[i, j] * self.coeff[j]
-            self.pmf[i] = _sum
-            if self.pmf[i] < 0.0:
+        if trilinear_interpolate4d_c(self.shcoeff, point, self.coeff):
+            for i in range(len_pmf):
                 self.pmf[i] = 0.0
+        else:
+            for i in range(len_pmf):
+                _sum = 0
+                for j in range(len_B):
+                    _sum += self.B[i, j] * self.coeff[j]
+                self.pmf[i] = _sum
+                if self.pmf[i] < 0.0:
+                    self.pmf[i] = 0.0
 
         return self.pmf

dipy/direction/tests/test_pmf.py

@@ -0,0 +1,43 @@
+import numpy as np
+import numpy.testing as npt
+
+from dipy.core.sphere import HemiSphere, unit_octahedron
+from dipy.direction.pmf import SimplePmfGen, SHCoeffPmfGen
+
+
+def test_pmf_from_sh():
+    sphere = HemiSphere.from_sphere(unit_octahedron)
+    pmfgen = SHCoeffPmfGen(np.ones([2, 2, 2, 28]), sphere, None)
+
+    # Test that the pmf is greater than 0 for a valid point
+    pmf = pmfgen.get_pmf(np.array([0, 0, 0], dtype='float'))
+    npt.assert_equal(np.sum(pmf) > 0, True)
+
+    # Test that the pmf is 0 for invalid Points
+    npt.assert_array_equal(pmfgen.get_pmf(np.array([-1, 0, 0], dtype='float')),
+                           np.zeros(len(sphere.vertices)))
+    npt.assert_array_equal(pmfgen.get_pmf(np.array([0, 0, 10], dtype='float')),
+                           np.zeros(len(sphere.vertices)))
+
+
+def test_pmf_from_array():
+    sphere = HemiSphere.from_sphere(unit_octahedron)
+    pmfgen = SimplePmfGen(np.ones([2, 2, 2, len(sphere.vertices)]))
+
+    # Test that the pmf is greater than 0 for a valid point
+    pmf = pmfgen.get_pmf(np.array([0, 0, 0], dtype='float'))
+    npt.assert_equal(np.sum(pmf) > 0, True)
+
+    # Test that the pmf is 0 for invalid Points
+    npt.assert_array_equal(pmfgen.get_pmf(np.array([-1, 0, 0], dtype='float')),
+                           np.zeros(len(sphere.vertices)))
+    npt.assert_array_equal(pmfgen.get_pmf(np.array([0, 0, 10], dtype='float')),
+                           np.zeros(len(sphere.vertices)))
+
+    npt.assert_raises(
+        ValueError,
+        lambda: SimplePmfGen(np.ones([2, 2, 2, len(sphere.vertices)])*-1))
+
+
+if __name__ == '__main__':
+    npt.run_module_suite()

dipy/segment/tests/test_mrf.py

@@ -56,7 +56,7 @@
 square_1[99:157, 99:157, :] = temp_3
 
 
-def test_greyscale_image():
+def test_grayscale_image():
 
     com = ConstantObservationModel()
     icm = IteratedConditionalModes()
@@ -124,7 +124,7 @@ def test_greyscale_image():
     npt.assert_(icm_segmentation.min() == 0)
 
 
-def test_greyscale_iter():
+def test_grayscale_iter():
 
     max_iter = 15
     beta = np.float64(0.1)
@@ -195,11 +195,11 @@ def test_greyscale_iter():
         npt.assert_(PLY[100, 100, 1, 3] > PLY[100, 100, 1, 1])
         npt.assert_(PLY[100, 100, 1, 3] > PLY[100, 100, 1, 2])
 
-        mu_upd, sigmasq_upd = com.update_param(image_gauss, PLY, mu, nclasses)        
+        mu_upd, sigmasq_upd = com.update_param(image_gauss, PLY, mu, nclasses)
         npt.assert_(mu_upd[0] >= 0.0)
         npt.assert_(mu_upd[1] >= 0.0)
         npt.assert_(mu_upd[2] >= 0.0)
-        npt.assert_(mu_upd[3] >= 0.0)    
+        npt.assert_(mu_upd[3] >= 0.0)
         npt.assert_(sigmasq_upd[0] >= 0.0)
         npt.assert_(sigmasq_upd[1] >= 0.0)
         npt.assert_(sigmasq_upd[2] >= 0.0)
@@ -294,7 +294,7 @@ def test_square_iter():
         npt.assert_(mu_upd[0] >= 0.0)
         npt.assert_(mu_upd[1] >= 0.0)
         npt.assert_(mu_upd[2] >= 0.0)
-        npt.assert_(mu_upd[3] >= 0.0)    
+        npt.assert_(mu_upd[3] >= 0.0)
         npt.assert_(sigmasq_upd[0] >= 0.0)
         npt.assert_(sigmasq_upd[1] >= 0.0)
         npt.assert_(sigmasq_upd[2] >= 0.0)

dipy/tracking/local/__init__.py

@@ -1,9 +1,15 @@
-from .localtracking import LocalTracking
-from .tissue_classifier import (
-    ActTissueClassifier, BinaryTissueClassifier, ThresholdTissueClassifier,
-    TissueClassifier)
 from .direction_getter import DirectionGetter
+from .localtracking import LocalTracking, ParticleFilteringTracking
+from .tissue_classifier import (ActTissueClassifier,
+                                BinaryTissueClassifier,
+                                CmcTissueClassifier,
+                                ConstrainedTissueClassifier,
+                                ThresholdTissueClassifier,
+                                TissueClassifier)
+
 from dipy.tracking import utils
 
-__all__ = ["ActTissueClassifier", "BinaryTissueClassifier", "LocalTracking",
-           "ThresholdTissueClassifier"]
+__all__ = ["ActTissueClassifier", "BinaryTissueClassifier",
+           "CmcTissueClassifier", "ConstrainedTissueClassifier",
+           "DirectionGetter", "LocalTracking", "ParticleFilteringTracking",
+           "ThresholdTissueClassifier", "TissueClassifier"]