def odf(self, Pr):
""" fill the odf by sampling radially on the pdf
crucial parameter here is self.radius
"""
odf = np.zeros(self.odfn)
"""
#for all odf vertices
for m in range(self.odfn):
xi=self.origin+self.radius*self.odf_vertices[m,0]
yi=self.origin+self.radius*self.odf_vertices[m,1]
zi=self.origin+self.radius*self.odf_vertices[m,2]
#apply linear 3d interpolation (trilinear)
PrI=map_coordinates(Pr,np.vstack((xi,yi,zi)),order=1)
for i in range(self.radiusn):
odf[m]=odf[m]+PrI[i]*self.radius[i]**2
"""
PrIs = map_coordinates(Pr, self.Xs, order=1)
#print PrIs.shape
""" in pdf_to_odf an optimized version of the function below
for m in range(self.odfn):
for i in range(self.radiusn):
odf[m]=odf[m]+PrIs[m*self.radiusn+i]*self.radius[i]**2
"""
pdf_to_odf(odf, PrIs, self.radius, self.odfn, self.radiusn)
return odf
def odf(self,Pr):
""" fill the odf by sampling radially on the pdf
crucial parameter here is self.radius
"""
odf = np.zeros(self.odfn)
"""
#for all odf vertices
for m in range(self.odfn):
xi=self.origin+self.radius*self.odf_vertices[m,0]
yi=self.origin+self.radius*self.odf_vertices[m,1]
zi=self.origin+self.radius*self.odf_vertices[m,2]
#apply linear 3d interpolation (trilinear)
PrI=map_coordinates(Pr,np.vstack((xi,yi,zi)),order=1)
for i in range(self.radiusn):
odf[m]=odf[m]+PrI[i]*self.radius[i]**2
"""
PrIs=map_coordinates(Pr,self.Xs,order=1)
#print PrIs.shape
""" in pdf_to_odf an optimized version of the function below
for m in range(self.odfn):
for i in range(self.radiusn):
odf[m]=odf[m]+PrIs[m*self.radiusn+i]*self.radius[i]**2
"""
pdf_to_odf(odf,PrIs, self.radius,self.odfn,self.radiusn)
return odf
def pdf_odf(Pr, sphere, rradius, interp_coords):
r""" Calculates the real ODF from the diffusion propagator(PDF) Pr
Parameters
----------
Pr : array, shape (X, X, X)
probability density function
sphere : Sphere
reconstruction sphere
rradius : array, shape (N,)
interpolation range on the radius
interp_coords : array, shape (N, 3)
coordinates in the pdf for interpolating the odf
"""
verts_no = sphere.vertices.shape[0]
odf = np.zeros(verts_no)
rradius_no = len(rradius)
#interp_coords = pdf_interp_coords(sphere, rradius, origin)
PrIs = map_coordinates(Pr, interp_coords, order=1)
pdf_to_odf(odf, PrIs, rradius, verts_no, rradius_no)
return odf
