diff --git a/amico/models.pyx b/amico/models.pyx index bd52cce..b51d952 100644 --- a/amico/models.pyx +++ b/amico/models.pyx @@ -248,7 +248,14 @@ class StickZeppelinBall( BaseModel ) : self.d_isos = np.array([ 3.0E-3 ]) # Isotropic diffusivitie(s) [mm^2/s] - def set( self, d_par, d_perps_zep, d_isos, d_par_zep=None, d_perp=0 ) : + def set( + self, + d_par=1.7E-3, + d_perps_zep=np.array([1.19E-3, 0.85E-3, 0.51E-3, 0.17E-3]), + d_isos=np.array([3.0E-3]), + d_par_zep=1.7E-3, + d_perp=0 + ): self.d_par = d_par self.d_perp = d_perp if d_par_zep is None: @@ -384,7 +391,13 @@ class CylinderZeppelinBall( BaseModel ) : self.isExvivo = False # Add dot compartment to dictionary (exvivo data) - def set( self, d_par, Rs, d_perps, d_isos ) : + def set( + self, + d_par=0.6E-3, + Rs=np.concatenate(([0.01], np.linspace(0.5, 8.0, 20))) * 1E-6, + d_perps=np.array([1.19E-3, 0.85E-3, 0.51E-3, 0.17E-3]), + d_isos=np.array([2.0E-3]) + ): self.d_par = d_par self.Rs = np.array(Rs) self.d_perps = np.array(d_perps) @@ -644,11 +657,18 @@ class NODDI( BaseModel ) : self.isExvivo = False - def set( self, dPar, dIso, IC_VFs, IC_ODs, isExvivo ): + def set( + self, + dPar=1.7E-33, + dIso=3.0E-3, + IC_VFs=np.linspace(0.1, 0.99, 12), + IC_ODs=np.hstack((np.array([0.03, 0.06]), np.linspace(0.09, 0.99, 10))), + isExvivo=False + ): self.dPar = dPar self.dIso = dIso - self.IC_VFs = np.array( IC_VFs ) - self.IC_ODs = np.array( IC_ODs ) + self.IC_VFs = np.array( IC_VFs ) if isinstance(IC_VFs, list) else IC_VFs + self.IC_ODs = np.array( IC_ODs ) if isinstance(IC_ODs, list) else IC_ODs self.isExvivo = isExvivo if isExvivo: self.maps_name.append('dot') @@ -969,7 +989,13 @@ class FreeWater( BaseModel ) : self.d_isos = [ 2.5E-3 ] # Isotropic diffusivities [mm^2/s] - def set( self, d_par, d_perps, d_isos, type ) : + def set( + self, + d_par=1.0E-3, + d_perps=np.linspace(0.1, 1.0, 10) * 1E-3, + d_isos=np.array([2.5E-3]), + type='Human' + ): self.d_par = d_par self.d_perps = d_perps self.d_isos = d_isos @@ -1296,7 +1322,13 @@ class SANDI( BaseModel ) : self.d_isos = np.linspace(0.25,3.0,5) * 1E-3 # Extra-cellular isotropic mean diffusivitie(s) [mm^2/s] - def set( self, d_is, Rs, d_in, d_isos ) : + def set( + self, + d_is=3.0E-3, + Rs=np.linspace(1.0, 12.0, 5) * 1E-6, + d_in=np.linspace(0.25, 3.0, 5) * 1E-3, + d_isos=np.linspace(0.25, 3.0, 5) * 1E-3 + ): self.d_is = d_is self.Rs = np.array(Rs) self.d_in = np.array(d_in)