Delete modelfunctions.h

NODDI_Watson_diff/development/modelfunctions.h

-
-#include "diffusivities.h"
-#include "WatsonFunctions.h"
-#include "LegendreFunctions.h"
-
-// Parameters in NODDI-Watson 
-// P[0]: fiso
-// P[1]: fintra
-// P[2]: kappa
-// P[3]: th
-// P[4]: ph
-
-// CFP[0:2] are bvecs 
-// CFP[3] are bvals
-// FixP[0] is S0
-
-MACRO T step_size(T param, T scale){
-  T step;
-  step = (T)TINY*nonzerosign(param)*fabs_gpu(param)*scale;
-  step = min_gpu(max_gpu(fabs_gpu(step),(T)MINSTEP),(T)MAXSTEP);
-  
-  return step;
-}
-
-MACRO T Calculate_ExtraCellular(T* P,
-				T* CFP,
-				T& xv)
-{
-  // Calculate Signal from ExtraCellular compartment //
-  
-  //dPerp = dPar*(1-f);
-  T Dperpendicular = Dparallel*(1-P[1]);
-  
-  T Dpar_equivalent;
-  T Dperp_equivalent;
-  
-  WatsonHinderedDiffusionCoeff(P[2],Dperpendicular,Dpar_equivalent,Dperp_equivalent);
-  
-  //exp(-bval.*((dPar - dPerp)*cosThetaSq + dPerp));
-  T ExtraCell = exp_gpu(-CFP[3]*((Dpar_equivalent - Dperp_equivalent)*xv*xv + Dperp_equivalent));
-  
-  return ExtraCell;
-}
-
-MACRO T Calculate_IntraCellular(T* P,
-				T* CFP,
-				T& xv)
-{
-  // Calculate Signal from IntraCellular compartment //
-
-  T parComp =-CFP[3]*Dparallel; // Parallel component: -bval * dintra
-  // Radius is 0, so no Perpendicular Component
-
-  // Compute Legendre weighted signal
-  T lgi[7]; // legendre  gaussian integral
-  legendreGaussianIntegral(-parComp,lgi);
-  
-  // Compute the spherical harmonic coefficients of the Watson's distribution
-  T coeff[7];
-  WatsonSHCoeff(P[2],coeff);
-  
-  for(int i=0;i<7;i++){
-    lgi[i]*=coeff[i];
-  }
-  
-  if(xv>1) xv=1;
-  if(xv<-1) xv=-1;
-  // Compute the SH values at cosTheta
-  T SH[7];
-  computeSH_values(xv,SH);
-  
-  for(int i=0;i<7;i++){
-    lgi[i]*=SH[i];
-  }
-  
-  T IntraCell = (T)0.0;
-  for(int i=0;i<7;i++){
-    IntraCell+=lgi[i];
-  }
-  
-  // Remove negative values
-  if(IntraCell<0) IntraCell=1e-3;
-  IntraCell *= (T)0.5;
-
-  return IntraCell;
-}
-
-MACRO T Predicted_Signal(
-			 int npar, // Number of Parameters to estimate
-			 T* P, 	// Estimated parameters
-			 T* CFP, // Fixed Parameters common to all the voxels
-			 T* FixP) // Fixed Parameters for each voxel
-{
-  T isoterm = exp_gpu(-CFP[3]*Diso); 	// exp(-bval*d)
-
-  T xv = CFP[0]*sin_gpu(P[3])*cos_gpu(P[4])	// (bvec(1)*sinth*cosph
-	+ CFP[1]*sin_gpu(P[3])*sin_gpu(P[4]) 	// + bvec(2)*sinth*sinph
-	+ CFP[2]*cos_gpu(P[3]);			// + bvec(3)*costh)
-
-  T ExtraCell = Calculate_ExtraCellular(P,CFP,xv);
-  T IntraCell = Calculate_IntraCellular(P,CFP,xv);
-		
-  T anisoterm = (1-P[1])*ExtraCell+P[1]*IntraCell;
-  
-  T pred_signal=FixP[0]*((1-P[0])*anisoterm + P[0]*isoterm);
-    
-  return pred_signal;
-}
-
-// Constraints checked during MCMC (if MCMC is used)
-MACRO bool ConstraintsMCMC(
-		       int npar, // Number of Parameters to estimate
-		       T* P) // Estimated parameters
-{
-  return true;
-}
-
-// Partial derivatives respect each model parameter
-MACRO void Partial_Derivatives(
-			       int npar, // Number of Parameters to estimate
-			       T* P, // Estimated parameters, use P*
-			       T* CFP, // Fixed Parameters common to all the voxels
-			       T* FixP, // Fixed Parameters for each voxel
-			       T* derivatives) // Derivative respect each model estimated parameter
-{
-  T isoterm = exp_gpu(-CFP[3]*Diso); 	// exp(-bval*d)
-
-  T xv = CFP[0]*sin_gpu(P[3])*cos_gpu(P[4])	// (bvec(1)*sinth*cosph
-	+ CFP[1]*sin_gpu(P[3])*sin_gpu(P[4]) 	// + bvec(2)*sinth*sinph
-	+ CFP[2]*cos_gpu(P[3]);			// + bvec(3)*costh)
-
-  T ExtraCell = Calculate_ExtraCellular(P,CFP,xv);
-  T IntraCell = Calculate_IntraCellular(P,CFP,xv);
-		
-  T anisoterm = (1-P[1])*ExtraCell+P[1]*IntraCell;
-  
-  //T pred_signal=FixP[0]*((1-P[0])*anisoterm + P[0]*isoterm);
- 
-  // df/fiso
-  derivatives[0]= FixP[0]*(isoterm-anisoterm);
- 
-  // df/fintra
-  derivatives[1]= FixP[0]*(1-P[0])*(IntraCell - ExtraCell);
-
-  // df/dk   
-  // numerical differentiation
-  derivatives[2]=NUMERICAL(2);
-
-  // df/dth   
-  // numerical differentiation
-  derivatives[3]=NUMERICAL(3);
-
-  // df/dph   
-  // numerical differentiation
-  derivatives[4]=NUMERICAL(4);
-}
-
-// Constraints run after LevenbergMarquardt (if LevenbergMarquardt is used)
-MACRO void FixConstraintsLM(	
-			    int npar, // Number of Parameters to estimate
-			    T* P) // Estimated parameters
-{
-}
-
-MACRO T custom_priors(
-       int id_p,   // the number of parameter in the model (starts at 0)
-			 T* P, 		// Estimated parameters
-       int nmeas, // Number of measurements per voxel
-			 T* CFP, 	// Fixed Parameters common to all the voxels for all measurements !!
-			 T* FixP) 	// Fixed Parameters for each voxel
-{
-	return (T)0.0;
-}
-