Changeset 554 for sans/XOP_Dev/SANSAnalysis

Timestamp:

Sep 10, 2009 3:56:43 PM (13 years ago)

Author:

srkline

Message:

(libTwoPhase):re-definition if DAB parameters so they are not correlated

(libSphere): correct integration ranges/normalization for simple cubic model

(elliptical cylinder): wholesale changes (JaeHie??). not really sure of these, but probably related to the definition of the relative orientation angles.

Location:

sans/XOP_Dev/SANSAnalysis/lib

Files:

• DANSE/c_extensions/elliptical_cylinder.c (modified) (6 diffs)
• libSphere.c (modified) (2 diffs)
• libTwoPhase.c (modified) (2 diffs)

sans/XOP_Dev/SANSAnalysis/lib/DANSE/c_extensions/elliptical_cylinder.c

@@ -18 +18 @@
 double elliptical_cylinder_analytical_1D(EllipticalCylinderParameters *pars, double q) {
         double dp[6];
-        
+
         // Fill paramater array
         dp[0] = pars->scale;
@@ -26 +26 @@
         dp[4] = pars->contrast;
         dp[5] = pars->background;
-        
+
         // Call library function to evaluate model
-        return EllipCyl20(dp, q);       
+        return EllipCyl20(dp, q);
 }
 
-double elliptical_cylinder_kernel(EllipticalCylinderParameters *pars, double q, double alpha, double psi) {
+double elliptical_cylinder_kernel(EllipticalCylinderParameters *pars, double q, double alpha, double psi, double nu) {
         double qr;
         double qL;
         double r_major;
         double kernel;
-        
+
         r_major = pars->r_ratio * pars->r_minor;
 
-        qr = q*sin(alpha)*sqrt( r_major*r_major*sin(psi)*sin(psi) + pars->r_minor*pars->r_minor*cos(psi)*cos(psi) );
+        qr = q*sin(alpha)*sqrt( r_major*r_major*sin(nu)*sin(nu) + pars->r_minor*pars->r_minor*cos(nu)*cos(nu) );
         qL = q*pars->length*cos(alpha)/2.0;
-        
+
         kernel = 2.0*NR_BessJ1(qr)/qr * sin(qL)/qL;
         return kernel*kernel;
@@ -56 +56 @@
         q = sqrt(qx*qx+qy*qy);
     return elliptical_cylinder_analytical_2D_scaled(pars, q, qx/q, qy/q);
-} 
+}
 
 /**
@@ -62 +62 @@
  * @param pars: parameters of the cylinder
  * @param q: q-value
- * @param phi: angle phi
+ * @param theta: angle theta = angle wrt z axis
+ * @param phi: angle phi = angle around y axis (starting from the x+-direction as phi = 0)
  * @return: function value
  */
 double elliptical_cylinder_analytical_2D(EllipticalCylinderParameters *pars, double q, double phi) {
     return elliptical_cylinder_analytical_2D_scaled(pars, q, cos(phi), sin(phi));
-} 
+}
 
 /**
@@ -79 +80 @@
 double elliptical_cylinder_analytical_2D_scaled(EllipticalCylinderParameters *pars, double q, double q_x, double q_y) {
         double cyl_x, cyl_y, cyl_z;
+        double ell_x, ell_y;
         double q_z;
         double alpha, vol, cos_val;
+        double nu, cos_nu;
         double answer;
-        
-    // Cylinder orientation
+
+    //Cylinder orientation
     cyl_x = sin(pars->cyl_theta) * cos(pars->cyl_phi);
     cyl_y = sin(pars->cyl_theta) * sin(pars->cyl_phi);
     cyl_z = cos(pars->cyl_theta);
-     
+
     // q vector
     q_z = 0;
-        
+
     // Compute the angle btw vector q and the
     // axis of the cylinder
     cos_val = cyl_x*q_x + cyl_y*q_y + cyl_z*q_z;
-    
+
     // The following test should always pass
     if (fabs(cos_val)>1.0) {
@@ -100 +103 @@
         return 0;
     }
-    
+
     // Note: cos(alpha) = 0 and 1 will get an
     // undefined value from CylKernel
         alpha = acos( cos_val );
-        
-        answer = elliptical_cylinder_kernel(pars, q, alpha, pars->cyl_psi);
-        
+
+    //ellipse orientation:
+        // the elliptical corss section was transformed and projected
+        // into the detector plane already through sin(alpha)and furthermore psi remains as same
+        // on the detector plane.
+        // So, all we need is to calculate the angle (nu) of the minor axis of the ellipse wrt
+        // the wave vector q.
+        // JaeHie Cho 12JUN09
+
+        //x- y- component on the detector plane.
+    ell_x =  cos(pars->cyl_psi);
+    ell_y =  sin(pars->cyl_psi);
+
+    // calculate the axis of the ellipse wrt q-coord.
+    cos_nu = ell_x*q_x + ell_y*q_y;
+    nu = acos(cos_nu);
+
+    // The following test should always pass
+    if (fabs(cos_nu)>1.0) {
+        printf("cyl_ana_2D: Unexpected error: cos(nu)>1\n");
+        return 0;
+    }
+
+        answer = elliptical_cylinder_kernel(pars, q, alpha, pars->cyl_psi,nu);
+
         // Multiply by contrast^2
         answer *= pars->contrast*pars->contrast;
-        
+
         //normalize by cylinder volume
         //NOTE that for this (Fournet) definition of the integral, one must MULTIPLY by Vcyl
     vol = acos(-1.0) * pars->r_minor * pars->r_minor * pars->r_ratio * pars->length;
         answer *= vol;
-        
+
         //convert to [cm-1]
         answer *= 1.0e8;
-        
+
         //Scale
         answer *= pars->scale;
-        
+
         // add in the background
         answer += pars->background;
-        
+
         return answer;
 }
-    
+

sans/XOP_Dev/SANSAnalysis/lib/libSphere.c

@@ -2038 +2038 @@
         Pi = 4.0*atan(1.0);
         va = 0.0;
-        vb = 2.0*Pi;            //orintational average, outer integral
+        vb = Pi/2.0;            //orintational average, outer integral
         vaj = 0.0;
-        vbj = Pi;               //endpoints of inner integral
+        vbj = Pi/2.0;           //endpoints of inner integral
         
         summ = 0.0;                     //initialize intergral
@@ -2104 +2104 @@
         
         retVal = temp2*SCeval(yy,xx,temp3,temp4,temp5);
-        retVal /= 4*Pi;
+        retVal *= 2.0/Pi;
         
         return(retVal);

sans/XOP_Dev/SANSAnalysis/lib/libTwoPhase.c

@@ -116 +116 @@
 }
 
+// 6 JUL 2009 SRK changed definition of Izero scale factor to be uncorrelated with range
+//
 double
 DAB_Model(double dp[], double q)
@@ -127 +129 @@
         incoh = dp[2]; 
         
-        inten = Izero/pow((1.0 + (qval*range)*(qval*range)),2) + incoh;
+        inten = (Izero*range*range*range)/pow((1.0 + (qval*range)*(qval*range)),2) + incoh;
         
         return(inten);