Changes in / [4ee041f:06aaa75d] in sasview

Files:

• sasview/default_categories.json (modified) (1 diff)
• sasview/test/1d_data/saxess_example.pdh (deleted)
• setup.py (modified) (1 diff)
• src/sas/models/c_extension/c_models/barbell.cpp (modified) (6 diffs)
• src/sas/sasgui/perspectives/fitting/models.py (modified) (2 diffs)

sasview/default_categories.json

@@ -1 @@
-{"Shapes": [["BarBellModel", true], ["PearlNecklaceModel", true], ["HollowCylinderModel", true], ["CoreMultiShellModel", true], ["FCCrystalModel", true], ["ParallelepipedModel", true], ["FuzzySphereModel", true], ["CoreShellEllipsoidXTModel", true], ["LamellarPCrystalModel", true], ["BCCrystalModel", true], ["EllipticalCylinderModel", true], ["RectangularHollowPrismInfThinWallsModel", true], ["CSParallelepipedModel", true], ["OnionExpShellModel", true], ["MultiShellModel", true], ["RaspBerryModel", true], ["CoreShellEllipsoidModel", true], ["CappedCylinderModel", true], ["CylinderModel", true], ["SphericalSLDModel", true], ["SCCrystalModel", true], ["StackedDisksModel", true], ["LamellarPSHGModel", true], ["CoreShellBicelleModel", true], ["RectangularHollowPrismModel", true], ["LamellarPSModel", true], ["EllipsoidModel", true], ["SphereModel", true], ["VesicleModel", true], ["TriaxialEllipsoidModel", true], ["LamellarModel", true], ["PringlesModel", true], ["RectangularPrismModel", true], ["CoreShellCylinderModel", true], ["BinaryHSModel", true], ["FlexibleCylinderModel", true], ["LamellarFFHGModel", true], ["FlexCylEllipXModel", true], ["LinearPearlsModel", true], ["CoreShellModel", true]], "Structure Factor": [["SquareWellStructure", true], ["HayterMSAStructure", true], ["HardsphereStructure", true], ["StickyHSStructure", true]], "Shape-Independent": [["TwoPowerLawModel", true], ["GelFitModel", true], ["DABModel", true], ["PowerLawAbsModel", true], ["PorodModel", true], ["GuinierModel", true], ["RPA10Model", true], ["TeubnerStreyModel", true], ["StarPolymer", true], ["UnifiedPowerRgModel", true], ["MassSurfaceFractal", true], ["Core2ndMomentModel", true], ["TwoLorentzianModel", true], ["DebyeModel", true], ["MassFractalModel", true], ["GuinierPorodModel", true], ["CorrLengthModel", true], ["PolymerExclVolume", true], ["FractalModel", true], ["PeakLorentzModel", true], ["BroadPeakModel", true], ["FractalCoreShellModel", true], ["PeakGaussModel", true], ["BEPolyelectrolyte", true], ["Poly_GaussCoil", true], ["SurfaceFractalModel", true], ["GaussLorentzGelModel", true], ["LorentzModel", true]], "Uncategorized": [["ReflectivityModel", true], ["ReflectivityIIModel", true], ["LineModel", true], ["MicelleSphCoreModel", true]]}
+{"Shapes": [["PearlNecklaceModel", true], ["HollowCylinderModel", true], ["CoreMultiShellModel", true], ["FCCrystalModel", true], ["CoreShellEllipsoidXTModel", true], ["FuzzySphereModel", true], ["CSParallelepipedModel", true], ["EllipticalCylinderModel", true], ["BCCrystalModel", true], ["LamellarFFHGModel", true], ["RectangularHollowPrismInfThinWallsModel", true], ["LamellarPCrystalModel", true], ["OnionExpShellModel", true], ["VesicleModel", true], ["MultiShellModel", true], ["RaspBerryModel", true], ["CoreShellEllipsoidModel", true], ["CappedCylinderModel", true], ["CylinderModel", true], ["SphericalSLDModel", true], ["StackedDisksModel", true], ["LamellarPSHGModel", true], ["CoreShellBicelleModel", true], ["RectangularHollowPrismModel", true], ["LamellarPSModel", true], ["EllipsoidModel", true], ["SphereModel", true], ["ParallelepipedModel", true], ["TriaxialEllipsoidModel", true], ["LamellarModel", true], ["PringlesModel", true], ["RectangularPrismModel", true], ["CoreShellCylinderModel", true], ["BinaryHSModel", true], ["FlexibleCylinderModel", true], ["SCCrystalModel", true], ["FlexCylEllipXModel", true], ["LinearPearlsModel", true], ["CoreShellModel", true]], "Structure Factor": [["SquareWellStructure", true], ["HayterMSAStructure", true], ["HardsphereStructure", true], ["StickyHSStructure", true]], "Shape-Independent": [["TwoPowerLawModel", true], ["GelFitModel", true], ["DABModel", true], ["PowerLawAbsModel", true], ["PorodModel", true], ["MassFractalModel", true], ["RPA10Model", true], ["TeubnerStreyModel", true], ["DebyeModel", true], ["MassSurfaceFractal", true], ["Core2ndMomentModel", true], ["TwoLorentzianModel", true], ["UnifiedPowerRgModel", true], ["PolymerExclVolume", true], ["BEPolyelectrolyte", true], ["GuinierModel", true], ["GuinierPorodModel", true], ["CorrLengthModel", true], ["StarPolymer", true], ["FractalModel", true], ["PeakLorentzModel", true], ["BroadPeakModel", true], ["PeakGaussModel", true], ["FractalCoreShellModel", true], ["Poly_GaussCoil", true], ["SurfaceFractalModel", true], ["GaussLorentzGelModel", true], ["LorentzModel", true]], "Uncategorized": [["ReflectivityModel", true], ["ReflectivityIIModel", true], ["LineModel", true], ["MicelleSphCoreModel", true]]}

setup.py

@@ -96 +96 @@
     try:
         darwin_ver = int(os.uname()[2].split('.')[0])
-        if darwin_ver >= 13 and darwin_ver < 14:
+        if darwin_ver >= 13:
             platform_copt = {'unix' : ['-Wno-error=unused-command-line-argument-hard-error-in-future']}
     except:

src/sas/models/c_extension/c_models/barbell.cpp

@@ -30 +30 @@
         #include "barbell.h"
 }
-
-// Convenience parameter structure
-typedef struct {
-    double scale;
-    double rad_bar;
-    double len_bar;
-    double rad_bell;
-    double sld_barbell;
-    double sld_solv;
-    double background;
-    double theta;
-    double phi;
-} BarBellParameters;
 
 BarBellModel :: BarBellModel() {
@@ -59 +46 @@
 }
 
-double barbell2d_kernel(double dp[], double q, double alpha) {
+double bar2d_kernel(double dp[], double q, double alpha) {
   int j;
   double Pi;
@@ -126 +113 @@
   return answer;
 }
-
-/**
- * Function to evaluate 2D scattering function
- * @param pars: parameters of the BarBell
- * @param q: q-value
- * @param q_x: q_x / q
- * @param q_y: q_y / q
- * @return: function value
- */
-static double barbell_analytical_2D_scaled(BarBellParameters *pars, double q, double q_x, double q_y) {
-  double cyl_x, cyl_y;//, cyl_z;
-  //double q_z;
-  double alpha, cos_val;
-  double answer;
-  double dp[7];
-  //convert angle degree to radian
-  double pi = 4.0*atan(1.0);
-  double theta = pars->theta * pi/180.0;
-  double phi = pars->phi * pi/180.0;
-
-  dp[0] = pars->scale;
-  dp[1] = pars->rad_bar;
-  dp[2] = pars->len_bar;
-  dp[3] = pars->rad_bell;
-  dp[4] = pars->sld_barbell;
-  dp[5] = pars->sld_solv;
-  dp[6] = pars->background;
-
-
-  //double Pi = 4.0*atan(1.0);
-    // Cylinder orientation
-    cyl_x = cos(theta) * cos(phi);
-    cyl_y = sin(theta);
-    //cyl_z = -cos(theta) * sin(phi);
-
-    // 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) {
-      printf("cyl_ana_2D: Unexpected error: cos(alpha)>1\n");
-      return 0;
-    }
-
-    // Note: cos(alpha) = 0 and 1 will get an
-    // undefined value from CylKernel
-  alpha = acos( cos_val );
-
-  answer = barbell2d_kernel(dp, q, alpha);
-
-
-  return answer;
-
-}
-
-/**
- * Function to evaluate 2D scattering function
- * @param pars: parameters of the BarBell
- * @param q: q-value
- * @return: function value
- */
-static double barbell_analytical_2DXY(BarBellParameters *pars, double qx, double qy){
-  double q;
-  q = sqrt(qx*qx+qy*qy);
-  return barbell_analytical_2D_scaled(pars, q, qx/q, qy/q);
-}
-
 /**
  * Function to evaluate 1D scattering function
@@ -274 +190 @@
  */
 double BarBellModel :: operator()(double qx, double qy) {
-  BarBellParameters dp;
-
-        // Fill parameter array for IGOR library
-        // Add the background after averaging
-        dp.scale = scale();
-        dp.rad_bar = rad_bar();
-        dp.len_bar = len_bar();
-        dp.rad_bell = rad_bell();
-        dp.sld_barbell = sld_barbell();
-        dp.sld_solv = sld_solv();
-        dp.background = 0.0;
-        dp.theta = theta();
-        dp.phi = phi();
+  double dp[7];
+
+  // Fill parameter array for IGOR library
+  // Add the background after averaging
+  dp[0] = scale();
+  dp[1] = rad_bar();
+  dp[2] = len_bar();
+  dp[3] = rad_bell();
+  dp[4] = sld_barbell();
+  dp[5] = sld_solv();
+  dp[6] = 0.0;
+
+  double _theta = theta();
+  double _phi = phi();
 
         // Get the dispersion points for the rad_bar
@@ -320 +237 @@
         // Loop over radius weight points
         for(size_t i=0; i<weights_rad_bar.size(); i++) {
-                dp.rad_bar = weights_rad_bar[i].value;
+                dp[1] = weights_rad_bar[i].value;
                 for(size_t j=0; j<weights_len_bar.size(); j++) {
-                        dp.len_bar = weights_len_bar[j].value;
+                        dp[2] = weights_len_bar[j].value;
                         for(size_t k=0; k<weights_rad_bell.size(); k++) {
-                                dp.rad_bell = weights_rad_bell[k].value;
+                                dp[3] = weights_rad_bell[k].value;
                                 // Average over theta distribution
                                 for(size_t l=0; l< weights_theta.size(); l++) {
-                                        dp.theta = weights_theta[l].value;
+                                        _theta = weights_theta[l].value;
                                         // Average over phi distribution
                                         for(size_t m=0; m< weights_phi.size(); m++) {
-                                                dp.phi = weights_phi[m].value;
+                                                _phi = weights_phi[m].value;
                                                 //Un-normalize Form by volume
-                                                hDist = -sqrt(fabs(dp.rad_bell*dp.rad_bell-dp.rad_bar*dp.rad_bar));
-                                                vol_i = pi*dp.rad_bar*dp.rad_bar*dp.len_bar+2.0*pi/3.0*((dp.rad_bell-hDist)*(dp.rad_bell-hDist)*
-                                                                                (2*dp.rad_bell+hDist));
+                                                hDist = sqrt(fabs(dp[3]*dp[3]-dp[1]*dp[1]));
+                                                vol_i = pi*dp[1]*dp[1]*dp[2]+2.0*pi*(2.0*dp[3]*dp[3]*dp[3]/3.0
+                                                                                +dp[3]*dp[3]*hDist-hDist*hDist*hDist/3.0);
+
+                                          const double q = sqrt(qx*qx+qy*qy);
+                                          //convert angle degree to radian
+                                          const double pi = 4.0*atan(1.0);
+
+                                          // Cylinder orientation
+                                    const double cyl_x = cos(_theta * pi/180.0) * cos(_phi * pi/180.0);
+                                    const double cyl_y = sin(_theta * pi/180.0);
+
+                                    // Compute the angle btw vector q and the
+                                    // axis of the cylinder (assume qz = 0)
+                                    const double cos_val = cyl_x*qx + cyl_y*qy;
+
+                                    // The following test should always pass
+                                    if (fabs(cos_val)>1.0) {
+                                      return 0;
+                                    }
+
+                                    // Note: cos(alpha) = 0 and 1 will get an
+                                    // undefined value from CylKernel
+                                    const double alpha = acos( cos_val );
+
+            // Call the IGOR library function to get the kernel
+            const double output = bar2d_kernel(dp, q, alpha)/sin(alpha);
+
                                                 double _ptvalue = weights_rad_bar[i].weight
                                                                                         * weights_len_bar[j].weight
@@ -341 +283 @@
                                                                                         * weights_phi[m].weight
                                                                                         * vol_i
-                                                                                        * barbell_analytical_2DXY(&dp, qx, qy);
-                                                                                        //* output;
+                                                                                        * output;
                                                                                         //* pow(weights_rad[i].value,3.0);
 

src/sas/sasgui/perspectives/fitting/models.py

@@ -315 +315 @@
         # regular model names only
         base_message = "Unable to load model {0}"
-        self.model_name_list = []
-        try:
+        try:
+            self.model_name_list = []
             from sas.models.SphereModel import SphereModel
             self.model_dictionary[SphereModel.__name__] = SphereModel
@@ -529 +529 @@
         except:
             logging.error(base_message.format(EllipticalCylinderModel.__name__))
-
-        try:
-            from sas.models.BarBellModel import BarBellModel
-
-            self.model_dictionary[BarBellModel.__name__] = BarBellModel
-            #       self.shape_list.append(BarBellModel)
-            self.model_name_list.append(BarBellModel.__name__)
-        except:
-            logging.error(base_message.format(BarBellModel.__name__))
 
         try: