upd script

devtools/fakeData/fake-gisas1.py

@@ -10,47 +10,51 @@ There are, however, some systematic distortions:
 """
 
 import bornagain as ba
-from bornagain import deg, nm
+from bornagain import deg, nm, ba_plot as bp
 import numpy as np
 
-mat_vacuum = ba.HomogeneousMaterial("Vacuum", 0, 0)
+mat_vacuum = ba.RefractiveMaterial("Vacuum", 0, 0)
 # nominal material constants are (6e-6, 2e-8) and (6e-4, 2e-8)
-mat_substrate = ba.HomogeneousMaterial("Substrate", 6.3e-6, 4e-7)
-mat_particle = ba.HomogeneousMaterial("Particle", 5.8e-4, 2e-7)
+mat_substrate = ba.RefractiveMaterial("Substrate", 6.3e-6, 4e-7)
+mat_particle = ba.RefractiveMaterial("Particle", 3e-5, 2e-7)
 
 
 def get_sample(params):
     h = params["cylinder_height"]
     r = params["cylinder_radius"]
+    ro = params["surface_density"]
 
-    ff1 = ba.FormFactorCone(1.1*r, h, 80*deg)
-    ff2 = ba.FormFactorTruncatedSpheroid(r, 3.3*h, 2.5*h/r, 2.2*h)
+    ff1 = ba.Cone(1.1*r, h, 80*deg)
+    ff2 = ba.TruncatedSpheroid(r, 3.3*h, 2.5*h/r, 2.2*h)
 
     layout = ba.ParticleLayout()
     layout.addParticle(ba.Particle(mat_particle, ff1), .4)
     layout.addParticle(ba.Particle(mat_particle, ff2), .6)
+    layout.setTotalParticleSurfaceDensity(ro)
 
     layer_1 = ba.Layer(mat_vacuum)
     layer_1.addLayout(layout)
     layer_2 = ba.Layer(mat_substrate)
 
+    sigma, hurst, corrLength = 0.2*nm, 0.3, 20*nm
+    roughness = ba.LayerRoughness(sigma, hurst, corrLength)
+
     sample = ba.MultiLayer()
     sample.addLayer(layer_1)
-    sample.addLayer(layer_2)
+    sample.addLayerWithTopRoughness(layer_2, roughness)
     return sample
 
 
 def get_simulation(params):
     # nominal beam parameters are 0.1*nm, 0.2*deg
-    beam = ba.Beam(10**params['lg(intensity)'], 0.0993*nm,
-                   ba.Direction(0.202*deg, 0))
+    beam = ba.Beam(10**params['lg(intensity)'], 0.0993*nm, 0.202*deg)
 
     # nominal detector x-axis starts from -1.5*deg
-    det = ba.SphericalDetector(100, -1.49*deg, 1.5*deg, 100, 0, 3*deg)
+    det = ba.SphericalDetector(120, -1.49*deg, 1.5*deg, 120, 0, 3*deg)
 
     sample = get_sample(params)
 
-    simulation = ba.GISASSimulation(beam, sample, det)
+    simulation = ba.ScatteringSimulation(beam, sample, det)
     if 'lg(background)' in params:
         simulation.setBackground(
             ba.ConstantBackground(10**params['lg(background)']))
@@ -60,10 +64,11 @@ def get_simulation(params):
 
 def model_parameters():
     return {
-        'lg(intensity)': 6,
-        'lg(background)': 0.5,
+        'lg(intensity)': 9,
+        'lg(background)': 1.2,
         'cylinder_height': 4*nm,
         'cylinder_radius': 5*nm,
+        'surface_density': 0.005
     }
 
 
@@ -76,14 +81,16 @@ def fake_data():
 
     # Compute model distribution
     simulation = get_simulation(params)
-    simulation.runSimulation()
-    theory = simulation.result().array()
+    result = simulation.simulate()
+    bp.plot_simulation_result(result)
+
+    theory = result.npArray()
 
     # Draw noisy data
     data = np.random.poisson(theory)
 
     # Save to numpy
-    np.savetxt("faked-gisas1.txt.gz", data)
+    np.savetxt("faked-gisas.txt", data)
 
 
 if __name__ == '__main__':