Merge pull request #7 from bh107/xraysim-workaround

Xraysim workaround

.gitignore

@@ -6,23 +6,22 @@ dist/
 benchmarks/**/bin
 MANIFEST
 bh-job-*
-benchmarks/_utils/cil/Utilities/obj
 *.mdb
+
+benchmarks/_utils/cil/Utilities/obj
 benchmarks/black_scholes/cil/src/obj
 benchmarks/black_scholes/cs_cil/src/obj
 benchmarks/black_scholes/csharp_numcil/src/obj
+benchmarks/heat_equation/csharp_numcil/src/obj
+benchmarks/heat_equation_fixed/csharp_numcil/src/obj
 benchmarks/jacobi/csharp_numcil/src/obj
-black_scholes.userprefs
-jacobi.userprefs
 benchmarks/jacobi_fixed/csharp_numcil/src/obj
 benchmarks/jacobi_solve/csharp_numcil/src/obj
 benchmarks/jacobi_stencil/csharp_numcil/src/obj
 benchmarks/nbody/csharp_numcil/src/obj
-benchmarks/shallow_water/csharp_numcil/src/obj
 benchmarks/nbody_nice/csharp_numcil/src/obj
-shallow_water.userprefs
 benchmarks/reactiondiffusion/csharp_numcil/src/obj
-reactiondiffusion.userprefs
-benchmarks/heat_equation/csharp_numcil/src/obj
-benchmarks/heat_equation_fixed/csharp_numcil/src/obj
+benchmarks/shallow_water/csharp_numcil/src/obj
+benchmarks/xraysim/python_numpy/materials
+
 *.userprefs

benchmarks/xraysim/python_numpy/xraysim.py

@@ -133,14 +133,11 @@ def xraysim(sourcelist,
             #raydst is now to be correlated with material/attenuation grid
             t = sceneattenuates[...,np.newaxis] * raydst
             #We sums the three dimensions
-            t = np.add.reduce(t)
-            t = np.add.reduce(t)
-            t = np.add.reduce(t)
+            t = np.sum(t, axis=(0, 1, 2))
             dtectattenuates = t.reshape(detector_resolution, detector_resolution)
-
-            pixelintensity = ((np.ones(raylengths.shape) * source[power] * Const.invsqr) / raylengths).reshape(dshape)
+            pixelintensity = ((Const.invsqr * source[power] * np.ones(raylengths.shape[0])[..., np.newaxis]) / raylengths).reshape(dshape)
             area = np.dot( rayudirs, pixelareavector.reshape(3,1) ).reshape(dshape)
-            result += pixelintensity * area * np.exp(- dtectattenuates)
+            result += pixelintensity * area * np.exp(-dtectattenuates)
             ret.append(result)
             if visualize:
                 low = np.minimum.reduce(result.flatten())
@@ -180,7 +177,7 @@ def main():
 
     B.start()
     for _ in xrange(iterations):
-        detector_results = xraysim(*scene,  visualize=B.visualize)
+        detector_results = xraysim(*scene, visualize=B.visualize)
         if util.Benchmark().bohrium:
             B.flush()
 

benchmarks/xraysim/python_numpy/xraysimgeometry.py

@@ -59,7 +59,7 @@ def raygeometry(src, detpixpos):
     origin         = np.array([src[0],src[1],src[2]])
     rays           = detpixpos.reshape(raycount,3)[:,0:3] - origin
 
-    raydistances   = np.sqrt( np.add.reduce( rays*rays , axis=1) ).reshape(raycount,1)
+    raydistances   = np.sqrt(np.sum(rays*rays, axis=1)).reshape(raycount,1)
     unitrays       = rays / raydistances
 
     rayinverses    = np.ones(unitrays.shape) / unitrays
@@ -149,5 +149,3 @@ def runAABB( scenegrid,
 
     voxelraydistances = (t_out-t_in)*(t_out>=t_in)
     return voxelraydistances
-
-