From 5bbf3f1ffee598904acb3d54997fda6b5927292b Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Tue, 26 Feb 2019 14:01:09 -0600
Subject: [PATCH] Using numpy array to transfer data rather than loops and
 additional double structure.

---
 scripts/openmc-voxel-to-vtk                 | 24 ++++++++++-----------
 tests/regression_tests/plot_voxel/plots.xml |  2 +-
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/scripts/openmc-voxel-to-vtk b/scripts/openmc-voxel-to-vtk
index c0d8e9a147..88172bb4c1 100755
--- a/scripts/openmc-voxel-to-vtk
+++ b/scripts/openmc-voxel-to-vtk
@@ -8,6 +8,7 @@ import numpy as np
 import h5py
 import vtk
 
+from vtk.util import numpy_support
 
 def main():
     # Process command line arguments
@@ -22,26 +23,25 @@ def main():
     dimension = fh.attrs['num_voxels']
     width = fh.attrs['voxel_width']
     lower_left = fh.attrs['lower_left']
-    voxel_data = fh['data'].value
 
     nx, ny, nz = dimension
     upper_right = lower_left + width*dimension
-    
+
     grid = vtk.vtkImageData()
     grid.SetDimensions(nx+1, ny+1, nz+1)
     grid.SetOrigin(*lower_left)
     grid.SetSpacing(*width)
-    
-    data = vtk.vtkDoubleArray()
+
+    # transpose data from OpenMC ordering (zyx) to VTK ordering (xyz)
+    # and flatten to 1-D array
+    h5data = fh['data'].value.T.flatten()
+    data = vtk.vtkIntArray()
     data.SetName("id")
-    data.SetNumberOfTuples(nx*ny*nz)
-    for x in range(nx):
-        sys.stdout.write(" {}%\r".format(int(x/nx*100)))
-        sys.stdout.flush()
-        for y in range(ny):
-            for z in range(nz):
-                i = z*nx*ny + y*nx + x
-                data.SetValue(i, voxel_data[x, y, z])
+    # pass h5data as a "hint" that no copy/allocation is necessary
+    data.SetArray(h5data, h5dara.size, True)
+    # set the data array
+    data.array = h5data
+    # add data to image grid
     grid.GetCellData().AddArray(data)
 
     writer = vtk.vtkXMLImageDataWriter()
diff --git a/tests/regression_tests/plot_voxel/plots.xml b/tests/regression_tests/plot_voxel/plots.xml
index 833329b427..e57992c2a7 100644
--- a/tests/regression_tests/plot_voxel/plots.xml
+++ b/tests/regression_tests/plot_voxel/plots.xml
@@ -2,7 +2,7 @@
 <plots>
 
   <plot id="4" type="voxel">
-    <pixels>50 50 10</pixels>
+    <pixels>500 500 100</pixels>
     <origin>0. 0. 0.</origin>
     <width>20 20 10</width>
   </plot>