From 8ad75f888c0a98235b34914ccc9df2c705277c89 Mon Sep 17 00:00:00 2001
From: Craig Warren <craig_warren@me.com>
Date: Fri, 15 Jul 2016 13:36:04 +0100
Subject: [PATCH] Added function to build voxels from a mask array.

---
 gprMax/geometry_primitives.pyx | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gprMax/geometry_primitives.pyx b/gprMax/geometry_primitives.pyx
index 821e0423..e4f3f74b 100644
--- a/gprMax/geometry_primitives.pyx
+++ b/gprMax/geometry_primitives.pyx
@@ -702,3 +702,36 @@ cpdef void build_voxels_from_array(int xs, int ys, int zs, int numexistmaterials
                     numID += numexistmaterials
                     build_voxel(i, j, k, numID, numID, numID, numID, False, solid, rigidE, rigidH, ID)
 
+
+cpdef void build_voxels_from_array_mask(int xs, int ys, int zs, int waternumID, int grassnumID, np.int8_t[:, :, ::1] mask, np.int16_t[:, :, ::1] data, np.uint32_t[:, :, ::1] solid, np.int8_t[:, :, :, ::1] rigidE, np.int8_t[:, :, :, ::1] rigidH, np.uint32_t[:, :, :, ::1] ID):
+    """Builds Yee voxels by reading integers from an array.
+        
+    Args:
+        xs, ys, zs (int): Cell coordinates of position of start of array in domain.
+        waternumID, grassnumID (int): Numeric ID of water and grass materials.
+        data (memoryview): Access to array containing numeric IDs of voxels to create.
+        mask (memoryview): Access to array containing a mask of voxels to create.
+        solid, rigidE, rigidH, ID (memoryviews): Access to solid, rigid and ID arrays.
+    """
+
+    cdef Py_ssize_t i, j, k
+    cdef int xf, yf, zf, numID, numIDx, numIDy, numIDz
+    
+    # Set upper bounds
+    xf = xs + data.shape[0]
+    yf = ys + data.shape[1]
+    zf = zs + data.shape[2]
+
+    for i in range(xs, xf):
+        for j in range(ys, yf):
+            for k in range(zs, zf):
+                if mask[i - xs, j - ys, k - zs] == 1:
+                    numID = numIDx = numIDy = numIDz = data[i - xs, j - ys, k - zs]
+                    build_voxel(i, j, k, numID, numIDx, numIDy, numIDz, False, solid, rigidE, rigidH, ID)
+                elif mask[i - xs, j - ys, k - zs] == 2:
+                    numID = numIDx = numIDy = numIDz = waternumID
+                    build_voxel(i, j, k, numID, numIDx, numIDy, numIDz, False, solid, rigidE, rigidH, ID)
+                elif mask[i - xs, j - ys, k - zs] == 3:
+                    numID = numIDx = numIDy = numIDz = grassnumID
+                    build_voxel(i, j, k, numID, numIDx, numIDy, numIDz, False, solid, rigidE, rigidH, ID)
+