Replace hits of uint8_t -> uint32_t for cell indices

When allowing larger block sizes, we may easily overflow 8-bit counters.
Note that this was *already* overflowing for nz > 6, but it appears
it was never tested.

Author: cphyc

yt/geometry/oct_container.pxd

@@ -86,7 +86,7 @@ cdef class OctreeContainer:
         self,
         const int level,
         const np.uint8_t[::1] level_inds,
-        const np.uint8_t[::1] cell_inds,
+        const np.uint32_t[::1] cell_inds,
         const np.int64_t[::1] file_inds,
         dict dest_fields,
         dict source_fields,
@@ -96,7 +96,7 @@ cdef class OctreeContainer:
         self,
         const int level,
         const np.uint8_t[::1] level_inds,
-        const np.uint8_t[::1] cell_inds,
+        const np.uint32_t[::1] cell_inds,
         const np.int64_t[::1] file_inds,
         const np.int32_t[::1] domain_inds,
         dict dest_fields,

yt/geometry/oct_container.pyx

@@ -754,7 +754,7 @@ cdef class OctreeContainer:
         self,
         const int level,
         const np.uint8_t[::1] levels,
-        const np.uint8_t[::1] cell_inds,
+        const np.uint32_t[::1] cell_inds,
         const np.int64_t[::1] file_inds,
         dict dest_fields,
         dict source_fields,
@@ -807,7 +807,7 @@ cdef class OctreeContainer:
         -------
         oct_inds : int64 ndarray (nocts*8, )
             The on-domain index of the octs containing each cell
-        cell_inds : uint8 ndarray (nocts*8, )
+        cell_inds : uint32 ndarray (nocts*8, )
             The index of the cell in its parent oct
 
         Note
@@ -819,10 +819,10 @@ cdef class OctreeContainer:
 
         cdef NeighbourCellIndexVisitor visitor
 
-        cdef np.uint8_t[::1] cell_inds
+        cdef np.uint32_t[::1] cell_inds
         cdef np.int64_t[::1] oct_inds
 
-        cell_inds = np.full(num_octs*4**3, self.nz[0] * self.nz[1] * self.nz[2], dtype=np.uint8)
+        cell_inds = np.full(num_octs*4**3, self.nz[0] * self.nz[1] * self.nz[2], dtype=np.uint32)
         oct_inds = np.full(num_octs*4**3, -1, dtype=np.int64)
 
         visitor = NeighbourCellIndexVisitor(self, -1, n_ghost_zones)
@@ -840,7 +840,7 @@ cdef class OctreeContainer:
         self,
         const int level,
         const np.uint8_t[::1] level_inds,
-        const np.uint8_t[::1] cell_inds,
+        const np.uint32_t[::1] cell_inds,
         const np.int64_t[::1] file_inds,
         const np.int32_t[::1] domain_inds,
         dict dest_fields,
@@ -896,7 +896,7 @@ cdef class OctreeContainer:
         -------
         levels : uint8, shape (num_cells,)
             The level of each cell of the super oct
-        cell_inds : uint8, shape (num_cells, )
+        cell_inds : uint32, shape (num_cells, )
             The index of each cell of the super oct within its own oct
         file_inds : int64, shape (num_cells, )
             The on-file position of the cell. See notes below.
@@ -933,12 +933,12 @@ cdef class OctreeContainer:
         cdef NeighbourCellVisitor visitor
 
         cdef np.ndarray[np.uint8_t, ndim=1] levels
-        cdef np.ndarray[np.uint8_t, ndim=1] cell_inds
+        cdef np.ndarray[np.uint32_t, ndim=1] cell_inds
         cdef np.ndarray[np.int64_t, ndim=1] file_inds
         cdef np.ndarray[np.int32_t, ndim=1] domains
         levels = np.full(num_cells, 255, dtype="uint8")
         file_inds = np.full(num_cells, -1, dtype="int64")
-        cell_inds = np.full(num_cells, self.nz[0] * self.nz[1] * self.nz[2], dtype="uint8")
+        cell_inds = np.full(num_cells, self.nz[0] * self.nz[1] * self.nz[2], dtype="uint32")
         domains = np.full(num_cells, -1, dtype="int32")
 
         visitor = NeighbourCellVisitor(self, -1, n_ghost_zones)

yt/geometry/oct_visitors.pxd

@@ -152,7 +152,7 @@ cdef class StoreIndex(OctVisitor):
 cdef class BaseNeighbourVisitor(OctVisitor):
     cdef int idim      # 0,1,2 for x,y,z
     cdef int direction # +1 for +x, -1 for -x
-    cdef np.uint8_t neigh_ind[3]
+    cdef np.uint32_t neigh_ind[3]
     cdef bint other_oct
     cdef Oct *neighbour
     cdef OctreeContainer octree
@@ -161,15 +161,15 @@ cdef class BaseNeighbourVisitor(OctVisitor):
 
     cdef void set_neighbour_info(self, Oct *o, int ishift[3])
 
-    cdef inline np.uint8_t neighbour_rind(self):
+    cdef inline np.uint32_t neighbour_rind(self):
         return (self.neigh_ind[2]*self.nz[1]+self.neigh_ind[1])*self.nz[0]+self.neigh_ind[0]
 
 cdef class NeighbourCellIndexVisitor(BaseNeighbourVisitor):
-    cdef np.uint8_t[::1] cell_inds
+    cdef np.uint32_t[::1] cell_inds
     cdef np.int64_t[::1] domain_inds
 
 cdef class NeighbourCellVisitor(BaseNeighbourVisitor):
     cdef np.uint8_t[::1] levels
     cdef np.int64_t[::1] file_inds
-    cdef np.uint8_t[::1] cell_inds
+    cdef np.uint32_t[::1] cell_inds
     cdef np.int32_t[::1] domains

yt/geometry/oct_visitors.pyx

@@ -412,7 +412,7 @@ cdef class BaseNeighbourVisitor(OctVisitor):
 
         # Index of neighbouring cell within its oct
         for i in range(3):
-            self.neigh_ind[i] = <np.uint8_t>(ishift[i]) % 2
+            self.neigh_ind[i] = <np.uint32_t>(ishift[i]) % 2
 
         self.other_oct = other_oct
         if other_oct:
@@ -452,7 +452,7 @@ cdef class NeighbourCellIndexVisitor(BaseNeighbourVisitor):
     cdef void visit(self, Oct* o, np.uint8_t selected):
         cdef int i, j, k
         cdef int ishift[3]
-        cdef np.uint8_t neigh_cell_ind
+        cdef np.uint32_t neigh_cell_ind
         cdef np.int64_t neigh_domain_ind
         if selected == 0: return
         # Work at oct level
@@ -497,7 +497,7 @@ cdef class NeighbourCellVisitor(BaseNeighbourVisitor):
         cdef int i, j, k
         cdef int ishift[3]
         cdef np.int64_t neigh_file_ind
-        cdef np.uint8_t neigh_cell_ind
+        cdef np.uint32_t neigh_cell_ind
         cdef np.int32_t neigh_domain
         cdef np.uint8_t neigh_level
         if selected == 0: return