[yt-svn] commit/yt: ngoldbaum: Merged in MatthewTurk/yt (pull request #1818)

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1 new commit in yt:

https://bitbucket.org/yt_analysis/yt/commits/75c9b92eb87a/
Changeset:   75c9b92eb87a
Branch:      yt
User:        ngoldbaum
Date:        2015-10-26 18:47:21+00:00
Summary:     Merged in MatthewTurk/yt (pull request #1818)

Adding grid_arrays to grid_container
Affected #:  6 files

diff -r 2096df33b692550e8090b58bf31da407b35cc2dd -r 75c9b92eb87a6e379461548c23f3b3902fa2b666 yt/geometry/grid_container.pxd
--- a/yt/geometry/grid_container.pxd
+++ b/yt/geometry/grid_container.pxd
@@ -21,7 +21,8 @@
 from libc.math cimport nearbyint, rint
 from yt.geometry.selection_routines cimport SelectorObject, _ensure_code
 from yt.utilities.lib.fp_utils cimport iclip
-from grid_visitors cimport GridTreeNode, GridVisitorData, grid_visitor_function
+from grid_visitors cimport GridTreeNode, GridVisitorData, \
+    grid_visitor_function, GridTreeNodePadded
 cimport grid_visitors 
 from yt.utilities.lib.bitarray cimport bitarray
 

diff -r 2096df33b692550e8090b58bf31da407b35cc2dd -r 75c9b92eb87a6e379461548c23f3b3902fa2b666 yt/geometry/grid_container.pyx
--- a/yt/geometry/grid_container.pyx
+++ b/yt/geometry/grid_container.pyx
@@ -124,6 +124,31 @@
             children.append(childs)
         return indices, levels, nchild, children
 
+    @property
+    def grid_arrays(self):
+        cdef GridTreeNodePadded[:] grids
+        grids = <GridTreeNodePadded[:self.num_grids]> \
+            (<GridTreeNodePadded*> self.grids)
+        grids_basic = np.asarray(grids)
+        # This next bit is necessary because as of 0.23.4, Cython can't make
+        # nested dtypes automatically where you have a property that is
+        # something like float[3].  So we unroll all of those, then re-roll
+        # them in a new dtype.
+        dtn = {}
+        dt = grids_basic.dtype
+        for name in dt.names:
+            d, o = dt.fields[name]
+            n = name
+            if name.endswith("_x"):
+                f = (d.char, 3)
+                n = name[:-2]
+            elif name.endswith("_y") or name.endswith("_z"):
+                continue
+            else:
+                f = (d.char, 1)
+            dtn[n] = (f, o)
+        return grids_basic.view(dtype=np.dtype(dtn))
+
     cdef void setup_data(self, GridVisitorData *data):
         # Being handed a new GVD object, we initialize it to sane defaults.
         data.index = 0

diff -r 2096df33b692550e8090b58bf31da407b35cc2dd -r 75c9b92eb87a6e379461548c23f3b3902fa2b666 yt/geometry/grid_visitors.pxd
--- a/yt/geometry/grid_visitors.pxd
+++ b/yt/geometry/grid_visitors.pxd
@@ -27,6 +27,27 @@
     int dims[3]
     np.float64_t dds[3]
 
+cdef struct GridTreeNodePadded:
+    int num_children
+    int level
+    long int index
+    double left_edge_x
+    double left_edge_y
+    double left_edge_z
+    double right_edge_x
+    double right_edge_y
+    double right_edge_z
+    long int children_pointers
+    long int start_index_x
+    long int start_index_y
+    long int start_index_z
+    int dims_x
+    int dims_y
+    int dims_z
+    double dds_x
+    double dds_y
+    double dds_z
+
 cdef struct GridVisitorData:
     GridTreeNode *grid
     np.uint64_t index

diff -r 2096df33b692550e8090b58bf31da407b35cc2dd -r 75c9b92eb87a6e379461548c23f3b3902fa2b666 yt/geometry/oct_container.pyx
--- a/yt/geometry/oct_container.pyx
+++ b/yt/geometry/oct_container.pyx
@@ -20,6 +20,7 @@
 from selection_routines cimport SelectorObject
 from libc.math cimport floor
 cimport selection_routines
+from yt.geometry.oct_visitors cimport OctPadded
 
 ORDER_MAX = 20
 _ORDER_MAX = ORDER_MAX
@@ -109,6 +110,19 @@
                 for k in range(self.nn[2]):
                     self.root_mesh[i][j][k] = NULL
 
+    @property
+    def oct_arrays(self):
+        cdef OctAllocationContainer *cur = self.cont
+        cdef Oct *this
+        cdef int i
+        cdef OctPadded[:] mm
+        rv = []
+        while cur != NULL:
+            mm = <OctPadded[:cur.n_assigned]> (<OctPadded*> cur.my_octs)
+            rv.append(np.asarray(mm))
+            cur = cur.next
+        return rv
+
     @classmethod
     def load_octree(cls, header):
         cdef np.ndarray[np.uint8_t, ndim=1] ref_mask

diff -r 2096df33b692550e8090b58bf31da407b35cc2dd -r 75c9b92eb87a6e379461548c23f3b3902fa2b666 yt/geometry/oct_visitors.pxd
--- a/yt/geometry/oct_visitors.pxd
+++ b/yt/geometry/oct_visitors.pxd
@@ -24,6 +24,12 @@
     np.int64_t domain       # (opt) addl int index
     Oct **children          # Up to 8 long
 
+cdef struct OctPadded:
+    np.int64_t file_ind
+    np.int64_t domain_ind
+    np.int64_t domain
+    np.int64_t padding
+
 cdef struct OctVisitorData:
     np.uint64_t index
     np.uint64_t last

diff -r 2096df33b692550e8090b58bf31da407b35cc2dd -r 75c9b92eb87a6e379461548c23f3b3902fa2b666 yt/geometry/tests/test_grid_container.py
--- a/yt/geometry/tests/test_grid_container.py
+++ b/yt/geometry/tests/test_grid_container.py
@@ -116,3 +116,12 @@
     # Test if find_points fails properly for non equal indices' array sizes
     yield assert_raises, AssertionError, test_ds.index._find_points, \
         [0], 1.0, [2, 3]
+
+def test_grid_arrays_view():
+    ds = setup_test_ds()
+    tree = ds.index._get_grid_tree()
+    grid_arr = tree.grid_arrays
+    yield assert_equal, grid_arr['left_edge'], ds.index.grid_left_edge
+    yield assert_equal, grid_arr['right_edge'], ds.index.grid_right_edge
+    yield assert_equal, grid_arr['dims'], ds.index.grid_dimensions
+    yield assert_equal, grid_arr['level'], ds.index.grid_levels[:,0]

Repository URL: https://bitbucket.org/yt_analysis/yt/

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