[yt-svn] commit/yt: MatthewTurk: Merged in MatthewTurk/yt/yt-3.0 (pull request #945)

[commits-noreply at bitbucket.org]

1 new commit in yt:

https://bitbucket.org/yt_analysis/yt/commits/af18fce402d7/
Changeset:   af18fce402d7
Branch:      yt-3.0
User:        MatthewTurk
Date:        2014-06-11 23:33:44
Summary:     Merged in MatthewTurk/yt/yt-3.0 (pull request #945)

Reduce memory usage for particle octrees
Affected #:  4 files

diff -r 122c45b92abbc439fa04107c58079932a19462d4 -r af18fce402d7e68f3620b4a0d6b322b50815f573 yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -599,6 +599,10 @@
             return
         elif self._locked == True:
             raise GenerationInProgress(fields)
+        # Track which ones we want in the end
+        ofields = set(self.field_data.keys()
+                    + fields_to_get
+                    + fields_to_generate)
         # At this point, we want to figure out *all* our dependencies.
         fields_to_get = self._identify_dependencies(fields_to_get,
             self._spatial)
@@ -627,6 +631,9 @@
 
         fields_to_generate += gen_fluids + gen_particles
         self._generate_fields(fields_to_generate)
+        for field in self.field_data.keys():
+            if field not in ofields:
+                self.field_data.pop(field)
 
     def _generate_fields(self, fields_to_generate):
         index = 0

diff -r 122c45b92abbc439fa04107c58079932a19462d4 -r af18fce402d7e68f3620b4a0d6b322b50815f573 yt/data_objects/octree_subset.py
--- a/yt/data_objects/octree_subset.py
+++ b/yt/data_objects/octree_subset.py
@@ -52,12 +52,6 @@
     _type_name = 'octree_subset'
     _skip_add = True
     _con_args = ('base_region', 'domain', 'pf')
-    _container_fields = (("index", "dx"),
-                         ("index", "dy"),
-                         ("index", "dz"),
-                         ("index", "x"),
-                         ("index", "y"),
-                         ("index", "z"))
     _domain_offset = 0
     _cell_count = -1
 
@@ -78,19 +72,6 @@
         self.base_region = base_region
         self.base_selector = base_region.selector
 
-    def _generate_container_field(self, field):
-        if self._current_chunk is None:
-            self.index._identify_base_chunk(self)
-        if isinstance(field, tuple): field = field[1]
-        if field == "dx":
-            return self._current_chunk.fwidth[:,0]
-        elif field == "dy":
-            return self._current_chunk.fwidth[:,1]
-        elif field == "dz":
-            return self._current_chunk.fwidth[:,2]
-        else:
-            raise RuntimeError
-
     def __getitem__(self, key):
         tr = super(OctreeSubset, self).__getitem__(key)
         try:
@@ -111,16 +92,20 @@
         return self._num_zones + 2*self._num_ghost_zones
 
     def _reshape_vals(self, arr):
-        if len(arr.shape) == 4: return arr
+        if len(arr.shape) == 4 and arr.flags["F_CONTIGUOUS"]:
+            return arr
         nz = self.nz
         n_oct = arr.shape[0] / (nz**3.0)
         if arr.size == nz*nz*nz*n_oct:
-            arr = arr.reshape((nz, nz, nz, n_oct), order="F")
+            new_shape = (nz, nz, nz, n_oct)
         elif arr.size == nz*nz*nz*n_oct * 3:
-            arr = arr.reshape((nz, nz, nz, n_oct, 3), order="F")
+            new_shape = (nz, nz, nz, n_oct, 3)
         else:
             raise RuntimeError
-        arr = np.asfortranarray(arr)
+        # This will retain units now.
+        arr.shape = new_shape
+        if not arr.flags["F_CONTIGUOUS"]:
+            arr = arr.reshape(new_shape, order="F")
         return arr
 
     _domain_ind = None

diff -r 122c45b92abbc439fa04107c58079932a19462d4 -r af18fce402d7e68f3620b4a0d6b322b50815f573 yt/geometry/coordinate_handler.py
--- a/yt/geometry/coordinate_handler.py
+++ b/yt/geometry/coordinate_handler.py
@@ -34,10 +34,10 @@
 
 def _get_coord_fields(axi, units = "code_length"):
     def _dds(field, data):
-        rv = data.pf.arr(data.fwidth[...,axi], units)
+        rv = data.pf.arr(data.fwidth[...,axi].copy(), units)
         return data._reshape_vals(rv)
     def _coords(field, data):
-        rv = data.pf.arr(data.fcoords[...,axi], units)
+        rv = data.pf.arr(data.fcoords[...,axi].copy(), units)
         return data._reshape_vals(rv)
     return _dds, _coords
 

diff -r 122c45b92abbc439fa04107c58079932a19462d4 -r af18fce402d7e68f3620b4a0d6b322b50815f573 yt/geometry/particle_oct_container.pyx
--- a/yt/geometry/particle_oct_container.pyx
+++ b/yt/geometry/particle_oct_container.pyx
@@ -300,6 +300,7 @@
             # Now we locate the particle
             for i in range(3):
                 ind[i] = <int> ((pos[p, i] - self.left_edge[i])*self.idds[i])
+                ind[i] = iclip(ind[i], 0, self.dims[i])
             mask[ind[0],ind[1],ind[2]] |= val
 
     def identify_data_files(self, SelectorObject selector):

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

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