[yt-svn] commit/yt: 2 new changesets

[commits-noreply at bitbucket.org]

2 new commits in yt:

https://bitbucket.org/yt_analysis/yt/commits/13f5af59d375/
Changeset:   13f5af59d375
Branch:      yt
User:        MatthewTurk
Date:        2014-10-17 18:17:01+00:00
Summary:     First pass at computing boxes, thanks to Andrew's suggestion.
Affected #:  2 files

diff -r 558d9f064464adf497d777b760b9e7ac12f9baea -r 13f5af59d37521a28bee3019f37068541caced59 yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -113,7 +113,8 @@
         self.directory = ds.fullpath
         self._handle = ds._handle
 
-        self.float_type = self._handle['Chombo_global'].attrs['testReal'].dtype.name
+        tr = self._handle['Chombo_global'].attrs.get("testReal", "float32")
+            
         self._levels = [key for key in self._handle.keys() if key.startswith('level')]
         GridIndex.__init__(self, ds, dataset_type)
 
@@ -161,7 +162,13 @@
     def _count_grids(self):
         self.num_grids = 0
         for lev in self._levels:
-            self.num_grids += self._handle[lev]['Processors'].len()
+            d = self._handle[lev]
+            if 'Processors' in d:
+                self.num_grids += d['Processors'].len()
+            elif 'boxes' in d:
+                self.num_grids += d['boxes'].len()
+            else:
+                raise RuntimeError("Uknown file specification")
 
     def _parse_index(self):
         f = self._handle # shortcut

diff -r 558d9f064464adf497d777b760b9e7ac12f9baea -r 13f5af59d37521a28bee3019f37068541caced59 yt/frontends/chombo/io.py
--- a/yt/frontends/chombo/io.py
+++ b/yt/frontends/chombo/io.py
@@ -25,6 +25,7 @@
     _dataset_type = "chombo_hdf5"
     _offset_string = 'data:offsets=0'
     _data_string = 'data:datatype=0'
+    _offsets = None
 
     def __init__(self, ds, *args, **kwargs):
         BaseIOHandler.__init__(self, ds, *args, **kwargs)
@@ -32,6 +33,29 @@
         self._handle = ds._handle
         self.dim = self._handle['Chombo_global/'].attrs['SpaceDim']
         self._read_ghost_info()
+        if self._offset_string not in self._handle['level_0']:
+            self._calculate_offsets()
+
+    def _calculate_offsets(self):
+        def box_size(corners):
+            size = 1
+            for idim in range(self.dim):
+                size *= (corners[idim+self.dim] - corners[idim] + 1)
+            return size
+
+        self._offsets = {}
+        num_comp = self._handle.attrs['num_components']
+        level = 0
+        while 1:
+            lname = 'level_%i' % level
+            if lname not in self._handle: break
+            boxes = self._handle['level_0']['boxes'].value
+            box_sizes = [box_size(box) for box in boxes]
+
+            offsets = np.cumsum(box_sizes*num_comp, dtype='int64') 
+            offsets -= offsets[0]
+            self._offsets[level] = offsets
+            level += 1
 
     def _read_ghost_info(self):
         try:
@@ -41,7 +65,7 @@
             self.ghost = np.array(self.ghost)
         except KeyError:
             # assume zero ghosts if outputGhosts not present
-            self.ghost = np.zeros(self.dim)
+            self.ghost = np.zeros(self.dim, 'int64')
 
     _field_dict = None
     @property
@@ -80,7 +104,10 @@
         shape = grid.ActiveDimensions + 2*self.ghost
         boxsize = shape.prod()
 
-        grid_offset = lev[self._offset_string][grid._level_id]
+        if self._offsets is not None:
+            grid_offset = self._offsets[grid.Level][grid._level_id]
+        else:
+            grid_offset = lev[self._offset_string][grid._level_id]
         start = grid_offset+self.field_dict[field]*boxsize
         stop = start + boxsize
         data = lev[self._data_string][start:stop]


https://bitbucket.org/yt_analysis/yt/commits/5da834fbf924/
Changeset:   5da834fbf924
Branch:      yt
User:        MatthewTurk
Date:        2014-10-17 18:46:46+00:00
Summary:     Thanks to Andrew for the fix!
Affected #:  1 file

diff -r 13f5af59d37521a28bee3019f37068541caced59 -r 5da834fbf92476bd5defa5f3f114287e07190888 yt/frontends/chombo/io.py
--- a/yt/frontends/chombo/io.py
+++ b/yt/frontends/chombo/io.py
@@ -50,7 +50,7 @@
             lname = 'level_%i' % level
             if lname not in self._handle: break
             boxes = self._handle['level_0']['boxes'].value
-            box_sizes = [box_size(box) for box in boxes]
+            box_sizes = np.array([box_size(box) for box in boxes])
 
             offsets = np.cumsum(box_sizes*num_comp, dtype='int64') 
             offsets -= offsets[0]

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

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