[yt-svn] commit/yt: ngoldbaum: Merged in atmyers/yt (pull request #1623)

[commits-noreply at bitbucket.org]

1 new commit in yt:

https://bitbucket.org/yt_analysis/yt/commits/b0ae2114ec60/
Changeset:   b0ae2114ec60
Branch:      yt
User:        ngoldbaum
Date:        2015-06-29 19:46:33+00:00
Summary:     Merged in atmyers/yt (pull request #1623)

Removing dead code / fixing a Pluto bug in the Chombo frontend
Affected #:  3 files

diff -r e69200450e5dd5263dd017b35c4e29f84f859b5b -r b0ae2114ec601caf0775412492d45e05289cc995 yt/frontends/chombo/api.py
--- a/yt/frontends/chombo/api.py
+++ b/yt/frontends/chombo/api.py
@@ -33,7 +33,6 @@
     PlutoFieldInfo
 
 from .io import \
-    IOHandlerChomboHDF5,\
-    IOHandlerPlutoHDF5
+    IOHandlerChomboHDF5
 
 from . import tests

diff -r e69200450e5dd5263dd017b35c4e29f84f859b5b -r b0ae2114ec601caf0775412492d45e05289cc995 yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -47,6 +47,7 @@
 class ChomboGrid(AMRGridPatch):
     _id_offset = 0
     __slots__ = ["_level_id", "stop_index"]
+
     def __init__(self, id, index, level, start, stop):
         AMRGridPatch.__init__(self, id, filename = index.index_filename,
                               index = index)
@@ -99,12 +100,6 @@
         self.domain_left_edge = ds.domain_left_edge
         self.domain_right_edge = ds.domain_right_edge
         self.dataset_type = dataset_type
-
-        if ds.dimensionality == 1:
-            self.dataset_type = "chombo1d_hdf5"
-        if ds.dimensionality == 2:
-            self.dataset_type = "chombo2d_hdf5"
-
         self.field_indexes = {}
         self.dataset = weakref.proxy(ds)
         # for now, the index file is the dataset!
@@ -114,7 +109,7 @@
         self._handle = ds._handle
 
         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)
 
@@ -256,17 +251,10 @@
         self._handle = HDF5FileHandler(filename)
         self.dataset_type = dataset_type
 
-        # look up the dimensionality of the dataset
-        D = self._handle['Chombo_global/'].attrs['SpaceDim']
-        if D == 1:
-            self.dataset_type = 'chombo1d_hdf5'
-        if D == 2:
-            self.dataset_type = 'chombo2d_hdf5'
-
         self.geometry = "cartesian"
         self.ini_filename = ini_filename
         self.fullplotdir = os.path.abspath(filename)
-        Dataset.__init__(self,filename, self.dataset_type,
+        Dataset.__init__(self, filename, self.dataset_type,
                          units_override=units_override)
         self.storage_filename = storage_filename
         self.cosmological_simulation = False
@@ -398,7 +386,7 @@
 
 class PlutoHierarchy(ChomboHierarchy):
 
-    def __init__(self, ds, dataset_type="pluto_chombo_native"):
+    def __init__(self, ds, dataset_type="chombo_hdf5"):
         ChomboHierarchy.__init__(self, ds, dataset_type)
 
     def _parse_index(self):
@@ -456,7 +444,7 @@
     _index_class = PlutoHierarchy
     _field_info_class = PlutoFieldInfo
 
-    def __init__(self, filename, dataset_type='pluto_chombo_native',
+    def __init__(self, filename, dataset_type='chombo_hdf5',
                  storage_filename = None, ini_filename = None,
                  units_override=None):
 

diff -r e69200450e5dd5263dd017b35c4e29f84f859b5b -r b0ae2114ec601caf0775412492d45e05289cc995 yt/frontends/chombo/io.py
--- a/yt/frontends/chombo/io.py
+++ b/yt/frontends/chombo/io.py
@@ -93,15 +93,11 @@
         self._particle_field_index = field_dict
         return self._particle_field_index
 
-    def _read_field_names(self, grid):
-        ncomp = int(self._handle.attrs['num_components'])
-        fns = [c[1] for c in f.attrs.items()[-ncomp-1:-1]]
-
     def _read_data(self, grid, field):
         lstring = 'level_%i' % grid.Level
         lev = self._handle[lstring]
         dims = grid.ActiveDimensions
-        shape = grid.ActiveDimensions + 2*self.ghost
+        shape = dims + 2*self.ghost
         boxsize = shape.prod()
 
         if self._offsets is not None:
@@ -112,7 +108,7 @@
         stop = start + boxsize
         data = lev[self._data_string][start:stop]
         data_no_ghost = data.reshape(shape, order='F')
-        ghost_slice = [slice(g, d-g, None) for g, d in zip(self.ghost, grid.ActiveDimensions)]
+        ghost_slice = [slice(g, d-g, None) for g, d in zip(self.ghost, dims)]
         ghost_slice = ghost_slice[0:self.dim]
         return data_no_ghost[ghost_slice]
 
@@ -201,43 +197,6 @@
         return np.asarray(data[field_index::items_per_particle], dtype=np.float64, order='F')
 
 
-class IOHandlerChombo2DHDF5(IOHandlerChomboHDF5):
-    _dataset_type = "chombo2d_hdf5"
-    _offset_string = 'data:offsets=0'
-    _data_string = 'data:datatype=0'
-
-    def __init__(self, ds, *args, **kwargs):
-        BaseIOHandler.__init__(self, ds, *args, **kwargs)
-        self.ds = ds
-        self._handle = ds._handle
-        self.dim = 2
-        self._read_ghost_info()
-
-
-class IOHandlerChombo1DHDF5(IOHandlerChomboHDF5):
-    _dataset_type = "chombo1d_hdf5"
-    _offset_string = 'data:offsets=0'
-    _data_string = 'data:datatype=0'
-
-    def __init__(self, ds, *args, **kwargs):
-        BaseIOHandler.__init__(self, ds, *args, **kwargs)
-        self.ds = ds
-        self.dim = 1
-        self._handle = ds._handle
-        self._read_ghost_info()
-
-
-class IOHandlerPlutoHDF5(IOHandlerChomboHDF5):
-    _dataset_type = "pluto_chombo_native"
-    _offset_string = 'data:offsets=0'
-    _data_string = 'data:datatype=0'
-
-    def __init__(self, ds, *args, **kwargs):
-        BaseIOHandler.__init__(self, ds, *args, **kwargs)
-        self.ds = ds
-        self._handle = ds._handle
-
-
 def parse_orion_sinks(fn):
     '''

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

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