[yt-svn] commit/yt: ngoldbaum: Merged in atmyers/yt (pull request #2030)

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1 new commit in yt:

https://bitbucket.org/yt_analysis/yt/commits/9c26b9791511/
Changeset:   9c26b9791511
Branch:      yt
User:        ngoldbaum
Date:        2016-03-13 18:22:41+00:00
Summary:     Merged in atmyers/yt (pull request #2030)

Adding a Simulation type for ExodusII Datasets.
Affected #:  4 files

diff -r e93907ab891413d8f78db4aac567852aa7e14cbe -r 9c26b97915111f171177465e79d6381aae16d4f0 doc/source/analyzing/time_series_analysis.rst
--- a/doc/source/analyzing/time_series_analysis.rst
+++ b/doc/source/analyzing/time_series_analysis.rst
@@ -79,7 +79,7 @@
 Analyzing an Entire Simulation
 ------------------------------
 
-.. note:: Implemented for: Enzo, Gadget, OWLS.
+.. note:: Implemented for the Enzo, Gadget, OWLS, and Exodus II frontends.
 
 The parameter file used to run a simulation contains all the information 
 necessary to know what datasets should be available.  The ``simulation`` 

diff -r e93907ab891413d8f78db4aac567852aa7e14cbe -r 9c26b97915111f171177465e79d6381aae16d4f0 yt/frontends/exodus_ii/api.py
--- a/yt/frontends/exodus_ii/api.py
+++ b/yt/frontends/exodus_ii/api.py
@@ -18,6 +18,9 @@
     ExodusIIUnstructuredIndex, \
     ExodusIIDataset
 
+from .simulation_handling import \
+    ExodusIISimulation
+
 from .fields import \
     ExodusIIFieldInfo
 

diff -r e93907ab891413d8f78db4aac567852aa7e14cbe -r 9c26b97915111f171177465e79d6381aae16d4f0 yt/frontends/exodus_ii/simulation_handling.py
--- /dev/null
+++ b/yt/frontends/exodus_ii/simulation_handling.py
@@ -0,0 +1,93 @@
+import glob
+import os
+from yt.extern.six import add_metaclass
+from yt.convenience import \
+    load
+from yt.funcs import \
+    only_on_root
+from yt.utilities.exceptions import \
+    YTOutputNotIdentified
+from yt.utilities.logger import ytLogger as \
+    mylog
+from yt.utilities.parallel_tools.parallel_analysis_interface import \
+    parallel_objects
+from yt.data_objects.time_series import \
+    DatasetSeries, \
+    RegisteredSimulationTimeSeries
+from yt.frontends.exodus_ii.api import ExodusIIDataset
+
+
+ at add_metaclass(RegisteredSimulationTimeSeries)
+class ExodusIISimulation(DatasetSeries):
+    r"""
+    Initialize an ExodusII Simulation object.
+
+    Upon creation, the input directoy is searched for valid ExodusIIDatasets.
+    The get_time_series can be used to generate a DatasetSeries object.
+
+    simulation_directory : str
+        The directory that contain the simulation data.
+    
+    Examples
+    --------
+    >>> import yt
+    >>> sim = yt.simulation("demo_second", "ExodusII")
+    >>> sim.get_time_series()
+    >>> for ds in sim:
+    ...     print ds.current_time
+
+    """
+    
+    def __init__(self, simulation_directory, find_outputs=False):
+        self.simulation_directory = simulation_directory
+        fn_pattern = "%s/*" % self.simulation_directory
+        potential_outputs = glob.glob(fn_pattern)
+        self.all_outputs = self._check_for_outputs(potential_outputs)
+        self.all_outputs.sort(key=lambda obj: obj["filename"])
+
+    def get_time_series(self, parallel=False, setup_function=None):
+        r"""
+        Instantiate a DatasetSeries object for a set of outputs.
+
+        If no additional keywords given, a DatasetSeries object will be
+        created with all potential datasets created by the simulation.
+
+        Fine-level filtering is currently not implemented.
+        
+        """
+        
+        all_outputs = self.all_outputs
+        ds_list = []
+        for output in all_outputs:
+            num_steps = output['num_steps']
+            fn = output['filename']
+            for step in range(num_steps):
+                ds = ExodusIIDataset(fn, step=step)
+                ds_list.append(ds)
+        super(ExodusIISimulation, self).__init__(ds_list, 
+                                                 parallel=parallel, 
+                                                 setup_function=setup_function)
+        
+    def _check_for_outputs(self, potential_outputs):
+        r"""
+        Check a list of files to see if they are valid datasets.
+        """
+
+        only_on_root(mylog.info, "Checking %d potential outputs.",
+                     len(potential_outputs))
+
+        my_outputs = {}
+        for my_storage, output in parallel_objects(potential_outputs,
+                                                   storage=my_outputs):
+            if os.path.exists(output):
+                try:
+                    ds = load(output)
+                    if ds is not None:
+                        num_steps = ds.num_steps
+                        my_storage.result = {"filename": output,
+                                             "num_steps": num_steps}
+                except YTOutputNotIdentified:
+                    mylog.error("Failed to load %s", output)
+        my_outputs = [my_output for my_output in my_outputs.values() \
+                      if my_output is not None]
+        return my_outputs

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

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