[TEP014] Simulation HDF and deprecated to_hdf cleanup.

tardis/io/util.py

@@ -311,63 +311,6 @@ def to_hdf(self, file_path, path='', name=None, collection=None):
         super(PlasmaWriterMixin, self).to_hdf(file_path, path, name)
 
 
-#Deprecated
-def to_hdf(path_or_buf, path, elements, complevel=9, complib='blosc'):
-    """
-    A function to uniformly store TARDIS data
-    to an HDF file.
-
-    Scalars will be stored in a Series under path/scalars
-    1D arrays will be stored under path/property_name as distinct Series
-    2D arrays will be stored under path/property_name as distinct DataFrames
-
-    Units will be stored as their CGS value
-
-    Parameters
-    ----------
-    path_or_buf:
-        Path or buffer to the HDF store
-    path: str
-        Path inside the HDF store to store the `elements`
-    elements: dict
-        A dict of property names and their values to be
-        stored.
-
-    Returns
-    -------
-
-    """
-    scalars = {}
-    for key, value in elements.iteritems():
-        if hasattr(value, 'cgs'):
-            value = value.cgs.value
-        if np.isscalar(value):
-            scalars[key] = value
-        elif hasattr(value, 'shape'):
-            if value.ndim == 1:
-                # This try,except block is only for model.plasma.levels
-                try:
-                    pd.Series(value).to_hdf(path_or_buf,
-                                            os.path.join(path, key))
-                except NotImplementedError:
-                    pd.DataFrame(value).to_hdf(path_or_buf,
-                                               os.path.join(path, key))
-            else:
-                pd.DataFrame(value).to_hdf(path_or_buf, os.path.join(path, key))
-        else:
-            data = pd.DataFrame([value])
-            data.to_hdf(path_or_buf, os.path.join(path, key))
-
-    if scalars:
-        scalars_series = pd.Series(scalars)
-
-        # Unfortunately, with to_hdf we cannot append, so merge beforehand
-        scalars_path = os.path.join(path, 'scalars')
-        with pd.HDFStore(path_or_buf, complevel=complevel, complib=complib) as store:
-            if scalars_path in store:
-                scalars_series = store[scalars_path].append(scalars_series)
-        scalars_series.to_hdf(path_or_buf, os.path.join(path, 'scalars'))
-
 '''
 Code for Custom Logger Classes (ColoredFormatter and ColorLogger) and its helper function
 (formatter_message) is used from this thread

tardis/simulation/base.py

@@ -8,12 +8,12 @@
 from tardis.montecarlo import MontecarloRunner
 from tardis.model import Radial1DModel
 from tardis.plasma.standard_plasmas import assemble_plasma
-
+from tardis.io.util import HDFWriterMixin
 # Adding logging support
 logger = logging.getLogger(__name__)
 
 
-class Simulation(object):
+class Simulation(HDFWriterMixin):
     """A composite object containing all the required information for a
     simulation.
 
@@ -36,6 +36,8 @@ class Simulation(object):
         .. note:: TARDIS must be built with OpenMP support in order for
         `nthreads` to have effect.
     """
+    hdf_properties = ['model', 'plasma', 'runner']
+    hdf_name = 'simulation'
     def __init__(self, iterations, model, plasma, runner,
                  no_of_packets, no_of_virtual_packets, luminosity_nu_start,
                  luminosity_nu_end, last_no_of_packets,
@@ -320,34 +322,6 @@ def remove_callback(self, id):
         except KeyError:
             return False
 
-    def to_hdf(self, path_or_buf, path='simulation', plasma_properties=None,
-               suffix_count=True):
-        """
-        Store the simulation to an HDF structure.
-
-        Parameters
-        ----------
-        path_or_buf
-            Path or buffer to the HDF store
-        path : str
-            Path inside the HDF store to store the simulation
-        plasma_properties
-            `None` or a `PlasmaPropertyCollection` which will
-            be passed as the collection argument to the
-            plasma.to_hdf method.
-        suffix_count : bool
-            If True, the path inside the HDF will be suffixed with the
-            number of the iteration being stored.
-        Returns
-        -------
-        None
-        """
-        if suffix_count:
-            path += str(self.iterations_executed)
-        self.runner.to_hdf(path_or_buf, path)
-        self.model.to_hdf(path_or_buf, path)
-        self.plasma.to_hdf(path_or_buf, path, plasma_properties)
-
     @classmethod
     def from_config(cls, config, **kwargs):
         """