[TEP006] Aggregate TARDIS restructure and configuration system cleanup

docs/physics/physical_quantities.rst

@@ -46,14 +46,14 @@ as Astropy `Quantities <http://astropy.readthedocs.org/en/v0.2.1/_generated/astr
 
 .. code-block:: python
 
-    model.t_rads.cgs
+    model.t_rad.cgs
 
 will give you a list of the :math:`T_{\rm rad}`-values for the model zones
 in cgs units. To obtain an array of the values (without units) use
 
 .. code-block:: python
 
-    model.t_rads.cgs.value
+    model.t_rad.cgs.value
 
 Similarly, the :math:`W`-values can be accessed using
 

scripts/tardis

@@ -1,8 +1,7 @@
 #!/usr/bin/env python
 from tardis.io import config_reader
 
-from tardis import model
-from tardis.simulation.base import run_radial1d
+from tardis.simulation import Simulation
 import numpy as np
 
 import logging
@@ -63,20 +62,20 @@ if args.packet_log_file:
     logger.addHandler(packet_logging_handler)
 
 tardis_config = config_reader.Configuration.from_yaml(args.config_fname)
-radial1d_mdl = model.Radial1DModel(tardis_config)
+simulation = Simulation.from_config(tardis_config)
 
 if args.gdb:
     import os; print(os.getpid()); raw_input() # Workaround to attach gdb
 if args.profile:
     import cProfile
-    cProfile.runctx('run_radial1d(radial1d_mdl)', locals(),
+    cProfile.runctx('simulation.run()', locals(),
                     globals(), filename=args.profiler_log_file)
 else:
-    run_radial1d(radial1d_mdl)
+    simulation.run()
 
 
-if not np.all(radial1d_mdl.spectrum_virtual.luminosity_density_lambda.value
+if not np.all(simulation.runner.spectrum_virtual.luminosity_density_lambda.value
         == 0.0):
-    radial1d_mdl.spectrum_virtual.to_ascii(args.spectrum_fname)
+    simulation.runner.spectrum_virtual.to_ascii(args.spectrum_fname)
 else:
-    radial1d_mdl.spectrum.to_ascii(args.spectrum_fname)
+    simulation.runner.spectrum.to_ascii(args.spectrum_fname)

tardis/base.py

@@ -19,23 +19,22 @@ def run_tardis(config, atom_data=None):
         atomic data will be loaded according to keywords set in the configuration
         [default=None]
     """
-    from tardis.io import config_reader
-    from tardis import model, simulation, atomic
+    from tardis.io.config_reader import Configuration
+    from tardis.simulation import Simulation
+    from tardis.atomic import AtomData
 
     if atom_data is not None:
         try:
-            atom_data = atomic.AtomData.from_hdf5(atom_data)
+            atom_data = AtomData.from_hdf5(atom_data)
         except TypeError:
             atom_data = atom_data
 
     try:
-        tardis_config = config_reader.Configuration.from_yaml(
-            config, atom_data=atom_data)
+        tardis_config = Configuration.from_yaml(config)
     except TypeError:
-        tardis_config = config_reader.Configuration.from_config_dict(
-            config, atom_data=atom_data)
+        tardis_config = Configuration.from_config_dict(config)
 
-    radial1d_mdl = model.Radial1DModel(tardis_config)
-    simulation.run_radial1d(radial1d_mdl)
+    simulation = Simulation.from_config(tardis_config, atom_data=atom_data)
+    simulation.run()
 
-    return radial1d_mdl
+    return simulation

tardis/gui/widgets.py

@@ -566,7 +566,7 @@ def change_model(self, model):
         """Reset the model set in the GUI."""
         self.model = model
         self.tablemodel.arraydata = []
-        self.tablemodel.add_data(model.t_rads.value.tolist())
+        self.tablemodel.add_data(model.t_rad.value.tolist())
         self.tablemodel.add_data(model.ws.tolist())
 
     def change_spectrum_to_spec_virtual_flux_angstrom(self):
@@ -626,7 +626,7 @@ def change_graph_to_ws(self):
 
     def change_graph_to_t_rads(self):
         """Change the graph back to radiation Temperature."""
-        self.change_graph(self.model.t_rads.value, 't_rads', '(K)')
+        self.change_graph(self.model.t_rad.value, 't_rad', '(K)')
 
     def change_graph(self, data, name, unit):
         """Called to change the shell plot by the two methods above."""
@@ -659,22 +659,22 @@ def plot_model(self):
         self.graph.ax1.set_ylabel('Rad. Temp (K)')
         self.graph.ax1.yaxis.get_major_formatter().set_powerlimits((0, 1))
         self.graph.dataplot = self.graph.ax1.plot(
-            range(len(self.model.t_rads.value)), self.model.t_rads.value)
+            range(len(self.model.t_rad.value)), self.model.t_rad.value)
         self.graph.ax2.clear()
         self.graph.ax2.set_title('Shell View')
         self.graph.ax2.set_xticklabels([])
         self.graph.ax2.set_yticklabels([])
         self.graph.ax2.grid = True
 
         self.shells = []
-        t_rad_normalizer = colors.Normalize(vmin=self.model.t_rads.value.min(), 
-            vmax=self.model.t_rads.value.max())
+        t_rad_normalizer = colors.Normalize(vmin=self.model.t_rad.value.min(),
+            vmax=self.model.t_rad.value.max())
         t_rad_color_map = plt.cm.ScalarMappable(norm=t_rad_normalizer, 
             cmap=plt.cm.jet)
-        t_rad_color_map.set_array(self.model.t_rads.value)
+        t_rad_color_map.set_array(self.model.t_rad.value)
         if self.graph.cb:
-            self.graph.cb.set_clim(vmin=self.model.t_rads.value.min(), 
-                vmax=self.model.t_rads.value.max())
+            self.graph.cb.set_clim(vmin=self.model.t_rad.value.min(),
+                vmax=self.model.t_rad.value.max())
             self.graph.cb.update_normal(t_rad_color_map)
         else:
             self.graph.cb = self.graph.figure.colorbar(t_rad_color_map)
@@ -685,7 +685,7 @@ def plot_model(self):
             self.model.tardis_config.structure.r_inner.value[0])
 
         #self.graph.normalizing_factor = 8e-16
-        for i, t_rad in enumerate(self.model.t_rads.value):
+        for i, t_rad in enumerate(self.model.t_rad.value):
             r_inner = (self.model.tardis_config.structure.r_inner.value[i] * 
                 self.graph.normalizing_factor)
             r_outer = (self.model.tardis_config.structure.r_outer.value[i] *