massive change of structure

tardis/atomic.py

@@ -439,7 +439,7 @@ def __init__(self, atom_data, ionization_data, levels_data, lines_data, macro_at
 
 
 
-
+        self.ion_cx_data = ion_cx_data
 
 
 

tardis/plasma/properties/__init__.py

@@ -0,0 +1 @@
+from ion_population import PhiSahaNebular, PhiSahaLTE

tardis/plasma/atomic_properties.py → tardis/plasma/properties/atomic.py

@@ -1,9 +1,9 @@
-from abc import ABCMeta
+from abc import ABCMeta, abstractmethod
 
 import numpy as np
 import pandas as pd
 
-from tardis.plasma.base_properties import ProcessingPlasmaProperty
+from tardis.plasma.properties.base import ProcessingPlasmaProperty
 from tardis.plasma.exceptions import IncompleteAtomicData
 
 class BaseAtomicDataProperty(ProcessingPlasmaProperty):
@@ -15,6 +15,15 @@ def __init__(self, plasma_parent):
         super(BaseAtomicDataProperty, self).__init__(plasma_parent)
         self.value = None
 
+    @abstractmethod
+    def _set_index(self, raw_atomic_property):
+        raise NotImplementedError('Needs to be implemented in subclasses')
+
+    @abstractmethod
+    def _filter_atomic_property(self, raw_atomic_property):
+        raise NotImplementedError('Needs to be implemented in subclasses')
+
+
     def calculate(self, atomic_data, selected_atoms):
         if self.value is not None:
             return self.value
@@ -70,6 +79,15 @@ def calculate(self, levels, lines):
         return np.array(levels_index.ix[lines_index])
 
 
+class IonCXData(BaseAtomicDataProperty):
+    name = 'ion_cx_data'
+
+    def _filter_atomic_property(self, ion_cx_data, selected_atoms):
+        return filtered_ion_cx_data
+
+    def _set_index(self, ion_cx_data):
+        return levels.set_index(['atomic_number', 'ion_number', 'level_number'])
+
 
 class AtomicMass(BaseAtomicDataProperty):
     name = 'atomic_mass'

tardis/plasma/general_properties.py → tardis/plasma/properties/general.py

@@ -1,11 +1,9 @@
 import logging
 
 import numpy as np
-import pandas as pd
-
 from astropy import constants as const
 
-from tardis.plasma.base_properties import ProcessingPlasmaProperty
+from tardis.plasma.properties.base import ProcessingPlasmaProperty
 
 logger = logging.getLogger(__name__)
 

tardis/plasma/ion_population.py → tardis/plasma/properties/ion_population.py

@@ -3,11 +3,12 @@
 import numpy as np
 import pandas as pd
 
-from tardis.plasma.base_properties import ProcessingPlasmaProperty
+from tardis.plasma.properties.base import ProcessingPlasmaProperty
 from tardis.plasma.exceptions import PlasmaIonizationError
 logger = logging.getLogger(__name__)
 
-
+__all__ = ['PhiSahaNebular', 'PhiSahaLTE', 'RadiationFieldCorrection',
+           'IonNumberDensity', ]
 
 class PhiSahaNebular(ProcessingPlasmaProperty):
     """

tardis/plasma/level_population.py → tardis/plasma/properties/level_population.py

@@ -1,9 +1,8 @@
 import logging
 
 import numpy as np
-import pandas as pd
 
-from tardis.plasma.base_properties import ProcessingPlasmaProperty
+from tardis.plasma.properties.base import ProcessingPlasmaProperty
 
 logger = logging.getLogger(__name__)
 

tardis/plasma/partition_function.py → tardis/plasma/properties/partition_function.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 
-from tardis.plasma.base_properties import ProcessingPlasmaProperty
+from tardis.plasma.properties.base import ProcessingPlasmaProperty
 
 logger = logging.getLogger(__name__)
 

tardis/plasma/plasma_input.py → tardis/plasma/properties/plasma_input.py

@@ -1,4 +1,4 @@
-from tardis.plasma.base_properties import BasePlasmaProperty
+from tardis.plasma.properties.base import BasePlasmaProperty
 
 
 

tardis/plasma/properties/properties.py

@@ -0,0 +1,3 @@
+#### Importing properties from other modules ########
+
+######################################################

tardis/plasma/radiative_properties.py → tardis/plasma/properties/radiative_properties.py

@@ -2,10 +2,9 @@
 
 import numpy as np
 import pandas as pd
-
 from astropy import units as u, constants as const
 
-from tardis.plasma.base_properties import ProcessingPlasmaProperty
+from tardis.plasma.properties.base import ProcessingPlasmaProperty
 
 logger = logging.getLogger(__name__)
 

tardis/plasma/standard_plasmas.py

@@ -1,10 +1,7 @@
 import logging
 
-import numpy as np
-import pandas as pd
-
 from tardis.plasma import BasePlasma
-from tardis.plasma.plasma_input import (TRadiative, AtomicData, Abundance,
+from tardis.plasma.properties.plasma_input import (TRadiative, AtomicData, Abundance,
                                         Density, TimeExplosion)
 from tardis.plasma.properties import (
     BetaRadiation, LevelBoltzmannFactor, Levels, Lines,

tardis/plasma/tests/conftest.py

@@ -1,10 +1,8 @@
-import pytest
 import numpy as np
-
 import pandas as pd
-
 from astropy import units as u
 
+import pytest
 from tardis.plasma.standard_plasmas import LTEPlasma
 
 

tardis/plasma/tests/test_general_properties.py

@@ -1,9 +1,7 @@
-
 import numpy as np
+from astropy import constants as const
 
-from astropy import units as u, constants as const
-
-from tardis.plasma.general_properties import (BetaRadiation, GElectron,
+from tardis.plasma.properties.general import (BetaRadiation, GElectron,
                                               NumberDensity, SelectedAtoms)
 
 

tardis/plasma/tests/test_simple_plasma.py

@@ -1,12 +1,3 @@
-import pytest
-
-import pandas as pd
-import numpy as np
-
-from astropy import units as u
-
-from tardis.plasma.plasma_input import TRadiative, AtomicData, Abundance, DilutionFactor
-
 from tardis.plasma.standard_plasmas import LTEPlasma