Schreiber+16 IR SED library - missing files

database_builder/__init__.py

@@ -19,9 +19,10 @@ import itertools
 import numpy as np
 from scipy import interpolate
 import scipy.constants as cst
+from astropy.table import Table
 from pcigale.data import (Database, Filter, M2005, BC03, Fritz2006,
                           Dale2014, DL2007, DL2014, NebularLines,
-                          NebularContinuum)
+                          NebularContinuum, Schreiber2016)
 
 
 def read_bc03_ssp(filename):
@@ -664,6 +665,40 @@ def build_nebular(base):
     base.add_nebular_continuum(models_cont)
     base.add_nebular_lines(models_lines)
 
+def build_schreiber2016(base):
+    models = []
+    schreiber2016_dir = os.path.join(os.path.dirname(__file__), 'schreiber2016/')
+    pah = Table.read(schreiber2016_dir + 'g15_pah.fits')
+    dust = Table.read(schreiber2016_dir + 'g15_dust.fits')
+    
+    # Getting the lambda grid for the templates and convert from microns to nm.
+    wave = dust[0][0][0] * 1E3
+
+    for td in range(15, 100, 1):
+        # Find the closest temperature in the model list of tdust
+        tsed = np.where(np.absolute(np.array(dust[0][6])-td) == np.min(np.absolute(np.array(dust[0][6])-td)))[0]
+        
+        # The models are in nuFnu.
+        # We convert this to W/nm.
+        lumin_dust = dust[0][1][tsed] / wave
+        lumin_dust = lumin_dust[0]
+        #norm = np.trapz(lumin_dust, x=wave)
+        #lumin_dust /= norm
+
+        models.append(Schreiber2016(0, np.float(td), wave, lumin_dust))
+
+        # The models are in nuFnu.
+        # We convert this to W/nm.
+        lumin_pah = pah[0][1][tsed] / wave
+        lumin_pah = lumin_pah[0]
+        #norm = np.trapz(lumin_pah, x=wave)
+        #lumin_pah /= norm
+
+        models.append(Schreiber2016(1, np.float(td), wave, lumin_pah))
+
+                                        
+    base.add_schreiber2016(models)
+
 def build_base():
     base = Database(writable=True)
     base.upgrade_base()
@@ -709,6 +744,11 @@ def build_base():
     print("\nDONE\n")
     print('#' * 78)
 
+    print("9- Importing Schreiber et al (2016) models\n")
+    build_schreiber2016(base)
+    print("\nDONE\n")
+    print('#' * 78)
+    
     base.session.close_all()
 
 

pcigale/data/__init__.py

@@ -30,6 +30,7 @@ from .dl2014 import DL2014
 from .fritz2006 import Fritz2006
 from .nebular_continuum import NebularContinuum
 from .nebular_lines import NebularLines
+from .schreiber2016 import Schreiber2016
 
 DATABASE_FILE = pkg_resources.resource_filename(__name__, 'data.db')
 
@@ -235,6 +236,21 @@ class _NebularContinuum(BASE):
         self.wave = nebular_continuum.wave
         self.lumin = nebular_continuum.lumin
 
+class _Schreiber2016(BASE):
+    """Storage for Schreiber et al (2016) infra-red templates
+        """
+    
+    __tablename__ = 'schreiber2016_templates'
+    type = Column(Float, primary_key=True)
+    tdust = Column(String, primary_key=True)
+    wave = Column(PickleType)
+    lumin = Column(PickleType)
+    
+    def __init__(self, ir):
+        self.type = ir.type
+        self.tdust = ir.tdust
+        self.wave = ir.wave
+        self.lumin = ir.lumin
 
 class Database(object):
     """Object giving access to pcigale database."""
@@ -611,6 +627,8 @@ class Database(object):
             dictionary of parameters and their values
         """
         return self._get_parameters(_Dale2014)
+    
+
 
     def add_fritz2006(self, models):
         """
@@ -792,6 +810,72 @@ class Database(object):
         """
         return self._get_parameters(_NebularContinuum)
 
+    def add_schreiber2016(self, models):
+        """
+        Add Schreiber et al (2016) templates the collection.
+        
+        Parameters
+        ----------
+        models: list of pcigale.data.Schreiber2016 objects
+        
+        """
+    
+        if self.is_writable:
+            for model in models:
+                self.session.add(_Schreiber2016(model))
+            try:
+                self.session.commit()
+            except exc.IntegrityError:
+                self.session.rollback()
+                raise DatabaseInsertError(
+                  'The Schreiber2016 template is already in the base.')
+        else:
+            raise Exception('The database is not writable.')
+
+    def get_schreiber2016(self, type, tdust):
+        """
+        Get the Schreiber et al (2016) template corresponding to the given set of
+        parameters.
+        
+        Parameters
+        ----------
+        type: float
+        Dust template or PAH template
+        tdust: float
+        Dust temperature
+        
+        Returns
+        -------
+        template: pcigale.data.Schreiber2016
+        The Schreiber et al. (2016) IR template.
+        
+        Raises
+        ------
+        DatabaseLookupError: if the requested template is not in the database.
+        
+        """
+        result = (self.session.query(_Schreiber2016).
+              filter(_Schreiber2016.type == type).
+              filter(_Schreiber2016.tdust == tdust).
+              first())
+        if result:
+            return Schreiber2016(result.type, result.tdust, result.wave,
+                                  result.lumin)
+        else:
+            raise DatabaseLookupError(
+                "The Schreiber2016 template for type <{0}> and tdust <{1}> "
+                "is not in the database.".format(type, tdust))
+
+    def get_schreiber2016_parameters(self):
+        """Get parameters for the Scnreiber 2016 models.
+        
+        Returns
+        -------
+        paramaters: dictionary
+        dictionary of parameters and their values
+        """
+        return self._get_parameters(_Schreiber2016)
+
     def _get_parameters(self, schema):
         """Generic function to get parameters from an arbitrary schema.