(Re?)-implemented AtomicTransition class, and made it play nicely with Spectrum1D

Author: andycasey

oracle/specutils/spectrum1d.py

@@ -106,6 +106,14 @@ def copy(self):
             variance=self.variance.copy(), headers=self.headers.copy())
 
 
+    def __contains__(self, value):
+        try:
+            # for AtomicTransitions
+            return self.disp[-1] >= value.wavelength >= self.disp[0]
+        except AttributeError:
+            return self.disp[-1] >= value >= self.disp[0]
+
+
     @property
     def v_helio(self):
         """

oracle/transitions/__init__.py

@@ -0,0 +1,4 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from atomic import AtomicTransition

oracle/transitions/atomic.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+""" Represent atomic transitions. """
+
+from __future__ import absolute_import, print_function
+
+__all__ = ["AtomicTransition"]
+__author__ = "Andy Casey <[email protected]>"
+
+import json
+import yaml
+
+from numpy import log, nan
+
+
+class AtomicTransition(object):
+
+    _DEFAULTS = {}
+
+    def __init__(self, wavelength, species, e_low, log_gf, mask=None, **kwargs):
+        """
+        Initialise the class.
+        """
+
+        self.wavelength = float(wavelength)
+        self.species = float(species)
+        self.e_low = float(e_low)
+        self.log_gf = float(log_gf)
+        self.mask = mask
+
+        self._raw = self._DEFAULTS.copy()
+        self._raw.update({
+            "wavelength": self.wavelength,
+            "species": self.species,
+            "e_low": self.e_low,
+            "log_gf": self.log_gf,
+            "mask": self.mask
+        })
+        self._raw.update(kwargs)
+
+    def __str__(self):
+        return unicode(self).encode("utf-8").strip()
+
+    def __unicode__(self):
+        return u"<{element} {ion} at {wavelength:.2f} Å>".format(
+            element=self.element, ion="I"*self.ion, wavelength=self.wavelength)
+
+    def __repr__(self):
+        return "<oracle.transitions.{klass} {element} {ion} at {wavelength:.1f}"\
+            " Angstroms at {location}>".format(klass=self.__class__.__name__,
+                element=self.element, ion="I" * self.ion,
+                wavelength=self.wavelength, location=hex(id(self)))
+
+    def to_json(self, **kwargs):
+        return json.dumps(self._raw, **kwargs)
+
+    def to_yaml(self, **kwargs):
+        return yaml.dump(self._raw, **kwargs)
+    
+    @property
+    def element(self):
+        periodictable = """H                                                  He
+                           Li Be                               B  C  N  O  F  Ne
+                           Na Mg                               Al Si P  S  Cl Ar
+                           K  Ca Sc Ti V  Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
+                           Rb Sr Y  Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I  Xe
+                           Cs Ba Lu Hf Ta W  Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
+                           Fr Ra Lr Rf Db Sg Bh Hs Mt Ds Rg Cn UUt"""
+        
+        lanthanoids    =  "La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb"
+        actinoids      =  "Ac Th Pa U  Np Pu Am Cm Bk Cf Es Fm Md No"
+        
+        periodictable = periodictable.replace("Ba ", "Ba " + lanthanoids) \
+            .replace("Ra ", "Ra " + actinoids).split()
+        return periodictable[self.atomic_number - 1]
+
+    @property
+    def atomic_number(self):
+        return int(self.species)
+
+    @property
+    def ion(self):
+        return int((self.species % 1) * 10) + 1
+
+    @property
+    def equivalent_width(self):
+        return self._raw.get("equivalent_width", nan)
+
+    @equivalent_width.setter
+    def equivalent_width(self, value):
+        self._raw["equivalent_width"] = value
+
+    @property
+    def log_eps(self):
+        return self._raw.get("log_eps", nan)
+
+    @log_eps.setter
+    def log_eps(self, value):
+        self._raw["log_eps"] = value
+
+    @property
+    def reduced_equivalent_width(self):
+        """
+        Return the reduced equivalent width of the line, if the equivalent width
+        has been measured.
+
+        The reduced equivalent width is defined by:
+
+        >> REW = log(equivalent width/wavelength)
+
+        :raise AttributeError:
+            If no equivalent width has been measured for this line.
+        """
+        return log(self.equivalent_width/self.wavelength)
+
+    # Some default line behaviour that we don't want passed to _raw unless
+    # explicitly defined.
+    @property
+    def continuum_degree(self):
+        return self._raw.get("continuum_degree", 0) # Assumes normalised spectra
+
+    @continuum_degree.setter
+    def continuum_degree(self, value):
+        self._raw["continuum_degree"] = value
+
+    @property
+    def fitting_region(self):
+        return self._raw.get("fitting_region",
+            [self.wavelength - 1.5, self.wavelength + 1.5])
+
+    @fitting_region.setter
+    def fitting_region(self, value):
+        self._raw["fitting_region"] = value
+
+    @property
+    def v_rad_tolerance(self):
+        return self._raw.get("v_rad_tolerance", 1.0) # km/s
+
+    @v_rad_tolerance.setter
+    def v_rad_tolerance(self, value):
+        self._raw["v_rad_tolerance"] = value

setup.py

@@ -83,8 +83,8 @@ def readfile(filename):
     author="Andrew R. Casey",
     author_email="[email protected]",
     packages=[
-        "oracle", "oracle.photospheres", "oracle.models", "oracle.specutils",
-        "oracle.synthesis"
+        "oracle", "oracle.photospheres", "oracle.models", "oracle.solvers",
+        "oracle.specutils", "oracle.synthesis", "oracle.transitions"
     ],
     url="http://www.github.com/andycasey/oracle/",
     description="the suppository of all wisdom",