fix snythetic spectra to work cleanly with wcs again

Author: keflavich

examples/ch3cn_110_synthspec.py

@@ -25,14 +25,15 @@
 
     R.temperature = temperature
     R.run_radex()
-    S = pyradex.synthspec.SyntheticSpectrum(110.326*u.GHz,110.388*u.GHz,R.get_table())
+    wcs = pyradex.synthspec.FrequencyArray(110.326*u.GHz,110.388*u.GHz, npts=1000)
+    S = pyradex.synthspec.SyntheticSpectrum.from_RADEX(wcs,R)
 
     # spectral colors
     color = mpl.cm.spectral(float(ii)/len(temperatures))
     S.plot(label='%i K' % temperature,color=color)
 
     for ii in xrange(nlines):
-        fluxes[ii].append(S.table[ii]['flux'])
+        fluxes[ii].append(S.T_B[ii].value)
 
 pl.savefig("CH3CN_6-5_synthetic_spectra.pdf",bbox_inches='tight')
 
@@ -42,7 +43,7 @@
 pl.clf()
 pl.subplot(1,2,1)
 for ii in xrange(nlines):
-    pl.plot(temperatures,fluxes[ii],label=linenames[ii])
+    pl.plot(temperatures,np.array(fluxes[ii]),label=linenames[ii])
 
 # Line #4 is the "reference line" at lowest energy
 pl.subplot(1,2,2)

examples/h2co_grids.py

@@ -43,7 +43,7 @@
         R.abundance = abundance # reset column to the appropriate value
         R.run_radex(reuse_last=False, reload_molfile=True)
 
-        TI = R.total_intensity
+        TI = R.source_brightness
         taugrid_6[jj,ii] = R.tau[0]
         texgrid_6[jj,ii] = R.tex[0].value
         fluxgrid_6[jj,ii] = TI[0].value

examples/h2cs_thermometer.py

@@ -50,7 +50,9 @@ def latex_float(f):
         for temperature in [10,50,100]:
             R.temperature = temperature
             R.run_radex()
-            S = pyradex.synthspec.SyntheticSpectrum(103.0*u.GHz,103.1*u.GHz,R.get_table(),linewidth=10*u.km/u.s)
+            wcs = pyradex.synthspec.FrequencyArray(103.0*u.GHz, 103.1*u.GHz, npts=1000)
+            S = pyradex.synthspec.SyntheticSpectrum.from_RADEX(wcs, R,
+                                                               linewidth=10*u.km/u.s)
             S.plot(label='%i K' % temperature)
 
         pl.legend(loc='best')

pyradex/synthspec.py

@@ -181,6 +181,8 @@ def from_RADEX(cls, wcs, rad,
 
             data = self.get_profile()
 
+            self.table = rad.get_table()
+
             super(Spectrum,self).__init__(data=data, wcs=self.wcs,
                                           unit=u.Unit(rad.T_B.unit))
 
@@ -211,14 +213,15 @@ def plot(self, update_data=False, *args, **kwargs):
             if update_data:
                 self.data = self.get_profile()
 
-            pl.gca().set_xlabel(self.dispersion.unit.to_string())
+            dispersion = self.wcs(np.arange(self.wcs.npts))
+            pl.gca().set_xlabel(dispersion.unit.to_string())
             if hasattr(self.data,'unit'):
                 pl.gca().set_ylabel(self.data.unit.to_string())
                 data = self.data.value
             else:
                 data = self.data
 
-            return pl.plot(self.dispersion.value, data, *args, **kwargs)
+            return pl.plot(dispersion.value, data, *args, **kwargs)
 
         def __call__(self, linewidth=None, velocity_offset=0*u.km/u.s, **kwargs):
             """