Merge abfce6f into 97492f0

linetools · Jul 11, 2018 · 2fb441f · 2fb441f
2 parents 97492f0 + abfce6f
commit 2fb441f
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Showing 3 changed files with 14 additions and 7 deletions.
diff --git a/linetools/isgm/abssystem.py b/linetools/isgm/abssystem.py
@@ -620,9 +620,10 @@ def to_dict(self):
         outdict['components'] = {}
         for component in self._components:
             outdict['components'][component.name] = ltu.jsonify(component.to_dict())
-        # Spectrum file?
-        if hasattr(self, 'spec_file'):
-            outdict['spec_file'] = self.spec_file
+        # Extras
+        for eattr in ['spec_file', 'kin']:
+            if hasattr(self, eattr):
+                outdict[eattr] = getattr(self,eattr)
         # Polish
         outdict = ltu.jsonify(outdict)
         # Return

diff --git a/linetools/spectra/io.py b/linetools/spectra/io.py
@@ -517,7 +517,7 @@ def parse_FITS_binary_table(hdulist, exten=None, wave_tag=None, flux_tag=None,
     if sig_tag is None:
         sig_tags = ['ERROR','ERR','SIGMA_FLUX','ERR_FLUX', 'ENORM', 'FLAM_SIG', 'SIGMA_UP',
                     'ERRSTIS', 'FLUXERR', 'SIGMA', 'sigma', 'sigma_flux',
-                    'er', 'err', 'error', 'sig', 'fluxerror']
+                    'er', 'err', 'error', 'sig', 'fluxerror', 'FLUX_ERROR']
     else:
         sig_tags = [sig_tag]
     sig, sig_tag = get_table_column(sig_tags, hdulist, idx=exten)

diff --git a/linetools/spectra/xspectrum1d.py b/linetools/spectra/xspectrum1d.py
@@ -830,7 +830,7 @@ def relative_vel(self, wv_obs):
         return velo
 
     #  Box car smooth
-    def box_smooth(self, nbox, preserve=True, **kwargs):
+    def box_smooth(self, nbox, preserve=True, scale_sig=True, **kwargs):
         """ Box car smooth the spectrum
 
         Parameters
@@ -840,6 +840,8 @@ def box_smooth(self, nbox, preserve=True, **kwargs):
         preserve: bool, optional
           If True, perform a convolution to ensure the new spectrum
           has the same number of pixels as the original.
+        scale_sig : bool, optional
+          If True, scale the smoothed sig array down by np.sqrt(nbox)
         **kwargs: dict
           If preserve=True, these keywords are passed on to
           astropy.convoution.convolve
@@ -853,7 +855,9 @@ def box_smooth(self, nbox, preserve=True, **kwargs):
             from astropy.convolution import convolve, Box1DKernel
             new_fx = convolve(self.flux, Box1DKernel(nbox), **kwargs)
             if self.sig_is_set:
-                new_sig = convolve(self.sig, Box1DKernel(nbox), **kwargs) / np.sqrt(nbox)
+                new_sig = convolve(self.sig, Box1DKernel(nbox), **kwargs)
+                if scale_sig:
+                    new_sig /= np.sqrt(nbox)
             else:
                 new_sig = None
             if self.co_is_set:
@@ -876,7 +880,9 @@ def box_smooth(self, nbox, preserve=True, **kwargs):
             new_fx = ltu.scipy_rebin(self.flux[orig_pix_trunc], new_npix)
             if self.sig_is_set:
                 new_sig = ltu.scipy_rebin(
-                    self.sig[orig_pix_trunc], new_npix) / np.sqrt(nbox)
+                    self.sig[orig_pix_trunc], new_npix)
+                if scale_sig:
+                    new_sig /= np.sqrt(nbox)
             else:
                 new_sig = None
             if self.co_is_set: