finish badpixel kludge

linetools/analysis/abskin.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 import pdb
+import warnings
 
 from astropy import units as u
 from astropy.convolution import convolve, Box1DKernel
@@ -33,15 +34,16 @@ def generate_stau(velo, flux, sig, kbin=22.*u.km/u.s, debug=False):
     # Calculate dv
     dv = np.abs(np.median(velo-np.roll(velo,1)))
 
-    # Test for bad pixels
+    # Test for and replace bad pixels
     badzero = np.where((flux == 0) | (sig <= 0))[0]
     if len(badzero) > 0:
         if np.max(badzero)-np.min(badzero) >= 5:
             raise ValueError('orig_kin: too many or too large sections of bad data')
-
+        warnings.warn("Input array to generate_stau has one or more bad pixels.  Replacing with the local mean")
         flux[badzero] = np.mean(np.array([flux[np.min(badzero)-1],
                                                     flux[np.max(badzero)+1]]))
-        pdb.set_trace() # Should add sig too
+        sig[badzero] = np.mean(np.array([sig[np.min(badzero)-1],
+                                          sig[np.max(badzero)+1]]))
 
     # Generate the tau array
     tau = np.zeros(npix)
@@ -56,19 +58,10 @@ def generate_stau(velo, flux, sig, kbin=22.*u.km/u.s, debug=False):
 
     # Smooth
     nbin = (np.round(kbin/dv)).value
-    try:
-        kernel = Box1DKernel(nbin, mode='center')
-    except:
-        pdb.set_trace()
+    kernel = Box1DKernel(nbin, mode='center')
     stau = convolve(tau, kernel, boundary='fill', fill_value=0.)
     if debug is True:
-        try:
-            from xastropy.xutils import xdebug as xdb
-        except ImportError:
-            pdb.set_trace()
-        else:
-            xdb.xplot(velo, tau, stau)
-            xdb.set_trace()
+        pdb.set_trace()
 
     # Return
     return stau