Merge branch 'develop' into cf_naming

pypeit/core/arc.py

@@ -485,12 +485,12 @@ def get_censpec(slit_cen, slitmask, arcimg, gpm=None, box_rad=3.0,
             continue
         # Check if this slit is masked
         if slit_bpm is not None and slit_bpm[islit]:
-            msgs.info('Ignoring masked slit {}'.format(islit))
+            msgs.info('Ignoring masked slit {}'.format(islit+1))
             # TODO -- Avoid using NaNs
             arc_spec[:,islit] = np.nan
             continue
         if verbose:
-            msgs.info('Extracting approximate arc spectrum along the center of slit {0}'.format(islit))
+            msgs.info('Extracting approximate arc spectrum along the center of slit {0}'.format(islit+1))
         # Create a mask for the pixels that will contribue to the arc
         arcmask = _gpm & (np.absolute(spat[None,:] - slit_cen[:,islit,None]) < box_rad)
         # Trimming the image makes this much faster

pypeit/core/wavecal/autoid.py

@@ -1736,10 +1736,12 @@ def run_brute(self, min_nlines=10):
         self._det_weak = {}
         self._det_stro = {}
         for slit in range(self._nslit):
-            msgs.info("Working on slit: {}".format(slit))
             if slit not in self._ok_mask:
                 self._all_final_fit[str(slit)] = None
+                msgs.info('Ignoring masked slit {}'.format(slit+1))
                 continue
+            else:
+                msgs.info("Working on slit: {}".format(slit+1))
             # TODO Pass in all the possible params for detect_lines to arc_lines_from_spec, and update the parset
             # Detect lines, and decide which tcent to use
             sigdetect = wvutils.parse_param(self._par, 'sigdetect', slit)
@@ -1751,7 +1753,7 @@ def run_brute(self, min_nlines=10):
 
             # Were there enough lines?  This mainly deals with junk slits
             if self._all_tcent.size < min_nlines:
-                msgs.warn("Not enough lines to identify in slit {0:d}!".format(slit))
+                msgs.warn("Not enough lines to identify in slit {0:d}!".format(slit+1))
                 self._det_weak[str(slit)] = [None,None]
                 self._det_stro[str(slit)] = [None,None]
                 # Remove from ok mask
@@ -1770,9 +1772,10 @@ def run_brute(self, min_nlines=10):
             # Print preliminary report
             good_fit[slit] = self.report_prelim(slit, best_patt_dict, best_final_fit)
 
-        # Now that all slits have been inspected, cross match to generate a
+        # Now that all slits have been inspected, cross match (if there are bad fit) to generate a
         # list of all lines in every slit, and refit all spectra
-        if self._nslit > 1:
+        # in self.cross_match() good fits are cross correlate with each other, so we need to have at least 2 good fits
+        if np.where(good_fit[self._ok_mask])[0].size > 1 and np.any(np.logical_not(good_fit[self._ok_mask])):
             msgs.info('Checking wavelength solution by cross-correlating with all slits')
 
             msgs.info('Cross-correlation iteration #1')
@@ -2034,7 +2037,7 @@ def cross_match(self, good_fit, detections):
         # to be classified as a bad slit here. Is this the behavior we want?? Maybe we should be more
         # conservative and call a bad any slit which results in an outlier here?
         good_slits = np.sort(sort_idx[np.unique(slit_ids[gdmsk, :].flatten())])
-        bad_slits = np.setdiff1d(np.arange(self._nslit), good_slits, assume_unique=True)
+        bad_slits = np.setdiff1d(np.arange(self._nslit)[self._ok_mask], good_slits, assume_unique=True)
         nbad = bad_slits.size
         if nbad > 0:
             msgs.info('Working on {:d}'.format(nbad) + ' bad slits: {:}'.format(bad_slits + 1))
@@ -2858,13 +2861,12 @@ def report_final(self):
         for slit in range(self._nslit):
             # Prepare a message for bad wavelength solutions
             badmsg = '---------------------------------------------------' + msgs.newline() +\
-                     'Final report for slit {0:d}/{1:d}:'.format(slit+1, self._nslit) + msgs.newline() +\
-                     '  Wavelength calibration not performed!'
+                     'Final report for slit {0:d}/{1:d}:'.format(slit+1, self._nslit) + msgs.newline()
             if slit not in self._ok_mask:
-                msgs.warn(badmsg)
+                msgs.warn(badmsg + 'Masked slit ignored')
                 continue
             if self._all_patt_dict[str(slit)] is None:
-                msgs.warn(badmsg)
+                msgs.warn(badmsg + '  Wavelength calibration not performed!')
                 continue
             st = str(slit)
             if self._all_patt_dict[st]['sign'] == +1: