Merge pull request #1718 from pypeit/hotfix_skysub

HotFix: SkyRegions GUI

doc/releases/1.14.1dev.rst

@@ -61,5 +61,7 @@ Bug Fixes
   detector for Keck/LRIS RED.
 - Fixed a bug with the ``pypeit_identify`` script when using echelle data. Previously,
   the sigdetect parameter was a list of all orders, instead of a single value.
+- Fixed a bug with the GUI ``pypeit_skysub_regions``. Previously, the calib header
+  information was not included, and this led to a calibration error.
 
 

pypeit/core/gui/skysub_regions.py

@@ -571,22 +571,41 @@ def operations(self, key, axisID):
         self.replot()
 
     def get_result(self):
-        """Save a mask containing the skysub regions, and print information
+        """Generate a calibration file containing a mask of the skysub regions, and print information
         for what the user should include in their .pypeit file
+
+        Returns
+        -------
+        msskyreg : :class:`SkyRegions`, None
+            Returns an instance of the :class:`SkyRegions` class. If None is returned,
+            the user has requested to not use the updates.
+        """
+        if not self._use_updates:
+            return None
+
+        # Generate the mask
+        inmask = skysub.generate_mask(self.pypeline, self._skyreg, self.slits, self.slits_left, self.slits_right)
+        if np.all(np.logical_not(inmask)):
+            msgs.warn("Sky regions are empty - A sky regions calibration frame will not be generated")
+            return None
+
+        # Build the Sky Regions calibration frame
+        return buildimage.SkyRegions(image=inmask.astype(float), PYP_SPEC=self.spectrograph)
+
+    def get_outname(self):
+        """ Get an output filename
+
+        Returns
+        -------
+        outfil : :obj:`str`
+            The output filename to use for the Sky Regions calibration frame
         """
-        # Only do this if the user wishes to save the result
-        if self._use_updates:
-            # Generate the mask
-            inmask = skysub.generate_mask(self.pypeline, self._skyreg, self.slits, self.slits_left, self.slits_right)
-            # Save the mask
-            outfil = self._outname
-            if os.path.exists(self._outname) and not self._overwrite:
-                outfil = 'temp.fits'
-                msgs.warn(f"A SkyRegions file already exists and you have not forced an overwrite:\n{self._outname}")
-                msgs.info(f"Saving regions to: {outfil}")
-                self._overwrite = True
-            msskyreg = buildimage.SkyRegions(image=inmask.astype(float), PYP_SPEC=self.spectrograph)
-            msskyreg.to_file(file_path=outfil)
+        outfil = self._outname
+        if os.path.exists(self._outname) and not self._overwrite:
+            outfil = 'temp.fits'
+            msgs.warn(f"A SkyRegions file already exists and you have not forced an overwrite:\n{self._outname}")
+            msgs.info(f"Adopting the following output filename: {outfil}")
+        return outfil
 
     def recenter(self):
         xlim = self.axes['main'].get_xlim()

pypeit/core/skysub.py

@@ -1592,13 +1592,14 @@ def generate_mask(pypeline, skyreg, slits, slits_left, slits_right, spat_flexure
             spec_min = np.append(spec_min, slits.specmin[sl])
             spec_max = np.append(spec_max, slits.specmax[sl])
 
+    # Check if no regions were added
+    if left_edg.shape[1] == 0:
+        return np.zeros((slits.nspec, slits.nspat), dtype=bool)
+
     # Now that we have sky region traces, utilise the SlitTraceSet to define the regions.
     # We will then use the slit_img task to create a mask of the sky regions.
-    # TODO: I don't understand why slmsk needs to be instantiated.  SlitTraceSet
-    # does this internally.
-    slmsk = np.zeros(left_edg.shape[1], dtype=slittrace.SlitTraceSet.bitmask.minimum_dtype())
     slitreg = slittrace.SlitTraceSet(left_edg, righ_edg, pypeline, nspec=slits.nspec,
-                                     nspat=slits.nspat, mask=slmsk, specmin=spec_min,
+                                     nspat=slits.nspat, specmin=spec_min,
                                      specmax=spec_max, binspec=slits.binspec,
                                      binspat=slits.binspat, pad=0)
     # Generate the mask, and return

pypeit/scripts/skysub_regions.py

@@ -95,7 +95,13 @@ def main(args):
                                       initial=args.initial, flexure=spat_flexure)
 
         # Get the results
-        skyreg.get_result()
+        msskyreg = skyreg.get_result()
+
+        if msskyreg is not None:
+            outfil = skyreg.get_outname()
+            setup, calib_id, detname = msskyreg.parse_calib_key(calib_key)
+            msskyreg.set_paths(calib_dir, setup, calib_id, detname)
+            msskyreg.to_file(file_path=outfil)
 
         # Reset the defaults
         skyreg.finalize()