Implementing manual flexure shift

pypeit/metadata.py

@@ -122,7 +122,7 @@ def __init__(self, spectrograph, par, files=None, data=None, usrdata=None,
             self.merge(usrdata)
 
         # Impose types on specific columns
-        self._impose_types(['comb_id', 'bkg_id', 'manual'], [int, int, str])
+        self._impose_types(['comb_id', 'bkg_id', 'manual', 'shift'], [int, int, str, float])
 
         # Initialize internal attributes
         self.configs = None
@@ -354,7 +354,7 @@ def remove_rows(self, rows, regroup=False):
         """
         self.table.remove_rows(np.atleast_1d(rows))
         if regroup:
-            for col in ['setup', 'calib', 'calibbit', 'comb_id', 'bkg_id']:
+            for col in ['setup', 'calib', 'calibbit', 'comb_id', 'bkg_id', 'shift']:
                 if col in self.keys():
                     del self.table[col]
             self.set_configurations()
@@ -1446,7 +1446,7 @@ def get_frame_types(self, flag_unknown=False, user=None, merge=True):
         msgs.info("Typing completed!")
         return self.set_frame_types(type_bits, merge=merge)
 
-    def set_pypeit_cols(self, write_bkg_pairs=False, write_manual=False):
+    def set_pypeit_cols(self, write_bkg_pairs=False, write_manual=False, write_shift = False):
         """
         Generate the list of columns to be included in the fitstbl
         (nearly the complete list).
@@ -1457,6 +1457,9 @@ def set_pypeit_cols(self, write_bkg_pairs=False, write_manual=False):
                 and bkg_id
             write_manual (:obj:`bool`, optional):
                 Add additional ``PypeIt`` columns for manual extraction
+            write_shift (:obj:`bool`, optional):
+                Add additional ``PypeIt`` columns for manual flexure
+                correction
 
 
         Returns:
@@ -1474,12 +1477,18 @@ def set_pypeit_cols(self, write_bkg_pairs=False, write_manual=False):
         # manual
         if write_manual:
             extras += ['manual']
+        if write_shift:
+            print('')
+            print('Adding Shift Column')
+            print('')
+            extras += ['shift']
         for key in extras:
             if key not in columns:
                 columns += [key]
-
+        print('Column list is: ', columns)
         # Take only those present
         output_cols = np.array(columns)
+        print('Output cols will be ', output_cols[np.isin(output_cols, self.keys())].tolist())
         return output_cols[np.isin(output_cols, self.keys())].tolist()
 
     def set_combination_groups(self, assign_objects=True):
@@ -1510,6 +1519,8 @@ def set_combination_groups(self, assign_objects=True):
             self['comb_id'] = -1
         if 'bkg_id' not in self.keys():
             self['bkg_id'] = -1
+        if 'shift' not in self.keys():
+            self['shift'] = 0
 
         # NOTE: Importantly, this if statement means that, if the user has
         # defined any non-negative combination IDs in their pypeit file, none of
@@ -1544,6 +1555,8 @@ def set_user_added_columns(self):
         """
         if 'manual' not in self.keys():
             self['manual'] = ''
+        if 'shift' not in self.keys():
+            self['shift'] = 0
 
     def write_sorted(self, ofile, overwrite=True, ignore=None, 
                      write_bkg_pairs=False, write_manual=False):
@@ -1586,7 +1599,7 @@ def write_sorted(self, ofile, overwrite=True, ignore=None,
         # Grab output columns
         output_cols = self.set_pypeit_cols(write_bkg_pairs=write_bkg_pairs,
                                            write_manual=write_manual)
-
+        print('Columns being used are: ', output_cols)
         cfgs = self.unique_configurations(copy=ignore is not None)
         if ignore is not None:
             for key in cfgs.keys():
@@ -1628,6 +1641,7 @@ def write_sorted(self, ofile, overwrite=True, ignore=None,
 
     def write_pypeit(self, output_path=None, cfg_lines=None,
                      write_bkg_pairs=False, write_manual=False,
+                     write_shift = False,
                      configs=None, config_subdir=True,
                      version_override=None, date_override=None):
         """
@@ -1656,6 +1670,9 @@ def write_pypeit(self, output_path=None, cfg_lines=None,
                 object and background frame pairs.  
             write_manual (:obj:`bool`, optional):
                 Add additional ``PypeIt`` columns for manual extraction
+            write_shift (:obj:`bool`, optional):
+                Add additional ``PypeIt`` columns for manual spatial flexure
+                correction
             configs (:obj:`str`, :obj:`list`, optional):
                 One or more strings used to select the configurations
                 to include in the returned objects. If ``'all'``,
@@ -1703,7 +1720,8 @@ def write_pypeit(self, output_path=None, cfg_lines=None,
 
         # Grab output columns
         output_cols = self.set_pypeit_cols(write_bkg_pairs=write_bkg_pairs,
-                                           write_manual=write_manual)
+                                           write_manual=write_manual,
+                                           write_shift = write_shift)
 
         # Write the pypeit files
         ofiles = [None]*len(cfg_keys)
@@ -1746,7 +1764,6 @@ def write_pypeit(self, output_path=None, cfg_lines=None,
             #with io.StringIO() as ff:
             #    subtbl.write(ff, format='ascii.fixed_width')
             #    data_lines = ff.getvalue().split('\n')[:-1]
-
             # Config lines
             if cfg_lines is None:
                 cfg_lines = ['[rdx]']

pypeit/pypeit.py

@@ -783,10 +783,19 @@ def objfind_one(self, frames, det, bg_frames=None, std_outfile=None):
 
         # Flexure
         spat_flexure = None
+        # use the flexure correction in the "shift" column
+        manual_flexure = self.fitstbl[frames[0]]['shift']
         if (self.objtype == 'science' and self.par['scienceframe']['process']['spat_flexure_correct']) or \
-                (self.objtype == 'standard' and self.par['calibrations']['standardframe']['process']['spat_flexure_correct']):
-            spat_flexure = sciImg.spat_flexure
+                (self.objtype == 'standard' and self.par['calibrations']['standardframe']['process']['spat_flexure_correct']) or \
+                    manual_flexure:
+            if manual_flexure:
+                msgs.info(f'Implementing manual flexure of {manual_flexure}')
+                spat_flexure = manual_flexure
+                sciImg.spat_flexure = spat_flexure
+            else:
+                spat_flexure = sciImg.spat_flexure
         # Build the initial sky mask
+        msgs.info(f'Flexure being used is: {spat_flexure}')
         initial_skymask = self.load_skyregions(initial_slits=self.spectrograph.pypeline != 'SlicerIFU',
                                                scifile=sciImg.files[0], frame=frames[0], spat_flexure=spat_flexure)
 

pypeit/scripts/setup.py

@@ -41,6 +41,8 @@ def get_parser(cls, width=None):
                                  '\'A,B\' or \'B,D,E\' or \'E\'.')
         parser.add_argument('-b', '--background', default=False, action='store_true',
                             help='Include the background-pair columns for the user to edit')
+        parser.add_argument('-f', '--flexure', default=False, action='store_true',
+                            help='Include the manual spatial shift (flexure) column for the user to edit')
         parser.add_argument('-m', '--manual_extraction', default=False, action='store_true',
                             help='Include the manual extraction column for the user to edit')
         parser.add_argument('-v', '--verbosity', type=int, default=1,
@@ -122,6 +124,7 @@ def main(args):
             pypeit_files = ps.fitstbl.write_pypeit(output_path=output_path, cfg_lines=ps.user_cfg, 
                                                    write_bkg_pairs=args.background,
                                                    write_manual=args.manual_extraction,
+                                                   write_shift = args.flexure,
                                                    configs=configs,
                                                    version_override=args.version_override,
                                                    date_override=args.date_override)

pypeit/spectrographs/keck_nirspec_high.py

@@ -80,7 +80,7 @@ def pypeit_file_keys(self):
         pypeit_keys = super().pypeit_file_keys()
         # TODO: Why are these added here? See
         # pypeit.metadata.PypeItMetaData.set_pypeit_cols
-        pypeit_keys += ['comb_id', 'bkg_id']
+        pypeit_keys += ['comb_id', 'bkg_id', 'shift']
         return pypeit_keys
 
     def get_echelle_angle_files(self, lamps_list, filter1, filter2):
@@ -593,7 +593,7 @@ def config_specific_par(self, scifile, inp_par=None):
             par['calibrations']['wavelengths']['xcorr_offset_minmax'] = 0.25
             par['calibrations']['wavelengths']['xcorr_percent_ceil'] = 99.9
             par['calibrations']['wavelengths']['echelle_pad'] = 1
-            par['calibrations']['slitedges']['rm_slits'] = '1:'
+            #par['calibrations']['slitedges']['rm_slits'] = '1:'
 
 
         if decker == '0.144x12':