Merge branch 'develop' into nirspec

doc/help/run_pypeit.rst

@@ -4,7 +4,7 @@
     usage: run_pypeit [-h] [-v VERBOSITY] [-r REDUX_PATH] [-m] [-s] [-o] [-c]
                       pypeit_file
     
-    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.15.1.dev151+g015ee23ce.d20240423[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.15.1.dev192+gf7d381a4b.d20240516[0m
     ##  
     ##  Available spectrographs include:
     ##   bok_bc, gemini_flamingos1, gemini_flamingos2, gemini_gmos_north_e2v,

pypeit/core/arc.py

@@ -69,7 +69,7 @@ def fit2darc(all_wv,all_pix,all_orders,nspec, nspec_coeff=4,norder_coeff=4,sigre
         utils.pyplot_rcparams()
         plt.figure(figsize=(7,5))
         msgs.info("Plot identified lines")
-        cm = plt.cm.get_cmap('RdYlBu_r')
+        cm = plt.get_cmap('RdYlBu_r')
         sc = plt.scatter(all_orders, all_pix,c=all_wv/10000., cmap=cm)
         cbar = plt.colorbar(sc)
         cbar.set_label(r'Wavelength [$\mu$m]', rotation=270,

pypeit/core/tracewave.py

@@ -8,7 +8,7 @@
 import numpy as np
 from scipy import interpolate, ndimage
 from matplotlib import pyplot as plt
-from matplotlib import cm, lines
+from matplotlib import lines, colormaps
 
 from IPython import embed
 
@@ -1061,7 +1061,7 @@ def arc_tilts_spat_qa(tilts_dspat, tilts, tilts_model, tilts_spec_fit, tot_mask,
     # Show the fit residuals as a function of spatial position
     line_indx = np.outer(np.ones(nspat), np.arange(nuse))
     lines_spec = tilts_spec_fit[0, :]
-    cmap = cm.get_cmap('coolwarm', nuse)
+    cmap = colormaps['coolwarm'].resampled(nuse)
 
     fig, ax = plt.subplots(figsize=(14, 12))
     # dummy mappable shows the spectral pixel

pypeit/core/wavecal/wvutils.py

@@ -282,6 +282,12 @@ def get_wave_grid(waves=None, gpms=None, wave_method='linear', iref=0, wave_grid
         elif wave_method == 'iref': # Use the iref index wavelength array
             wave_tmp = waves[iref]
             wave_grid = wave_tmp[wave_tmp > 1.0]
+            if spec_samp_fact != 1: # adjust sampling via internal interpolation
+                nwave = len(wave_grid)
+                indx = np.arange(nwave)
+                indx_new = np.linspace(0,nwave-1,int(nwave/spec_samp_fact))
+                wave_tmp = np.interp(indx_new,indx,wave_grid)
+                wave_grid = wave_tmp
 
         else:
             msgs.error("Bad method for wavelength grid: {:s}".format(wave_method))

pypeit/metadata.py

@@ -176,7 +176,7 @@ def _vet_instrument(self, meta_tbl):
                     msgs.warn(f'More than one instrument in your dataset! {instr_names} \n'
                               'Proceed with great caution...')
                 # Check the name
-                if instr_names[0] != self.spectrograph.header_name:
+                if not instr_names[0].startswith(self.spectrograph.header_name):
                     msgs.warn('The instrument name in the headers of the raw files does not match the '
                               f'expected one! Found {instr_names[0]}, expected {self.spectrograph.header_name}.  '
                               'You may have chosen the wrong PypeIt spectrograph name!')
@@ -857,7 +857,7 @@ def set_configurations(self, configs=None, force=False, fill=None):
                 mod_cfg = self.spectrograph.modify_config(self.table[i], cfg)
                 this_cfg = self.get_configuration(i, modified=True)
                 if self.spectrograph.same_configuration([this_cfg, mod_cfg], check_keys=False):
-                    if d in self.table['setup'][i]:
+                    if d in self.table['setup'][i].split(','):
                         continue
                     elif self.table['setup'][i] == 'None':
                         self.table['setup'][i] = d
@@ -882,7 +882,7 @@ def set_configurations(self, configs=None, force=False, fill=None):
         # For each configuration, determine if any of the frames with
         # the ignored frame types should be assigned to it:
         for cfg_key in _configs.keys():
-            in_cfg = np.array([cfg_key in _setup for _setup in self.table['setup']])
+            in_cfg = np.array([cfg_key in _setup.split(',') for _setup in self.table['setup']])
             for ftype, metakey in ignore_frames.items():
 
                 # TODO: For now, use this assert to check that the
@@ -937,7 +937,7 @@ def set_configurations(self, configs=None, force=False, fill=None):
                 # assign
                 new_cfg_key = np.full(len(self.table['setup'][indx]), 'None', dtype=object)
                 for c in range(len(self.table['setup'][indx])):
-                    if cfg_key in self.table['setup'][indx][c]:
+                    if cfg_key in self.table['setup'][indx][c].split(','):
                         new_cfg_key[c] = self.table['setup'][indx][c]
                     elif self.table['setup'][indx][c] == 'None':
                         new_cfg_key[c] = cfg_key
@@ -1168,7 +1168,7 @@ def set_calibration_groups(self, global_frames=None, default=False, force=False)
         # any changes to the strings will be truncated at 4 characters.
         self.table['calib'] = np.full(len(self), 'None', dtype=object)
         for i in range(n_cfg):
-            in_cfg = np.array([configs[i] in _set for _set in self.table['setup']]) # & (self['framebit'] > 0)
+            in_cfg = np.array([configs[i] in _set.split(',') for _set in self.table['setup']]) # & (self['framebit'] > 0)
             if not any(in_cfg):
                 continue
             icalibs = np.full(len(self['calib'][in_cfg]), 'None', dtype=object)
@@ -1638,7 +1638,7 @@ def write_sorted(self, ofile, overwrite=True, ignore=None,
         ff = open(_ofile, 'w')
         for setup in cfgs.keys():
             # Get the subtable of frames taken in this configuration
-            indx = np.array([setup in _set for _set in self['setup']])
+            indx = np.array([setup in _set.split(',') for _set in self['setup']])
             if not np.any(indx):
                 continue
             subtbl = self.table[output_cols][indx]
@@ -1772,7 +1772,7 @@ def write_pypeit(self, output_path=None, cfg_lines=None,
                 setup_dict[f'Setup {setup}'][key] = cfg[setup][key]
 
             # Get the paths
-            in_cfg = np.array([setup in _set for _set in self.table['setup']])
+            in_cfg = np.array([setup in _set.split(',') for _set in self.table['setup']])
             if not np.any(in_cfg):
                 continue
             paths = np.unique(self['directory'][in_cfg]).tolist()

pypeit/scripts/setup.py

@@ -81,25 +81,35 @@ def main(args):
         msgs.set_logfile_and_verbosity('setup', args.verbosity)
 
         if args.spectrograph is None:
-            raise IOError('spectrograph is a required argument.  Use the -s, --spectrograph '
-                          'command-line option.')
-
-        # Check that input spectrograph is supported
-        if args.spectrograph not in available_spectrographs:
-            raise ValueError(f'Instrument "{args.spectrograph}" unknown to PypeIt.\n'
-                             f'\tOptions are: {", ".join(available_spectrographs)}\n'
-                             '\tSelect an available instrument or consult the documentation '
-                             'on how to add a new instrument.')
+            if args.gui is False:
+                raise IOError('spectrograph is a required argument.  Use the -s, --spectrograph '
+                            'command-line option.')
+        else:
+            # Check that input spectrograph is supported
+            if args.spectrograph not in available_spectrographs:
+                raise ValueError(f'Instrument "{args.spectrograph}" unknown to PypeIt.\n'
+                                 f'\tOptions are: {", ".join(available_spectrographs)}\n'
+                                 '\tSelect an available instrument or consult the documentation '
+                                 'on how to add a new instrument.')
 
         if args.gui:
             from pypeit.scripts.setup_gui import SetupGUI
-            if isinstance(args.root,list):
-                root_args = args.root
-            else:
-                # If the root argument is a single string, convert it to a lsit.
-                # This can happen when the default for --root is used
-                root_args = [args.root]
-            gui_args = SetupGUI.parse_args(["-s", args.spectrograph, "-e", args.extension, "-r", *root_args])
+            # Build up arguments to the GUI
+            setup_gui_argv = ["-e", args.extension]
+            if args.spectrograph is not None:
+                setup_gui_argv += ["-s", args.spectrograph]
+
+                # Pass root but only if there's a spectrograph, because
+                # root has a default value but can't be acted upon by the GUI
+                # without a spectrograph.
+                if isinstance(args.root,list):
+                    root_args = args.root
+                else:
+                    # If the root argument is a single string, convert it to a list.
+                    # This can happen when the default for --root is used
+                    root_args = [args.root]
+                setup_gui_argv += ["-r"] + root_args
+            gui_args = SetupGUI.parse_args(setup_gui_argv)
             SetupGUI.main(gui_args)
 
         # Initialize PypeItSetup based on the arguments

pypeit/scripts/setup_gui.py

@@ -10,8 +10,7 @@
 
 from pypeit.scripts import scriptbase
 from pypeit.setup_gui.controller import SetupGUIController
-from pypeit.setup_gui import model
-
+from pypeit.spectrographs import available_spectrographs
 class SetupGUI(scriptbase.ScriptBase):
 
     @classmethod
@@ -21,7 +20,7 @@ def get_parser(cls, width=None):
                                     width=width)
         parser.add_argument('-s', '--spectrograph', default=None, type=str,
                             help='A valid spectrograph identifier: {0}'.format(
-                                    ', '.join(model.available_spectrographs())))
+                                    ', '.join(available_spectrographs)))
         parser.add_argument('-r', '--root', default=[], type=str,nargs='+',
                             help='Root to search for data files.  You can provide the top-level '
                                  'directory  (e.g., /data/Kast) or the search string up through '
@@ -54,6 +53,3 @@ def main(combined_args):
         app = QApplication(qt_args)
         controller = SetupGUIController(args)
         controller.start(app)
-
-if __name__ == '__main__':
-    SetupGUI.entry_point()