docstrings and cleanup

pypeit/core/extract.py

@@ -478,9 +478,9 @@ def extract_hist_spectrum(waveimg, frame, gpm=None, bins=1000):
     if waveimg.shape != _gpm.shape:
         msgs.error("Wavelength image is not the same shape as the GPM")
     # Set the bins
-    if type(bins) is int:
+    if isinstance(bins, int):
         _bins = np.linspace(np.min(waveimg[_gpm]), np.max(waveimg[_gpm]), bins)
-    elif type(bins) is np.ndarray:
+    elif isinstance(bins, np.ndarray):
         _bins = bins
     else:
         msgs.error("Argument 'bins' should be an integer or a numpy array")

pypeit/inputfiles.py

@@ -796,16 +796,16 @@ def options(self):
             Dictionary containing cube options.
         """
         # Define the list of allowed parameters
-        opts = dict(scale_corr=None, skysub_frame=None)
+        opts = dict(scale_corr=None, skysub_frame=None, ra_offset=None, dec_offset=None)
 
         # Get the scale correction files
-        scale_corr = self.path_and_files('scale_corr', skip_blank=True)
+        scale_corr = self.path_and_files('scale_corr', skip_blank=False, check_exists=False)
         if scale_corr is None:
             opts['scale_corr'] = [None]*len(self.filenames)
         elif len(scale_corr) == 1 and len(self.filenames) > 1:
             opts['scale_corr'] = scale_corr.lower()*len(self.filenames)
         elif len(scale_corr) != 0:
-            opts['scale_corr'] = scale_corr.lower()
+            opts['scale_corr'] = scale_corr
 
         # Get the skysub files
         skysub_frame = self.path_and_files('skysub_frame', skip_blank=False, check_exists=False)

pypeit/par/pypeitpar.py

@@ -1456,6 +1456,7 @@ def __init__(self, slit_spec=None, relative_weights=None, align=None, combine=No
                                     'line map to register two frames.' \
 
         defaults['method'] = "subpixel"
+        options['method'] = ["subpixel", "ngp"]
         dtypes['method'] = str
         descr['method'] = 'What method should be used to generate the datacube. There are currently two options: ' \
                           '(1) "subpixel" (default) - this algorithm divides each pixel in the spec2d frames ' \
@@ -1588,19 +1589,12 @@ def from_dict(cls, cfg):
         return cls(**kwargs)
 
     def validate(self):
-        # Check the method options
-        allowed_methods = ["subpixel", "ngp"]
-        if self.data['method'] not in allowed_methods:
-            # Check if the supplied name exists
-            if not os.path.exists(self.data['method']):
-                raise ValueError("The 'method' must be one of:\n"+", ".join(allowed_methods) +
-                                 "\nor, the relative path to a spec2d file.")
         # Check the skysub options
         allowed_skysub_options = ["none", "image", ""]  # Note, "None" is treated as None which gets assigned to the default value "image".
         if self.data['skysub_frame'] not in allowed_skysub_options:
             # Check if the supplied name exists
             if not os.path.exists(self.data['method']):
-                raise ValueError("The 'skysub_frame' must be one of:\n" + ", ".join(allowed_methods) +
+                raise ValueError("The 'skysub_frame' must be one of:\n" + ", ".join(allowed_skysub_options) +
                                  "\nor, the relative path to a spec2d file.")
         if len(self.data['whitelight_range']) != 2:
             raise ValueError("The 'whitelight_range' must be a two element list of either NoneType or float")

pypeit/scripts/coadd_datacube.py

@@ -52,9 +52,16 @@ def main(args):
             msgs.info("Restricting to detector={}".format(args.det))
             parset['rdx']['detnum'] = int(args.det)
 
+        # Extract the options
+        ra_offsets = coadd3dfile.options['ra_offset']
+        dec_offsets = coadd3dfile.options['dec_offset']
+        skysub_frame = coadd3dfile.options['skysub_frame']
+        scale_corr = coadd3dfile.options['scale_corr']
+
         # Instantiate CoAdd3d
         tstart = time.time()
-        coadd = CoAdd3D.get_instance(coadd3dfile.filenames, coadd3dfile.options, spectrograph=spectrograph, par=parset,
+        coadd = CoAdd3D.get_instance(coadd3dfile.filenames, parset, skysub_frame=skysub_frame, scale_corr=scale_corr,
+                                     ra_offsets=ra_offsets, dec_offsets=dec_offsets, spectrograph=spectrograph,
                                      det=args.det, overwrite=args.overwrite)
 
         # Coadd the files

pypeit/slittrace.py

@@ -447,6 +447,7 @@ def get_radec_image(self, wcs, alignSplines, tilts, initial=True, flexure=None):
             reference (usually the centre of the slit) and the edges of the
             slits. Shape is (nslits, 2).
         """
+        msgs.info("Generating an RA/DEC image")
         # Initialise the output
         raimg = np.zeros((self.nspec, self.nspat))
         decimg = np.zeros((self.nspec, self.nspat))