Blaze function fix

pypeit/extraction.py

@@ -15,8 +15,7 @@
 
 from pypeit import msgs, utils
 from pypeit.display import display
-from pypeit.core import skysub, extract, flexure
-
+from pypeit.core import skysub, extract, flexure, flat
 from IPython import embed
 
 
@@ -64,7 +63,7 @@ class Extract:
     @classmethod
     def get_instance(cls, sciImg, slits, sobjs_obj, spectrograph, par, objtype, global_sky=None,
                      bkg_redux_global_sky=None, waveTilts=None, tilts=None, wv_calib=None, waveimg=None,
-                     flatimg=None, bkg_redux=False, return_negative=False, std_redux=False, show=False, basename=None):
+                     flatimages=None, bkg_redux=False, return_negative=False, std_redux=False, show=False, basename=None):
         """
         Instantiate the Extract subclass appropriate for the provided
         spectrograph.
@@ -101,9 +100,9 @@ def get_instance(cls, sciImg, slits, sobjs_obj, spectrograph, par, objtype, glob
                 This is the waveCalib object which is optional, but either wv_calib or waveimg must be provided.
             waveimg (`numpy.ndarray`_, optional):
                 Wave image. Either a wave image or wv_calib object (above) must be provided
-            flatimg (`numpy.ndarray`_, optional):
-                Flat image. This is optional, but if provided, it is used to extract the
-                normalized blaze profile. Same shape as ``sciImg``.
+            flatimages (:class:`~pypeit.flatfield.FlatImages`, optional):
+                FlatImages class. This is optional, but if provided, it is used to extract the
+                normalized blaze profile.
             bkg_redux (:obj:`bool`, optional):
                 If True, the sciImg has been subtracted by
                 a background image (e.g. standard treatment in the IR)
@@ -131,12 +130,12 @@ def get_instance(cls, sciImg, slits, sobjs_obj, spectrograph, par, objtype, glob
                     if c.__name__ == (spectrograph.pypeline + 'Extract'))(
             sciImg, slits, sobjs_obj, spectrograph, par, objtype, global_sky=global_sky,
             bkg_redux_global_sky=bkg_redux_global_sky, waveTilts=waveTilts, tilts=tilts,
-            wv_calib=wv_calib, waveimg=waveimg, flatimg=flatimg, bkg_redux=bkg_redux, return_negative=return_negative,
-            std_redux=std_redux, show=show, basename=basename)
+            wv_calib=wv_calib, waveimg=waveimg, flatimages=flatimages, bkg_redux=bkg_redux,
+            return_negative=return_negative, std_redux=std_redux, show=show, basename=basename)
 
     def __init__(self, sciImg, slits, sobjs_obj, spectrograph, par, objtype, global_sky=None,
                  bkg_redux_global_sky=None, waveTilts=None, tilts=None, wv_calib=None, waveimg=None,
-                 flatimg=None, bkg_redux=False, return_negative=False, std_redux=False, show=False,
+                 flatimages=None, bkg_redux=False, return_negative=False, std_redux=False, show=False,
                  basename=None):
 
         # Setup the parameters sets for this object. NOTE: This uses objtype, not frametype!
@@ -149,7 +148,6 @@ def __init__(self, sciImg, slits, sobjs_obj, spectrograph, par, objtype, global_
         self.par = par
         self.global_sky = global_sky if global_sky is not None else np.zeros_like(sciImg.image)
         self.bkg_redux_global_sky = bkg_redux_global_sky
-        self.flatimg = flatimg
 
         self.basename = basename
         # Parse
@@ -247,6 +245,18 @@ def __init__(self, sciImg, slits, sobjs_obj, spectrograph, par, objtype, global_
         else:
             msgs.warn("Spectral FWHM image could not be generated")
 
+        # get flatfield image for blaze function
+        self.flatimg = None
+        if flatimages is not None:
+            # This way of getting the flat image (instead of just reading flatimages.pixelflat_model) ensures that the
+            # flat image is available also when an archival pixel flat is used.
+            flat_raw = flatimages.pixelflat_raw if flatimages.pixelflat_raw is not None else flatimages.illumflat_raw
+            if flat_raw is not None and flatimages.pixelflat_norm is not None:
+                # TODO: Can we just use flat_raw if flatimages.pixelflat_norm is None?
+                self.flatimg, _ = flat.flatfield(flat_raw, flatimages.pixelflat_norm)
+        if self.flatimg is None:
+            msgs.warn("No flat image was found. A spectrum of the flatfield will not be extracted!")
+
         # Now apply a global flexure correction to each slit provided it's not a standard star
         if self.par['flexure']['spec_method'] != 'skip' and not self.std_redux:
             # Update slitshift values

pypeit/pypeit.py

@@ -1029,18 +1029,14 @@ def extract_one(self, frames, det, sciImg, bkg_redux_sciimg, objFind, initial_sk
 
         if not self.par['reduce']['extraction']['skip_extraction']:
             msgs.info(f"Extraction begins for {self.basename} on det={det}")
-            # set the flatimg, if it exists
-            flatimg = None if self.caliBrate.flatimages is None else self.caliBrate.flatimages.pixelflat_model
-            if flatimg is None:
-                msgs.warn("No flat image was found. A spectrum of the flatfield will not be extracted!")
             # Instantiate Reduce object
             # Required for pipeline specific object
             # At instantiation, the fullmask in self.sciImg is modified
             # TODO Are we repeating steps in the init for FindObjects and Extract??
             self.exTract = extraction.Extract.get_instance(
                 sciImg, slits, sobjs_obj, self.spectrograph,
                 self.par, self.objtype, global_sky=final_global_sky, bkg_redux_global_sky=bkg_redux_global_sky,
-                waveTilts=self.caliBrate.wavetilts, wv_calib=self.caliBrate.wv_calib, flatimg=flatimg,
+                waveTilts=self.caliBrate.wavetilts, wv_calib=self.caliBrate.wv_calib, flatimages=self.caliBrate.flatimages,
                 bkg_redux=self.bkg_redux, return_negative=self.par['reduce']['extraction']['return_negative'],
                 std_redux=self.std_redux, basename=self.basename, show=self.show)
             # Perform the extraction

pypeit/specobjs.py

@@ -237,8 +237,8 @@ def unpack_object(self, ret_flam=False, log10blaze=False, min_blaze_value=1e-3,
 
         # Check for missing data
         none_flux = [f is None for f in getattr(self, flux_key)]
+        other = 'OPT' if extract_type == 'BOX' else 'BOX'
         if np.any(none_flux):
-            other = 'OPT' if extract_type == 'BOX' else 'BOX'
             msg = f"{extract_type} extracted flux is not available for all slits/orders. " \
                   f"Consider trying the {other} extraction."
             if not remove_missing:
@@ -249,6 +249,12 @@ def unpack_object(self, ret_flam=False, log10blaze=False, min_blaze_value=1e-3,
                 # Remove missing data
                 r_indx = np.where(none_flux)[0]
                 self.remove_sobj(r_indx)
+        # check for missing blaze
+        if extract_blaze:
+            none_blaze = [f is None for f in getattr(self, blaze_key)]
+            if np.any(none_blaze):
+                msgs.error(f"{extract_type} extracted blaze is not available for all slits/orders. "
+                           f"Consider trying the {other} extraction, or NOT using the flat.")
 
         #
         norddet = self.nobj
@@ -299,7 +305,7 @@ def unpack_object(self, ret_flam=False, log10blaze=False, min_blaze_value=1e-3,
         # Return
         if self[0].PYPELINE in ['MultiSlit', 'SlicerIFU'] and self.nobj == 1:
             meta_spec['ECH_ORDERS'] = None
-            blaze_ret = blaze_function.reshape(nspec) if extract_blaze else None
+            blaze_ret = blaze_function.reshape(nspec) if blaze_function is not None else None
             return wave.reshape(nspec), flux.reshape(nspec), flux_ivar.reshape(nspec), \
                    flux_gpm.reshape(nspec), blaze_ret, meta_spec, self.header
         else: