Spatial flexure options

deprecated/find_objects.py

@@ -191,7 +191,7 @@ def illum_profile_spatial(self, skymask=None, trim_edg=(0, 0), debug=False):
     skymask_now = skymask if (skymask is not None) else np.ones_like(self.sciImg.image, dtype=bool)
     hist_trim = 0  # Trim the edges of the histogram to take into account edge effects
     gpm = self.sciImg.select_flag(invert=True)
-    slitid_img_init = self.slits.slit_img(pad=0, initial=True, flexure=self.spat_flexure_shift)
+    slitid_img_init = self.slits.slit_img(pad=0, initial=True, spat_flexure=self.spat_flexure_shift)
     spatScaleImg = np.ones_like(self.sciImg.image)
     # For each slit, grab the spatial coordinates and a spline
     # representation of the spatial profile from the illumflat
@@ -290,7 +290,7 @@ def illum_profile_spectral(self, global_sky, skymask=None):
     # relative spectral sensitivity is calculated at a given wavelength for all slits simultaneously.
     scaleImg = flatfield.illum_profile_spectral(self.sciImg.image.copy(), self.waveimg, self.slits,
                                                 slit_illum_ref_idx=sl_ref, model=global_sky, gpmask=gpm,
-                                                skymask=skymask, trim=trim, flexure=self.spat_flexure_shift,
+                                                skymask=skymask, trim=trim, spat_flexure=self.spat_flexure_shift,
                                                 smooth_npix=smooth_npix)
     # Now apply the correction to the science frame
     self.apply_relative_scale(scaleImg)

deprecated/flat.py

@@ -226,7 +226,7 @@ def fit_flat(flat, tilts_dict, tslits_dict_in, slit, inmask = None,
     slitmask_pad = pixels.tslits2mask(tslits_dict_in, pad = pad)
     thismask = (slitmask_pad == slit) # mask enclosing the wider slit bounadries
     # Create a tilts image using this padded thismask, rather than using the original thismask_in slit pixels
-    tilts = tracewave.fit2tilts(shape, tilts_dict['coeffs'], tilts_dict['func2d'])
+    tilts = tracewave.fit2tilts(tilts_dict['coeffs'], tilts_dict['func2d'], shape=shape)
     piximg = tilts * (nspec-1)
     pixvec = np.arange(nspec)
 

deprecated/ql_keck_lris.py

@@ -59,7 +59,7 @@ def config_lines(args):
     cfg_lines += ['        refframe = observed']
     cfg_lines += ['[scienceframe]']
     cfg_lines += ['    [[process]]']
-    cfg_lines += ['        spat_flexure_correct = False']
+    cfg_lines += ['        spat_flexure_method = skip']
     if not args.mask_cr:
         cfg_lines += ['        mask_cr = False']
     cfg_lines += ['[reduce]']

deprecated/ql_multislit.py

@@ -75,7 +75,7 @@ def config_lines(args):
     cfg_lines += ['        refframe = observed']
     cfg_lines += ['[scienceframe]']
     cfg_lines += ['    [[process]]']
-    cfg_lines += ['        spat_flexure_correct = False']
+    cfg_lines += ['        spat_flexure_method = skip']
     if not args.mask_cr:
         cfg_lines += ['        mask_cr = False']
     cfg_lines += ['[reduce]']

deprecated/reduce.py

@@ -222,10 +222,10 @@ def initialise_slits(self, initial=False):
         self.slits = self.caliBrate.slits
         # Select the edges to use
         self.slits_left, self.slits_right, _ \
-            = self.slits.select_edges(initial=initial, flexure=self.spat_flexure_shift)
+            = self.slits.select_edges(initial=initial, spat_flexure=self.spat_flexure_shift)
 
         # Slitmask
-        self.slitmask = self.slits.slit_img(initial=initial, flexure=self.spat_flexure_shift,
+        self.slitmask = self.slits.slit_img(initial=initial, spat_flexure=self.spat_flexure_shift,
                                             exclude_flag=self.slits.bitmask.exclude_for_reducing+['BOXSLIT'])
         # Now add the slitmask to the mask (i.e. post CR rejection in proc)
         # NOTE: this uses the par defined by EdgeTraceSet; this will
@@ -339,7 +339,7 @@ def run_objfind(self, std_trace=None, show_peaks=False):
         else:
             tilt_flexure_shift = self.spat_flexure_shift
         msgs.info("Generating tilts image")
-        self.tilts = self.waveTilts.fit2tiltimg(self.slitmask, flexure=tilt_flexure_shift)
+        self.tilts = self.waveTilts.fit2tiltimg(self.slitmask, spat_flexure=tilt_flexure_shift)
         #
 
         # First pass object finding
@@ -375,7 +375,7 @@ def prepare_extraction(self, global_sky):
                           (np.invert(self.slits.bitmask.flagged(self.slits.mask,
                                                                 flag=self.slits.bitmask.exclude_for_reducing)))
         # Update Slitmask to remove `BOXSLIT`, i.e., we don't want to extract those
-        self.slitmask = self.slits.slit_img(flexure=self.spat_flexure_shift,
+        self.slitmask = self.slits.slit_img(spat_flexure=self.spat_flexure_shift,
                                             exclude_flag=self.slits.bitmask.exclude_for_reducing)
         # use the tweaked traces if they exist - DP: I'm not sure this is necessary
         self.sciImg.update_mask_slitmask(self.slitmask)
@@ -391,7 +391,7 @@ def prepare_extraction(self, global_sky):
         else:
             tilt_flexure_shift = self.spat_flexure_shift
         msgs.info("Generating tilts image")
-        self.tilts = self.waveTilts.fit2tiltimg(self.slitmask, flexure=tilt_flexure_shift)
+        self.tilts = self.waveTilts.fit2tiltimg(self.slitmask, spat_flexure=tilt_flexure_shift)
 
         # Wavelengths (on unmasked slits)
         msgs.info("Generating wavelength image")
@@ -1605,7 +1605,7 @@ def illum_profile_spatial(self, skymask=None, trim_edg=(0, 0)):
         skymask_now = skymask if (skymask is not None) else np.ones_like(self.sciImg.image, dtype=bool)
         hist_trim = 0  # Trim the edges of the histogram to take into account edge effects
         gpm = self.sciImg.select_flag(invert=True)
-        slitid_img_init = self.slits.slit_img(pad=0, initial=True, flexure=self.spat_flexure_shift)
+        slitid_img_init = self.slits.slit_img(pad=0, initial=True, spat_flexure=self.spat_flexure_shift)
         spatScaleImg = np.ones_like(self.sciImg.image)
         # For each slit, grab the spatial coordinates and a spline
         # representation of the spatial profile from the illumflat
@@ -1701,7 +1701,7 @@ def illum_profile_spectral(self, global_sky, skymask=None):
         gpm = self.sciImg.select_flag(invert=True)
         scaleImg = flatfield.illum_profile_spectral(self.sciImg.image.copy(), self.waveimg, self.slits,
                                                     slit_illum_ref_idx=ref_idx, model=global_sky, gpmask=gpm,
-                                                    skymask=skymask, trim=trim, flexure=self.spat_flexure_shift)
+                                                    skymask=skymask, trim=trim, spat_flexure=self.spat_flexure_shift)
         # Now apply the correction to the science frame
         self.apply_relative_scale(scaleImg)
 

doc/calibrations/flexure.rst

@@ -26,11 +26,22 @@ Spatial Flexure
 The code has a simple yet relatively robust method to cross-correlate
 the slits against any input image to determine a rigid, spatial offset.
 This algorithm is performed for any frame type by setting
-``spat_flexure_correct = True`` in the ``process`` block
-of :ref:`processimagespar`.
+``spat_flexure_method = <method>`` in the ``process`` block
+of :ref:`processimagespar`, where you should replace ``<method>`` with one of the
+following valid methods:
+``skip`` - this will skip the spatial flexure correction
+``detector`` - this will calculate one spatial flexure value for all slits on the detector
+``slit`` - this will calculate the spatial flexure for each slit separately
+``edge`` - this will calculate the spatial flexure for each slit edge separately
 
 We have made our own determinations for which instruments to enable this as the
 default. Inspect the :ref:`instr_par` list to see if your instrument is included
+(search for the value of ``spat_flexure_method``). We recommend that you use the
+``detector`` method for most instruments, unless you have good reason to believe
+that the spatial flexure is different for different slits or slit edges. Also note
+that some spectrographs post-process the spatial flexure values when using the ``slit``
+or ``edge`` methods (e.g. perform a linear fit to the spatial flexure values) to improve
+the result. Consult the documentation for your instrument to see if this is the case.
 (search for the value of ``spat_flexure_correct``).
 A QA plot is generated for each frame for which the spatial flexure correction
 is applied. We recommend the user to inspect these plots to ensure the flexure
@@ -52,11 +63,11 @@ add this to your PypeIt file:
 
     [scienceframe]
         [[process]]
-            spat_flexure_correct = True
+            spat_flexure_method = detector
     [calibrations]
         [[standardframe]]
             [[[process]]]
-                spat_flexure_correct = True
+                spat_flexure_method = detector
 
 This will:
 
@@ -78,7 +89,7 @@ following to your :doc:`../pypeit_file`:
     [calibrations]
         [[tiltframe]]
             [[[process]]]
-                spat_flexure_correct = True
+                spat_flexure_method = detector
 
 This will:
 

doc/calibrations/image_proc.rst

@@ -288,8 +288,8 @@ Spatial Flexure Shift
 
 A spatial shift in the slit positions due to instrument flexure is calculated
 using :func:`~pypeit.core.flexure.spat_flexure_shift` if the
-``spat_flexure_correct`` parameter is true.  See :ref:`flexure` for additional
-discussion.
+``spat_flexure_method`` parameter is set to an option other than ``skip``.
+See :ref:`flexure` for additional discussion.
 
 Flat-fielding
 -------------