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/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/coadd1d.rst

@@ -312,7 +312,7 @@ This tool is developed by Michael Murphy and is available at
 `this link <https://github.com/MTMurphy77/UVES_popler/>`__.
 Here is an example of a coadded spectrum using UVES_popler:
 
-.. image:: ../figures/uves_popler.png
+.. image:: figures/uves_popler.png
    :scale: 60%
 
 UVES_popler was originally written to coadd ESO/UVES echelle spectra

doc/help/pypeit_sensfunc.rst

@@ -2,7 +2,7 @@
 
     $ pypeit_sensfunc -h
     usage: pypeit_sensfunc [-h] [--extr {OPT,BOX}] [--algorithm {UVIS,IR}]
-                           [--multi MULTI] [-o OUTFILE] [-s SENS_FILE] [-f FLATFILE]
+                           [--multi MULTI] [-o OUTFILE] [-s SENS_FILE] [-f]
                            [--debug] [--par_outfile PAR_OUTFILE] [-v VERBOSITY]
                            spec1dfile
 
@@ -71,20 +71,20 @@
                             in the filename.
       -s SENS_FILE, --sens_file SENS_FILE
                             Configuration file with sensitivity function parameters
-      -f FLATFILE, --flatfile FLATFILE
-                            Use a flat calibration file to compute the blaze
-                            function when generating the sensitivity function.  This
-                            is helpful to account for small scale undulations in the
-                            sensitivity function.  Note that it is not possible to
-                            set --flatfile and simultaneously use a .sens file with
-                            the --sens_file option. If you are using a .sens file,
-                            set the flatfile there via e.g.:
+      -f, --use_flat        Use the extracted spectrum of the flatfield calibration
+                            to estimate the blaze function when generating the
+                            sensitivity function. This is helpful to account for
+                            small scale undulations in the sensitivity function. The
+                            spec1dfile must contain the extracted flatfield response
+                            in order to use this option. This spectrum is extracted
+                            by default, unless you did not compute a pixelflat
+                            frame. Note that it is not possible to set --use_flat
+                            and simultaneously use a .sens file with the --sens_file
+                            option. If you are using a .sens file, set the use_flat
+                            flag with the argument:
 
                                 [sensfunc]
-                                     flatfile = Calibrations/Flat_A_0_DET01.fits
-
-                            Where Flat_A_0_DET01.fits is the flat file in your
-                            Calibrations directory
+                                     use_flat = True
       --debug               show debug plots?
       --par_outfile PAR_OUTFILE
                             Name of output file to save the parameters used by the