convert to spat_flexure

pypeit/coadd3d.py

@@ -1109,7 +1109,8 @@ def load(self):
             crval_wv = self.cubepar['wave_min'] if self.cubepar['wave_min'] is not None else wave0
             cd_wv = self.cubepar['wave_delta'] if self.cubepar['wave_delta'] is not None else dwv
             self.all_wcs.append(self.spec.get_wcs(spec2DObj.head0, slits, detector.platescale, crval_wv, cd_wv))
-            ra_img, dec_img, minmax = slits.get_radec_image(self.all_wcs[ff], alignSplines, spec2DObj.tilts, flexure=spat_flexure)
+            ra_img, dec_img, minmax = slits.get_radec_image(self.all_wcs[ff], alignSplines, spec2DObj.tilts,
+                                                            spat_flexure=spat_flexure)
 
             # Extract wavelength and delta wavelength arrays from the images
             wave_ext = waveimg[onslit_gpm]

pypeit/core/flexure.py

@@ -189,8 +189,8 @@ def spat_flexure_qa(img, slits, shift, gpm=None, vrange=None, outfile=None):
         vrange = None
 
     # TODO: should we use initial or tweaked slits in this plot?
-    left_slits, right_slits, mask_slits = slits.select_edges(initial=True, flexure=None)
-    left_flex, right_flex, mask = slits.select_edges(initial=True, flexure=shift)
+    left_slits, right_slits, mask_slits = slits.select_edges(initial=True, spat_flexure=None)
+    left_flex, right_flex, mask = slits.select_edges(initial=True, spat_flexure=shift)
 
     if debug:
         # where to start and end the plot in the spatial&spectral direction

pypeit/core/gui/skysub_regions.py

@@ -41,7 +41,7 @@ class SkySubGUI:
     """
 
     def __init__(self, canvas, image, frame, outname, det, slits, axes, pypeline, spectrograph, printout=False,
-                 runtime=False, resolution=None, initial=False, flexure=None, overwrite=False):
+                 runtime=False, resolution=None, initial=False, spat_flexure=None, overwrite=False):
         """Controls for the interactive sky regions definition tasks in PypeIt.
 
         The main goal of this routine is to interactively select sky background
@@ -73,8 +73,8 @@ def __init__(self, canvas, image, frame, outname, det, slits, axes, pypeline, sp
         initial : bool, optional
             To use the initial edges regardless of the presence of
             the tweaked edges, set this to True.
-        flexure : float, optional
-            If provided, offset each slit by this amount
+        spat_flexure : float, optional
+            If provided, offset each slit in the spatial direction by this amount
         runtime : bool
             Is the GUI being launched during data reduction?
         resolution : int
@@ -137,7 +137,7 @@ def __init__(self, canvas, image, frame, outname, det, slits, axes, pypeline, sp
         self._fitr = []  # Matplotlib shaded fit region
         self._fita = None
 
-        self.slits_left, self.slits_right, _ = slits.select_edges(initial=initial, spat_flexure=flexure)
+        self.slits_left, self.slits_right, _ = slits.select_edges(initial=initial, spat_flexure=spat_flexure)
         self.initialize_menu()
         self.reset_regions()
 
@@ -149,7 +149,7 @@ def __init__(self, canvas, image, frame, outname, det, slits, axes, pypeline, sp
     @classmethod
     def initialize(cls, det, frame, slits, pypeline, spectrograph, outname="skyregions.fits",
                    overwrite=False, initial=False,
-                   flexure=None, runtime=False, printout=False):
+                   spat_flexure=None, runtime=False, printout=False):
         """
         Initialize the 'ObjFindGUI' window for interactive object tracing
 
@@ -167,6 +167,8 @@ def initialize(cls, det, frame, slits, pypeline, spectrograph, outname="skyregio
             Name of the spectrograph
         printout : bool
             Should the results be printed to screen
+        spat_flexure : float, optional
+            If provided, offset each slit in the spatial direction by this amount
         runtime : bool
             Is this GUI being launched during a data reduction?
 
@@ -178,7 +180,7 @@ def initialize(cls, det, frame, slits, pypeline, spectrograph, outname="skyregio
         # NOTE: SlitTraceSet objects always store the left and right
         # traces as 2D arrays, even if there's only one slit.
         nslit = slits.nslits
-        lordloc, rordloc, _ = slits.select_edges(initial=initial, spat_flexure=flexure)
+        lordloc, rordloc, _ = slits.select_edges(initial=initial, spat_flexure=spat_flexure)
 
         # Determine the scale of the image
         med = np.median(frame)
@@ -210,7 +212,7 @@ def initialize(cls, det, frame, slits, pypeline, spectrograph, outname="skyregio
         # Initialise the object finding window and display to screen
         fig.canvas.manager.set_window_title('PypeIt - Sky regions')
         srgui = SkySubGUI(fig.canvas, image, frame, outname, det, slits, axes, pypeline, spectrograph,
-                          printout=printout, runtime=runtime, initial=initial, flexure=flexure, overwrite=overwrite)
+                          printout=printout, runtime=runtime, initial=initial, spat_flexure=spat_flexure, overwrite=overwrite)
         plt.show()
 
         return srgui

pypeit/scripts/skysub_regions.py

@@ -96,7 +96,7 @@ def main(args):
         # Finally, initialise the GUI
         skyreg = SkySubGUI.initialize(det, frame, slits, pypeline, specname, outname=regfile,
                                       overwrite=args.overwrite, runtime=False, printout=True,
-                                      initial=args.initial, flexure=spat_flexure)
+                                      initial=args.initial, spat_flexure=spat_flexure)
 
         # Get the results
         msskyreg = skyreg.get_result()

pypeit/slittrace.py

@@ -479,7 +479,7 @@ def get_slitlengths(self, initial=False, median=False):
         slitlen = right - left
         return np.median(slitlen, axis=1) if median else slitlen
 
-    def get_radec_image(self, wcs, alignSplines, tilts, slit_compute=None, slice_offset=None, initial=False, flexure=None):
+    def get_radec_image(self, wcs, alignSplines, tilts, slit_compute=None, slice_offset=None, initial=False, spat_flexure=None):
         """Generate an RA and DEC image for every pixel in the frame
         NOTE: This function is currently only used for SlicerIFU reductions.
 
@@ -504,8 +504,8 @@ def get_radec_image(self, wcs, alignSplines, tilts, slit_compute=None, slice_off
             is set to 0.0.
         initial : bool
             Select the initial slit edges?
-        flexure : float, optional
-            If provided, offset each slit by this amount.
+        spat_flexure : float, optional
+            If provided, offset each slit in the spatial direction by this amount.
 
         Returns
         -------
@@ -542,7 +542,7 @@ def get_radec_image(self, wcs, alignSplines, tilts, slit_compute=None, slice_off
         decimg = np.zeros((self.nspec, self.nspat))
         minmax = np.zeros((self.nslits, 2))
         # Get the slit information
-        slitid_img_init = self.slit_img(pad=0, initial=initial, spat_flexure=flexure)
+        slitid_img_init = self.slit_img(pad=0, initial=initial, spat_flexure=spat_flexure)
         for slit_idx, spatid in enumerate(self.spat_id):
             if slit_idx not in slit_compute:
                 continue