Trace fix improvements

py/desispec/scripts/trace_shifts.py

@@ -148,12 +148,14 @@ def fit_trace_shifts(image, args):
 
     spectrum_filename = args.spectrum
     if args.sky :
+        continuum_subtract = True
         srch_file = "data/spec-sky.dat"
         if not resources.files('desispec').joinpath(srch_file).is_file():
             log.error("Cannot find sky spectrum file {:s}".format(srch_file))
             raise RuntimeError("Cannot find sky spectrum file {:s}".format(srch_file))
         spectrum_filename = resources.files('desispec').joinpath(srch_file)
     elif args.arc_lamps :
+        continuum_subtract = False
         srch_file = "data/spec-arc-lamps.dat"
         if not resources.files('desispec').joinpath(srch_file).is_file():
             log.error("Cannot find arc lamps spectrum file {:s}".format(srch_file))
@@ -196,7 +198,7 @@ def fit_trace_shifts(image, args):
         x_for_dx,y_for_dx,dx,ex,fiber_for_dx,wave_for_dx = compute_dx_from_cross_dispersion_profiles(xcoef,ycoef,wavemin,wavemax, image=image, fibers=fibers, width=args.width, deg=args.degxy,image_rebin=args.ccd_rows_rebin)
         if internal_wavelength_calib :
             # measure y shifts
-            x_for_dy,y_for_dy,dy,ey,fiber_for_dy,wave_for_dy = compute_dy_using_boxcar_extraction(tset, image=image, fibers=fibers, width=args.width)
+            x_for_dy,y_for_dy,dy,ey,fiber_for_dy,wave_for_dy = compute_dy_using_boxcar_extraction(tset, image=image, fibers=fibers, width=args.width, continuum_subtract=continuum_subtract)
             mdy = np.median(dy)
             log.info("Subtract median(dy)={}".format(mdy))
             dy -= mdy # remove median, because this is an internal calibration
@@ -216,17 +218,14 @@ def fit_trace_shifts(image, args):
     degyy=args.degyy
 
     # if any quadrant is masked, reduce to a single offset
-    hy=image.pix.shape[0]//2
-    hx=image.pix.shape[1]//2
-    allgood=True
-    allgood &= (np.sum((x_for_dx<hx)&(y_for_dx<hy))>0) # some data in this quadrant
-    allgood &= (np.sum((x_for_dx<hx)&(y_for_dx>hy))>0) # some data in this quadrant
-    allgood &= (np.sum((x_for_dx>hx)&(y_for_dx<hy))>0) # some data in this quadrant
-    allgood &= (np.sum((x_for_dx>hx)&(y_for_dx>hy))>0) # some data in this quadrant
-    allgood &= (np.sum((x_for_dy<hx)&(y_for_dy<hy))>0) # some data in this quadrant
-    allgood &= (np.sum((x_for_dy<hx)&(y_for_dy>hy))>0) # some data in this quadrant
-    allgood &= (np.sum((x_for_dy>hx)&(y_for_dy<hy))>0) # some data in this quadrant
-    allgood &= (np.sum((x_for_dy>hx)&(y_for_dy>hy))>0) # some data in this quadrant
+    hy = image.pix.shape[0] // 2
+    hx = image.pix.shape[1] // 2
+    allgood = True
+    for _curx, _cury in [(x_for_dx,y_for_dx),(x_for_dy, y_for_dy)]:
+        for curxop in [np.less, np.greater]:
+            for curyop in [np.less, np.greater]:
+                allgood &= np.any(curxop(_curx, hx) & curyop(_cury, hy))
+        # some data in this quadrant
     if not allgood :
         log.warning("No shift data for at least one quadrant of the CCD, falls back to deg=0 shift")
         degxx=0