Merge branch 'develop' into hotfix_cif_meta

pypeit/find_objects.py

@@ -334,12 +334,9 @@ def run(self, std_trace=None, show_peaks=False, show_skysub_fit=False):
         initial_sky0 = self.global_skysub(skymask=self.initial_skymask, update_crmask=False,
                                           objs_not_masked=True, show_fit=show_skysub_fit)
         # First pass object finding
-        save_objfindQA = self.par['reduce']['findobj']['skip_second_find'] or self.std_redux \
-                            or self.initial_skymask is not None
         sobjs_obj, self.nobj = \
             self.find_objects(self.sciImg.image-initial_sky0, self.sciImg.ivar, std_trace=std_trace,
-                              show_peaks=show_peaks, show=self.findobj_show and not self.std_redux,
-                              save_objfindQA=save_objfindQA)
+                              show_peaks=show_peaks, show=self.findobj_show and not self.std_redux)
 
         if self.nobj == 0 or self.initial_skymask is not None:
             # Either no objects were found, or the initial sky mask was provided by the user.

pypeit/spectrographs/keck_lris.py

@@ -599,14 +599,20 @@ def get_maskdef_slitedges(self, ccdnum=None, filename=None, debug=None,
 
         # Trim down by detector
         # TODO -- Deal with Mark4
-        max_spat = 2048//bin_spat
+        if self.name == 'keck_lris_red_mark4':
+            max_spat = 4112//bin_spat
+        else:
+            max_spat = 2048//bin_spat
         if ccdnum == 1:
             if self.name == 'keck_lris_red':
                 good = centers < 0.
                 xstart = max_spat + 160//bin_spat  # The 160 is for the chip gap
             elif self.name == 'keck_lris_blue':
                 good = centers < 0.
-                xstart = max_spat + 30//bin_spat  
+                xstart = max_spat + 30//bin_spat
+            elif self.name == 'keck_lris_red_mark4':
+                xstart = 2073//bin_spat
+                good = centers < max_spat # No chip gap
             else:
                 msgs.error(f'Not ready to use slitmasks for {self.name}.  Develop it!')
         else:
@@ -1401,8 +1407,8 @@ def get_detector_par(self, det, hdu=None):
             dataext=0,
             specaxis=0,
             specflip=True,  
-            spatflip=False,
-            platescale=0.123,  # From the web page
+            spatflip=True,
+            platescale=0.135,  # From the web page
             darkcurr=0.0,
             saturation=65535.,
             nonlinear=0.76,

pypeit/wavetilts.py

@@ -188,34 +188,41 @@ def show(self, waveimg=None, wcs_match=True, in_ginga=True, show_traces=False):
                 If True, show the traces of the tilts on the image.
 
         """
+        # get tilt_img_dict
+        if (Path(self.calib_dir).resolve() / self.tiltimg_filename).exists():
+            tilt_img_dict = buildimage.TiltImage.from_file(Path(self.calib_dir).resolve() / self.tiltimg_filename)
+        else:
+            msgs.error(f'Tilt image {str((Path(self.calib_dir).resolve() / self.tiltimg_filename))} NOT FOUND.')
+
         # get slits
+        slitmask = None
         if (Path(self.calib_dir).resolve() / self.slits_filename).exists():
             slits = slittrace.SlitTraceSet.from_file(Path(self.calib_dir).resolve() / self.slits_filename)
-            slitmask = slits.slit_img(initial=True, flexure=self.spat_flexure)
-            left, right, mask = slits.select_edges(flexure=self.spat_flexure)
-            gpm = mask == 0
+            _slitmask = slits.slit_img(initial=True, flexure=self.spat_flexure)
+            _left, _right, _mask = slits.select_edges(flexure=self.spat_flexure)
+            gpm = _mask == 0
+            # resize
+            slitmask = arc.resize_mask2arc(tilt_img_dict.image.shape, _slitmask)
+            left = arc.resize_slits2arc(tilt_img_dict.image.shape, _slitmask.shape, _left)
+            right = arc.resize_slits2arc(tilt_img_dict.image.shape, _slitmask.shape, _right)
         else:
             slits = None
             msgs.warn('Could not load slits to show with tilts image.')
 
-        # get tiltimg
-        if (Path(self.calib_dir).resolve() / self.tiltimg_filename).exists():
-            tilt_img_dict = buildimage.TiltImage.from_file(Path(self.calib_dir).resolve() / self.tiltimg_filename)
-            tilt_img = tilt_img_dict.image * (slitmask > -1) if slits is not None else tilt_img_dict.image
-        else:
-            msgs.error('Tilt image not found.')
-
         # get waveimg
-        if waveimg is None and in_ginga:
+        same_size = (slits.nspec, slits.nspat) == tilt_img_dict.image.shape
+        if waveimg is None and slits is not None and same_size and in_ginga:
             wv_calib_name = wavecalib.WaveCalib.construct_file_name(self.calib_key, calib_dir=self.calib_dir)
-            if Path(wv_calib_name).resolve().exists() and slits is not None:
+            if Path(wv_calib_name).resolve().exists():
                 wv_calib = wavecalib.WaveCalib.from_file(wv_calib_name)
                 tilts = self.fit2tiltimg(slitmask, flexure=self.spat_flexure)
                 waveimg = wv_calib.build_waveimg(tilts, slits, spat_flexure=self.spat_flexure)
             else:
                 msgs.warn('Could not load Wave image to show with tilts image.')
 
         # Show
+        # tilt image
+        tilt_img = tilt_img_dict.image * (slitmask > -1) if slitmask is not None else tilt_img_dict.image
         # set cuts
         zmax = stats.sigma_clip(tilt_img, sigma=10, return_bounds=True)[2]
         zmin = stats.sigma_clip(tilt_img, sigma=5, return_bounds=True)[1] * 2