sort out min_line_length in determineDistortion() to be the fraction of the illuminated slit length

Author: chris-simpson

geminidr/core/parameters_spect.py

@@ -145,8 +145,8 @@ class determineDistortionConfig(config.Config):
     max_shift = config.RangeField("Maximum shift per pixel in line position",
                                   float, 0.05, min=0.001, max=0.1)
     max_missed = config.RangeField("Maximum number of steps to miss before a line is lost", int, 5, min=0)
-    min_line_length = config.RangeField("Exclude line traces shorter than this fraction of spatial dimension",
-                                        float, 0., min=0., max=1.)
+    min_line_length = config.RangeField("Exclude line traces shorter than this fraction of slit length",
+                                        float, 0.8, min=0., max=1.)
     debug_reject_bad = config.Field("Reject lines with suspiciously high SNR (e.g. bad columns)?", bool, True)
     debug = config.Field("Display line traces on image display?", bool, False)
 

geminidr/core/primitives_spect.py

@@ -1473,11 +1473,23 @@ def determineDistortion(self, adinputs=None, **params):
                     initial_peaks, _ = peak_finding.find_wavelet_peaks(
                         data, widths=widths, mask=mask & DQ.not_signal,
                         variance=variance, min_snr=min_snr, reject_bad=debug_reject_bad)
-                    log.stdinfo(f"Found {len(initial_peaks)} peaks")
-                    print(initial_peaks)
+                    #log.stdinfo(f"Found {len(initial_peaks)} peaks")
+
                 # The coordinates are always returned as (x-coords, y-coords)
                 rwidth = 0.42466 * fwidth
 
+                # The slit length may be smaller than the width of the slice,
+                # so we need to estimate the slit length and
+                # "min_line_length" is the fraction of that, not the fraction
+                # of the slice width.
+                loc = int(np.median(initial_peaks))
+                if dispaxis == 0:
+                    _slice = ext.mask[loc] & DQ.unilluminated
+                else:
+                    _slice = ext.mask[:, loc] & DQ.unilluminated
+                slit_length_frac = 1 - ((_slice.argmin() +
+                                         _slice[::-1].argmin()) / _slice.size)
+
                 # Straight slits, such as in longslit, can have all the lines
                 # traced simultaneously since they all have the same starting
                 # point. "Curved" slits need to be handled one-by-one. This is
@@ -1492,7 +1504,7 @@ def determineDistortion(self, adinputs=None, **params):
                         nsum=nsum, max_missed=max_missed,
                         max_shift=max_shift * ybin / xbin,
                         viewer=self.viewer if debug else None,
-                        min_line_length=min_line_length)
+                        min_line_length=min_line_length*slit_length_frac)
 
                 else:
                     traces = []
@@ -1501,14 +1513,20 @@ def determineDistortion(self, adinputs=None, **params):
                         # along the dispersion axis. `extract_info` here is the
                         # polynomial describing that midway line.
                         start = extract_info(peak)
+                        print("peak, start:", peak, start)
                         traces.extend(tracing.trace_lines(
                             ext, axis=1 - dispaxis,
                             start=start, initial=[peak],
                             rwidth=rwidth, cwidth=max(int(fwidth), 5), step=step,
                             nsum=nsum, max_missed=max_missed,
                             max_shift=max_shift * ybin / xbin,
                             viewer=self.viewer if debug else None,
-                            min_line_length=0.1))
+                            min_line_length=min_line_length*slit_length_frac))
+
+                log.stdinfo(f"Traced {len(traces)} lines")
+                if ext.id == 6 and ad.filename.startswith("S20060311S0321"):
+                    for trace in traces:
+                        print(trace.input_coordinates())
 
                 # List of traced peak positions
                 in_coords = np.array([coord for trace in traces for

geminidr/f2/parameters_f2_spect.py

@@ -31,7 +31,6 @@ class determineDistortionConfig(parameters_spect.determineDistortionConfig):
     def setDefaults(self):
         self.spectral_order = 3
         self.min_snr = 10.
-        self.min_line_length = 0.3
         self.debug_reject_bad = False
 
 

geminidr/gnirs/parameters_gnirs_crossdispersed.py

@@ -19,13 +19,12 @@ def setDefaults(self):
 
 class determineDistortionConfig(parameters_spect.determineDistortionConfig):
     spectral_order = config.RangeField("Fitting order in spectral direction", int, None, min=1, optional=True)
-    min_line_length = config.RangeField("Exclude line traces shorter than this fraction of spatial dimension",
-                                        float, None, min=0., max=1., optional=True)
     max_missed = config.RangeField("Maximum number of steps to miss before a line is lost",
                                int, None, min=0, optional=True)
     def setDefaults(self):
         self.min_snr = 10
         self.spatial_order = 2
+        self.step = 5
         self.debug_reject_bad = False
 
 

geminidr/gnirs/parameters_gnirs_longslit.py

@@ -13,8 +13,6 @@ def list_of_ints_check(value):
 
 class determineDistortionConfig(parameters_spect.determineDistortionConfig):
     spectral_order = config.RangeField("Fitting order in spectral direction", int, None, min=1, optional=True)
-    min_line_length = config.RangeField("Exclude line traces shorter than this fraction of spatial dimension",
-                                        float, None, min=0., max=1., optional=True)
     max_missed = config.RangeField("Maximum number of steps to miss before a line is lost",
                                int, None, min=0, optional=True)
     def setDefaults(self):

geminidr/gnirs/primitives_gnirs_spect.py

@@ -121,14 +121,6 @@ def determineDistortion(self, adinputs=None, **params):
                 self.log.stdinfo(f'Parameter "spectral_order" is set to None. '
                                  f'Using spectral_order={these_params["spectral_order"]} for {ad.filename}')
 
-            if these_params["min_line_length"] is None:
-                if cam.startswith('Long'):
-                    these_params["min_line_length"] = 0.8
-                else:
-                    these_params["min_line_length"] = 0.6
-                self.log.stdinfo(f'Parameter "min_line_length" is set to None. '
-                 f'Using min_line_length={these_params["min_line_length"]} for {ad.filename}')
-
             if these_params["max_missed"] is None:
                 if "ARC" in ad.tags:
                     # In arcs with few lines tracing strong horizontal noise pattern can