Merge branch 'bugfix/fitTelluric_infs_nans_crash' into release/4.x

Author: chris-simpson

geminidr/core/parameters_telluric.py

@@ -34,6 +34,10 @@ class fitTelluricConfig(config.core_1Dfitting_config):
     apply_shift = config.Field("Permanently apply pixel shift?", bool, True)  # debug?
     debug_lsf_sampling = config.RangeField("Number of sample points for each LSF parameter",
                                            int, 5, min=3, optional=False)
+    debug_stellar_mask_threshold = config.RangeField(
+        "Absorption threshold for stellar mask", float, 0.9, min=0.5, max=1.0)
+    debug_stellar_mask_max_extent = config.RangeField(
+        "Maximum extent of a stellar mask region (nm)", float, 40., min=0.)
 
     def setDefaults(self):
         self.niter = 1

geminidr/core/primitives_telluric.py

@@ -256,7 +256,7 @@ def fitTelluric(self, adinputs=None, **params):
                 if (len(ext.shape) == 1 and
                         ext.hdr.get('APERTURE') == aperture_to_use):
                     tspek = tspek_list[result_index]
-                    absorption = tspek.data / m_final.models[result_index].continuum(tspek.waves)
+                    absorption = at.divide0(tspek.data, m_final.models[result_index].continuum(tspek.waves))
                     goodpix = ~(tspek.mask | tcal.stellar_mask[result_index]).astype(bool)
                     spline = make_interp_spline(tcal.spectra[result_index].waves[goodpix],
                                                 absorption[goodpix], k=3)

geminidr/interactive/fit/telluric.py

@@ -376,7 +376,7 @@ def model_change_handler(self, model):
 
         good = get_good_pixels(model.x, model.aux_data.data['waves'])
 
-        absorption = model.y / model.aux_data.data['continuum'][good]
+        absorption = at.divide0(model.y, model.aux_data.data['continuum'][good])
         goodpix = [m == 'good' for m in model.mask]
         spline = make_interp_spline(model.x[goodpix],
                                     absorption[goodpix], k=3)

gempy/library/calibrator.py

@@ -143,8 +143,17 @@ def __init__(self, telluric_spectra, ui_params=None):
         # We store this as an attribute here since it's not handled fully
         # by TelluricSpectrum (you can make the mask but it's not applied)
         # and it needs to be accessed by the Visualizer
-        self.stellar_mask = [tspek.make_stellar_mask(r=self.resolution)
-                             for tspek in self.spectra]
+        if ui_params is None:
+            stellar_mask_threshold = 1.0
+            stellar_mask_max_extent = 0.
+        else:
+            stellar_mask_threshold = ui_params.debug_stellar_mask_threshold
+            stellar_mask_max_extent = ui_params.debug_stellar_mask_max_extent
+        self.stellar_mask = [tspek.make_stellar_mask(
+            threshold=stellar_mask_threshold,
+            max_contiguous=stellar_mask_max_extent,
+            r=self.resolution)
+            for tspek in self.spectra]
 
         # Allow instantiation without this and can call later
         if ui_params is not None: