Merge branch 'enh/wavecal_3.2' into release/3.2.x

geminidr/core/parameters_spect.py

@@ -113,6 +113,7 @@ class determineWavelengthSolutionConfig(config.core_1Dfitting_config):
                                    check=list_of_ints_check)
     debug_alternative_centers = config.Field("Try alternative wavelength centers?", bool, False)
     interactive = config.Field("Display interactive fitter?", bool, False)
+    verbose = config.Field("Print additional fitting information?", bool, False)
 
     def setDefaults(self):
         del self.function

geminidr/core/primitives_spect.py

@@ -806,7 +806,7 @@ def _get_fit1d_input_data(ext, exptime, spec_table):
                 uiparams = UIParameters(config)
                 visualizer = fit1d.Fit1DVisualizer({"x": all_waves, "y": all_zpt, "weights": all_weights},
                                                    fitting_parameters=all_fp_init,
-                                                   tab_name_fmt="CCD {}",
+                                                   tab_name_fmt=lambda i: f"CCD {i+1}",
                                                    xlabel=f'Wavelength ({xunits})',
                                                    ylabel=f'Sensitivity ({yunits})',
                                                    domains=all_domains,
@@ -1354,7 +1354,7 @@ def determineWavelengthSolution(self, adinputs=None, **params):
                 visualizer = WavelengthSolutionVisualizer(
                     reconstruct_points, all_fp_init,
                     modal_message="Re-extracting 1D spectra",
-                    tab_name_fmt="Slit {}",
+                    tab_name_fmt=lambda i: f"Slit {i+1}",
                     xlabel="Fitted wavelength (nm)", ylabel="Non-linear component (nm)",
                     domains=domains,
                     title="Wavelength Solution",
@@ -1375,12 +1375,12 @@ def determineWavelengthSolution(self, adinputs=None, **params):
                     input_data, fit1d, acceptable_fit = wavecal.get_automated_fit(
                         ext, uiparams, p=self, linelist=linelist, bad_bits=DQ.not_signal)
                     if not acceptable_fit:
-                        log.warning("No acceptable wavelength solution found "
-                                    f"for {ext.id}")
-
-                    wavecal.update_wcs_with_solution(ext, fit1d, input_data, config)
-                    wavecal.save_fit_as_pdf(input_data["spectrum"], fit1d.points[~fit1d.mask],
-                                            fit1d.image[~fit1d.mask], ad.filename)
+                        log.warning("No acceptable wavelength solution found")
+                    else:
+                        wavecal.update_wcs_with_solution(ext, fit1d, input_data, config)
+                        wavecal.save_fit_as_pdf(
+                            input_data["spectrum"], fit1d.points[~fit1d.mask],
+                            fit1d.image[~fit1d.mask], ad.filename)
 
             # Timestamp and update the filename
             gt.mark_history(ad, primname=self.myself(), keyword=timestamp_key)
@@ -2987,7 +2987,7 @@ def recalc_fn(ad: AstroData, ui_parms: UIParameters):
                 ui_params = UIParameters(config, reinit_params=reinit_params, extras=reinit_extras)
                 visualizer = fit1d.Fit1DVisualizer(lambda ui_params: recalc_fn(ad, ui_params),
                                                    fitting_parameters=[fit1d_params]*count,
-                                                   tab_name_fmt="Slit {}",
+                                                   tab_name_fmt=lambda i: f"Slit {i+1}",
                                                    xlabel='Row',
                                                    ylabel='Signal',
                                                    domains=all_shapes,
@@ -3529,6 +3529,18 @@ def _get_spectrophotometry(self, filename, in_vacuo=False):
                                   * u.Unit("erg cm-2 s-1") / u.Hz)
         return spec_table
 
+    def _apply_wavelength_model_bounds(self, model=None, ext=None):
+        # Apply bounds to an astropy.modeling.models.Chebyshev1D to indicate
+        # the range of parameter space to explore
+        # The default here is 2% tolerance in central wavelength and dispersion
+        for i, (pname, pvalue) in enumerate(zip(model.param_names, model.parameters)):
+            if i == 0:  # central wavelength
+                prange = 0.02 * pvalue
+            elif i == 1:  # half the wavelength extent (~dispersion)
+                prange = 0.02 * abs(pvalue)
+            else:  # higher-order terms
+                prange = 1
+            getattr(model, pname).bounds = (pvalue - prange, pvalue + prange)
 
 # -----------------------------------------------------------------------------
 

geminidr/gmos/primitives_gmos_longslit.py

@@ -793,7 +793,7 @@ def reconstruct_points(ui_params=None):
                 extras = {"row": RangeField("Row of data to operate on", int, int(nrows/2), min=1, max=nrows)}
                 uiparams = UIParameters(config, reinit_params=reinit_params, extras=extras)
                 visualizer = fit1d.Fit1DVisualizer(reconstruct_points, all_fp_init,
-                                                   tab_name_fmt="CCD {}",
+                                                   tab_name_fmt=lambda i: f"CCD {i+1}",
                                                    xlabel='x (pixels)', ylabel='counts',
                                                    domains=all_domains,
                                                    title="Normalize Flat",

geminidr/gmos/primitives_gmos_spect.py

@@ -581,3 +581,15 @@ def _get_arc_linelist(self, waves=None):
         filename = os.path.join(lookup_dir,
                                 'CuAr_GMOS{}.dat'.format('_mixord' if use_second_order else ''))
         return wavecal.LineList(filename)
+
+    def _apply_wavelength_model_bounds(self, model=None, ext=None):
+        # Apply bounds to an astropy.modeling.models.Chebyshev1D to indicate
+        # the range of parameter space to explore
+        for i, (pname, pvalue) in enumerate(zip(model.param_names, model.parameters)):
+            if i == 0:  # central wavelength
+                prange = 10
+            elif i == 1:  # half the wavelength extent (~dispersion)
+                prange = 0.02 * abs(pvalue)
+            else:  # higher-order terms
+                prange = 1
+            getattr(model, pname).bounds = (pvalue - prange, pvalue + prange)

geminidr/interactive/fit/fit1d.py

@@ -154,6 +154,7 @@ def __init__(
         listeners=None,
         band_model=None,
         extra_masks=None,
+        default_model=None,
     ):
         """Create base class with given parameters as initial model inputs.
 
@@ -179,6 +180,9 @@ def __init__(
 
         extra_masks : dict of boolean arrays
             points to display but not use in fit
+
+        default_model : callable
+            function to evaluate model if self.fit is None
         """
         super().__init__()
 
@@ -195,6 +199,7 @@ def __init__(
         self.domain = domain
         self.fit = None
         self.listeners = listeners
+        self.default_model = default_model
 
         self.section = section
         self.data = bm.ColumnDataSource({"x": [], "y": [], "mask": []})
@@ -514,6 +519,12 @@ def update_mask(self):
         self.data.data["mask"] = mask
 
     def evaluate(self, x):
+        if self.fit is None:
+            # fit_1D.evaluate() always returns an array so we need to also
+            retval = self.default_model(x)
+            if isinstance(retval, float):
+                return np.array([retval])
+            return retval
         return self.fit.evaluate(x)
 
 
@@ -887,7 +898,10 @@ def model_change_handler(self, model):
         model : :class:`~geminidr.interactive.fit.fit1d.InteractiveModel1D`
             The model that has changed.
         """
-        rms_str = "--" if np.isnan(model.fit.rms) else f"{model.fit.rms:.4f}"
+        try:
+            rms_str = "--" if np.isnan(model.fit.rms) else f"{model.fit.rms:.4f}"
+        except AttributeError:
+            rms_str = "--"
 
         rms = (
             f'<div class="info_panel">'
@@ -968,6 +982,7 @@ def __init__(
         enable_regions=True,
         central_plot=True,
         extra_masks=None,
+        default_model=None,
     ):
         """Panel for visualizing a 1-D fit, perhaps in a tab.
 
@@ -1021,6 +1036,9 @@ def __init__(
 
         extra_masks : dict of boolean arrays
             points to display but not use in the fit
+
+        default_model : callable
+            function to evaluate model if self.fit is None
         """
         # Just to get the doc later
         self.visualizer = visualizer
@@ -1050,6 +1068,7 @@ def __init__(
             weights,
             band_model=band_model,
             extra_masks=extra_masks,
+            default_model=default_model,
         )
 
         self.model.add_listener(self.model_change_handler)
@@ -1528,7 +1547,7 @@ def __init__(
         fitting_parameters,
         modal_message=None,
         modal_button_label=None,
-        tab_name_fmt="{}",
+        tab_name_fmt=None,
         xlabel="x",
         ylabel="y",
         domains=None,
@@ -1571,8 +1590,8 @@ def __init__(
             If set and if modal_message was set, this will be used for the
             label on the recalculate button.  It is not required.
 
-        tab_name_fmt : str
-            Format string for naming the tabs
+        tab_name_fmt : callable
+            Turns ext.id into a title for the tab name
 
         xlabel : str
             String label for X axis
@@ -1751,6 +1770,9 @@ def kickoff_modal(attr, old, new):
 
         elif turbo_tabs:
             self.turbo = TabsTurboInjector(self.tabs)
+
+        if tab_name_fmt is None:
+            tab_name_fmt = lambda i: f"Extension {i+1}"
 
         for i in range(self.nfits):
             extra_masks = {}
@@ -1780,12 +1802,12 @@ def kickoff_modal(attr, old, new):
 
             if turbo_tabs:
                 self.turbo.add_tab(
-                    tui.component, title=tab_name_fmt.format(i + 1)
+                    tui.component, title=str(tab_name_fmt(i))
                 )
 
             else:
                 tab = bm.TabPanel(
-                    child=tui.component, title=tab_name_fmt.format(i + 1)
+                    child=tui.component, title=str(tab_name_fmt(i))
                 )
 
                 self.tabs.tabs.append(tab)

geminidr/interactive/fit/tracing.py

@@ -65,7 +65,7 @@ def interactive_trace_apertures(ext, fit1d_params, ui_params: UIParameters):
         fitting_parameters=fit_par_list,
         help_text=help_text,
         primitive_name="traceApertures",
-        tab_name_fmt="Aperture {}",
+        tab_name_fmt=lambda i: f"Aperture {i+1}",
         title="Interactive Trace Apertures",
         xlabel=xlabel,
         ylabel=ylabel,

geminidr/interactive/fit/wavecal.py

@@ -26,6 +26,7 @@
 
 from gempy.library.matching import match_sources
 from gempy.library.tracing import cwt_ricker, pinpoint_peaks
+from gempy.library.fitting import fit_1D
 
 from .fit1d import (
     Fit1DPanel,
@@ -117,7 +118,7 @@ def __init__(
             The weights of the fit.
 
         meta : dict
-            A dictionary of metadata.
+            A dictionary of metadata. This is the "all_input_data"
 
         kwargs : dict
             Any additional keyword arguments.
@@ -132,6 +133,7 @@ def __init__(
             "wavelengths": np.zeros_like(meta["spectrum"]),
             "spectrum": meta["spectrum"],
         }
+        kwargs["default_model"] = meta["init_models"][0]
 
         self.spectrum = bm.ColumnDataSource(spectrum_data_dict)
 
@@ -483,7 +485,10 @@ def linear_model(model):
         """Return only the linear part of a model. It doesn't work for
         splines, which is why it's not in the InteractiveModel1D class
         """
-        model = model.fit._models
+        if model.fit is None:
+            model = model.default_model
+        else:
+            model = model.fit.model
         new_model = model.__class__(
             degree=1, c0=model.c0, c1=model.c1, domain=model.domain
         )

gempy/library/matching.py

@@ -372,7 +372,8 @@ def __call__(self, model, in_coords, ref_coords, in_weights=None,
         farg = (model_copy, in_coords, tree)
         p0, *_ = model_to_fit_params(model_copy)
 
-        arg_names = inspect.getfullargspec(self._opt_method).args
+        argspec = inspect.getfullargspec(self._opt_method)
+        arg_names, kwarg_names = argspec.args, argspec.kwonlyargs
         args = [self.objective_function]
         if arg_names[1] == 'x0':
             args.append(p0)
@@ -381,15 +382,15 @@ def __call__(self, model, in_coords, ref_coords, in_weights=None,
         else:
             raise ValueError("Don't understand argument {}".format(arg_names[1]))
 
-        if 'args' in arg_names:
+        if 'args' in arg_names or 'args' in kwarg_names:
             kwargs['args'] = farg
 
         if 'method' in arg_names:
             kwargs['method'] = self._method
 
-        if 'minimizer_kwargs' in arg_names:
-            kwargs['minimizer_kwargs'] = {'args': farg,
-                                          'method': 'Nelder-Mead'}
+        #if 'minimizer_kwargs' in arg_names:
+        #    kwargs['minimizer_kwargs'] = {'args': farg,
+        #                                  'method': 'Nelder-Mead'}
 
         result = self._opt_method(*args, **kwargs)