Add option of using self derived interpolated profile for horne extra…

…ct in specviz2d/spectral extraction plugin (#2845)

* add option for self profile for horne extract in spectral extraction

* bump up specreduce version

* review comments

* move change log entry to 3.11

* typo

CHANGES.rst

@@ -39,6 +39,7 @@ Specviz
 Specviz2d
 ^^^^^^^^^
 
+
 API Changes
 -----------
 
@@ -132,6 +133,7 @@ Specviz
 
 Specviz2d
 ^^^^^^^^^
+- Add option to use self-derived spatial profile for Horne extract in spectral extraction plugin. [#2845]
 
 API Changes
 -----------

jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py

@@ -92,6 +92,17 @@ class SpectralExtraction(PluginTemplateMixin):
     * ``ext_type`` (:class:`~jdaviz.core.template_mixin.SelectPluginComponent`)
     * :attr:`ext_width` :
       full width of the extraction window.
+    * ``horne_ext_profile`` (:class:`~jdaviz.core.template_mixin.SelectPluginComponent`):
+      For Horne extract, choice of 'Gaussian' or 'Self (interpolated)' to use
+      empirical profile from data.
+    * :attr:`self_prof_n_bins` :
+      Number of bins to use when computing the self-derived profile for Horne Extract.
+    * :attr:`self_prof_interp_degree_x` :
+      Interpolation degree (in X) to use when computing the self-derived profile
+      for Horne Extract.
+    * :attr:`self_prof_interp_degree_y` :
+      Interpolation degree (in Y) to use when computing the self-derived profile
+      for Horne Extract.
     * ``ext_add_results`` (:class:`~jdaviz.core.template_mixin.AddResults`)
     * :meth:`import_extract`
     * :meth:`export_extract`
@@ -190,6 +201,13 @@ class SpectralExtraction(PluginTemplateMixin):
     ext_type_items = List().tag(sync=True)
     ext_type_selected = Unicode().tag(sync=True)
 
+    horne_ext_profile_items = List().tag(sync=True)
+    horne_ext_profile_selected = Unicode().tag(sync=True)
+
+    self_prof_n_bins = IntHandleEmpty(10).tag(sync=True)
+    self_prof_interp_degree_x = IntHandleEmpty(1).tag(sync=True)
+    self_prof_interp_degree_y = IntHandleEmpty(1).tag(sync=True)
+
     ext_width = FloatHandleEmpty(0).tag(sync=True)
 
     ext_uncert_warn = Bool(False).tag(sync=True)
@@ -313,6 +331,11 @@ def __init__(self, *args, **kwargs):
                                               selected='ext_type_selected',
                                               manual_options=['Boxcar', 'Horne'])
 
+        self.horne_ext_profile = SelectPluginComponent(self,
+                                                       items='horne_ext_profile_items',
+                                                       selected='horne_ext_profile_selected',
+                                                       manual_options=['Gaussian', 'Self (interpolated)'])  # noqa
+
         self.ext_add_results = AddResults(self, 'ext_results_label',
                                           'ext_results_label_default',
                                           'ext_results_label_auto',
@@ -350,6 +373,10 @@ def user_api(self):
                                            'export_bg', 'export_bg_img', 'export_bg_sub',
                                            'ext_dataset', 'ext_trace', 'ext_type',
                                            'ext_width', 'ext_add_results',
+                                           'horne_ext_profile',
+                                           'self_prof_n_bins',
+                                           'self_prof_interp_degree_x',
+                                           'self_prof_interp_degree_y',
                                            'import_extract',
                                            'export_extract', 'export_extract_spectrum'))
 
@@ -600,7 +627,9 @@ def _interaction_in_bg_step(self, event={}):
         self.active_step = 'bg'
 
     @observe('is_active', 'ext_dataset_selected', 'ext_trace_selected',
-             'ext_type_selected', 'ext_width', 'active_step')
+             'ext_type_selected', 'ext_width', 'active_step',
+             'horne_ext_profile_selected', 'self_prof_n_bins',
+             'self_prof_interp_degree_x', 'self_prof_interp_degree_y')
     @skip_if_not_tray_instance()
     @skip_if_no_updates_since_last_active()
     def _interaction_in_ext_step(self, event={}):
@@ -925,11 +954,37 @@ def export_extract(self, **kwargs):
         if self.ext_type_selected == 'Boxcar':
             ext = extract.BoxcarExtract(inp_sp2d, trace, width=self.ext_width)
         elif self.ext_type_selected == 'Horne':
+            spatial_profile = None
             if inp_sp2d.uncertainty is None:
                 inp_sp2d.uncertainty = VarianceUncertainty(np.ones_like(inp_sp2d.data))
+
             if not hasattr(inp_sp2d.uncertainty, 'uncertainty_type'):
                 inp_sp2d.uncertainty = StdDevUncertainty(inp_sp2d.uncert)
-            ext = extract.HorneExtract(inp_sp2d, trace)
+
+            if self.horne_ext_profile_selected == 'Self (interpolated)':
+
+                # check inputs
+                if self.self_prof_n_bins <= 0:
+                    raise ValueError('`self_prof_n_bins` must be greater than 0.')
+                if self.self_prof_interp_degree_x <= 0:
+                    raise ValueError('`self_prof_interp_degree_x` must be greater than 0.')
+                if self.self_prof_interp_degree_y <= 0:
+                    raise ValueError('`self_prof_interp_degree_y` must be greater than 0.')
+
+                # setup dict of interpolation options
+                n_bins_interpolated_profile = self.self_prof_n_bins
+                interp_degree = (self.self_prof_interp_degree_x, self.self_prof_interp_degree_y)
+                spatial_profile = {'name': 'interpolated_profile',
+                                   'n_bins_interpolated_profile': n_bins_interpolated_profile,
+                                   'interp_degree': interp_degree}
+
+            elif self.horne_ext_profile_selected == 'Gaussian':
+                spatial_profile = 'gaussian'
+
+            else:
+                raise ValueError("Horne extraction profile must either be 'Gaussian' or 'Self (interpolated)'")  # noqa
+
+            ext = extract.HorneExtract(inp_sp2d, trace, spatial_profile=spatial_profile)
         else:
             raise NotImplementedError(f"extraction type '{self.ext_type_selected}' not supported")  # noqa
 

jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.vue

@@ -406,6 +406,59 @@
         </v-text-field>
       </v-row>
 
+      <v-row v-if="ext_type_selected === 'Horne'">
+        <v-select
+          attach
+          :menu-props="{ left: true }"
+          :items=" horne_ext_profile_items.map(i => i.label)"
+          v-model="horne_ext_profile_selected"
+          label="Profile Type"
+          hint="Profile to use for Horne extractoin."
+          persistent-hint
+        ></v-select>
+      </v-row>
+
+      <v-row v-if="horne_ext_profile_selected === 'Self (interpolated)'">
+        <v-text-field
+          label="N Bins"
+          type="number"
+          v-model.number=self_prof_n_bins
+          :rules="[() => self_prof_n_bins !== '' || 'This field is required',
+                   () => self_prof_n_bins >0 || 'Number of bins must be greater than zero']"
+          hint="Number of bins used to measure self profile."
+          persistent-hint
+        >
+        </v-text-field>
+      </v-row>
+
+      <div v-if="ext_type_selected === 'Horne'">
+        <v-row v-if="horne_ext_profile_selected === 'Self (interpolated)'">
+          <v-text-field
+            label="Interpolation Degree (X)"
+            type="number"
+            v-model.number=self_prof_interp_degree_x
+            :rules="[() => self_prof_interp_degree_x !== '' || 'This field is required',
+                     () => self_prof_interp_degree_x >0 || 'X interpolation degree must be be greater than zero']"
+            hint="Interpolation degree (X) to measure self profile."
+            persistent-hint
+          >
+          </v-text-field>
+        </v-row>
+
+        <v-row v-if="horne_ext_profile_selected === 'Self (interpolated)'">
+          <v-text-field
+            label="Interpolation Degree (Y)"
+            type="number"
+            v-model.number=self_prof_interp_degree_y
+            :rules="[() => self_prof_interp_degree_y !== '' || 'This field is required',
+                     () => self_prof_interp_degree_y >0 || 'Y interpolation degree must be be greater than zero']"
+            hint="Interpolation degree (Y) to measure self profile."
+            persistent-hint
+          >
+          </v-text-field>
+        </v-row>
+      </div>
+
       <plugin-add-results
         :label.sync="ext_results_label"
         :label_default="ext_results_label_default"

jdaviz/configs/specviz2d/plugins/spectral_extraction/tests/test_spectral_extraction.py

@@ -1,6 +1,11 @@
 import gwcs
 import pytest
+from astropy.modeling import models
+from astropy.nddata import VarianceUncertainty
+from astropy.tests.helper import assert_quantity_allclose
+import astropy.units as u
 from astropy.utils.data import download_file
+import numpy as np
 from packaging.version import Version
 from specreduce import tracing, background, extract
 from specutils import Spectrum1D
@@ -185,3 +190,78 @@ def test_spectrum_on_top(specviz2d_helper):
     pext = specviz2d_helper.app.get_tray_item_from_name('spectral-extraction')
     assert pext.bg_type_selected == 'OneSided'
     assert pext.bg_separation < 0
+
+
+@pytest.mark.filterwarnings('ignore')
+def test_horne_extract_self_profile(specviz2d_helper):
+
+    spec2d = np.zeros((40, 100))
+    spec2dvar = np.ones((40, 100))
+
+    for ii in range(spec2d.shape[1]):
+        mgaus = models.Gaussian1D(amplitude=10,
+                                  mean=(9.+(20/spec2d.shape[1])*ii),
+                                  stddev=2)
+        rg = np.arange(0, spec2d.shape[0], 1)
+        gaus = mgaus(rg)
+        spec2d[:, ii] = gaus
+
+    wave = np.arange(0, spec2d.shape[1], 1)
+    objectspec = Spectrum1D(spectral_axis=wave*u.m,
+                            flux=spec2d*u.Jy,
+                            uncertainty=VarianceUncertainty(spec2dvar*u.Jy*u.Jy))
+
+    specviz2d_helper.load_data(objectspec)
+    pext = specviz2d_helper.app.get_tray_item_from_name('spectral-extraction')
+
+    trace_fit = tracing.FitTrace(objectspec,
+                                 trace_model=models.Polynomial1D(degree=1),
+                                 window=13, peak_method='gaussian', guess=20)
+    pext.import_trace(trace_fit)
+
+    pext.ext_type.selected = "Horne"
+    pext.horne_ext_profile.selected = "Self (interpolated)"
+
+    # check that correct defaults are set
+    assert pext.self_prof_n_bins == 10
+    assert pext.self_prof_interp_degree_x == 1
+    assert pext.self_prof_interp_degree_y == 1
+
+    sp_ext = pext.export_extract_spectrum()
+
+    bg_sub = pext.export_bg_sub()
+
+    extract_horne_interp = extract.HorneExtract(bg_sub, trace_fit,
+                                                spatial_profile='interpolated_profile')
+
+    assert_quantity_allclose(extract_horne_interp.spectrum.flux, sp_ext.flux)
+
+    # now try changing from defaults
+    pext.self_prof_n_bins = 5
+    pext.self_prof_interp_degree_x = 2
+    pext.self_prof_interp_degree_y = 2
+
+    sp_ext = pext.export_extract_spectrum()
+    bg_sub = pext.export_bg_sub()
+
+    extract_horne_interp = extract.HorneExtract(bg_sub, trace_fit,
+                                                spatial_profile={'name': 'interpolated_profile',
+                                                                 'n_bins_interpolated_profile': 5,
+                                                                 'interp_degree': (2, 2)})
+
+    assert_quantity_allclose(extract_horne_interp.spectrum.flux, sp_ext.flux)
+
+    # test that correct errors are raised
+    pext.self_prof_n_bins = 0
+    with pytest.raises(ValueError, match='must be greater than 0'):
+        sp_ext = pext.export_extract_spectrum()
+
+    pext.self_prof_n_bins = 1
+    pext.self_prof_interp_degree_x = 0
+    with pytest.raises(ValueError, match='must be greater than 0'):
+        sp_ext = pext.export_extract_spectrum()
+
+    pext.self_prof_interp_degree_x = 1
+    pext.self_prof_interp_degree_y = 0
+    with pytest.raises(ValueError, match='`self_prof_interp_degree_y` must be greater than 0.'):
+        sp_ext = pext.export_extract_spectrum()

pyproject.toml

@@ -24,7 +24,7 @@ dependencies = [
     "voila>=0.4,<0.5",
     "pyyaml>=5.4.1",
     "specutils>=1.15",
-    "specreduce>=1.3.0,<1.4.0",
+    "specreduce>=1.4.1",
     "photutils>=1.4",
     "glue-astronomy>=0.10",
     "asteval>=0.9.23",