Background subtraction in spectral extraction (cubeviz) (spacetelesco…

…pe#2859)
gibsongreen · May 24, 2024 · 616dfdc · 616dfdc
1 parent 930125f
commit 616dfdc
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Showing 8 changed files with 378 additions and 183 deletions.
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -16,6 +16,8 @@ Cubeviz
   the label of the flux cube) as well as to several plugins: model fitting, gaussian smooth,
   line analysis, and moment maps. [#2827]
 
+- Background subtraction support within Spectral Extraction. [#2859]
+
 Imviz
 ^^^^^
 
@@ -49,6 +51,8 @@ Cubeviz
   ``wavelength_unit`` (use ``value_unit``), ``show_wavelength`` (use ``show_value``),
   ``slice`` (use ``value``). [#2878]
 
+- Spectral Extraction: renamed ``collapse_to_spectrum(...)`` to ``extract(...)``. [#2859]
+
 Imviz
 ^^^^^
 

diff --git a/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py b/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py
diff --git a/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.vue b/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.vue
@@ -85,7 +85,7 @@
       </div>
     </div>
 
-    <div v-if="dev_bg_support" @mouseover="() => active_step='bg'">
+    <div @mouseover="() => active_step='bg'">
       <j-plugin-section-header :active="active_step==='bg'">Background</j-plugin-section-header>
       <plugin-subset-select
         :items="bg_items"
@@ -133,6 +133,40 @@
           </v-row>
         </div>
       </div>
+
+      <v-row v-if="bg_selected !== 'None'">
+        <v-expansion-panels accordion>
+          <v-expansion-panel>
+            <v-expansion-panel-header v-slot="{ open }">
+              <span style="padding: 6px">Export Background Spectrum</span>
+            </v-expansion-panel-header>
+            <v-expansion-panel-content class="plugin-expansion-panel-content">
+              <v-row v-if="function_selected === 'Sum'">
+                <v-switch
+                  v-model="bg_spec_per_spaxel"
+                  label="Normalize per-spaxel"
+                  hint="Whether to normalize the background per spaxel (not shown in preview). Otherwise, the spectrum will be scaled by the ratio between the areas of the extraction aperture to the background aperture."
+                  persistent-hint
+                ></v-switch>
+              </v-row>
+              <plugin-add-results
+                :label.sync="bg_spec_results_label"
+                :label_default="bg_spec_results_label_default"
+                :label_auto.sync="bg_spec_results_label_auto"
+                :label_invalid_msg="bg_spec_results_label_invalid_msg"
+                :label_overwrite="bg_spec_results_label_overwrite"
+                label_hint="Label for the background spectrum"
+                :add_to_viewer_items="bg_spec_add_to_viewer_items"
+                :add_to_viewer_selected.sync="bg_spec_add_to_viewer_selected"
+                action_label="Export"
+                action_tooltip="Create Background Spectrum"
+                @click:action="create_bg_spec"
+              ></plugin-add-results>
+            </v-expansion-panel-content>
+          </v-expansion-panel>
+        </v-expansion-panels>
+      </v-row>
+
     </div>
 
     <div @mouseover="() => active_step='ext'">

diff --git a/jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py b/jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py
@@ -30,7 +30,7 @@ def test_version_after_nddata_update(cubeviz_helper, spectrum1d_cube_with_uncert
     collapsed_cube_nddata = spectral_cube.sum(axis=(0, 1))  # return NDDataArray
 
     # Collapse the spectral cube using the methods in jdaviz:
-    collapsed_cube_s1d = plg.collapse_to_spectrum(add_data=False)  # returns Spectrum1D
+    collapsed_cube_s1d = plg.extract(add_data=False)  # returns Spectrum1D
 
     assert plg._obj.disabled_msg == ''
     assert isinstance(spectral_cube, NDDataArray)
@@ -80,7 +80,7 @@ def test_gauss_smooth_before_spec_extract(cubeviz_helper, spectrum1d_cube_with_u
     expected_uncert = 2
 
     extract_plugin.aperture = 'Subset 1'
-    collapsed_spec = extract_plugin.collapse_to_spectrum()
+    collapsed_spec = extract_plugin.extract()
 
     # this single pixel has two wavelengths, and all uncertainties are unity
     # irrespective of which collapse function is applied:
@@ -89,7 +89,7 @@ def test_gauss_smooth_before_spec_extract(cubeviz_helper, spectrum1d_cube_with_u
 
     # this two-pixel region has four unmasked data points per wavelength:
     extract_plugin.aperture = 'Subset 2'
-    collapsed_spec_2 = extract_plugin.collapse_to_spectrum()
+    collapsed_spec_2 = extract_plugin.extract()
     assert_array_equal(collapsed_spec_2.uncertainty.array, expected_uncert)
 
 
@@ -120,7 +120,7 @@ def test_subset(
 
     # single pixel region:
     plg.aperture = 'Subset 1'
-    collapsed_spec_1 = plg.collapse_to_spectrum()
+    collapsed_spec_1 = plg.extract()
 
     # this single pixel has two wavelengths, and all uncertainties are unity
     # irrespective of which collapse function is applied:
@@ -129,7 +129,7 @@ def test_subset(
 
     # this two-pixel region has four unmasked data points per wavelength:
     plg.aperture = 'Subset 2'
-    collapsed_spec_2 = plg.collapse_to_spectrum()
+    collapsed_spec_2 = plg.extract()
 
     assert_array_equal(collapsed_spec_2.uncertainty.array, expected_uncert)
 
@@ -251,13 +251,13 @@ def test_cone_aperture_with_different_methods(cubeviz_helper, spectrum1d_cube_la
     extract_plg.wavelength_dependent = True
     extract_plg.function = 'Sum'
 
-    collapsed_spec = extract_plg.collapse_to_spectrum()
+    collapsed_spec = extract_plg.extract()
 
     assert_allclose(collapsed_spec.flux.value[1000:1010], expected_flux_1000, rtol=1e-6)
     assert_allclose(collapsed_spec.flux.value[2400:2410], expected_flux_2400, rtol=1e-6)
 
     extract_plg.function = 'Mean'
-    collapsed_spec_mean = extract_plg.collapse_to_spectrum()
+    collapsed_spec_mean = extract_plg.extract()
 
     assert_allclose(collapsed_spec_mean.flux.value, 1)
 
@@ -283,12 +283,12 @@ def test_cylindrical_aperture_with_different_methods(cubeviz_helper, spectrum1d_
     extract_plg.wavelength_dependent = False
     extract_plg.function = 'Sum'
 
-    collapsed_spec = extract_plg.collapse_to_spectrum()
+    collapsed_spec = extract_plg.extract()
 
     assert_allclose(collapsed_spec.flux.value, expected_flux_wav)
 
     extract_plg.function = 'Mean'
-    collapsed_spec_mean = extract_plg.collapse_to_spectrum()
+    collapsed_spec_mean = extract_plg.extract()
 
     assert_allclose(collapsed_spec_mean.flux.value, 1)
 
@@ -304,7 +304,7 @@ def test_rectangle_aperture_with_exact(cubeviz_helper, spectrum1d_cube_largest):
     extract_plg.aperture_method.selected = "Exact"
     extract_plg.wavelength_dependent = True
     extract_plg.function = 'Sum'
-    collapsed_spec = extract_plg.collapse_to_spectrum()
+    collapsed_spec = extract_plg.extract()
 
     # The extracted spectrum has "steps" (aliased) but perhaps that is due to
     # how photutils is extracting a boxy aperture. There is still a slope.
@@ -313,11 +313,44 @@ def test_rectangle_aperture_with_exact(cubeviz_helper, spectrum1d_cube_largest):
     assert_allclose(collapsed_spec.flux.value[::301], expected_flux_step)
 
     extract_plg.wavelength_dependent = False
-    collapsed_spec = extract_plg.collapse_to_spectrum()
+    collapsed_spec = extract_plg.extract()
 
     assert_allclose(collapsed_spec.flux.value, 16)  # 4 x 4
 
 
+def test_background_subtraction(cubeviz_helper, spectrum1d_cube_largest):
+    cubeviz_helper.load_data(spectrum1d_cube_largest)
+    center = PixCoord(5, 10)
+    cubeviz_helper.load_regions([
+        CirclePixelRegion(center, radius=2.5),
+        EllipsePixelRegion(center, width=5, height=5)])
+
+    extract_plg = cubeviz_helper.plugins['Spectral Extraction']
+    with extract_plg.as_active():
+        extract_plg.aperture = 'Subset 1'
+        spec_no_bg = extract_plg.extract()
+
+        extract_plg.background = 'Subset 2'
+
+        # test visiblity of background aperture and preview based on "active step"
+        assert extract_plg.background.marks[0].visible
+        assert not extract_plg._obj.marks['bg_spec'].visible
+        extract_plg._obj.active_step = 'ap'
+        assert not extract_plg.background.marks[0].visible
+        assert not extract_plg._obj.marks['bg_spec'].visible
+        extract_plg._obj.active_step = 'bg'
+        assert extract_plg.background.marks[0].visible
+        assert extract_plg._obj.marks['bg_spec'].visible
+
+        bg_spec = extract_plg.extract_bg_spectrum()
+        extract_plg.bg_spec_per_spaxel = True
+        bg_spec_normed = extract_plg.extract_bg_spectrum()
+        assert np.all(bg_spec_normed.flux.value < bg_spec.flux.value)
+        spec = extract_plg.extract()
+
+    assert np.allclose(spec.flux, spec_no_bg.flux - bg_spec.flux)
+
+
 def test_cone_and_cylinder_errors(cubeviz_helper, spectrum1d_cube_largest):
     cubeviz_helper.load_data(spectrum1d_cube_largest)
     center = PixCoord(5, 10)
@@ -333,16 +366,16 @@ def test_cone_and_cylinder_errors(cubeviz_helper, spectrum1d_cube_largest):
 
     extract_plg.function = 'Min'
     with pytest.raises(ValueError, match=extract_plg._obj.conflicting_aperture_error_message):
-        extract_plg.collapse_to_spectrum()
+        extract_plg.extract()
 
     extract_plg.function = 'Max'
     with pytest.raises(ValueError, match=extract_plg._obj.conflicting_aperture_error_message):
-        extract_plg.collapse_to_spectrum()
+        extract_plg.extract()
 
     extract_plg.function = 'Sum'
     extract_plg.aperture = 'Subset 2'
     with pytest.raises(NotImplementedError, match=".* is not supported"):
-        extract_plg.collapse_to_spectrum()
+        extract_plg.extract()
 
 
 def test_cone_aperture_with_frequency_units(cubeviz_helper, spectral_cube_wcs):
@@ -358,19 +391,19 @@ def test_cone_aperture_with_frequency_units(cubeviz_helper, spectral_cube_wcs):
     extract_plg.function = 'Sum'
 
     with pytest.raises(ValueError, match="Spectral axis unit physical type is"):
-        extract_plg.collapse_to_spectrum()
+        extract_plg.extract()
 
 
 def test_cube_extraction_with_nan(cubeviz_helper, image_cube_hdu_obj):
     image_cube_hdu_obj[1].data[:, :2, :2] = np.nan
     cubeviz_helper.load_data(image_cube_hdu_obj, data_label="with_nan")
     extract_plg = cubeviz_helper.plugins['Spectral Extraction']
-    sp = extract_plg.collapse_to_spectrum()  # Default settings (sum)
+    sp = extract_plg.extract()  # Default settings (sum)
     assert_allclose(sp.flux.value, 96)  # (10 x 10) - 4
 
     cubeviz_helper.load_regions(RectanglePixelRegion(PixCoord(1.5, 1.5), width=4, height=4))
     extract_plg.aperture = 'Subset 1'
-    sp_subset = extract_plg.collapse_to_spectrum()  # Default settings but on Subset
+    sp_subset = extract_plg.extract()  # Default settings but on Subset
     assert_allclose(sp_subset.flux.value, 12)  # (4 x 4) - 4
 
 
@@ -383,7 +416,7 @@ def test_autoupdate_results(cubeviz_helper, spectrum1d_cube_largest):
     extract_plg.aperture = 'Subset 1'
     extract_plg.add_results.label = 'extracted'
     extract_plg.add_results._obj.auto_update_result = True
-    _ = extract_plg.collapse_to_spectrum()
+    _ = extract_plg.extract()
 
 #    orig_med_flux = np.median(cubeviz_helper.get_data('extracted').flux)
 
@@ -445,10 +478,10 @@ def test_extraction_composite_subset(cubeviz_helper, spectrum1d_cube):
     flux_viewer.apply_roi(upper_aperture)
 
     spec_extr_plugin.aperture_selected = 'Subset 1'
-    spectrum_1 = spec_extr_plugin.collapse_to_spectrum()
+    spectrum_1 = spec_extr_plugin.extract()
 
     spec_extr_plugin.aperture_selected = 'Subset 2'
-    spectrum_2 = spec_extr_plugin.collapse_to_spectrum()
+    spectrum_2 = spec_extr_plugin.extract()
 
     subset_plugin.subset_selected = 'Create New'
     rectangle = RectangularROI(-0.5, 1.5, -0.5, 3.5)
@@ -465,7 +498,7 @@ def test_extraction_composite_subset(cubeviz_helper, spectrum1d_cube):
 
     assert spec_extr_plugin.aperture.is_composite
 
-    spectrum_3 = spec_extr_plugin.collapse_to_spectrum()
+    spectrum_3 = spec_extr_plugin.extract()
 
     np.testing.assert_allclose(
         (spectrum_1 + spectrum_2).flux.value,

diff --git a/jdaviz/configs/specviz/plugins/unit_conversion/tests/test_unit_conversion.py b/jdaviz/configs/specviz/plugins/unit_conversion/tests/test_unit_conversion.py
@@ -153,7 +153,7 @@ def test_unit_translation(cubeviz_helper):
 
     # all spectra will pass through spectral extraction,
     # this will store a scale factor for use in translations.
-    collapsed_spec = extract_plg.collapse_to_spectrum()
+    collapsed_spec = extract_plg.extract()
 
     # test that the scale factor was set
     assert collapsed_spec.meta['_pixel_scale_factor'] != 1
@@ -224,7 +224,7 @@ def test_sb_unit_conversion(cubeviz_helper):
     extract_plg.wavelength_dependent = True
     extract_plg.function = 'Sum'
     extract_plg.reference_spectral_value = 0.000001
-    extract_plg.collapse_to_spectrum()
+    extract_plg.extract()
 
     uc_plg._obj.show_translator = True
     uc_plg._obj.flux_or_sb_selected = 'Flux'

diff --git a/jdaviz/core/marks.py b/jdaviz/core/marks.py
@@ -17,7 +17,7 @@
            'LineAnalysisContinuum', 'LineAnalysisContinuumCenter',
            'LineAnalysisContinuumLeft', 'LineAnalysisContinuumRight',
            'LineUncertainties', 'ScatterMask', 'SelectedSpaxel', 'MarkersMark', 'FootprintOverlay',
-           'ApertureMark', 'SpectralExtractionPreview']
+           'ApertureMark']
 
 accent_color = "#c75d2c"
 
@@ -612,11 +612,6 @@ def __init__(self, viewer, id, **kwargs):
         super().__init__(viewer, **kwargs)
 
 
-class SpectralExtractionPreview(PluginLine):
-    def __init__(self, viewer, **kwargs):
-        super().__init__(viewer, **kwargs)
-
-
 class HistogramMark(Lines):
     def __init__(self, min_max_value, scales, **kwargs):
         # Vertical line in LinearScale