Export spectral subsets

CHANGES.rst

@@ -8,6 +8,9 @@ New Features
 
 - Adding Data Quality plugin for Imviz and Cubeviz. [#2767, #2817]
 
+- Enable exporting spectral regions to ECSV files readable by ``astropy.table.QTable`` or
+  ``specutils.SpectralRegion`` [#2843]
+
 Cubeviz
 ^^^^^^^
 
@@ -73,6 +76,8 @@ Other Changes and Additions
 
 - Line menu in Redshift from Centroid section of Line Analysis now shows values in current units. [#2816, #2831]
 
+- Bump required specutils version to 1.15. [#2843]
+
 3.9.2 (unreleased)
 ==================
 

docs/specviz/export_data.rst

@@ -14,7 +14,7 @@ those data currently back into your Jupyter notebook:
 
     specviz.get_spectra()
 
-which yields a either a single `specutils.Spectrum1D` object or a dictionary of 
+which yields a either a single `specutils.Spectrum1D` object or a dictionary of
 `specutils.Spectrum1D` (if there are multiple displayed spectra) that you can
 manipulate however you wish.  You can then load the modified spectrum back into
 the notebook via the API described in :ref:`specviz-import-api`.
@@ -70,6 +70,11 @@ To extract the spectral region you want:
 
     myregion = regions["Subset 2"]
 
+.. seealso::
+
+    :ref:`Export From Plugins <specviz-plugins>`
+        Spectral region subsets can also be exported to disk as an ECSV file.
+
 .. _specviz-export-model:
 
 Model Fits

docs/specviz/plugins.rst

@@ -320,4 +320,8 @@ using the |icon-line-select| (line selector) tool in the spectrum viewer.
 Export
 ======
 
-This plugin allows a given viewer's plot to be exported to various image formats.
+This plugin allows exporting a the contents of a viewer or a plot within a plugin to various image formats.
+Additionally, spatial and spectral regions can be exported to files, as astropy regions saves as FITS or REG
+files (in the case of spatial regions), or as ECSV files in the case of spectral regions via specutils SpectralRegion.
+Note that multiple spectral regions can be saved out to the same file, as long as they are subregions of a single
+subset rather than independent subsets.

jdaviz/configs/default/plugins/export/export.py

@@ -111,9 +111,6 @@ def __init__(self, *args, **kwargs):
         self.dataset.filters = ['is_not_wcs_only', 'not_child_layer',
                                 'from_plugin']
 
-        # NOTE: if/when adding support for spectral subsets, update the languange in the UI
-        self.subset.filters = ['is_spatial']
-
         viewer_format_options = ['png', 'svg']
         if self.config == 'cubeviz':
             if not self.app.state.settings.get('server_is_remote'):
@@ -135,7 +132,9 @@ def __init__(self, *args, **kwargs):
                                                          selected='plugin_table_format_selected',
                                                          manual_options=plugin_table_format_options)
 
-        subset_format_options = ['fits', 'reg']
+        subset_format_options = [{'label': 'fits', 'value': 'fits', 'disabled': False},
+                                 {'label': 'reg', 'value': 'reg', 'disabled': False},
+                                 {'label': 'ecsv', 'value': 'ecsv', 'disabled': True}]
         self.subset_format = SelectPluginComponent(self,
                                                    items='subset_format_items',
                                                    selected='subset_format_selected',
@@ -226,6 +225,8 @@ def _sync_singleselect(self, event):
             if name != attr:
                 setattr(self, attr, '')
             if attr == 'subset_selected':
+                if self.subset.selected != '':
+                    self._update_subset_format_disabled()
                 self._set_subset_not_supported_msg()
             if attr == 'dataset_selected':
                 self._set_dataset_not_supported_msg()
@@ -258,6 +259,46 @@ def _is_filename_changed(self, event):
         # Clear overwrite warning when user changes filename
         self.overwrite_warn = False
 
+    def _update_subset_format_disabled(self):
+        new_items = []
+        if self.subset.selected is not None:
+            subset = self.app.get_subsets(self.subset.selected)
+            if self.app._is_subset_spectral(subset[0]):
+                good_formats = ["ecsv"]
+            else:
+                good_formats = ["fits", "reg"]
+            for item in self.subset_format_items:
+                if item["label"] in good_formats:
+                    item["disabled"] = False
+                else:
+                    item["disabled"] = True
+                    if item["label"] == self.subset_format.selected:
+                        self.subset_format.selected = good_formats[0]
+                new_items.append(item)
+        self.subset_format_items = []
+        self.subset_format_items = new_items
+
+    @observe('subset_format_selected')
+    def _disable_subset_format_combo(self, event):
+        # Disable selecting a bad subset+format combination from the API
+        if self.subset.selected == '' or self.subset.selected is None:
+            return
+        subset = self.app.get_subsets(self.subset.selected)
+        bad_combo = False
+        if self.app._is_subset_spectral(subset[0]):
+            if event['new'] != "ecsv":
+                bad_combo = True
+        elif event['new'] == "ecsv":
+            bad_combo = True
+
+        if bad_combo:
+            # Set back to a good value and raise error
+            good_format = [format["label"] for format in self.subset_format_items if
+                           format["disabled"] is False][0]
+            self.subset_format.selected = good_format
+            raise ValueError(f"Cannot export {self.subset.selected} in {event['new']}"
+                             f" format, reverting selection to {self.subset_format.selected}")
+
     def _set_subset_not_supported_msg(self, msg=None):
         """
         Check if selected subset is spectral or composite, and warn and
@@ -269,7 +310,7 @@ def _set_subset_not_supported_msg(self, msg=None):
             if self.subset.selected == '':
                 self.subset_invalid_msg = ''
             elif self.app._is_subset_spectral(subset[0]):
-                self.subset_invalid_msg = 'Export for spectral subsets not yet supported.'
+                self.subset_invalid_msg = ''
             elif len(subset) > 1:
                 self.subset_invalid_msg = 'Export for composite subsets not yet supported.'
             else:
@@ -422,7 +463,11 @@ def export(self, filename=None, show_dialog=None, overwrite=False,
                 if raise_error_for_overwrite:
                     raise FileExistsError(f"{filename} exists but overwrite=False")
                 return
-            self.save_subset_as_region(selected_subset_label, filename)
+
+            if self.subset_format.selected in ('fits', 'reg'):
+                self.save_subset_as_region(selected_subset_label, filename)
+            elif self.subset_format.selected == 'ecsv':
+                self.save_subset_as_table(filename)
 
         elif len(self.dataset.selected):
             filetype = self.dataset_format.selected
@@ -655,6 +700,10 @@ def save_subset_as_region(self, selected_subset_label, filename):
 
         region.write(filename, overwrite=True)
 
+    def save_subset_as_table(self, filename):
+        region = self.app.get_subsets(subset_name=self.subset.selected)
+        region.write(filename)
+
     def vue_interrupt_recording(self, *args):  # pragma: no cover
         self.movie_interrupt = True
         # TODO: this will need updating when batch/multiselect support is added

jdaviz/configs/default/plugins/export/export.vue

@@ -33,7 +33,7 @@
           :items="viewer_format_items.map(i => i.label)"
           label="Format"
           hint="Image format for exporting viewers."
-          :disabled="viewer_selected.length == 0" 
+          :disabled="viewer_selected.length == 0"
           persistent-hint
         >
         </v-select>
@@ -126,9 +126,9 @@
     </div>
 
     <div v-if="subset_items.length > 0">
-      <span class="export-category">Spatial Subsets</span>
+      <span class="export-category">Subsets</span>
       <v-row>
-        <span class="category-content v-messages v-messages__message text--secondary">Export spatial subset as astropy region.</span>
+        <span class="category-content v-messages v-messages__message text--secondary">Export spatial subset as astropy region or spectral subset as specutils SpectralRegion.</span>
       </v-row>
       <plugin-inline-select
         :items="subset_items"
@@ -150,7 +150,9 @@
           :menu-props="{ left: true }"
           attach
           v-model="subset_format_selected"
-          :items="subset_format_items.map(i => i.label)"
+          :items="subset_format_items"
+          item-text="label"
+          item-disabled="disabled"
           label="Format"
           hint="Format for exporting subsets."
           :disabled="subset_selected == null || subset_selected.length == 0"
@@ -200,10 +202,10 @@
         :single_select_allow_blank="false"
       >
       </plugin-inline-select>
-      <jupyter-widget 
+      <jupyter-widget
           v-if='plugin_plot_selected_widget.length > 0'
           style="position: absolute; left: -100%"
-          :widget="plugin_plot_selected_widget"/> 
+          :widget="plugin_plot_selected_widget"/>
       <v-row class="row-min-bottom-padding">
         <v-select
           class="category-content"
@@ -222,7 +224,7 @@
 
     <div style="display: grid; position: relative"> <!-- overlay container -->
     <div style="grid-area: 1/1">
-      
+
     <plugin-auto-label
       :value.sync="filename_value"
       :default="filename_default"
@@ -297,7 +299,7 @@
    display: block;
    text-align: center;
    overflow: hidden;
-   white-space: nowrap; 
+   white-space: nowrap;
    text-transform: uppercase;
    color: gray;
    font-weight: 500;

jdaviz/configs/default/plugins/export/tests/test_export.py

@@ -66,7 +66,7 @@ def test_basic_export_subsets_imviz(self, imviz_helper):
 
         # test that invalid file extension raises an error
         with pytest.raises(ValueError,
-                           match=re.escape("x not one of ['fits', 'reg'], reverting selection to reg")):  # noqa
+                           match=re.escape("x not one of ['fits', 'reg', 'ecsv'], reverting selection to reg")):  # noqa
             export_plugin.subset_format.selected = 'x'
 
     def test_not_implemented(self, cubeviz_helper, spectral_cube_wcs):
@@ -93,10 +93,6 @@ def test_not_implemented(self, cubeviz_helper, spectral_cube_wcs):
 
         assert export_plugin.subset_invalid_msg == 'Export for composite subsets not yet supported.'
 
-        cubeviz_helper.app.session.edit_subset_mode.mode = NewMode
-        cubeviz_helper.app.get_viewer("spectrum-viewer").apply_roi(XRangeROI(5, 15.5))
-        assert 'Subset 2' not in export_plugin.subset.choices
-
     def test_export_subsets_wcs(self, imviz_helper, spectral_cube_wcs):
 
         # using cube WCS instead of 2d imaging wcs for consistancy with
@@ -193,9 +189,13 @@ def test_basic_export_subsets_cubeviz(self, cubeviz_helper, spectral_cube_wcs):
 
         # test that invalid file extension raises an error
         with pytest.raises(ValueError,
-                           match=re.escape("x not one of ['fits', 'reg'], reverting selection to reg")):  # noqa
+                           match=re.escape("x not one of ['fits', 'reg', 'ecsv'], reverting selection to reg")):  # noqa
             export_plugin.subset_format.selected = 'x'
 
+        # Test that selecting disabled option raises an error
+        with pytest.raises(ValueError, match="Cannot export Subset 1 in ECSV format"):
+            export_plugin.subset_format.selected = 'ecsv'
+
         # test that attempting to save a composite subset raises an error
         cubeviz_helper.app.session.edit_subset_mode.mode = AndMode
         cubeviz_helper.app.get_viewer('flux-viewer').apply_roi(CircularROI(xc=25, yc=25, radius=5))
@@ -205,6 +205,23 @@ def test_basic_export_subsets_cubeviz(self, cubeviz_helper, spectral_cube_wcs):
                            match='Subset can not be exported - Export for composite subsets not yet supported.'):  # noqa
             export_plugin.export()
 
+        # Test saving spectral subset
+        cubeviz_helper.app.session.edit_subset_mode.mode = NewMode
+        cubeviz_helper.app.get_viewer("spectrum-viewer").apply_roi(XRangeROI(5, 15.5))
+        export_plugin.subset.selected = 'Subset 2'
+
+        # Format should auto-update to first non-disabled entry
+        assert export_plugin.subset_format.selected == 'ecsv'
+        for format in export_plugin.subset_format.items:
+            if format['label'] != 'ecsv':
+                assert format['disabled']
+            else:
+                assert format['disabled'] is False
+
+        export_plugin.filename_value = "test_spectral_region"
+        export_plugin.export()
+        assert os.path.isfile('test_spectral_region.ecsv')
+
 
 @pytest.mark.usefixtures('_jail')
 def test_export_cubeviz_spectrum_viewer(cubeviz_helper, spectrum1d_cube):

jdaviz/core/template_mixin.py

@@ -725,7 +725,7 @@ def __init__(self, *args, **kwargs):
             manual_options = [default_text] + manual_options
         self._manual_options = manual_options
 
-        self.items = [{"label": opt} for opt in manual_options]
+        self.items = [{"label": opt} if isinstance(opt, str) else opt for opt in manual_options]
         # set default values for traitlets
         if default_text is not None:
             self.selected = default_text

pyproject.toml

@@ -23,7 +23,7 @@ dependencies = [
     "ipywidgets>=8.0.6",
     "voila>=0.4,<0.5",
     "pyyaml>=5.4.1",
-    "specutils>=1.9",
+    "specutils>=1.15",
     "specreduce>=1.3.0,<1.4.0",
     "photutils>=1.4",
     "glue-astronomy>=0.10",