Plugin: spectral extraction

CHANGES.rst

@@ -20,6 +20,11 @@ Mosviz
 Specviz
 ^^^^^^^
 
+Specviz2d
+^^^^^^^^^
+
+- Spectral extraction plugin. [#1514]
+
 API Changes
 -----------
 

docs/index.rst

@@ -174,6 +174,7 @@ Using Jdaviz
   imviz/index.rst
   specviz/index.rst
   cubeviz/index.rst
+  specviz2d/index.rst
   mosviz/index.rst
   save_state.rst
   display.rst

docs/reference/api.rst

@@ -138,6 +138,9 @@ Plugins
 .. automodapi:: jdaviz.configs.specviz.plugins.unit_conversion.unit_conversion
    :no-inheritance-diagram:
 
+.. automodapi:: jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction
+   :no-inheritance-diagram:
+
 .. _jdaviz-api-nuts-bolts:
 
 Nuts and Bolts

docs/specviz2d/index.rst

@@ -0,0 +1,19 @@
+.. image:: ../logos/specviz2d.svg
+   :width: 400
+
+.. _specviz2d:
+
+#########
+Specviz2D
+#########
+
+Specviz2d is a tool for visualization and quick-look analysis of 2D astronomical spectra.
+
+.. We do not want a real section here so navbar shows toc directly.
+
+**Using Specviz**
+
+.. toctree::
+  :maxdepth: 2
+
+  plugins

docs/specviz2d/plugins.rst

@@ -0,0 +1,172 @@
+.. _specviz2d-plugins:
+
+*********************
+Data Analysis Plugins
+*********************
+
+The Specviz2D data analysis plugins are meant to aid quick-look analysis
+of 2D spectroscopic data. All plugins are accessed via the :guilabel:`plugin`
+icon in the upper right corner of the Specviz application. 
+
+.. _specviz2d-metadata-viewer:
+
+Metadata Viewer
+===============
+
+.. seealso::
+
+    :ref:`Metadata Viewer <imviz_metadata-viewer>`
+        Imviz documentation on using the metadata viewer.
+
+.. _specviz2d-plot-options:
+
+Plot Options
+============
+
+.. seealso::
+
+    :ref:`Spectral Plot Options <specviz-plot-settings>`
+        Documentation on further details regarding the plot setting controls.
+
+.. _specviz2d-subset-plugin:
+
+Subset Tools
+============
+
+.. seealso::
+
+    :ref:`Subset Tools <imviz-subset-plugin>`
+        Imviz documentation describing the concept of subsets in Jdaviz.
+
+.. _specviz2d-spectral-extraction:
+
+Spectral Extraction
+===================
+
+The Spectral Extraction plugin exposes `specreduce <https://specreduce.readthedocs.io>`_
+methods for tracing, background subtraction, and spectral extraction from 2D spectra.
+
+Trace
+-----
+
+The first section of the plugin allows for creating and visualizing 
+`specreduce Trace <https://specreduce.readthedocs.io/en/latest/#module-specreduce.tracing>`_
+objects.
+
+Once you interact with any of the inputs in the extract step or hover over that area
+of the plugin, the live visualization will change to show the trace as a solid line.
+
+To create a new trace in the plugin, choose the desired "Trace Type" and edit any input arguments.
+A preview of the trace will update in real time in the 2D spectrum viewer.
+
+To export the trace as a data object into the 2D spectrum viewer (to access via the API or to 
+adjust plotting options), open the "Export Trace" panel, choose a label for the new data entry,
+and click "Create".  Note that this step is not required to create an extraction with simple
+workflows.
+
+Trace objects created outside of jdaviz can be loaded into the app via::
+
+    viz.app.add_data(my_trace)
+
+and then added to the viewer through the data menu.
+
+Once trace objects are loaded into the app, they can be offset (in the cross-dispersion direction)
+by selecting the trace label, entering an offset, and overwriting the existing data entry (or
+creating a new one) with the modified trace.
+
+Background
+----------
+
+The background step of the plugin allows for creating background and background-subtracted
+images via `specreduce.background <https://specreduce.readthedocs.io/en/latest/#module-specreduce.background>`_.
+
+Once you interact with any of the inputs in the background step or hover over that area
+of the plugin, the live visualization will change to show the center (dotted line) and edges
+(solid lines) of the background region(s).  Choose between creating the background
+around the trace defined in the Trace section, or around a "Manual" flat trace.
+
+To visualize the resulting background or background-subtracted image, click on the respective panel,
+and choose a label for the new data entry.  The exported images will now appear in the data dropdown
+menu in the 2D spectrum viewer.  To refine the trace based on the background-subtracted image, return
+to the Trace step and select the exported background-subtracted image as input. 
+
+Extract
+-------
+
+The extraction step of the plugin extracts a 1D spectrum from an input 2D spectrum via
+`specreduce.extract <https://specreduce.readthedocs.io/en/latest/#module-specreduce.extract>`_.
+
+Once you interact with any of the inputs in the extract step or hover over that area
+of the plugin, the live visualization will change to show the center (dotted line) and
+edges (solid lines) of the extraction region.```
+
+The input 2D spectrum defaults to "From Plugin", which will use the settings defined in the Background
+step to create a background-subtracted image without needing to export it into the app itself.
+To use a different 2D spectrum loaded in the app (or exported from the Background step), choose
+that from the dropdown instead.  To skip background subtraction, choose the original 2D spectrum
+as input.
+
+To visualize or export the resulting 2D spectrum, provide a data label and click "Extract".  The 
+resulting spectrum object can be accessed from the API in the same way as any other
+data product in the spectrum viewer.
+
+
+.. _specviz2d-gaussian-smooth:
+
+Gaussian Smooth
+===============
+
+.. seealso::
+
+    :ref:`Gaussian Smooth <gaussian-smooth>`
+        Specviz documentation on Gaussian Smooth.
+
+.. _specviz2d-model-fitting:
+
+Model Fitting
+=============
+
+.. seealso::
+
+    :ref:`Model Fitting <specviz-model-fitting>`
+        Specviz documentation on Model Fitting.
+
+
+.. _specviz2d-unit-conversion:
+
+Unit Conversion
+===============
+
+.. seealso::
+
+    :ref:`Unit Conversion <unit-conversion>`
+        Specviz documentation on Unit Conversion.
+
+
+.. _specviz2d-line-lists:
+
+Line Lists
+==========
+
+.. seealso::
+
+    :ref:`Line Lists <line-lists>`
+        Specviz documentation on Line Lists.
+
+
+.. _specviz2d-line-analysis:
+
+Line Analysis
+=============
+
+.. seealso::
+
+    :ref:`Line Analysis <line-analysis>`
+        Specviz documentation on Line Analysis.
+
+.. _specviz2d-export-plot:
+
+Export Plot
+===========
+
+This plugin allows exporting the plot in a given viewer to various image formats.

jdaviz/app.py

@@ -403,6 +403,18 @@ def _link_new_data(self, reference_data=None, data_to_be_linked=None):
         ref_data = dc[reference_data] if reference_data else dc[0]
         linked_data = dc[data_to_be_linked] if data_to_be_linked else dc[-1]
 
+        if linked_data.meta.get('Plugin', None) == 'SpectralExtraction':
+            if 'Trace' in linked_data.meta:
+                links = [LinkSame(linked_data.components[2], ref_data.components[0]),
+                         LinkSame(linked_data.components[0], ref_data.components[1])]
+                dc.add_link(links)
+                return
+            else:
+                links = [LinkSame(linked_data.components[0], ref_data.components[0]),
+                         LinkSame(linked_data.components[1], ref_data.components[1])]
+                dc.add_link(links)
+                return
+
         # The glue-astronomy SpectralCoordinates currently seems incompatible with glue
         # WCSLink. This gets around it until there's an upstream fix.
         if isinstance(linked_data.coords, SpectralCoordinates):
@@ -623,7 +635,9 @@ def get_data_from_viewer(self, viewer_reference, data_label=None,
                     if cls is not None:
                         # If data is one-dimensional, assume that it can be
                         #  collapsed via the defined statistic
-                        if cls == Spectrum1D:
+                        if 'Trace' in layer_data.meta:
+                            layer_data = layer_data.get_object()
+                        elif cls == Spectrum1D:
                             layer_data = layer_data.get_object(cls=cls,
                                                                statistic=statistic)
                         else:
@@ -1238,8 +1252,13 @@ def vue_data_item_visibility(self, event):
 
         replace = event.get('replace', False)
         selected_items = viewer_item['selected_data_items']
+
         if replace and visible:
-            selected_items = {id: 'visible' if id == item_id else 'hidden' for id in selected_items.keys()}  # noqa
+            # trace items remain selected, even if the mode is in replace
+            keep_selected = [k for k, v in viewer_item['selected_data_items'].items()
+                             if v != 'hidden' and
+                             self._get_data_item_by_id(k).get('type') == 'trace']
+            selected_items = {id: 'visible' if id == item_id or id in keep_selected else 'hidden' for id in selected_items.keys()}  # noqa
         else:
             selected_items[item_id] = 'visible' if visible else 'hidden'
 
@@ -1261,6 +1280,10 @@ def vue_call_viewer_method(self, event):
         kwargs = event.get('kwargs', {})
         return getattr(self._viewer_store[viewer_id], method)(*args, **kwargs)
 
+    def _get_data_item_by_id(self, data_id):
+        return next((x for x in self.state.data_items
+                     if x['id'] == data_id), None)
+
     def _update_selected_data_items(self, viewer_id, selected_items):
         # Find the active viewer
         viewer_item = self._viewer_item_by_id(viewer_id)
@@ -1275,8 +1298,7 @@ def _update_selected_data_items(self, viewer_id, selected_items):
 
         # Include any selected data in the viewer
         for data_id, visibility in selected_items.items():
-            label = next((x['name'] for x in self.state.data_items
-                          if x['id'] == data_id), None)
+            label = self._get_data_item_by_id(data_id)['name']
 
             if label is None:
                 warnings.warn(f"No data item with id '{data_id}' found in "
@@ -1370,6 +1392,8 @@ def _create_data_item(data):
             component_ids = [str(c) for c in data.component_ids()]
         if data.label == 'MOS Table':
             typ = 'table'
+        elif 'Trace' in data.meta:
+            typ = 'trace'
         elif ndims == 1:
             typ = '1d spectrum'
         elif ndims == 2 and wcsaxes is not None:

jdaviz/components/plugin_dataset_select.vue

@@ -15,15 +15,15 @@
     <template slot="selection" slot-scope="data">
       <div class="single-line">
         <span>
-          <v-icon style='margin-right: 2px'>{{ data.item.icon }}</v-icon>
+          <v-icon v-if="data.item.icon" style='margin-right: 2px'>{{ data.item.icon }}</v-icon>
           {{ data.item.label }}
         </span>
       </div>
     </template>
     <template slot="item" slot-scope="data">
       <div class="single-line">
         <span>
-          <v-icon style='margin-right: 2px'>{{ data.item.icon }}</v-icon>
+          <v-icon v-if="data.item.icon" style='margin-right: 2px'>{{ data.item.icon }}</v-icon>
           {{ data.item.label }}
         </span>
       </div>

jdaviz/components/plugin_layer_select.vue

@@ -18,12 +18,12 @@
       <div class="single-line" style="width: 100%">
         <v-chip v-if="multiselect" style="width: calc(100% - 20px)">
           <span>
-            <v-icon style='margin-left: -10px; margin-right: 2px'>{{ data.item.icon }}</v-icon>
+            <v-icon v-if="data.item.icon" style='margin-left: -10px; margin-right: 2px'>{{ data.item.icon }}</v-icon>
             {{ data.item.label }}
           </span>
         </v-chip>
         <span v-else>
-          <v-icon style='margin-right: 2px'>{{ data.item.icon }}</v-icon>
+          <v-icon v-if="data.item.icon" style='margin-right: 2px'>{{ data.item.icon }}</v-icon>
           {{ data.item.label }}
         </span>
       </div>

jdaviz/components/plugin_viewer_select.vue

@@ -18,12 +18,12 @@
       <div class="single-line" style="width: 100%">
         <v-chip v-if="multiselect" style="width: calc(100% - 20px)">
           <span>
-            <v-icon style='margin-left: -10px; margin-right: 2px'>{{ data.item.icon }}</v-icon>
+            <v-icon v-if="data.item.icon" style='margin-left: -10px; margin-right: 2px'>{{ data.item.icon }}</v-icon>
             {{ data.item.label }}
           </span>
         </v-chip>
         <span v-else>
-          <v-icon style='margin-right: 2px'>{{ data.item.icon }}</v-icon>
+          <v-icon v-if="data.item.icon" style='margin-right: 2px'>{{ data.item.icon }}</v-icon>
           {{ data.item.label }}
         </span>
       </div>

jdaviz/components/viewer_data_select.vue

@@ -104,6 +104,10 @@ module.exports = {
       if (['image-viewer', 'spectrum-2d-viewer'].indexOf(this.$props.viewer.reference) !== -1) {
         multi_select = false
       }
+    } else if (this.$props.viewer.config === 'specviz2d') {
+      if (this.$props.viewer.reference === 'spectrum-2d-viewer') {
+        multi_select = false
+      }
     }
     return {
       // default to passed values, whenever value or uncertainty are changed
@@ -161,9 +165,9 @@ module.exports = {
         }
       } else if (this.$props.viewer.config === 'specviz2d') {
         if (this.$props.viewer.reference === 'spectrum-viewer') {
-          return item.ndims === 1 && this.dataItemInViewer(item, returnExtraItems)
+          return item.ndims === 1 && item.type!=='trace' && this.dataItemInViewer(item, returnExtraItems)
         } else if (this.$props.viewer.reference === 'spectrum-2d-viewer') {
-          return item.ndims === 2 && this.dataItemInViewer(item, returnExtraItems)
+          return (item.ndims === 2 || item.type==='trace') && this.dataItemInViewer(item, returnExtraItems)
         }
       }
       // for any situation not covered above, default to showing the entry