Add tool that shows spectrum at spaxel in cubeviz

CHANGES.rst

@@ -38,6 +38,9 @@ API Changes
 Cubeviz
 ^^^^^^^
 
+- New tool for visualizing spectrum at a pixel's coordinate location
+  in the image viewer [#1317]
+
 Imviz
 ^^^^^
 

docs/cubeviz/displaycubes.rst

@@ -110,6 +110,19 @@ of the selected area, but will expand or limit the y range to preserve the aspec
 ratio of the image. The 1D spectrum viewer allows panning and zooming along a single
 axis as in Specviz.
 
+.. _cubeviz-spectrum-at-spaxel:
+
+Spectrum At Spaxel
+==================
+
+This tool allows a user to select one pixel in the image viewer and visualize the spectrum
+at that point in the spectrum viewer. The selected pixel will be highlighted in the image viewer
+and the spectrum will have the same color. If there are multiple data selected in the image viewer
+a spectrum will be created for each data. Once the tool is deselected, the highlighted pixel will
+revert back to normal but the created spectrum/spectra will remain in the spectrum viewer.
+The zoom level of the spectrum viewer will then revert to what it was when the tool was first
+activated.
+
 .. _display-settings:
 
 Display Settings

jdaviz/configs/cubeviz/plugins/tools.py

@@ -3,10 +3,14 @@
 
 from glue.config import viewer_tool
 from glue.viewers.common.tool import CheckableTool
+from glue.core.link_helpers import LinkSame
+from echo import delay_callback
+from specutils import Spectrum1D
 
 from jdaviz.core.events import SliceSelectWavelengthMessage, SliceToolStateMessage
+from jdaviz.core.marks import SelectedPixel
 
-__all__ = ['SelectSlice']
+__all__ = ['SelectSlice', 'SpectrumPerSpaxel']
 
 ICON_DIR = os.path.join(os.path.dirname(__file__), '..', '..', '..', 'data', 'icons')
 
@@ -42,3 +46,123 @@ def on_mouse_event(self, data):
         self.viewer.session.hub.broadcast(msg)
 
         self._time_last = time.time()
+
+
+@viewer_tool
+class SpectrumPerSpaxel(CheckableTool):
+
+    icon = os.path.join(ICON_DIR, 'pixelspectra.svg')
+    tool_id = 'jdaviz:spectrumperspaxel'
+    action_text = 'See spectrum at a single spaxel'
+    tool_tip = 'Click on the viewer and see the spectrum at that spaxel in the spectrum viewer'
+
+    def __init__(self, viewer, **kwargs):
+        self.old_y_min = 0
+        self.old_y_max = 0
+        self.spectrum_viewer = None
+
+        # #b515d1 is magenta
+        self.colors = ['#b515d1']
+        super().__init__(viewer, **kwargs)
+
+    def activate(self):
+        self.viewer.add_event_callback(self.on_mouse_event,
+                                       events=['click'])
+        self.spectrum_viewer = self.viewer.jdaviz_app.get_viewer_by_id("cubeviz-3")
+        self.old_y_min, self.old_y_max = (self.spectrum_viewer.state.y_min,
+                                          self.spectrum_viewer.state.y_max)
+
+    def deactivate(self):
+        self.viewer.remove_event_callback(self.on_mouse_event)
+        with delay_callback(self.spectrum_viewer.state, 'y_min', 'y_max'):
+            self.spectrum_viewer.state.y_min, self.spectrum_viewer.state.y_max = (self.old_y_min,
+                                                                                  self.old_y_max)
+        self.remove_highlight_on_pixel()
+
+    def on_mouse_event(self, data):
+        event = data['event']
+
+        if event == 'click':
+            event_x = data['domain']['x']
+            event_y = data['domain']['y']
+
+            x = round(event_x)
+            y = round(event_y)
+
+            self.remove_highlight_on_pixel()
+            self.highlight_pixel(x, y)
+
+            new_y_min = 0
+            new_y_max = 0
+
+            # Spectrum is created for each active layer in the viewer
+            for data in self.viewer.data():
+                if len(data.shape) != 3:
+                    return
+
+                cube = data.get_object(cls=Spectrum1D, statistic=None)
+                if x > cube.shape[0] or y > cube.shape[1] or x < 0 or y < 0:
+                    return
+
+                spec = Spectrum1D(flux=cube.flux[x][y], spectral_axis=cube.spectral_axis)
+                label = f"{data.label}_at_pixel"
+
+                # Remove data from viewer, re-add data to app, and then add data
+                # back to spectrum viewer
+                self.viewer.jdaviz_app.remove_data_from_viewer("spectrum-viewer", label)
+                self.viewer.jdaviz_app.add_data(spec, label)
+                self.viewer.jdaviz_app.add_data_to_viewer("spectrum-viewer",
+                                                          label,
+                                                          clear_other_data=False)
+
+                # Add meta data for reference data and pixel
+                dc = self.viewer.session.data_collection
+                dc[label].meta["reference_data"] = data.label
+                dc[label].meta["created_from_pixel"] = f"({x}, {y})"
+
+                # Set color of spectrum to magenta to not conflict with subset colors
+                self.spectrum_viewer.figure.marks[-1].colors = self.colors
+
+                # Link newly created spectrum to reference data
+                ref_cube = self.spectrum_viewer.state.reference_data
+                new_spec = dc[label]
+                self.link_data(ref_cube, new_spec)
+
+                # Set y limits based on the new spectrum or spectra being created
+                if max(spec.flux.value) > new_y_max:
+                    new_y_max = max(spec.flux.value)
+                if min(spec.flux.value) < new_y_min:
+                    new_y_min = min(spec.flux.value)
+
+            with delay_callback(self.spectrum_viewer.state, 'y_min', 'y_max'):
+                self.spectrum_viewer.state.y_min, self.spectrum_viewer.state.y_max = (new_y_min,
+                                                                                      new_y_max)
+
+    def link_data(self, data1, data2):
+        if data1.label == data2.label:
+            return
+        world1 = data1.world_component_ids
+        world2 = data2.world_component_ids
+        if len(world1) == 3 and len(world2) == 1:
+            links = [LinkSame(world1[2], world2[0])]
+        elif len(world1) == 1 and len(world2) == 1:
+            links = [LinkSame(world1[0], world2[0])]
+        else:
+            return
+
+        self.viewer.session.data_collection.add_link(links)
+
+    def highlight_pixel(self, x, y):
+        # Creates a box that outlines the pixel at coordinate (x, y)
+        x_coords = [x - 0.5, x + 0.5, x + 0.5, x - 0.5]
+        y_coords = [y - 0.5, y - 0.5, y + 0.5, y + 0.5]
+
+        # Create LinearScale that is the same size as the image viewer
+        scales = {'x': self.viewer.figure.interaction.x_scale, 'y': self.viewer.figure.interaction.y_scale}
+        highlight = SelectedPixel(x=x_coords, y=y_coords, scales=scales,
+                                  fill='none', colors=self.colors, stroke_width=2,
+                                  close_path=True)
+        self.viewer.figure.marks = self.viewer.figure.marks + [highlight]
+
+    def remove_highlight_on_pixel(self):
+        self.viewer.figure.marks = [x for x in self.viewer.figure.marks if not isinstance(x, SelectedPixel)]

jdaviz/configs/cubeviz/plugins/viewers.py

@@ -28,7 +28,7 @@ class CubevizImageView(BqplotImageView, JdavizViewerMixin):
     tools_nested = [
                     ['bqplot:home'],
                     ['jdaviz:boxzoom', 'bqplot:panzoom'],
-                    ['bqplot:circle', 'bqplot:rectangle'],
+                    ['bqplot:circle', 'bqplot:rectangle', 'jdaviz:spectrumperspaxel'],
                     ['jdaviz:sidebar_plot', 'jdaviz:sidebar_export']
                 ]
 

jdaviz/core/marks.py

@@ -463,3 +463,8 @@ def __init__(self, **kwargs):
 class ScatterMask(Scatter):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
+
+
+class SelectedPixel(Lines):
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)