Link mosviz data as a batch after they are loaded

jdaviz/app.py

@@ -15,6 +15,7 @@
 from regions import RectanglePixelRegion, PixCoord
 from specutils import Spectrum1D
 
+from glue.core.exceptions import IncompatibleAttribute
 from glue.config import data_translator
 from glue.config import settings as glue_settings
 from glue.core import BaseData, HubListener, Data, DataCollection
@@ -148,6 +149,10 @@ def __init__(self, configuration=None, *args, **kwargs):
         # Parse the yaml configuration file used to compose the front-end UI
         self.load_configuration(configuration)
 
+        # If true, link data on load. If false, do not link data to speed up
+        # data loading
+        self.auto_link = kwargs.pop('auto_link', True)
+
         # Subscribe to messages indicating that a new viewer needs to be
         #  created. When received, information is passed to the application
         #  handler to generate the appropriate viewer instance.
@@ -244,6 +249,11 @@ def _link_new_data(self):
         any components are compatible with already loaded data. If so, link
         them so that they can be displayed on the same profile1D plot.
         """
+        # Allow for batch linking of data in the parser rather than on
+        # data load
+        if not self.auto_link:
+            return
+
         new_len = len(self.data_collection)
         # Can't link if there's no world_component_ids
         wc_new = self.data_collection[new_len-1].world_component_ids
@@ -442,8 +452,11 @@ def get_data_from_viewer(self, viewer_reference, data_label=None,
 
                         if cls is not None:
                             handler, _ = data_translator.get_handler_for(cls)
-                            layer_data = handler.to_object(layer_data,
-                                                           statistic=statistic)
+                            try:
+                                layer_data = handler.to_object(layer_data,
+                                                               statistic=statistic)
+                            except IncompatibleAttribute:
+                                continue
 
                         data[label] = layer_data
 

jdaviz/configs/mosviz/helper.py

@@ -14,8 +14,8 @@ class MosViz(ConfigHelper):
 
     _default_configuration = "mosviz"
 
-    def __init__(self):
-        super().__init__()
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
 
         spec1d = self.app.get_viewer("spectrum-viewer")
         spec1d.scales['x'].observe(self._update_spec2d_x_axis)
@@ -131,6 +131,7 @@ def load_data(self, spectra_1d, spectra_2d, images=None, spectra_1d_label=None,
             ``images``. Can be a list of strings representing data labels
             for each item in ``data_obj`` if  ``data_obj`` is a list.
         """
+        self.app.auto_link = False
 
         # If we have a single image for multiple spectra, tell the table viewer
         if not isinstance(images, (list, tuple)) and isinstance(spectra_1d, (list, tuple)):
@@ -145,6 +146,21 @@ def load_data(self, spectra_1d, spectra_2d, images=None, spectra_1d_label=None,
 
         self.load_2d_spectra(spectra_2d, spectra_2d_label)
         self.load_1d_spectra(spectra_1d, spectra_1d_label)
+        self.link_table_data(None)
+
+        self.app.auto_link = True
+
+    def link_table_data(self, data_obj):
+        """
+        Batch link data in the Mosviz table rather than doing it on
+        data load.
+
+        Parameters
+        ----------
+        data_obj : obj
+            Input for Mosviz data parsers.
+        """
+        super().load_data(data_obj, parser_reference="mosviz-link-data")
 
     def load_metadata(self, data_obj):
         """
@@ -195,7 +211,12 @@ def load_2d_spectra(self, data_obj, data_labels=None):
                           data_labels=data_labels)
 
     def load_niriss_data(self, data_obj, data_labels=None):
+        self.app.auto_link = False
+
         super().load_data(data_obj, parser_reference="mosviz-niriss-parser")
+        self.link_table_data(data_obj)
+
+        self.app.auto_link = True
 
     def load_images(self, data_obj, data_labels=None, share_image=0):
         """

jdaviz/configs/mosviz/plugins/parsers.py

@@ -13,6 +13,8 @@
 from astropy.wcs import WCS
 from asdf.fits_embed import AsdfInFits
 from pathlib import Path
+from glue.core.link_helpers import LinkSame
+
 
 __all__ = ['mos_spec1d_parser', 'mos_spec2d_parser', 'mos_image_parser']
 
@@ -87,6 +89,41 @@ def _fields_from_ecsv(fname, fields, delimiter=","):
     return parsed_fields
 
 
+@data_parser_registry("mosviz-link-data")
+def link_data_in_table(app, data_obj=None):
+    """
+    Batch links data in the mosviz table viewer.
+
+    Parameters
+    ----------
+    app : `~jdaviz.app.Application`
+        The application-level object used to reference the viewers.
+    data_obj : None
+        Passed in in order to use the data_parser_registry, otherwise
+        not used.
+    """
+    mos_data = app.session.data_collection['MOS Table']
+    wc_spec_ids = []
+
+    # Optimize linking speed through a) delaying link manager updates with a
+    # context manager, b) handling intra-row linkage of 1D and 2D spectra in a
+    # loop, and c) handling inter-row linkage after that in one fell swoop.
+    with app.data_collection.delay_link_manager_update():
+        for index in range(len(mos_data.get_component('1D Spectra').data)):
+            spec_1d = mos_data.get_component('1D Spectra').data[index]
+            spec_2d = mos_data.get_component('2D Spectra').data[index]
+            # image = mos_data.get_component('Images').data[index] # include?
+
+            wc_spec_1d = app.session.data_collection[spec_1d].world_component_ids
+            wc_spec_2d = app.session.data_collection[spec_2d].world_component_ids
+            # wc_image = app.session.data_collection[image].world_component_ids
+            # [RA, Dec] instead of [World]
+
+            wc_spec_ids.append(LinkSame(wc_spec_1d[0], wc_spec_2d[0]))
+
+    app.session.data_collection.add_link(wc_spec_ids)
+
+
 @data_parser_registry("mosviz-spec1d-parser")
 def mos_spec1d_parser(app, data_obj, data_labels=None):
     """

jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py

@@ -74,7 +74,8 @@ def _on_viewer_data_changed(self, msg=None):
         if msg is not None and msg.viewer_id != self._viewer_id:
             return
 
-        self._viewer_data = self.app.get_data_from_viewer('spectrum-viewer')
+        self._viewer_data = self.app.get_data_from_viewer('spectrum-viewer',
+                                                          include_subsets=False)
 
         self.dc_items = [data.label
                          for data in self.app.data_collection

jdaviz/configs/specviz/plugins/viewers.py

@@ -6,6 +6,7 @@
 from glue.core.subset import Subset
 from glue.config import data_translator
 from glue_jupyter.bqplot.profile import BqplotProfileView
+from glue.core.exceptions import IncompatibleAttribute
 
 import astropy
 from astropy.utils.introspection import minversion
@@ -66,8 +67,11 @@ def data(self, cls=None):
 
                     if _class is not None:
                         handler, _ = data_translator.get_handler_for(_class)
-                        layer_data = handler.to_object(layer_data,
-                                                       statistic=statistic)
+                        try:
+                            layer_data = handler.to_object(layer_data,
+                                                           statistic=statistic)
+                        except IncompatibleAttribute:
+                            continue
                     data.append(layer_data)
 
         return data

jdaviz/core/helpers.py

@@ -31,9 +31,9 @@ class ConfigHelper(HubListener):
     """
     _default_configuration = 'default'
 
-    def __init__(self, app=None):
+    def __init__(self, app=None, auto_link=True):
         if app is None:
-            self.app = Application(configuration=self._default_configuration)
+            self.app = Application(configuration=self._default_configuration, auto_link=auto_link)
         else:
             self.app = app
 

notebooks/MosvizExample.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# MOSViz example notebook"
+    "# Mosviz example notebook"
    ]
   },
   {
@@ -28,7 +28,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This starts MOSViz."
+    "Next, start Mosviz. Set the `auto_link` argument to `False` to speed up its data loading process. (We'll encounter that later.)"
    ]
   },
   {
@@ -51,7 +51,7 @@
    "source": [
     "But before we can use it, we need some data.\n",
     "\n",
-    "The MOSViz parsers accept lists of `Spectrum1D`, `SpectralCube`, and `CCDData` for 1D, 2D, and image data, respectively. Alternatively, users can also provide lists of file paths and MOSViz will internally attempt to parse them as their respective data types."
+    "The Mosviz parsers accept lists of `Spectrum1D`, `SpectralCube`, and `CCDData` for 1D, 2D, and image data, respectively. Alternatively, users can also provide lists of file paths and Mosviz will internally attempt to parse them as their respective data types."
    ]
   },
   {
@@ -108,7 +108,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now that we have the data files extracted into `data_dir`, we can generate lists for MOSViz."
+    "Now that we have the data files extracted into `data_dir`, we can generate lists for Mosviz."
    ]
   },
   {
@@ -176,7 +176,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If no images are provided, MOSViz can still display the spectra."
+    "If no images are provided, Mosviz can still display the spectra."
    ]
   },
   {
@@ -236,7 +236,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -250,7 +250,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.5"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

notebooks/MosvizNIRISSExample.ipynb

@@ -5,7 +5,7 @@
    "id": "2b2fcea7",
    "metadata": {},
    "source": [
-    "# MOSViz NIRISS example notebook"
+    "# Mosviz NIRISS example notebook"
    ]
   },
   {
@@ -32,7 +32,7 @@
    "id": "e3d6f12f",
    "metadata": {},
    "source": [
-    "This starts MOSViz."
+    "Next, start Mosviz."
    ]
   },
   {
@@ -44,9 +44,9 @@
    },
    "outputs": [],
    "source": [
-    "from jdaviz.configs.mosviz.helper import MosViz\n",
+    "from jdaviz.configs.mosviz.helper import MosViz as Mosviz\n",
     "\n",
-    "mosviz = MosViz()\n",
+    "mosviz = Mosviz()\n",
     "mosviz.app"
    ]
   },
@@ -116,6 +116,14 @@
    "source": [
     "mosviz.load_niriss_data(data_dir)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "03884229",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -134,7 +142,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,