From cc13d6bee53f7e34ddea90cac556387aa179bb00 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Mon, 12 Jul 2021 13:09:44 -0400
Subject: [PATCH 01/21] Add mosviz example notebook with updated nirspec data

---
 notebooks/concepts/MosvizUpdatedData.ipynb | 191 +++++++++++++++++++++
 1 file changed, 191 insertions(+)
 create mode 100644 notebooks/concepts/MosvizUpdatedData.ipynb

diff --git a/notebooks/concepts/MosvizUpdatedData.ipynb b/notebooks/concepts/MosvizUpdatedData.ipynb
new file mode 100644
index 0000000000..4664de6c74
--- /dev/null
+++ b/notebooks/concepts/MosvizUpdatedData.ipynb
@@ -0,0 +1,191 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from jdaviz import MosViz"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "b445e0e7fef14169b97ec3eda3f99ee4",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Application(components={'g-viewer-tab': '<template>\\n  <component :is=\"stack.container\">\\n    <g-viewer-tab\\n …"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "mosviz = MosViz()\n",
+    "mosviz.app"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The MOSViz parsers accepts lists of `Spectrum1D`, `SpectralCube`, and `CCDData` for 1D, 2D, and image data respectively. Alternatively, and the method used below, users can provide lists of file paths and MOSViz will internally attempt to parse them as their respective data type."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [],
+   "source": [
+    "import glob\n",
+    "from astropy.utils.data import download_file\n",
+    "import tempfile\n",
+    "import pathlib\n",
+    "from zipfile import ZipFile\n",
+    "\n",
+    "# Lists of data products\n",
+    "slit_id = []\n",
+    "spectra_1d = []\n",
+    "spectra_2d = []\n",
+    "cutouts = []\n",
+    "\n",
+    "#Central Store data directories\n",
+    "file_location = \"central\"\n",
+    "if file_location == \"central\":\n",
+    "    cutouts_path = \"/user/jotor/mosviz-cutouts/\"\n",
+    "    level3_path = \"/grp/jwst/wit4/nirspec/Muzerolle/Sim_products/CEERS_PRISM/\"\n",
+    "else:\n",
+    "    #Local data directories\n",
+    "    level3_path = \"/Users/pogle/Desktop/newcomputer/CEERS/CEERS_PRISM/\"\n",
+    "    cutouts_path = \"/Users/pogle/Desktop/newcomputer/CEERS/CEERS_PRISM_cutouts/\"\n",
+    "\n",
+    "for file_path in glob.glob(str(level3_path+'*')):\n",
+    "    if ('x1d' in file_path) & ('combined' in file_path):\n",
+    "        spectra_1d.append(file_path)\n",
+    "        if file_location == \"central\":\n",
+    "            slitid = file_path[88:93]\n",
+    "        else:\n",
+    "            slitid = file_path[81:86]\n",
+    "        slit_id.append(slitid)\n",
+    "    elif ('s2d' in file_path) & ('combined' in file_path):\n",
+    "        spectra_2d.append(file_path)\n",
+    "#for file_path in glob.glob(str(cutouts_path+'*')):\n",
+    "#    if ('cutout' in file_path) & ('.fits' in file_path):\n",
+    "#        cutouts.append(file_path)   \n",
+    " \n",
+    "#Sort the slit ids and filenames\n",
+    "slit_id_sorted = sorted (slit_id)    \n",
+    "spectra_1d_sorted = sorted(spectra_1d)\n",
+    "spectra_2d_sorted = sorted(spectra_2d)\n",
+    "\n",
+    "#Cutout filenames\n",
+    "cutouts_sorted = []\n",
+    "for s_id in slit_id_sorted: cutouts_sorted.append(cutouts_path+\"cutout\"+s_id+\".fits\")\n",
+    "    \n",
+    "#Print out the matched filenames for each slit\n",
+    "for s_id, f_1d, f_2d, f_cut in zip(slit_id_sorted, spectra_1d_sorted, spectra_2d_sorted, cutouts_sorted): \n",
+    "    if file_location == \"central\":\n",
+    "        print(s_id, \"...\"+f_1d[87:], \"...\"+f_2d[87:], \"...\"+f_cut[27:])\n",
+    "    else:\n",
+    "        print(s_id, \"...\"+f_1d[80:], \"...\"+f_2d[80:], \"...\"+f_cut[59:])    \n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#mosviz.load_data(spectra_1d, spectra_2d, images=images)\n",
+    "\n",
+    "# Or alternatively: \n",
+    "mosviz.load_metadata(cutouts_sorted[0:15])           #Only show the first 15, otherwise it takes too long (8min)  \n",
+    "mosviz.load_1d_spectra(spectra_1d_sorted[0:15])  \n",
+    "mosviz.load_2d_spectra(spectra_2d_sorted[0:15]) \n",
+    "mosviz.load_images(cutouts_sorted[0:15])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If no images are provided, MOSViz can still display the spectra."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mosviz_no_images = MosViz()\n",
+    "mosviz_no_images.app"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mosviz_no_images.load_data(spectra_1d, spectra_2d)\n",
+    "\n",
+    "# Or alternatively: \n",
+    "# mosviz_no_images.load_1d_spectra(spectra_1d)\n",
+    "# mosviz_no_images.load_2d_spectra(spectra_2d)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Images can be added later."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mosviz_no_images.load_images(images)\n",
+    "mosviz_no_images.load_metadata(images)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

From 1f7604ad37207bc4dc4c191542c806e5f9265d79 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Thu, 5 Aug 2021 14:21:23 -0400
Subject: [PATCH 02/21] Link data as one batch rather than at data load

---
 jdaviz/app.py                            | 11 +++++++++-
 jdaviz/configs/mosviz/helper.py          | 19 ++++++++++++++--
 jdaviz/configs/mosviz/plugins/parsers.py | 28 ++++++++++++++++++++++++
 jdaviz/core/helpers.py                   |  4 ++--
 4 files changed, 57 insertions(+), 5 deletions(-)

diff --git a/jdaviz/app.py b/jdaviz/app.py
index 9e33007a6d..786416a92f 100644
--- a/jdaviz/app.py
+++ b/jdaviz/app.py
@@ -129,7 +129,7 @@ class Application(VuetifyTemplate, HubListener):
 
     loading = Bool(False).tag(sync=True)
 
-    def __init__(self, configuration=None, *args, **kwargs):
+    def __init__(self, configuration=None, auto_link=True, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
         # Generate a state object for this application to maintain the state of
@@ -148,6 +148,10 @@ 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 = auto_link
+
         # 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 +248,11 @@ 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
diff --git a/jdaviz/configs/mosviz/helper.py b/jdaviz/configs/mosviz/helper.py
index aaa6be41b6..0a83991c4a 100644
--- a/jdaviz/configs/mosviz/helper.py
+++ b/jdaviz/configs/mosviz/helper.py
@@ -14,8 +14,8 @@ class MosViz(ConfigHelper):
 
     _default_configuration = "mosviz"
 
-    def __init__(self):
-        super().__init__()
+    def __init__(self, auto_link):
+        super().__init__(app=None, auto_link=auto_link)
 
         spec1d = self.app.get_viewer("spectrum-viewer")
         spec1d.scales['x'].observe(self._update_spec2d_x_axis)
@@ -145,6 +145,20 @@ 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)
+
+    def link_table_data(self, data_obj):
+        """
+        Batch link data in the mosviz table rather than doing it on
+        data load.
+
+        Parameters
+        ----------
+        data_obj : None
+            Not used in this method, only included to be able to access the
+            mosviz data parsers.
+        """
+        super().load_data(data_obj, parser_reference="mosviz-link-data")
 
     def load_metadata(self, data_obj):
         """
@@ -196,6 +210,7 @@ def load_2d_spectra(self, data_obj, data_labels=None):
 
     def load_niriss_data(self, data_obj, data_labels=None):
         super().load_data(data_obj, parser_reference="mosviz-niriss-parser")
+        self.link_table_data(data_obj)
 
     def load_images(self, data_obj, data_labels=None, share_image=0):
         """
diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index 1b062e31aa..393280440a 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/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 +89,32 @@ 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, data_labels=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.
+    data_labels : None
+        Not used.
+    """
+    mos_data = app.session.data_collection['MOS Table']
+
+    # Loop through mos table rows and link Spectra 1D and Spectra 2D
+    # data objects. This speeds up performance significantly over linking
+    # data when loaded into the application.
+    for index in range(0, 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]
+        app.session.data_collection.add_link(LinkSame(spec_1d, spec_2d))
+
+
 @data_parser_registry("mosviz-spec1d-parser")
 def mos_spec1d_parser(app, data_obj, data_labels=None):
     """
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index b45280d21e..ea5ec07121 100644
--- a/jdaviz/core/helpers.py
+++ b/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
 

From 93cd2499ba10076846a2a33bbcb4b542ccfbd6da Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Thu, 5 Aug 2021 14:23:33 -0400
Subject: [PATCH 03/21] Remove unused file

---
 notebooks/concepts/MosvizUpdatedData.ipynb | 191 ---------------------
 1 file changed, 191 deletions(-)
 delete mode 100644 notebooks/concepts/MosvizUpdatedData.ipynb

diff --git a/notebooks/concepts/MosvizUpdatedData.ipynb b/notebooks/concepts/MosvizUpdatedData.ipynb
deleted file mode 100644
index 4664de6c74..0000000000
--- a/notebooks/concepts/MosvizUpdatedData.ipynb
+++ /dev/null
@@ -1,191 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from jdaviz import MosViz"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {
-    "scrolled": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b445e0e7fef14169b97ec3eda3f99ee4",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Application(components={'g-viewer-tab': '<template>\\n  <component :is=\"stack.container\">\\n    <g-viewer-tab\\n …"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "mosviz = MosViz()\n",
-    "mosviz.app"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "The MOSViz parsers accepts lists of `Spectrum1D`, `SpectralCube`, and `CCDData` for 1D, 2D, and image data respectively. Alternatively, and the method used below, users can provide lists of file paths and MOSViz will internally attempt to parse them as their respective data type."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {
-    "scrolled": false
-   },
-   "outputs": [],
-   "source": [
-    "import glob\n",
-    "from astropy.utils.data import download_file\n",
-    "import tempfile\n",
-    "import pathlib\n",
-    "from zipfile import ZipFile\n",
-    "\n",
-    "# Lists of data products\n",
-    "slit_id = []\n",
-    "spectra_1d = []\n",
-    "spectra_2d = []\n",
-    "cutouts = []\n",
-    "\n",
-    "#Central Store data directories\n",
-    "file_location = \"central\"\n",
-    "if file_location == \"central\":\n",
-    "    cutouts_path = \"/user/jotor/mosviz-cutouts/\"\n",
-    "    level3_path = \"/grp/jwst/wit4/nirspec/Muzerolle/Sim_products/CEERS_PRISM/\"\n",
-    "else:\n",
-    "    #Local data directories\n",
-    "    level3_path = \"/Users/pogle/Desktop/newcomputer/CEERS/CEERS_PRISM/\"\n",
-    "    cutouts_path = \"/Users/pogle/Desktop/newcomputer/CEERS/CEERS_PRISM_cutouts/\"\n",
-    "\n",
-    "for file_path in glob.glob(str(level3_path+'*')):\n",
-    "    if ('x1d' in file_path) & ('combined' in file_path):\n",
-    "        spectra_1d.append(file_path)\n",
-    "        if file_location == \"central\":\n",
-    "            slitid = file_path[88:93]\n",
-    "        else:\n",
-    "            slitid = file_path[81:86]\n",
-    "        slit_id.append(slitid)\n",
-    "    elif ('s2d' in file_path) & ('combined' in file_path):\n",
-    "        spectra_2d.append(file_path)\n",
-    "#for file_path in glob.glob(str(cutouts_path+'*')):\n",
-    "#    if ('cutout' in file_path) & ('.fits' in file_path):\n",
-    "#        cutouts.append(file_path)   \n",
-    " \n",
-    "#Sort the slit ids and filenames\n",
-    "slit_id_sorted = sorted (slit_id)    \n",
-    "spectra_1d_sorted = sorted(spectra_1d)\n",
-    "spectra_2d_sorted = sorted(spectra_2d)\n",
-    "\n",
-    "#Cutout filenames\n",
-    "cutouts_sorted = []\n",
-    "for s_id in slit_id_sorted: cutouts_sorted.append(cutouts_path+\"cutout\"+s_id+\".fits\")\n",
-    "    \n",
-    "#Print out the matched filenames for each slit\n",
-    "for s_id, f_1d, f_2d, f_cut in zip(slit_id_sorted, spectra_1d_sorted, spectra_2d_sorted, cutouts_sorted): \n",
-    "    if file_location == \"central\":\n",
-    "        print(s_id, \"...\"+f_1d[87:], \"...\"+f_2d[87:], \"...\"+f_cut[27:])\n",
-    "    else:\n",
-    "        print(s_id, \"...\"+f_1d[80:], \"...\"+f_2d[80:], \"...\"+f_cut[59:])    \n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#mosviz.load_data(spectra_1d, spectra_2d, images=images)\n",
-    "\n",
-    "# Or alternatively: \n",
-    "mosviz.load_metadata(cutouts_sorted[0:15])           #Only show the first 15, otherwise it takes too long (8min)  \n",
-    "mosviz.load_1d_spectra(spectra_1d_sorted[0:15])  \n",
-    "mosviz.load_2d_spectra(spectra_2d_sorted[0:15]) \n",
-    "mosviz.load_images(cutouts_sorted[0:15])"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "If no images are provided, MOSViz can still display the spectra."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "mosviz_no_images = MosViz()\n",
-    "mosviz_no_images.app"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "mosviz_no_images.load_data(spectra_1d, spectra_2d)\n",
-    "\n",
-    "# Or alternatively: \n",
-    "# mosviz_no_images.load_1d_spectra(spectra_1d)\n",
-    "# mosviz_no_images.load_2d_spectra(spectra_2d)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Images can be added later."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "mosviz_no_images.load_images(images)\n",
-    "mosviz_no_images.load_metadata(images)"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

From 60ca838fcf2781501cb00353be3118dcfa5bc870 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Thu, 5 Aug 2021 14:38:34 -0400
Subject: [PATCH 04/21] Update notebooks with auto_link option

---
 notebooks/MosvizExample.ipynb       |  2 +-
 notebooks/MosvizNIRISSExample.ipynb | 12 ++++++++++--
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/notebooks/MosvizExample.ipynb b/notebooks/MosvizExample.ipynb
index c286503659..9d1b3351e3 100644
--- a/notebooks/MosvizExample.ipynb
+++ b/notebooks/MosvizExample.ipynb
@@ -41,7 +41,7 @@
    "source": [
     "from jdaviz.configs.mosviz.helper import MosViz as Mosviz\n",
     "\n",
-    "mosviz = Mosviz()\n",
+    "mosviz = Mosviz(auto_link=False)\n",
     "mosviz.app"
    ]
   },
diff --git a/notebooks/MosvizNIRISSExample.ipynb b/notebooks/MosvizNIRISSExample.ipynb
index a6f24171af..edf8ab760e 100644
--- a/notebooks/MosvizNIRISSExample.ipynb
+++ b/notebooks/MosvizNIRISSExample.ipynb
@@ -46,7 +46,7 @@
    "source": [
     "from jdaviz.configs.mosviz.helper import MosViz\n",
     "\n",
-    "mosviz = MosViz()\n",
+    "mosviz = MosViz(auto_link=False)\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,

From aab771a6a13ea2a5c30c8ea8adb50361ca01bb93 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Thu, 5 Aug 2021 15:08:47 -0400
Subject: [PATCH 05/21] Move auto_link parameter to kwargs

---
 jdaviz/app.py                            | 4 ++--
 jdaviz/configs/mosviz/helper.py          | 4 ++--
 jdaviz/configs/mosviz/plugins/parsers.py | 5 ++++-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/jdaviz/app.py b/jdaviz/app.py
index 786416a92f..e4293000b1 100644
--- a/jdaviz/app.py
+++ b/jdaviz/app.py
@@ -129,7 +129,7 @@ class Application(VuetifyTemplate, HubListener):
 
     loading = Bool(False).tag(sync=True)
 
-    def __init__(self, configuration=None, auto_link=True, *args, **kwargs):
+    def __init__(self, configuration=None, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
         # Generate a state object for this application to maintain the state of
@@ -150,7 +150,7 @@ def __init__(self, configuration=None, auto_link=True, *args, **kwargs):
 
         # If true, link data on load. If false, do not link data to speed up
         # data loading
-        self.auto_link = auto_link
+        self.auto_link = kwargs.pop('auto_link')
 
         # Subscribe to messages indicating that a new viewer needs to be
         #  created. When received, information is passed to the application
diff --git a/jdaviz/configs/mosviz/helper.py b/jdaviz/configs/mosviz/helper.py
index 0a83991c4a..b9dd3fcfed 100644
--- a/jdaviz/configs/mosviz/helper.py
+++ b/jdaviz/configs/mosviz/helper.py
@@ -14,8 +14,8 @@ class MosViz(ConfigHelper):
 
     _default_configuration = "mosviz"
 
-    def __init__(self, auto_link):
-        super().__init__(app=None, auto_link=auto_link)
+    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)
diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index 393280440a..68f8230a4c 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -112,7 +112,10 @@ def link_data_in_table(app, data_obj=None, data_labels=None):
     for index in range(0, 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]
-        app.session.data_collection.add_link(LinkSame(spec_1d, spec_2d))
+
+        wc_spec_1d = app.session.data_collection[spec_1d].world_component_ids
+        wc_spec_2d = app.session.data_collection[spec_2d].world_component_ids
+        app.session.data_collection.add_link(LinkSame(wc_spec_1d[0], wc_spec_2d[0]))
 
 
 @data_parser_registry("mosviz-spec1d-parser")

From 61932e93ec3471d3b033af95a72943c23c608e69 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Thu, 5 Aug 2021 15:27:40 -0400
Subject: [PATCH 06/21] Update jdaviz/app.py

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>
---
 jdaviz/app.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jdaviz/app.py b/jdaviz/app.py
index e4293000b1..4dff4218b4 100644
--- a/jdaviz/app.py
+++ b/jdaviz/app.py
@@ -150,7 +150,7 @@ def __init__(self, configuration=None, *args, **kwargs):
 
         # If true, link data on load. If false, do not link data to speed up
         # data loading
-        self.auto_link = kwargs.pop('auto_link')
+        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

From 51352a7e48e47cca9bc0f910ab9acc1eb0f2ec00 Mon Sep 17 00:00:00 2001
From: ojustino <ojustino@users.noreply.github.com>
Date: Wed, 18 Aug 2021 13:07:41 -0400
Subject: [PATCH 07/21] Use link manager delay when linking Mosviz tables

---
 jdaviz/configs/mosviz/plugins/parsers.py | 26 ++++++++++++++++--------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index 68f8230a4c..cc0a3c57a4 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -105,17 +105,25 @@ def link_data_in_table(app, data_obj=None, data_labels=None):
         Not used.
     """
     mos_data = app.session.data_collection['MOS Table']
+    wc_spec_ids = []
 
-    # Loop through mos table rows and link Spectra 1D and Spectra 2D
-    # data objects. This speeds up performance significantly over linking
-    # data when loaded into the application.
-    for index in range(0, 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]
+    # 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(0, 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)
 
-        wc_spec_1d = app.session.data_collection[spec_1d].world_component_ids
-        wc_spec_2d = app.session.data_collection[spec_2d].world_component_ids
-        app.session.data_collection.add_link(LinkSame(wc_spec_1d[0], wc_spec_2d[0]))
 
 
 @data_parser_registry("mosviz-spec1d-parser")

From 7f63f27d510f21995f7ff0793afa95994ed4165d Mon Sep 17 00:00:00 2001
From: Thomas Robitaille <thomas.robitaille@gmail.com>
Date: Tue, 24 Aug 2021 17:18:54 +0100
Subject: [PATCH 08/21] Don't convert subsets to user-facing objects if they
 are incompatible

---
 jdaviz/app.py                                             | 8 ++++++--
 .../specviz/plugins/unit_conversion/unit_conversion.py    | 3 ++-
 jdaviz/configs/specviz/plugins/viewers.py                 | 8 ++++++--
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/jdaviz/app.py b/jdaviz/app.py
index 4dff4218b4..dfd7adc4cc 100644
--- a/jdaviz/app.py
+++ b/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
@@ -451,8 +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
 
diff --git a/jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py b/jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py
index 3d96e64c20..55dc241185 100644
--- a/jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py
+++ b/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
diff --git a/jdaviz/configs/specviz/plugins/viewers.py b/jdaviz/configs/specviz/plugins/viewers.py
index 1450244bda..54a81120f9 100644
--- a/jdaviz/configs/specviz/plugins/viewers.py
+++ b/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

From c62fbdbeccbc0fc26e9b40e8ab0bb6c643140d6e Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Thu, 26 Aug 2021 09:54:16 -0400
Subject: [PATCH 09/21] Fix codestyle checks

---
 jdaviz/app.py                             | 2 +-
 jdaviz/configs/mosviz/plugins/parsers.py  | 6 +++---
 jdaviz/configs/specviz/plugins/viewers.py | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/jdaviz/app.py b/jdaviz/app.py
index dfd7adc4cc..4f894727ca 100644
--- a/jdaviz/app.py
+++ b/jdaviz/app.py
@@ -454,7 +454,7 @@ def get_data_from_viewer(self, viewer_reference, data_label=None,
                             handler, _ = data_translator.get_handler_for(cls)
                             try:
                                 layer_data = handler.to_object(layer_data,
-                                                            statistic=statistic)
+                                                               statistic=statistic)
                             except IncompatibleAttribute:
                                 continue
 
diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index cc0a3c57a4..5ca8cc36ca 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -114,18 +114,18 @@ def link_data_in_table(app, data_obj=None, data_labels=None):
         for index in range(0, 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?
+            # 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_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):
     """
diff --git a/jdaviz/configs/specviz/plugins/viewers.py b/jdaviz/configs/specviz/plugins/viewers.py
index 54a81120f9..22737d66fc 100644
--- a/jdaviz/configs/specviz/plugins/viewers.py
+++ b/jdaviz/configs/specviz/plugins/viewers.py
@@ -69,7 +69,7 @@ def data(self, cls=None):
                         handler, _ = data_translator.get_handler_for(_class)
                         try:
                             layer_data = handler.to_object(layer_data,
-                                                        statistic=statistic)
+                                                           statistic=statistic)
                         except IncompatibleAttribute:
                             continue
                     data.append(layer_data)

From 4504a24e182fdb82e4b6f29082f527e764f58836 Mon Sep 17 00:00:00 2001
From: ojustino <ojustino@users.noreply.github.com>
Date: Thu, 26 Aug 2021 19:25:11 -0400
Subject: [PATCH 10/21] Accepted suggestions from code review

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>
---
 jdaviz/configs/mosviz/helper.py          | 7 +++----
 jdaviz/configs/mosviz/plugins/parsers.py | 2 +-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/jdaviz/configs/mosviz/helper.py b/jdaviz/configs/mosviz/helper.py
index b9dd3fcfed..e29de2ec8d 100644
--- a/jdaviz/configs/mosviz/helper.py
+++ b/jdaviz/configs/mosviz/helper.py
@@ -149,14 +149,13 @@ def load_data(self, spectra_1d, spectra_2d, images=None, spectra_1d_label=None,
 
     def link_table_data(self, data_obj):
         """
-        Batch link data in the mosviz table rather than doing it on
+        Batch link data in the Mosviz table rather than doing it on
         data load.
 
         Parameters
         ----------
-        data_obj : None
-            Not used in this method, only included to be able to access the
-            mosviz data parsers.
+        data_obj : obj
+            Input for Mosviz data parsers.
         """
         super().load_data(data_obj, parser_reference="mosviz-link-data")
 
diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index 5ca8cc36ca..8e10b55293 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -111,7 +111,7 @@ def link_data_in_table(app, data_obj=None, data_labels=None):
     # 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(0, len(mos_data.get_component('1D Spectra').data)):
+        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?

From 25725680712c97af5b5b11c59e5718437ef372ce Mon Sep 17 00:00:00 2001
From: ojustino <ojustino@users.noreply.github.com>
Date: Thu, 26 Aug 2021 19:24:25 -0400
Subject: [PATCH 11/21] Implemented suggestions from @pllim

---
 jdaviz/configs/mosviz/plugins/parsers.py | 2 +-
 notebooks/MosvizExample.ipynb            | 2 +-
 notebooks/MosvizNIRISSExample.ipynb      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index 8e10b55293..eec1209624 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -92,7 +92,7 @@ def _fields_from_ecsv(fname, fields, delimiter=","):
 @data_parser_registry("mosviz-link-data")
 def link_data_in_table(app, data_obj=None, data_labels=None):
     """
-    Batch links data in the mosviz table viewer
+    Batch links data in the mosviz table viewer.
 
     Parameters
     ----------
diff --git a/notebooks/MosvizExample.ipynb b/notebooks/MosvizExample.ipynb
index 9d1b3351e3..38279a96c8 100644
--- a/notebooks/MosvizExample.ipynb
+++ b/notebooks/MosvizExample.ipynb
@@ -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.)"
    ]
   },
   {
diff --git a/notebooks/MosvizNIRISSExample.ipynb b/notebooks/MosvizNIRISSExample.ipynb
index edf8ab760e..c3e518e906 100644
--- a/notebooks/MosvizNIRISSExample.ipynb
+++ b/notebooks/MosvizNIRISSExample.ipynb
@@ -32,7 +32,7 @@
    "id": "e3d6f12f",
    "metadata": {},
    "source": [
-    "This starts MOSViz."
+    "Next, start MOSviz. Set the `auto_link` argument to `False` to speed up data loading once we reach that step."
    ]
   },
   {

From 19ac2ad051a4a6fb8a75fee5eeef5516cbbc4610 Mon Sep 17 00:00:00 2001
From: ojustino <ojustino@users.noreply.github.com>
Date: Fri, 27 Aug 2021 12:33:43 -0400
Subject: [PATCH 12/21] Standardized Mosviz spelling in example notebooks

---
 notebooks/MosvizExample.ipynb       | 10 +++++-----
 notebooks/MosvizNIRISSExample.ipynb |  8 ++++----
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/notebooks/MosvizExample.ipynb b/notebooks/MosvizExample.ipynb
index 38279a96c8..3012ad678b 100644
--- a/notebooks/MosvizExample.ipynb
+++ b/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": [
-    "Next, start MOSviz. Set the `auto_link` argument to `False` to speed up its data loading process. (We'll encounter that later.)"
+    "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."
    ]
   },
   {
diff --git a/notebooks/MosvizNIRISSExample.ipynb b/notebooks/MosvizNIRISSExample.ipynb
index c3e518e906..7e41c0cd89 100644
--- a/notebooks/MosvizNIRISSExample.ipynb
+++ b/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": [
-    "Next, start MOSviz. Set the `auto_link` argument to `False` to speed up data loading once we reach that step."
+    "Next, start Mosviz. Set the `auto_link` argument to `False` to speed up data loading once we reach that step."
    ]
   },
   {
@@ -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(auto_link=False)\n",
+    "mosviz = Mosviz(auto_link=False)\n",
     "mosviz.app"
    ]
   },

From d5a6ba78d1a525d2eda9502009c8d8da00b1ccf0 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 27 Aug 2021 14:33:06 -0400
Subject: [PATCH 13/21] Move auto_link from app call to inside load_data method

---
 jdaviz/app.py                       |   3 +-
 jdaviz/configs/mosviz/helper.py     |   7 ++
 notebooks/MosvizExample.ipynb       |   6 +-
 notebooks/MosvizNIRISSExample.ipynb | 135 ++++++++++++++++++++++++++--
 4 files changed, 138 insertions(+), 13 deletions(-)

diff --git a/jdaviz/app.py b/jdaviz/app.py
index 4f894727ca..27e1929bf9 100644
--- a/jdaviz/app.py
+++ b/jdaviz/app.py
@@ -252,8 +252,9 @@ def _link_new_data(self):
         # Allow for batch linking of data in the parser rather than on
         # data load
         if not self.auto_link:
+            print("auto_link false")
             return
-
+        print("auto_link true")
         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
diff --git a/jdaviz/configs/mosviz/helper.py b/jdaviz/configs/mosviz/helper.py
index e29de2ec8d..9347684b5d 100644
--- a/jdaviz/configs/mosviz/helper.py
+++ b/jdaviz/configs/mosviz/helper.py
@@ -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)):
@@ -147,6 +148,8 @@ def load_data(self, spectra_1d, spectra_2d, images=None, spectra_1d_label=None,
         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
@@ -208,9 +211,13 @@ 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):
         """
         Load and parse a set of image objects. If providing a file path, it
diff --git a/notebooks/MosvizExample.ipynb b/notebooks/MosvizExample.ipynb
index 3012ad678b..1c4a69f9c8 100644
--- a/notebooks/MosvizExample.ipynb
+++ b/notebooks/MosvizExample.ipynb
@@ -41,7 +41,7 @@
    "source": [
     "from jdaviz.configs.mosviz.helper import MosViz as Mosviz\n",
     "\n",
-    "mosviz = Mosviz(auto_link=False)\n",
+    "mosviz = Mosviz()\n",
     "mosviz.app"
    ]
   },
@@ -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,
diff --git a/notebooks/MosvizNIRISSExample.ipynb b/notebooks/MosvizNIRISSExample.ipynb
index 7e41c0cd89..69d8d08398 100644
--- a/notebooks/MosvizNIRISSExample.ipynb
+++ b/notebooks/MosvizNIRISSExample.ipynb
@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "869727c8",
    "metadata": {},
    "outputs": [],
@@ -32,27 +32,42 @@
    "id": "e3d6f12f",
    "metadata": {},
    "source": [
-    "Next, start Mosviz. Set the `auto_link` argument to `False` to speed up data loading once we reach that step."
+    "Next, start Mosviz."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "f2233e63",
    "metadata": {
     "scrolled": false
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "afc0762f0c224cb0bbdc660a0506d6c2",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Application(components={'g-viewer-tab': '<template>\\n  <component :is=\"stack.container\">\\n    <g-viewer-tab\\n …"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "from jdaviz.configs.mosviz.helper import MosViz as Mosviz\n",
     "\n",
-    "mosviz = Mosviz(auto_link=False)\n",
+    "mosviz = Mosviz()\n",
     "mosviz.app"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "75d0e918",
    "metadata": {},
    "outputs": [],
@@ -77,7 +92,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "2ac93c58",
    "metadata": {},
    "outputs": [],
@@ -109,10 +124,112 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "1c75b8a1",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:astropy:first HDU with data is extension 1.\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Loading: Images\n",
+      "INFO: first HDU with data is extension 1. [astropy.nddata.ccddata]\n",
+      "Loading: 2D Spectra C sources\n",
+      "Loading: 2D Spectra R sources\n",
+      "Loading: 1D Spectra C sources\n",
+      "Loading: 1D Spectra R sources\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "auto_link false\n",
+      "Populating table\n",
+      "auto_link false\n",
+      "Done\n"
+     ]
+    }
+   ],
    "source": [
     "mosviz.load_niriss_data(data_dir)"
    ]

From 7939d2c240723443ce0c68e82cecf2e36a9589f8 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Fri, 27 Aug 2021 14:59:55 -0400
Subject: [PATCH 14/21] Clean up notebooks

---
 jdaviz/app.py                            |   3 +-
 jdaviz/configs/mosviz/plugins/parsers.py |   4 +-
 notebooks/MosvizNIRISSExample.ipynb      | 131 ++---------------------
 3 files changed, 9 insertions(+), 129 deletions(-)

diff --git a/jdaviz/app.py b/jdaviz/app.py
index 27e1929bf9..4f894727ca 100644
--- a/jdaviz/app.py
+++ b/jdaviz/app.py
@@ -252,9 +252,8 @@ def _link_new_data(self):
         # Allow for batch linking of data in the parser rather than on
         # data load
         if not self.auto_link:
-            print("auto_link false")
             return
-        print("auto_link true")
+
         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
diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index eec1209624..b4cabdf3d4 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -90,7 +90,7 @@ def _fields_from_ecsv(fname, fields, delimiter=","):
 
 
 @data_parser_registry("mosviz-link-data")
-def link_data_in_table(app, data_obj=None, data_labels=None):
+def link_data_in_table(app, data_obj=None):
     """
     Batch links data in the mosviz table viewer.
 
@@ -101,8 +101,6 @@ def link_data_in_table(app, data_obj=None, data_labels=None):
     data_obj : None
         Passed in in order to use the data_parser_registry, otherwise
         not used.
-    data_labels : None
-        Not used.
     """
     mos_data = app.session.data_collection['MOS Table']
     wc_spec_ids = []
diff --git a/notebooks/MosvizNIRISSExample.ipynb b/notebooks/MosvizNIRISSExample.ipynb
index 69d8d08398..badf20160d 100644
--- a/notebooks/MosvizNIRISSExample.ipynb
+++ b/notebooks/MosvizNIRISSExample.ipynb
@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "869727c8",
    "metadata": {},
    "outputs": [],
@@ -37,27 +37,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "f2233e63",
    "metadata": {
     "scrolled": false
    },
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "afc0762f0c224cb0bbdc660a0506d6c2",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Application(components={'g-viewer-tab': '<template>\\n  <component :is=\"stack.container\">\\n    <g-viewer-tab\\n …"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "from jdaviz.configs.mosviz.helper import MosViz as Mosviz\n",
     "\n",
@@ -67,7 +52,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "75d0e918",
    "metadata": {},
    "outputs": [],
@@ -92,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "2ac93c58",
    "metadata": {},
    "outputs": [],
@@ -124,112 +109,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "1c75b8a1",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "INFO:astropy:first HDU with data is extension 1.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Loading: Images\n",
-      "INFO: first HDU with data is extension 1. [astropy.nddata.ccddata]\n",
-      "Loading: 2D Spectra C sources\n",
-      "Loading: 2D Spectra R sources\n",
-      "Loading: 1D Spectra C sources\n",
-      "Loading: 1D Spectra R sources\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "auto_link false\n",
-      "Populating table\n",
-      "auto_link false\n",
-      "Done\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "mosviz.load_niriss_data(data_dir)"
    ]

From 60ce746c5320ed8e7ca310cd3dbb6f0a99977ff8 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Mon, 30 Aug 2021 09:31:31 -0400
Subject: [PATCH 15/21] Add comments

---
 jdaviz/configs/mosviz/helper.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/jdaviz/configs/mosviz/helper.py b/jdaviz/configs/mosviz/helper.py
index 9347684b5d..bb184d2152 100644
--- a/jdaviz/configs/mosviz/helper.py
+++ b/jdaviz/configs/mosviz/helper.py
@@ -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.
         """
+        # Link data after everything is loaded
         self.app.auto_link = False
 
         # If we have a single image for multiple spectra, tell the table viewer
@@ -148,6 +149,8 @@ def load_data(self, spectra_1d, spectra_2d, images=None, spectra_1d_label=None,
         self.load_1d_spectra(spectra_1d, spectra_1d_label)
         self.link_table_data(None)
 
+        # Any subsequently added data will automatically be linked
+        # with data already loaded in the app
         self.app.auto_link = True
 
     def link_table_data(self, data_obj):

From dbafddf79b50b083b7182209fe35390936b41040 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Tue, 31 Aug 2021 13:29:10 -0400
Subject: [PATCH 16/21] Fix codestyle checks

---
 jdaviz/configs/mosviz/helper.py          | 4 ++--
 jdaviz/configs/mosviz/plugins/parsers.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/jdaviz/configs/mosviz/helper.py b/jdaviz/configs/mosviz/helper.py
index fc325b550e..ecc70b3c2b 100644
--- a/jdaviz/configs/mosviz/helper.py
+++ b/jdaviz/configs/mosviz/helper.py
@@ -182,13 +182,13 @@ def load_data(self, spectra_1d=None, spectra_2d=None, images=None,
             logging.warning(msg)
             msg = SnackbarMessage(msg, color='warning', sender=self)
             self.app.hub.broadcast(msg)
-            
+
         self.link_table_data(None)
 
         # Any subsequently added data will automatically be linked
         # with data already loaded in the app
         self.app.auto_link = True
-        
+
     def link_table_data(self, data_obj):
         """
         Batch link data in the Mosviz table rather than doing it on
diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index f074efb2e9..ce0195ff9a 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -125,7 +125,7 @@ def link_data_in_table(app, data_obj=None):
 
     app.session.data_collection.add_link(wc_spec_ids)
 
-    
+
 @data_parser_registry("mosviz-nirspec-directory-parser")
 def mos_nirspec_directory_parser(app, data_obj, data_labels=None):
 

From 8486e8230bd8e2cd311e22e5746385fb7b287088 Mon Sep 17 00:00:00 2001
From: Jesse Averbukh <javerbukh@gmail.com>
Date: Tue, 31 Aug 2021 14:36:17 -0400
Subject: [PATCH 17/21] Remove reference to auto_link from app calls

---
 jdaviz/core/helpers.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index ea5ec07121..b45280d21e 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -31,9 +31,9 @@ class ConfigHelper(HubListener):
     """
     _default_configuration = 'default'
 
-    def __init__(self, app=None, auto_link=True):
+    def __init__(self, app=None):
         if app is None:
-            self.app = Application(configuration=self._default_configuration, auto_link=auto_link)
+            self.app = Application(configuration=self._default_configuration)
         else:
             self.app = app
 

From 7e2369e5f23712058a289de1a14114c2ea978f55 Mon Sep 17 00:00:00 2001
From: ojustino <ojustino@users.noreply.github.com>
Date: Tue, 31 Aug 2021 14:50:04 -0400
Subject: [PATCH 18/21] Removed auto_link reference from notebook

---
 notebooks/MosvizExample.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/notebooks/MosvizExample.ipynb b/notebooks/MosvizExample.ipynb
index 061991770f..90c0b8d27e 100644
--- a/notebooks/MosvizExample.ipynb
+++ b/notebooks/MosvizExample.ipynb
@@ -28,7 +28,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next, start Mosviz. Set the `auto_link` argument to `False` to speed up its data loading process. (We'll encounter that later.)"
+    "Next, start Mosviz."
    ]
   },
   {

From 8084945c6af66d910503ffe363fa2b95dffceb86 Mon Sep 17 00:00:00 2001
From: "P. L. Lim" <2090236+pllim@users.noreply.github.com>
Date: Thu, 2 Sep 2021 08:53:24 -0400
Subject: [PATCH 19/21] Fix PEP 8

---
 jdaviz/configs/mosviz/helper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jdaviz/configs/mosviz/helper.py b/jdaviz/configs/mosviz/helper.py
index 7549eaf740..87feb9e30f 100644
--- a/jdaviz/configs/mosviz/helper.py
+++ b/jdaviz/configs/mosviz/helper.py
@@ -265,7 +265,7 @@ def load_data(self, spectra_1d=None, spectra_2d=None, images=None,
         # Any subsequently added data will automatically be linked
         # with data already loaded in the app
         self.app.auto_link = True
-        
+
         # Load the first object into the viewers automatically
         self.app.get_viewer("table-viewer").figure_widget.highlighted = 0
 

From 6d25c70837aff7d017a342c42cfbcce085be4b59 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <39831871+rosteen@users.noreply.github.com>
Date: Tue, 7 Sep 2021 14:41:37 -0400
Subject: [PATCH 20/21] Update jdaviz/configs/mosviz/plugins/parsers.py

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>
---
 jdaviz/configs/mosviz/plugins/parsers.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index 51b87b15b7..780cd560ed 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -141,7 +141,6 @@ def link_data_in_table(app, data_obj=None):
         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

From 592b3f6787fdaeee98a54286346c346b58bdb68a Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <39831871+rosteen@users.noreply.github.com>
Date: Tue, 7 Sep 2021 14:42:02 -0400
Subject: [PATCH 21/21] Update jdaviz/configs/mosviz/plugins/parsers.py

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>
---
 jdaviz/configs/mosviz/plugins/parsers.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index 780cd560ed..695dbaaa05 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -144,8 +144,6 @@ def link_data_in_table(app, data_obj=None):
 
             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]))