From d6745a58dda4fc6f42ada9fd4dd3d45a5177b2e5 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Fri, 18 Oct 2024 09:04:10 -0400
Subject: [PATCH 01/16] Add ability to load 2D flux arrays in Specviz by
 splitting into separate spectra

---
 jdaviz/configs/specviz/plugins/parsers.py | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index 51fbfc1ee6..1947b0370f 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -56,8 +56,24 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
         raise TypeError("SpectrumCollection detected."
                         " Please provide a Spectrum1D or SpectrumList")
     elif isinstance(data, Spectrum1D):
-        data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
-        data = [data]
+        # Handle the possibility of 2D spectra by splitting into separate spectra
+        if data.flux.ndim == 1:
+            data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
+            data = [data]
+        elif data.flux.ndim == 2:
+            temp_data = []
+            data_label = []
+            for i in range(data.flux.shape[0]):
+                unc = None
+                mask = None
+                if data.uncertainty is not None:
+                    unc = data.uncertainty[i, :]
+                if mask is not None:
+                    mask = data.mask[i, :]
+                temp_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
+                                            uncertainty=unc))
+                data_label.append(f'{app.return_data_label(data_label, alt_name="specviz_data")}[{i}]')  # noqa
+            data = temp_data
     # No special processing is needed in this case, but we include it for completeness
     elif isinstance(data, SpectrumList):
         pass

From ccc30fac37605723e0b756bd91dbf11789d1055a Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Fri, 18 Oct 2024 09:09:47 -0400
Subject: [PATCH 02/16] Changelog

---
 CHANGES.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGES.rst b/CHANGES.rst
index 732515e20b..e67d19118e 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -15,6 +15,7 @@ Mosviz
 
 Specviz
 ^^^^^^^
+- Specviz parser will now split a spectrum with a 2D flux array into multiple spectra on load. [#3229]
 
 Specviz2d
 ^^^^^^^^^

From 91242019e11a5c9d5c2b9430c4b28841f66ca22d Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Fri, 18 Oct 2024 09:40:53 -0400
Subject: [PATCH 03/16] Handle this in file load case

---
 jdaviz/configs/specviz/plugins/parsers.py | 39 ++++++++++++++---------
 1 file changed, 24 insertions(+), 15 deletions(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index 1947b0370f..04a30c68ab 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -61,19 +61,7 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
             data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
             data = [data]
         elif data.flux.ndim == 2:
-            temp_data = []
-            data_label = []
-            for i in range(data.flux.shape[0]):
-                unc = None
-                mask = None
-                if data.uncertainty is not None:
-                    unc = data.uncertainty[i, :]
-                if mask is not None:
-                    mask = data.mask[i, :]
-                temp_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
-                                            uncertainty=unc))
-                data_label.append(f'{app.return_data_label(data_label, alt_name="specviz_data")}[{i}]')  # noqa
-            data = temp_data
+            data, data_label = _split_spectrum_with_2D_flux_array(data)
     # No special processing is needed in this case, but we include it for completeness
     elif isinstance(data, SpectrumList):
         pass
@@ -95,8 +83,12 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
 
         if path.is_file():
             try:
-                data = [Spectrum1D.read(str(path), format=format)]
-                data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
+                data = Spectrum1D.read(str(path), format=format)
+                if data.flux.ndim == 2:
+                    data, data_label = split_spectrum_with_2D_flux_array(data)
+                else:
+                    data = [data]
+                    data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
 
             except IORegistryError:
                 # Multi-extension files may throw a registry error
@@ -262,3 +254,20 @@ def combine_lists_to_1d_spectrum(wl, fnu, dfnu, wave_units, flux_units):
     spec = Spectrum1D(flux=fnuall * flux_units, spectral_axis=wlall * wave_units,
                       uncertainty=unc)
     return spec
+
+
+def split_spectrum_with_2D_flux_array(data):
+    temp_data = []
+    data_label = []
+    for i in range(data.flux.shape[0]):
+        unc = None
+        mask = None
+        if data.uncertainty is not None:
+            unc = data.uncertainty[i, :]
+        if mask is not None:
+            mask = data.mask[i, :]
+        temp_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
+                                    uncertainty=unc))
+        data_label.append(f'{app.return_data_label(data_label, alt_name="specviz_data")}[{i}]')  # noqa
+
+    return temp_data, data_label

From aa0cb56233e292e6f003d78b6e831f48b087d0c4 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Fri, 18 Oct 2024 09:44:17 -0400
Subject: [PATCH 04/16] Fix typo

---
 jdaviz/configs/specviz/plugins/parsers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index 04a30c68ab..ddc665d9b1 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -61,7 +61,7 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
             data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
             data = [data]
         elif data.flux.ndim == 2:
-            data, data_label = _split_spectrum_with_2D_flux_array(data)
+            data, data_label = split_spectrum_with_2D_flux_array(data)
     # No special processing is needed in this case, but we include it for completeness
     elif isinstance(data, SpectrumList):
         pass

From 180467a9fd4c4de6d15ab8ca7771e950b50e5534 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Fri, 18 Oct 2024 10:10:25 -0400
Subject: [PATCH 05/16] Add test and debug

---
 jdaviz/configs/specviz/plugins/parsers.py   | 12 ++++++------
 jdaviz/configs/specviz/tests/test_helper.py |  9 +++++++++
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index ddc665d9b1..165bc19dd1 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -61,7 +61,7 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
             data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
             data = [data]
         elif data.flux.ndim == 2:
-            data, data_label = split_spectrum_with_2D_flux_array(data)
+            data, data_label = split_spectrum_with_2D_flux_array(data, data_label, app)
     # No special processing is needed in this case, but we include it for completeness
     elif isinstance(data, SpectrumList):
         pass
@@ -85,7 +85,7 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
             try:
                 data = Spectrum1D.read(str(path), format=format)
                 if data.flux.ndim == 2:
-                    data, data_label = split_spectrum_with_2D_flux_array(data)
+                    data, data_label = split_spectrum_with_2D_flux_array(data, data_label, app)
                 else:
                     data = [data]
                     data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
@@ -256,9 +256,9 @@ def combine_lists_to_1d_spectrum(wl, fnu, dfnu, wave_units, flux_units):
     return spec
 
 
-def split_spectrum_with_2D_flux_array(data):
+def split_spectrum_with_2D_flux_array(data, data_label, app):
     temp_data = []
-    data_label = []
+    temp_data_label = []
     for i in range(data.flux.shape[0]):
         unc = None
         mask = None
@@ -268,6 +268,6 @@ def split_spectrum_with_2D_flux_array(data):
             mask = data.mask[i, :]
         temp_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
                                     uncertainty=unc))
-        data_label.append(f'{app.return_data_label(data_label, alt_name="specviz_data")}[{i}]')  # noqa
+        temp_data_label.append(f'{app.return_data_label(data_label, alt_name="specviz_data")}[{i}]')  # noqa
 
-    return temp_data, data_label
+    return temp_data, temp_data_label
diff --git a/jdaviz/configs/specviz/tests/test_helper.py b/jdaviz/configs/specviz/tests/test_helper.py
index 6ca8c67064..1a3d6b1dc4 100644
--- a/jdaviz/configs/specviz/tests/test_helper.py
+++ b/jdaviz/configs/specviz/tests/test_helper.py
@@ -405,6 +405,15 @@ def test_load_spectrum_list_directory_concat(tmpdir, specviz_helper):
     assert len(specviz_helper.app.data_collection) == 41
 
 
+def test_load_spectrum1d_2d_flux(specviz_helper):
+    spec = Spectrum1D(spectral_axis=np.linspace(4000,6000,100)*u.Angstrom,
+                        flux=np.ones((4,100))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
+    specviz_helper.load_data(spec, data_label="test")
+
+    assert len(specviz_helper.app.data_collection) == 4
+    assert specviz_helper.app.data_collection[0].label == "test[0]"
+
+
 def test_plot_uncertainties(specviz_helper, spectrum1d):
     specviz_helper.load_data(spectrum1d)
 

From 620c6ae5b25d5b8aee4314e03f0ab32f4dc380e3 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Fri, 18 Oct 2024 10:29:02 -0400
Subject: [PATCH 06/16] Codestyle again, whoops

---
 jdaviz/configs/specviz/tests/test_helper.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/jdaviz/configs/specviz/tests/test_helper.py b/jdaviz/configs/specviz/tests/test_helper.py
index 1a3d6b1dc4..9552fe1315 100644
--- a/jdaviz/configs/specviz/tests/test_helper.py
+++ b/jdaviz/configs/specviz/tests/test_helper.py
@@ -406,8 +406,8 @@ def test_load_spectrum_list_directory_concat(tmpdir, specviz_helper):
 
 
 def test_load_spectrum1d_2d_flux(specviz_helper):
-    spec = Spectrum1D(spectral_axis=np.linspace(4000,6000,100)*u.Angstrom,
-                        flux=np.ones((4,100))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
+    spec = Spectrum1D(spectral_axis=np.linspace(4000, 6000, 100)*u.Angstrom,
+                      flux=np.ones((4, 100))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
     specviz_helper.load_data(spec, data_label="test")
 
     assert len(specviz_helper.app.data_collection) == 4

From 4703b9ddeeed1cecf1afa15065cdf65cbfb8f0e9 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Fri, 18 Oct 2024 11:53:27 -0400
Subject: [PATCH 07/16] Add keyword to force Specviz parser to use
 SpectrumList.read

---
 jdaviz/configs/specviz/plugins/parsers.py | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index 165bc19dd1..10c9b2015b 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -18,7 +18,8 @@
 
 @data_parser_registry("specviz-spectrum1d-parser")
 def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_viewer=True,
-                              concat_by_file=False, cache=None, local_path=os.curdir, timeout=None):
+                              concat_by_file=False, cache=None, local_path=os.curdir, timeout=None,
+                              load_as_list=False):
     """
     Loads a data file or `~specutils.Spectrum1D` object into Specviz.
 
@@ -46,6 +47,9 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
         remote requests in seconds (passed to
         `~astropy.utils.data.download_file` or
         `~astroquery.mast.Conf.timeout`).
+    load_as_list : bool, optional
+        Force the parser to load the input file with the `~specutils.SpectrumList` read function
+        instead of `~specutils.Spectrum1D`.
     """
 
     spectrum_viewer_reference_name = app._jdaviz_helper._default_spectrum_viewer_reference_name
@@ -81,7 +85,12 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
 
         path = pathlib.Path(data)
 
-        if path.is_file():
+        if path.is_dir() or load_as_list:
+            data = SpectrumList.read(str(path), format=format)
+            if data == []:
+                raise ValueError(f"`specutils.SpectrumList.read('{str(path)}')` "
+                                 "returned an empty list")
+        elif path.is_file():
             try:
                 data = Spectrum1D.read(str(path), format=format)
                 if data.flux.ndim == 2:
@@ -93,11 +102,6 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
             except IORegistryError:
                 # Multi-extension files may throw a registry error
                 data = SpectrumList.read(str(path), format=format)
-        elif path.is_dir():
-            data = SpectrumList.read(str(path), format=format)
-            if data == []:
-                raise ValueError(f"`specutils.SpectrumList.read('{str(path)}')` "
-                                 "returned an empty list")
         else:
             raise FileNotFoundError("No such file: " + str(path))
 

From fd5dc1767dc2ba1ff8b9b36ae466d9788db6d45e Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Fri, 18 Oct 2024 13:49:10 -0400
Subject: [PATCH 08/16] Add new keyword to helper load_data

---
 jdaviz/configs/specviz/helper.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 7eefe9e212..c13ac67175 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -41,7 +41,8 @@ def __init__(self, *args, **kwargs):
                                handler=self._redshift_listener)
 
     def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
-                  concat_by_file=False, cache=None, local_path=None, timeout=None):
+                  concat_by_file=False, cache=None, local_path=None, timeout=None,
+                  load_as_list=False):
         """
         Load data into Specviz.
 
@@ -80,7 +81,8 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
                           concat_by_file=concat_by_file,
                           cache=cache,
                           local_path=local_path,
-                          timeout=timeout)
+                          timeout=timeout,
+                          load_as_list=load_as_list)
 
     def get_spectra(self, data_label=None, spectral_subset=None, apply_slider_redshift="Warn"):
         """Returns the current data loaded into the main viewer

From cec0bea021af58559910e3ad78d3da9cde85a9e3 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Tue, 22 Oct 2024 13:12:42 -0400
Subject: [PATCH 09/16] Implement suggestions from @rileythai

Co-authored-by: rileythai <rtha0022@student.monash.edu>
---
 jdaviz/configs/specviz/plugins/parsers.py | 41 +++++++++++++++++------
 1 file changed, 30 insertions(+), 11 deletions(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index 10c9b2015b..c4e7719946 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -79,9 +79,7 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
             data = SpectrumList.read(data, format=format)
     else:
         # try parsing file_obj as a URI/URL:
-        data = download_uri_to_path(
-            data, cache=cache, local_path=local_path, timeout=timeout
-        )
+        data = download_uri_to_path(data, cache=cache, local_path=local_path, timeout=timeout)
 
         path = pathlib.Path(data)
 
@@ -105,11 +103,21 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
         else:
             raise FileNotFoundError("No such file: " + str(path))
 
+    # step through SpectrumList and convert any 2D spectra to 1D spectra
     if isinstance(data, SpectrumList):
+        new_data = SpectrumList()
+        for spec in data:
+            if spec.flux.ndim == 2:
+                temp_data, _ = split_spectrum_with_2D_flux_array(spec)
+                new_data.extend(temp_data)
+            else:
+                new_data.append(spec)
+        data = new_data
+
         if not isinstance(data_label, (list, tuple)):
             temp_labels = []
             for i in range(len(data)):
-                temp_labels.append(f"{data_label} {i}")
+                temp_labels.append(f"{data_label} [{i}]")
             data_label = temp_labels
         elif len(data_label) != len(data):
             raise ValueError(f"Length of data labels list ({len(data_label)}) is different"
@@ -261,17 +269,28 @@ def combine_lists_to_1d_spectrum(wl, fnu, dfnu, wave_units, flux_units):
 
 
 def split_spectrum_with_2D_flux_array(data, data_label, app):
-    temp_data = []
-    temp_data_label = []
+    """
+    Helper function to split Spectrum1D of 2D flux to a SpectrumList of nD objects.
+    Parameters
+    ----------
+    data : `~specutils.Spectrum1D`
+        Spectrum with 2D flux array
+    Returns
+    -------
+    new_data : `~specutils.SpectrumList`
+        list of unpacked spectra
+    """
+    new_data = []
+    new_data_label = []
     for i in range(data.flux.shape[0]):
         unc = None
         mask = None
         if data.uncertainty is not None:
             unc = data.uncertainty[i, :]
-        if mask is not None:
+        if data.mask is not None:
             mask = data.mask[i, :]
-        temp_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
-                                    uncertainty=unc))
-        temp_data_label.append(f'{app.return_data_label(data_label, alt_name="specviz_data")}[{i}]')  # noqa
+        new_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
+                                   uncertainty=unc, mask=mask))
+        new_data_label.append(f'{app.return_data_label(data_label, alt_name="specviz_data")}[{i}]')  # noqa
 
-    return temp_data, temp_data_label
+    return new_data, new_data_label

From 505674ef6f31671f2f77c7b274d75841a73a7a41 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Tue, 22 Oct 2024 14:01:46 -0400
Subject: [PATCH 10/16] Add more test coverage, debug

---
 jdaviz/configs/specviz/plugins/parsers.py   | 29 +++++++++------------
 jdaviz/configs/specviz/tests/test_helper.py | 16 +++++++++---
 2 files changed, 25 insertions(+), 20 deletions(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index c4e7719946..a8e005d1ec 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -56,16 +56,18 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
     # If no data label is assigned, give it a unique name
     if not data_label:
         data_label = app.return_data_label(data, alt_name="specviz_data")
+
     if isinstance(data, SpectrumCollection):
         raise TypeError("SpectrumCollection detected."
                         " Please provide a Spectrum1D or SpectrumList")
     elif isinstance(data, Spectrum1D):
         # Handle the possibility of 2D spectra by splitting into separate spectra
         if data.flux.ndim == 1:
-            data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
+            data_label = [data_label]
             data = [data]
         elif data.flux.ndim == 2:
-            data, data_label = split_spectrum_with_2D_flux_array(data, data_label, app)
+            data = split_spectrum_with_2D_flux_array(data)
+            data_label = [f"{data_label} [{i}]" for i in range(len(data))]
     # No special processing is needed in this case, but we include it for completeness
     elif isinstance(data, SpectrumList):
         pass
@@ -73,7 +75,7 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
         # special processing for HDUList
         if isinstance(data, fits.HDUList):
             data = [Spectrum1D.read(data)]
-            data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
+            data_label = [data_label]
         else:
             # list treated as SpectrumList if not an HDUList
             data = SpectrumList.read(data, format=format)
@@ -92,7 +94,7 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
             try:
                 data = Spectrum1D.read(str(path), format=format)
                 if data.flux.ndim == 2:
-                    data, data_label = split_spectrum_with_2D_flux_array(data, data_label, app)
+                    data = split_spectrum_with_2D_flux_array(data)
                 else:
                     data = [data]
                     data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
@@ -108,17 +110,13 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
         new_data = SpectrumList()
         for spec in data:
             if spec.flux.ndim == 2:
-                temp_data, _ = split_spectrum_with_2D_flux_array(spec)
-                new_data.extend(temp_data)
+                new_data.extend(split_spectrum_with_2D_flux_array(spec))
             else:
                 new_data.append(spec)
-        data = new_data
+        data = SpectrumList(new_data)
 
         if not isinstance(data_label, (list, tuple)):
-            temp_labels = []
-            for i in range(len(data)):
-                temp_labels.append(f"{data_label} [{i}]")
-            data_label = temp_labels
+            data_label = [f"{data_label} [{i}]" for i in range(len(data))]
         elif len(data_label) != len(data):
             raise ValueError(f"Length of data labels list ({len(data_label)}) is different"
                              f" than length of list of data ({len(data)})")
@@ -141,7 +139,7 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
                 # if the concatenated list of uncertanties is all nan (meaning
                 # they were all nan to begin with, or all None), it will be set
                 # to None on the final Spectrum1D
-                if spec.uncertainty[wlind] is not None:
+                if spec.uncertainty is not None and spec.uncertainty[wlind] is not None:
                     dfnuallorig.append(spec.uncertainty[wlind].array)
                 else:
                     dfnuallorig.append(np.nan)
@@ -268,20 +266,20 @@ def combine_lists_to_1d_spectrum(wl, fnu, dfnu, wave_units, flux_units):
     return spec
 
 
-def split_spectrum_with_2D_flux_array(data, data_label, app):
+def split_spectrum_with_2D_flux_array(data):
     """
     Helper function to split Spectrum1D of 2D flux to a SpectrumList of nD objects.
     Parameters
     ----------
     data : `~specutils.Spectrum1D`
         Spectrum with 2D flux array
+
     Returns
     -------
     new_data : `~specutils.SpectrumList`
         list of unpacked spectra
     """
     new_data = []
-    new_data_label = []
     for i in range(data.flux.shape[0]):
         unc = None
         mask = None
@@ -291,6 +289,5 @@ def split_spectrum_with_2D_flux_array(data, data_label, app):
             mask = data.mask[i, :]
         new_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
                                    uncertainty=unc, mask=mask))
-        new_data_label.append(f'{app.return_data_label(data_label, alt_name="specviz_data")}[{i}]')  # noqa
 
-    return new_data, new_data_label
+    return new_data
\ No newline at end of file
diff --git a/jdaviz/configs/specviz/tests/test_helper.py b/jdaviz/configs/specviz/tests/test_helper.py
index 9552fe1315..228e263faa 100644
--- a/jdaviz/configs/specviz/tests/test_helper.py
+++ b/jdaviz/configs/specviz/tests/test_helper.py
@@ -405,14 +405,22 @@ def test_load_spectrum_list_directory_concat(tmpdir, specviz_helper):
     assert len(specviz_helper.app.data_collection) == 41
 
 
-def test_load_spectrum1d_2d_flux(specviz_helper):
-    spec = Spectrum1D(spectral_axis=np.linspace(4000, 6000, 100)*u.Angstrom,
-                      flux=np.ones((4, 100))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
+def test_load_2d_flux(specviz_helper):
+    spec = Spectrum1D(spectral_axis=np.linspace(4000, 6000, 10)*u.Angstrom,
+                      flux=np.ones((4, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
     specviz_helper.load_data(spec, data_label="test")
 
     assert len(specviz_helper.app.data_collection) == 4
-    assert specviz_helper.app.data_collection[0].label == "test[0]"
+    assert specviz_helper.app.data_collection[0].label == "test [0]"
 
+    spec2 = Spectrum1D(spectral_axis=np.linspace(4000, 6000, 10)*u.Angstrom,
+                      flux=np.ones((2, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
+
+    spec_list = SpectrumList([spec, spec2])
+    specviz_helper.load_data(spec_list, data_label="second test")
+
+    assert len(specviz_helper.app.data_collection) == 10
+    assert specviz_helper.app.data_collection[-1].label == "second test [5]"
 
 def test_plot_uncertainties(specviz_helper, spectrum1d):
     specviz_helper.load_data(spectrum1d)

From 2147377ea6c67f49b50345d1d94c74d1f84be5cd Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Tue, 22 Oct 2024 14:03:16 -0400
Subject: [PATCH 11/16] Codestyle

Codestyle
---
 jdaviz/configs/specviz/plugins/parsers.py   | 2 +-
 jdaviz/configs/specviz/tests/test_helper.py | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index a8e005d1ec..06aa04d8b0 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -290,4 +290,4 @@ def split_spectrum_with_2D_flux_array(data):
         new_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
                                    uncertainty=unc, mask=mask))
 
-    return new_data
\ No newline at end of file
+    return new_data
diff --git a/jdaviz/configs/specviz/tests/test_helper.py b/jdaviz/configs/specviz/tests/test_helper.py
index 228e263faa..ea4e25dd71 100644
--- a/jdaviz/configs/specviz/tests/test_helper.py
+++ b/jdaviz/configs/specviz/tests/test_helper.py
@@ -414,7 +414,7 @@ def test_load_2d_flux(specviz_helper):
     assert specviz_helper.app.data_collection[0].label == "test [0]"
 
     spec2 = Spectrum1D(spectral_axis=np.linspace(4000, 6000, 10)*u.Angstrom,
-                      flux=np.ones((2, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
+                       flux=np.ones((2, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
 
     spec_list = SpectrumList([spec, spec2])
     specviz_helper.load_data(spec_list, data_label="second test")
@@ -422,6 +422,7 @@ def test_load_2d_flux(specviz_helper):
     assert len(specviz_helper.app.data_collection) == 10
     assert specviz_helper.app.data_collection[-1].label == "second test [5]"
 
+
 def test_plot_uncertainties(specviz_helper, spectrum1d):
     specviz_helper.load_data(spectrum1d)
 

From 47a69b1b7e08438804dbd709b081328b6b607bf4 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Tue, 22 Oct 2024 14:18:07 -0400
Subject: [PATCH 12/16] Apparently need this to standardize the input label

---
 jdaviz/configs/specviz/plugins/parsers.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index 06aa04d8b0..1dce93e07c 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -56,6 +56,9 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
     # If no data label is assigned, give it a unique name
     if not data_label:
         data_label = app.return_data_label(data, alt_name="specviz_data")
+    else:
+        # Still need to standardize the label
+        data_label = app.return_data_label(data_label, alt_name="specviz_data")
 
     if isinstance(data, SpectrumCollection):
         raise TypeError("SpectrumCollection detected."

From 44dcb6d60f916759d9b87d8d3db6a1b376ad45ab Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Tue, 22 Oct 2024 15:41:39 -0400
Subject: [PATCH 13/16] One more label handling fix

---
 jdaviz/configs/specviz/plugins/parsers.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index 1dce93e07c..8180e38aa3 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -56,8 +56,10 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
     # If no data label is assigned, give it a unique name
     if not data_label:
         data_label = app.return_data_label(data, alt_name="specviz_data")
+    # Still need to standardize the label
+    elif isinstance(data_label, (list, tuple)):
+        data_label = [app.return_data_label(label, alt_name="specviz_data") for label in data_label]  # noqa
     else:
-        # Still need to standardize the label
         data_label = app.return_data_label(data_label, alt_name="specviz_data")
 
     if isinstance(data, SpectrumCollection):

From fbba848c557bb0ad5fa54736eabc0cf915db03f7 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <39831871+rosteen@users.noreply.github.com>
Date: Thu, 24 Oct 2024 11:40:26 -0400
Subject: [PATCH 14/16] Apply suggestions from code review

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

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index 8180e38aa3..128d9f595f 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -118,7 +118,6 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
                 new_data.extend(split_spectrum_with_2D_flux_array(spec))
             else:
                 new_data.append(spec)
-        data = SpectrumList(new_data)
 
         if not isinstance(data_label, (list, tuple)):
             data_label = [f"{data_label} [{i}]" for i in range(len(data))]
@@ -274,6 +273,7 @@ def combine_lists_to_1d_spectrum(wl, fnu, dfnu, wave_units, flux_units):
 def split_spectrum_with_2D_flux_array(data):
     """
     Helper function to split Spectrum1D of 2D flux to a SpectrumList of nD objects.
+
     Parameters
     ----------
     data : `~specutils.Spectrum1D`
@@ -282,7 +282,7 @@ def split_spectrum_with_2D_flux_array(data):
     Returns
     -------
     new_data : `~specutils.SpectrumList`
-        list of unpacked spectra
+        List of unpacked spectra.
     """
     new_data = []
     for i in range(data.flux.shape[0]):

From 8680144e6a1f5c59061d3faf4ecb06bb053f36d5 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Thu, 24 Oct 2024 12:34:32 -0400
Subject: [PATCH 15/16] Add clarity to test and changelog

---
 CHANGES.rst                                 | 3 ++-
 jdaviz/configs/specviz/tests/test_helper.py | 3 +++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGES.rst b/CHANGES.rst
index e67d19118e..b06628a43b 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -15,7 +15,8 @@ Mosviz
 
 Specviz
 ^^^^^^^
-- Specviz parser will now split a spectrum with a 2D flux array into multiple spectra on load. [#3229]
+- Specviz parser will now split a spectrum with a 2D flux array into multiple spectra on load
+  (useful for certain SDSS file types). [#3229]
 
 Specviz2d
 ^^^^^^^^^
diff --git a/jdaviz/configs/specviz/tests/test_helper.py b/jdaviz/configs/specviz/tests/test_helper.py
index ea4e25dd71..8e87125071 100644
--- a/jdaviz/configs/specviz/tests/test_helper.py
+++ b/jdaviz/configs/specviz/tests/test_helper.py
@@ -406,6 +406,8 @@ def test_load_spectrum_list_directory_concat(tmpdir, specviz_helper):
 
 
 def test_load_2d_flux(specviz_helper):
+    # Test loading a spectrum with a 2D flux, which should be split into separate
+    # 1D Spectrum1D objects to load in Specviz.
     spec = Spectrum1D(spectral_axis=np.linspace(4000, 6000, 10)*u.Angstrom,
                       flux=np.ones((4, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
     specviz_helper.load_data(spec, data_label="test")
@@ -416,6 +418,7 @@ def test_load_2d_flux(specviz_helper):
     spec2 = Spectrum1D(spectral_axis=np.linspace(4000, 6000, 10)*u.Angstrom,
                        flux=np.ones((2, 10))*u.Unit("1e-17 erg / (Angstrom cm2 s)"))
 
+    # Make sure 2D spectra in a SpectrumList also get split properly.
     spec_list = SpectrumList([spec, spec2])
     specviz_helper.load_data(spec_list, data_label="second test")
 

From f5e2f290a31089725f3cd3d7c3fd968655044824 Mon Sep 17 00:00:00 2001
From: Ricky O'Steen <rosteen@stsci.edu>
Date: Thu, 24 Oct 2024 13:20:45 -0400
Subject: [PATCH 16/16] Add meta, debug

---
 jdaviz/configs/specviz/plugins/parsers.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/jdaviz/configs/specviz/plugins/parsers.py b/jdaviz/configs/specviz/plugins/parsers.py
index 128d9f595f..8af49c2bc3 100644
--- a/jdaviz/configs/specviz/plugins/parsers.py
+++ b/jdaviz/configs/specviz/plugins/parsers.py
@@ -112,12 +112,13 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
 
     # step through SpectrumList and convert any 2D spectra to 1D spectra
     if isinstance(data, SpectrumList):
-        new_data = SpectrumList()
+        new_data = []
         for spec in data:
             if spec.flux.ndim == 2:
                 new_data.extend(split_spectrum_with_2D_flux_array(spec))
             else:
                 new_data.append(spec)
+        data = SpectrumList(new_data)
 
         if not isinstance(data_label, (list, tuple)):
             data_label = [f"{data_label} [{i}]" for i in range(len(data))]
@@ -293,6 +294,6 @@ def split_spectrum_with_2D_flux_array(data):
         if data.mask is not None:
             mask = data.mask[i, :]
         new_data.append(Spectrum1D(flux=data.flux[i, :], spectral_axis=data.spectral_axis,
-                                   uncertainty=unc, mask=mask))
+                                   uncertainty=unc, mask=mask, meta=data.meta))
 
     return new_data