From 9f6d11c6d759bc0787dee60b2de8b8292ffebd1e Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 16 Jan 2025 14:41:21 -0500
Subject: [PATCH 01/14] remove unused specviz2d parser

* 2d->1d spectra have been handled by the spectral extraction plugin for a while and logic no longer goes through here
---
 jdaviz/configs/specviz2d/plugins/__init__.py |  1 -
 jdaviz/configs/specviz2d/plugins/parsers.py  | 76 --------------------
 2 files changed, 77 deletions(-)
 delete mode 100644 jdaviz/configs/specviz2d/plugins/parsers.py

diff --git a/jdaviz/configs/specviz2d/plugins/__init__.py b/jdaviz/configs/specviz2d/plugins/__init__.py
index 76a3e76214..389f6386e0 100644
--- a/jdaviz/configs/specviz2d/plugins/__init__.py
+++ b/jdaviz/configs/specviz2d/plugins/__init__.py
@@ -1,2 +1 @@
-from .parsers import *  # noqa
 from .spectral_extraction.spectral_extraction import * # noqa
diff --git a/jdaviz/configs/specviz2d/plugins/parsers.py b/jdaviz/configs/specviz2d/plugins/parsers.py
deleted file mode 100644
index 199e0fd622..0000000000
--- a/jdaviz/configs/specviz2d/plugins/parsers.py
+++ /dev/null
@@ -1,76 +0,0 @@
-from pathlib import Path
-
-from specutils import Spectrum1D
-from astropy.io import fits
-import astropy.units as u
-import numpy as np
-
-from jdaviz.core.registries import data_parser_registry
-from jdaviz.utils import standardize_metadata, PRIHDR_KEY
-
-__all__ = ['spec2d_1d_parser']
-
-
-def _check_is_file(path):
-    return isinstance(path, str) and Path(path).is_file()
-
-
-@data_parser_registry("spec2d-1d-parser")
-def spec2d_1d_parser(app, data_obj, data_label=None, show_in_viewer=True):
-    """
-    Generate a quicklook 1D spectrum from an input 2D spectrum by summing
-    over the cross-dispersion axis.
-
-    Notes
-    -----
-    This currently only works with JWST-type data in which the data is in the
-    second hdu of the fits file.
-
-    Parameters
-    ----------
-    app : `~jdaviz.app.Application`
-        The application-level object used to reference the viewers.
-    data_obj : str or list or spectrum-like
-        File path, list, or spectrum-like object to be read as a new row in
-        the mosviz table.
-    data_labels : str, optional
-        The label applied to the glue data component.
-    """
-    if _check_is_file(data_obj):
-        with fits.open(data_obj) as hdulist:
-            data = hdulist[1].data
-            header = hdulist[1].header
-            prihdr = hdulist[0].header
-
-        # Should only be 2D, so DISPAXIS-1 should be 0 or -1 and sum over the
-        # correct axis. If Unit doesn't understand the BUNIT we leave flux
-        # unitless
-        try:
-            flux = np.sum(data, header['DISPAXIS']-1)*u.Unit(header["BUNIT"])
-        except ValueError:
-            flux = u.Quantity(np.sum(data, header['DISPAXIS']-1))
-
-        if "WAVEND" in header and "WAVSTART" in header:
-            step = (header["WAVEND"] - header["WAVSTART"]) / flux.size
-            spectral_axis = np.arange(header["WAVSTART"], header["WAVEND"],
-                                      step) * u.m
-        else:
-            # u.Unit("m") is used if WAVEND and WAVSTART are present so
-            # we use it here as well, even though the actual unit is pixels
-            spectral_axis = np.arange(1, flux.size + 1, 1) * u.m
-
-        metadata = standardize_metadata(header)
-        metadata[PRIHDR_KEY] = standardize_metadata(prihdr)
-
-        data_obj = Spectrum1D(flux, spectral_axis=spectral_axis, meta=metadata)
-
-        data_label = app.return_data_label(data_label, alt_name="specviz2d_data")
-        app.data_collection[data_label] = data_obj
-
-    else:
-        raise NotImplementedError("Spectrum2d parser only takes a filename")
-
-    if show_in_viewer:
-        app.add_data_to_viewer(
-            app._default_spectrum_viewer_reference_name, data_label
-        )

From a2082f35cd3948ea6eb696d3ebe519e6079c8a70 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Tue, 21 Jan 2025 10:19:59 -0500
Subject: [PATCH 02/14] use existing data_format detection logic

---
 jdaviz/configs/mosviz/plugins/parsers.py |  8 ++++----
 jdaviz/configs/specviz/helper.py         | 23 +++++++++++++++--------
 jdaviz/core/data_formats.py              |  9 ++++++---
 3 files changed, 25 insertions(+), 15 deletions(-)

diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index 31579799ac..689044f1bc 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -301,10 +301,10 @@ def mos_spec2d_parser(app, data_obj, data_labels=None, add_to_table=True,
 
     """
     spectrum_2d_viewer_reference_name = (
-        app._jdaviz_helper._default_spectrum_2d_viewer_reference_name
+        getattr(app._jdaviz_helper, "_default_spectrum_2d_viewer_reference_name", None)
     )
     table_viewer_reference_name = (
-        app._jdaviz_helper._default_table_viewer_reference_name
+        getattr(app._jdaviz_helper, "_default_table_viewer_reference_name", None)
     )
 
     # Note: This is also used by Specviz2D
@@ -388,13 +388,13 @@ def _parse_as_spectrum1d(hdulist, ext, transpose):
             label = data_labels[index]
             app.data_collection[label] = data
 
-        if add_to_table:
+        if add_to_table and table_viewer_reference_name is not None:
             _add_to_table(
                 app, data_labels, '2D Spectra',
                 table_viewer_reference_name=table_viewer_reference_name
             )
 
-    if show_in_viewer:
+    if show_in_viewer and spectrum_2d_viewer_reference_name is not None:
         if len(data_labels) > 1:
             raise ValueError("More than one data label provided, unclear " +
                              "which to show in viewer")
diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 066456198b..7f123ea803 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -74,16 +74,23 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
             `~astropy.utils.data.download_file` or
             `~astroquery.mast.Conf.timeout`).
         """
+        from jdaviz.core import data_formats
+        format, conf = data_formats.get_valid_format(data)
+        parsers = {'specviz': 'specviz-spectrum1d-parser', 'specviz2d': 'mosviz-spec2d-parser'}
+        parser_kwargs = {'mosviz-spec2d-parser': {},
+                         'specviz-spectrum1d-parser': {'format': format,
+                                                       'show_in_viewer': show_in_viewer,
+                                                       'concat_by_file': concat_by_file,
+                                                       'cache': cache,
+                                                       'local_path': local_path,
+                                                       'timeout': timeout,
+                                                       'load_as_list': load_as_list}}
+        parser = parsers.get(conf)
+        kwargs = parser_kwargs.get(parser, {})
         super().load_data(data,
-                          parser_reference='specviz-spectrum1d-parser',
+                          parser_reference=parser,
                           data_label=data_label,
-                          format=format,
-                          show_in_viewer=show_in_viewer,
-                          concat_by_file=concat_by_file,
-                          cache=cache,
-                          local_path=local_path,
-                          timeout=timeout,
-                          load_as_list=load_as_list)
+                          **kwargs)
 
     def get_spectra(self, data_label=None, spectral_subset=None, apply_slider_redshift="Warn"):
         """Returns the current data loaded into the main viewer
diff --git a/jdaviz/core/data_formats.py b/jdaviz/core/data_formats.py
index 32f464f704..88ceff8741 100644
--- a/jdaviz/core/data_formats.py
+++ b/jdaviz/core/data_formats.py
@@ -75,9 +75,12 @@ def get_valid_format(filename):
     config : str
         The recommended application configuration
     """
-
-    valid_file_format = identify_spectrum_format(filename, SpectrumList)
-    ndim = guess_dimensionality(filename)
+    if isinstance(filename, (str, pathlib.Path)):
+        valid_file_format = identify_spectrum_format(filename, SpectrumList)
+        ndim = guess_dimensionality(filename)
+    elif isinstance(filename, (Spectrum1D)):
+        valid_file_format = None
+        ndim = filename.flux.ndim
 
     if valid_file_format:
         recommended_config = file_to_config_mapping.get(valid_file_format, 'default')

From fb23045235eb6838c713e30647cdd032d3da6400 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Tue, 21 Jan 2025 11:36:07 -0500
Subject: [PATCH 03/14] add custom parser for specreduce trace objects

---
 jdaviz/configs/mosviz/plugins/parsers.py | 30 +++++++++++++++++++++++-
 jdaviz/configs/specviz/helper.py         |  6 ++---
 jdaviz/core/data_formats.py              | 22 +++++++++++++++++
 3 files changed, 54 insertions(+), 4 deletions(-)

diff --git a/jdaviz/configs/mosviz/plugins/parsers.py b/jdaviz/configs/mosviz/plugins/parsers.py
index 689044f1bc..59893a3657 100644
--- a/jdaviz/configs/mosviz/plugins/parsers.py
+++ b/jdaviz/configs/mosviz/plugins/parsers.py
@@ -18,7 +18,7 @@
 from jdaviz.core.events import SnackbarMessage
 from jdaviz.utils import standardize_metadata, PRIHDR_KEY, download_uri_to_path
 
-__all__ = ['mos_spec1d_parser', 'mos_spec2d_parser', 'mos_image_parser']
+__all__ = ['mos_spec1d_parser', 'mos_spec2d_parser', 'mos_image_parser', 'specreduce_trace_parser']
 
 FALLBACK_NAME = "Unspecified"
 EXPECTED_FILES = {"niriss": ['1D Spectra C', '1D Spectra R',
@@ -403,6 +403,34 @@ def _parse_as_spectrum1d(hdulist, ext, transpose):
     return len(data_obj)
 
 
+@data_parser_registry("specreduce-trace")
+def specreduce_trace_parser(app, data_obj, data_label=None, show_in_viewer=False):
+    """
+    Loads a specreduce trace object.
+
+    Parameters
+    ----------
+    app : `~jdaviz.app.Application`
+        The application-level object used to reference the viewers.
+    data_obj : str or list or spectrum-like
+        File path, list, or spectrum-like object to be read as a new row in
+        the mosviz table.
+    data_label : str, optional
+        The label applied to the glue data component.
+    show_in_viewer : bool
+        Show data in viewer(s).
+    """
+    spectrum_2d_viewer_reference_name = (
+        getattr(app._jdaviz_helper, "_default_spectrum_2d_viewer_reference_name", None)
+    )
+
+    app.add_data(data_obj, data_label=data_label)
+    if show_in_viewer and spectrum_2d_viewer_reference_name:
+        app.add_data_to_viewer(
+            spectrum_2d_viewer_reference_name, data_label
+        )
+
+
 def _load_fits_image_from_filename(filename, app):
     with fits.open(filename) as hdulist:
         # We do not use the generated labels
diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 7f123ea803..c9ffa8d51f 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -75,9 +75,10 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
             `~astroquery.mast.Conf.timeout`).
         """
         from jdaviz.core import data_formats
-        format, conf = data_formats.get_valid_format(data)
-        parsers = {'specviz': 'specviz-spectrum1d-parser', 'specviz2d': 'mosviz-spec2d-parser'}
+        parser = data_formats.get_parser(data)
+
         parser_kwargs = {'mosviz-spec2d-parser': {},
+                         'specreduce-trace': {'show_in_viewer': show_in_viewer},
                          'specviz-spectrum1d-parser': {'format': format,
                                                        'show_in_viewer': show_in_viewer,
                                                        'concat_by_file': concat_by_file,
@@ -85,7 +86,6 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
                                                        'local_path': local_path,
                                                        'timeout': timeout,
                                                        'load_as_list': load_as_list}}
-        parser = parsers.get(conf)
         kwargs = parser_kwargs.get(parser, {})
         super().load_data(data,
                           parser_reference=parser,
diff --git a/jdaviz/core/data_formats.py b/jdaviz/core/data_formats.py
index 88ceff8741..8f19ce64f2 100644
--- a/jdaviz/core/data_formats.py
+++ b/jdaviz/core/data_formats.py
@@ -8,6 +8,7 @@
 
 from specutils.io.registers import identify_spectrum_format
 from specutils import Spectrum1D, SpectrumList, SpectrumCollection
+from specreduce.tracing import Trace
 from stdatamodels import asdf_in_fits
 
 from jdaviz.core.config import list_configurations
@@ -90,6 +91,27 @@ def get_valid_format(filename):
     return valid_file_format, recommended_config
 
 
+def get_parser(obj):
+    """
+    Identify the data parser from a filename or data object
+
+    Parameters
+    ----------
+    obj : str or `pathlib.Path` or file-like object
+        The filename of the loaded data
+
+    Returns
+    -------
+    parser : str
+        The parser for the data object
+    """
+    if isinstance(obj, Trace):
+        return 'specreduce-trace'
+    _, config = get_valid_format(obj)
+    parsers = {'specviz': 'specviz-spectrum1d-parser', 'specviz2d': 'mosviz-spec2d-parser'}
+    return parsers.get(config)
+
+
 def identify_data(filename, current=None):
     """Identify the data format and application configuration from a filename.
 

From b2ed1ed5221e042577058d89eebb9fae5d85f331 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Tue, 21 Jan 2025 12:46:56 -0500
Subject: [PATCH 04/14] pass data_labels for mosviz parser

---
 jdaviz/configs/specviz/helper.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index c9ffa8d51f..12b2c8986f 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -77,19 +77,21 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
         from jdaviz.core import data_formats
         parser = data_formats.get_parser(data)
 
-        parser_kwargs = {'mosviz-spec2d-parser': {},
-                         'specreduce-trace': {'show_in_viewer': show_in_viewer},
+        parser_kwargs = {'mosviz-spec2d-parser': {'show_in_viewer': show_in_viewer,
+                                                  'data_labels': data_label},
+                         'specreduce-trace': {'show_in_viewer': show_in_viewer,
+                                              'data_label': data_label},
                          'specviz-spectrum1d-parser': {'format': format,
                                                        'show_in_viewer': show_in_viewer,
                                                        'concat_by_file': concat_by_file,
                                                        'cache': cache,
                                                        'local_path': local_path,
                                                        'timeout': timeout,
-                                                       'load_as_list': load_as_list}}
+                                                       'load_as_list': load_as_list,
+                                                       'data_label': data_label}}
         kwargs = parser_kwargs.get(parser, {})
         super().load_data(data,
                           parser_reference=parser,
-                          data_label=data_label,
                           **kwargs)
 
     def get_spectra(self, data_label=None, spectral_subset=None, apply_slider_redshift="Warn"):

From e9ed7989e63c83f73019543f4662a3bc50790898 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Tue, 21 Jan 2025 12:57:35 -0500
Subject: [PATCH 05/14] new functionality behind dev flag

---
 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 12b2c8986f..e3a0bcd77e 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -6,6 +6,7 @@
 from glue.core.subset_group import GroupedSubset
 from specutils import SpectralRegion, Spectrum1D
 
+from jdaviz.core import data_formats
 from jdaviz.core.helpers import ConfigHelper
 from jdaviz.core.events import RedshiftMessage
 from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
@@ -33,6 +34,7 @@ class Specviz(ConfigHelper, LineListMixin):
 
     _default_configuration = "specviz"
     _default_spectrum_viewer_reference_name = "spectrum-viewer"
+    _dev_deconfig = False
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
@@ -74,9 +76,9 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
             `~astropy.utils.data.download_file` or
             `~astroquery.mast.Conf.timeout`).
         """
-        from jdaviz.core import data_formats
         parser = data_formats.get_parser(data)
-
+        if not self._dev_deconfig and parser != 'specviz-spectrum1d-parser':
+            raise NotImplementedError("Only Spectrum1D data is supported in Specviz.")
         parser_kwargs = {'mosviz-spec2d-parser': {'show_in_viewer': show_in_viewer,
                                                   'data_labels': data_label},
                          'specreduce-trace': {'show_in_viewer': show_in_viewer,

From 5e52cf3d8d2f23faf20f1f0b2d3c9d6bfd4d8fc7 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Tue, 21 Jan 2025 13:07:02 -0500
Subject: [PATCH 06/14] remove automodapi for unused specviz2d parsers

---
 docs/reference/api_parsers.rst | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/docs/reference/api_parsers.rst b/docs/reference/api_parsers.rst
index 99665e245c..d82a0070d6 100644
--- a/docs/reference/api_parsers.rst
+++ b/docs/reference/api_parsers.rst
@@ -15,8 +15,5 @@ Parsers API
 .. automodapi:: jdaviz.configs.specviz.plugins.parsers
    :no-inheritance-diagram:
 
-.. automodapi:: jdaviz.configs.specviz2d.plugins.parsers
-   :no-inheritance-diagram:
-
 .. automodapi:: jdaviz.configs.rampviz.plugins.parsers
    :no-inheritance-diagram:
\ No newline at end of file

From 182fc119cb2cc10c37a7b03c5267d795df6d044c Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Tue, 21 Jan 2025 13:11:47 -0500
Subject: [PATCH 07/14] avoid calling get_valid_format for data objects

---
 jdaviz/core/data_formats.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/jdaviz/core/data_formats.py b/jdaviz/core/data_formats.py
index 8f19ce64f2..e959391ade 100644
--- a/jdaviz/core/data_formats.py
+++ b/jdaviz/core/data_formats.py
@@ -76,12 +76,8 @@ def get_valid_format(filename):
     config : str
         The recommended application configuration
     """
-    if isinstance(filename, (str, pathlib.Path)):
-        valid_file_format = identify_spectrum_format(filename, SpectrumList)
-        ndim = guess_dimensionality(filename)
-    elif isinstance(filename, (Spectrum1D)):
-        valid_file_format = None
-        ndim = filename.flux.ndim
+    valid_file_format = identify_spectrum_format(filename, SpectrumList)
+    ndim = guess_dimensionality(filename)
 
     if valid_file_format:
         recommended_config = file_to_config_mapping.get(valid_file_format, 'default')
@@ -107,6 +103,12 @@ def get_parser(obj):
     """
     if isinstance(obj, Trace):
         return 'specreduce-trace'
+    elif isinstance(obj, Spectrum1D):
+        if obj.flux.ndim == 1:
+            return 'specviz-spectrum1d-parser'
+        else:
+            # TODO: how to determine if multiple spectra or an image?
+            return 'mosviz-spec2d-parser'
     _, config = get_valid_format(obj)
     parsers = {'specviz': 'specviz-spectrum1d-parser', 'specviz2d': 'mosviz-spec2d-parser'}
     return parsers.get(config)

From c64f14ccd58e76f41ac0c05689b941220919c90b Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Wed, 22 Jan 2025 12:22:04 -0500
Subject: [PATCH 08/14] handle show_in_viewer in load_data instead of parsers

---
 jdaviz/configs/specviz/helper.py | 25 ++++++++++++++++++++++---
 1 file changed, 22 insertions(+), 3 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index e3a0bcd77e..ca491f2ac0 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -79,12 +79,20 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
         parser = data_formats.get_parser(data)
         if not self._dev_deconfig and parser != 'specviz-spectrum1d-parser':
             raise NotImplementedError("Only Spectrum1D data is supported in Specviz.")
-        parser_kwargs = {'mosviz-spec2d-parser': {'show_in_viewer': show_in_viewer,
+
+        default_labels = {'mosviz-spec2d-parser': '2D Spectrum',
+                          'specreduce-trace': 'Trace',
+                          'specviz-spectrum1d-parser': 'Spectrum 1D'}
+        if data_label is None:
+            data_label = default_labels.get(parser, 'Unknown')
+        data_label = self.app.return_unique_name(data_label)
+
+        parser_kwargs = {'mosviz-spec2d-parser': {'show_in_viewer': False,
                                                   'data_labels': data_label},
-                         'specreduce-trace': {'show_in_viewer': show_in_viewer,
+                         'specreduce-trace': {'show_in_viewer': False,
                                               'data_label': data_label},
                          'specviz-spectrum1d-parser': {'format': format,
-                                                       'show_in_viewer': show_in_viewer,
+                                                       'show_in_viewer': False,
                                                        'concat_by_file': concat_by_file,
                                                        'cache': cache,
                                                        'local_path': local_path,
@@ -96,6 +104,17 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
                           parser_reference=parser,
                           **kwargs)
 
+        if show_in_viewer:
+            # loop through existing viewers and show in any that support this data type
+            added = 0
+            for viewer in self.viewers.values():
+                if data_label in viewer.data_menu.data_labels_unloaded:
+                    added += 1
+                    viewer.data_menu.add_data(data_label)
+            if added == 0:
+                # TODO: in the future open a new viewer with some default type based on the data
+                print(f"*** No viewer found to display \'{data_label}\'")
+
     def get_spectra(self, data_label=None, spectral_subset=None, apply_slider_redshift="Warn"):
         """Returns the current data loaded into the main viewer
 

From 03449c5c17021df6a9b656d9089c43acf2c39b59 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Wed, 22 Jan 2025 12:23:38 -0500
Subject: [PATCH 09/14] support load_as_list for 2d spectra

---
 jdaviz/configs/specviz/helper.py | 2 +-
 jdaviz/core/data_formats.py      | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index ca491f2ac0..dd3791cce0 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -76,7 +76,7 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
             `~astropy.utils.data.download_file` or
             `~astroquery.mast.Conf.timeout`).
         """
-        parser = data_formats.get_parser(data)
+        parser = data_formats.get_parser(data, load_as_list=load_as_list)
         if not self._dev_deconfig and parser != 'specviz-spectrum1d-parser':
             raise NotImplementedError("Only Spectrum1D data is supported in Specviz.")
 
diff --git a/jdaviz/core/data_formats.py b/jdaviz/core/data_formats.py
index e959391ade..13ec295bbe 100644
--- a/jdaviz/core/data_formats.py
+++ b/jdaviz/core/data_formats.py
@@ -87,7 +87,7 @@ def get_valid_format(filename):
     return valid_file_format, recommended_config
 
 
-def get_parser(obj):
+def get_parser(obj, load_as_list=False):
     """
     Identify the data parser from a filename or data object
 
@@ -107,7 +107,8 @@ def get_parser(obj):
         if obj.flux.ndim == 1:
             return 'specviz-spectrum1d-parser'
         else:
-            # TODO: how to determine if multiple spectra or an image?
+            if load_as_list:
+                return 'specviz-spectrumlist-parser'
             return 'mosviz-spec2d-parser'
     _, config = get_valid_format(obj)
     parsers = {'specviz': 'specviz-spectrum1d-parser', 'specviz2d': 'mosviz-spec2d-parser'}

From bcef7718244a37e479bb86a062efd5cf651d8450 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Wed, 22 Jan 2025 12:47:00 -0500
Subject: [PATCH 10/14] support lists of objects when parsing

---
 jdaviz/configs/specviz/helper.py            |  2 +-
 jdaviz/configs/specviz/tests/test_helper.py |  4 ++--
 jdaviz/core/data_formats.py                 | 18 ++++++++++++++++--
 3 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index dd3791cce0..321ada4efa 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -82,7 +82,7 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
 
         default_labels = {'mosviz-spec2d-parser': '2D Spectrum',
                           'specreduce-trace': 'Trace',
-                          'specviz-spectrum1d-parser': 'Spectrum 1D'}
+                          'specviz-spectrum1d-parser': 'Spectrum'}
         if data_label is None:
             data_label = default_labels.get(parser, 'Unknown')
         data_label = self.app.return_unique_name(data_label)
diff --git a/jdaviz/configs/specviz/tests/test_helper.py b/jdaviz/configs/specviz/tests/test_helper.py
index 3c0f7f5223..bd144f3e86 100644
--- a/jdaviz/configs/specviz/tests/test_helper.py
+++ b/jdaviz/configs/specviz/tests/test_helper.py
@@ -60,7 +60,7 @@ def test_load_spectrum_list_no_labels(self):
         self.spec_app.load_data(self.spec_list)
         assert len(self.spec_app.app.data_collection) == 4
         for i in (1, 2, 3):
-            assert "specviz_data" in self.spec_app.app.data_collection[i].label
+            assert "Spectrum" in self.spec_app.app.data_collection[i].label
 
     def test_load_spectrum_list_with_labels(self):
         # now load three more spectra from a SpectrumList, with labels:
@@ -412,7 +412,7 @@ def test_load_2d_flux(specviz_helper):
     # 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")
+    specviz_helper.load_data(spec, data_label="test", load_as_list=True)
 
     assert len(specviz_helper.app.data_collection) == 4
     assert specviz_helper.app.data_collection[0].label == "test [0]"
diff --git a/jdaviz/core/data_formats.py b/jdaviz/core/data_formats.py
index 13ec295bbe..56b05468a4 100644
--- a/jdaviz/core/data_formats.py
+++ b/jdaviz/core/data_formats.py
@@ -101,15 +101,29 @@ def get_parser(obj, load_as_list=False):
     parser : str
         The parser for the data object
     """
+    if isinstance(obj, (SpectrumList, SpectrumCollection)):
+        return 'specviz-spectrum1d-parser'
     if isinstance(obj, Trace):
         return 'specreduce-trace'
-    elif isinstance(obj, Spectrum1D):
+    if isinstance(obj, Spectrum1D):
         if obj.flux.ndim == 1:
             return 'specviz-spectrum1d-parser'
         else:
             if load_as_list:
-                return 'specviz-spectrumlist-parser'
+                return 'specviz-spectrum1d-parser'
             return 'mosviz-spec2d-parser'
+    if isinstance(obj, fits.HDUList):
+        columns = [c.name.lower() for hduitem in obj for c in getattr(hduitem, 'columns', [])]
+        if 'wavelength' in columns and 'flux' in columns:
+            return 'specviz-spectrum1d-parser'
+        else:
+            raise ValueError("cannot find valid parser for HDUList")
+    if isinstance(obj, list):
+        parsers = [get_parser(o, load_as_list=load_as_list) for o in obj]
+        if len(set(parsers)) > 1:
+            raise ValueError("cannot find single parser for list of objects")
+        return parsers[0]
+
     _, config = get_valid_format(obj)
     parsers = {'specviz': 'specviz-spectrum1d-parser', 'specviz2d': 'mosviz-spec2d-parser'}
     return parsers.get(config)

From c06bf777533e2d285998042d2fe640f54b05fc0e Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 23 Jan 2025 13:48:58 -0500
Subject: [PATCH 11/14] support downloading from URI

---
 jdaviz/configs/specviz/helper.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index 321ada4efa..be362527b6 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -1,3 +1,4 @@
+import pathlib
 import warnings
 
 from astropy import units as u
@@ -10,6 +11,7 @@
 from jdaviz.core.helpers import ConfigHelper
 from jdaviz.core.events import RedshiftMessage
 from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
+from jdaviz.utils import download_uri_to_path
 
 __all__ = ['Specviz']
 
@@ -87,6 +89,12 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
             data_label = default_labels.get(parser, 'Unknown')
         data_label = self.app.return_unique_name(data_label)
 
+        if isinstance(data, str):
+            path = pathlib.Path(data)
+            if not path.is_file() and not path.is_dir():
+                data = download_uri_to_path(data, cache=cache,
+                                            local_path=local_path, timeout=timeout)
+
         parser_kwargs = {'mosviz-spec2d-parser': {'show_in_viewer': False,
                                                   'data_labels': data_label},
                          'specreduce-trace': {'show_in_viewer': False,
@@ -94,9 +102,6 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
                          'specviz-spectrum1d-parser': {'format': format,
                                                        'show_in_viewer': False,
                                                        'concat_by_file': concat_by_file,
-                                                       'cache': cache,
-                                                       'local_path': local_path,
-                                                       'timeout': timeout,
                                                        'load_as_list': load_as_list,
                                                        'data_label': data_label}}
         kwargs = parser_kwargs.get(parser, {})

From 4727516be7d2c918afca3352b7d21de311b7d6a7 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Thu, 23 Jan 2025 15:20:12 -0500
Subject: [PATCH 12/14] WIP: deconfigged data parser registry

---
 jdaviz/configs/specviz/helper.py |  81 +++++++--------
 jdaviz/core/parsers.py           | 173 +++++++++++++++++++++++++++++++
 jdaviz/core/registries.py        |  14 ++-
 3 files changed, 221 insertions(+), 47 deletions(-)
 create mode 100644 jdaviz/core/parsers.py

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index be362527b6..e5d1c3a9c2 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -45,27 +45,24 @@ def __init__(self, *args, **kwargs):
         self.app.hub.subscribe(self, RedshiftMessage,
                                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,
-                  load_as_list=False):
+    def load_data(self, input, data_label=None, parser=None,
+                  show_in_viewer=True,
+                  cache=None, local_path=None, timeout=None):
         """
         Load data into Specviz.
 
         Parameters
         ----------
-        data : str, `~specutils.Spectrum1D`, or `~specutils.SpectrumList`
+        input : str, `~specutils.Spectrum1D`, or `~specutils.SpectrumList`
             Spectrum1D, SpectrumList, or path to compatible data file.
         data_label : str
             The Glue data label found in the ``DataCollection``.
-        format : str
-            Loader format specification used to indicate data format in
-            `~specutils.Spectrum1D.read` io method.
+        parser : str
+            The name of the parser to use to load the data.  Will automatically
+            be determined if only a single registered parser is capable of parsing
+            ``input``.
         show_in_viewer : bool
             Show data in viewer(s).
-        concat_by_file : bool
-            If True and there is more than one available extension, concatenate
-            the extensions within each spectrum file passed to the parser and
-            add a concatenated spectrum to the data collection.
         cache : None, bool, or str
             Cache the downloaded file if the data are retrieved by a query
             to a URL or URI.
@@ -78,47 +75,39 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
             `~astropy.utils.data.download_file` or
             `~astroquery.mast.Conf.timeout`).
         """
-        parser = data_formats.get_parser(data, load_as_list=load_as_list)
-        if not self._dev_deconfig and parser != 'specviz-spectrum1d-parser':
+        from jdaviz.core import parsers
+
+        if isinstance(input, str):
+            path = pathlib.Path(input)
+            if not path.is_file() and not path.is_dir():
+                input = download_uri_to_path(input, cache=cache,
+                                             local_path=local_path, timeout=timeout)
+
+        parser = parsers.parse(input, parser=parser)
+        if not self._dev_deconfig and parser.registry_name != '1D Spectrum':
             raise NotImplementedError("Only Spectrum1D data is supported in Specviz.")
 
-        default_labels = {'mosviz-spec2d-parser': '2D Spectrum',
-                          'specreduce-trace': 'Trace',
-                          'specviz-spectrum1d-parser': 'Spectrum'}
         if data_label is None:
-            data_label = default_labels.get(parser, 'Unknown')
-        data_label = self.app.return_unique_name(data_label)
+            data_label = parser.default_data_label
 
-        if isinstance(data, str):
-            path = pathlib.Path(data)
-            if not path.is_file() and not path.is_dir():
-                data = download_uri_to_path(data, cache=cache,
-                                            local_path=local_path, timeout=timeout)
-
-        parser_kwargs = {'mosviz-spec2d-parser': {'show_in_viewer': False,
-                                                  'data_labels': data_label},
-                         'specreduce-trace': {'show_in_viewer': False,
-                                              'data_label': data_label},
-                         'specviz-spectrum1d-parser': {'format': format,
-                                                       'show_in_viewer': False,
-                                                       'concat_by_file': concat_by_file,
-                                                       'load_as_list': load_as_list,
-                                                       'data_label': data_label}}
-        kwargs = parser_kwargs.get(parser, {})
-        super().load_data(data,
-                          parser_reference=parser,
-                          **kwargs)
+        data_labels = []
+        for data in parser.glue_data:
+            data_label = self.app.return_unique_name(data_label)
+            data_labels.append(data_label)
+            self.app.add_data(data, data_label)
 
         if show_in_viewer:
-            # loop through existing viewers and show in any that support this data type
-            added = 0
-            for viewer in self.viewers.values():
-                if data_label in viewer.data_menu.data_labels_unloaded:
-                    added += 1
-                    viewer.data_menu.add_data(data_label)
-            if added == 0:
-                # TODO: in the future open a new viewer with some default type based on the data
-                print(f"*** No viewer found to display \'{data_label}\'")
+            for data_label in data_labels:
+                # loop through existing viewers and show in any that support this data type
+                added = 0
+                for viewer in self.viewers.values():
+                    if data_label in viewer.data_menu.data_labels_unloaded:
+                        added += 1
+                        viewer.data_menu.add_data(data_label)
+                if added == 0:
+                    # TODO: in the future open a new viewer with some default type based on the data
+                    # using parser.default_viewer
+                    print(f"*** No viewer found to display \'{data_label}\'")
 
     def get_spectra(self, data_label=None, spectral_subset=None, apply_slider_redshift="Warn"):
         """Returns the current data loaded into the main viewer
diff --git a/jdaviz/core/parsers.py b/jdaviz/core/parsers.py
new file mode 100644
index 0000000000..9b030724d0
--- /dev/null
+++ b/jdaviz/core/parsers.py
@@ -0,0 +1,173 @@
+from functools import cached_property
+
+from jdaviz.core.registries import parser_registry
+
+from specutils import Spectrum1D
+from specutils.io.registers import identify_spectrum_format
+
+__all__ = ['parse']
+
+
+class BaseParser:
+    registry_name = None  # populated by parser_registry decorator
+
+    def __init__(self, input, shared_info={}):
+        self.shared_info = shared_info  # dictionary of parsed objects to be re-used between parsers
+        self._input = input
+        # trigger the cached_property
+        _ = self.can_parse
+
+    @property
+    def input(self):
+        return self._input
+
+    @cached_property
+    def default_data_label(self):
+        # optional override by subclass
+        # has access to self.input and anything stored by can_parse
+        return self.registry_name
+
+    @cached_property
+    def default_viewer(self):
+        # override by subclass
+        # has access to self.input and anything stored by can_parse
+        return 'scatter'
+
+    @cached_property
+    def can_parse(self):
+        # override by subclass, ONLY use self.input
+        # anything that needs to be opened can be stored internally for other methods (i.e. _input_to_object)
+        return False
+
+    def _input_to_object(self):
+        # override by subclass
+        # has access to self.input and anything stored by can_parse
+        # can return single object or list (in which case _object_to_glue_data should also handle)
+        return self.input
+
+    @cached_property
+    def object(self):
+        if not self.can_parse:
+            raise ValueError("Cannot parse input")
+        return self._input_to_object()
+
+    def _object_to_glue_data(self):
+        # override by subclass
+        # has access to self.input and self.object and can return single entry or list
+        return self.object
+
+    @cached_property
+    def glue_data(self):
+        if not self.can_parse:
+            raise ValueError("Cannot parse input")
+        data = self._object_to_glue_data()
+        if not isinstance(data, list):
+            data = [data]
+        return data
+
+
+@parser_registry('1D Spectrum')
+class Spectrum1DParser(BaseParser):
+    def default_viewer(self):
+        return 'spectrum-viewer'
+
+    @cached_property
+    def can_parse(self):
+        if 'Spectrum1D' in self.shared_info:
+            pass
+        elif isinstance(self.input, Spectrum1D):
+            self.shared_info['Spectrum1D'] = self.input
+        if isinstance(self.input, str):
+            if 'specutils_format' not in self.shared_info:
+                try:
+                    format = identify_spectrum_format(self.input, Spectrum1D)
+                except ValueError:
+                    return False
+                else:
+                    self.shared_info['specutils_format'] = format
+            if self.shared_info['specutils_format'] in ('JWST x1d',):
+                self.shared_info['Spectrum1D'] = Spectrum1D.read(self.input)
+            else:
+                return False
+        else:
+            return False
+        return self.shared_info['Spectrum1D'].flux.ndim == 1
+
+    def _input_to_object(self):
+        # has access to self.input and anything stored by can_parse
+        return self.shared_info['Spectrum1D']
+
+
+@parser_registry('2D Spectrum')
+class Spectrum2DParser(BaseParser):
+    def default_viewer(self):
+        return 'spectrum-2d-viewer'
+
+    @cached_property
+    def can_parse(self):
+        if 'Spectrum1D' in self.shared_info:
+            pass
+        elif isinstance(self.input, str):
+            if 'specutils_format' not in self.shared_info:
+                try:
+                    format = identify_spectrum_format(self.input, Spectrum1D)
+                except ValueError:
+                    return False
+                else:
+                    self.shared_info['specutils_format'] = format
+            if self.shared_info['specutils_format'] in ('JWST s2d',):
+                self.shared_info['Spectrum1D'] = Spectrum1D.read(self.input)
+            else:
+                return False
+        elif isinstance(self.input, Spectrum1D):
+            self.shared_info['Spectrum1D'] = self.input
+        else:
+            return False
+        return self.shared_info['Spectrum1D'].flux.ndim == 2
+
+    def _input_to_object(self):
+        # has access to self.input and anything stored by can_parse
+        return self.shared_info['Spectrum1D']
+
+
+@parser_registry('2D Spectral Trace')
+class SpectralTraceParser(BaseParser):
+    def default_viewer(self):
+        return 'spectrum-2d-viewer'
+
+    @cached_property
+    def can_parse(self):
+        from specreduce.tracing import Trace
+        return isinstance(self.input, Trace)
+
+
+def parse(input, parser=None):
+    # if input is a string, but not path/file, then download first
+
+    # by default, search through all registered parsers, but also allow
+    # passing a Parser class or name of registered parser.
+    # could also be extended to allow pre-parsing of MOS data
+    if isinstance(parser, BaseParser):
+        all_parsers = {parser.__name__: parser}
+    if isinstance(parser, str):
+        if parser not in parser_registry.members:
+            raise ValueError(f"\'{parser}\' not one of {list(parser_registry.members.keys())}")
+        all_parsers = {parser: parser_registry.members.get(parser)}
+    else:
+        all_parsers = parser_registry.members
+
+    # loop through all registered parsers to see which can parse the file
+    valid_parsers = {}
+    shared_info = {}
+    for parser_name, Parser in all_parsers.items():
+        this_parser = Parser(input, shared_info)
+        shared_info.update(this_parser.shared_info)
+        if this_parser.can_parse:
+            valid_parsers[parser_name] = this_parser
+    if not len(valid_parsers):
+        all_parsers_str = ', '.join(list(all_parsers.keys()))
+        raise ValueError(f"No valid parsers found for input, tried {all_parsers_str}.")
+    if len(valid_parsers) > 1:
+        valid_parsers_str = ', '.join(list(valid_parsers.keys()))
+        raise ValueError(f"Multiple valid parsers found, please pass parser as one of: {valid_parsers_str}")  # noqa
+    return list(valid_parsers.values())[0]
\ No newline at end of file
diff --git a/jdaviz/core/registries.py b/jdaviz/core/registries.py
index 84ddc4370b..1b69d242f4 100644
--- a/jdaviz/core/registries.py
+++ b/jdaviz/core/registries.py
@@ -8,7 +8,7 @@
 __all__ = ['convert', 'UniqueDictRegistry', 'ViewerRegistry', 'TrayRegistry',
            'ToolRegistry', 'MenuRegistry', 'DataParserRegistry',
            'viewer_registry', 'tray_registry', 'tool_registry', 'menu_registry',
-           'data_parser_registry']
+           'data_parser_registry', 'parser_registry']
 
 
 def _to_snake(s):
@@ -221,8 +221,20 @@ def decorator(func):
         return decorator
 
 
+class ParserRegistry(UniqueDictRegistry):
+    """Registry containing data parsing classes
+    """
+    def __call__(self, name=None):
+        def decorator(cls):
+            cls.registry_name = name
+            self.add(name, cls)
+            return cls
+        return decorator
+
+
 viewer_registry = ViewerRegistry()
 tray_registry = TrayRegistry()
 tool_registry = ToolRegistry()
 menu_registry = MenuRegistry()
 data_parser_registry = DataParserRegistry()
+parser_registry = ParserRegistry()  # replacement for data_parser_registry as part of deconfigging

From b285cbdcd8f7973a796d3b6984e86ffee5200654 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Fri, 24 Jan 2025 09:09:57 -0500
Subject: [PATCH 13/14] 3-step parser infrastructure

---
 jdaviz/configs/specviz/helper.py |  54 +++---
 jdaviz/core/parsers.py           | 285 ++++++++++++++++---------------
 jdaviz/core/registries.py        |  15 +-
 3 files changed, 184 insertions(+), 170 deletions(-)

diff --git a/jdaviz/configs/specviz/helper.py b/jdaviz/configs/specviz/helper.py
index e5d1c3a9c2..bb96ba3b67 100644
--- a/jdaviz/configs/specviz/helper.py
+++ b/jdaviz/configs/specviz/helper.py
@@ -45,9 +45,10 @@ def __init__(self, *args, **kwargs):
         self.app.hub.subscribe(self, RedshiftMessage,
                                handler=self._redshift_listener)
 
-    def load_data(self, input, data_label=None, parser=None,
-                  show_in_viewer=True,
-                  cache=None, local_path=None, timeout=None):
+    def load_data(self, input, data_label=None,
+                  resolver=None, parser=None, loader=None,
+                  resolver_kwargs={}, parser_kwargs={}, loader_kwargs={},
+                  show_in_viewer=True):
         """
         Load data into Specviz.
 
@@ -57,44 +58,31 @@ def load_data(self, input, data_label=None, parser=None,
             Spectrum1D, SpectrumList, or path to compatible data file.
         data_label : str
             The Glue data label found in the ``DataCollection``.
-        parser : str
-            The name of the parser to use to load the data.  Will automatically
-            be determined if only a single registered parser is capable of parsing
-            ``input``.
         show_in_viewer : bool
             Show data in viewer(s).
-        cache : None, bool, or str
-            Cache the downloaded file if the data are retrieved by a query
-            to a URL or URI.
-        local_path : str, optional
-            Cache remote files to this path. This is only used if data is
-            requested from `astroquery.mast`.
-        timeout : float, optional
-            If downloading from a remote URI, set the timeout limit for
-            remote requests in seconds (passed to
-            `~astropy.utils.data.download_file` or
-            `~astroquery.mast.Conf.timeout`).
         """
         from jdaviz.core import parsers
 
-        if isinstance(input, str):
-            path = pathlib.Path(input)
-            if not path.is_file() and not path.is_dir():
-                input = download_uri_to_path(input, cache=cache,
-                                             local_path=local_path, timeout=timeout)
+        data_labels = []
+        inputs = input if isinstance(input, list) else [input]
 
-        parser = parsers.parse(input, parser=parser)
-        if not self._dev_deconfig and parser.registry_name != '1D Spectrum':
-            raise NotImplementedError("Only Spectrum1D data is supported in Specviz.")
+        for input in inputs:
+            objects, loader = parsers.parse(input,
+                                            resolver=resolver, parser=parser, loader=loader,
+                                            resolver_kwargs=resolver_kwargs,
+                                            parser_kwargs=parser_kwargs,
+                                            loader_kwargs=loader_kwargs)
 
-        if data_label is None:
-            data_label = parser.default_data_label
+            if not self._dev_deconfig and loader.registry_name != '1D Spectrum':
+                raise NotImplementedError("Only Spectrum1D data is supported in Specviz.")
 
-        data_labels = []
-        for data in parser.glue_data:
-            data_label = self.app.return_unique_name(data_label)
-            data_labels.append(data_label)
-            self.app.add_data(data, data_label)
+            if data_label is None:
+                data_label = getattr(loader, 'default_data_label', 'data')
+
+            for data in objects:
+                data_label = self.app.return_unique_name(data_label)
+                data_labels.append(data_label)
+                self.app.add_data(data, data_label)
 
         if show_in_viewer:
             for data_label in data_labels:
diff --git a/jdaviz/core/parsers.py b/jdaviz/core/parsers.py
index 9b030724d0..1e73c0efc8 100644
--- a/jdaviz/core/parsers.py
+++ b/jdaviz/core/parsers.py
@@ -1,173 +1,192 @@
+import os
+#import numpy as np
 from functools import cached_property
 
-from jdaviz.core.registries import parser_registry
+from jdaviz.core.registries import resolver_registry, parser_registry, loader_registry
+from jdaviz.utils import download_uri_to_path
 
 from specutils import Spectrum1D
-from specutils.io.registers import identify_spectrum_format
 
 __all__ = ['parse']
 
 
-class BaseParser:
-    registry_name = None  # populated by parser_registry decorator
+"""
+Three registries for 3 steps:
+1. Resolver: for resolving string to a path or object(s)
+    input: string
+    output: path to file or directory or object itself (skip parsing step)
+2. Parser: for parsing a file into an object(s)
+    input: string or path to file or directory
+    output: python object
+3. Loader: for manipulating the object(s) and passing to glue (potentially in a loop)
+    input: python object
+    output: glue data or python object able to directly be input to glue parsers
+"""
 
-    def __init__(self, input, shared_info={}):
-        self.shared_info = shared_info  # dictionary of parsed objects to be re-used between parsers
+
+class BaseParsingStep:
+    def __init__(self, input):
         self._input = input
-        # trigger the cached_property
-        _ = self.can_parse
 
     @property
     def input(self):
         return self._input
 
-    @cached_property
-    def default_data_label(self):
-        # optional override by subclass
-        # has access to self.input and anything stored by can_parse
-        return self.registry_name
+#    def validate_call_kwargs(self, kwargs):
+#        # hmmm not sure where this belongs (in original is_valid or while calling)
+#        import inspect
+#        allowed_kwargs = inspect.signature(self.__call__).parameters.keys()
+#        valid = np.all([k in allowed_kwargs for k in kwargs])
+#        if not valid:
+#            raise ValueError(f"Invalid keyword arguments passed to __call__, allowed: {allowed_kwargs}")
 
-    @cached_property
-    def default_viewer(self):
+    @property
+    def is_valid(self):
         # override by subclass
-        # has access to self.input and anything stored by can_parse
-        return 'scatter'
-
-    @cached_property
-    def can_parse(self):
-        # override by subclass, ONLY use self.input
-        # anything that needs to be opened can be stored internally for other methods (i.e. _input_to_object)
         return False
 
-    def _input_to_object(self):
-        # override by subclass
-        # has access to self.input and anything stored by can_parse
-        # can return single object or list (in which case _object_to_glue_data should also handle)
+    def __call__(self):
         return self.input
 
-    @cached_property
-    def object(self):
-        if not self.can_parse:
-            raise ValueError("Cannot parse input")
-        return self._input_to_object()
 
-    def _object_to_glue_data(self):
-        # override by subclass
-        # has access to self.input and self.object and can return single entry or list
-        return self.object
+class BaseParsingStepLoader(BaseParsingStep):
+    @property
+    def default_data_label(self):
+        return self.registry_name
 
-    @cached_property
-    def glue_data(self):
-        if not self.can_parse:
-            raise ValueError("Cannot parse input")
-        data = self._object_to_glue_data()
-        if not isinstance(data, list):
-            data = [data]
-        return data
 
+class ParsingStepSearch:
+    valid = {}
+
+    def __init__(self, registry, parser, input, kwargs):
+        self._step = registry._step
+        self._input = input
+        self._kwargs = kwargs
+
+        if isinstance(parser, BaseParsingStep):
+            all_parsers = {parser.__name__: parser}
+        if isinstance(parser, str):
+            if parser not in registry.members:
+                raise ValueError(f"\'{parser}\' not one of {list(registry.members.keys())}")
+            all_parsers = {parser: registry.members.get(parser)}
+        else:
+            all_parsers = registry.members
+        self.all_parsers = all_parsers
 
-@parser_registry('1D Spectrum')
-class Spectrum1DParser(BaseParser):
-    def default_viewer(self):
-        return 'spectrum-viewer'
+        # loop through all registered parsers to see which can parse the file
+        valid_parsers = {}
+        for parser_name, Parser in all_parsers.items():
+            this_parser = Parser(input)
+            if this_parser.is_valid:
+                valid_parsers[parser_name] = this_parser
+        self.valid_parsers = valid_parsers
 
     @cached_property
-    def can_parse(self):
-        if 'Spectrum1D' in self.shared_info:
-            pass
-        elif isinstance(self.input, Spectrum1D):
-            self.shared_info['Spectrum1D'] = self.input
-        if isinstance(self.input, str):
-            if 'specutils_format' not in self.shared_info:
-                try:
-                    format = identify_spectrum_format(self.input, Spectrum1D)
-                except ValueError:
-                    return False
-                else:
-                    self.shared_info['specutils_format'] = format
-            if self.shared_info['specutils_format'] in ('JWST x1d',):
-                self.shared_info['Spectrum1D'] = Spectrum1D.read(self.input)
-            else:
-                return False
-        else:
-            return False
-        return self.shared_info['Spectrum1D'].flux.ndim == 1
+    def single_match(self):
+        if not len(self.valid_parsers):
+            all_parsers_str = ', '.join(list(self.all_parsers.keys()))
+            raise ValueError(f"No valid {self._step}s found for input, tried {all_parsers_str}.")
+        if len(self.valid_parsers) > 1:
+            valid_parsers_str = ', '.join(list(self.valid_parsers.keys()))
+            raise ValueError(f"Multiple valid {self._step}s found, please pass {self._step} as one of: {valid_parsers_str}")  # noqa
+        return list(self.valid_parsers.values())[0]
+
+    def __call__(self):
+        print(f"{self._step} using {self.single_match.registry_name}")
+        return self.single_match(**self._kwargs)
+
+
+@resolver_registry('Local Path')
+class LocalFileResolver(BaseParsingStep):
+    @property
+    def is_valid(self):
+        return os.path.exists(self.input)
 
-    def _input_to_object(self):
-        # has access to self.input and anything stored by can_parse
-        return self.shared_info['Spectrum1D']
+    def __call__(self):
+        return self.input
 
 
-@parser_registry('2D Spectrum')
-class Spectrum2DParser(BaseParser):
-    def default_viewer(self):
-        return 'spectrum-2d-viewer'
+@resolver_registry('URL')
+class URLResolver(BaseParsingStep):
+    @property
+    def is_valid(self):
+        return not os.path.exists(self.input)
 
-    @cached_property
-    def can_parse(self):
-        if 'Spectrum1D' in self.shared_info:
-            pass
-        elif isinstance(self.input, str):
-            if 'specutils_format' not in self.shared_info:
-                try:
-                    format = identify_spectrum_format(self.input, Spectrum1D)
-                except ValueError:
-                    return False
-                else:
-                    self.shared_info['specutils_format'] = format
-            if self.shared_info['specutils_format'] in ('JWST s2d',):
-                self.shared_info['Spectrum1D'] = Spectrum1D.read(self.input)
-            else:
-                return False
-        elif isinstance(self.input, Spectrum1D):
-            self.shared_info['Spectrum1D'] = self.input
-        else:
+    def __call__(self, cache=True, local_path=None, timeout=60):
+        return download_uri_to_path(self.input, cache=cache,
+                                    local_path=local_path, timeout=timeout)
+
+
+@parser_registry('specutils.Spectrum')
+class SpecutilsSpectrumParser(BaseParsingStep):
+    def is_valid(self):
+        if isinstance(self.input, Spectrum1D):
+            return True
+        if not isinstance(self.input, str):
+            return False
+        try:
+            self.spectrum1d
+        except Exception as e:
+            print("spectrum1d read failed", str(e))
             return False
-        return self.shared_info['Spectrum1D'].flux.ndim == 2
+        return True
 
-    def _input_to_object(self):
-        # has access to self.input and anything stored by can_parse
-        return self.shared_info['Spectrum1D']
+    @cached_property
+    def spectrum1d(self):
+        return Spectrum1D.read(self.input)
 
+    def __call__(self):
+        if isinstance(self.input, Spectrum1D):
+            return self.input
+        return self.spectrum1d
 
-@parser_registry('2D Spectral Trace')
-class SpectralTraceParser(BaseParser):
-    def default_viewer(self):
-        return 'spectrum-2d-viewer'
 
-    @cached_property
-    def can_parse(self):
+@loader_registry('1D Spectrum')
+class Spectrum1DLoader(BaseParsingStepLoader):
+    @property
+    def is_valid(self):
+        return isinstance(self.input, Spectrum1D) and self.input.flux.ndim == 1
+
+
+@loader_registry('2D Spectrum')
+class Spectrum2DLoader(BaseParsingStepLoader):
+    @property
+    def is_valid(self):
+        return isinstance(self.input, Spectrum1D) and self.input.flux.ndim == 2
+
+
+@loader_registry('Specreduce Trace')
+class SpecreduceTraceLoader(BaseParsingStepLoader):
+    @property
+    def is_valid(self):
         from specreduce.tracing import Trace
         return isinstance(self.input, Trace)
 
+    @property
+    def default_data_label(self):
+        return 'Trace'
+
+
+def parse(input,
+          resolver=None, parser=None, loader=None,
+          resolver_kwargs={}, parser_kwargs={}, loader_kwargs={}):
+
+    if isinstance(input, str) or resolver is not None:
+        resolver_search = ParsingStepSearch(resolver_registry, resolver, input, resolver_kwargs)
+        input = resolver_search()
+
+    if isinstance(input, str) or parser is not None:
+        parser_search = ParsingStepSearch(parser_registry, parser, input, parser_kwargs)
+        input = parser_search()
+
+    loader_search = ParsingStepSearch(loader_registry, loader, input, loader_kwargs)
+    # need access to the loader itself for viewer/data_label defaults
+    loader = loader_search.single_match
+    # identical to loader(**loader_kwargs)
+    objects = loader_search()
+    if not isinstance(objects, list):
+        objects = [objects]
+    return objects, loader
+
 
-def parse(input, parser=None):
-    # if input is a string, but not path/file, then download first
-
-    # by default, search through all registered parsers, but also allow
-    # passing a Parser class or name of registered parser.
-    # could also be extended to allow pre-parsing of MOS data
-    if isinstance(parser, BaseParser):
-        all_parsers = {parser.__name__: parser}
-    if isinstance(parser, str):
-        if parser not in parser_registry.members:
-            raise ValueError(f"\'{parser}\' not one of {list(parser_registry.members.keys())}")
-        all_parsers = {parser: parser_registry.members.get(parser)}
-    else:
-        all_parsers = parser_registry.members
-
-    # loop through all registered parsers to see which can parse the file
-    valid_parsers = {}
-    shared_info = {}
-    for parser_name, Parser in all_parsers.items():
-        this_parser = Parser(input, shared_info)
-        shared_info.update(this_parser.shared_info)
-        if this_parser.can_parse:
-            valid_parsers[parser_name] = this_parser
-    if not len(valid_parsers):
-        all_parsers_str = ', '.join(list(all_parsers.keys()))
-        raise ValueError(f"No valid parsers found for input, tried {all_parsers_str}.")
-    if len(valid_parsers) > 1:
-        valid_parsers_str = ', '.join(list(valid_parsers.keys()))
-        raise ValueError(f"Multiple valid parsers found, please pass parser as one of: {valid_parsers_str}")  # noqa
-    return list(valid_parsers.values())[0]
\ No newline at end of file
+# TODO: concept of "only_if_requested" for spectrum2d loaded as list
\ No newline at end of file
diff --git a/jdaviz/core/registries.py b/jdaviz/core/registries.py
index 1b69d242f4..f0f5a1c834 100644
--- a/jdaviz/core/registries.py
+++ b/jdaviz/core/registries.py
@@ -8,7 +8,8 @@
 __all__ = ['convert', 'UniqueDictRegistry', 'ViewerRegistry', 'TrayRegistry',
            'ToolRegistry', 'MenuRegistry', 'DataParserRegistry',
            'viewer_registry', 'tray_registry', 'tool_registry', 'menu_registry',
-           'data_parser_registry', 'parser_registry']
+           'data_parser_registry',
+           'resolver_registry', 'parser_registry', 'loader_registry']
 
 
 def _to_snake(s):
@@ -221,9 +222,13 @@ def decorator(func):
         return decorator
 
 
-class ParserRegistry(UniqueDictRegistry):
+class ParserStepRegistry(UniqueDictRegistry):
     """Registry containing data parsing classes
     """
+    def __init__(self, *args, **kwargs):
+        self._step = kwargs.pop('step')
+        super().__init__(*args, **kwargs)
+
     def __call__(self, name=None):
         def decorator(cls):
             cls.registry_name = name
@@ -236,5 +241,7 @@ def decorator(cls):
 tray_registry = TrayRegistry()
 tool_registry = ToolRegistry()
 menu_registry = MenuRegistry()
-data_parser_registry = DataParserRegistry()
-parser_registry = ParserRegistry()  # replacement for data_parser_registry as part of deconfigging
+data_parser_registry = DataParserRegistry()  # remove once deconfigging is completed
+resolver_registry = ParserStepRegistry(step='resolver')
+parser_registry = ParserStepRegistry(step='parser')
+loader_registry = ParserStepRegistry(step='loader')
\ No newline at end of file

From ad9fce34a5d0c44cd45684ec6de52c913b524cd1 Mon Sep 17 00:00:00 2001
From: Kyle Conroy <kyleconroy@gmail.com>
Date: Fri, 24 Jan 2025 10:19:27 -0500
Subject: [PATCH 14/14] basic SpectrumList support

---
 jdaviz/core/parsers.py | 83 ++++++++++++++++++++++++++++++++++--------
 1 file changed, 68 insertions(+), 15 deletions(-)

diff --git a/jdaviz/core/parsers.py b/jdaviz/core/parsers.py
index 1e73c0efc8..fc1db2b55b 100644
--- a/jdaviz/core/parsers.py
+++ b/jdaviz/core/parsers.py
@@ -5,7 +5,7 @@
 from jdaviz.core.registries import resolver_registry, parser_registry, loader_registry
 from jdaviz.utils import download_uri_to_path
 
-from specutils import Spectrum1D
+from specutils import Spectrum1D, SpectrumList
 
 __all__ = ['parse']
 
@@ -54,6 +54,12 @@ class BaseParsingStepLoader(BaseParsingStep):
     def default_data_label(self):
         return self.registry_name
 
+    @property
+    def default_viewer(self):
+        # returns the registry name of the default viewer
+        # only used if `show_in_viewer=True` and no existing viewers can accept the data
+        return 'specviz-profile-viewer'
+
 
 class ParsingStepSearch:
     valid = {}
@@ -63,8 +69,10 @@ def __init__(self, registry, parser, input, kwargs):
         self._input = input
         self._kwargs = kwargs
 
-        if isinstance(parser, BaseParsingStep):
-            all_parsers = {parser.__name__: parser}
+        # TODO: could eventually allow passing unregistered parser classes/objects
+        # which could then be used to allow pre-parsing of MOS data (selecting individual rows)
+#        if isinstance(parser, BaseParsingStep):
+#            all_parsers = {parser.__name__: parser}
         if isinstance(parser, str):
             if parser not in registry.members:
                 raise ValueError(f"\'{parser}\' not one of {list(registry.members.keys())}")
@@ -96,6 +104,8 @@ def __call__(self):
         return self.single_match(**self._kwargs)
 
 
+### RESOLVERS (string -> path or object(s))
+
 @resolver_registry('Local Path')
 class LocalFileResolver(BaseParsingStep):
     @property
@@ -117,29 +127,41 @@ def __call__(self, cache=True, local_path=None, timeout=60):
                                     local_path=local_path, timeout=timeout)
 
 
+### PARSERS (path -> object(s))
+
 @parser_registry('specutils.Spectrum')
 class SpecutilsSpectrumParser(BaseParsingStep):
+    SpecutilsCls = Spectrum1D
+
+    @property
     def is_valid(self):
-        if isinstance(self.input, Spectrum1D):
-            return True
-        if not isinstance(self.input, str):
-            return False
         try:
-            self.spectrum1d
+            self.object
         except Exception as e:
-            print("spectrum1d read failed", str(e))
+            print(f"{self.SpecutilsCls.__name__} read failed", str(e))
             return False
         return True
 
     @cached_property
-    def spectrum1d(self):
-        return Spectrum1D.read(self.input)
+    def object(self):
+        if isinstance(self.input, self.SpecutilsCls):
+            return self.input
+        return self.SpecutilsCls.read(self.input)
 
     def __call__(self):
-        if isinstance(self.input, Spectrum1D):
-            return self.input
-        return self.spectrum1d
+        return self.object
+
+
+@parser_registry('specutils.SpectrumList')
+class SpecutilsSpectrumListParser(SpecutilsSpectrumParser):
+    SpecutilsCls = SpectrumList
+
+    @property
+    def is_valid(self):
+        return super().is_valid and len(self.object) > 1
+
 
+### LOADERS (object(s) -> object(s) ready for ingesting in glue)
 
 @loader_registry('1D Spectrum')
 class Spectrum1DLoader(BaseParsingStepLoader):
@@ -155,6 +177,37 @@ def is_valid(self):
         return isinstance(self.input, Spectrum1D) and self.input.flux.ndim == 2
 
 
+@loader_registry('1D Spectrum List')
+class Spectrum1DListLoader(BaseParsingStepLoader):
+    @property
+    def is_valid(self):
+        # TODO: should this be split into two loaders? 
+        # should a loader take a single input type, output a single output type, or just have a consistent data_label and viewer?
+        return isinstance(self.input, SpectrumList) or (isinstance(self.input, Spectrum1D) and self.input.flux.ndim == 2)
+
+    def __call__(self):
+        if isinstance(self.input, SpectrumList):
+            return self.input
+        elif isinstance(self.input, Spectrum1D):
+            def this_row(field, i):
+                if field is None:
+                    return None
+                return field[i, :]
+    
+            return SpectrumList([Spectrum1D(spectral_axis=self.input.spectral_axis,
+                                            flux=this_row(self.input.flux, i),
+                                            uncertainty=this_row(self.input.uncertainty, i),
+                                            mask=this_row(self.input.mask, i),
+                                            meta=self.input.meta)
+                                 for i in range(self.input.flux.shape[0])])
+        else:
+            raise NotImplementedError()
+
+    @property
+    def default_data_label(self):
+        return '1D Spectrum'
+
+
 @loader_registry('Specreduce Trace')
 class SpecreduceTraceLoader(BaseParsingStepLoader):
     @property
@@ -189,4 +242,4 @@ def parse(input,
     return objects, loader
 
 
-# TODO: concept of "only_if_requested" for spectrum2d loaded as list
\ No newline at end of file
+# TODO: concept of "only_if_requested"/priority/enabled for spectrum2d loaded as list
\ No newline at end of file