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] 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.