POC: 3-step generalized data parsing

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:

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',
@@ -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")
@@ -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

jdaviz/configs/specviz/helper.py

@@ -1,3 +1,4 @@
+import pathlib
 import warnings
 
 from astropy import units as u
@@ -6,9 +7,11 @@
 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
+from jdaviz.utils import download_uri_to_path
 
 __all__ = ['Specviz']
 
@@ -33,6 +36,7 @@ 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)
@@ -41,49 +45,57 @@ 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,
+                  resolver=None, parser=None, loader=None,
+                  resolver_kwargs={}, parser_kwargs={}, loader_kwargs={},
+                  show_in_viewer=True):
         """
         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.
         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.
-        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`).
         """
-        super().load_data(data,
-                          parser_reference='specviz-spectrum1d-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)
+        from jdaviz.core import parsers
+
+        data_labels = []
+        inputs = input if isinstance(input, list) else [input]
+
+        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 not self._dev_deconfig and loader.registry_name != '1D Spectrum':
+                raise NotImplementedError("Only Spectrum1D data is supported in Specviz.")
+
+            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:
+                # 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

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]"

jdaviz/configs/specviz2d/plugins/__init__.py

@@ -1,2 +1 @@
-from .parsers import *  # noqa
 from .spectral_extraction.spectral_extraction import * # noqa

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
@@ -75,7 +76,6 @@ def get_valid_format(filename):
     config : str
         The recommended application configuration
     """
-
     valid_file_format = identify_spectrum_format(filename, SpectrumList)
     ndim = guess_dimensionality(filename)
 
@@ -87,6 +87,48 @@ def get_valid_format(filename):
     return valid_file_format, recommended_config
 
 
+def get_parser(obj, load_as_list=False):
+    """
+    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, (SpectrumList, SpectrumCollection)):
+        return 'specviz-spectrum1d-parser'
+    if isinstance(obj, Trace):
+        return 'specreduce-trace'
+    if isinstance(obj, Spectrum1D):
+        if obj.flux.ndim == 1:
+            return 'specviz-spectrum1d-parser'
+        else:
+            if load_as_list:
+                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)
+
+
 def identify_data(filename, current=None):
     """Identify the data format and application configuration from a filename.