import base64
import pathlib
import uuid
from astropy.io.registry import IORegistryError
from specutils import Spectrum1D, SpectrumList, SpectrumCollection
from jdaviz.core.registries import data_parser_registry
__all__ = ["specviz_spectrum1d_parser"]
[docs]@data_parser_registry("specviz-spectrum1d-parser")
def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_viewer=True):
"""
Loads a data file or `~specutils.Spectrum1D` object into Specviz.
Parameters
----------
data : 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.
"""
# If no data label is assigned, give it a unique identifier
if not data_label:
data_label = "specviz_data|" + str(
base64.b85encode(uuid.uuid4().bytes), "utf-8"
)
if isinstance(data, SpectrumCollection):
raise TypeError("SpectrumCollection detected."
" Please provide a Spectrum1D or SpectrumList")
elif isinstance(data, Spectrum1D):
data = [data]
data_label = [data_label]
elif isinstance(data, SpectrumList):
pass
else:
path = pathlib.Path(data)
if path.is_file():
try:
data = [Spectrum1D.read(str(path), format=format)]
data_label = [data_label]
except IORegistryError:
# Multi-extension files may throw a registry error
data = SpectrumList.read(str(path), format=format)
else:
raise FileNotFoundError("No such file: " + str(path))
if isinstance(data, SpectrumList):
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
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)})")
# If there's already data in the viewer, convert units if needed
current_unit = None
current_spec = app.get_data_from_viewer("spectrum-viewer")
if current_spec != {} and current_spec is not None:
spec_key = list(current_spec.keys())[0]
current_unit = current_spec[spec_key].spectral_axis.unit
with app.data_collection.delay_link_manager_update():
for i in range(len(data)):
spec = data[i]
if current_unit is not None and spec.spectral_axis.unit != current_unit:
spec = Spectrum1D(flux=spec.flux,
spectral_axis=spec.spectral_axis.to(current_unit))
app.add_data(spec, data_label[i])
# Only auto-show the first spectrum in a list
if i == 0 and show_in_viewer:
app.add_data_to_viewer("spectrum-viewer", data_label[i])