import base64
import pathlib
import uuid
import numpy as np
from astropy.io.registry import IORegistryError
from astropy.nddata import StdDevUncertainty
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]
# No special processing is needed in this case, but we include it for completeness
elif isinstance(data, SpectrumList):
pass
elif isinstance(data, list):
data = SpectrumList.read(data, format=format)
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)
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))
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():
# these are used to build a combined spectrum with all
# input spectra included (taken from https://github.com/spacetelescope/
# dat_pyinthesky/blob/main/jdat_notebooks/MRS_Mstar_analysis/
# JWST_Mstar_dataAnalysis_analysis.ipynb)
wlallorig = []
fnuallorig = []
dfnuallorig = []
for i, spec in enumerate(data):
wave_units = spec.spectral_axis.unit
flux_units = spec.flux.unit
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])
# handle display, with the SpectrumList special case in mind.
if show_in_viewer:
if isinstance(data, SpectrumList):
# add spectrum to combined result
for wlind in range(len(spec.spectral_axis)):
wlallorig.append(spec.spectral_axis[wlind].value)
fnuallorig.append(spec.flux[wlind].value)
dfnuallorig.append(spec.uncertainty[wlind].array)
elif i == 0:
app.add_data_to_viewer("spectrum-viewer", data_label[i])
# reset display ranges, or build combined spectrum, when input is a SpectrumList instance
if isinstance(data, SpectrumList):
# build combined spectrum
wlallarr = np.array(wlallorig)
fnuallarr = np.array(fnuallorig)
dfnuallarr = np.array(dfnuallorig)
srtind = np.argsort(wlallarr)
wlall = wlallarr[srtind]
fnuall = fnuallarr[srtind]
fnuallerr = dfnuallarr[srtind]
# units are not being handled properly yet.
unc = StdDevUncertainty(fnuallerr * flux_units)
spec = Spectrum1D(flux=fnuall * flux_units, spectral_axis=wlall * wave_units,
uncertainty=unc)
# needs perhaps a better way to label the combined spectrum
label = "Combined " + data_label[0]
app.add_data(spec, label)
if show_in_viewer:
app.add_data_to_viewer("spectrum-viewer", label)