from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
from jdaviz.configs.specviz import Specviz
from jdaviz.core.events import AddDataMessage, SnackbarMessage
from jdaviz.core.helpers import CubeConfigHelper
from jdaviz.configs.cubeviz.plugins.viewers import CubevizImageView
__all__ = ['Cubeviz']
_spectral_axis_names = ["Wave", "Wavelength", "Freq", "Frequency",
"Wavenumber", "Velocity", "Energy"]
[docs]
class Cubeviz(CubeConfigHelper, LineListMixin):
"""Cubeviz Helper class"""
_default_configuration = 'cubeviz'
_default_spectrum_viewer_reference_name = "spectrum-viewer"
_default_uncert_viewer_reference_name = "uncert-viewer"
_default_flux_viewer_reference_name = "flux-viewer"
_default_image_viewer_reference_name = "image-viewer"
_cube_viewer_default_label = _default_flux_viewer_reference_name
_loaded_flux_cube = None
_loaded_uncert_cube = None
_loaded_mask_cube = None
_cube_viewer_cls = CubevizImageView
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.app.hub.subscribe(self, AddDataMessage,
handler=self._set_spectrum_x_axis)
def _set_spectrum_x_axis(self, msg):
viewer = self.app.get_viewer(self._default_spectrum_viewer_reference_name)
if msg.viewer_id != viewer.reference_id:
return
ref_data = viewer.state.reference_data
if ref_data and ref_data.ndim == 3:
for att_name in _spectral_axis_names:
if att_name in ref_data.component_ids():
if viewer.state.x_att != ref_data.id[att_name]:
viewer.state.x_att = ref_data.id[att_name]
viewer.state.reset_limits()
break
else:
viewer.state.x_att = ref_data.id["Pixel Axis 2 [x]"]
viewer.state.reset_limits()
[docs]
def load_data(self, data, data_label=None, override_cube_limit=False, **kwargs):
"""
Load and parse a data cube with Cubeviz.
(Note that only one cube may be loaded per Cubeviz instance.)
Parameters
----------
data : str, `~astropy.io.fits.HDUList`, `~specutils.Spectrum1D`, or ndarray
A string file path, astropy FITS object pointing to the
data cube, a spectrum object, or a Numpy array cube.
If plain array is given, axes order must be ``(x, y, z)``.
data_label : str or `None`
Data label to go with the given data. If not given,
one will be automatically generated.
override_cube_limit : bool
Override internal cube count limitation and load the data anyway.
Setting this to `True` is not recommended unless you know what
you are doing.
**kwargs : dict
Extra keywords accepted by Jdaviz application-level parser.
"""
if not override_cube_limit and len(self.app.state.data_items) != 0:
raise RuntimeError('Only one cube may be loaded per Cubeviz instance')
if data_label:
kwargs['data_label'] = data_label
super().load_data(data, parser_reference="cubeviz-data-parser", **kwargs)
if 'Spectral Extraction' not in self.plugins: # pragma: no cover
msg = SnackbarMessage(
"Automatic spectral extraction requires the Spectral Extraction plugin to be enabled", # noqa
color='error', sender=self, timeout=10000)
self.app.hub.broadcast(msg)
else:
try:
self.plugins['Spectral Extraction']._obj._extract_in_new_instance(auto_update=False, add_data=True) # noqa
except Exception:
msg = SnackbarMessage(
"Automatic spectrum extraction for the entire cube failed."
" See the spectral extraction plugin to perform a custom extraction",
color='error', sender=self, timeout=10000)
else:
msg = SnackbarMessage(
"The extracted 1D spectrum was generated automatically for the entire cube."
" See the spectral extraction plugin for details or to"
" perform a custom extraction.",
color='warning', sender=self, timeout=10000)
self.app.hub.broadcast(msg)
[docs]
def select_wavelength(self, wavelength):
"""
Select the slice closest to the provided wavelength.
Parameters
----------
wavelength : float
Wavelength to select in units of the x-axis of the spectrum. The nearest slice will
be selected if "snap to slice" is enabled in the slice plugin.
"""
if not isinstance(wavelength, (int, float)):
raise TypeError("wavelength must be a float or int")
self.select_slice(wavelength)
@property
def specviz(self):
"""
A Specviz helper (:class:`~jdaviz.configs.specviz.helper.Specviz`) for the Jdaviz
application that is wrapped by Cubeviz.
"""
if not hasattr(self, '_specviz'):
self._specviz = Specviz(app=self.app)
return self._specviz
[docs]
def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
cls=None, use_display_units=False):
"""
Returns data with name equal to ``data_label`` of type ``cls`` with subsets applied from
``spectral_subset``, if applicable.
Parameters
----------
data_label : str, optional
Provide a label to retrieve a specific data set from data_collection.
spatial_subset : str, optional
Spatial subset applied to data. Only applicable if ``data_label`` points to a cube or
image. To extract a spectrum from a cube, use the spectral extraction plugin instead.
spectral_subset : str, optional
Spectral subset applied to data.
cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
The type that data will be returned as.
Returns
-------
data : cls
Data is returned as type cls with subsets applied.
"""
return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
spectral_subset=spectral_subset,
cls=cls, use_display_units=use_display_units)
# Need this method for Imviz Aperture Photometry plugin.
[docs]
def get_aperture_photometry_results(self):
"""Return aperture photometry results, if any.
Results are calculated using :ref:`cubeviz-aper-phot` plugin.
Returns
-------
results : `~astropy.table.QTable` or `None`
Photometry results if available or `None` otherwise.
"""
return self.plugins['Aperture Photometry']._obj.export_table()
