import numpy as np
from jdaviz.core.helpers import ConfigHelper
from jdaviz.core.events import SnackbarMessage
[docs]class Specviz2d(ConfigHelper):
"""Specviz2D Helper class"""
_default_configuration = "specviz2d"
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
spec1d = self.app.get_viewer("spectrum-viewer")
spec1d.scales['x'].observe(self._update_spec2d_x_axis)
spec2d = self.app.get_viewer("spectrum-2d-viewer")
spec2d.scales['x'].observe(self._update_spec1d_x_axis)
def _extend_world(self, spec1d, ext):
# Extend 1D spectrum world axis to enable panning (within reason) past
# the bounds of data
world = self.app.data_collection[spec1d]["World 0"].copy()
dw = world[1]-world[0]
prepend = np.linspace(world[0]-dw*ext, world[0]-dw, ext)
dw = world[-1]-world[-2]
append = np.linspace(world[-1]+dw, world[-1]+dw*ext, ext)
world = np.hstack((prepend, world, append))
return world
def _update_spec2d_x_axis(self, change):
# This assumes the two spectrum viewers have the same x-axis shape and
# wavelength solution, which should always hold
if change['old'] is None:
pass
else:
name = change['name']
if name not in ['min', 'max']:
return
new_val = change['new']
spec1d = self.app.get_viewer('spectrum-viewer').state.reference_data.label
extend_by = int(self.app.data_collection[spec1d]["World 0"].shape[0])
world = self._extend_world(spec1d, extend_by)
# Warn the user if they've panned far enough away from the data
# that the viewers will desync
if new_val > world[-1] or new_val < world[0]:
msg = "Warning: panning too far away from the data may desync\
the 1D and 2D spectrum viewers"
msg = SnackbarMessage(msg, color='warning', sender=self)
self.app.hub.broadcast(msg)
idx = float((np.abs(world - new_val)).argmin()) - extend_by
scales = self.app.get_viewer('spectrum-2d-viewer').scales
old_idx = getattr(scales['x'], name)
if idx != old_idx:
setattr(scales['x'], name, idx)
def _update_spec1d_x_axis(self, change):
# This assumes the two spectrum viewers have the same x-axis shape and
# wavelength solution, which should always hold
if change['old'] is None:
pass
else:
name = change['name']
if name not in ['min', 'max']:
return
new_idx = int(np.around(change['new']))
spec1d = self.app.get_viewer('spectrum-viewer').state.reference_data.label
extend_by = int(self.app.data_collection[spec1d]["World 0"].shape[0])
world = self._extend_world(spec1d, extend_by)
scales = self.app.get_viewer('spectrum-viewer').scales
old_val = getattr(scales['x'], name)
# Warn the user if they've panned far enough away from the data
# that the viewers will desync
try:
val = world[new_idx+extend_by]
except IndexError:
val = old_val
msg = "Warning: panning too far away from the data may desync \
the 1D and 2D spectrum viewers"
msg = SnackbarMessage(msg, color='warning', sender=self)
self.app.hub.broadcast(msg)
if val != old_val:
setattr(scales['x'], name, val)
[docs] def load_data(self, spectrum_2d=None, spectrum_1d=None, spectrum_1d_label=None,
spectrum_2d_label=None, show_in_viewer=True):
"""
Load and parse a pair of corresponding 1D and 2D spectra
Parameters
----------
spectrum_1d: str or Spectrum1D
A spectrum as translatable container objects (e.g.
``Spectrum1D``) that can be read by glue-jupyter. Alternatively,
can be a string file path.
spectrum_2d: str
A spectrum as translatable container objects (e.g.
``Spectrum1D``) that can be read by glue-jupyter. Alternatively,
can be a string file path.
spectrum_1d_label : str
String representing the label for the data item loaded via
``onedspectra``. Can be a list of strings representing data labels
for each item in ``data_obj`` if ``data_obj`` is a list.
spectrum_2d_label : str
String representing the label for the data item loaded via
``twodspectra``. Can be a list of strings representing data labels
for each item in ``data_obj`` if ``data_obj`` is a list.
"""
if spectrum_2d_label is None:
spectrum_2d_label = "Spectrum 2D"
elif spectrum_2d_label[-2:] != "2D":
spectrum_2d_label = "{} 2D".format(spectrum_2d_label)
if spectrum_1d_label is None:
spectrum_1d_label = spectrum_2d_label.replace("2D", "1D")
if spectrum_2d is not None:
self.app.load_data(spectrum_2d, parser_reference="mosviz-spec2d-parser",
data_labels=spectrum_2d_label,
show_in_viewer=show_in_viewer,
add_to_table=False)
# Collapse the 2D spectrum to 1D if no 1D spectrum provided
if spectrum_1d is None:
self.app.load_data(spectrum_2d,
parser_reference="spec2d-1d-parser",
data_label=spectrum_1d_label,
show_in_viewer=show_in_viewer)
# Warn that this shouldn't be used for science
msg = "Warning: The collapsed 1D spectrum is for quicklook" +\
" purposes only. A robust extraction should be used for" +\
" scientific use cases."
msg = SnackbarMessage(msg, color='warning', sender=self,
timeout=10000)
self.app.hub.broadcast(msg)
return
self.app.load_data(spectrum_1d, data_label=spectrum_1d_label,
parser_reference="specviz-spectrum1d-parser",
show_in_viewer=show_in_viewer)