import warnings
from astropy import units as u
from glue.core.message import (DataCollectionAddMessage,
DataCollectionDeleteMessage)
from glue.core import Data
from glue.core.link_helpers import LinkSame
from specutils import Spectrum1D
from specutils.manipulation import spectral_slab
from traitlets import List, Unicode, observe
from jdaviz.core.events import SnackbarMessage
from jdaviz.core.registries import tray_registry
from jdaviz.core.template_mixin import PluginTemplateMixin, SpectralSubsetSelectMixin
__all__ = ['Collapse']
[docs]@tray_registry('g-collapse', label="Collapse")
class Collapse(PluginTemplateMixin, SpectralSubsetSelectMixin):
template_file = __file__, "collapse.vue"
data_items = List([]).tag(sync=True)
selected_data_item = Unicode().tag(sync=True)
funcs = List(['Mean', 'Median', 'Min', 'Max', 'Sum']).tag(sync=True)
selected_func = Unicode('Sum').tag(sync=True)
# selected_viewer for spatial-spatial image.
# NOTE: this is currently cubeviz-specific so will need to be updated
# to be config-specific if using within other viewer configurations.
viewer_to_id = {'Left': 'cubeviz-0', 'Center': 'cubeviz-1', 'Right': 'cubeviz-2'}
viewers = List(['None', 'Left', 'Center', 'Right']).tag(sync=True)
selected_viewer = Unicode('None').tag(sync=True)
spectral_unit = Unicode().tag(sync=True)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.hub.subscribe(self, DataCollectionAddMessage,
handler=self._on_data_updated)
self.hub.subscribe(self, DataCollectionDeleteMessage,
handler=self._on_data_updated)
self._selected_data = None
self._selected_cube = None
self._label_counter = 0
def _on_data_updated(self, msg):
self.data_items = [x.label for x in self.data_collection]
# Default to selecting the first loaded cube
if self._selected_data is None:
for i in range(len(self.data_items)):
try:
self.selected_data_item = self.data_items[i]
except (ValueError, TypeError):
continue
@observe('selected_data_item')
def _on_data_item_selected(self, event):
data_label = event['new']
if data_label not in self.data_collection.labels:
return
self._selected_data = self.data_collection[self.data_collection.labels.index(data_label)]
self._selected_cube = self._selected_data.get_object(cls=Spectrum1D, statistic=None)
self.spectral_unit = self._selected_cube.spectral_axis.unit.to_string()
[docs] def vue_collapse(self, *args, **kwargs):
# Collapsing over the spectral axis. Cut out the desired spectral
# region. Defaults to the entire spectrum.
spec_min = float(self.spectral_subset.selected_min(self._selected_cube)) * u.Unit(self.spectral_unit) # noqa
spec_max = float(self.spectral_subset.selected_max(self._selected_cube)) * u.Unit(self.spectral_unit) # noqa
with warnings.catch_warnings():
warnings.filterwarnings('ignore', message='No observer defined on WCS')
spec = spectral_slab(self._selected_cube, spec_min, spec_max)
# Spatial-spatial image only.
collapsed_spec = spec.collapse(self.selected_func.lower(), axis=-1).T # Quantity
data = Data()
data['flux'] = collapsed_spec.value
data.get_component('flux').units = str(collapsed_spec.unit)
self._label_counter += 1
label = f"Collapsed {self._label_counter} {self._selected_data.label}"
data.meta["Plugin"] = "Collapse"
self.app.add_data(data, label)
self._link_collapse_data()
snackbar_message = SnackbarMessage(
f"Data set '{self._selected_data.label}' collapsed successfully.",
color="success",
sender=self)
self.hub.broadcast(snackbar_message)
# Spatial-spatial image only.
if self.selected_viewer != 'None':
# replace the contents in the selected viewer with the results from this plugin
self.app.add_data_to_viewer(self.viewer_to_id.get(self.selected_viewer),
label, clear_other_data=True)
def _link_collapse_data(self):
"""
Link the new dataset pixel-wise to the original dataset. In general
direct pixel to pixel links are the most efficient and should be
used in cases like this where we know there is a 1-to-1 mapping of
pixel coordinates.
"""
new_len = len(self.app.data_collection)
pc_new = self.app.data_collection[-1].pixel_component_ids
# Link to the first dataset with compatible coordinates
for i in range(new_len - 1):
pc_old = self.app.data_collection[i].pixel_component_ids
# If data_collection[i] is also from the collapse plugin
if ("Plugin" in self.app.data_collection[i].meta and
self.app.data_collection[i].meta["Plugin"] == "Collapse"):
links = [LinkSame(pc_old[0], pc_new[0]),
LinkSame(pc_old[1], pc_new[1])]
# Else, link collapse data to cube (pc_old)
else:
links = [[LinkSame(pc_new[1], pc_old[2]),
LinkSame(pc_new[0], pc_old[1])]]
self.app.data_collection.add_link(links)
break