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re-implement get_spectra
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(undeprecated for now to see if existing tests pass)
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@kecnry
kecnry committed Jan 14, 2025
1 parent 819abf7 commit 9ae61ce
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Showing 2 changed files with 45 additions and 67 deletions.
15 changes: 14 additions & 1 deletion jdaviz/configs/default/plugins/data_menu/data_menu.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,8 @@ class DataMenu(TemplateMixin, LayerSelectMixin, DatasetSelectMixin):
* :meth:`data_labels_loaded`
* :meth:`data_labels_visible`
* :meth:`data_labels_unloaded`
* :meth:`subset_labels_loaded`
* :meth:`subset_labels_visible`
* ``layer`` (:class:`~jdaviz.core.template_mixin.LayerSelect`):
actively selected layer(s)
* ``orientation`` (:class:`~jdaviz.core.template_mixin.LayerSelect`):
Expand Down Expand Up @@ -156,7 +158,8 @@ def user_api(self):
expose = ['open_menu', 'layer', 'set_layer_visibility', 'toggle_layer_visibility',
'create_subset', 'modify_subset', 'add_data', 'view_info',
'remove_from_viewer', 'remove_from_app']
readonly = ['data_labels_loaded', 'data_labels_visible', 'data_labels_unloaded']
readonly = ['subset_labels_loaded', 'subset_labels_visible',
'data_labels_loaded', 'data_labels_visible', 'data_labels_unloaded']
if self.app.config == 'imviz':
expose += ['orientation']
return UserApiWrapper(self, expose=expose, readonly=readonly)
Expand All @@ -171,6 +174,16 @@ def open_menu(self):
def existing_subset_labels(self):
return [sg.label for sg in self.app.data_collection.subset_groups]

@property
def subset_labels_loaded(self):
return [layer['label'] for layer in self.layer_items
if layer['label'] in self.existing_subset_labels]

@property
def subset_labels_visible(self):
return [layer['label'] for layer in self.layer_items
if layer['label'] in self.existing_subset_labels and layer['visible']]

@property
def data_labels_loaded(self):
return [layer['label'] for layer in self.layer_items
Expand Down
97 changes: 31 additions & 66 deletions jdaviz/configs/specviz/helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,70 +85,6 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
timeout=timeout,
load_as_list=load_as_list)

@deprecated(since="4.2", alternative="get_data")
def get_spectra(self, data_label=None, spectral_subset=None, apply_slider_redshift="Warn"):
"""Returns the current data loaded into the main viewer
"""
spectra = {}
# Just to save line length
get_data_method = self.app._jdaviz_helper.get_data
viewer = self.app.get_viewer(self._default_spectrum_viewer_reference_name)
all_subsets = self.app.get_subsets(object_only=True)

if data_label is not None:
spectrum = get_data_method(data_label=data_label,
spectral_subset=spectral_subset,
cls=Spectrum1D)
spectra[data_label] = spectrum
else:
for layer_state in viewer.state.layers:
lyr = layer_state.layer
if spectral_subset is not None:
if lyr.label == spectral_subset:
spectrum = get_data_method(data_label=lyr.data.label,
spectral_subset=spectral_subset,
cls=Spectrum1D)
spectra[lyr.data.label] = spectrum
else:
continue
elif (isinstance(lyr, GroupedSubset) and lyr.label in all_subsets.keys() and
isinstance(all_subsets[lyr.label][0], Region)):
# spatial subsets appear as automatically extracted entries, we can skip
# the layer representing the subset itself.
continue
elif (isinstance(lyr, GroupedSubset) and lyr.label in all_subsets.keys() and
isinstance(all_subsets[lyr.label], SpectralRegion)):
spectrum = get_data_method(data_label=lyr.data.label,
spectral_subset=lyr.label,
cls=Spectrum1D)
spectra[f'{lyr.data.label} ({lyr.label})'] = spectrum
else:
spectrum = get_data_method(data_label=lyr.label,
cls=Spectrum1D)
spectra[lyr.label] = spectrum

if not apply_slider_redshift:
if data_label is not None:
return spectra[data_label]
return spectra
else:
output_spectra = {}
# We need to create new Spectrum1D outputs with the redshifts set
for key in spectra.keys():
output_spectra[key] = _apply_redshift_to_spectra(spectra[key], self._redshift)

if apply_slider_redshift == "Warn":
warnings.warn("Applying the value from the redshift "
"slider to the output spectra. To avoid seeing this "
"warning, explicitly set the apply_slider_redshift "
"keyword option to True or False.")

if data_label is not None:
output_spectra = output_spectra[data_label]

return output_spectra

@deprecated(since="4.1", alternative="subset_tools.get_regions")
def get_spectral_regions(self, use_display_units=False):
"""
Expand Down Expand Up @@ -305,7 +241,7 @@ def set_spectrum_tick_format(self, fmt, axis=None):
sv.set_tick_format(fmt, axis=['x', 'y'][axis])

def get_data(self, data_label=None, spectral_subset=None, cls=None,
use_display_units=False):
use_display_units=False, apply_slider_redshift="Warn"):
"""
Returns data with name equal to data_label of type cls with subsets applied from
spectral_subset.
Expand All @@ -320,12 +256,41 @@ def get_data(self, data_label=None, spectral_subset=None, cls=None,
The type that data will be returned as.
use_display_units: bool, optional
Whether to convert to the display units defined in the <unit-conversion> plugin.
apply_slider_redshift : bool, optional
Whether to apply the redshift slider value to the output spectra. If set to "Warn",
a warning will be issued if the redshift slider is not set to 0. To avoid seeing this
warning, explicitly set the apply_slider_redshift keyword option to True or False.
Returns
-------
data : cls
Data is returned as type cls with subsets applied.
"""
return self._get_data(data_label=data_label, spectral_subset=spectral_subset,
data = self._get_data(data_label=data_label, spectral_subset=spectral_subset,
cls=cls, use_display_units=use_display_units)

if apply_slider_redshift and isinstance(data, Spectrum1D):
return _apply_redshift_to_spectra(data, self._redshift)
return data

def get_spectra(self, data_label=None, spectral_subset=None, apply_slider_redshift="Warn"):
"""Returns the current data loaded into the main viewer
"""
sv = self.viewers[self._default_spectrum_viewer_reference_name]
spectra_labels = sv.data_menu.data_labels_loaded if data_label is None else [data_label]
subset_labels = sv.data_menu.subset_labels_visible if spectral_subset is None else [spectral_subset] # noqa

spectra = {}
for spec_label in spectra_labels:
spectra[spec_label] = self.get_data(data_label=spec_label,
cls=Spectrum1D,
apply_slider_redshift=apply_slider_redshift)
for subset_label in subset_labels:
spectrum = self.get_data(data_label=spec_label,
spectral_subset=subset_label,
cls=Spectrum1D,
apply_slider_redshift=apply_slider_redshift)
spectra[f"{spec_label} ({subset_label})"] = spectrum
return spectra

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