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updates for Spectrum1D support in specreduce
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@kecnry
kecnry committed Dec 2, 2022
1 parent dd7ffa2 commit 0465147
Showing 1 changed file with 14 additions and 33 deletions.
47 changes: 14 additions & 33 deletions jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,7 @@
from jdaviz.core.custom_traitlets import IntHandleEmpty, FloatHandleEmpty
from jdaviz.core.marks import PluginLine

from astropy.nddata import NDData, StdDevUncertainty, VarianceUncertainty, UnknownUncertainty
from specutils import Spectrum1D
from astropy.nddata import UnknownUncertainty
from specreduce import tracing
from specreduce import background
from specreduce import extract
Expand Down Expand Up @@ -644,18 +643,18 @@ def export_trace(self, add_data=False, **kwargs):
# being able to load back into the plugin)
orig_trace = self.trace_trace.selected_obj
if isinstance(orig_trace, tracing.FlatTrace):
trace = tracing.FlatTrace(self.trace_dataset.selected_obj.data,
trace = tracing.FlatTrace(self.trace_dataset.selected_obj,
orig_trace.trace_pos+self.trace_offset)
else:
trace = tracing.ArrayTrace(self.trace_dataset.selected_obj.data,
trace = tracing.ArrayTrace(self.trace_dataset.selected_obj,
self.trace_trace.selected_obj.trace+self.trace_offset)

elif self.trace_type_selected == 'Flat':
trace = tracing.FlatTrace(self.trace_dataset.selected_obj.data,
trace = tracing.FlatTrace(self.trace_dataset.selected_obj,
self.trace_pixel)

elif self.trace_type_selected == 'Auto':
trace = tracing.KosmosTrace(self.trace_dataset.selected_obj.data,
trace = tracing.KosmosTrace(self.trace_dataset.selected_obj,
guess=self.trace_pixel,
bins=int(self.trace_bins),
window=self.trace_window,
Expand All @@ -674,7 +673,7 @@ def vue_create_trace(self, *args):

def _get_bg_trace(self):
if self.bg_type_selected == 'Manual':
trace = tracing.FlatTrace(self.trace_dataset.selected_obj.data,
trace = tracing.FlatTrace(self.trace_dataset.selected_obj,
self.bg_trace_pixel)
elif self.bg_trace_selected == 'From Plugin':
trace = self.export_trace(add_data=False)
Expand Down Expand Up @@ -736,15 +735,15 @@ def export_bg(self, **kwargs):
trace = self._get_bg_trace()

if self.bg_type_selected == 'Manual':
bg = background.Background(self.bg_dataset.selected_obj.data,
bg = background.Background(self.bg_dataset.selected_obj,
[trace], width=self.bg_width)
elif self.bg_type_selected == 'OneSided':
bg = background.Background.one_sided(self.bg_dataset.selected_obj.data,
bg = background.Background.one_sided(self.bg_dataset.selected_obj,
trace,
self.bg_separation,
width=self.bg_width)
elif self.bg_type_selected == 'TwoSided':
bg = background.Background.two_sided(self.bg_dataset.selected_obj.data,
bg = background.Background.two_sided(self.bg_dataset.selected_obj,
trace,
self.bg_separation,
width=self.bg_width)
Expand All @@ -763,10 +762,7 @@ def export_bg_img(self, add_data=False, **kwargs):
Whether to add the resulting image to the application, according to the options
defined in the plugin.
"""
bg = self.export_bg(**kwargs)

bg_spec = Spectrum1D(spectral_axis=self.bg_dataset.selected_obj.spectral_axis,
flux=bg.bkg_image()*self.bg_dataset.selected_obj.flux.unit)
bg_spec = self.export_bg(**kwargs).bkg_image()

if add_data:
self.bg_add_results.add_results_from_plugin(bg_spec, replace=True)
Expand All @@ -792,8 +788,7 @@ def export_bg_spectrum(self, add_data=False, **kwargs):
Whether to add the resulting spectrum to the application, according to the options
defined in the plugin.
"""
bg = self.export_bg(**kwargs)
spec = bg.bkg_spectrum()
spec = self.export_bg(**kwargs).bkg_spectrum()

if add_data:
self.bg_spec_add_results.add_results_from_plugin(spec, replace=False)
Expand All @@ -813,10 +808,7 @@ def export_bg_sub(self, add_data=False, **kwargs):
Whether to add the resulting image to the application, according to the options
defined in the plugin.
"""
bg = self.export_bg(**kwargs)

bg_sub_spec = Spectrum1D(spectral_axis=self.bg_dataset.selected_obj.spectral_axis,
flux=bg.sub_image()*self.bg_dataset.selected_obj.flux.unit)
bg_sub_spec = self.export_bg(**kwargs).sub_image()

if add_data:
self.bg_sub_add_results.add_results_from_plugin(bg_sub_spec, replace=True)
Expand Down Expand Up @@ -867,13 +859,9 @@ def export_extract(self, **kwargs):
inp_sp2d = self._get_ext_input_spectrum()

if self.ext_type_selected == 'Boxcar':
ext = extract.BoxcarExtract(inp_sp2d.data, trace, width=self.ext_width)
ext = extract.BoxcarExtract(inp_sp2d, trace, width=self.ext_width)
elif self.ext_type_selected == 'Horne':
uncert = inp_sp2d.uncertainty if inp_sp2d.uncertainty is not None else VarianceUncertainty(np.ones_like(inp_sp2d.data)) # noqa
if not hasattr(uncert, 'uncertainty_type'):
uncert = StdDevUncertainty(uncert)
image = NDData(inp_sp2d.data, uncertainty=uncert)
ext = extract.HorneExtract(image, trace)
ext = extract.HorneExtract(inp_sp2d, trace)
else:
raise NotImplementedError(f"extraction type '{self.ext_type_selected}' not supported") # noqa

Expand All @@ -892,13 +880,6 @@ def export_extract_spectrum(self, add_data=False, **kwargs):
extract = self.export_extract(**kwargs)
spectrum = extract.spectrum

# Specreduce returns a spectral axis in pixels, so we'll replace with input spectral_axis
# NOTE: this is currently disabled until proper handling of axes-limit linking between
# the 2D spectrum image (plotted in pixels) and a 1D spectrum (plotted in freq or
# wavelength) is implemented.

# spectrum = Spectrum1D(spectral_axis=inp_sp2d.spectral_axis, flux=spectrum.flux)

if add_data:
self.ext_add_results.add_results_from_plugin(spectrum, replace=False)

Expand Down

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