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support specreduce 1.3 #1889

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merged 12 commits into from
Dec 13, 2022
Merged

support specreduce 1.3 #1889

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3da9aa2
updates for Spectrum1D support in specreduce
kecnry Nov 15, 2022
f2c0099
TEMP: force spectrum to plot in pixel-space
kecnry Nov 15, 2022
0313848
update spectral extraction with new model types
kecnry Dec 2, 2022
9f30a41
update to make use of FitTrace
kecnry Dec 2, 2022
81c10ea
binning toggle
kecnry Dec 2, 2022
b8bd460
update units in parser test
kecnry Dec 2, 2022
72116ed
order-dependent validation for number of bins
kecnry Dec 2, 2022
9e2aedc
pin specreduce 1.3
kecnry Dec 2, 2022
69574d6
re-introduce uncertainty fallbacks for HorneExtract
kecnry Dec 8, 2022
4dc4aae
fix minor typo in UI
kecnry Dec 8, 2022
dd4ec24
add support for Chebyshev traces
kecnry Dec 13, 2022
8a2c7a6
add UI warning for slow FitTrace
kecnry Dec 13, 2022
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3 changes: 3 additions & 0 deletions CHANGES.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,9 @@ Specviz
Specviz2d
^^^^^^^^^

- Update to be compatible with changes in specreduce 1.3, including FitTrace
with Polynomial, Spline, and Legendre options. [#1889]

API Changes
-----------

Expand Down
110 changes: 62 additions & 48 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 @@ -13,14 +13,20 @@
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.modeling import models
from astropy.nddata import StdDevUncertainty, VarianceUncertainty, UnknownUncertainty
from astropy import units
from specreduce import tracing
from specreduce import background
from specreduce import extract

__all__ = ['SpectralExtraction']

_model_cls = {'Spline': models.Spline1D,
'Polynomial': models.Polynomial1D,
'Legendre': models.Legendre1D,
'Chebyshev': models.Chebyshev1D}


@tray_registry('spectral-extraction', label="Spectral Extraction",
viewer_requirements=['spectrum', 'spectrum-2d'])
Expand All @@ -42,12 +48,15 @@ class SpectralExtraction(PluginTemplateMixin):
* ``trace_type`` (:class:`~jdaviz.core.template_mixin.SelectPluginComponent`):
controls the type of trace to be generated.
* ``trace_peak_method`` (:class:`~jdaviz.core.template_mixin.SelectPluginComponent`):
only applicable if ``trace_type`` is set to ``Auto``.
only applicable if ``trace_type`` is not ``Flat``.
* :attr:`trace_pixel` :
pixel of the trace. If ``trace_type`` is set to ``Auto``, then this
pixel of the trace. If ``trace_type`` is not ``Flat``, then this
is the "guess" for the automated trace.
* :attr:`trace_do_binning` :
only applicable if ``trace_type`` is not ``Flat``. Bin the input data when fitting the
trace.
* :attr:`trace_bins` :
only applicable if ``trace_type`` is set to ``Auto``.
only applicable if ``trace_type`` is not ``Flat`` and ``trace_do_binning``.
* :attr:`trace_window` :
full width of the trace.
* :meth:`import_trace`
Expand Down Expand Up @@ -101,10 +110,12 @@ class SpectralExtraction(PluginTemplateMixin):
trace_type_selected = Unicode().tag(sync=True)

trace_pixel = FloatHandleEmpty(0).tag(sync=True)
trace_order = IntHandleEmpty(3).tag(sync=True)

trace_peak_method_items = List().tag(sync=True)
trace_peak_method_selected = Unicode().tag(sync=True)

trace_do_binning = Bool(True).tag(sync=True)
trace_bins = IntHandleEmpty(20).tag(sync=True)
trace_window = IntHandleEmpty(0).tag(sync=True)

Expand Down Expand Up @@ -205,7 +216,9 @@ def __init__(self, *args, **kwargs):
self.trace_type = SelectPluginComponent(self,
items='trace_type_items',
selected='trace_type_selected',
manual_options=['Flat', 'Auto'])
manual_options=['Flat', 'Polynomial',
'Legendre', 'Chebyshev',
'Spline'])

self.trace_peak_method = SelectPluginComponent(self,
items='trace_peak_method_items',
Expand Down Expand Up @@ -302,8 +315,10 @@ def __init__(self, *args, **kwargs):
@property
def user_api(self):
return PluginUserApi(self, expose=('interactive_extract',
'trace_dataset', 'trace_type', 'trace_peak_method',
'trace_pixel', 'trace_bins', 'trace_window',
'trace_dataset', 'trace_type',
'trace_order', 'trace_peak_method',
'trace_pixel',
'trace_do_binning', 'trace_bins', 'trace_window',
'import_trace',
'export_trace',
'bg_dataset', 'bg_type',
Expand Down Expand Up @@ -407,7 +422,7 @@ def _update_plugin_marks(self, *args):
sp1d = self.export_extract_spectrum(add_data=False)
except Exception as e:
# NOTE: ignore error, but will be raised when clicking ANY of the export buttons
# NOTE: KosmosTrace or manual background are often giving a
# NOTE: FitTrace or manual background are often giving a
# "background regions overlapped" error from specreduce
self.ext_specreduce_err = repr(e)
self.marks['extract'].clear()
Expand Down Expand Up @@ -473,9 +488,9 @@ def marks(self):
return self._marks

@observe('trace_dataset_selected', 'trace_type_selected',
'trace_trace_selected', 'trace_offset',
'trace_trace_selected', 'trace_offset', 'trace_order',
'trace_pixel', 'trace_peak_method_selected',
'trace_bins', 'trace_window', 'active_step')
'trace_do_binning', 'trace_bins', 'trace_window', 'active_step')
def _interaction_in_trace_step(self, event={}):
if not self.plugin_opened or not self._do_marks:
return
Expand Down Expand Up @@ -613,11 +628,14 @@ def import_trace(self, trace):
if isinstance(trace, tracing.FlatTrace):
self.trace_type_selected = 'Flat'
self.trace_pixel = trace.trace_pos
elif isinstance(trace, tracing.KosmosTrace):
self.trace_type_selected = 'Auto'
elif isinstance(trace, tracing.FitTrace):
self.trace_type_selected = trace.trace_model.__class__.__name__.strip('1D')
self.trace_pixel = trace.guess
self.trace_window = trace.window
self.trace_bins = trace.bins
self.trace_do_binning = True
if hasattr(trace.trace_model, 'degree'):
self.trace_order = trace.trace_model.degree
elif isinstance(trace, tracing.ArrayTrace): # pragma: no cover
raise NotImplementedError(f"cannot import ArrayTrace into plugin. Use viz.load_trace instead") # noqa
else: # pragma: no cover
Expand All @@ -644,22 +662,24 @@ 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,
guess=self.trace_pixel,
bins=int(self.trace_bins),
window=self.trace_window,
peak_method=self.trace_peak_method_selected.lower())
elif self.trace_type_selected in _model_cls:
trace_model = _model_cls[self.trace_type_selected](degree=self.trace_order)
trace = tracing.FitTrace(self.trace_dataset.selected_obj,
guess=self.trace_pixel,
bins=int(self.trace_bins) if self.trace_do_binning else None,
window=self.trace_window,
peak_method=self.trace_peak_method_selected.lower(),
trace_model=trace_model)

else:
raise NotImplementedError(f"trace_type={self.trace_type_selected} not implemented")
Expand All @@ -674,7 +694,7 @@ 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 +756,15 @@ 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 +783,7 @@ 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 @@ -792,12 +809,15 @@ 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)

# TEMPORARY: override spectral axis to be in pixels until properly supporting plotting
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What issue will fix this? Is this future work?

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This is the general effort to support wavelengths (waiting for glue/bqplot work in order to sync the axes correctly). So yes, this is intentionally added to keep the current behavior.

# in wavelength/frequency
spec._spectral_axis = np.arange(len(spec.spectral_axis)) * units.pix

return spec

def vue_create_bg_spec(self, *args):
Expand All @@ -813,10 +833,7 @@ 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 +884,13 @@ 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)
if inp_sp2d.uncertainty is None:
inp_sp2d.uncertainty = VarianceUncertainty(np.ones_like(inp_sp2d.data))
if not hasattr(inp_sp2d.uncertainty, 'uncertainty_type'):
inp_sp2d.uncertainty = StdDevUncertainty(inp_sp2d.uncert)
ext = extract.HorneExtract(inp_sp2d, trace)
else:
raise NotImplementedError(f"extraction type '{self.ext_type_selected}' not supported") # noqa

Expand All @@ -892,12 +909,9 @@ 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)
# TEMPORARY: override spectral axis to be in pixels until properly supporting plotting
# in wavelength/frequency
spectrum._spectral_axis = np.arange(len(spectrum.spectral_axis)) * units.pix

if add_data:
self.ext_add_results.add_results_from_plugin(spectrum, replace=False)
Expand Down
48 changes: 41 additions & 7 deletions jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.vue
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Expand Up @@ -75,43 +75,77 @@
></v-select>
</v-row>

<v-row v-if="trace_type_selected!=='Flat'">
<v-text-field
label="Order"
type="number"
v-model.number="trace_order"
:rules="[() => trace_order!=='' || 'This field is required',
() => trace_order>=0 || 'Order must be positive',
() => (trace_type_selected!=='Spline' || (trace_order > 0 && trace_order <= 5)) || 'Spline order must be between 1 and 5']"
hint="Order of the trace model."
persistent-hint
>
</v-text-field>
</v-row>

<v-row>
<v-text-field
label="Pixel"
type="number"
v-model.number="trace_pixel"
:rules="[() => trace_pixel!=='' || 'This field is required']"
:hint="trace_type_selected === 'Flat' ? 'Pixel row for flat trace.' : 'Pixel row initial guess for auto trace.'"
:hint="trace_type_selected === 'Flat' ? 'Pixel row for flat trace.' : 'Pixel row initial guess for fitting the trace.'"
persistent-hint
>
</v-text-field>
</v-row>

<v-row v-if="trace_type_selected==='Auto'">
<v-row v-if="trace_type_selected!=='Flat'">
<v-switch
v-model="trace_do_binning"
label="Bin input spectrum"
></v-switch>
<v-text-field
v-if="trace_do_binning"
label="Bins"
type="number"
v-model.number="trace_bins"
:rules="[() => trace_bins!=='' || 'This field is required']"
:rules="[() => trace_bins!=='' || 'This field is required',
() => trace_bins>=Math.max(4, trace_order+1) || 'Bins must be >= '+Math.max(4, trace_order+1)]"
hint="Number of bins in the dispersion direction."
persistent-hint
>
</v-text-field>
</v-row>

<v-row v-if="trace_type_selected==='Auto'">
<v-row v-if="trace_type_selected!=='Flat' && !trace_do_binning">
<span class="v-messages v-messages__message text--secondary">
<b style="color: red !important">WARNING:</b> Trace fitting may be slow without binning.
</span>
</v-row>

<v-row v-if="trace_type_selected!=='Flat' && trace_do_binning && trace_bins > 20">
<span class="v-messages v-messages__message text--secondary">
<b style="color: red !important">WARNING:</b> Trace fitting may be slow with a large number of bins.
</span>
</v-row>


<v-row v-if="trace_type_selected!=='Flat'">
<v-text-field
label="Window Width"
type="number"
v-model.number="trace_window"
:rules="[() => trace_window!=='' || 'This field is required']"
:rules="[() => trace_window!=='' || 'This field is required',
() => trace_window > 0 || 'Window must be positive']"
hint="Width in rows to consider for peak finding."
persistent-hint
>
</v-text-field>
</v-row>

<v-row v-if="trace_type_selected==='Auto'">
<v-row v-if="trace_type_selected!=='Flat'">
<v-select
attach
:menu-props="{ left: true }"
Expand Down Expand Up @@ -313,7 +347,7 @@
:selected.sync="ext_dataset_selected"
:show_if_single_entry="false"
label="2D Spectrum"
hint="Select the data used to extract the spectrum. 'From Plugin' uses background-subtraced image defined in Background section above."
hint="Select the data used to extract the spectrum. 'From Plugin' uses background-subtracted image defined in Background section above."
/>

<plugin-dataset-select
Expand Down
8 changes: 4 additions & 4 deletions jdaviz/configs/specviz2d/plugins/spectral_extraction/tests/test_spectral_extraction.py
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Expand Up @@ -45,11 +45,11 @@ def test_plugin(specviz2d_helper):
trace = pext.export_trace(add_data=True) # overwrite
assert isinstance(trace, tracing.FlatTrace)

# create KosmosTrace
# create FitTrace
pext.trace_trace_selected = 'New Trace'
pext.trace_type_selected = 'Auto'
pext.trace_type_selected = 'Polynomial'
trace = pext.export_trace(add_data=True)
assert isinstance(trace, tracing.KosmosTrace)
assert isinstance(trace, tracing.FitTrace)
assert trace.guess == 27
trace = pext.export_trace(trace_pixel=26, add_data=False)
assert trace.guess == 26
Expand Down Expand Up @@ -135,7 +135,7 @@ def test_plugin(specviz2d_helper):
pext.update_marks(step)

# test exception handling
pext.trace_type = 'Auto'
pext.trace_type = 'Polynomial'
pext.bg_type_selected = 'TwoSided'
pext.bg_separation = 1
pext.bg_width = 5
Expand Down
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