SpectralExtraction#

class jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction(*args, **kwargs)[source]#

Bases: PluginTemplateMixin

The Spectral Extraction plugin exposes specreduce methods for tracing, background subtraction, and spectral extraction from 2D spectra. See the Spectral Extraction Plugin Documentation for more details.

Only the following attributes and methods are available through the public plugin API:

show()
open_in_tray()
close_in_tray()
interactive_extract
trace_dataset (SelectPluginComponent): controls the input dataset for generating the trace.
trace_type (SelectPluginComponent): controls the type of trace to be generated.
trace_peak_method (SelectPluginComponent): only applicable if trace_type is not Flat.
trace_pixel : pixel of the trace. If trace_type is not Flat, then this is the “guess” for the automated trace.
trace_do_binning : only applicable if trace_type is not Flat. Bin the input data when fitting the trace.
trace_bins : only applicable if trace_type is not Flat and trace_do_binning.
trace_window : full width of the trace.
import_trace()
export_trace()
bg_dataset (DatasetSelect): controls the input dataset for generating the background.
bg_type (SelectPluginComponent): controls the type of background to be generated.
bg_trace_pixel : only applicable if bg_type is set to Manual
bg_separation : only applicable if bg_type set set to OneSided or TwoSided. Separation from the referenced trace for the center of each of the background window(s).
bg_width : full width of each background window(s).
bg_statistic (SelectPluginComponent): statistic to use when computing the background. ‘Average’ will account for partial pixel weights, ‘Median’ will include all partial pixels.
bg_add_results (AddResults)
bg_sub_add_results
import_bg()
export_bg()
export_bg_img()
export_bg_sub()
ext_dataset (DatasetSelect): controls the input dataset for generating the extracted spectrum. “From Plugin” will use the background-subtracted image as defined by the background options above. To skip background extraction, select the original input 2D spectrum.
ext_trace (DatasetSelect)
ext_type (SelectPluginComponent)
ext_width : full width of the extraction window.
ext_add_results (AddResults)
import_extract()
export_extract()
export_extract_spectrum()

Public constructor

Attributes Summary

`active_step`	A trait for unicode strings.
`bg_add_to_viewer_items`	An instance of a Python list.
`bg_add_to_viewer_selected`	A trait for unicode strings.
`bg_dataset_items`	An instance of a Python list.
`bg_dataset_selected`	A trait for unicode strings.
`bg_img_spinner`	A boolean (True, False) trait.
`bg_results_label`	A trait for unicode strings.
`bg_results_label_auto`	A boolean (True, False) trait.
`bg_results_label_default`	A trait for unicode strings.
`bg_results_label_invalid_msg`	A trait for unicode strings.
`bg_results_label_overwrite`	A boolean (True, False) trait.
`bg_separation`	Mixin to handle empty floating point field.
`bg_spec_add_to_viewer_items`	An instance of a Python list.
`bg_spec_add_to_viewer_selected`	A trait for unicode strings.
`bg_spec_results_label`	A trait for unicode strings.
`bg_spec_results_label_auto`	A boolean (True, False) trait.
`bg_spec_results_label_default`	A trait for unicode strings.
`bg_spec_results_label_invalid_msg`	A trait for unicode strings.
`bg_spec_results_label_overwrite`	A boolean (True, False) trait.
`bg_spec_spinner`	A boolean (True, False) trait.
`bg_statistic_items`	An instance of a Python list.
`bg_statistic_selected`	A trait for unicode strings.
`bg_sub_add_to_viewer_items`	An instance of a Python list.
`bg_sub_add_to_viewer_selected`	A trait for unicode strings.
`bg_sub_results_label`	A trait for unicode strings.
`bg_sub_results_label_auto`	A boolean (True, False) trait.
`bg_sub_results_label_default`	A trait for unicode strings.
`bg_sub_results_label_invalid_msg`	A trait for unicode strings.
`bg_sub_results_label_overwrite`	A boolean (True, False) trait.
`bg_sub_spinner`	A boolean (True, False) trait.
`bg_trace_items`	An instance of a Python list.
`bg_trace_pixel`	Mixin to handle empty floating point field.
`bg_trace_selected`	A trait for unicode strings.
`bg_type_items`	An instance of a Python list.
`bg_type_selected`	A trait for unicode strings.
`bg_width`	Mixin to handle empty floating point field.
`dialog`	A boolean (True, False) trait.
`ext_add_to_viewer_items`	An instance of a Python list.
`ext_add_to_viewer_selected`	A trait for unicode strings.
`ext_dataset_items`	An instance of a Python list.
`ext_dataset_selected`	A trait for unicode strings.
`ext_results_label`	A trait for unicode strings.
`ext_results_label_auto`	A boolean (True, False) trait.
`ext_results_label_default`	A trait for unicode strings.
`ext_results_label_invalid_msg`	A trait for unicode strings.
`ext_results_label_overwrite`	A boolean (True, False) trait.
`ext_specreduce_err`	A trait for unicode strings.
`ext_trace_items`	An instance of a Python list.
`ext_trace_selected`	A trait for unicode strings.
`ext_type_items`	An instance of a Python list.
`ext_type_selected`	A trait for unicode strings.
`ext_uncert_warn`	A boolean (True, False) trait.
`ext_width`	Mixin to handle empty floating point field.
`interactive_extract`	A boolean (True, False) trait.
`marks`	Access the marks created by this plugin in both the spectrum-viewer and spectrum-2d-viewer.
`template_file`
`trace_add_to_viewer_items`	An instance of a Python list.
`trace_add_to_viewer_selected`	A trait for unicode strings.
`trace_bins`	Mixin to handle empty integer field.
`trace_dataset_items`	An instance of a Python list.
`trace_dataset_selected`	A trait for unicode strings.
`trace_do_binning`	A boolean (True, False) trait.
`trace_offset`	Mixin to handle empty integer field.
`trace_order`	Mixin to handle empty integer field.
`trace_peak_method_items`	An instance of a Python list.
`trace_peak_method_selected`	A trait for unicode strings.
`trace_pixel`	Mixin to handle empty floating point field.
`trace_results_label`	A trait for unicode strings.
`trace_results_label_auto`	A boolean (True, False) trait.
`trace_results_label_default`	A trait for unicode strings.
`trace_results_label_invalid_msg`	A trait for unicode strings.
`trace_results_label_overwrite`	A boolean (True, False) trait.
`trace_spinner`	A boolean (True, False) trait.
`trace_trace_items`	An instance of a Python list.
`trace_trace_selected`	A trait for unicode strings.
`trace_type_items`	An instance of a Python list.
`trace_type_selected`	A trait for unicode strings.
`trace_window`	Mixin to handle empty integer field.
`user_api`
`uses_active_status`	A boolean (True, False) trait.

Methods Summary

`export_bg`(args, *kwargs)
`export_bg_img`(args, *kwargs)
`export_bg_spectrum`(args, *kwargs)
`export_bg_sub`(args, *kwargs)
`export_extract`(**kwargs)	Create a specreduce extraction object from the input parameters defined in the plugin.
`export_extract_spectrum`(args, *kwargs)
`export_trace`(args, *kwargs)
`import_bg`(bg)	Import the input parameters from an existing specreduce Background object into the plugin.
`import_extract`(ext)	Import the input parameters from an existing specreduce extract object into the plugin.
`import_trace`(trace)	Import the input parameters from an existing specreduce Trace object into the plugin.
`update_marks`([step])	Manually update the live-preview marks for a given step in spectral extraction.
`vue_create_bg_img`(*args)
`vue_create_bg_spec`(*args)
`vue_create_bg_sub`(*args)
`vue_create_trace`(*args)
`vue_extract_spectrum`(*args)

Attributes Documentation

active_step#: A trait for unicode strings.

bg_add_to_viewer_items#: An instance of a Python list.

bg_add_to_viewer_selected#: A trait for unicode strings.

bg_dataset_items#: An instance of a Python list.

bg_dataset_selected#: A trait for unicode strings.

bg_img_spinner#: A boolean (True, False) trait.

bg_results_label#: A trait for unicode strings.

bg_results_label_auto#: A boolean (True, False) trait.

bg_results_label_default#: A trait for unicode strings.

bg_results_label_invalid_msg#: A trait for unicode strings.

bg_results_label_overwrite#: A boolean (True, False) trait.

bg_separation#: Mixin to handle empty floating point field.

bg_spec_add_to_viewer_items#: An instance of a Python list.

bg_spec_add_to_viewer_selected#: A trait for unicode strings.

bg_spec_results_label#: A trait for unicode strings.

bg_spec_results_label_auto#: A boolean (True, False) trait.

bg_spec_results_label_default#: A trait for unicode strings.

bg_spec_results_label_invalid_msg#: A trait for unicode strings.

bg_spec_results_label_overwrite#: A boolean (True, False) trait.

bg_spec_spinner#: A boolean (True, False) trait.

bg_statistic_items#: An instance of a Python list.

bg_statistic_selected#: A trait for unicode strings.

bg_sub_add_to_viewer_items#: An instance of a Python list.

bg_sub_add_to_viewer_selected#: A trait for unicode strings.

bg_sub_results_label#: A trait for unicode strings.

bg_sub_results_label_auto#: A boolean (True, False) trait.

bg_sub_results_label_default#: A trait for unicode strings.

bg_sub_results_label_invalid_msg#: A trait for unicode strings.

bg_sub_results_label_overwrite#: A boolean (True, False) trait.

bg_sub_spinner#: A boolean (True, False) trait.

bg_trace_items#: An instance of a Python list.

bg_trace_pixel#: Mixin to handle empty floating point field.

bg_trace_selected#: A trait for unicode strings.

bg_type_items#: An instance of a Python list.

bg_type_selected#: A trait for unicode strings.

bg_width#: Mixin to handle empty floating point field.

dialog#: A boolean (True, False) trait.

ext_add_to_viewer_items#: An instance of a Python list.

ext_add_to_viewer_selected#: A trait for unicode strings.

ext_dataset_items#: An instance of a Python list.

ext_dataset_selected#: A trait for unicode strings.

ext_results_label#: A trait for unicode strings.

ext_results_label_auto#: A boolean (True, False) trait.

ext_results_label_default#: A trait for unicode strings.

ext_results_label_invalid_msg#: A trait for unicode strings.

ext_results_label_overwrite#: A boolean (True, False) trait.

ext_specreduce_err#: A trait for unicode strings.

ext_trace_items#: An instance of a Python list.

ext_trace_selected#: A trait for unicode strings.

ext_type_items#: An instance of a Python list.

ext_type_selected#: A trait for unicode strings.

ext_uncert_warn#: A boolean (True, False) trait.

ext_width#: Mixin to handle empty floating point field.

interactive_extract#: A boolean (True, False) trait.

marks#: Access the marks created by this plugin in both the spectrum-viewer and spectrum-2d-viewer.

template_file = ('/home/docs/checkouts/readthedocs.org/user_builds/jdaviz/envs/latest/lib/python3.11/site-packages/jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py', 'spectral_extraction.vue')#

trace_add_to_viewer_items#: An instance of a Python list.

trace_add_to_viewer_selected#: A trait for unicode strings.

trace_bins#: Mixin to handle empty integer field.

trace_dataset_items#: An instance of a Python list.

trace_dataset_selected#: A trait for unicode strings.

trace_do_binning#: A boolean (True, False) trait.

trace_offset#: Mixin to handle empty integer field.

trace_order#: Mixin to handle empty integer field.

trace_peak_method_items#: An instance of a Python list.

trace_peak_method_selected#: A trait for unicode strings.

trace_pixel#: Mixin to handle empty floating point field.

trace_results_label#: A trait for unicode strings.

trace_results_label_auto#: A boolean (True, False) trait.

trace_results_label_default#: A trait for unicode strings.

trace_results_label_invalid_msg#: A trait for unicode strings.

trace_results_label_overwrite#: A boolean (True, False) trait.

trace_spinner#: A boolean (True, False) trait.

trace_trace_items#: An instance of a Python list.

trace_trace_selected#: A trait for unicode strings.

trace_type_items#: An instance of a Python list.

trace_type_selected#: A trait for unicode strings.

trace_window#: Mixin to handle empty integer field.

user_api#

uses_active_status#: A boolean (True, False) trait.

Methods Documentation

export_bg(*args, **kwargs)#

export_bg_img(*args, **kwargs)#

export_bg_spectrum(*args, **kwargs)#

export_bg_sub(*args, **kwargs)#

export_extract(**kwargs)[source]#: Create a specreduce extraction object from the input parameters defined in the plugin.

export_extract_spectrum(*args, **kwargs)#

export_trace(*args, **kwargs)#

import_bg(bg)[source]#

Import the input parameters from an existing specreduce Background object into the plugin.

Parameters:

bgspecreduce.background.Background: Background object to import

import_extract(ext)[source]#

Import the input parameters from an existing specreduce extract object into the plugin.

Parameters:

extspecreduce.extract.BoxcarExtract: Extract object to import

import_trace(trace)[source]#

Import the input parameters from an existing specreduce Trace object into the plugin.

Parameters:

tracespecreduce.tracing.Trace: Trace object to import

update_marks(step=None)[source]#

Manually update the live-preview marks for a given step in spectral extraction. This API mimics opening the plugin and interacting with one of the steps.

Parameters:

stepstr: Step in the extraction process to visualize. Must be one of: ‘trace’, ‘bg’, ‘ext’.

vue_create_bg_img(*args)[source]#

vue_create_bg_spec(*args)[source]#

vue_create_bg_sub(*args)[source]#

vue_create_trace(*args)[source]#

vue_extract_spectrum(*args)[source]#