SpectralExtraction

class jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction(*args, **kwargs)

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()

• 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_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_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_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_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

Methods Summary

clear_marks()	Manually clear the live-preview marks.
export_bg(**kwargs)	Create a specreduce Background object from the input parameters defined in the plugin.
export_bg_img([add_data])	Create a background 2D spectrum from the input parameters defined in the plugin.
export_bg_spectrum([add_data])	Create a background 1D spectrum from the input parameters defined in the plugin.
export_bg_sub([add_data])	Create a background-subtracted 2D spectrum from the input parameters defined in the plugin.
export_extract(**kwargs)	Create a specreduce extraction object from the input parameters defined in the plugin.
export_extract_spectrum([add_data])	Create an extracted 1D spectrum from the input parameters defined in the plugin.
export_trace([add_data])	Create a specreduce Trace object from the input parameters defined in the plugin.
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_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_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_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/v3.5.0/lib/python3.9/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_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

Methods Documentation

clear_marks()

Manually clear the live-preview marks.

export_bg(**kwargs)

Create a specreduce Background object from the input parameters defined in the plugin.

Parameters:

add_databool

Whether to add the resulting image to the application, according to the options defined in the plugin.

export_bg_img(add_data=False, **kwargs)

Create a background 2D spectrum from the input parameters defined in the plugin.

Parameters:

add_databool

Whether to add the resulting image to the application, according to the options defined in the plugin.

export_bg_spectrum(add_data=False, **kwargs)

Create a background 1D spectrum from the input parameters defined in the plugin.

Parameters:

add_databool

Whether to add the resulting spectrum to the application, according to the options defined in the plugin.

export_bg_sub(add_data=False, **kwargs)

Create a background-subtracted 2D spectrum from the input parameters defined in the plugin.

Parameters:

add_databool

Whether to add the resulting image to the application, according to the options defined in the plugin.

export_extract(**kwargs)

Create a specreduce extraction object from the input parameters defined in the plugin.

export_extract_spectrum(add_data=False, **kwargs)

Create an extracted 1D spectrum from the input parameters defined in the plugin.

Parameters:

add_databool

Whether to add the resulting spectrum to the application, according to the options defined in the plugin.

export_trace(add_data=False, **kwargs)

Create a specreduce Trace object from the input parameters defined in the plugin.

Parameters:

add_databool

Whether to add the resulting trace to the application, according to the options defined in the plugin.

import_bg(bg)

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

Parameters:

bgspecreduce.background.Background

Background object to import

import_extract(ext)

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

Parameters:

extspecreduce.extract.BoxcarExtract

Extract object to import

import_trace(trace)

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)

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)

vue_create_bg_spec(*args)

vue_create_bg_sub(*args)

vue_create_trace(*args)

vue_extract_spectrum(*args)