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Export Data From Jdaviz to Notebook

Specific instructions on exporting data from Jdaviz to your notebook vary slightly for each instance of Jdaviz, including for :ref:`Specviz <specviz-notebook>`, :ref:`Cubeviz <cubeviz-notebook>`, :ref:`Mosviz <mosviz-notebook>`, and :ref:`Imviz <imviz-notebook>`. In all instances, however, you can export data products from the Jdaviz into your notebook and, ultimately, save those variables locally.

Export Position Regions (Imviz)

In ~jdaviz.configs.imviz.helper.Imviz, you can extract positional regions:

regions = myviz.get_interactive_regions()
regions

Export Spectra

To export spectra currently loaded into the instance of your app back into your notebook do:

spectra = myviz.get_spectra()

which yields a specutils.Spectrum1D object that you can manipulate however you wish. You can then load the modified spectrum back into the notebook via the API described in :ref:`api-import`.

Alternatively, if you want more control over Specviz, you can access it the via the lower-level application interface that connects to the glue-jupyter application level. This is accessed via the .app attribute of the ~jdaviz.configs.specviz.helper.Specviz helper class. For more on what you can do with this lower-level object, see the API sections and the glue-jupyter documentation

For a list of available subsets to extract, you can type:

spectra = myviz.app.get_data_from_viewer('spectrum-viewer')
spectra

To extract data from you spectrum-viewer:

spectrum = myviz.app.get_data_from_viewer('spectrum-viewer','Subset 1')

Export Spectral Regions

If you have spectral region subsets, you can extract the parameters of these subsets as an Astropy spectral region. For a list of available spectral regions to extract, you can type:

regions = myviz.specviz.get_spectral_regions()
regions

To extract the spectral region you want:

myregion = regions["Subset 2"]

Export Data from Image Viewer

In Cubeviz, three image viewers display your data:

Top Left: flux-viewer
Center: uncert-viewer
Top Right: mask-viewer

If you have modified your data cube and have new data in one of your image viewers, you can extract it. To list the data available in a particular viewer:

data = myviz.app.get_data_from_viewer("uncert-viewer")
data

To extract the data you want:

mydata = myviz.app.get_data_from_viewer("uncert-viewer", "contents")

The data is returned as a glue-jupyter object. To convert to a numpy array:

mydata_flux = mydata["flux"]

Alternatively, you can wrap this all into a single command:

mydata = myviz.app.get_data_from_viewer("uncert-viewer", "contents[FLUX]")

Export Model and Model Parameters

After fitting a :ref:`specviz-plugins`, you can extract the Astropy model and/or model parameters. For a list of models:

models = myviz.get_models()
models

To extract a specific model:

mymodel = myviz.get_model_parameters(model_label="ModelLabel", x=x, y=y)

where the model_label parameter identifies which model should be returned and the x and y parameters identify specifically which spaxel fits are to be returned, for models applied to every spaxel using the Apply to Cube button. Leaving x or y as None will mean that the models fit to every spaxel across that axis will be returned.

To extract the model parameters:

myparams = myviz.get_model_parameters(model_label="ModelLabel", x=x, y=y)

You can then access the model parameter values:

myparams['ModelLabel']['parameter']