export_data.rst

Exporting Data from Cubeviz

After data have been manipulated or analyzed, it is possible to export those data currently back into your Jupyter notebook.

Spatial Regions

Export Spatial Regions <imviz_export>

Documentation on how to export spatial regions.

Since Specviz can be accessed from Cubeviz, the following line of code can be used to extract the spectrum of a spatial subset named "Subset 1":

subset1_spec1d = cubeviz.specviz.get_spectra(subset_to_apply="Subset 1")

An example without accessing Specviz:

subset1_spec1d = cubeviz.get_data(data_label=flux_data_label, 
                                  subset_to_apply="Subset 1",
                                  statistic="mean")

Note that in the above example, the statistic keyword is used to tell Cubeviz how to collapse the flux cube down to a one dimensional spectrum - this is not necessarily equivalent to the collapsed spectrum in the spectrum viewer, which may have used a different collapse statistic.

To get all subsets from the spectrum viewer:

subset1_spec1d = cubeviz.app.get_subsets_from_viewer("spectrum-viewer")

To access the spatial regions themselves:

regions = cubeviz.get_interactive_regions()
regions

1D Spectra and Spectral Regions

Export Spectra <specviz-export-data>

Documentation on how to export data from the spectrum-viewer.

The following line of code can be used to extract a spectral subset named "Subset 2":

subset2_spec1d = cubeviz.specviz.get_spectra("Subset 2")

3D Data Cubes

To extract the entire cube, you can run the following code (replace "data_name" with the name of the data you want to extract):

mydata = cubeviz.get_data(data_label="data_name")

The data is returned as a 3D specutils.Spectrum1D object.

To write out a specutils.Spectrum1D cube from Cubeviz (e.g., a fitted cube from model-fitting), where the mask (if available) is as defined in Spectrum1D masks:

mydata.write("mydata.fits", format="jdaviz-cube")

Data can also be accessed directly from data_collection using the following code:

cubeviz.app.data_collection[0]

Which is returned as a ~glue.core.data.Data object. The ~glue.core.data_collection.DataCollection object can be indexed to return all available data (i.e., not just using 0 like in the previous example).

Model Fits

For a list of model labels:

models = cubeviz.get_models()
models

Once you know the model labels, to get a specific model:

mymodel = cubeviz.get_models(model_label="ModelLabel", x=10)

To extract all of the model parameters:

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

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.

Markers Table

All mouseover information in the markers plugin <markers-plugin> can be exported to an astropy table <astropy:astropy-table> by calling ~jdaviz.core.template_mixin.TableMixin.export_table (see plugin-apis).