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Updates to docs and images in docs for cubeviz import and display cubes
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Camilla Pacifici committed Mar 26, 2024
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7 changes: 4 additions & 3 deletions docs/cubeviz/displaycubes.rst
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Expand Up @@ -7,7 +7,7 @@ Displaying Cubes
The Cubeviz layout includes two image viewers (at the top of the app)
and one spectrum viewer (at the bottom of the app), which it attempts to
populate automatically when the first dataset is loaded. By default, Cubeviz
attempts to parse and display the flux in the top left viewer, the uncertainty
attempts to parse and display the flux in the top left viewer and the uncertainty
in the top right viewer. The spectrum
viewer is populated by default by collapsing the spatial axes using the "Sum"
function. The indicators that the load machinery looks for in each HDU to
Expand All @@ -34,8 +34,8 @@ Jupyter notebook using an API. The Toolbar below gives you several spectroscopic
display options. Right click will open a dropdown with access to different options
for each button.

.. image:: ./img/cubeviztoolbar.jpg
:alt: Speciz Toolbar
.. image:: ./img/cubeviztoolbar.png
:alt: Cubeviz Toolbar

.. _cubeviz-selecting-data:

Expand Down Expand Up @@ -93,6 +93,7 @@ over the region, and the resulting spectrum will be displayed in the 1D spectrum
the bottom of the UI.

.. image:: img/subset_creation.png
:alt: Subset creation in Cubeviz

.. _cubeviz-spectrum-at-spaxel:

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10 changes: 8 additions & 2 deletions docs/cubeviz/import_data.rst
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Expand Up @@ -6,7 +6,7 @@ Importing Data into Cubeviz

By design, Cubeviz only supports data that can be parsed as
:class:`~specutils.Spectrum1D` objects. Despite the name, :class:`~specutils.Spectrum1D`
now supports 3D cubes and allows the Python-level interface and parsing tools to
supports 3D cubes and allows the Python-level interface and parsing tools to
be defined in ``specutils`` instead of being duplicated in Jdaviz.
:class:`~specutils.Spectrum1D` objects are very flexible in their capabilities, however,
and hence should address most astronomical spectrum use cases.
Expand Down Expand Up @@ -139,8 +139,14 @@ object, you can load it into Cubeviz as follows:
.. code-block:: python
import numpy as np
import astropy.wcs as fitswcs
from astropy.wcs import wcs
import astropy.units as u
from specutils import Spectrum1D
from jdaviz import Cubeviz
from jwst import datamodels
file = "/path/to/data/file.fits"
mydatamodel = datamodels.open(file)
# mydatamodel is a jwst.datamodels object
# Due to current schema in jwst.datamodels, you'll need to create your own WCS object before you create your Spectrum1D object
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10 changes: 5 additions & 5 deletions docs/cubeviz/index.rst
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Expand Up @@ -18,18 +18,17 @@ with IFU data cubes. It uses
the `specutils <https://specutils.readthedocs.io/en/latest/>`_ package
from `Astropy <https://www.astropy.org>`_ .

Cubeviz is a tool for visualization and quick-look analysis of 3D data cubes,
primarily from integral field units (IFUs). It incorporates visualization tools
Cubeviz incorporates visualization tools
with analysis capabilities, such as Astropy regions and :ref:`specutils` packages.
Users can interact with their data from within the tool.
Cubeviz allows spectra of regions within the cube to be easily plotted and examined,
offering all the same capabilities as :ref:`specviz`.

In addition, Cubeviz also allows users to interacting with their cube to:
In addition, Cubeviz also allows users to interact with their cube to:

* view the wavelength slices (RA, DEC),

* view flux, error, and data quality cubes simultaneously,
* view flux and error or data quality cubes simultaneously,

* view spectra from selected spatial (RA, DEC) regions,

Expand All @@ -41,7 +40,8 @@ In addition, Cubeviz also allows users to interacting with their cube to:

* fit spectral lines,

* create moment maps, including line flux and kinematic maps (rotation velocity and velocity dispersion),
* create moment maps, including line flux and kinematic maps
(rotation velocity and velocity dispersion),

* overlay spectral line lists,

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