Jdaviz

================

New Features
------------
- Stretch bounds tool now enables dynamic adjustment of spline knots. [2545, 2623]

- Stretch histogram shows a spinner when the histogram data is updating. [2644]

- Spectrum and image viewer bounds can now be set through the Plot Options UI. [2604, 2649]

- Opacity for spatial subsets is now adjustable from within Plot Options. [2663]

- Live-preview of aperture selection in plugins. [2664, 2684]

- "Export Plot" plugin is now replaced with the more general "Export" plugin. [2722, 2782]

- "Export" plugin supports exporting plugin tables, plugin plots, data, and
non-composite spatial subsets.[2755, 2774, 2760, 2772, 2770, 2780, 2784]

- Opening a plugin in the tray (from the API or the toolbar buttons) now scrolls to that plugin.
[2768]

Cubeviz
^^^^^^^

- Calculated moments can now be output in velocity units. [2584, 2588, 2665, 2697]

- Added functionality to Collapse and Spectral Extraction plugins to save results to FITS file. [2586]

- Moment map plugin now supports linear per-spaxel continuum subtraction. [2587]

- Single-pixel subset tool now shows spectrum-at-spaxel on hover. [2647]

- Spectral extraction plugin re-organized into subsections to be more consistent with specviz2d. [2676]

- Add conical aperture support to cubeviz in the spectral extraction plugin. [2679]

- New aperture photometry plugin that can perform aperture photometry on selected cube slice. [2666]

- Live previews in spectral extraction plugin. [2733]

- Slice plugin is refactored to rely on the spectral value instead of the slice index. This removes
both the slider and slice-index input. [2715]

Imviz
^^^^^

- There is now option for image rotation in Orientation (was Links Control) plugin.
This feature requires WCS linking. [2179, 2673, 2699, 2734, 2759]

- Add "Random" colormap for visualizing image segmentation maps. [2671]

- Enabling any matched zoom tool in a viewer disables other matched zoom tools in other viewers
to avoid recursion. [2764]

Specviz2d
^^^^^^^^^

- Spectral extraction plugin: highlighting of active header section. [2676]

API Changes
-----------

- ``width`` argument in Line Analysis plugin is renamed to ``continuum_width`` and ``width``
will be removed in a future release. [2587]

- New API access to ``viz.data_labels``, ``viewer.data_labels_visible``, and
``viewer.data_labels_loaded``. [2626]

Cubeviz
^^^^^^^

- ``spatial_subset`` in the spectral extraction plugin is now renamed to ``aperture`` and the deprecated name will
be removed in a future release. [2664]

- Slice plugin's ``wavelength``, ``wavelength_unit``, and ``show_wavelength`` are deprecated in favor
of ``value``, ``value_unit``, and ``show_value``, respectively. ``slice`` is also deprecated
and should be replaced with accessing/setting ``value`` directly. [2706, 2715]

- Disabled exporting spectrum-viewer to PNG in Cubeviz; pending investigation/bugfix. [2777]

Imviz
^^^^^

- Links Control plugin is now called Orientation. [2179]

- Linking by WCS will now always generate a hidden reference data layer
without distortion. As a result, when WCS linked, the first loaded data
is no longer the reference data. Additionally, if data is distorted,
its distortion will show when linked by WCS. If there is also data without WCS,
it can no longer be displayed when WCS linked. [2179]

- ``imviz.link_data()`` inputs and behaviors are now consistent with the Orientation plugin. [2179]

- Single-pixel tool is no longer available. To mark a single-pixel area, use Markers plugin. [2710]

Bug Fixes
---------

- Fix redshifted line lists that were displaying at rest wavelengths, by assuming a global redshift. [2726]

- Order of RGB preset colors now matches for less than and greater than 5 layers. [2731]

Cubeviz
^^^^^^^

- Spectral extraction now ignores NaNs. [2737]

Imviz
^^^^^

- Apertures that are selected and later modified to be invalid properly show a warning. [2684]

- Histogram in Plot Options no longer stalls for a very large image. [2735]

Specviz
^^^^^^^

- Check unit type (e.g., flux density, surface brightness, counts, etc) for generating
display label for the y axis in spectral viewer. Previously it was hard coded
to always display ``flux density`` no matter the input unit. [2703]

==================

Bug Fixes
---------

* Fix app top-bar alignment in popouts and when embedded in websites. [2648]

* Viewer data-menu is no-longer synced between different instances of the app to avoid recursion
between click events. [2670]

* Fix data-menu cutoff in smaller viewers, ensuring full visibility regardless of viewer dimensions. [2630, 2707]

Cubeviz
^^^^^^^
- Fixes Spectral Extraction's assumptions of one data per viewer, and flux data only in
flux-viewer/uncertainty data only in uncert-viewer. [2646]

- Fixed a bug where cube model fitting could fail (endless spinner) if input cube
has invalid 3D WCS. [2685]

==================

Bug Fixes
---------

- Compatibility with glue-core 1.17. [2591, 2595]

- Fix image layer visibility toggle in plot options. [2595]

- Fixes viewer toolbar items losing ability to bring up right-click menu. [2605]

Cubeviz
^^^^^^^

- Fixes ability to remove cube data from the app. [2608]

- Fixes [SCI] data not showing in the spectrum viewer's data menu. [2631]

Imviz
^^^^^

- Line Profile (XY) plugin no longer malfunctions when image contains NaN values. [2594]

- Stretch histogram now represents mixed state for any of the inputs (when multiple viewers are
selected) with an overlay appropriately. [2606]

- Fixes viewer keys in ``viz.viewers`` for additionally created viewers. [2624]

Mosviz
^^^^^^

Specviz
^^^^^^^

- Fixed parser bug where an HDUList would load as SpectrumList, even though it was a Spectrum1D. [2576]

Specviz2d
^^^^^^^^^

================

New Features
------------

- Plots in plugins now include basic zoom/pan tools for Plot Options,
Imviz Line Profiles, and Imviz's aperture photometry. [2498]

- Histogram plot in Plot Options now includes tool to set stretch vmin and vmax. [2513, 2556]

- The Plot Options plugin now include a 'spline' stretch feature. [2525]

- User can now remove data from the app completely after removing it from viewers. [2409, 2531]

- Colorbar now shown on top of the histogram in Plot Options for image viewers. [2517]

- Reorder viewer and layer settings in Plot Options. [2543, 2557]

- Add button in Plot Options to apply preset RBG options to visible layers when in Monochromatic mode. [2558, 2568]

- Plugin "action" buttons disable and show icon indicating that an action is in progress. [2560, 2571]

- Plugin APIs now include a ``close_in_tray()`` method. [2562]

- Convert the layer select dropdown in Plot Options into a horizontal panel of buttons. [2566, 2574, 2582]

Cubeviz
^^^^^^^

- Add circular annulus subset to toolbar. [2438]

- Expose sky regions in get_subsets. If 'include_sky_region' is True, a sky Region will be returned (in addition to a pixel Region) for spatial subsets with parent data that was a WCS. [2496]

Imviz
^^^^^

- Aperture photometry (previously "Imviz Simple Aperture Photometry") now supports batch mode. [2465]

- Aperture photometry sum is now presented in scientific notation consistently. [2530]

- Expose sky regions in get_subsets. If 'include_sky_region' is True, a sky Region will be returned (in addition to a pixel Region) for spatial subsets with parent data that was a WCS. [2496]

Mosviz
^^^^^^

- Matched mouseover indicator to show same position in 1d and 2d spectral viewers. [2575]

Specviz2d
^^^^^^^^^

- Matched mouseover indicator to show same position in 1d and 2d spectral viewers. [2575]

API Changes
-----------

- Deprecated ``app.get_data_from_viewer`` is removed, use ``viz_helper.get_data`` instead. [2578]

- Deprecated ``app.get_subsets_from_viewer`` is removed, use ``viz_helper.get_subsets`` instead. [2578]

- User APIs now raise a warning when attempting to set a non-existing attribute to avoid confusion
caused by typos, etc. [2577]

- Viewer API now exposed via ``viz.viewers`` dictionary, currently containing APIs to set axes
limits as well as astrowidgets API commands for Imviz. [2563]

Imviz
^^^^^

- Deprecated ``do_link`` argument of ``imviz.load_data`` is removed, use ``batch_load`` context manager instead. [2578]

Specviz
^^^^^^^

- Deprecated ``specviz.load_spectrum`` is removed, use ``specviz.load_data`` instead. [2578]

Bug Fixes
---------

- Fix Plot Options stretch histogram's curve for non-gray colormaps. [2537]

Imviz
^^^^^

- Plot options layer selection no longer gets stuck in some cases when deleting
the currently selected viewer. [2541]

Other Changes and Additions
---------------------------

- Better handling of non-finite uncertainties in model fitting. The 'filter_non_finite' flag (for the
LevMarLSQFitter) now filters datapoints with non-finite weights. In Specviz, if a fully-finite spectrum
with non-finite uncertainties is loaded, the uncertainties will be dropped so every datapoint isn't
filtered. For other scenarios with non-finite uncertainties, there are appropriate warning messages
displayed to alert users that data points are being filtered because of non-finite uncertainties (when
flux is finite). [2437]

- Add swatches to color picker. [2494]

- Plot options now includes better support for scatter viewers, including toggling line visibility. [2449]

==================

Bug Fixes
---------

- Fixed bug which did not update all references to a viewer's ID when
updating a viewer's reference name. [2479]

- Deleting a subset while actively editing it now deselects the subset tool,
preventing the appearance of "ghost" subsets. [2497]

- Fixes a bug in plot options where switching from multi to single-select mode
failed to properly update the selection. [2505]

Cubeviz
^^^^^^^

- Fixed moment map losing WCS when being written out to FITS file. [2431]

- Fixed parsing for VLT MUSE data cube so spectral axis unit is correctly converted. [2504]

- Updated glue-core pin to fix the green layer that would appear if 2D data was added to
image viewers while spectral subsets were defined. [2527]

Imviz
^^^^^

Mosviz
^^^^^^

Specviz
^^^^^^^

- Spectrum that has incompatible flux unit with what is already loaded
will no longer be loaded as ghost spectrum. It will now be rejected
with an error message on the snackbar. [2485]

Specviz2d
^^^^^^^^^

Other Changes and Additions
---------------------------

- Compatibility with Python 3.12. [2473]

================

New Features
------------

- Improved design of Launcher and pass filepath arg from cli when no config specified. [2311, 2417]

- Subset Tools plugin now displays the parent data of a spatial (ROI) subset. [2154]

- Data color cycler and marker color updates for increased accessibility. [2453]

- Add support for ``MultiMaskSubsetState`` in ``viz.app.get_subsets()`` and in
the Subset Plugin [2462]

Cubeviz
^^^^^^^

- Add Spectral Extraction plugin for Cubeviz, which converts spectral cubes
to 1D spectra with propagated uncertainties [2039]

Imviz
^^^^^

- The stretch histogram within plot options can now be popped-out into its own window. [2314]

- vmin/vmax step size in the plot options plugin is now dynamic based on the full range of the
image. [2388]

- Footprints plugin for plotting overlays of instrument footprints or custom regions in the image
viewer. [2341, 2377, 2413]

- Add a curve to stretch histograms in the Plot Options plugin representing the colormap
stretch function. [2390]

- The stretch histogram is now downsampled for large images for improved performance. [2408]

- Add multiselect support to the subset plugin for recentering only. [2430]

Mosviz
^^^^^^

- Plot options now includes the stretch histogram previously implemented for Imviz/Cubeviz. [2407]

Specviz
^^^^^^^

- Improve visibility of live-collapsed spectra from spatial regions in Cubeviz [2387]

Specviz2d
^^^^^^^^^

- Plot options now includes the stretch histogram previously implemented for Imviz/Cubeviz. [2407]

API Changes
-----------

- Adjusted axis ticks and labels for spectrum viewers to be more readable.
Axes on image viewers no longer show by default. [2372]

Cubeviz
^^^^^^^

Imviz
^^^^^

- Fixed Subset Tools unable to re-center non-composite spatial subset on an image
that is not the reference data when linked by WCS. [2154]

- Fixed inaccurate results when aperture photometry is performed on non-reference data
that are of a different pixel scale or are rotated w.r.t. the reference data when
linked by WCS. [2154]

- Fixed wrong angle translations between sky regions in ``regions`` and ``photutils``.
They were previously off by 90 degrees. [2154]

Mosviz
^^^^^^

Specviz
^^^^^^^

Specviz2d
^^^^^^^^^

Bug Fixes
---------

- Circle tool to create a circular Subset no longer results in an ellipse
under certain conditions. [2332]

- Fixes turning off multiselect mode for a dropdown when no selections are currently made.
Previously this resulted in a traceback, but now applies the default selection for
single-select mode. [2404]

- Fixes tracebacks from plugins opened in popout windows. [2411]

- Fixes app not displaying properly in Notebook 7. [2420]

Cubeviz
^^^^^^^

Imviz
^^^^^

Mosviz
^^^^^^

- Fixes slit overlay angle in cutout viewer. [2434]

Specviz
^^^^^^^

Specviz2d
^^^^^^^^^

Other Changes and Additions
---------------------------

- Improved logic for handling active state of plugins. [2386, 2450]

- API framework for batch aperture photometry. [2401]