v4.0.0

4.0 (2024-10-17)

New Features

• Added ability to load remote data from a URI or URL. [#2875, #2923]

• Added flux/surface brightness translation and surface brightness
  unit conversion in Cubeviz and Specviz. [#2781, #2940, #3088, #3111, #3113, #3129,
  #3139, #3149, #3155, #3178, #3185, #3187, #3190, #3156, #3200, #3192, #3206, #3211, #3216, #3219]

• Plugin tray is now open by default. [#2892]

• New "About" plugin to show Jdaviz version info. [#2886]

• Descriptions are shown in the color mode dropdown for image layers to help describe the use-cases
  for Colormap vs Color. [#2894]

• The colormap menu for image layers now shows in-line previews of the colormaps. [#2900]

• Plugins can now expose in-UI API hints. [#3137, #3159]

• The standalone version of jdaviz now uses solara instead of voila, resulting in faster load times. [#2909]

• New configuration for ramp/Level 1 and rate image/Level 2 data products from Roman WFI and
  JWST [#3120, #3148, #3167, #3171, #3194]

• Unit columns are now visible by default in the results table in model fitting. [#3196]

Cubeviz

• Automatic spectral extraction now goes through the logic of the spectral extraction plugin for
  self-consistency. This results in several breaking changes to data-labels and get_data
  (the extracted spectra are now given dedicated data-labels instead of referring to them by
  the label of the flux cube) as well as to several plugins: model fitting, gaussian smooth,
  line analysis, and moment maps. [#2827]

• Background subtraction support within Spectral Extraction. [#2859]

• Aperture photometry plugin now listens to changes in display unit. [#3118]

Imviz

• Added a table with catalog search results. [#2915, #3101, #3099]

• "Imviz Line Profiles (XY)" plugin is renamed to "Image Profiles (XY)". [#3121]

• Added Gaia catalog to Catalog plugin. [#3090]

• Updated link_type to align_by and wcs_use_affine to wcs_fast_approximation in
  Orientation plugin API to better match UI text. [#3128]

Specviz

• Fixed viz.app.get_subsets() for XOR mode. [#3124]

Specviz2d

• Add option to use self-derived spatial profile for Horne extract in spectral extraction plugin. [#2845]

API Changes

• The Monochromatic option for color_mode in plot options is now renamed to Color.
  Monochromatic will continue to work with a deprecation warning, but may be removed in a
  future release. [#2894]

• Plugin Table components now support row selection. [#2856]

Cubeviz

• get_data no longer supports function or spatial_subset as arguments. To access
  an extracted 1D spectrum, use the Spectral Extraction plugin or the automatic extraction of
  spatial subsets, and refer to the data-label assigned to the resulting 1D spectrum. [#2827]

• Several plugins that take 1D spectra replace spatial_subset with referring to the 1D
  spectrum in dataset. This affects: model fitting, gaussian smooth, line analysis,
  and moment maps. [#2827]

• Removed deprecated cubeviz.select_slice() method. Use cubeviz.select_wavelength()
  instead. [#2878]

• In the Slice plugin, the following deprecated properties were removed: wavelength (use value),
  wavelength_unit (use value_unit), show_wavelength (use show_value),
  slice (use value). [#2878]

• Spectral Extraction: renamed collapse_to_spectrum(...) to extract(...). [#2859]

• Generic FITS parsing now goes through specutils loaders first, if possible.
  If a specutils loader is used, uncertainty is converted to standard deviation type. [#3119]

• Custom Spectrum1D writer format jdaviz-cube is removed. Use wcs1d-fits from
  specutils instead. [#2094]

• Aperture Photometry plugin now uses TRFLSQFitter to fit radial profile because LevMarLSQFitter
  is no longer recommended by Astropy. [#3202]

Imviz

• Deprecated Rotate Canvas plugin was removed; use Orientation plugin instead. [#2878]

• Aperture Photometry plugin now uses TRFLSQFitter to fit radial profile because LevMarLSQFitter
  is no longer recommended by Astropy. [#3202]

Specviz

• In the Line Analysis plugin, deprecated width was removed (use continuum_width). [#2878]

Bug Fixes

• Markers table can now export to CSV but its columns had to be changed to accomodate this fix:
  world and pixel (previously containing SkyCoord and pixel location tuples, respectively) are now
  each two separate columns for world_ra/world_dec and pixel_x/pixel_y, respectively. [#3089]

• Stretch histogram in zoom limits no longer attempts unnecessary updates when zoom limits are changed. [#3151]

• Aperture Photometry plugin no longer allows negative counts conversion factor. [#3154]

• Fixed multiple select handling for batch mode aperture photometry in Cubeviz. [#3163]

Cubeviz

• Moment map plugin now reflects selected flux / surface brightness unit for moment zero. [#2877]

• Update the scale factor used to convert a spectrum between surface brightness and flux
  to use wavelength-dependent aperture area instead of the cone slice scale factor. [#2860]

• Handle display units when doing flux / surface brightness conversions. [#2910]

• Flux units are now correct for collapsed spectra when using the sum function
  when units are in per steradian. [#2873]

• Mouse over coordinates now responds to the selected surface brightness unit. [#2931]

• Fixed MaNGA cube loading. Uncertainty type is also handled properly now. [#3119]

• Fixed spectral axis value display in Markers plugin. Previously, it failed to display
  very small values, resulting in zeroes. [#3119]

• No longer incorrectly swap RA and Dec axes when loading Spectrum1D objects. [#3133]

• Fixed fitting a model to the entire cube when NaNs are present. [#3191]

Specviz2d

• Fixed Subset unit when it is created in 2D spectrum viewer. [#3201]

• Fix matched mouseover marker for 1d spectrum viewer when mouse is over 2d spectrum viewer. [#3203]

Other Changes and Additions

• Bump required specutils version to 1.18. Moment 0 calculation is now in units
  of flux*dx (rather than flux) [#3184]

v3.10.3

3.10.3 (2024-07-22)

Bug Fixes

• Fixes exporting the stretch histogram from Plot Options before the Plot Options plugin is ever opened. [#2934]

• Previous zoom tool is optimized to only issue one zoom update to the viewer. [#2949]

• Fixes overwrite behavior for plugin plots, and properly closes overwrite warning overlay after confirmation. [#3094]

• Disable all non-image exporting when the server is not running locally, to avoid confusion with the file being saved on the server. [#3096]

Cubeviz

• Fixed a bug with filename handling for movie exports. [#2942]

Imviz

• Fix multiple footprints bug that prevented footprint updates on changes to the
  viewer orientation. [#2918]

v3.10.2

3.10.2 (2024-06-06)

Bug Fixes

• Update button in the subset plugin is now disabled when no subset is selected. [#2880]

v3.10.1

3.10.1 (2024-05-14)

Bug Fixes

Cubeviz

• Fix Data Quality plugin bug that attempted to apply array compositing logic to
  spatial subsets. [#2854]

Specviz2d

• Prevent laggy behavior in trace previews for spectral extraction. [#2862]

v3.10.0

New Features

• The filename entry in the export plugin is now automatically populated based on the selection. [#2824]

• Adding Data Quality plugin for Imviz and Cubeviz. [#2767, #2817, #2844]

• Enable exporting spectral regions to ECSV files readable by astropy.table.QTable or
  specutils.SpectralRegion [#2843]

Cubeviz

• Enable spectral unit conversion in cubeviz. [#2758, #2803]

• Enable spectral extraction for composite subsets. [#2837]

API Changes

Cubeviz

• ERROR and DATA_QUALITY extension names are now recognized as
  uncertainty and mask, respectively. [#2840]

Bug Fixes

Cubeviz

• Re-enable support for exporting spectrum-viewer. [#2825]

• Loading a specific extension with ext keyword no longer crashes. [#2830]

Other Changes and Additions

• Bump required Python version to 3.10. [#2757]

• Line menu in Redshift from Centroid section of Line Analysis now shows values in current units. [#2816, #2831]

• Bump required specutils version to 1.15. [#2843]

v3.9.1

3.9.1 (2024-04-19)

Bug Fixes

• Fix dropdown selection for table format in export plugin. [#2793]

• Standalone mode: stop jdaviz/voila processes when closing app. [#2791]

• Fix mouseover display's top-layer logic to account for the visibility and contour toggles in
  the plot options plugin. [#2818]

• Fixes compatibility with glue >= 1.19. [#2820]

Cubeviz

• Spectral extraction errors will show in snackbar. [#2807]

Imviz

• Fix bugs where API created footprints did not overlay and only last
  footprint displayed if added before linking. [#2790, #2797]

• Improved behavior when orientations are created or selected without having data loaded in the viewer. [#2789]

• Fixed a bug in the Orientation plugin where a WCS orientation could sometimes be flipped. [#2802]

Specviz

• H-Paschen-Brackett HI 5-4 line's rest wavelength is now correct. It was previously off by 0.5 micron. [#2819]

v3.9.0

3.9 (2024-04-05)

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]

v3.8.2

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]

v3.8.1 Release Notes

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]

Specviz

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

v3.8.0

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]