v4.1.0

4.1 (2024-12-23)

New Features

• New design for viewer legend and future data-menu. [#3220, #3254, #3263, #3264, #3271, #3272, #3274, #3289, #3310, #3370]

• Improve performance while importing multiple regions. [#3321]

• API method to toggle API hints. [#3336]

• Changing flux/SB display units no longer resets viewer zoom levels. [#3335]

Cubeviz

• Add Sonify Data plugin which uses the Strauss package to turn a data cube into sound. [#3269]

Imviz

• Orientation plugin API now exposes create_north_up_east_left and create_north_up_east_right methods. [#3308]

• Add Roman WFI and CGI footprints to the Footprints plugin. [#3322, #3345]

• Catalog Search plugin now exposes a maximum sources limit for all catalogs and resolves an edge case
  when loading a catalog from a file that only contains one source. [#3337]

• Catalog Search plugin zoom_to_selected is now in the public API. The default
  zoom level changed from a fixed 50 pixels to a zoom window that is a fraction of
  the image size (default 2%) to address and issue with zooming when using a small
  image or WCS linked. [#3369]

Specviz

• Specviz parser will now split a spectrum with a 2D flux array into multiple spectra on load
  (useful for certain SDSS file types). [#3229]

API Changes

• Removed API access to plugins that have passed the deprecation period: Links Control, Canvas Rotation, Export Plot. [#3270]

• Subset Tools plugin now exposes the subset, combination_mode, recenter_dataset,
  recenter, get_center, and set_center in the user API. [#3293, #3304, #3325]

• Metadata plugin: metadata_plugin.metadata API has been deprecated; use
  metadata_plugin.meta instead, which will return a Python dictionary instead of
  list of tuples. [#3292]

• Add get_regions method to subset plugin to retrieve spatial/spectral subsets as
  regions or SpectralRegions, deprecate get_interactive_regions and get_spectral_regions. [#3340]

Bug Fixes

• Fixed broken flux unit conversions in all plugins that respond to changes in flux unit changes. These cases
  occured when certain flux-to flux-conversions occured, as well as certain conversions between flux and surface
  brightness. This PR also fixed an issue with unit string formatting in the aperture photometry plugin. [#3228]

• Fixed broken histogram pan/zoom in Plot Options plugin. [#3361]

• Fixed bug with Plot Options select_all when data is float32. [#3366]

• Fixed an issue with back-to-back calls of set_limits and get_limits. [#3371]

Cubeviz

• Removed the deprecated save as fits option from the Collapse, Moment Maps, and Spectral Extraction plugins; use the Export plugin instead. [#3256]

• Fixed bugs where cube model fitting could fail if Jdaviz custom equivalencies were required. [#3343]

Other Changes and Additions

• Added a short description of each plugin in the side menu, visible before the plugin is opened. Removes redundant descriptions above link
  out to documentation when plugin is opened. Enable search on plugin description in addition to title. [#3268]

• Improved performance of app.get_subsets for the single-subset case. [#3363]

v4.0.1

Bug Fixes

• Improved performance and removed jittering for the matched box zoom tool. [#3215]

• Fixed Aperture Photometry radial profile fit crashing when NaN is present in
  aperture data for Cubeviz and Imviz. [#3246]

• Prevent PluginMarks from converting y-range so they maintain their position
  in the spectrum-viewer when spectral y units are converted. [#3242]

• Added nbclassic dependency to fix solara-based popouts. [#3282]

• Fixed viewer widgets displaying improperly if initialized out of view in Jupyter Lab. [#3299]

• Fixed width of sliders in plugins to use full-width of plugin. [#3303]

• Raise an error when attempting to open in a popout or sidecar when not supported (i.e. within VSCode). [#3309]

Cubeviz

• Add missing styling to API hints entry for aperture_method in the spectral extraction plugin. [#3231]

• Fixed "spectrum at spaxel" tool so it no longer resets spectral axis zoom. [#3249]

• Fixed initializing a Gaussian1D model component when Cube Fit is toggled on. [#3295]

• Spectral extraction now correctly respects the loaded mask cube. [#3319, #3358]

Imviz

• Remove "From File.." option when running on an external server. [#3239]

• Button in the footprints plugin to change the link-type now redirects to the orientation plugin
  when the change fails due to the presence of subsets or markers. [#3276]

• Updates UI language in the orientation plugin to better match API. [#3276]

• Update Roman L2 example files in example notebook. [#3346]

v3.10.4

3.10.4 (2024-10-29)

Bug Fixes

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

Imviz

• Remove "From File.." option when running on an external server. [#3239]

Specviz2d

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

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]