Jdaviz

Latest version: v4.1.1

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4.2

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

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

- Added API and UI for renaming subsets to Subset Tools plugin. [3356, 3392]

- Viewer data-menus are now found in the legend on the right of the viewer. [3281]

- Added 'select_rows' method to plugin tables to enable changing
curent selection by indicies or slice. Also added 'select_all' and 'select_none'
methods to change active selection to all table items or clear all selected
items without clearing the table. [3381]

- Plugin API methods and attributes are now searchable from the plugin tray (and visible when API hints are enabled). [3384]

Cubeviz
^^^^^^^

- Enhancements for the cube sonification plugin. [3377, 3387]

Imviz
^^^^^

- Enhance the Catalog Search plugin to support additional columns when loading catalog data from files. [3359]

- Catalog Search ``clear_table`` now removes all associated markers from the viewer. [3359]

Mosviz
^^^^^^

Specviz
^^^^^^^

Specviz2d
^^^^^^^^^

- Implement the Unit Conversion plugin in Specviz2D. [3253]

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

Cubeviz
^^^^^^^

Imviz
^^^^^

- Orientation plugin: ``link_type`` and ``wcs_use_affine`` (previously deprecated) have now been removed. [3385]

Mosviz
^^^^^^

Specviz
^^^^^^^

- Specviz-specific helper-level methods are deprecated and will be removed in the future in favor of plugin APIs as configs are centralized. [3388]

Specviz2d
^^^^^^^^^

- Specviz2d-specific helper-level methods are deprecated and will be removed in the future in favor of plugin APIs as configs are centralized. [3388]

Bug Fixes
---------

Cubeviz
^^^^^^^

- Fixed copious warnings from spaxel tool when data has INF. [3368]

- Cubeviz-specific helper-level methods are deprecated and will be removed in the future in favor of plugin APIs as configs are centralized. [3388]

Imviz
^^^^^

- ``get_aperture_photometry_results`` helper-level method is deprecated and will be removed in the future in favor of plugin APIs as configs are centralized. [3388]

Mosviz
^^^^^^

Specviz
^^^^^^^

- Fixed traceback in model fitting due to units not being represented as strings. [3412]

Specviz2d
^^^^^^^^^

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

4.1.2

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

Bug Fixes
---------

Cubeviz
^^^^^^^

Imviz
^^^^^

Mosviz
^^^^^^

Specviz
^^^^^^^

Specviz2d
^^^^^^^^^

4.1.1

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

Bug Fixes
---------

- Fixes traceback from the data-menu that can be caused by a viewer rename. [3383]

- Fixes data-menu visibility when app is scrolled out of view. [3391]

- Fix Slice plugin for indexing through temporal slices. [3235]

Cubeviz
^^^^^^^

Imviz
^^^^^

- Spatial subsets no longer show as having mixed visibility (in the legend and plot options tab) when aligned by WCS. [3373]

- Fixed Gaia catalog search sometimes failing with invalid ``SOURCE_ID`` look-up. [3400]

Mosviz
^^^^^^

Specviz
^^^^^^^

Specviz2d
^^^^^^^^^

4.1

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

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]

4.0.1

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

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]

Mosviz
^^^^^^

Specviz
^^^^^^^

Specviz2d
^^^^^^^^^

4.0

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

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 1.16. Moment 0 calculation is now in units
of flux*dx (rather than flux) [3184]

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