Display units support for markers plugin #2130

kecnry · 2023-04-05T18:08:48Z

Description

This pull request adds display units support for the markers plugin and (by the changes introduced to the marks themselves) fixes support for plotting uncertainties.

Note that the values logged in the table are intentionally still stored with their original units, but the drawn markers are now aware of units and will be drawn in the correct location when the display units on the figure are changed.

Screen.Recording.2023-04-05.at.2.07.05.PM.mov

Changelog will point to #2127 so is ignored from CI here.

Change log entry

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list the proposed change log here for review and add to CHANGES.rst before merge. If no, maintainer
should add a no-changelog-entry-needed label.

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pllim · 2023-04-06T19:13:18Z

Does this need glue-core v1.9.0? Because we cannot right now, see #2136

duytnguyendtn

Code changes are straight forward and the PR works as expected. Thanks!

kecnry · 2023-04-07T12:24:12Z

Does this need glue-core v1.9.0?

Yes, that will likely block the eventual merging of #2127 into main, but should still be able to be tested locally with glue 1.9 or glue-viz/glue#2379.

javerbukh · 2023-04-10T15:09:40Z

Works in Specviz but in Cubeviz I get the following traceback:

File ~\Documents\STScI\jdaviz\jdaviz\core\marks.py:521, in PluginMark.set_x_unit(self, unit)
    519 def set_x_unit(self, unit=None):
    520     if unit is None:
--> 521         unit = self.viewer.state.x_display_unit
    522     unit = u.Unit(unit)
    523     if self.xunit is not None:

AttributeError: 'BqplotImageViewerState' object has no attribute 'x_display_unit'

kecnry · 2023-04-11T13:02:07Z

@javerbukh - good catch now that this was rebased on top of #2131, that should be fixed now 🤞

javerbukh

Works, thanks!

* update markers plugin for display units * move unit-updating logic to mark itself * LineUncertainties to be unit-aware * fix support for markers in cubeviz

* Added .ico and .svg files * app-wide display unit in specviz (#2048) * basic app-wide display unit in specviz (not all plugins are updated yet) * unit-aware select component which maps to glue-supported unit strings * implement use_display_units option for get_data, get_subsets Co-authored-by: Jesse Averbukh <javerbukh@gmail.com> Co-authored-by: Kyle Conroy <kyleconroy@gmail.com> * bump glue-core to necessary version for display units * change PR number in changelog to main PR * Display units line analysis (#2128) * emit event when display unit changed * update line analysis for unit changes * cubeviz/slice plugin unit conversion support (we might want to generalize some of this logic more into the mark's _update_data when adding support for spectral lines as well) * Display units support for markers plugin (#2130) * update markers plugin for display units * move unit-updating logic to mark itself * LineUncertainties to be unit-aware * fix support for markers in cubeviz * display units: fix failing tests (#2132) * fix error raised when spectrum uncertainty is None * fix RTD build failure because of missing mixin available in import * fix test setting display unit now that um is preferred to micron * add disabled unit conversion plugin to mosviz * avoid unit-conversion error in cubeviz tests * bump versions of glue/glue-jupyter * fix deg intialization in cubeviz slice plugin * add LinesAutoUnit to __all__ so RTD can find it * add use_display_units kwarg to get_spectral_regions * fix setting display units for unitless data * Apply suggestions from code review Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com> * Display units: line lists (#2148) * BaseSpectrumVerticalLine to inherit unit-support from PluginMark * convert units on internal rest value * code cleanup * remove unit conversion plugin from all bug specviz * for initial implementation - eventually we'll want to implement across all plugins/viewers * get_display_unit fallback for configs without unit conversion plugin * Update glue-core dependency * Update Subset Tools plugin to use display units (#2195) * bump glue-core to necessary version for display units * cubeviz/slice plugin unit conversion support (we might want to generalize some of this logic more into the mark's _update_data when adding support for spectral lines as well) * display units: fix failing tests (#2132) * fix error raised when spectrum uncertainty is None * fix RTD build failure because of missing mixin available in import * fix test setting display unit now that um is preferred to micron * add disabled unit conversion plugin to mosviz * avoid unit-conversion error in cubeviz tests * bump versions of glue/glue-jupyter * fix deg intialization in cubeviz slice plugin * add LinesAutoUnit to __all__ so RTD can find it * add use_display_units kwarg to get_spectral_regions * fix setting display units for unitless data * Apply suggestions from code review Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com> * remove unit conversion plugin from all bug specviz * for initial implementation - eventually we'll want to implement across all plugins/viewers * Working on unit conversion handling in subset plugin * Get subset updating working in non-default units * Add changelog * Update jdaviz/configs/default/plugins/subset_plugin/subset_plugin.vue Co-authored-by: Kyle Conroy <kyleconroy@gmail.com> --------- Co-authored-by: Kyle Conroy <kyleconroy@gmail.com> Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com> * allow downstream apps to set what classes are considered native marks * Fix unit conversion for PluginMarks and y-limits (#2215) * Fix unit conversion for PluginMarks and y-limits * Only use equivalency if it's a spec viewer * Store wavelength unit on data update * Remove redundant line * Better check in marks * Replace subset_to_apply in docs where possible (#2223) * Replace subset_to_apply in docs where possible (#2223) * Avoid trying to convert units of empty marks arrays * Add open method to automatically detect config and load data * Update demo notebooks * Codestyle * Add autoconfig test coverage * Revert "Update demo notebooks" This reverts commit cc513b3. * Add mention of open to relevant example notebooks * Prepare to support open via cli * Remove the need to open file twice for autoconfig detection * Fix Helper vs App Docstring * TST: Change PIP_EXTRA_INDEX_URL because packages moved where they upload nightly builds. * Display units: model fitting (#2216) * model component compatibility based on display units * equation validity based on display units * allow re-estimating model parameters to update compat checks * test coverage * get_data(use_display_units) to pass spectral_density equivalency * handle whitespace in model equation * Add clarity for kwargs * plugin results: support overwriting when data loaded in multiple viewers (#2222) * reverts removal of call to set_plot_axes when loading data into viewer (#2235) * fixes a bug in the axes labels on cube viewers in cubeviz as well as setting the correct attributes in lcviz * Subsume failing identifier test into autoconfig test * Update subset plugin UI (#2234) * Update subset plugin UI * Apply suggestions from code review Co-authored-by: Kyle Conroy <kyleconroy@gmail.com> --------- Co-authored-by: Kyle Conroy <kyleconroy@gmail.com> * Changelog * Add docs page to explain how to create jdaviz-readable products (#2228) * Add page for data products * Update index * Fix title * Capital letters * Address first review comments * Edit format * Apply suggestions from code review Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com> * Including reference in import_data * Update docs/create_products.rst * Update docs/create_products.rst --------- Co-authored-by: Camilla Pacifici <cpacifici@stsci.edu> Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com> Co-authored-by: Ricky O'Steen <39831871+rosteen@users.noreply.github.com> * FEAT: Load annulus from file and allow IMPORT DATA to load reg files. Annulus support provided by glue-viz/glue#2403 and glue-viz/glue-astronomy#92 Add test for exception. Bump minimum requirements for glue-core and glue-astronomy. * disallow gaussian smooth output as input * BUG: Fix ellipse translation in app.get_subsets() * DOC: Use pydata-sphinx-theme (#2243) * DOC: Use pydata-sphinx-theme that has dark mode, modern design, and mobile friendly DOC: No longer need tomli DOC: Now requires sphinx-astropy 1.9.1 * Add cards to index page with icons * Remove iframe hardcoding so it scales in mobile mode * DOC: Insert small logo next to title instead of a giant logo above the title * Add app method to simplify spectral subset (#2237) * Add app method to simplify spectral subset Add simplify button to subset plugin * Fix xor bug exposed by simplify button * Fix style checks * Remove print statements * Add tooltip to simplify button * Make button appear only if the subset can be simplified * Make simplify button appear only when applicable * Apply suggestions from code review Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com> * Update changes file --------- Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com> * Fix missed conflict --------- Co-authored-by: Jennifer Kotler <jkotler@esme.stsci.edu> Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com> Co-authored-by: Jesse Averbukh <javerbukh@gmail.com> Co-authored-by: Ricky O'Steen <rosteen@stsci.edu> Co-authored-by: Ricky O'Steen <39831871+rosteen@users.noreply.github.com> Co-authored-by: Duy Nguyen <duytnguyendtn.open@gmail.com> Co-authored-by: Camilla Pacifici <camilla.pacifici@gmail.com> Co-authored-by: Camilla Pacifici <cpacifici@stsci.edu>

kecnry added the no-changelog-entry-needed changelog bot directive label Apr 5, 2023

kecnry added this to the 3.5 milestone Apr 5, 2023

kecnry requested review from duytnguyendtn, rosteen, javerbukh, pllim, bmorris3, haticekaratay and cshanahan1 as code owners April 5, 2023 18:08

kecnry mentioned this pull request Apr 5, 2023

Display units (unit conversion refactor) #2127

Merged

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duytnguyendtn approved these changes Apr 6, 2023

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kecnry added the Ready for final review label Apr 7, 2023

kecnry added 3 commits April 10, 2023 10:54

update markers plugin for display units

6a86f6c

move unit-updating logic to mark itself

7bd825c

LineUncertainties to be unit-aware

3e3e778

kecnry force-pushed the display-units-markers branch from 043a837 to 3e3e778 Compare April 10, 2023 14:54

fix support for markers in cubeviz

1123061

javerbukh approved these changes Apr 11, 2023

View reviewed changes

kecnry merged commit 5a33d08 into spacetelescope:dev-display-units Apr 11, 2023

kecnry deleted the display-units-markers branch April 11, 2023 14:08

kecnry added a commit that referenced this pull request Apr 17, 2023

Display units support for markers plugin (#2130)

bdd2223

* update markers plugin for display units * move unit-updating logic to mark itself * LineUncertainties to be unit-aware * fix support for markers in cubeviz

kecnry added a commit that referenced this pull request Apr 18, 2023

Display units support for markers plugin (#2130)

7e48396

* update markers plugin for display units * move unit-updating logic to mark itself * LineUncertainties to be unit-aware * fix support for markers in cubeviz

kecnry added a commit that referenced this pull request Apr 19, 2023

Display units support for markers plugin (#2130)

ae0e3d0

* update markers plugin for display units * move unit-updating logic to mark itself * LineUncertainties to be unit-aware * fix support for markers in cubeviz

kecnry added a commit that referenced this pull request May 4, 2023

Display units support for markers plugin (#2130)

c2db26e

* update markers plugin for display units * move unit-updating logic to mark itself * LineUncertainties to be unit-aware * fix support for markers in cubeviz

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Display units support for markers plugin #2130

Display units support for markers plugin #2130

kecnry commented Apr 5, 2023

pllim commented Apr 6, 2023

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kecnry commented Apr 7, 2023

javerbukh commented Apr 10, 2023

kecnry commented Apr 11, 2023

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Display units support for markers plugin #2130

Display units support for markers plugin #2130

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kecnry commented Apr 5, 2023

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