Glue unit conversion in Specviz #2048

pllim · 2023-02-28T22:55:14Z

Description

This pull request is to continue the work of the following but integrating glue unit conversion into Jdaviz instead of a concept notebook. This PR is part of a larger effort and will be merged into a temporary development branch until the full refactor is complete - not all plugins/tests are expected to work/pass yet, but reviewers please do note any issues so that we can add to the list of things to check before eventual merge into main.

The goal of this individual PR is to create the concept of a "global display unit" in jdaviz in the old unit conversion plugin and sync state between that and the internal glue viewer's display units. Once the unit is changed, other plugins/behaviors are expected to break and will be updated in follow-up efforts.

This builds on:

Added ability to convert units in profile viewer glue-viz/glue#2296

Fix world_axis_units for SpectralCoordinates glue-viz/glue-astronomy#87 (need to bump glue-astronomy minversion)
Add a LinkSameWithUnits class that links respecting units glue-viz/glue#2379 (need to check if this actually works; need to bump glue minversion) 🐱

Closes #895
Closes #1187
Closes #1260

TODO

Change log entry

Is a change log needed? If yes, is it added to CHANGES.rst? If you want to avoid merge conflicts,
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.

Checklist for package maintainer(s)

This checklist is meant to remind the package maintainer(s) who will review this pull request of some common things to look for. This list is not exhaustive.

Are two approvals required? Branch protection rule does not check for the second approval. If a second approval is not necessary, please apply the trivial label.
Do the proposed changes actually accomplish desired goals? Also manually run the affected example notebooks, if necessary.
Do the proposed changes follow the STScI Style Guides?
Are tests added/updated as required? If so, do they follow the STScI Style Guides?
Are docs added/updated as required? If so, do they follow the STScI Style Guides?
Did the CI pass? If not, are the failures related?
Is a milestone set? Set this to bugfix milestone if this is a bug fix and needs to be released ASAP; otherwise, set this to the next major release milestone.
After merge, any internal documentations need updating (e.g., JIRA, Innerspace)?

jdaviz/configs/specviz/plugins/viewers.py

pllim · 2023-03-02T15:12:55Z

Took me a while to make this work, so I need to write this down:

viewer.state.__class__.x_display_unit.get_choices(viewer.state)

Co-authored-by: Jesse Averbukh <javerbukh@gmail.com>

still not quite working yet [ci skip] [rtd skip]

and add change log. [ci skip] [rtd skip]

but still needs unreleased glue [ci skip] [rtd skip]

[ci skip] [rtd skip]

jdaviz/configs/specviz2d/tests/test_parsers.py

pllim · 2023-03-29T01:52:35Z

jdaviz/core/validunits.py

-    return [u.Unit(unit).name
-            if u.Unit(unit) == u.Unit("Angstrom")
-            else u.Unit(unit).long_names[0] if (
-                hasattr(u.Unit(unit), "long_names") and len(u.Unit(unit).long_names) > 0)


Note: Long name does not round-trip well with the display axis stuff. Let's not use it.

pllim · 2023-03-29T01:53:22Z

jdaviz/core/validunits.py


    # Get local units.
    locally_defined_flux_units = ['Jy', 'mJy', 'uJy',
                                  'W / (m2 Hz)',
                                  'eV / (s m2 Hz)',
                                  'erg / (s cm2)',
-                                  'erg / (s cm2 um)',


Note: This fails unit conversion in astropy. Do we really need this?

pllim · 2023-03-29T01:54:20Z

jdaviz/tests/test_subsets.py

@@ -135,12 +133,10 @@ def test_region_from_subset_3d(cubeviz_helper):


 def test_region_from_subset_profile(cubeviz_helper, spectral_cube_wcs):
-    data = Data(flux=np.ones((128, 128, 256)), label='Test 1D Flux', coords=spectral_cube_wcs)


For the glue display axis to initialize properly, we cannot hack-load like this anymore.

kecnry · 2023-03-29T17:50:06Z

the latest commit updates the implementation to make use of callbacks (so manually calling set_plot_axes is no longer required) and plugin dropdown components (so clicking apply is no longer necessary) and syncs the state between the UI, plugin API, and glue-state. Note that this is still somewhat hardcoded to the single-spectrum-viewer specviz case. We'll either need to generalize the code or disable across other configs until that work can be done.

Screen.Recording.2023-03-29.at.1.47.50.PM.mov

jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py

kecnry · 2023-03-29T18:01:50Z

jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py

+        self.spectrum_viewer.set_plot_axes()
+        if x_unit != self.spectral_unit.selected:
+            x_u = u.Unit(x_unit)
+            self.spectral_unit.choices = [x_unit] + create_spectral_equivalencies_list(x_u)


this is probably overkill to recompute each time - can we get away with only computing it once?

I started out with hardcoding it altogether but that didn't behave well. You think we can get away with only doing it once, especially in cases like Specviz2d with extraction, or Cubeviz with collapse? If so, when should it trigger?

for the spectral axis, we probably can get away with it (except for the pixel case which we might need to handle separately). For the flux, maybe not - we'll at least need to trigger on changes to reference data as well as changes to the spectral units 🤔 . For now this is the most conservative and I don't expect it to cause any noticeable lagging.

kecnry · 2023-03-31T18:05:23Z

Agreed, I think the simplest way is to force the UI list to our "preferred" representation - the API will still accept any valid string that can be mapped to the choices.

rosteen · 2023-03-31T18:19:42Z

Next two things I've noticed while testing plugins:

It looks like changing from um to Hz and then fitting a constant+gaussian works, but fitting a linear+gaussian fails because the slope parameter of the linear model is still estimated in MJy / sr / um.
While displaying with frequency units, spectral lines will still be plotted at the numerical values corresponding to their wavelengths rather than having that converted to freqency.

rosteen · 2023-03-31T18:23:05Z

Ah, and one more: with spectral units converted to frequency, selecting a spectral region in Line Analysis fails with the following traceback:

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
File ~/opt/anaconda3/envs/viz_dev/lib/python3.11/site-packages/ipywidgets/widgets/widget.py:773, in Widget._handle_msg(self, msg)
    771         if 'buffer_paths' in data:
    772             _put_buffers(state, data['buffer_paths'], msg['buffers'])
--> 773         self.set_state(state)
    775 # Handle a state request.
    776 elif method == 'request_state':

File ~/opt/anaconda3/envs/viz_dev/lib/python3.11/site-packages/ipywidgets/widgets/widget.py:650, in Widget.set_state(self, sync_data)
    645         self._send(msg, buffers=echo_buffers)
    647 # The order of these context managers is important. Properties must
    648 # be locked when the hold_trait_notification context manager is
    649 # released and notifications are fired.
--> 650 with self._lock_property(**sync_data), self.hold_trait_notifications():
    651     for name in sync_data:
    652         if name in self.keys:

File ~/opt/anaconda3/envs/viz_dev/lib/python3.11/contextlib.py:144, in _GeneratorContextManager.__exit__(self, typ, value, traceback)
    142 if typ is None:
    143     try:
--> 144         next(self.gen)
    145     except StopIteration:
    146         return False

File ~/opt/anaconda3/envs/viz_dev/lib/python3.11/site-packages/traitlets/traitlets.py:1502, in HasTraits.hold_trait_notifications(self)
   1500 for changes in cache.values():
   1501     for change in changes:
-> 1502         self.notify_change(change)

File ~/opt/anaconda3/envs/viz_dev/lib/python3.11/site-packages/ipywidgets/widgets/widget.py:701, in Widget.notify_change(self, change)
    698     if name in self.keys and self._should_send_property(name, getattr(self, name)):
    699         # Send new state to front-end
    700         self.send_state(key=name)
--> 701 super().notify_change(change)

File ~/opt/anaconda3/envs/viz_dev/lib/python3.11/site-packages/traitlets/traitlets.py:1517, in HasTraits.notify_change(self, change)
   1515 def notify_change(self, change):
   1516     """Notify observers of a change event"""
-> 1517     return self._notify_observers(change)

File ~/opt/anaconda3/envs/viz_dev/lib/python3.11/site-packages/traitlets/traitlets.py:1564, in HasTraits._notify_observers(self, event)
   1561 elif isinstance(c, EventHandler) and c.name is not None:
   1562     c = getattr(self, c.name)
-> 1564 c(event)

File ~/projects/jdaviz/jdaviz/configs/specviz/plugins/line_analysis/line_analysis.py:338, in LineAnalysis._calculate_statistics(self, *args, **kwargs)
    336 else:
    337     spectrum = extract_region(full_spectrum, sr, return_single_spectrum=True)
--> 338     sr_lower = spectrum.spectral_axis[spectrum.spectral_axis.value >= sr.lower.value][0]
    339     sr_upper = spectrum.spectral_axis[spectrum.spectral_axis.value <= sr.upper.value][-1]
    341 # compute continuum

File ~/opt/anaconda3/envs/viz_dev/lib/python3.11/site-packages/astropy/units/quantity.py:1272, in Quantity.__getitem__(self, key)
   1269     return self._new_view(self.view(np.ndarray)[key], self.unit[key])
   1271 try:
-> 1272     out = super().__getitem__(key)
   1273 except IndexError:
   1274     # We want zero-dimensional Quantity objects to behave like scalars,
   1275     # so they should raise a TypeError rather than an IndexError.
   1276     if self.isscalar:

IndexError: index 0 is out of bounds for axis 0 with size 0

pllim · 2023-03-31T18:24:14Z

I wonder if plugins should disable themselves if they detect the data unit is different from display units... 👀

kecnry · 2023-03-31T18:25:29Z

Once this PR is in, we'll go through each plugin one-by-one to update them before eventually merging the whole thing into main. I expect most plugins to currently break once the units are changed.

rosteen · 2023-03-31T18:30:51Z

"Once the unit is changed, other plugins/behaviors are expected to break and will be updated in follow-up efforts." - almost like that was in the description 😆 . Still, not bad to catalog what's breaking.

kecnry · 2023-03-31T18:32:11Z

Still, not bad to catalog what's breaking.

By all means, feel free, but don't feel like you need to be thorough - that will lead you to insanity! 😂

docs/specviz/plugins.rst

rosteen · 2023-03-31T19:54:24Z

notebooks/concepts/specviz_glue_unit_conversion.ipynb

+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "viewer.state.x_display_unit = \"GHz\""


This fails now, seems like the notebook should refer to Hz instead of GHz:

File ~/projects/jdaviz/jdaviz/core/template_mixin.py:674, in UnitSelectPluginComponent._selected_changed(self, event) 672 if new_u not in self.unit_choices: 673 self.selected = event['old'] --> 674 raise ValueError(f"{event['new']} not one of {self.labels}, reverting selection to {event['old']}") # noqa 676 # convert to default string representation from the valid choices 677 ind = self.unit_choices.index(new_u) ValueError: GHz not one of ['Angstrom', 'Hz', 'erg', 'nm', 'um', 'Ci', 'J', 'Ry', 'cm', 'eV', 'k', 'm'], reverting selection to Hz

The string compare stuff is annoying like that, you have to include all the possible prefixes or it is going to fail.

I wonder if @astrofrog can make it less annoying but if not, we need to use the "include prefix" option in some of these base units.

I pushed a commit which now allows setting any unit accepted by glue via the API. If that unit does not appear in the list of dropdown choices, it will be appended to the end of the available list for the remainder of the session.

For example:

uc = specviz.plugins['Unit Conversion'] uc.open_in_tray() print(uc.spectral_unit.choices) # ['Angstrom', 'Hz', 'erg', 'nm', 'um', 'Ci', 'J', 'Ry', 'cm', 'eV', 'k', 'm'] uc.spectral_unit = 'GHz' print(uc.spectral_unit.selected) # GHz print(uc.spectra_unit.choices) # ['Angstrom', 'Hz', 'erg', 'nm', 'um', 'Ci', 'J', 'Ry', 'cm', 'eV', 'k', 'm', 'GHz']

rosteen

I left one more comment on the notebook, but I'm going to go ahead and approve. Code looks codely, plugins will be dealt with after this is merged.

* in which case the plugin select component appends that option to its curated list of options going forward. This allows supporting a large number of options/prefixes without having to show them all in the dropdown.

javerbukh

Sounds like most existing bugs are documented and we are moving to a development branch, so I think this is good to go!

* 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>

* 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>

pllim added this to the 3.4 milestone Feb 28, 2023

github-actions bot added documentation Explanation of code and concepts imviz specviz labels Feb 28, 2023

pllim commented Feb 28, 2023

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astrofrog mentioned this pull request Mar 2, 2023

Fix world_axis_units for SpectralCoordinates glue-viz/glue-astronomy#87

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pllim mentioned this pull request Mar 2, 2023

Added ability to convert units in profile viewer glue-viz/glue#2296

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pllim mentioned this pull request Mar 20, 2023

Refactor get subsets to work with composite subset state #2087

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pllim force-pushed the sticky-unit-conversion branch from 842707b to 96f241d Compare March 28, 2023 18:58

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WIP: Glue unit conversion in Jdaviz. [ci skip] [rtd skip]

91bcb84

Co-authored-by: Jesse Averbukh <javerbukh@gmail.com>

WIP: Moar stuff but

fa03af3

still not quite working yet [ci skip] [rtd skip]

Use glue-viz/glue#2379

46024af

and add change log. [ci skip] [rtd skip]

Fix unit conversion plugin

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but still needs unreleased glue [ci skip] [rtd skip]

pllim force-pushed the sticky-unit-conversion branch from 29d8b96 to f64890b Compare March 29, 2023 01:31

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Fix tests again

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Fix change log

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Add back v-if

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use callbacks and plugin components for setting display unit

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implement use_display_units option for get_data, get_subsets

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minor code/style cleanup

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remove mention of apply button in plugin docs

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allow setting to ANY glue-valid unit from the API

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* in which case the plugin select component appends that option to its curated list of options going forward. This allows supporting a large number of options/prefixes without having to show them all in the dropdown.

kecnry mentioned this pull request Apr 3, 2023

subset fails to create after glue display unit changed using spectral equivalency #2125

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pass use_display_units through get_range_subset_bounds

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axes limits do not update correctly when changing display unit #2126

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Display units (unit conversion refactor) #2127

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Glue unit conversion in Specviz #2048

Glue unit conversion in Specviz #2048

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		@@ -135,12 +133,10 @@ def test_region_from_subset_3d(cubeviz_helper):


		def test_region_from_subset_profile(cubeviz_helper, spectral_cube_wcs):
		data = Data(flux=np.ones((128, 128, 256)), label='Test 1D Flux', coords=spectral_cube_wcs)

Glue unit conversion in Specviz #2048

Glue unit conversion in Specviz #2048

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pllim commented Feb 28, 2023 • edited by kecnry Loading

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TODO

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