implement unit conversion in specviz2d

CHANGES.rst

@@ -36,6 +36,8 @@ Specviz
 Specviz2d
 ^^^^^^^^^
 
+- Implement the Unit Conversion plugin in Specviz2D. [#3253]
+
 API Changes
 -----------
 

jdaviz/configs/cubeviz/helper.py

@@ -141,6 +141,8 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None,
             Spectral subset applied to data.
         cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
             The type that data will be returned as.
+        use_display_units : bool, optional
+            Specify whether the returned data is in native units or the current display units.
 
         Returns
         -------

jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py

@@ -520,9 +520,18 @@ def test_spectral_extraction_with_correct_sum_units(cubeviz_helper,
     cubeviz_helper.load_data(spectrum1d_cube_fluxunit_jy_per_steradian)
     spec_extr_plugin = cubeviz_helper.plugins['Spectral Extraction']._obj
     collapsed = spec_extr_plugin.extract()
+
+    assert '_pixel_scale_factor' in collapsed.meta
+
+    # Original units in Jy / sr
+    # After collapsing, sr is removed via the scale factor and the extracted spectrum is in Jy
+    expected_flux_values = (np.array([190., 590., 990., 1390., 1790.,
+                                      2190., 2590., 2990., 3390., 3790.]) *
+                            collapsed.meta.get('_pixel_scale_factor'))
+
     np.testing.assert_allclose(
         collapsed.flux.value,
-        [190., 590., 990., 1390., 1790., 2190., 2590., 2990., 3390., 3790.]
+        expected_flux_values
     )
     assert collapsed.flux.unit == u.Jy
     assert collapsed.uncertainty.unit == u.Jy

jdaviz/configs/default/plugins/markers/markers.py

@@ -64,10 +64,12 @@ def __init__(self, *args, **kwargs):
         elif self.config == 'specviz':
             headers = ['spectral_axis', 'spectral_axis:unit',
                        'index', 'value', 'value:unit']
+
         elif self.config == 'specviz2d':
             # TODO: add "index" if/when specviz2d supports plotting spectral_axis
             headers = ['spectral_axis', 'spectral_axis:unit',
                        'pixel_x', 'pixel_y', 'value', 'value:unit', 'viewer']
+
         elif self.config == 'mosviz':
             headers = ['spectral_axis', 'spectral_axis:unit',
                        'pixel_x', 'pixel_y', 'world_ra', 'world_dec', 'index',
@@ -223,7 +225,6 @@ def _on_is_active_changed(self, *args):
     def _on_viewer_key_event(self, viewer, data):
         if data['event'] == 'keydown' and data['key'] == 'm':
             row_info = self.coords_info.as_dict()
-
             if 'viewer' in self.table.headers_avail:
                 row_info['viewer'] = viewer.reference if viewer.reference is not None else viewer.reference_id  # noqa
 

jdaviz/configs/default/plugins/markers/tests/test_markers_plugin.py

@@ -4,6 +4,7 @@
 import numpy as np
 from numpy.testing import assert_allclose
 import pytest
+from specutils import Spectrum1D
 
 from jdaviz.core.custom_units_and_equivs import PIX2, SPEC_PHOTON_FLUX_DENSITY_UNITS
 from jdaviz.core.marks import MarkersMark
@@ -242,6 +243,61 @@ def test_markers_cubeviz_flux_unit_conversion(cubeviz_helper,
     assert last_row['value:unit'] == new_cube_unit_str
 
 
+def test_markers_specviz2d_unit_conversion(specviz2d_helper, spectrum2d):
+    data = np.zeros((5, 10))
+    data[3] = np.arange(10)
+    spectrum2d = Spectrum1D(flux=data*u.MJy, spectral_axis=data[3]*u.AA)
+    specviz2d_helper.load_data(spectrum2d)
+
+    uc = specviz2d_helper.plugins['Unit Conversion']
+    uc.open_in_tray()
+    mp = specviz2d_helper.plugins['Markers']
+    mp.keep_active = True
+
+    label_mouseover = specviz2d_helper.app.session.application._tools["g-coords-info"]
+    viewer2d = specviz2d_helper.app.get_viewer("spectrum-2d-viewer")
+    label_mouseover._viewer_mouse_event(viewer2d, {"event": "mousemove",
+                                                   "domain": {"x": 6, "y": 3}})
+    assert label_mouseover.as_text() == ('Pixel x=06.0 y=03.0 Value +6.00000e+00 MJy',
+                                         'Wave 6.00000e+00 Angstrom',
+                                         '')
+    mp._obj._on_viewer_key_event(viewer2d, {'event': 'keydown',
+                                            'key': 'm'})
+
+    # make sure last marker added to table reflects new unit selection
+    last_row = mp.export_table()[-1]
+    assert last_row['value:unit'] == uc.flux_unit
+    assert last_row['spectral_axis:unit'] == uc.spectral_unit
+
+    # ensure marks work with flux conversion where spectral axis is required and
+    # spectral axis conversion
+    uc.flux_unit = 'erg / (Angstrom s cm2)'
+    uc.spectral_unit = 'Ry'
+    label_mouseover._viewer_mouse_event(viewer2d, {"event": "mousemove",
+                                                   "domain": {"x": 4, "y": 3}})
+    assert label_mouseover.as_text() == ('Pixel x=04.0 y=03.0 Value +7.49481e+00 erg / (Angstrom s cm2)',  # noqa
+                                         'Wave 2.27817e+02 Ry',
+                                         '')
+    mp._obj._on_viewer_key_event(viewer2d, {'event': 'keydown',
+                                            'key': 'm'})
+
+    # make sure last marker added to table reflects new unit selection
+    last_row = mp.export_table()[-1]
+    assert last_row['value:unit'] == uc.flux_unit
+    assert last_row['spectral_axis:unit'] == uc.spectral_unit
+
+    second_marker_flux_unit = uc.flux_unit.selected
+    second_marker_spectral_unit = uc.spectral_unit.selected
+
+    # test edge case two non-native spectral axis required conversions
+    uc.flux_unit = 'ph / (Angstrom s cm2)'
+    uc.spectral_unit = 'eV'
+
+    # make sure table flux and spectral unit doesn't update
+    assert last_row['value:unit'] == second_marker_flux_unit
+    assert last_row['spectral_axis:unit'] == second_marker_spectral_unit
+
+
 class TestImvizMultiLayer(BaseImviz_WCS_NoWCS):
     def test_markers_layer_cycle(self):
         label_mouseover = self.imviz.app.session.application._tools['g-coords-info']

jdaviz/configs/default/plugins/model_fitting/model_fitting.py

@@ -1113,8 +1113,11 @@ def _fit_model_to_spectrum(self, add_data):
             return
         models_to_fit = self._reinitialize_with_fixed()
 
-        masked_spectrum = self._apply_subset_masks(self.dataset.selected_spectrum,
+        spec = self.dataset.get_selected_spectrum(use_display_units=True)
+
+        masked_spectrum = self._apply_subset_masks(spec,
                                                    self.spectral_subset)
+
         try:
             fitted_model, fitted_spectrum = fit_model_to_spectrum(
                 masked_spectrum,

jdaviz/configs/default/plugins/model_fitting/tests/test_fitting.py

@@ -312,6 +312,8 @@ def test_results_table(specviz_helper, spectrum1d):
     mf = specviz_helper.plugins['Model Fitting']
     mf.create_model_component('Linear1D')
 
+    uc = specviz_helper.plugins['Unit Conversion']
+
     mf.add_results.label = 'linear model'
     with warnings.catch_warnings():
         warnings.filterwarnings('ignore', message='Model is linear in parameters.*')
@@ -325,6 +327,9 @@ def test_results_table(specviz_helper, spectrum1d):
                                  'L:intercept_0', 'L:intercept_0:unit',
                                  'L:intercept_0:fixed', 'L:intercept_0:std']
 
+    # verify units in table match the current display unit
+    assert mf_table['L:intercept_0:unit'][-1] == uc.flux_unit
+
     mf.create_model_component('Gaussian1D')
     mf.add_results.label = 'composite model'
     with warnings.catch_warnings():
@@ -346,6 +351,19 @@ def test_results_table(specviz_helper, spectrum1d):
                                  'G:stddev_1', 'G:stddev_1:unit',
                                  'G:stddev_1:fixed', 'G:stddev_1:std']
 
+    mf.remove_model_component('G')
+    assert len(mf_table) == 2
+
+    # verify Spectrum1D model fitting plugin and table can handle spectral density conversions
+    uc.flux_unit = 'erg / (Angstrom s cm2)'
+    mf.reestimate_model_parameters()
+
+    with warnings.catch_warnings():
+        warnings.filterwarnings('ignore', message='Model is linear in parameters.*')
+        mf.calculate_fit(add_data=True)
+
+    assert mf_table['L:intercept_0:unit'][-1] == uc.flux_unit
+
 
 def test_equation_validation(specviz_helper, spectrum1d):
     data_label = 'test'

jdaviz/configs/imviz/plugins/coords_info/coords_info.py

@@ -22,6 +22,7 @@
 from jdaviz.core.unit_conversion_utils import (all_flux_unit_conversion_equivs,
                                                check_if_unit_is_per_solid_angle,
                                                flux_conversion_general)
+from jdaviz.utils import flux_conversion
 
 __all__ = ['CoordsInfo']
 
@@ -433,6 +434,12 @@ def _image_viewer_update(self, viewer, x, y):
             # use WCS to expose the wavelength for a 2d spectrum shown in pixel space
             try:
                 wave, pixel = image.coords.pixel_to_world(x, y)
+                if wave is not None:
+                    equivalencies = all_flux_unit_conversion_equivs(cube_wave=wave)
+                    wave = wave.to(self.app._get_display_unit('spectral'),
+                                   equivalencies=equivalencies)
+                    self._dict['spectral_axis'] = wave.value
+                    self._dict['spectral_axis:unit'] = wave.unit.to_string()
             except Exception:  # WCS might not be valid  # pragma: no cover
                 coords_status = False
             else:
@@ -483,12 +490,21 @@ def _image_viewer_update(self, viewer, x, y):
 
             if isinstance(viewer, (ImvizImageView, MosvizImageView, MosvizProfile2DView)):
                 value = image.get_data(attribute)[int(round(y)), int(round(x))]
+
                 if associated_dq_layers is not None:
                     associated_dq_layer = associated_dq_layers[0]
                     dq_attribute = associated_dq_layer.state.attribute
                     dq_data = associated_dq_layer.layer.get_data(dq_attribute)
                     dq_value = dq_data[int(round(y)), int(round(x))]
+
                 unit = u.Unit(image.get_component(attribute).units)
+                if (isinstance(viewer, MosvizProfile2DView) and unit != ''
+                   and unit != self.app._get_display_unit(attribute)):
+                    equivalencies = all_flux_unit_conversion_equivs(cube_wave=wave)
+                    value = flux_conversion(value, unit, self.app._get_display_unit(attribute),
+                                            eqv=equivalencies)
+                    unit = self.app._get_display_unit(attribute)
+
             elif isinstance(viewer, (CubevizImageView, RampvizImageView)):
                 arr = image.get_component(attribute).data
                 unit = u.Unit(image.get_component(attribute).units)
@@ -543,7 +559,10 @@ def _image_viewer_update(self, viewer, x, y):
             else:
                 dq_text = ''
             self.row1b_text = f'{value:+10.5e} {unit}{dq_text}'
-            self._dict['value'] = float(value)
+            if not isinstance(value, (float, np.floating)):
+                self._dict['value'] = float(value)
+            else:
+                self._dict['value'] = value
             self._dict['value:unit'] = str(unit)
             self._dict['value:unreliable'] = unreliable_pixel
         else:

jdaviz/configs/mosviz/plugins/tools.py

@@ -1,6 +1,7 @@
 import os
 
 from glue.config import viewer_tool
+from astropy import units as u
 
 from jdaviz.configs.mosviz.plugins.viewers import MosvizProfileView, MosvizProfile2DView
 from jdaviz.core.tools import _MatchedZoomMixin, HomeZoom, BoxZoom, XRangeZoom, PanZoom, PanZoomX
@@ -18,12 +19,45 @@ def _is_matched_viewer(self, viewer):
         return isinstance(viewer, (MosvizProfile2DView, MosvizProfileView))
 
     def _map_limits(self, from_viewer, to_viewer, limits={}):
+        components = self.viewer.state.data_collection[0]._components
+        # Determine cid for spectral axis
+        cid = None
+        for key in components.keys():
+            if 'Wavelength' in str(key):
+                cid = str(key)
+                break
+            elif 'Wave' in str(key):
+                cid = str(key)
+                break
+
+        if cid is None:
+            raise ValueError("Neither 'Wavelength' nor 'Wave' component'" +
+                             "found in the data collection.")
+
+        native_unit = u.Unit(self.viewer.state.data_collection[0].get_component(cid).units)
+        current_display_unit = u.Unit(self.viewer.jdaviz_helper.app._get_display_unit('spectral'))
+
         if isinstance(from_viewer, MosvizProfileView) and isinstance(to_viewer, MosvizProfile2DView):  # noqa
+            if native_unit != current_display_unit:
+                limits['x_min'] = (limits['x_min'] * native_unit).to_value(
+                                   current_display_unit, equivalencies=u.spectral()
+                                )
+
+                limits['x_max'] = (limits['x_max'] * native_unit).to_value(
+                                   current_display_unit, equivalencies=u.spectral()
+                                   )
             limits['x_min'], limits['x_max'] = to_viewer.world_to_pixel_limits((limits['x_min'],
                                                                                 limits['x_max']))
         elif isinstance(from_viewer, MosvizProfile2DView) and isinstance(to_viewer, MosvizProfileView):  # noqa
             limits['x_min'], limits['x_max'] = from_viewer.pixel_to_world_limits((limits['x_min'],
                                                                                   limits['x_max']))
+            if native_unit != current_display_unit:
+                limits['x_min'] = (limits['x_min'] * native_unit).to_value(
+                                   current_display_unit, equivalencies=u.spectral()
+                                   )
+                limits['x_max'] = (limits['x_max'] * native_unit).to_value(
+                                   current_display_unit, equivalencies=u.spectral()
+                                   )
         return limits
 
 

jdaviz/configs/mosviz/tests/test_data_loading.py

@@ -222,8 +222,11 @@ def test_load_single_image_multi_spec(mosviz_helper, mos_image, spectrum1d, mos_
 
     label_mouseover._viewer_mouse_event(spec2d_viewer,
                                         {'event': 'mousemove', 'domain': {'x': 10, 'y': 100}})
+
+    # Note: spectra2d Wave loaded in meters, but we respect one spectral unit, so the meters in
+    # converted to Angstrom (the spectra1d spectral unit).
     assert label_mouseover.as_text() == ('Pixel x=00010.0 y=00100.0 Value +8.12986e-01',
-                                         'Wave 1.10000e-05 m', '')
+                                         'Wave 1.10000e+05 Angstrom', '')
     assert label_mouseover.icon == 'c'
 
     # need to trigger a mouseleave or mouseover to reset the traitlets

jdaviz/configs/specviz/plugins/line_analysis/tests/test_line_analysis.py

@@ -6,6 +6,7 @@
 from numpy.testing import assert_allclose
 from regions import RectanglePixelRegion, PixCoord
 from specutils import Spectrum1D, SpectralRegion
+from glue.core.roi import XRangeROI
 
 from jdaviz.configs.specviz.plugins.line_analysis.line_analysis import _coerce_unit
 from jdaviz.core.custom_units_and_equivs import PIX2
@@ -91,7 +92,7 @@ def test_cubeviz_units(cubeviz_helper, spectrum1d_cube_custom_fluxunit,
     is in flux/pix2 and flux/sr, and that the results remain consistant
     between translations of the spectral y axis flux<>surface brightness.
     """
-    cube = spectrum1d_cube_custom_fluxunit(fluxunit=u.Jy / sq_angle_unit,
+    cube = spectrum1d_cube_custom_fluxunit(fluxunit=u.MJy / sq_angle_unit,
                                            shape=(25, 25, 4), with_uncerts=True)
     cubeviz_helper.load_data(cube, data_label="Test Cube")
 
@@ -107,9 +108,46 @@ def test_cubeviz_units(cubeviz_helper, spectrum1d_cube_custom_fluxunit,
     results = plugin.results
     assert results[0]['unit'] == 'W / m2'
 
+    viewer = cubeviz_helper.app.get_viewer('spectrum-viewer')
+    viewer.apply_roi(XRangeROI(4.63e-7, 4.64e-7))
+
+    la = cubeviz_helper.plugins['Line Analysis']
+    la.keep_active = True
+    la.spectral_subset.selected = 'Subset 1'
+
+    marks_before = [la._obj.continuum_marks['left'].y,
+                    la._obj.continuum_marks['right'].y]
+
+    # change flux unit and make sure result stays the same after conversion
+    uc.flux_unit.selected = 'Jy'
+
+    marks_after = [la._obj.continuum_marks['left'].y,
+                   la._obj.continuum_marks['right'].y]
+
+    # ensure continuum marks update when spectral_y is changed by
+    # multiply converted continuum marks by expected scale factor (MJy -> Jy)
+    scaling_factor = 1e6
+    assert_allclose([mark * scaling_factor for mark in marks_before], marks_after, rtol=1e-5)
+
+    # reset to test again after spectral_y_type is changed
+    marks_before = marks_after
+
     # now change to surface brightness
     uc.spectral_y_type = 'Surface Brightness'
 
+    if sq_angle_unit == PIX2:
+        # translation does not alter spectral_y values in viewer
+        scaling_factor = 1
+    else:
+        scaling_factor = cube.meta.get('PIXAR_SR')
+
+    marks_after = [la._obj.continuum_marks['left'].y,
+                   la._obj.continuum_marks['right'].y]
+
+    # ensure continuum marks update when spectral_y_type is changed
+    # multiply converted continuum marks by expected pixel scale factor
+    assert_allclose([mark / scaling_factor for mark in marks_before], marks_after, rtol=1e-5)
+
     results = plugin.results
     line_flux_before_unit_conversion = results[0]
     # convert back and forth between unit<>str for string format consistency