implement unit conversion in specviz2d

CHANGES.rst

@@ -29,6 +29,8 @@ Specviz
 Specviz2d
 ^^^^^^^^^
 
+- Implement the Unit Conversion plugin the Specviz2D. [#3253]
+
 API Changes
 -----------
 - Removed API access to plugins that have passed the deprecation period: Links Control, Canvas Rotation, Export Plot. [#3270]

jdaviz/configs/cubeviz/helper.py

@@ -138,6 +138,8 @@ 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/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',

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

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

@@ -154,3 +154,40 @@ def test_flux_unit_choices(specviz_helper, flux_unit, expected_choices):
 
     assert uc_plg.flux_unit.selected == flux_unit.to_string()
     assert uc_plg.flux_unit.choices == expected_choices
+
+
+def test_mosviz_profile_view_mouseover(specviz2d_helper, spectrum2d):
+    data = np.zeros((5, 10))
+    data[3] = np.arange(10)
+    spectrum2d = Spectrum1D(flux=data*u.MJy, spectral_axis=data[3]*u.um)
+
+    specviz2d_helper.load_data(spectrum2d)
+    viewer = specviz2d_helper.app.get_viewer("spectrum-viewer")
+    plg = specviz2d_helper.plugins["Unit Conversion"]
+
+    # make sure we don't expose angle, sb, nor spectral-y units when native
+    # units are in flux
+    assert hasattr(plg, 'flux_unit')
+    assert not hasattr(plg, 'angle_unit')
+    assert not hasattr(plg, 'sb_unit')
+    assert not hasattr(plg, 'spectral_y_type')
+
+    label_mouseover = specviz2d_helper.app.session.application._tools['g-coords-info']
+    label_mouseover._viewer_mouse_event(viewer,
+                                        {'event': 'mousemove',
+                                         'domain': {'x': 5, 'y': 3}})
+
+    assert label_mouseover.as_text() == ('Cursor 5.00000e+00, 3.00000e+00',
+                                         'Wave 5.00000e+00 um (5 pix)',
+                                         'Flux 5.00000e+00 MJy')
+
+    plg._obj.flux_unit_selected = 'Jy'
+    assert label_mouseover.as_text() == ('Cursor 5.00000e+00, 3.00000e+00',
+                                         'Wave 5.00000e+00 um (5 pix)',
+                                         'Flux 5.00000e+06 Jy')
+
+    # test mouseover when spectral density equivalencies are required for conversion
+    plg._obj.flux_unit_selected = 'erg / (Angstrom s cm2)'
+    assert label_mouseover.as_text() == ('Cursor 5.00000e+00, 3.00000e+00',
+                                         'Wave 5.00000e+00 um (5 pix)',
+                                         'Flux 5.99585e-08 erg / (Angstrom s cm2)')

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

@@ -113,7 +113,7 @@ def __init__(self, *args, **kwargs):
 
         self._cached_properties = ['image_layers']
 
-        if self.config not in ['specviz', 'cubeviz']:
+        if self.config not in ['specviz', 'specviz2d', 'cubeviz']:
             # TODO [specviz2d, mosviz] x_display_unit is not implemented in glue for image viewer
             # used by spectrum-2d-viewer
             # TODO [mosviz]: add to yaml file
@@ -141,7 +141,7 @@ def __init__(self, *args, **kwargs):
         # initialize flux choices to empty list, will be populated when data is loaded
         self.flux_unit.choices = []
 
-        self.has_angle = self.config in ('cubeviz', 'specviz', 'mosviz')
+        self.has_angle = self.config in ('cubeviz', 'specviz', 'mosviz', 'specviz2d')
         self.angle_unit = UnitSelectPluginComponent(self,
                                                     items='angle_unit_items',
                                                     selected='angle_unit_selected')
@@ -211,7 +211,6 @@ def _on_add_data_to_viewer(self, msg):
                 or not len(self.flux_unit_selected)
                 or not len(self.angle_unit_selected)
                 or (self.config == 'cubeviz' and not len(self.spectral_y_type_selected))):
-
             data_obj = msg.data.get_object()
             if isinstance(data_obj, Spectrum1D):
 
@@ -237,9 +236,13 @@ def _on_add_data_to_viewer(self, msg):
 
                     try:
                         if angle_unit is None:
-                            # default to sr if input spectrum is not in surface brightness units
-                            # TODO: for cubeviz, should we check the cube itself?
-                            self.angle_unit.selected = 'sr'
+                            if self.config in ['specviz', 'specviz2d']:
+                                self.has_angle = False
+                                self.has_sb = False
+                            else:
+                                # default to pix2 if input data is not in surface brightness units
+                                # TODO: for cubeviz, should we check the cube itself?
+                                self.angle_unit.selected = 'pix2'
                         else:
                             self.angle_unit.selected = str(angle_unit)
                     except ValueError:

jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.vue

@@ -49,7 +49,7 @@
       hint="Solid angle unit."
     />
 
-    <v-row v-if="has_spectral">
+    <v-row v-if="has_sb">
       <v-text-field
         v-model="sb_unit_selected"
         :label="api_hints_enabled ? 'plg.sb_unit' : 'Surface Brightness Unit'"

jdaviz/configs/specviz2d/helper.py

@@ -171,7 +171,8 @@ def load_trace(self, trace, data_label, show_in_viewer=True):
                 self._default_spectrum_2d_viewer_reference_name, data_label
             )
 
-    def get_data(self, data_label=None, spectral_subset=None, cls=None):
+    def get_data(self, data_label=None, spectral_subset=None,
+                 cls=None, use_display_units=False):
         """
         Returns data with name equal to data_label of type cls with subsets applied from
         spectral_subset.
@@ -184,11 +185,14 @@ def get_data(self, data_label=None, spectral_subset=None, cls=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
         -------
         data : cls
             Data is returned as type cls with subsets applied.
 
         """
-        return self._get_data(data_label=data_label, spectral_subset=spectral_subset, cls=cls)
+        return self._get_data(data_label=data_label, spectral_subset=spectral_subset,
+                              cls=cls, use_display_units=use_display_units)

jdaviz/configs/specviz2d/specviz2d.yaml

@@ -19,6 +19,7 @@ tray:
   - g-plot-options
   - g-subset-tools
   - g-markers
+  - g-unit-conversion
   - spectral-extraction
   - g-gaussian-smooth
   - g-model-fitting

jdaviz/conftest.py

@@ -260,7 +260,7 @@ def _create_spectrum1d_cube_with_fluxunit(fluxunit=u.Jy, shape=(2, 2, 4), with_u
     wcs_dict = {"CTYPE1": "RA---TAN", "CTYPE2": "DEC--TAN", "CTYPE3": "WAVE-LOG",
                 "CRVAL1": 205, "CRVAL2": 27, "CRVAL3": 4.622e-7,
                 "CDELT1": -0.0001, "CDELT2": 0.0001, "CDELT3": 8e-11,
-                "CRPIX1": 0, "CRPIX2": 0, "CRPIX3": 0,
+                "CRPIX1": 0, "CRPIX2": 0, "CRPIX3": 0, "PIXAR_SR": 10,
                 # Need these for aperture photometry test.
                 "TELESCOP": "JWST", "BUNIT": fluxunit.to_string(), "PIXAR_A2": 0.01}
     w = WCS(wcs_dict)

jdaviz/core/helpers.py

@@ -480,16 +480,12 @@ def _handle_display_units(self, data, use_display_units=True):
                                                                new_uncert.unit, y_unit, spec=data)
                         new_uncert = StdDevUncertainty(new_uncert_converted, unit=y_unit)
                     else:
-                        new_uncert = StdDevUncertainty(new_uncert, unit=data.flux.unit)
+                        new_uncert = StdDevUncertainty(new_uncert, unit=y_unit)
 
                 else:
                     new_uncert = None
-                if ('_pixel_scale_factor' in data.meta):
-                    new_y = flux_conversion(data.flux.value, data.flux.unit,
-                                            y_unit, data) * u.Unit(y_unit)
-                else:
-                    new_y = flux_conversion(data.flux.value, data.flux.unit,
-                                            data.flux.unit, spec=data) * u.Unit(data.flux.unit)
+                new_y = flux_conversion(data.flux.value, data.flux.unit,
+                                        y_unit, spec=data) * u.Unit(y_unit)
                 new_spec = (spectral_axis_conversion(data.spectral_axis.value,
                                                      data.spectral_axis.unit,
                                                      spectral_unit)

jdaviz/core/marks.py

@@ -11,7 +11,8 @@
                                 SpectralMarksChangedMessage,
                                 RedshiftMessage)
 from jdaviz.core.unit_conversion_utils import (all_flux_unit_conversion_equivs,
-                                               flux_conversion_general)
+                                               flux_conversion_general,
+                                               check_if_unit_is_per_solid_angle)
 
 
 __all__ = ['OffscreenLinesMarks', 'BaseSpectrumVerticalLine', 'SpectralLine',
@@ -129,15 +130,21 @@ def set_y_unit(self, unit=None):
             unit = self.viewer.state.y_display_unit
         unit = u.Unit(unit)
 
+        # spectrum y-values in viewer have already been converted, don't convert again
+        # if a spectral_y_type is changed, just update the unit
+        if self.yunit is not None and check_if_unit_is_per_solid_angle(self.yunit) != check_if_unit_is_per_solid_angle(unit):  # noqa
+            self.yunit = unit
+            return
+
         if self.yunit is not None and not np.all([s == 0 for s in self.y.shape]):
+
             if self.viewer.default_class is Spectrum1D:
 
                 spec = self.viewer.state.reference_data.get_object(cls=Spectrum1D)
 
                 pixar_sr = spec.meta.get('PIXAR_SR', 1)
                 cube_wave = self.x * self.xunit
                 equivs = all_flux_unit_conversion_equivs(pixar_sr, cube_wave)
-
                 y = flux_conversion_general(self.y, self.yunit, unit, equivs,
                                             with_unit=False)
 
@@ -148,14 +155,22 @@ def set_y_unit(self, unit=None):
     def _on_global_display_unit_changed(self, msg):
         if not self.auto_update_units:
             return
-        if self.viewer.__class__.__name__ in ['SpecvizProfileView', 'CubevizProfileView']:
+        if self.viewer.__class__.__name__ in ['SpecvizProfileView',
+                                              'CubevizProfileView',
+                                              'MosvizProfileView']:
             axis_map = {'spectral': 'x', 'spectral_y': 'y'}
         elif self.viewer.__class__.__name__ == 'MosvizProfile2DView':
             axis_map = {'spectral': 'x'}
         else:
             return
         axis = axis_map.get(msg.axis, None)
         if axis is not None:
+            scale = self.scales.get(axis, None)
+            # if PluginMark mark is LinearScale(0, 1), prevent it from entering unit conversion
+            # machinery so it maintains it's position in viewer.
+            if isinstance(scale, LinearScale) and (scale.min, scale.max) == (0, 1):
+                return
+
             getattr(self, f'set_{axis}_unit')(msg.unit)
 
     def clear(self):