Unit conversion plugin

docs/plugins.rst

@@ -72,6 +72,34 @@ This plugin allows choosing which column in the underlying data should be used a
     * :meth:`lightkurve.LightCurve.select_flux`
 
 
+.. _unit-conversion
+
+Unit Conversion
+===============
+
+This plugin allows choosing app-wide units to use for the time and flux axes.
+
+
+.. admonition:: User API Example
+    :class: dropdown
+
+    See the :class:`~lcviz.plugins.unit_conversion.unit_conversion.UnitConversion` user API documentation for more details.
+
+    .. code-block:: python
+
+      from lcviz import LCviz
+      from lightkurve import search_lightcurve
+      lc = search_lightcurve("HAT-P-11", mission="Kepler",
+                             cadence="long", quarter=10).download().flatten()
+      lcviz = LCviz()
+      lcviz.load_data(lc)
+      lcviz.show()
+
+      units = lcviz.plugins['Unit Conversion']
+      print(units.time_unit.choices)
+      units.time_unit = 'hr'
+
+
 .. _plot-options:
 
 Plot Options

docs/reference/api_plugins.rst

@@ -38,3 +38,6 @@ Plugins API
 
 .. automodapi:: lcviz.plugins.time_selector.time_selector
   :no-inheritance-diagram:
+
+.. automodapi:: lcviz.plugins.unit_conversion.unit_conversion
+  :no-inheritance-diagram:

lcviz/helper.py

@@ -103,7 +103,7 @@ class LCviz(ConfigHelper):
                      'dense_toolbar': False,
                      'context': {'notebook': {'max_height': '600px'}}},
         'toolbar': ['g-data-tools', 'g-subset-tools', 'g-viewer-creator', 'lcviz-coords-info'],
-        'tray': ['lcviz-metadata-viewer', 'flux-column',
+        'tray': ['lcviz-metadata-viewer', 'flux-column', 'lcviz-unit-conversion',
                  'lcviz-plot-options', 'lcviz-subset-plugin',
                  'lcviz-markers', 'time-selector',
                  'stitch', 'flatten', 'frequency-analysis', 'ephemeris',

lcviz/plugins/__init__.py

@@ -13,3 +13,4 @@
 from .plot_options.plot_options import *  # noqa
 from .stitch.stitch import *  # noqa
 from .subset_plugin.subset_plugin import *  # noqa
+from .unit_conversion.unit_conversion import *  # noqa

lcviz/plugins/unit_conversion/__init__.py

@@ -0,0 +1 @@
+from .unit_conversion import *  # noqa

lcviz/plugins/unit_conversion/unit_conversion.py

@@ -0,0 +1,107 @@
+from jdaviz.configs.specviz.plugins.unit_conversion.unit_conversion import (UnitConversion,
+                                                                            _valid_glue_display_unit,  # noqa
+                                                                            _flux_to_sb_unit)
+from jdaviz.core.events import GlobalDisplayUnitChanged
+from jdaviz.core.registries import tray_registry
+
+from lcviz.viewers import (CubeView, TimeScatterView)
+
+__all__ = ['UnitConversion']
+
+
+@tray_registry('lcviz-unit-conversion', label="Unit Conversion")
+class UnitConversion(UnitConversion):
+    """
+    See the :ref:`Unit Conversion Plugin Documentation <unit-conversion>` for more details.
+
+    For a full list of exposed attributes, call ``dir(plugin)``.  Note that some attributes are
+    applicable depending on the selection of ``viewer`` and/or ``layer``.  Below are
+    a list of some common attributes and methods are available through the
+    :ref:`public plugin API <plugin-apis>`:
+
+    * :meth:`~jdaviz.core.template_mixin.PluginTemplateMixin.show`
+    * :meth:`~jdaviz.core.template_mixin.PluginTemplateMixin.open_in_tray`
+    * :meth:`~jdaviz.core.template_mixin.PluginTemplateMixin.close_in_tray`
+    """
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.docs_link = f"https://lcviz.readthedocs.io/en/{self.vdocs}/plugins.html#unit-conversion"
+        self.docs_description = "Choose units for the time and flux axes."
+        self.disabled_msg = ""  # otherwise disabled upstream - remove once upstream no longer has a config check
+
+        self.has_time = True
+        self.has_flux = True
+
+    @property
+    def spectrum_viewer(self):
+        if hasattr(self, '_default_time_viewer_reference_name'):
+            viewer_reference = self._default_time_viewer_reference_name
+        else:
+            viewer_reference = self.app._get_first_viewer_reference_name(
+            )
+
+        return self.app.get_viewer(viewer_reference)
+
+    def _on_add_data_to_viewer(self, msg):
+        viewer = msg.viewer
+
+        if (not len(self.time_unit_selected) or not len(self.flux_unit_selected)):
+            # TODO: default based on the native units of the data (LC or TPF)
+            self.time_unit.choices = ['d', 'hr', 'min', 's']
+            self.time_unit_selected = 'd'
+            self.flux_unit.choices = ['erg / (Angstrom cm2 s)']
+            self.flux_unit_selected = 'erg / (Angstrom cm2 s)'
+            # setting default values will trigger the observes to set the units
+            # in _on_unit_selected, so return here to avoid setting twice
+            return
+
+        # TODO: when enabling unit-conversion in rampviz, this may need to be more specific
+        # or handle other cases for ramp profile viewers
+        if isinstance(viewer, TimeScatterView):
+            if (viewer.state.x_display_unit == self.time_unit_selected
+                    and viewer.state.y_display_unit == self.flux_unit_selected):
+                # data already existed in this viewer and display units were already set
+                return
+
+            # this spectral viewer was empty (did not have display units set yet),˜
+            # but global selections are available in the plugin,
+            # so we'll set them to the viewer here
+            viewer.state.x_display_unit = self.time_unit_selected
+            viewer.state.y_display_unit = self.flux_unit_selected
+
+        elif isinstance(viewer, CubeView):
+            # set the attribute display unit (contour and stretch units) for the new layer
+            # NOTE: this assumes that all image data is coerced to surface brightness units
+            layers = [lyr for lyr in msg.viewer.layers if lyr.layer.data.label == msg.data.label]
+            self._handle_attribute_display_unit(self.flux_unit_selected, layers=layers)
+            self._clear_cache('image_layers')
+
+    def _on_unit_selected(self, msg):
+        """
+        When any user selection is made, update the relevant viewer(s) with the new unit,
+        and then emit a GlobalDisplayUnitChanged message to notify other plugins of the change.
+        """
+        print("*** _on_unit_selected", msg.get('name'), msg.get('new'))
+        if not len(msg.get('new', '')):
+            # empty string, nothing to set yet
+            return
+
+        axis = msg.get('name').split('_')[0]
+
+        if axis == 'time':
+            xunit = _valid_glue_display_unit(self.time_unit.selected, self.spectrum_viewer, 'x')
+            # TODO: iterate over all TimeScatterViewers
+            self.spectrum_viewer.state.x_display_unit = xunit
+            self.spectrum_viewer.set_plot_axes()
+
+        elif axis == 'flux':
+            yunit = _valid_glue_display_unit(self.flux_unit.selected, self.spectrum_viewer, 'y')
+            # TODO: iterate over all Time and Phase Scatter Viewers
+            self.spectrum_viewer.state.y_display_unit = yunit
+            self.spectrum_viewer.set_plot_axes()
+
+            # TODO: handle setting surface brightness units for CubeView
+
+        # axis (first) argument will be one of: time, flux
+        self.hub.broadcast(GlobalDisplayUnitChanged(axis,
+                           msg.new, sender=self))

lcviz/state.py

@@ -35,6 +35,7 @@ def _reset_y_limits(self, *event):
         self._reset_att_limits('y')
 
     def reset_limits(self, *event):
+        # TODO: this is not working correctly when units are changed (probably the same for _reset_att_limits)
         x_min, x_max = np.inf, -np.inf
         y_min, y_max = np.inf, -np.inf
 

lcviz/viewers.py

@@ -164,7 +164,7 @@ def set_plot_axes(self):
     def _set_plot_x_axes(self, dc, component_labels, light_curve):
         self.state.x_att = dc[0].components[component_labels.index('dt')]
 
-        x_unit = self.time_unit
+        x_unit = self.time_unit  # TODO: use get display unit instead?  Or at least update self.time_unit
         reference_time = light_curve.meta.get('reference_time', None)
 
         if reference_time is not None:
@@ -176,7 +176,10 @@ def _set_plot_x_axes(self, dc, component_labels, light_curve):
         self.figure.axes[0].num_ticks = 5
 
     def _set_plot_y_axes(self, dc, component_labels, light_curve):
-        self.state.y_att = dc[0].components[component_labels.index('flux')]
+        try:
+            self.state.y_att = dc[0].components[component_labels.index('flux')]
+        except ValueError:
+            pass
 
         y_unit = light_curve.flux.unit
         y_unit_physical_type = str(y_unit.physical_type).title()