Time Selector (adapted version of cubeviz's slice) plugin (#85)

docs/plugins.rst

@@ -179,6 +179,40 @@ visible when the plugin is opened.
         Jdaviz documentation on the Markers plugin.
 
 
+.. _time-indicator:
+
+Time Selector
+==============
+
+The time selector plugin allows defining the time indicated in all light curve viewers
+(time and phase viewers) as well as the time at which all image cubes are displayed.
+
+
+.. admonition:: User API Example
+    :class: dropdown
+
+    See the :class:`~lcviz.plugins.time_selector.time_selector.TimeSelector` user API documentation for more details.
+
+    .. code-block:: python
+
+      from lcviz import LCviz
+      lc = search_lightcurve("HAT-P-11", mission="Kepler",
+                             cadence="long", quarter=10).download().flatten()
+      lcviz = LCviz()
+      lcviz.load_data(lc)
+      lcviz.show()
+
+      ts = lcviz.plugins['Time Selector']
+      ts.open_in_tray()
+
+
+.. seealso::
+
+    :ref:`Jdaviz Slice Plugin <jdaviz:slice>`
+        Jdaviz documentation on the Slice plugin.
+
+
+
 .. _flatten:
 
 Flatten

docs/reference/api_plugins.rst

@@ -29,3 +29,6 @@ Plugins API
 
 .. automodapi:: lcviz.plugins.subset_plugin.subset_plugin
   :no-inheritance-diagram:
+
+.. automodapi:: lcviz.plugins.time_selector.time_selector
+  :no-inheritance-diagram:

lcviz/helper.py

@@ -74,7 +74,8 @@ class LCviz(ConfigHelper):
         'toolbar': ['g-data-tools', 'g-subset-tools', 'lcviz-coords-info'],
         'tray': ['lcviz-metadata-viewer', 'flux-column',
                  'lcviz-plot-options', 'lcviz-subset-plugin',
-                 'lcviz-markers', 'flatten', 'frequency-analysis', 'ephemeris',
+                 'lcviz-markers', 'time-selector',
+                 'flatten', 'frequency-analysis', 'ephemeris',
                  'binning', 'lcviz-export-plot'],
         'viewer_area': [{'container': 'col',
                          'children': [{'container': 'row',

lcviz/marks.py

@@ -1,11 +1,21 @@
+from astropy import units as u
 import numpy as np
 
-from jdaviz.core.marks import PluginLine, PluginScatter
+from jdaviz.core.marks import PluginLine, PluginScatter, SliceIndicatorMarks
 from lcviz.viewers import PhaseScatterView
 
 __all__ = ['LivePreviewTrend', 'LivePreviewFlattened', 'LivePreviewBinning']
 
 
+def _slice_indicator_get_slice_axis(self, data):
+    if hasattr(data, 'time'):
+        return data.time.value * u.d
+    return [] * u.dimensionless_unscaled
+
+
+SliceIndicatorMarks._get_slice_axis = _slice_indicator_get_slice_axis
+
+
 class WithoutPhaseSupport:
     def update_ty(self, times, y):
         self.times = np.asarray(times)

lcviz/plugins/__init__.py

@@ -6,6 +6,7 @@
 from .flux_column.flux_column import *  # noqa
 from .frequency_analysis.frequency_analysis import *  # noqa
 from .markers.markers import *  # noqa
+from .time_selector.time_selector import *  # noqa
 from .metadata_viewer.metadata_viewer import *  # noqa
 from .plot_options.plot_options import *  # noqa
 from .subset_plugin.subset_plugin import *  # noqa

lcviz/plugins/time_selector/__init__.py

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

lcviz/plugins/time_selector/time_selector.py

@@ -0,0 +1,70 @@
+from jdaviz.configs.cubeviz.plugins import Slice
+from jdaviz.core.registries import tray_registry
+
+from lcviz.viewers import CubeView, PhaseScatterView
+
+__all__ = ['TimeSelector']
+
+
+@tray_registry('time-selector', label="Time Selector")
+class TimeSelector(Slice):
+    """
+    See the :ref:`Time Selector Plugin Documentation <time-selector>` for more details.
+
+    Only the following 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`
+    * ``value``  Time of the indicator.  When setting this directly, it will
+      update automatically to the value corresponding to the nearest slice, if ``snap_to_slice`` is
+      enabled and a cube is loaded.
+    * ``show_indicator``
+      Whether to show indicator in spectral viewer when slice tool is inactive.
+    * ``show_value``
+      Whether to show slice value in label to right of indicator.
+    * ``snap_to_slice``
+      Whether the indicator (and ``value``) should snap to the value of the nearest slice in the
+      cube (if one exists).
+    """
+    _cube_viewer_cls = CubeView
+    _cube_viewer_default_label = 'image'
+
+    def __init__(self, *args, **kwargs):
+        """
+
+        """
+        super().__init__(*args, **kwargs)
+        self.docs_link = f"https://lcviz.readthedocs.io/en/{self.vdocs}/plugins.html#time-selector"
+        self.docs_description = "Select time to sync across all viewers (as an indicator in all time/phase viewers or to select the active slice in any image/cube viewers).  The slice can also be changed interactively in any time viewer by activating the slice tool."  # noqa
+        self.value_label = 'Time'
+        self.value_unit = 'd'
+        self.allow_disable_snapping = True
+
+    @property
+    def slice_axis(self):
+        # global display unit "axis" corresponding to the slice axis
+        return 'time'
+
+    @property
+    def valid_slice_att_names(self):
+        return ["time", "dt"]
+
+    @property
+    def user_api(self):
+        api = super().user_api
+        # can be removed after deprecated upstream attributes for wavelength/wavelength_value
+        # are removed in the lowest supported version of jdaviz
+        api._expose = [e for e in api._expose if e not in ('slice', 'wavelength',
+                                                           'wavelength_value', 'show_wavelength')]
+        return api
+
+    def _on_select_slice_message(self, msg):
+        viewer = msg.sender.viewer
+        if isinstance(viewer, PhaseScatterView):
+            prev_phase = viewer.times_to_phases(self.value)
+            new_phase = msg.value
+            self.value = self.value + (new_phase - prev_phase) * viewer.ephemeris.get('period', 1.0)
+        else:
+            super()._on_select_slice_message(msg)

lcviz/viewers.py

@@ -12,7 +12,8 @@
 
 from jdaviz.core.events import NewViewerMessage
 from jdaviz.core.registries import viewer_registry
-from jdaviz.configs.cubeviz.plugins.viewers import CubevizImageView
+from jdaviz.configs.cubeviz.plugins.viewers import (CubevizImageView,
+                                                    WithSliceIndicator, WithSliceSelection)
 from jdaviz.configs.default.plugins.viewers import JdavizViewerMixin
 from jdaviz.configs.specviz.plugins.viewers import SpecvizProfileView
 
@@ -60,13 +61,14 @@ def clone_viewer(self):
 
 
 @viewer_registry("lcviz-time-viewer", label="flux-vs-time")
-class TimeScatterView(JdavizViewerMixin, CloneViewerMixin, BqplotScatterView):
+class TimeScatterView(JdavizViewerMixin, CloneViewerMixin, WithSliceIndicator, BqplotScatterView):
     # categories: zoom resets, zoom, pan, subset, select tools, shortcuts
     tools_nested = [
                     ['jdaviz:homezoom', 'jdaviz:prevzoom'],
                     ['jdaviz:boxzoom', 'jdaviz:xrangezoom', 'jdaviz:yrangezoom'],
                     ['jdaviz:panzoom', 'jdaviz:panzoom_x', 'jdaviz:panzoom_y'],
                     ['bqplot:xrange', 'bqplot:yrange', 'bqplot:rectangle'],
+                    ['jdaviz:selectslice'],
                     ['lcviz:viewer_clone', 'jdaviz:sidebar_plot', 'jdaviz:sidebar_export']
                 ]
     default_class = LightCurve
@@ -79,7 +81,7 @@ def __init__(self, *args, **kwargs):
 
         self.display_mask = False
         self.time_unit = kwargs.get('time_unit', u.d)
-        self.initialize_toolbar()
+        self.initialize_toolbar(default_tool_priority=['jdaviz:selectslice'])
         self._subscribe_to_layers_update()
         # hack to inherit a small subset of methods from SpecvizProfileView
         # TODO: refactor jdaviz so these can be included in some mixin
@@ -89,6 +91,12 @@ def __init__(self, *args, **kwargs):
         self._clean_error = lambda: SpecvizProfileView._clean_error(self)
         self.density_map = kwargs.get('density_map', False)
 
+    @property
+    def slice_component_label(self):
+        # label of the component in the lightcurves corresponding to the slice axis
+        # calling data_collection_item.get_component(slice_component_label) must work
+        return 'dt'
+
     def data(self, cls=None):
         data = []
 
@@ -252,6 +260,13 @@ class PhaseScatterView(TimeScatterView):
     def ephemeris_component(self):
         return self.reference.split('[')[0].split(':')[-1]
 
+    @property
+    def ephemeris(self):
+        ephem = self.jdaviz_helper.plugins.get('Ephemeris', None)
+        if ephem is None:
+            raise ValueError("must have ephemeris plugin loaded to access ephemeris")
+        return ephem.ephemerides.get(self.ephemeris_component)
+
     def _set_plot_x_axes(self, dc, component_labels, light_curve):
         # setting of y_att will be handled by ephemeris plugin
         self.state.x_att = dc[0].components[component_labels.index(f'phase:{self.ephemeris_component}')]  # noqa
@@ -265,9 +280,13 @@ def times_to_phases(self, times):
 
         return ephem.times_to_phases(times, ephem_component=self.ephemeris_component)
 
+    def _set_slice_indicator_value(self, value):
+        # NOTE: on first call, this will initialize the indicator itself
+        self.slice_indicator.value = self.times_to_phases(value)
+
 
 @viewer_registry("lcviz-cube-viewer", label="cube")
-class CubeView(CloneViewerMixin, CubevizImageView):
+class CubeView(CloneViewerMixin, CubevizImageView, WithSliceSelection):
     # categories: zoom resets, zoom, pan, subset, select tools, shortcuts
     tools_nested = [
                     ['jdaviz:homezoom', 'jdaviz:prevzoom'],
@@ -297,6 +316,18 @@ def __init__(self, *args, **kwargs):
         # * _default_flux_viewer_reference_name
         # * _default_uncert_viewer_reference_name
 
+    @property
+    def slice_component_label(self):
+        # label of the component in the cubes corresponding to the slice axis
+        # calling data_collection_item.get_component(slice_component_label) on any
+        # input cube-data must work
+        return 'dt'
+
+    @property
+    def slice_index(self):
+        # index in viewer.slices corresponding to the slice axis
+        return 0
+
     def _initial_x_axis(self, *args):
         # Make sure that the x_att/y_att is correct on data load
         # called via a callback set upstream in CubevizImageView when reference_data is changed

pyproject.toml

@@ -20,7 +20,7 @@ classifiers = [
 ]
 dependencies = [
     "astropy>=5.2",
-    "jdaviz==3.8.*",
+    "jdaviz==3.9.*",
     "lightkurve>=2.4.1",
 ]
 dynamic = [