re-rename origin->column

CHANGES.rst

@@ -3,10 +3,10 @@
 
 * Clone viewer tool. [#74]
 
-* Flux origin plugin to choose which column is treated as the flux column for each dataset. [#77]
+* Flux column plugin to choose which column is treated as the flux column for each dataset. [#77]
 
 * Flatten plugin no longer creates new data entries, but instead appends a new column to the input
-  light curve and selects as the flux origin. [#77]
+  light curve and selects as the flux column (origin). [#77]
 
 0.1.0 (12-14-2023)
 ------------------

docs/plugins.rst

@@ -35,13 +35,13 @@ This plugin allows viewing of any metadata associated with the selected data.
     :ref:`Jdaviz Metadata Viewer <jdaviz:imviz_metadata-viewer>`
         Jdaviz documentation on the Metadata Viewer plugin.
 
-.. _flux-origin:
+.. _flux-column:
 
-Flux Origin
+Flux Column
 ===========
 
-This plugin allows choosing which column in the underlying data should be used as the flux origin
-throughout the app (when plotting and in any data analysis plugins).
+This plugin allows choosing which column in the underlying data should be used as the flux column
+(origin) throughout the app (when plotting and in any data analysis plugins).
 
 
 .. admonition:: User API Example
@@ -58,9 +58,9 @@ throughout the app (when plotting and in any data analysis plugins).
       lcviz.load_data(lc)
       lcviz.show()
 
-      flux_origin = lcviz.plugins['Flux Origin']
-      print(flux_origin.flux_origin.choices)
-      flux_origin.flux_origin = 'sap_flux'
+      flux_col = lcviz.plugins['Flux Column']
+      print(flux_col.flux_column.choices)
+      flux_col.flux_column = 'sap_flux'
 
 
 .. seealso::

lcviz/components/components.py

@@ -5,12 +5,12 @@
 
 from jdaviz.core.template_mixin import SelectPluginComponent
 
-from lcviz.events import FluxOriginChangedMessage
+from lcviz.events import FluxColumnChangedMessage
 
-__all__ = ['FluxOriginSelect', 'FluxOriginSelectMixin']
+__all__ = ['FluxColumnSelect', 'FluxColumnSelectMixin']
 
 
-class FluxOriginSelect(SelectPluginComponent):
+class FluxColumnSelect(SelectPluginComponent):
     def __init__(self, plugin, items, selected, dataset):
         super().__init__(plugin,
                          items=items,
@@ -22,8 +22,8 @@ def __init__(self, plugin, items, selected, dataset):
                          self._on_change_dataset)
 
         # sync between instances in different plugins
-        self.hub.subscribe(self, FluxOriginChangedMessage,
-                           handler=self._on_flux_origin_changed_msg)
+        self.hub.subscribe(self, FluxColumnChangedMessage,
+                           handler=self._on_flux_column_changed_msg)
 
     def _on_change_dataset(self, *args):
         def _include_col(lk_obj, col):
@@ -53,28 +53,28 @@ def _include_col(lk_obj, col):
         if lk_obj is None:
             return
         self.choices = [col for col in lk_obj.columns if _include_col(lk_obj, col)]
-        flux_origin = lk_obj.meta.get('FLUX_ORIGIN')
-        if flux_origin in self.choices:
-            self.selected = flux_origin
+        flux_column = lk_obj.meta.get('FLUX_ORIGIN')
+        if flux_column in self.choices:
+            self.selected = flux_column
         else:
             self.selected = ''
 
-    def _on_flux_origin_changed_msg(self, msg):
+    def _on_flux_column_changed_msg(self, msg):
         if msg.dataset != self.dataset.selected:
             return
 
         # need to clear the cache due to the change in metadata made to the data-collection entry
         self.dataset._clear_cache('selected_obj', 'selected_dc_item')
         self._on_change_dataset()
-        self.selected = msg.flux_origin
+        self.selected = msg.flux_column
 
     def _on_change_selected(self, *args):
         if self.selected == '':
             return
 
         dc_item = self.dataset.selected_dc_item
-        old_flux_origin = dc_item.meta.get('FLUX_ORIGIN')
-        if self.selected == old_flux_origin:
+        old_flux_column = dc_item.meta.get('FLUX_ORIGIN')
+        if self.selected == old_flux_column:
             # nothing to do here!
             return
 
@@ -85,8 +85,8 @@ def _on_change_selected(self, *args):
         self.app._jdaviz_helper._set_data_component(dc_item, 'flux_err', dc_item[self.selected+"_err"])  # noqa
         dc_item.meta['FLUX_ORIGIN'] = self.selected
 
-        self.hub.broadcast(FluxOriginChangedMessage(dataset=self.dataset.selected,
-                                                    flux_origin=self.selected,
+        self.hub.broadcast(FluxColumnChangedMessage(dataset=self.dataset.selected,
+                                                    flux_column=self.selected,
                                                     sender=self))
 
     def add_new_flux_column(self, flux, flux_err, label, selected=False):
@@ -99,19 +99,19 @@ def add_new_flux_column(self, flux, flux_err, label, selected=False):
                                                     flux_err)
 
         # broadcast so all instances update to get the new column and selection (if applicable)
-        self.hub.broadcast(FluxOriginChangedMessage(dataset=self.dataset.selected,
-                                                    flux_origin=label if selected else self.selected,  # noqa
+        self.hub.broadcast(FluxColumnChangedMessage(dataset=self.dataset.selected,
+                                                    flux_column=label if selected else self.selected,  # noqa
                                                     sender=self))
 
 
-class FluxOriginSelectMixin(VuetifyTemplate, HubListener):
-    flux_origin_items = List().tag(sync=True)
-    flux_origin_selected = Unicode().tag(sync=True)
+class FluxColumnSelectMixin(VuetifyTemplate, HubListener):
+    flux_column_items = List().tag(sync=True)
+    flux_column_selected = Unicode().tag(sync=True)
     # assumes DatasetSelectMixin is also used (DatasetSelectMixin must appear after in inheritance)
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.flux_origin = FluxOriginSelect(self,
-                                            'flux_origin_items',
-                                            'flux_origin_selected',
+        self.flux_column = FluxColumnSelect(self,
+                                            'flux_column_items',
+                                            'flux_column_selected',
                                             dataset='dataset')

lcviz/events.py

@@ -2,7 +2,7 @@
 
 __all__ = ['EphemerisComponentChangedMessage',
            'EphemerisChangedMessage',
-           'FluxOriginChangedMessage']
+           'FluxColumnChangedMessage']
 
 
 class EphemerisComponentChangedMessage(Message):
@@ -30,10 +30,10 @@ def __init__(self, ephemeris_label, *args, **kwargs):
         self.ephemeris_label = ephemeris_label
 
 
-class FluxOriginChangedMessage(Message):
-    """Message emitted by the FluxOriginSelect component when the selection has been changed.
-    To subscribe to a change for a particular dataset, consider using FluxOriginSelect directly
+class FluxColumnChangedMessage(Message):
+    """Message emitted by the FluxColumnSelect component when the selection has been changed.
+    To subscribe to a change for a particular dataset, consider using FluxColumnSelect directly
     and observing the traitlet, rather than subscribing to this message"""
-    def __init__(self, dataset, flux_origin, *args, **kwargs):
+    def __init__(self, dataset, flux_column, *args, **kwargs):
         self.dataset = dataset
-        self.flux_origin = flux_origin
+        self.flux_column = flux_column

lcviz/helper.py

@@ -72,7 +72,7 @@ class LCviz(ConfigHelper):
                      'dense_toolbar': False,
                      'context': {'notebook': {'max_height': '600px'}}},
         'toolbar': ['g-data-tools', 'g-subset-tools', 'lcviz-coords-info'],
-        'tray': ['lcviz-metadata-viewer', 'flux-origin',
+        'tray': ['lcviz-metadata-viewer', 'flux-column',
                  'lcviz-plot-options', 'lcviz-subset-plugin',
                  'lcviz-markers', 'flatten', 'frequency-analysis', 'ephemeris',
                  'binning', 'lcviz-export-plot'],

lcviz/plugins/__init__.py

@@ -3,7 +3,7 @@
 from .ephemeris.ephemeris import *  # noqa
 from .export_plot.export_plot import *  # noqa
 from .flatten.flatten import *  # noqa
-from .flux_origin.flux_origin import *  # noqa
+from .flux_column.flux_column import *  # noqa
 from .frequency_analysis.frequency_analysis import *  # noqa
 from .markers.markers import *  # noqa
 from .metadata_viewer.metadata_viewer import *  # noqa

lcviz/plugins/binning/binning.py

@@ -13,7 +13,7 @@
                                         with_spinner)
 from jdaviz.core.user_api import PluginUserApi
 
-from lcviz.components import FluxOriginSelectMixin
+from lcviz.components import FluxColumnSelectMixin
 from lcviz.events import EphemerisChangedMessage
 from lcviz.helper import _default_time_viewer_reference_name
 from lcviz.marks import LivePreviewBinning
@@ -25,7 +25,7 @@
 
 
 @tray_registry('binning', label="Binning")
-class Binning(PluginTemplateMixin, FluxOriginSelectMixin, DatasetSelectMixin,
+class Binning(PluginTemplateMixin, FluxColumnSelectMixin, DatasetSelectMixin,
               EphemerisSelectMixin, AddResultsMixin):
     """
     See the :ref:`Binning Plugin Documentation <binning>` for more details.
@@ -152,7 +152,7 @@ def _toggle_marks(self, event={}):
             # then the marks themselves need to be updated
             self._live_update(event)
 
-    @observe('flux_origin_selected', 'dataset_selected',
+    @observe('flux_column_selected', 'dataset_selected',
              'ephemeris_selected',
              'n_bins', 'previews_temp_disable')
     @skip_if_no_updates_since_last_active()

lcviz/plugins/flatten/flatten.py

@@ -13,7 +13,7 @@
                                         with_spinner)
 from jdaviz.core.user_api import PluginUserApi
 
-from lcviz.components import FluxOriginSelectMixin
+from lcviz.components import FluxColumnSelectMixin
 from lcviz.marks import LivePreviewTrend, LivePreviewFlattened
 from lcviz.utils import data_not_folded
 from lcviz.viewers import TimeScatterView, PhaseScatterView
@@ -23,7 +23,7 @@
 
 
 @tray_registry('flatten', label="Flatten")
-class Flatten(PluginTemplateMixin, FluxOriginSelectMixin, DatasetSelectMixin):
+class Flatten(PluginTemplateMixin, FluxColumnSelectMixin, DatasetSelectMixin):
     """
     See the :ref:`Flatten Plugin Documentation <flatten>` for more details.
 
@@ -44,7 +44,7 @@ class Flatten(PluginTemplateMixin, FluxOriginSelectMixin, DatasetSelectMixin):
     * ``unnormalize``
     * ``flux_label`` (:class:`~jdaviz.core.template_mixin.AutoTextField`):
       Label for the resulting flux column added to ``dataset`` and automatically selected as the new
-      flux origin.
+      flux column (origin).
     * :meth:`flatten`
     """
     template_file = __file__, "flatten.vue"
@@ -122,19 +122,19 @@ def marks(self):
 
         return trend_marks, flattened_marks
 
-    @observe('dataset_selected', 'flux_origin_selected')
+    @observe('dataset_selected', 'flux_column_selected')
     def _set_default_label(self, event={}):
         '''Generate a label and set the results field to that value'''
         if not hasattr(self, 'dataset'):  # pragma: no cover
             return
 
         # TODO: have an option to create new data entry and drop other columns?
         # (or should that just go through future data cloning)
-        self.flux_label.default = f"{self.flux_origin_selected}_flattened"
+        self.flux_label.default = f"{self.flux_column_selected}_flattened"
 
     @observe('flux_label_label', 'dataset')
     def _update_label_valid(self, event={}):
-        if self.flux_label.value in self.flux_origin.choices:
+        if self.flux_label.value in self.flux_column.choices:
             self.flux_label.invalid_msg = ''
             self.flux_label_overwrite = True
         elif self.flux_label.value in getattr(self.dataset.selected_obj, 'columns', []):
@@ -152,7 +152,7 @@ def flatten(self, add_data=True):
         ----------
         add_data : bool
             Whether to add the resulting light curve as a flux column and select that as the new
-            flux origin for that data entry.
+            flux column (origin) for that data entry.
 
         Returns
         -------
@@ -180,9 +180,9 @@ def flatten(self, add_data=True):
 
         if add_data:
             # add data as a new flux and corresponding err columns in the existing data entry
-            # and select as flux origin
+            # and select as flux column (origin)
             data = _data_with_reftime(self.app, output_lc)
-            self.flux_origin.add_new_flux_column(flux=data['flux'],
+            self.flux_column.add_new_flux_column(flux=data['flux'],
                                                  flux_err=data['flux_err'],
                                                  label=self.flux_label.value,
                                                  selected=True)
@@ -212,14 +212,14 @@ def _toggle_marks(self, event={}):
             # then the marks themselves need to be updated
             self._live_update(event)
 
-    @observe('dataset_selected', 'flux_origin_selected',
+    @observe('dataset_selected', 'flux_column_selected',
              'window_length', 'polyorder', 'break_tolerance',
              'niters', 'sigma', 'previews_temp_disable')
     @skip_if_no_updates_since_last_active()
     def _live_update(self, event={}):
         if self.previews_temp_disable:
             return
-        if self.dataset_selected == '' or self.flux_origin_selected == '':
+        if self.dataset_selected == '' or self.flux_column_selected == '':
             self._clear_marks()
             return
 

lcviz/plugins/flatten/flatten.vue

@@ -157,7 +157,7 @@
     </v-alert>
 
     <v-row justify="end">
-      <j-tooltip tooltipcontent="Flatten and select new column as flux origin">
+      <j-tooltip tooltipcontent="Flatten and select the new column as the adopted flux column">
         <plugin-action-button 
           :spinner="spinner"
           :disabled="flux_label_invalid_msg.length > 0"

lcviz/plugins/flux_column/__init__.py

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

lcviz/plugins/flux_origin/flux_origin.py → lcviz/plugins/flux_column/flux_column.py

@@ -3,28 +3,29 @@
                                         DatasetSelectMixin)
 from jdaviz.core.user_api import PluginUserApi
 
-from lcviz.components import FluxOriginSelectMixin
+from lcviz.components import FluxColumnSelectMixin
 
-__all__ = ['FluxOrigin']
+__all__ = ['FluxColumn']
 
 
-@tray_registry('flux-origin', label="Flux Origin")
-class FluxOrigin(PluginTemplateMixin, FluxOriginSelectMixin, DatasetSelectMixin):
+@tray_registry('flux-column', label="Flux Column")
+class FluxColumn(PluginTemplateMixin, FluxColumnSelectMixin, DatasetSelectMixin):
     """
-    See the :ref:`Flux Origin Plugin Documentation <flux-origin>` for more details.
+    See the :ref:`Flux Column Plugin Documentation <flux-column>` for more details.
 
     Only the following attributes and methods are available through the
     public plugin API.
 
     * ``dataset`` (:class:`~jdaviz.core.template_mixin.DatasetSelect`):
       Dataset to bin.
+    * ``flux_column`` (:class:`~lcviz.components.FluxColumnSelect`)
     """
-    template_file = __file__, "flux_origin.vue"
+    template_file = __file__, "flux_column.vue"
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
     @property
     def user_api(self):
-        expose = ['dataset', 'flux_origin']
+        expose = ['dataset', 'flux_column']
         return PluginUserApi(self, expose=expose)

lcviz/plugins/flux_origin/flux_origin.vue → lcviz/plugins/flux_column/flux_column.vue

@@ -1,7 +1,7 @@
 <template>
   <j-tray-plugin
     description='Choose which column to use as flux across lcviz.'
-    :link="'https://lcviz.readthedocs.io/en/'+vdocs+'/plugins.html#flux-origin'"
+    :link="'https://lcviz.readthedocs.io/en/'+vdocs+'/plugins.html#flux-column'"
     :uses_active_status="uses_active_status"
     @plugin-ping="plugin_ping($event)"
     :keep_active.sync="keep_active"
@@ -19,8 +19,8 @@
       <v-select
         :menu-props="{ left: true }"
         attach
-        :items="flux_origin_items.map(i => i.label)"
-        v-model="flux_origin_selected"
+        :items="flux_column_items.map(i => i.label)"
+        v-model="flux_column_selected"
         label="Flux Column"
         hint="Select the column to adopt as flux."
         persistent-hint

lcviz/tests/test_plugin_flatten.py

@@ -59,12 +59,12 @@ def test_plugin_flatten(helper, light_curve_like_kepler_quarter):
         after_update = marks[0].y
         assert not np.allclose(before_update, after_update)
 
-        orig_flux_origin = f._obj.flux_origin.selected
+        orig_flux_column = f._obj.flux_column.selected
         assert f.dataset.selected_obj is not None
         assert f._obj.flux_label_overwrite is False
-        assert f._obj.flux_label.value == f'{orig_flux_origin}_flattened'
+        assert f._obj.flux_label.value == f'{orig_flux_column}_flattened'
         f._obj.vue_apply(add_data=True)
-        assert f._obj.flux_origin.selected == f'{orig_flux_origin}_flattened'
+        assert f._obj.flux_column.selected == f'{orig_flux_column}_flattened'
         assert f._obj.flatten_err == ''
 
     # marks are hidden