Stitch plugin (#107)

* stitch plugin: basic implementation
* only shown in plugin tray if at least two light curves are loaded into a viewer
* optionally replace input datasets when stitching

CHANGES.rst

@@ -5,6 +5,8 @@
 
 * Default data labels no longer include flux-origin, but do include quarter/campaign/sector. [#111]
 
+* Basic stitch plugin to combine light curves into a single entry. [#107]
+
 0.3.1 (unreleased)
 ------------------
 

docs/plugins.rst

@@ -213,6 +213,47 @@ The time selector plugin allows defining the time indicated in all light curve v
 
 
 
+.. _stitch:
+
+Stitch
+======
+
+This plugin allows for combining multiple light curves into a single entry.  Note that this plugin
+is only available if there are at least two light curves loaded into a light curve viewer.
+
+.. admonition:: User API Example
+    :class: dropdown
+
+    See the :class:`~lcviz.plugins.stitch.stitch.Stitch` user API documentation for more details.
+
+    .. code-block:: python
+
+      from lcviz import LCviz
+      lc1 = search_lightcurve("HAT-P-11", mission="Kepler",
+                              cadence="long", quarter=9).download()
+      lc2 = search_lightcurve("HAT-P-11", mission="Kepler",
+                              cadence="long", quarter=10).download()
+      lcviz = LCviz()
+      lcviz.load_data(lc1, 'lc1')
+      lcviz.load_data(lc2, 'lc2')
+      # NOTE: this line is not technically considered public API - alternatively manually add
+      # the second light curve to the light curve viewer from the data menu
+      lcviz.app.add_data_to_viewer('flux-vs-time', 'lc1')
+      lcviz.show()
+
+      stitch = lcviz.plugins['Stitch']
+      stitch.open_in_tray()
+      stitch.dataset.select_all()
+      stitched_lc = stitch.stitch()
+      print(stitched_lc)
+
+.. seealso::
+
+    This plugin uses the following ``lightkurve`` implementations:
+
+    * :meth:`lightkurve.LightCurveCollection.stitch`
+
+
 .. _flatten:
 
 Flatten

lcviz/helper.py

@@ -70,7 +70,7 @@ class LCviz(ConfigHelper):
         'tray': ['lcviz-metadata-viewer', 'flux-column',
                  'lcviz-plot-options', 'lcviz-subset-plugin',
                  'lcviz-markers', 'time-selector',
-                 'flatten', 'frequency-analysis', 'ephemeris',
+                 'stitch', 'flatten', 'frequency-analysis', 'ephemeris',
                  'binning', 'lcviz-export'],
         'viewer_area': [{'container': 'col',
                          'children': [{'container': 'row',

lcviz/plugins/__init__.py

@@ -11,4 +11,5 @@
 from .time_selector.time_selector import *  # noqa
 from .metadata_viewer.metadata_viewer import *  # noqa
 from .plot_options.plot_options import *  # noqa
+from .stitch.stitch import *  # noqa
 from .subset_plugin.subset_plugin import *  # noqa

lcviz/plugins/stitch/__init__.py

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

lcviz/plugins/stitch/stitch.py

@@ -0,0 +1,96 @@
+from traitlets import Bool, Unicode, observe
+from lightkurve import LightCurve, LightCurveCollection
+
+from jdaviz.core.registries import tray_registry
+from jdaviz.core.template_mixin import (PluginTemplateMixin,
+                                        DatasetMultiSelectMixin,
+                                        AddResultsMixin,
+                                        with_spinner)
+from jdaviz.core.user_api import PluginUserApi
+
+from lcviz.utils import data_not_folded
+
+__all__ = ['Stitch']
+
+
+@tray_registry('stitch', label="Stitch")
+class Stitch(PluginTemplateMixin, DatasetMultiSelectMixin, AddResultsMixin):
+    """
+    See the :ref:`Stitch Plugin Documentation <stitch>` 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`
+    * ``dataset`` (:class:`~jdaviz.core.template_mixin.DatasetSelect`):
+      Datasets to stitch.
+    * ``remove_input_datasets``
+    * ``add_results`` (:class:`~jdaviz.core.template_mixin.AddResults`)
+    * :meth:`stitch`
+    """
+    template_file = __file__, "stitch.vue"
+    uses_active_status = Bool(False).tag(sync=False)
+
+    remove_input_datasets = Bool(False).tag(sync=True)
+    stitch_err = Unicode().tag(sync=True)
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        self.dataset.multiselect = True
+        # do not support stitching data in phase-space
+        self.dataset.add_filter(data_not_folded)
+
+        self.results_label_default = 'stitched'
+
+    @property
+    def user_api(self):
+        expose = ['dataset', 'stitch', 'remove_input_datasets', 'add_results']
+        return PluginUserApi(self, expose=expose)
+
+    @observe('dataset_items')
+    def _set_relevent(self, *args):
+        if len(self.dataset_items) < 2:
+            self.irrelevant_msg = 'Requires at least two datasets loaded into viewers'
+        else:
+            self.irrelevant_msg = ''
+
+    @with_spinner()
+    def stitch(self, add_data=True):
+        """
+        Stitch multiple light curves (``dataset``) together using lightkurve.stitch.
+
+        Parameters
+        ----------
+        add_data : bool
+            Whether to add the resulting light curve to the app.
+
+        Returns
+        -------
+        output_lc : `~lightkurve.LightCurve`
+            The flattened light curve.
+        """
+        if not self.dataset.multiselect:
+            raise ValueError("dataset must be in multiselect mode")
+        if len(self.dataset.selected) < 2:
+            raise ValueError("multiple datasets must be selected")
+        lcc = LightCurveCollection([dci.get_object(LightCurve)
+                                    for dci in self.dataset.selected_dc_item])
+        stitched_lc = lcc.stitch(corrector_func=lambda x: x)
+
+        if add_data:
+            self.add_results.add_results_from_plugin(stitched_lc)
+            if self.remove_input_datasets:
+                for dataset in self.dataset.selected:
+                    self.app.vue_data_item_remove({'item_name': dataset})
+        return stitched_lc
+
+    def vue_apply(self, *args, **kwargs):
+        try:
+            self.stitch(add_data=True)
+        except Exception as e:
+            self.stitch_err = str(e)
+        else:
+            self.stitch_err = ''

lcviz/plugins/stitch/stitch.vue

@@ -0,0 +1,55 @@
+<template>
+  <j-tray-plugin
+    description='Stitch light curves together.'
+    :link="'https://lcviz.readthedocs.io/en/'+vdocs+'/plugins.html#stitch'"
+    :popout_button="popout_button">
+
+    <plugin-dataset-select
+      :items="dataset_items"
+      :selected.sync="dataset_selected"
+      :show_if_single_entry="true"
+      :multiselect="true"
+      label="Data"
+      hint="Select the light curves as input."
+    />
+
+    <v-row v-if="dataset_selected.length < 2">
+      <span class="v-messages v-messages__message text--secondary">
+        <b style="color: red !important">Must select at least two input light curves to stitch.</b>
+      </span>
+    </v-row>
+
+    <plugin-add-results v-else
+      :label.sync="results_label"
+      :label_default="results_label_default"
+      :label_auto.sync="results_label_auto"
+      :label_invalid_msg="results_label_invalid_msg"
+      :label_overwrite="results_label_overwrite"
+      label_hint="Label for the binned data."
+      :add_to_viewer_items="add_to_viewer_items"
+      :add_to_viewer_selected.sync="add_to_viewer_selected"
+      action_label="Stitch"
+      action_tooltip="Stitch data"
+      :action_disabled="dataset_selected.length < 2"
+      :action_spinner="spinner"
+      @click:action="apply"
+    >
+      <v-row>
+        <v-switch
+          v-model="remove_input_datasets"
+          label="Remove input datasets"
+          hint='Delete input datasets from the app'
+          persistent-hint
+        >
+        </v-switch>
+      </v-row>
+    </plugin-add-results>
+
+    <v-row v-if="stitch_err">
+      <span class="v-messages v-messages__message text--secondary">
+        <b style="color: red !important">ERROR:</b> {{stitch_err}}
+      </span>
+    </v-row>
+
+  </j-tray-plugin>
+</template>

lcviz/tests/test_plugin_stitch.py

@@ -0,0 +1,30 @@
+def test_docs_snippets(helper, light_curve_like_kepler_quarter):
+    lcviz, lc = helper, light_curve_like_kepler_quarter
+    lc1 = lc
+    lc2 = lc.copy()
+
+    lcviz.load_data(lc1, 'lc1')
+    lcviz.load_data(lc2, 'lc2')
+    lcviz.app.add_data_to_viewer('flux-vs-time', 'lc2')
+    # lcviz.show()
+
+    stitch = lcviz.plugins['Stitch']
+    stitch.open_in_tray()
+    stitch.dataset.select_all()
+    stitched_lc = stitch.stitch()
+    print(stitched_lc)
+
+
+def test_plugin_stitch(helper, light_curve_like_kepler_quarter):
+    helper.load_data(light_curve_like_kepler_quarter)
+
+    assert "Stitch" not in helper.plugins.keys()
+
+    helper.load_data(light_curve_like_kepler_quarter.copy())
+    assert "Stitch" in helper.plugins.keys()
+
+    stitch = helper.plugins['Stitch']
+    stitch.dataset.select_all()
+    stitched_lc = stitch.stitch()
+
+    assert len(stitched_lc) == 2 * len(light_curve_like_kepler_quarter)