Photometric Extraction plugin

CHANGES.rst

@@ -5,6 +5,8 @@
 
 * Prevent duplicate sub-intervals (quarter/sector/campaign) in data labels. [#120]
 
+* Photometric extraction plugin. [#115]
+
 * Add feature to query the NASA Exoplanet Archive for exoplanet ephemerides. [#127]
 
 0.4.3 (09.05.2024)
@@ -41,7 +43,6 @@
 * 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]
-
 * Metadata plugin: show undefined entries as empty string instead of object repr. [#108]
 
 * Raise error when parser can't identify file_obj [#106]

docs/plugins.rst

@@ -218,6 +218,39 @@ The time selector plugin allows defining the time indicated in all light curve v
         Jdaviz documentation on the Slice plugin.
 
 
+.. _photometric-extraction:
+
+Photometric Extraction
+======================
+
+Note that this plugin is only available if TPF data is loaded into the app.
+
+.. 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
+      from lightkurve import search_targetpixelfile
+      tpf = search_targetpixelfile("KIC 001429092",
+                                   mission="Kepler",
+                                   cadence="long",
+                                   quarter=10).download()
+      lcviz = LCviz()
+      lcviz.load_data(tpf)
+      lcviz.show()
+
+      ext = lcviz.plugins['Photometric Extraction']
+      ext.open_in_tray()
+
+
+.. seealso::
+
+    This plugin uses the following ``lightkurve`` implementations:
+
+    * :meth:`lightkurve.KeplerTargetPixelFile.extract_aperture_photometry`
 
 .. _stitch:
 

docs/reference/api_plugins.rst

@@ -27,6 +27,9 @@ Plugins API
 .. automodapi:: lcviz.plugins.metadata_viewer.metadata_viewer
   :no-inheritance-diagram:
 
+.. automodapi:: lcviz.plugins.photometric_extraction.photometric_extraction
+  :no-inheritance-diagram:
+
 .. automodapi:: lcviz.plugins.plot_options.plot_options
   :no-inheritance-diagram:
 

lcviz/helper.py

@@ -105,7 +105,7 @@ class LCviz(ConfigHelper):
         'toolbar': ['g-data-tools', 'g-subset-tools', 'g-viewer-creator', 'lcviz-coords-info'],
         'tray': ['lcviz-metadata-viewer', 'flux-column',
                  'lcviz-plot-options', 'lcviz-subset-plugin',
-                 'lcviz-markers', 'time-selector',
+                 'lcviz-markers', 'time-selector', 'photometric-extraction',
                  'stitch', 'flatten', 'frequency-analysis', 'ephemeris',
                  'binning', 'lcviz-export'],
         'viewer_area': [{'container': 'col',

lcviz/plugins/__init__.py

@@ -10,6 +10,7 @@
 from .markers.markers import *  # noqa
 from .time_selector.time_selector import *  # noqa
 from .metadata_viewer.metadata_viewer import *  # noqa
+from .photometric_extraction.photometric_extraction import *  # noqa
 from .plot_options.plot_options import *  # noqa
 from .stitch.stitch import *  # noqa
 from .subset_plugin.subset_plugin import *  # noqa

lcviz/plugins/photometric_extraction/__init__.py

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

lcviz/plugins/photometric_extraction/photometric_extraction.py

@@ -0,0 +1,98 @@
+from astropy import units as u
+from traitlets import Bool, Unicode, observe
+from lightkurve import LightCurve
+
+from jdaviz.core.registries import tray_registry
+from jdaviz.configs.cubeviz.plugins import SpectralExtraction
+from jdaviz.core.user_api import PluginUserApi
+
+
+__all__ = ['PhotometricExtraction']
+
+
+@tray_registry('photometric-extraction', label="Photometric Extraction")
+class PhotometricExtraction(SpectralExtraction):
+    """
+    See the :ref:`Photometric Extraction Plugin Documentation <photometric-extraction>`
+    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`):
+      Dataset to extract.
+    * ``add_results`` (:class:`~jdaviz.core.template_mixin.AddResults`)
+    * :meth:`extract`
+    """
+    resulting_product_name = Unicode("light curve").tag(sync=True)
+    do_auto_extraction = False
+    wavelength_dependent_available = Bool(False).tag(sync=True)
+    bg_export_available = Bool(False).tag(sync=True)
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.docs_link = f"https://lcviz.readthedocs.io/en/{self.vdocs}/plugins.html#photometric-extraction"  # noqa
+        self.docs_description = "Extract light curve from target pixel file cube."  # noqa
+
+        def is_tpf(data):
+            return len(data.shape) == 3
+        self.dataset.filters = [is_tpf]
+
+        # only allow for Sum
+        self.function._manual_options = ['Sum']
+        self.function.items = [{"label": "Sum"}]
+
+        self._set_relevant()  # move upstream?
+
+    @property
+    def user_api(self):
+        expose = ['dataset', 'aperture',
+                  'background',
+                  'add_results', 'extract',
+                  'aperture_method']
+
+        return PluginUserApi(self, expose=expose)
+
+    @observe('dataset_items')
+    def _set_relevant(self, *args):
+        # NOTE: upstream will set disabled_msg to something similar, but mentioning
+        if len(self.dataset_items) < 1:
+            self.irrelevant_msg = 'Requires at least one TPF cube to be loaded'
+        else:
+            self.irrelevant_msg = ''
+
+    def _on_global_display_unit_changed(self, msg=None):
+        if msg is None:
+            self.flux_units = str(self.app._get_display_unit('flux'))
+            self.time_units = str(self.app._get_display_unit('time'))
+        elif msg.axis == 'flux':
+            self.flux_units = str(msg.unit)
+        elif msg.axis == 'time':
+            self.time_units = str(msg.unit)
+        else:
+            # ignore
+            return
+        # update results_units based on flux_units, sb_units, and currently selected function
+        self._update_results_units()
+
+    @property
+    def slice_display_unit_name(self):
+        return 'time'
+
+    @property
+    def spatial_axes(self):
+        return (1, 2)
+
+    def _return_extracted(self, cube, wcs, collapsed_nddata):
+        lc = LightCurve(time=cube.get_object(LightCurve).time, flux=collapsed_nddata.data)
+        return lc
+
+    def _preview_x_from_extracted(self, extracted):
+        return extracted.time.value - self.dataset.selected_obj.meta.get('reference_time',
+                                                                         0.0 * u.d).value
+
+    def _preview_y_from_extracted(self, extracted):
+        return extracted.flux.value

lcviz/plugins/photometric_extraction/photometric_extraction.vue

@@ -0,0 +1,55 @@
+<template>
+  <j-tray-plugin
+    description='Extract light curve from TPF data.'
+    :link="'https://lcviz.readthedocs.io/en/'+vdocs+'/plugins.html#photometric-extraction'"
+    :uses_active_status="uses_active_status"
+    @plugin-ping="plugin_ping($event)"
+    :keep_active.sync="keep_active"
+    :popout_button="popout_button">
+
+    <v-row>
+      <v-expansion-panels popout>
+        <v-expansion-panel>
+          <v-expansion-panel-header v-slot="{ open }">
+            <span style="padding: 6px">Settings</span>
+          </v-expansion-panel-header>
+          <v-expansion-panel-content>
+            <v-row>
+              <v-switch
+                v-model="show_live_preview"
+                label="Show live preview"
+                hint="Whether to show live preview of binning options."
+                persistent-hint
+              ></v-switch>
+            </v-row>
+          </v-expansion-panel-content>
+        </v-expansion-panel>
+      </v-expansion-panels>
+    </v-row>
+
+    <plugin-dataset-select
+      :items="dataset_items"
+      :selected.sync="dataset_selected"
+      :show_if_single_entry="false"
+      label="Data"
+      hint="Select the TPF as input."
+    />
+
+    <plugin-add-results
+      :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 extracted light curve."
+      :add_to_viewer_items="add_to_viewer_items"
+      :add_to_viewer_selected.sync="add_to_viewer_selected"
+      action_label="Extract"
+      action_tooltip="Extract photometry"
+      :action_disabled="!apply_enabled"
+      :action_spinner="spinner"
+      @click:action="apply"
+    ></plugin-add-results>
+
+  </j-tray-plugin>
+</template>

lcviz/plugins/plot_options/plot_options.py

@@ -3,6 +3,9 @@
 from traitlets import observe
 from jdaviz.configs.default.plugins import PlotOptions
 from jdaviz.core.registries import tray_registry
+from jdaviz.utils import get_subset_type
+
+from lcviz.viewers import CubeView
 
 __all__ = ['PlotOptions']
 
@@ -33,6 +36,17 @@ class PlotOptions(PlotOptions):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
+        def not_spatial_subset_in_scatter_viewer(lyr):
+            # note: have to check the classname instead of isinstance to avoid circular import
+            if np.any([isinstance(viewer, CubeView)
+                       for viewer in self.layer.viewer_objs]):
+                return True
+            # at this point, NO selected viewers are TPF Cube viewers,
+            # so we want to exclude spatial subsets
+            return get_subset_type(lyr) != 'spatial'
+
+        self.layer.add_filter(not_spatial_subset_in_scatter_viewer)
+
     @observe('vdocs')
     def _update_docs_link(self, *args):
         self.docs_link = f"https://lcviz.readthedocs.io/en/{self.vdocs}/plugins.html#plot-options"

lcviz/plugins/stitch/stitch.py

@@ -45,14 +45,15 @@ def __init__(self, *args, **kwargs):
         self.dataset.add_filter(data_not_folded, is_not_tpf)
 
         self.results_label_default = 'stitched'
+        self._set_relevant()
 
     @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):
+    def _set_relevant(self, *args):
         if len(self.dataset_items) < 2:
             self.irrelevant_msg = 'Requires at least two datasets loaded into viewers'
         else:

lcviz/utils.py

@@ -357,7 +357,7 @@ def to_data(self, obj, reference_time=None, unit=u.d):
             data[cid] = component_data
             if hasattr(component_data, 'unit'):
                 try:
-                    data.get_component(cid).units = str(component_data.unit)
+                    data.get_component(cid).units = str(component_data.unit/u.pix**2)
                 except KeyError:  # pragma: no cover
                     continue
 

lcviz/viewers.py

@@ -151,6 +151,13 @@ def _apply_layer_defaults(self, layer_state):
             layer_state.size = 5
         layer_state.points_mode = 'markers'
 
+    def _layer_included_in_legend(self, layer, subset_type):
+        print("***", layer.layer.label, subset_type)
+        if subset_type == 'spatial':
+            # do not show spatial subsets in time or phase viewers
+            return False
+        return super()._layer_included_in_legend(layer, subset_type)
+
     def set_plot_axes(self):
         # set which components should be plotted
         dc = self.jdaviz_app.data_collection
@@ -361,6 +368,13 @@ def _on_layers_update(self, layers=None):
             if hasattr(layer, 'attribute') and layer.attribute != flux_comp:
                 layer.attribute = flux_comp
 
+    def _layer_included_in_legend(self, layer, subset_type):
+        print("***", layer.layer.label, subset_type)
+        if subset_type == 'spectral':  # NOTE: spectral here means xrange (i.e. not spatial)
+            # ONLY show spatial subsets in image/cube viewer
+            return False
+        return super()._layer_included_in_legend(layer, subset_type)
+
     def data(self, cls=None):
         # TODO: generalize upstream in jdaviz.
         # This method is generalized from