Merge pull request #12 from bmorris3/lightkurve-parser

Adding support for subsets in time

lcviz/conftest.py

@@ -1,7 +1,6 @@
 import numpy as np
 import pytest
 from astropy import units as u
-from astropy.utils.masked import Masked
 from lightkurve import LightCurve
 
 from lcviz import __version__, LCviz
@@ -22,7 +21,6 @@ def light_curve_like_kepler_quarter(seed=42):
     """
     np.random.seed(seed)
     exp_per_day = (30 * u.min).to_value(u.day)
-    masked_fraction = 0.01
 
     # approx start and stop JD for Kepler Quarter 10:
     time = np.arange(2455739, 2455833, exp_per_day)
@@ -32,19 +30,10 @@ def light_curve_like_kepler_quarter(seed=42):
     ) * u.dimensionless_unscaled
     flux_err = scale * np.ones_like(flux)
 
-    # randomly apply mask to fraction of the data:
-    mask_indices = np.random.randint(
-        low=0,
-        high=len(flux),
-        size=int(masked_fraction * len(flux))
-    )
-    mask = np.zeros(len(flux), dtype=bool)
-    mask[mask_indices] = True
+    quality = np.zeros(len(time), dtype=np.int32)
 
-    flux = Masked(flux, mask)
-    flux_err = Masked(flux_err, mask)
     return LightCurve(
-        time=time, flux=flux, flux_err=flux_err
+        time=time, flux=flux, flux_err=flux_err, quality=quality
     )
 
 

lcviz/helper.py

@@ -1,8 +1,32 @@
+import astropy.units as u
+
+from lightkurve import LightCurve
+
 from jdaviz.core.helpers import ConfigHelper
 
 __all__ = ['LCviz']
 
 
+def _get_range_subset_bounds(self, subset_state, *args, **kwargs):
+    # Instead of overriding the jdaviz version of this method on jdaviz.Application,
+    # we could put in jdaviz by (1) checking if helper has a
+    # _default_time_viewer_reference_name, (2) using the LCviz version if so, and (3)
+    # using the jdaviz version otherwise.
+    viewer = self.get_viewer(self._jdaviz_helper._default_time_viewer_reference_name)
+    reference_time = viewer.state.reference_data.meta['reference_time']
+    if viewer:
+        units = u.Unit(viewer.state.x_display_unit)
+    else:
+        raise ValueError("Unable to find time axis units")
+
+    region = reference_time + u.Quantity([subset_state.lo * units, subset_state.hi * units])
+
+    return [{"name": subset_state.__class__.__name__,
+             "glue_state": subset_state.__class__.__name__,
+             "region": region,
+             "subset_state": subset_state}]
+
+
 class LCviz(ConfigHelper):
     _default_configuration = {
         'settings': {'configuration': 'lcviz',
@@ -13,7 +37,10 @@ class LCviz(ConfigHelper):
                      'dense_toolbar': False,
                      'context': {'notebook': {'max_height': '600px'}}},
         'toolbar': ['g-data-tools', 'g-subset-tools'],
-        'tray': ['g-metadata-viewer', 'g-plot-options', 'HelloWorldPlugin', 'g-export-plot'],
+        'tray': [
+            'g-metadata-viewer', 'g-plot-options', 'g-subset-plugin',
+            'HelloWorldPlugin', 'g-export-plot'
+        ],
         'viewer_area': [{'container': 'col',
                          'children': [{'container': 'row',
                                        'viewers': [{'name': 'time-viewer',
@@ -24,6 +51,11 @@ def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self._default_time_viewer_reference_name = 'time-viewer'
 
+        # override jdaviz behavior to support temporal subsets
+        self.app._get_range_subset_bounds = (
+            lambda *args, **kwargs: _get_range_subset_bounds(self.app, *args, **kwargs)
+        )
+
     def load_data(self, data, data_label=None):
         """
         Load data into LCviz.
@@ -47,3 +79,24 @@ def load_data(self, data, data_label=None):
             parser_reference='light_curve_parser',
             data_label=data_label
         )
+
+    def get_data(self, data_label=None, cls=LightCurve, subset_to_apply=None):
+        """
+        Returns data with name equal to data_label of type cls with subsets applied from
+        subset_to_apply.
+
+        Parameters
+        ----------
+        data_label : str, optional
+            Provide a label to retrieve a specific data set from data_collection.
+        cls : light curve class, optional
+            The type that data will be returned as.
+        subset_to_apply : str, optional
+            Subset that is to be applied to data before it is returned.
+
+        Returns
+        -------
+        data : cls
+            Data is returned as type cls with subsets applied.
+        """
+        return super()._get_data(data_label=data_label, cls=cls, subset_to_apply=subset_to_apply)

lcviz/tests/test_parser.py

@@ -1,12 +1,13 @@
 # import pytest
 import numpy as np
+from glue.core.roi import XRangeROI
 from astropy.time import Time
 # from astropy.utils.data import download_file
 from lightkurve import LightCurve
 # from lightkurve.io import kepler
-from gwcs.wcs import WCS
 import astropy.units as u
 
+from lcviz.utils import TimeCoordinates
 
 # @pytest.mark.remote_data
 # def test_kepler_via_mast_local_file(helper):
@@ -23,7 +24,7 @@
 #     flux_unit = u.Unit(data.get_component('flux').units)
 #     flux = flux_arr * flux_unit
 #
-#     assert isinstance(data.coords, WCS)
+#     assert isinstance(data.coords, TimeCoordinates)
 #     assert isinstance(flux, u.Quantity)
 #     assert flux.unit.is_equivalent(u.electron / u.s)
 #
@@ -43,7 +44,7 @@
 #     flux_unit = u.Unit(data.get_component('flux').units)
 #     flux = flux_arr * flux_unit
 #
-#     assert isinstance(data.coords, WCS)
+#     assert isinstance(data.coords, TimeCoordinates)
 #     assert isinstance(flux, u.Quantity)
 #     assert flux.unit.is_equivalent(u.electron / u.s)
 
@@ -60,6 +61,31 @@ def test_synthetic_lc(helper):
     flux_unit = u.Unit(data.get_component('flux').units)
     flux = flux_arr * flux_unit
 
-    assert isinstance(data.coords, WCS)
+    assert isinstance(data.coords, TimeCoordinates)
     assert isinstance(flux, u.Quantity)
     assert flux.unit.is_equivalent(u.electron / u.s)
+
+
+def test_apply_xrangerois(helper, light_curve_like_kepler_quarter):
+    lc = light_curve_like_kepler_quarter
+    helper.load_data(lc)
+    viewer = helper.app.get_viewer("time-viewer")
+    subset_plugin = helper.plugins['Subset Tools']
+
+    # the min/max of temporal regions can be defined in two ways:
+    time_ranges = [
+        [6, 8],  # in same units as the x axis, OR
+        Time(['2011-07-19', '2011-07-23'])  # directly with a Time object
+    ]
+
+    for time_range in time_ranges:
+        subset_plugin._obj.subset_selected = "Create New"
+        viewer.apply_roi(XRangeROI(*time_range))
+
+    subsets = helper.app.get_subsets_from_viewer('time-viewer')
+
+    subset_1_bounds_jd = subsets['Subset 1'][0]['region'].jd
+    subset_2_bounds_jd = subsets['Subset 2'][0]['region'].jd
+
+    np.testing.assert_allclose(subset_1_bounds_jd, [2455745., 2455747.])
+    np.testing.assert_allclose(subset_2_bounds_jd, [2455761.50076602, 2455765.50076602])