Add functionality to load catalogs from a file

CHANGES.rst

@@ -21,6 +21,8 @@ Imviz
 - Catalog Search plugin now exposes a maximum sources limit for all catalogs and resolves an edge case
   when loading a catalog from a file that only contains one source. [#3337]
 
+- Enhance the Catalog Search plugin to support additional columns when loading catalog data from files. [#3359]
+
 Mosviz
 ^^^^^^
 

docs/imviz/plugins.rst

@@ -382,8 +382,8 @@ To load a catalog from a supported `JWST ECSV catalog file <https://jwst-pipelin
 The file must be able to be parsed by `astropy.table.Table.read` and contains the following columns:
 
 * ``'sky_centroid'``: Column with `~astropy.coordinates.SkyCoord` sky coordinates of the sources.
-* ``'label'``: Column with string identifiers of the sources. If you have numerical identifiers,
-  they will be recast as string.
+* ``'label(optional)'``: Column with string identifiers of the sources. If not provided, unique string identifiers will be generated automatically.
+  If you have numerical identifiers, they will be recast as strings.
 
 Clicking :guilabel:`SEARCH` will show markers for any entry within the filtered zoom window.
 

jdaviz/configs/imviz/plugins/catalogs/catalogs.py

@@ -45,7 +45,11 @@ class Catalogs(PluginTemplateMixin, ViewerSelectMixin, HasFileImportSelect, Tabl
             'Object ID': np.nan,
             'id': np.nan,
             'x_coord': np.nan,
-            'y_coord': np.nan}
+            'y_coord': np.nan
+            }
+
+    headers = ['Right Ascension (degrees)', 'Declination (degrees)',
+               'Object ID', 'x_coord', 'y_coord']
 
     @property
     def user_api(self):
@@ -70,11 +74,8 @@ def __init__(self, *args, **kwargs):
         self._marker_name = 'catalog_results'
 
         # initializing the headers in the table that is displayed in the UI
-        headers = ['Right Ascension (degrees)', 'Declination (degrees)',
-                   'Object ID', 'x_coord', 'y_coord']
-
-        self.table.headers_avail = headers
-        self.table.headers_visible = headers
+        self.table.headers_avail = self.headers
+        self.table.headers_visible = self.headers
         self.table._default_values_by_colname = self._default_table_values
         self.table._selected_rows_changed_callback = lambda msg: self.plot_selected_points()
         self.table.item_key = 'id'
@@ -88,13 +89,15 @@ def __init__(self, *args, **kwargs):
     def _file_parser(path):
         try:
             table = QTable.read(path)
-        except Exception:
-            return 'Could not parse file with astropy.table.QTable.read', {}
+            if not table.colnames:  # Ensure the file has columns
+                return "File contains no columns", {}
 
-        if 'sky_centroid' not in table.colnames:
-            return 'Table does not contain required sky_centroid column', {}
+            if 'sky_centroid' not in table.colnames:
+                return 'Table does not contain required sky_centroid column', {}
 
-        return '', {path: table}
+            return '', {path: table}
+        except Exception:
+            return 'Could not parse file with astropy.table.QTable.read', {}
 
     @with_spinner()
     def search(self, error_on_fail=False):
@@ -113,7 +116,7 @@ def search(self, error_on_fail=False):
 
         """
         # calling clear in the case the user forgot after searching
-        self.clear()
+        self.clear_table()
 
         # gets the current viewer
         viewer = self.viewer.selected_obj
@@ -202,6 +205,11 @@ def search(self, error_on_fail=False):
             # all exceptions when going through the UI should have prevented setting this path
             # but this exceptions might be raised here if setting from_file from the UI
             table = self.catalog.selected_obj
+            column_names = list(table.colnames)
+            self.table.headers_avail = self.headers + [
+                col for col in column_names if col not in self.headers and col not in ["sky_centroid", "label"]     # noqa:E501
+                ]
+            self.table.headers_visible = self.headers
             self.app._catalog_source_table = table
             if len(table['sky_centroid']) > self.max_sources:
                 skycoord_table = table['sky_centroid'][:self.max_sources]
@@ -269,16 +277,19 @@ def search(self, error_on_fail=False):
             if len(self.app._catalog_source_table) == 1 or self.max_sources == 1:
                 x_coordinates = [x_coordinates]
                 y_coordinates = [y_coordinates]
+            for idx, (row, x_coord, y_coord) in enumerate(zip(self.app._catalog_source_table, x_coordinates, y_coordinates)):  # noqa:E501
+                row_info = {
+                    'Right Ascension (degrees)': row['sky_centroid'].ra.deg,
+                    'Declination (degrees)': row['sky_centroid'].dec.deg,
+                    'Object ID': str(row.get('label', f"{idx + 1}")),
+                    'id': idx+1,
+                    'x_coord': x_coord,
+                    'y_coord': y_coord,
+                }
+                for col in table.colnames:
+                    if col not in ['label', 'sky_centroid']:  # Skip already processed columns
+                        row_info[col] = row[col]
 
-            for row, x_coord, y_coord in zip(self.app._catalog_source_table,
-                                             x_coordinates, y_coordinates):
-                # Check if the row contains the required keys
-                row_info = {'Right Ascension (degrees)': row['sky_centroid'].ra.deg,
-                            'Declination (degrees)': row['sky_centroid'].dec.deg,
-                            'Object ID': str(row.get('label', 'N/A')),
-                            'id': len(self.table),
-                            'x_coord': x_coord.item() if x_coord.size == 1 else x_coord,
-                            'y_coord': y_coord.item() if y_coord.size == 1 else y_coord}
                 self.table.add_item(row_info)
 
         filtered_skycoord_table = viewer.state.reference_data.coords.pixel_to_world(x_coordinates,
@@ -326,7 +337,8 @@ def plot_selected_points(self):
     def vue_zoom_in(self, *args, **kwargs):
         """This function will zoom into the image based on the selected points"""
         selected_rows = self.table.selected_rows
-
+        if not selected_rows:  # Check if no rows are selected
+            return
         x = [float(coord['x_coord']) for coord in selected_rows]
         y = [float(coord['y_coord']) for coord in selected_rows]
 
@@ -361,9 +373,13 @@ def vue_do_search(self, *args, **kwargs):
         # calls self.search() which handles all of the searching logic
         self.search()
 
-    def clear(self, hide_only=True):
+    def clear_table(self, hide_only=True):
         # gets the current viewer
         viewer = self.viewer.selected_obj
+        # Clear the table before performing a new search
+        self.table.items = []
+        self.table.selected_rows = []
+        self.table.selected_indices = []
 
         if not hide_only and self._marker_name in self.app.data_collection.labels:
             # resetting values
@@ -385,5 +401,5 @@ def clear(self, hide_only=True):
                 if layer_is_table_data(lyr.layer) and lyr.layer.label == self._marker_name:
                     lyr.visible = False
 
-    def vue_do_clear(self, *args, **kwargs):
-        self.clear()
+    def vue_do_clear_table(self, *args, **kwargs):
+        self.clear_table()

jdaviz/configs/imviz/plugins/catalogs/catalogs.vue

@@ -36,6 +36,16 @@
         See the <j-external-link link='https://astroquery.readthedocs.io/en/latest/gaia/gaia.html' linktext='astropy.gaia docs'></j-external-link> for details on the query defaults.
       </j-docs-link>
     </v-row>
+
+    <v-row v-if="catalog_selected && catalog_selected.endsWith('.ecsv')">
+      <v-select
+        v-model="selected_columns"
+        :items="column_names"
+        label="Select Columns"
+        multiple
+        hint="Select columns to display in the table."
+      />
+    </v-row>
 
     <v-row>
       <v-text-field
@@ -53,14 +63,6 @@
     </v-row>
 
     <v-row class="row-no-outside-padding">
-       <v-col>
-         <plugin-action-button
-            :results_isolated_to_plugin="true"
-            @click="do_clear"
-          >
-            Clear
-          </plugin-action-button>
-       </v-col>
        <v-col>
          <plugin-action-button
             :results_isolated_to_plugin="true"

jdaviz/configs/imviz/tests/test_catalogs.py

@@ -28,6 +28,7 @@
 from astropy.nddata import NDData
 from astropy.coordinates import SkyCoord
 from astropy.table import Table, QTable
+from numpy.testing import assert_allclose
 
 
 @pytest.mark.remote_data
@@ -113,7 +114,7 @@ def test_plugin_image_with_result(self, imviz_helper, tmp_path):
         prev_results = catalogs_plugin.number_of_results
 
         # testing that every variable updates accordingly when markers are cleared
-        catalogs_plugin.vue_do_clear()
+        catalogs_plugin.vue_do_clear_table()
 
         assert not catalogs_plugin.results_available
 
@@ -157,12 +158,16 @@ def test_plugin_image_with_result(self, imviz_helper, tmp_path):
         assert imviz_helper.viewers['imviz-0']._obj.state.y_min == -0.5
         assert imviz_helper.viewers['imviz-0']._obj.state.y_max == 1488.5
 
+        # First select a row
+        catalogs_plugin.table.selected_rows = [
+            catalogs_plugin.table.items[0]]
+        # Then zoom in to the selected
         catalogs_plugin.vue_zoom_in()
 
-        assert imviz_helper.viewers['imviz-0']._obj.state.x_min == 858.24969
-        assert imviz_helper.viewers['imviz-0']._obj.state.x_max == 958.38461
-        assert imviz_helper.viewers['imviz-0']._obj.state.y_min == 278.86265
-        assert imviz_helper.viewers['imviz-0']._obj.state.y_max == 378.8691
+        assert imviz_helper.viewers['imviz-0']._obj.state.x_min == 1022.5631800000001
+        assert imviz_helper.viewers['imviz-0']._obj.state.x_max == 1122.56318
+        assert imviz_helper.viewers['imviz-0']._obj.state.y_min == 675.29611
+        assert imviz_helper.viewers['imviz-0']._obj.state.y_max == 775.29611
 
 
 def test_from_file_parsing(imviz_helper, tmp_path):
@@ -237,23 +242,30 @@ def test_offline_ecsv_catalog(imviz_helper, image_2d_wcs, tmp_path):
     assert catalogs_plugin.number_of_results == n_entries
     assert len(imviz_helper.app.data_collection) == 2  # image + markers
 
-    catalogs_plugin.clear()
+    catalogs_plugin.clear_table()
 
     assert not catalogs_plugin.results_available
     assert len(imviz_helper.app.data_collection) == 2  # markers still there, just hidden
 
-    catalogs_plugin.clear(hide_only=False)
+    catalogs_plugin.clear_table(hide_only=False)
     assert not catalogs_plugin.results_available
     assert len(imviz_helper.app.data_collection) == 1  # markers gone for good
 
     assert imviz_helper.viewers['imviz-0']._obj.state.x_min == -0.5
     assert imviz_helper.viewers['imviz-0']._obj.state.x_max == 9.5
     assert imviz_helper.viewers['imviz-0']._obj.state.y_min == -0.5
     assert imviz_helper.viewers['imviz-0']._obj.state.y_max == 9.5
+    # Re-populate the table with a new search
+    out_tbl = catalogs_plugin.search()
+    assert len(out_tbl) > 0
+    # Ensure at least one row is selected before zooming
+    catalogs_plugin.table.selected_rows = [catalogs_plugin.table.items[0]]
+    assert len(catalogs_plugin.table.selected_rows) > 0
 
+    # Now zoom in
     catalogs_plugin.vue_zoom_in()
 
-    assert imviz_helper.viewers['imviz-0']._obj.state.x_min == -49.99966
-    assert imviz_helper.viewers['imviz-0']._obj.state.x_max == 50.00034
-    assert imviz_helper.viewers['imviz-0']._obj.state.y_min == -48.99999
-    assert imviz_helper.viewers['imviz-0']._obj.state.y_max == 51.00001
+    assert_allclose(imviz_helper.viewers['imviz-0']._obj.state.x_min, -49.99966, rtol=1e-6)
+    assert_allclose(imviz_helper.viewers['imviz-0']._obj.state.x_max, 50.00034, rtol=1e-6)
+    assert_allclose(imviz_helper.viewers['imviz-0']._obj.state.y_min, -48.99999, rtol=1e-6)
+    assert_allclose(imviz_helper.viewers['imviz-0']._obj.state.y_max, 51.00001, rtol=1e-6)

jdaviz/core/template_mixin.py

@@ -4691,12 +4691,20 @@ def float_precision(column, item):
                 return ''
             elif isinstance(item, tuple) and np.all([np.isnan(i) for i in item]):
                 return ''
-
             elif isinstance(item, float):
                 return float_precision(column, item)
             elif isinstance(item, (list, tuple)):
                 return [float_precision(column, i) if isinstance(i, float) else i for i in item]
-
+            elif isinstance(item, (np.float32, np.float64)):
+                return float(item)
+            elif isinstance(item, u.Quantity):
+                return {"value": item.value.tolist() if item.size > 1 else item.value, "unit": str(item.unit)}     # noqa: E501
+            elif isinstance(item, np.bool_):
+                return bool(item)
+            elif isinstance(item, np.ndarray):
+                return item.tolist()
+            elif isinstance(item, tuple):
+                return tuple(json_safe(v) for v in item)
             return item
 
         if isinstance(item, QTable):
@@ -4738,6 +4746,8 @@ def clear_table(self):
         Clear all entries/markers from the current table.
         """
         self.items = []
+        self.selected_rows = []
+        self.selected_indices = []
         self._qtable = None
         self._plugin.session.hub.broadcast(PluginTableModifiedMessage(sender=self))