Fix coords assignment in CombineAdjustFeatures.run

Use explicit parameter calls when building table coordinates Fix shape definition for the IntensityTable docs
spacetx · Oct 19, 2021 · ef6cc21 · ef6cc21
1 parent 8741af1
commit ef6cc21
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diff --git a/starfish/core/intensity_table/intensity_table.py b/starfish/core/intensity_table/intensity_table.py
@@ -33,7 +33,7 @@ class IntensityTable(xr.DataArray):
     An IntensityTable records the numeric intensity of a set of features in each
     :code:`(round, channel)` tile in which the feature is identified.
     The :py:class:`IntensityTable` has shape
-    :code:`(n_feature, n_channel, n_round)`.
+    :code:`(n_feature, n_round, n_channel)`.
 
     Some :py:class:`SpotFinder` methods identify a position and search for
     Gaussian blobs in a small radius, only recording intensities if they are

diff --git a/starfish/core/spots/DetectPixels/combine_adjacent_features.py b/starfish/core/spots/DetectPixels/combine_adjacent_features.py
@@ -422,10 +422,13 @@ def run(
         # create new indexes for the output IntensityTable
         channel_index = mean_pixel_traces.indexes[Axes.CH]
         round_index = mean_pixel_traces.indexes[Axes.ROUND]
-        coords = IntensityTable._build_xarray_coords(spot_attributes, channel_index, round_index)
+        coords = IntensityTable._build_xarray_coords(
+            spot_attributes,
+            round_values=round_index,
+            channel_values=channel_index)
 
         # create the output IntensityTable
-        dims = (Features.AXIS, Axes.CH.value, Axes.ROUND.value)
+        dims = (Features.AXIS, Axes.ROUND.value, Axes.CH.value)
         intensity_table = DecodedIntensityTable(
             data=mean_pixel_traces, coords=coords, dims=dims
         )