bugfix/squeeze-extra-dims (#32)

* Squeeze data before return * Catch more squeezes and update tests
AllenCellModeling · Sep 25, 2021 · 7605974 · 7605974
1 parent 0e888bc
commit 7605974
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/napari_aicsimageio/core.py b/napari_aicsimageio/core.py
@@ -38,9 +38,9 @@ def _get_full_image_data(
     if DimensionNames.MosaicTile in img.reader.dims.order:
         try:
             if in_memory:
-                return img.reader.mosaic_xarray_data
+                return img.reader.mosaic_xarray_data.squeeze()
 
-            return img.reader.mosaic_xarray_dask_data
+            return img.reader.mosaic_xarray_dask_data.squeeze()
 
         # Catch reader does not support tile stitching
         except NotImplementedError:
@@ -50,9 +50,9 @@ def _get_full_image_data(
             )
 
     if in_memory:
-        return img.reader.xarray_data
+        return img.reader.xarray_data.squeeze()
 
-    return img.reader.xarray_dask_data
+    return img.reader.xarray_dask_data.squeeze()
 
 
 # Function to get Metadata to provide with data

diff --git a/napari_aicsimageio/tests/test_core.py b/napari_aicsimageio/tests/test_core.py
@@ -50,29 +50,29 @@
         ),
         (
             OME_TIFF,
-            (1, 4, 65, 600, 900),
+            (4, 65, 600, 900),
             {
                 "name": [
                     "0 :: Image:0 :: Bright_2",
                     "0 :: Image:0 :: EGFP",
                     "0 :: Image:0 :: CMDRP",
                     "0 :: Image:0 :: H3342",
                 ],
-                "channel_axis": 1,
+                "channel_axis": 0,
                 "scale": (0.29, 0.10833333333333332, 0.10833333333333332),
             },
         ),
         (
             LIF_FILE,
-            (1, 4, 1, 5622, 7666),
+            (4, 5622, 7666),
             {
                 "name": [
                     "0 :: TileScan_002 :: Gray",
                     "0 :: TileScan_002 :: Red",
                     "0 :: TileScan_002 :: Green",
                     "0 :: TileScan_002 :: Cyan",
                 ],
-                "channel_axis": 1,
+                "channel_axis": 0,
                 "scale": (0.20061311154598827, 0.20061311154598827),
             },
         ),
@@ -126,7 +126,7 @@ def test_reader(
 @pytest.mark.parametrize(
     "filename, expected_shape",
     [
-        (SINGLESCENE_FILE, (1, 325, 475)),
+        (SINGLESCENE_FILE, (325, 475)),
         (MULTISCENE_FILE, (3, 5, 325, 475)),
     ],
 )