bugfix/invert-lif-scales (#288)

* Invert LIF scale sizes * Apply scale changes to tests
AllenCellModeling · Aug 9, 2021 · c9e2af9 · c9e2af9
1 parent 3b71939
commit c9e2af9
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Showing 3 changed files with 18 additions and 9 deletions.
diff --git a/aicsimageio/readers/lif_reader.py b/aicsimageio/readers/lif_reader.py
@@ -380,6 +380,12 @@ def _get_coords_and_physical_px_sizes(
         # Unpack short info scales
         scale_x, scale_y, scale_z, scale_t = image_short_info["scale"]
 
+        # Scales from readlif are returned as px/µm
+        # We want to return as µm/px
+        scale_x = 1 / scale_x if scale_x is not None else None
+        scale_y = 1 / scale_y if scale_y is not None else None
+        scale_z = 1 / scale_z if scale_z is not None else None
+
         # Handle Spatial Dimensions
         if scale_z is not None:
             coords[DimensionNames.SpatialZ] = Reader._generate_coord_array(
@@ -596,6 +602,9 @@ def _construct_mosaic_xarray(self, data: types.ArrayLike) -> xr.DataArray:
 
         # Add expanded Y and X coords
         scale_x, scale_y, _, _ = selected_scene.info["scale"]
+        scale_x = 1 / scale_x if scale_x is not None else None
+        scale_y = 1 / scale_y if scale_y is not None else None
+
         if scale_y is not None:
             coords[DimensionNames.SpatialY] = Reader._generate_coord_array(
                 0, stitched.shape[-2], scale_y

diff --git a/aicsimageio/tests/readers/test_lif_reader.py b/aicsimageio/tests/readers/test_lif_reader.py
@@ -37,7 +37,7 @@
             np.uint16,
             dimensions.DEFAULT_DIMENSION_ORDER,
             ["Gray--TL-BF--EMP_BF", "Green--FLUO--GFP"],
-            (None, 3.076923076923077, 3.076923076923077),
+            (None, 0.32499999999999996, 0.32499999999999996),
         ),
         (
             "s_1_t_4_c_2_z_1.lif",
@@ -47,7 +47,7 @@
             np.uint16,
             dimensions.DEFAULT_DIMENSION_ORDER,
             ["Gray--TL-PH--EMP_BF", "Green--FLUO--GFP"],
-            (None, 2.9485556406398508, 2.9485556406398508),
+            (None, 0.33914910277324634, 0.33914910277324634),
         ),
         (
             "tiled.lif",
@@ -57,7 +57,7 @@
             np.uint8,
             dimensions.DEFAULT_DIMENSION_ORDER_WITH_MOSAIC_TILES,
             ["Gray", "Red", "Green", "Cyan"],
-            (None, 4.984719055966396, 4.984719055966396),
+            (None, 0.20061311154598827, 0.20061311154598827),
         ),
         pytest.param(
             "example.txt",
@@ -306,10 +306,10 @@ def test_lif_reader_mosaic_tile_inspection(
     [
         (
             "tiled.lif",
-            np.arange(0, 2552.176156654795, 4.984719055966396),
-            np.arange(0, 2552.176156654795, 4.984719055966396),
-            np.arange(0, 28024.09053264308, 4.984719055966396),
-            np.arange(0, 38212.85628303839, 4.984719055966396),
+            np.arange(0, 102.71391311154599, 0.20061311154598827),
+            np.arange(0, 102.71391311154599, 0.20061311154598827),
+            np.arange(0, 1127.846913111546, 0.20061311154598827),
+            np.arange(0, 1537.900113111546, 0.20061311154598827),
         ),
     ],
 )

diff --git a/aicsimageio/tests/test_aics_image.py b/aicsimageio/tests/test_aics_image.py
@@ -168,7 +168,7 @@
             np.uint16,
             dimensions.DEFAULT_DIMENSION_ORDER,
             ["Gray--TL-PH--EMP_BF", "Green--FLUO--GFP"],
-            (None, 2.9485556406398508, 2.9485556406398508),
+            (None, 0.33914910277324634, 0.33914910277324634),
             ET.Element,
         ),
         (
@@ -179,7 +179,7 @@
             np.uint8,
             dimensions.DEFAULT_DIMENSION_ORDER,
             ["Gray", "Red", "Green", "Cyan"],
-            (None, 4.984719055966396, 4.984719055966396),
+            (None, 0.20061311154598827, 0.20061311154598827),
             ET.Element,
         ),
         #######################################################################