added sd_utils

Author: hschryver

src/xenium_analysis_tools/utils/sd_utils.py

@@ -0,0 +1,71 @@
+import spatialdata as sd
+from spatialdata.transformations import Scale, Identity, set_transformation
+
+def add_micron_coord_sys(sdata, pixel_size=None, z_step=None):
+    # Define the pixel scaling factor
+    if pixel_size is None and 'table' in sdata:
+        pixel_size = sdata['table'].uns['section_metadata']['pixel_size']
+    if z_step is None and 'table' in sdata:
+        z_step = sdata['table'].uns['section_metadata']['z_step_size']
+    else:
+        z_step = 1.0
+
+    # 2D Images (channel, y, x)
+    # c = 1.0 (channels are discrete)
+    scale_yx = Scale([pixel_size, pixel_size], axes=("y", "x"))
+    scale_cyx = Scale([1.0, pixel_size, pixel_size], axes=("c", "y", "x"))
+
+    # For 3D Z-Stacks (c, z, y, x)
+    # c = 1.0 (channels are discrete)
+    # z = 3.0 (microns per plane)
+    # y, x = 0.2125 (microns per pixel)
+    scale_czyx = Scale(
+        [1.0, z_step, pixel_size, pixel_size], 
+        axes=("c", "z", "y", "x")
+    )
+
+    # Identity transform for elements already in microns
+    identity = Identity()
+
+    # --- Images ---
+    # dapi_zstack is (c, z, y, x)
+    if 'dapi_zstack' in sdata.images:
+        set_transformation(
+            sdata.images['dapi_zstack'], 
+            scale_czyx, 
+            to_coordinate_system="microns"
+        )
+
+    # morphology_focus is (c, y, x)
+    if 'morphology_focus' in sdata.images:
+        set_transformation(
+            sdata.images['morphology_focus'], 
+            scale_cyx, 
+            to_coordinate_system="microns"
+        )
+
+    # --- Labels ---
+    # Both labels are (y, x)
+    for label_name in sdata.labels:
+        set_transformation(
+            sdata.labels[label_name], 
+            scale_yx, 
+            to_coordinate_system="microns"
+        )
+
+    # --- Shapes & Points ---
+    # Already in microns
+    for shape_name in sdata.shapes:
+        set_transformation(
+            sdata.shapes[shape_name], 
+            identity, 
+            to_coordinate_system="microns"
+        )
+
+    for point_name in sdata.points:
+        set_transformation(
+            sdata.points[point_name], 
+            identity, 
+            to_coordinate_system="microns"
+        )
+    return sdata