Automatic detection of XZ pixel-size anisotropy, for per-FOV labeling…

… (ref #64 #112)

fractal/tasks/image_labeling.py

@@ -17,6 +17,7 @@
 import time
 from concurrent.futures import ThreadPoolExecutor
 
+import anndata as ad
 import dask
 import dask.array as da
 import numpy as np
@@ -126,8 +127,23 @@ def image_labeling(
     do_3D = data_zyx.shape[0] > 1
     if do_3D:
         if anisotropy is None:
-            # Reasonable value for level 0 (for some of our UZH datasets)
-            anisotropy = 1.0 / 0.1625
+
+            adata = ad.read_zarr(f"{zarrurl}tables/FOV_ROI_table")
+            pixel_size_x = adata["pixel_size_x"][0]
+            pixel_size_y = adata["pixel_size_y"][0]
+            pixel_size_z = adata["pixel_size_z"][0]
+            if not np.allclose(pixel_size_x, pixel_size_y):
+                raise Exception(
+                    "ERROR: XY anisotropy detected\n"
+                    f"pixel_size_x={pixel_size_x}\n"
+                    f"pixel_size_y={pixel_size_y}"
+                )
+            anisotropy = pixel_size_z / pixel_size_x
+            if labeling_level > 0:
+                raise NotImplementedError(
+                    "TODO: fix automatic anisotropy "
+                    "detection for higher levels"
+                )
 
     # Check model_type
     if model_type not in ["nuclei", "cyto2", "cyto"]: