Merge pull request #359 from bioimage-io/fix-tiling

Fix critical bug in predict with tiling

Author: FynnBe

bioimageio/core/prediction.py

@@ -330,13 +330,16 @@ def check_tiling(tiling):
         # override metadata defaults with provided dict
         if isinstance(tiling, dict):
             for key in ["halo", "tile", "scale"]:
-                default_tiling.update(tiling.get(key, dict()))
+                default_tiling[key].update(tiling.get(key, dict()))
         tiling = default_tiling
         check_tiling(tiling)
+
     elif isinstance(tiling, bool) and not tiling:
         raise NotImplementedError("Should be unreachable")
+
     else:
         raise ValueError(f"Invalid argument for tiling: {tiling}")
+
     return tiling
 
 

setup.py

@@ -26,7 +26,7 @@
     ],
     packages=find_namespace_packages(exclude=["tests"]),  # Required
     install_requires=[
-        "bioimageio.spec==0.4.9.*",
+        "bioimageio.spec==0.4.9",
         "imageio>=2.5",
         "numpy",
         "ruamel.yaml",

tests/test_bioimageio_spec_version.py

@@ -26,11 +26,16 @@ def test_bioimageio_spec_version():
     # get currently pinned bioimageio.spec version
     meta = metadata("bioimageio.core")
     req = meta["Requires-Dist"]
-    assert req.startswith("bioimageio.spec (==")
-    pmaj, pmin, ppatch, *asterisk_and_rest = req[len("bioimageio.spec (==") :].split(".")
-    assert asterisk_and_rest[0].startswith(
-        "*"
-    ), "bioimageio.spec version should be pinned down to patch, e.g. '0.4.9.*'"
+    print(req)
+    assert req.startswith("bioimageio.spec ==")
+    spec_ver = req[len("bioimageio.spec ==") :]
+    assert spec_ver.count(".") == 2
+    pmaj, pmin, ppatchand_and_post = spec_ver.split(".")
+    assert (ppatchand_and_post.isdigit() or ppatchand_and_post[:-1].isdigit()) and (
+        ppatchand_and_post[-1] == "*" or ppatchand_and_post[-1].isdigit()
+    ), "bioimageio.spec version should be pinned down to patch, e.g. '0.4.9*'"
+
+    ppatch = ppatchand_and_post[:-1] if ppatchand_and_post[-1] == "*" else ppatchand_and_post
     pinned = Version(f"{pmaj}.{pmin}.{ppatch}")
 
     assert pinned >= released, "bioimageio.spec pinned to an old version!"

tests/test_prediction.py

@@ -110,9 +110,7 @@ def check_result():
     check_result()
 
     # test with fixed padding
-    predict_image(
-        model, in_path, out_path, padding={"x": original_shape[0], "y": original_shape[1], "mode": "fixed"}
-    )
+    predict_image(model, in_path, out_path, padding={"x": original_shape[0], "y": original_shape[1], "mode": "fixed"})
     check_result()
 
     # test with automated padding
@@ -135,7 +133,7 @@ def test_predict_image_with_padding_channel_last(stardist, tmp_path):
     _test_predict_with_padding(stardist, tmp_path)
 
 
-def _test_predict_image_with_tiling(model, tmp_path, exp_mean_deviation):
+def _test_predict_image_with_tiling(model, tmp_path: Path, exp_mean_deviation):
     from bioimageio.core.prediction import predict_image
 
     spec = load_resource_description(model)
@@ -168,27 +166,27 @@ def check_result():
 
 # prediction with tiling with the parameters above may not be suited for any model
 # so we only run it for the pytorch unet2d here
-def test_predict_image_with_tiling_1(unet2d_nuclei_broad_model, tmp_path):
+def test_predict_image_with_tiling_1(unet2d_nuclei_broad_model, tmp_path: Path):
     _test_predict_image_with_tiling(unet2d_nuclei_broad_model, tmp_path, 0.012)
 
 
-def test_predict_image_with_tiling_2(unet2d_diff_output_shape, tmp_path):
-    _test_predict_image_with_tiling(unet2d_diff_output_shape, tmp_path, 0.012)
+def test_predict_image_with_tiling_2(unet2d_diff_output_shape, tmp_path: Path):
+    _test_predict_image_with_tiling(unet2d_diff_output_shape, tmp_path, 0.06)
 
 
-def test_predict_image_with_tiling_3(shape_change_model, tmp_path):
+def test_predict_image_with_tiling_3(shape_change_model, tmp_path: Path):
     _test_predict_image_with_tiling(shape_change_model, tmp_path, 0.012)
 
 
-def test_predict_image_with_tiling_channel_last(stardist, tmp_path):
+def test_predict_image_with_tiling_channel_last(stardist, tmp_path: Path):
     _test_predict_image_with_tiling(stardist, tmp_path, 0.13)
 
 
-def test_predict_image_with_tiling_fixed_output_shape(unet2d_fixed_shape, tmp_path):
+def test_predict_image_with_tiling_fixed_output_shape(unet2d_fixed_shape, tmp_path: Path):
     _test_predict_image_with_tiling(unet2d_fixed_shape, tmp_path, 0.025)
 
 
-def test_predict_images(unet2d_nuclei_broad_model, tmp_path):
+def test_predict_images(unet2d_nuclei_broad_model, tmp_path: Path):
     from bioimageio.core.prediction import predict_images
 
     n_images = 5