test_output_ref_shape_too_small

Author: FynnBe

bioimageio/spec/model/v0_5.py

@@ -193,7 +193,7 @@ def convert_name_to_id(cls, data: Dict[str, Any], info: ValidationInfo):
             "name" in data
             and "id" not in data
             and "original_format" in context
-            and context["original_format"].release[:2] == (0, 4)
+            and context["original_format"].release[:2] <= (0, 4)
         ):
             data["id"] = data.pop("name")
 

example_specs/models/unet2d_nuclei_broad/rdf.yaml

@@ -40,11 +40,12 @@ inputs:
       - type: batch
       - type: channel
         channel_names: [raw_intensity]
+        size: 1
       - type: space # todo: scale/unit
-        name: y
+        id: y
         size: 512
       - type: space
-        name: x
+        id: x
         size: 512
     test_tensor: test_input.npy
     sample_tensor: test_input.npy
@@ -66,13 +67,14 @@ outputs:
       - type: batch
       - type: channel
         channel_names: [probability]
+        size: 1
       - type: space
-        name: y
+        id: y
         size: raw.y
         halo: 32
       - type: space
         size: raw.x
-        name: x
+        id: x
         halo: 32
     test_tensor: test_output.npy
     sample_tensor: test_output.npy

tests/test_bioimageio_collection.py

@@ -44,6 +44,13 @@
     "zero/Notebook_U-Net_3D_ZeroCostDL4Mic/latest/rdf.yaml",
 }
 KNOWN_INVALID_AS_LATEST = {
+    "deepimagej/DeepSTORMZeroCostDL4Mic/latest/rdf.yaml",
+    "deepimagej/Mt3VirtualStaining/latest/rdf.yaml",
+    "deepimagej/WidefieldDapiSuperResolution/latest/rdf.yaml",
+    "deepimagej/WidefieldFitcSuperResolution/latest/rdf.yaml",
+    "deepimagej/DeepSTORMZeroCostDL4Mic/latest/rdf.yaml",
+    "deepimagej/DeepSTORMZeroCostDL4Mic/latest/rdf.yaml",
+    "deepimagej/DeepSTORMZeroCostDL4Mic/latest/rdf.yaml",
     "10.5281/zenodo.6559929/6559930/rdf.yaml",
     "10.5281/zenodo.7380171/7405349/rdf.yaml",
     "bioimageio/stardist/latest/rdf.yaml",

tests/test_model/test_v0_5.py

@@ -124,8 +124,8 @@ def test_tensor_base_invalid(kwargs: Dict[str, Any]):
             "description": "Input 1",
             "data": {"type": "float32"},
             "axes": [
-                dict(type="space", name="x", size=10),
-                dict(type="space", name="y", size=11),
+                dict(type="space", id="x", size=10),
+                dict(type="space", id="y", size=11),
                 dict(type="channel", channel_names=tuple("abc")),
             ],
             "preprocessing": [
@@ -155,7 +155,7 @@ def test_batch_axis(kwargs: Dict[str, Any]):
 @pytest.mark.parametrize(
     "kwargs",
     [
-        {"type": "space", "name": "x", "size": 10},
+        {"type": "space", "id": "x", "size": 10},
         SpaceInputAxis(id=AxisId("x"), size=10),
         {"type": "batch"},
     ],
@@ -274,17 +274,17 @@ def test_output_fixed_shape_too_small(model_data: Dict[str, Any]):
 
 
 def test_output_ref_shape_mismatch(model_data: Dict[str, Any]):
-    model_data["outputs"][0]["axes"][0] = {"type": "space", "name": "x", "size": {"reference": "input_1.x"}, "halo": 2}
+    model_data["outputs"][0]["axes"][0] = {"type": "space", "id": "x", "size": {"reference": "input_1.x"}, "halo": 2}
     summary = validate_format(model_data)
     assert summary.status == "passed", summary.format()
     # input_1.x -> input_1.z
-    model_data["outputs"][0]["axes"][0] = {"type": "space", "name": "x", "size": {"reference": "input_1.z"}, "halo": 2}
+    model_data["outputs"][0]["axes"][0] = {"type": "space", "id": "x", "size": {"reference": "input_1.z"}, "halo": 2}
     summary = validate_format(model_data)
     assert summary.status == "failed", summary.format()
 
 
 def test_output_ref_shape_too_small(model_data: Dict[str, Any]):
-    model_data["outputs"][0]["axes"][0] = {"type": "space", "name": "x", "size": {"reference": "input_1.x"}, "halo": 2}
+    model_data["outputs"][0]["axes"][0] = {"type": "space", "id": "x", "size": {"reference": "input_1.x"}, "halo": 2}
     summary = validate_format(model_data)
     assert summary.status == "passed", summary.format()
 
@@ -301,9 +301,9 @@ def test_model_has_parent_with_id(model_data: Dict[str, Any]):
 
 def test_model_with_expanded_output(model_data: Dict[str, Any]):
     model_data["outputs"][0]["axes"] = [
-        {"type": "space", "name": "x", "size": {"reference": "input_1.x"}},
-        {"type": "space", "name": "y", "size": {"reference": "input_1.y"}},
-        {"type": "space", "name": "z", "size": 7},
+        {"type": "space", "id": "x", "size": {"reference": "input_1.x"}},
+        {"type": "space", "id": "y", "size": {"reference": "input_1.y"}},
+        {"type": "space", "id": "z", "size": 7},
         {"type": "channel", "size": {"reference": "input_1.channel"}},
     ]