Merge pull request #385 from bioimage-io/fix_data_dep_size

Fix data dep size

.gitignore

@@ -1,3 +1,4 @@
+.env
 .idea/
 .tox/
 *.egg-info/

README.md

@@ -124,6 +124,10 @@ The model specification and its validation tools can be found at <https://github
 
 ## Changelog
 
+### 0.6.2
+
+* Fix [#384](https://github.com/bioimage-io/core-bioimage-io-python/issues/384)
+
 ### 0.6.1
 
 * Fix [#378](https://github.com/bioimage-io/core-bioimage-io-python/pull/378) (with [#379](https://github.com/bioimage-io/core-bioimage-io-python/pull/379))*

bioimageio/core/VERSION

@@ -1,3 +1,3 @@
 {
-    "version": "0.6.1"
+    "version": "0.6.2"
 }

bioimageio/core/block.py

@@ -16,6 +16,7 @@
     Halo,
     HaloLike,
     PadMode,
+    SliceInfo,
     TotalNumberOfBlocks,
 )
 from .tensor import Tensor
@@ -34,6 +35,7 @@ def inner_data(self):
 
     def __post_init__(self):
         super().__post_init__()
+        assert not any(v == -1 for v in self.sample_shape.values()), self.sample_shape
         for a, s in self.data.sizes.items():
             slice_ = self.inner_slice[a]
             halo = self.halo.get(a, Halo(0, 0))
@@ -65,6 +67,27 @@ def get_transformed(
     ) -> Self:
         raise NotImplementedError
 
+    @classmethod
+    def from_meta(cls, meta: BlockMeta, data: Tensor) -> Self:
+        return cls(
+            sample_shape={
+                k: data.tagged_shape[k] if v == -1 else v
+                for k, v in meta.sample_shape.items()
+            },
+            inner_slice={
+                k: (
+                    SliceInfo(start=v.start, stop=data.tagged_shape[k])
+                    if v.stop == -1
+                    else v
+                )
+                for k, v in meta.inner_slice.items()
+            },
+            halo=meta.halo,
+            block_index=meta.block_index,
+            blocks_in_sample=meta.blocks_in_sample,
+            data=data,
+        )
+
 
 def split_tensor_into_blocks(
     tensor: Tensor,

bioimageio/core/sample.py

@@ -251,18 +251,16 @@ def get_member_halo(m: MemberId, round: Callable[[float], int]):
 
     def with_data(self, data: PerMember[Tensor], *, stat: Stat) -> SampleBlock:
         return SampleBlock(
-            sample_shape=self.sample_shape,
+            sample_shape={
+                m: {
+                    a: data[m].tagged_shape[a] if s == -1 else s
+                    for a, s in member_shape.items()
+                }
+                for m, member_shape in self.sample_shape.items()
+            },
             sample_id=self.sample_id,
             blocks={
-                m: Block(
-                    sample_shape=self.sample_shape[m],
-                    inner_slice=b.inner_slice,
-                    halo=b.halo,
-                    block_index=b.block_index,
-                    blocks_in_sample=b.blocks_in_sample,
-                    data=data[m],
-                )
-                for m, b in self.blocks.items()
+                m: Block.from_meta(b, data=data[m]) for m, b in self.blocks.items()
             },
             stat=stat,
             block_index=self.block_index,