Merge pull request #169 from bioimage-io/fix-deepij-conf

Fix issues with build_model with deepimagej config

Author: constantinpape

bioimageio/core/build_spec/build_model.py

@@ -323,15 +323,19 @@ def _get_deepimagej_config(export_folder, sample_inputs, sample_outputs, pixel_s
 
     if any(preproc is not None for preproc in preprocessing):
         assert len(preprocessing) == 1
-        preprocess_ij = [_get_deepimagej_macro(name, kwargs) for name, kwargs in preprocessing[0].items()]
+        preprocess_ij = [
+            _get_deepimagej_macro(name, kwargs, export_folder) for name, kwargs in preprocessing[0].items()
+        ]
         attachments = [preproc["kwargs"] for preproc in preprocess_ij]
     else:
         preprocess_ij = [{"spec": None}]
         attachments = None
 
     if any(postproc is not None for postproc in postprocessing):
         assert len(postprocessing) == 1
-        postprocess_ij = [_get_deepimagej_macro(name, kwargs) for name, kwargs in postprocessing[0].items()]
+        postprocess_ij = [
+            _get_deepimagej_macro(name, kwargs, export_folder) for name, kwargs in postprocessing[0].items()
+        ]
         if attachments is None:
             attachments = [postproc["kwargs"] for postproc in postprocess_ij]
         else:
@@ -609,7 +613,7 @@ def build_model(
     else:
         assert len(pixel_sizes) == n_inputs
         for pix_size, axes in zip(pixel_sizes, spatial_axes):
-            assert isinstance(pixel_sizes, dict)
+            assert isinstance(pix_size, dict)
             assert set(pix_size.keys()) == set(axes)
 
     #
@@ -730,17 +734,6 @@ def build_model(
         if tmp_source is not None:
             os.remove(tmp_source)
 
-    # breakpoint()
-    # debugging: for some reason this causes a validation error for the sample_input / output,
-    # although they are passed in the same format as test inputs / outputs:
-    # (Pdb) model.sample_inputs
-    # [PosixPath('/tmp/bioimageio_cache/extracted_packages/efae734f36ff8634977c9174f01c854c4e2cfc799bc92751a4558a0edd963da6/sample_input_0.tif')]
-    # (Pdb) model.sample_outputs
-    # [PosixPath('/tmp/bioimageio_cache/extracted_packages/efae734f36ff8634977c9174f01c854c4e2cfc799bc92751a4558a0edd963da6/sample_output_0.tif')]
-    # (Pdb) model.test_inputs
-    # [PosixPath('/tmp/bioimageio_cache/extracted_packages/efae734f36ff8634977c9174f01c854c4e2cfc799bc92751a4558a0edd963da6/test_input.npy')]
-    # (Pdb) model.test_outputs
-    # [PosixPath('/tmp/bioimageio_cache/extracted_packages/efae734f36ff8634977c9174f01c854c4e2cfc799bc92751a4558a0edd963da6/test_output.npy')]
     model = load_raw_resource_description(model_package)
     return model
 

tests/build_spec/test_build_spec.py

@@ -36,6 +36,14 @@ def _test_build_spec(
     dep_file = None if model_spec.dependencies is missing else resolve_source(model_spec.dependencies.file, root)
     authors = [{"name": auth.name, "affiliation": auth.affiliation} for auth in model_spec.authors]
     covers = resolve_source(model_spec.covers, root)
+    preprocessing = [
+        None if input_.preprocessing == missing else {preproc.name: preproc.kwargs for preproc in input_.preprocessing}
+        for input_ in model_spec.inputs
+    ]
+    postprocessing = [
+        None if output.postprocessing == missing else {preproc.name: preproc.kwargs for preproc in output.preprocessing}
+        for output in model_spec.outputs
+    ]
     kwargs = dict(
         source=model_source,
         model_kwargs=model_spec.kwargs,
@@ -53,6 +61,8 @@ def _test_build_spec(
         cite=cite,
         root=model_spec.root_path,
         weight_type=weight_type_,
+        preprocessing=preprocessing,
+        postprocessing=postprocessing,
         output_path=out_path,
         add_deepimagej_config=add_deepimagej_config,
     )
@@ -63,6 +73,8 @@ def _test_build_spec(
         kwargs["output_reference"] = ["input"]
         kwargs["output_scale"] = [[1.0, 1.0, 1.0, 1.0]]
         kwargs["output_offset"] = [[0.0, 0.0, 0.0, 0.0]]
+    if add_deepimagej_config:
+        kwargs["pixel_sizes"] = [{"x": 5.0, "y": 5.0}]
 
     build_model(**kwargs)
     assert out_path.exists()