adapt to new bmz format

bioimage-io · Nov 25, 2024 · 689ad55 · 689ad55
1 parent 59a4ccb
commit 689ad55
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Showing 7 changed files with 66 additions and 5 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/AxisV05.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/AxisV05.java
@@ -61,7 +61,7 @@ else if (this.id == null && this.type.equals("space"))
 				    "Current configuration: type='%s', id=%s", 
 				    type, "null"
 				));
-		else if (this.id == null && this.type.equals("batch"))
+		else if ((this.id == null || this.id != "b") && this.type.equals("batch"))
 			this.abreviation = "b";
 		else if (this.id != null && id.equals("channel"))
 			this.abreviation = "c";

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV04.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV04.java
@@ -91,6 +91,10 @@ protected TensorSpecV04(Map<String, Object> tensorSpecMap, boolean input)
             preprocessing = new ArrayList<TransformSpec>(preprocessingTensors.size());
             for (Object elem : preprocessingTensors)
             {
+            	// TODO fix
+            	if (((Map<String, Object>) elem).get("id") != null 
+            			&& ((Map<String, Object>) elem).get("id").equals("ensure_dtype"))
+            		continue;
                 preprocessing.add(TransformSpec.build((Map<String, Object>) elem));
             }
         }
@@ -105,6 +109,10 @@ protected TensorSpecV04(Map<String, Object> tensorSpecMap, boolean input)
             postprocessing = new ArrayList<TransformSpec>(postprocessingTensors.size());
             for (Object elem : postprocessingTensors)
             {
+            	// TODO fix
+            	if (((Map<String, Object>) elem).get("id") != null 
+            			&& ((Map<String, Object>) elem).get("id").equals("ensure_dtype"))
+            		continue;
                 postprocessing.add(TransformSpec.build((Map<String, Object>) elem));
             }
         }

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV05.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV05.java
@@ -94,6 +94,10 @@ protected TensorSpecV05(Map<String, Object> tensorSpecMap, boolean input)
             preprocessing = new ArrayList<TransformSpec>(preprocessingTensors.size());
             for (Object elem : preprocessingTensors)
             {
+            	// TODO fix
+            	if (((Map<String, Object>) elem).get("id") != null 
+            			&& ((Map<String, Object>) elem).get("id").equals("ensure_dtype"))
+            		continue;
                 preprocessing.add(TransformSpec.build((Map<String, Object>) elem));
             }
         }
@@ -108,6 +112,10 @@ protected TensorSpecV05(Map<String, Object> tensorSpecMap, boolean input)
             postprocessing = new ArrayList<TransformSpec>(postprocessingTensors.size());
             for (Object elem : postprocessingTensors)
             {
+            	// TODO fix
+            	if (((Map<String, Object>) elem).get("id") != null 
+            			&& ((Map<String, Object>) elem).get("id").equals("ensure_dtype"))
+            		continue;
                 postprocessing.add(TransformSpec.build((Map<String, Object>) elem));
             }
         }

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/TransformSpec.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/TransformSpec.java
@@ -68,7 +68,11 @@ public Map<String, Object> getSpecMap()
      */
     public String getName()
     {
-        return specMap == null ? null : (String) specMap.get("name");
+    	if (specMap == null)
+    		return null;
+    	if (specMap.get("name") != null)
+    		return (String) specMap.get("name");
+    	return (String) specMap.get("id");
     }
 
     /**

diff --git a/src/main/java/io/bioimage/modelrunner/model/processing/Processing.java b/src/main/java/io/bioimage/modelrunner/model/processing/Processing.java
@@ -73,6 +73,9 @@ private void buildPreprocessing() throws IllegalArgumentException, RuntimeExcept
 			List<TransformSpec> preprocessing = tt.getPreprocessing();
 			List<TransformationInstance> list = new ArrayList<TransformationInstance>();
 			for (TransformSpec transformation : preprocessing) {
+				// TODO fix
+				if (transformation.getName() == null)
+					continue;
 				list.add(TransformationInstance.create(transformation));
 			}
 			preMap.put(tt.getName(), list);
@@ -85,6 +88,9 @@ private void buildPostprocessing() throws IllegalArgumentException, RuntimeExcep
 			List<TransformSpec> preprocessing = tt.getPostprocessing();
 			List<TransformationInstance> list = new ArrayList<TransformationInstance>();
 			for (TransformSpec transformation : preprocessing) {
+				// TODO fix
+				if (transformation.getName() == null)
+					continue;
 				list.add(TransformationInstance.create(transformation));
 			}
 			postMap.put(tt.getName(), list);

diff --git a/src/main/java/io/bioimage/modelrunner/numpy/DecodeNumpy.java b/src/main/java/io/bioimage/modelrunner/numpy/DecodeNumpy.java
@@ -140,9 +140,9 @@ public class DecodeNumpy {
     /**
      * PAttern that matches the metadata description of a numpy file
      */
-    public static final Pattern HEADER_PATTERN =
-            Pattern.compile("\\{'descr': '(.+)', 'fortran_order': (True|False), 'shape': \\((.*)\\),");
-	
+    public static final Pattern HEADER_PATTERN = 
+            Pattern.compile("\\{'descr': '(.+)', 'fortran_order': (True|False), 'shape': \\((.+?)\\)(?:\\s*,\\s*|\\s*)\\}");
+    
     /**
      * Main method to test the ImgLib2 creation
      * @param <T>

diff --git a/src/main/java/io/bioimage/modelrunner/transformations/EnsureDtypeTransformation.java b/src/main/java/io/bioimage/modelrunner/transformations/EnsureDtypeTransformation.java
@@ -0,0 +1,35 @@
+/*-
+ * #%L
+ * Use deep learning frameworks from Java in an agnostic and isolated way.
+ * %%
+ * Copyright (C) 2022 - 2024 Institut Pasteur and BioImage.IO developers.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+package io.bioimage.modelrunner.transformations;
+
+
+/**
+ * TODO do it
+ */
+public class EnsureDtypeTransformation extends AbstractTensorPixelTransformation
+{
+
+	private static String name = "ensure_dtype";
+
+	public EnsureDtypeTransformation()
+	{
+		super(name);
+	}
+}