Merge remote-tracking branch 'upstream/main' into public-axes

Author: alanocallaghan

README.md

@@ -2,7 +2,7 @@
 
 Support for parsing the [BioImage Model Zoo spec](https://github.com/bioimage-io/spec-bioimage-io) in Java.
 
-With thanks to the @bioimage-io for all their work in creating this spec and the model zoo.
+With thanks to @bioimage-io for all their work in creating this spec and the model zoo.
 
 ## Purpose
 
@@ -12,7 +12,7 @@ It's separated out from QuPath's code in case it could be useful to anyone else.
 
 ## Dependencies
 
-The spec is implemented in a single Java file with 3 dependencies:
+The spec has 3 dependencies:
 
 * SnakeYAML
 * Gson
@@ -22,9 +22,9 @@ Gson might be removed as a dependency in the future.
 
 ## Compatibility
 
-The code here should be compatible with Java 11.
+The code here should be compatible with Java 17.
 
-It was written for the model spec v0.4.x, but attempts too also handle most yaml files written with the model spec v0.3.x.
+It was written for the model spec v0.4.x, and updated to handle v0.5.x models, but attempts to also handle most yaml files written with the model spec v0.3.x.
 
 ## Building
 
@@ -39,4 +39,4 @@ To test more, you can pass a base directory and the test code will search recurs
 gradlew test -Ptest.models=path/to/base/directory
 ```
 
-> Note: The testing isn't very extensive. Currently, it just checks the models can be parsed without exceptions.
+> Note: The testing isn't very extensive. Currently, it just checks the models can be parsed without exceptions.

build.gradle

@@ -19,7 +19,7 @@ repositories {
 
 description = 'Support for parsing the BioImage Model Zoo spec in Java'
 
-version = "0.2.0-SNAPSHOT"
+version = "0.2.0"
 
 dependencies {
     // These are included in QuPath distribution

src/main/java/qupath/bioimageio/spec/Model.java

@@ -426,13 +426,12 @@ private static Path findRdf(Path path, Collection<String> names) throws IOExcept
             }
         } else if (path.toAbsolutePath().toString().toLowerCase().endsWith(".zip")) {
             // Check zip file
-            try (var fs = FileSystems.newFileSystem(path, (ClassLoader) null)) {
-                for (var dir : fs.getRootDirectories()) {
-                    for (var name : MODEL_NAMES) {
-                        var p = dir.resolve(name);
-                        if (Files.exists(p))
-                            return p;
-                    }
+            var fs = FileSystems.newFileSystem(path, (ClassLoader) null);
+            for (var dir : fs.getRootDirectories()) {
+                for (var name : MODEL_NAMES) {
+                    var p = dir.resolve(name);
+                    if (Files.exists(p))
+                        return p;
                 }
             }
         }

src/main/java/qupath/bioimageio/spec/tensor/axes/Axes.java

@@ -73,7 +73,7 @@ public Axis[] deserialize(JsonElement jsonElement, Type type, JsonDeserializatio
                     axes[i] = switch (oj.get("type").getAsString()) {
                         case "time" -> new TimeAxes.TimeAxis(
                                 id, desc,
-                                TimeAxes.TimeUnit.valueOf(oj.get("unit").getAsString().toUpperCase()),
+                                TimeAxes.TimeUnit.getUnit(oj.get("unit").getAsString()),
                                 oj.get("scale").getAsDouble(),
                                 size
                         );

src/main/java/qupath/bioimageio/spec/tensor/axes/SpaceAxes.java

@@ -16,19 +16,19 @@
 
 package qupath.bioimageio.spec.tensor.axes;
 
+import java.util.List;
+
+import qupath.bioimageio.spec.tensor.BaseTensor;
 import qupath.bioimageio.spec.tensor.sizes.ReferencedSize;
 import qupath.bioimageio.spec.tensor.sizes.Size;
-import qupath.bioimageio.spec.tensor.BaseTensor;
-
-import java.util.List;
 
 /**
  * Axes relating to physical space.
  */
 public class SpaceAxes {
 
     /**
-     * Possible SI and imperial units for distance in physical space (some more likely to be used than others).
+     * Possible SI and imperial units for distance in physical space.
      */
     public enum SpaceUnit {
         ATTOMETER("attometer"),
@@ -61,22 +61,22 @@ public enum SpaceUnit {
 
         private final String unit;
 
-        SpaceUnit(String s) {
-            this.unit = s;
+        SpaceUnit(String unit) {
+            this.unit = unit;
         }
 
         /**
          * Get the SpaceUnit corresponding to a String value.
-         * @param unit The unit as a string
-         * @return The corresponding unit, or null if not found.
+         * @param unit the unit as a string
+         * @return the corresponding unit, or NO_UNIT if not found.
          */
         public static SpaceUnit getUnit(String unit) {
-            for (var su: SpaceUnit.values()) {
+            for (var su: values()) {
                 if (su.unit.equalsIgnoreCase(unit)) {
                     return su;
                 }
             }
-            return null;
+            return NO_UNIT;
         }
     }
 
@@ -90,7 +90,7 @@ public static class SpaceAxis extends AxisBase implements ScaledAxis {
         private final boolean concatenable = false;
 
         SpaceAxis(String id, String description, String unit, double scale, Size size) {
-            this(id, description, SpaceUnit.valueOf(unit.toUpperCase()), scale, size);
+            this(id, description, SpaceUnit.getUnit(unit), scale, size);
         }
 
         SpaceAxis(String id, String description, SpaceUnit unit, double scale, Size size) {

src/main/java/qupath/bioimageio/spec/tensor/axes/TimeAxes.java

@@ -88,32 +88,55 @@ public int getHalo() {
     }
 
     /**
-     * Possible SI units for time.
+     * Possible units for time.
      */
     public enum TimeUnit {
-        ATTOSECOND,
-        CENTISECOND,
-        DAY,
-        DECISECOND,
-        EXASECOND,
-        FEMTOSECOND,
-        GIGASECOND,
-        HECTOSECOND,
-        HOUR,
-        KILOSECOND,
-        MEGASECOND,
-        MICROSECOND,
-        MILLISECOND,
-        MINUTE,
-        NANOSECOND,
-        PETASECOND,
-        PICOSECOND,
-        SECOND,
-        TERASECOND,
-        YOCTOSECOND,
-        YOTTASECOND,
-        ZEPTOSECOND,
-        ZETTASECOND
+        ATTOSECOND("attosecond"),
+        CENTISECOND("centisecond"),
+        DAY("day"),
+        DECISECOND("decisecond"),
+        EXASECOND("exasecond"),
+        FEMTOSECOND("femtosecond"),
+        GIGASECOND("gigasecond"),
+        HECTOSECOND("hectosecond"),
+        HOUR("hour"),
+        KILOSECOND("kilosecond"),
+        MEGASECOND("megasecond"),
+        MICROSECOND("microsecond"),
+        MILLISECOND("millisecond"),
+        MINUTE("minute"),
+        NANOSECOND("nanosecond"),
+        PETASECOND("petasecond"),
+        PICOSECOND("picosecond"),
+        SECOND("second"),
+        TERASECOND("terasecond"),
+        YOCTOSECOND("yoctosecond"),
+        YOTTASECOND("yottasecond"),
+        ZEPTOSECOND("zeptosecond"),
+        ZETTASECOND("zettasecond"),
+        NO_UNIT("");
+
+        private final String unit;
+
+        TimeUnit(String unit) {
+            this.unit = unit;
+        }
+
+        /**
+         * Get the TimeUnit corresponding to a String value.
+         * @param unit the unit as a string
+         * @return the corresponding unit, or NO_UNIT if not found.
+         */
+        public static TimeUnit getUnit(String unit) {
+            for (var tu: values()) {
+                if (tu.unit.equalsIgnoreCase(unit)) {
+                    return tu;
+                }
+            }
+            return NO_UNIT;
+        }
     }
 
+
+
 }

src/test/java/qupath/bioimageio/spec/TestBioImageIoSpec.java

@@ -45,7 +45,7 @@ static Collection<Path> provideYamlPaths() throws IOException, URISyntaxExceptio
 		else if (Files.isDirectory(path)) {
 			try (var fstream = Files.walk(path, testDepth)) {
 				return fstream
-						.filter(TestBioImageIoSpec::containsModel)
+						.filter(p -> containsModel(p) || p.toString().endsWith(".zip"))
 						.collect(Collectors.toSet());
 			}
 		} else {