Tischi hackathon

.gitignore

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+**/.classpath
+**/.project
+**/.settings
+**/target
+.DS_Store
+.classpath
+.project
+.settings
+.factorypath
+.idea
+target
+*.iml
+*.class
+*~
+*.orig
+# For Fiji #
+*.jar

pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>ome</groupId>
+    <artifactId>ome-ngff-java</artifactId>
+    <version>0.0.0-SNAPSHOT</version>
+
+    <url>https://github.com/ome/ome-ngff-java</url>
+    <name>OME NGFF Java</name>
+    <description>Java code for OME NGFF metadata</description>
+    <inceptionYear>2022</inceptionYear>
+    <organization>
+        <name>Open Microscopy Environment</name>
+        <url>http://www.openmicroscopy.org/</url>
+    </organization>
+    <issueManagement>
+        <system>Trac</system>
+        <url>https://trac.openmicroscopy.org/ome</url>
+    </issueManagement>    
+    <licenses>
+        <license>
+             <!-- TODO -->
+            <name>???</name>
+            <distribution>repo</distribution>
+        </license>
+    </licenses>
+    <developers>
+        <!-- TODO -->
+        <developer>
+            <id>tischi</id>
+            <name>Christian Tischer</name>
+            <roles>
+                <role>lead</role>
+                <role>developer</role>
+                <role>debugger</role>
+                <role>reviewer</role>
+                <role>support</role>
+                <role>maintainer</role>
+            </roles>
+        </developer>
+    </developers>
+    <contributors>
+    </contributors>
+    <mailingLists>
+        <!-- TODO -->
+    </mailingLists>
+    <properties>
+        <!-- TODO -->
+    </properties>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.22.0</version>
+                <configuration>
+                    <argLine>-Xmx4024m</argLine>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <repositories>
+      <repository>
+        <id>central</id>
+        <name>Central Repository</name>
+        <url>https://repo.maven.apache.org/maven2</url>
+      </repository>
+      <repository>
+        <id>ome</id>
+        <name>OME Artifactory</name>
+        <url>https://artifacts.openmicroscopy.org/artifactory/maven/</url>
+      </repository>
+    </repositories>
+
+    <dependencies>
+        <dependency>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
+            <version>10.0.1</version>
+        </dependency>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>2.9.1</version>
+        </dependency>
+    </dependencies>
+</project>

src/main/java/ome/ngff/MultiscalesV04.java

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+package ome.ngff;
+
+import com.google.common.collect.Lists;
+import com.google.gson.JsonElement;
+
+import java.util.Arrays;
+import java.util.List;
+
+public class MultiscalesV04
+{
+    // key in json for multiscales
+    public static final String MULTI_SCALE_KEY = "multiscales";
+
+    // Serialisation
+    private String version;
+    private String name;
+    private String type;
+    private Axis[] axes; // from v0.4+ within JSON
+    private Dataset[] datasets;
+    private CoordinateTransformations[] coordinateTransformations; // from v0.4+ within JSON
+
+    // Runtime
+
+    // Simply contains the {@codeAxes[] axes}
+    // but in reversed order to accommodate
+    // the Java array ordering of the image data.
+    private List< Axis > axisList;
+    private int numDimensions;
+
+    public MultiscalesV04() {
+    }
+
+    public static class Dataset {
+        public String path;
+        public CoordinateTransformations[] coordinateTransformations;
+    }
+
+    public static class CoordinateTransformations {
+        public String type;
+        public double[] scale;
+        public double[] translation;
+        public String path;
+    }
+
+    public static class Axis
+    {
+        public static final String CHANNEL_TYPE = "channel";
+        public static final String TIME_TYPE = "time";
+        public static final String SPATIAL_TYPE = "space";
+
+        public String name;
+        public String type;
+        public String unit;
+    }
+
+    public void init()
+    {
+        axisList = Lists.reverse( Arrays.asList( axes ) );
+        numDimensions = axisList.size();
+    }
+
+    // TODO Can this be done with a JSONAdapter ?
+    public void applyVersionFixes( JsonElement multiscales )
+    {
+        String version = multiscales.getAsJsonObject().get("version").getAsString();
+        if ( version.equals("0.3") ) {
+            JsonElement axes = multiscales.getAsJsonObject().get("axes");
+            // FIXME
+            //   - populate Axes[]
+            //   - populate coordinateTransformations[]
+            throw new RuntimeException("Parsing version 0.3 not yet implemented.");
+        } else if ( version.equals("0.4") ) {
+            // This should just work automatically
+        } else {
+            JsonElement axes = multiscales.getAsJsonObject().get("axes");
+            // FIXME
+            //   - populate Axes[]
+            //   - populate coordinateTransformations[]
+            throw new RuntimeException("Parsing version "+ version + " is not yet implemented.");
+        }
+    }
+
+    public int getChannelAxisIndex()
+    {
+        for ( int d = 0; d < numDimensions; d++ )
+            if ( axisList.get( d ).type.equals( Axis.CHANNEL_TYPE ) )
+                return d;
+        return -1;
+    }
+
+    public int getTimePointAxisIndex()
+    {
+        for ( int d = 0; d < numDimensions; d++ )
+            if ( axisList.get( d ).type.equals( Axis.TIME_TYPE ) )
+                return d;
+        return -1;
+    }
+
+    public int getSpatialAxisIndex( String axisName )
+    {
+        for ( int d = 0; d < numDimensions; d++ )
+            if ( axisList.get( d ).type.equals( Axis.SPATIAL_TYPE )
+                 && axisList.get( d ).name.equals( axisName ) )
+                return d;
+        return -1;
+    }
+
+    public List< Axis > getAxes()
+    {
+        return axisList;
+    }
+
+    public CoordinateTransformations[] getCoordinateTransformations()
+    {
+        return coordinateTransformations;
+    }
+
+    public Dataset[] getDatasets()
+    {
+        return datasets;
+    }
+
+    public int numDimensions()
+    {
+        return numDimensions;
+    }
+}