Merge pull request #3 from tomburke-rse/switch-bson-with-json

Rewrite to json from bson

labeling.iml

@@ -19,7 +19,7 @@
     <orderEntry type="library" name="Maven: com.googlecode.efficient-java-matrix-library:ejml:0.24" level="project" />
     <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
     <orderEntry type="library" name="Maven: net.sf.trove4j:trove4j:3.0.3" level="project" />
-    <orderEntry type="library" name="Maven: org.mongodb:bson:4.2.3" level="project" />
+    <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.8.6" level="project" />
     <orderEntry type="library" name="Maven: io.scif:scifio:0.41.1" level="project" />
     <orderEntry type="library" name="Maven: io.scif:scifio-jai-imageio:1.1.1" level="project" />
     <orderEntry type="library" name="Maven: net.imagej:imagej-common:0.34.0" level="project" />

pom.xml

@@ -1,12 +1,13 @@
 <?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 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>org.scijava</groupId>
         <artifactId>pom-scijava</artifactId>
         <version>30.0.0</version>
-        <relativePath />
+        <relativePath/>
     </parent>
 
     <groupId>net.imglib2</groupId>
@@ -110,14 +111,18 @@
 
         <!-- Other dependencies -->
         <dependency>
-            <groupId>org.mongodb</groupId>
-            <artifactId>bson</artifactId>
-            <version>4.2.3</version>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>${gson.version}</version>
         </dependency>
         <dependency>
             <groupId>io.scif</groupId>
             <artifactId>scifio</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.scijava</groupId>
+            <artifactId>scijava-common</artifactId>
+        </dependency>
 
         <!-- Test dependencies -->
         <dependency>

src/main/java/net/imglib2/labeling/LabelingIOService.java

@@ -11,13 +11,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -34,11 +34,9 @@
 package net.imglib2.labeling;
 
 import net.imagej.ImageJService;
-import net.imglib2.labeling.codecs.LabelingMappingCodec;
 import net.imglib2.labeling.data.Container;
 import net.imglib2.roi.labeling.ImgLabeling;
 import net.imglib2.type.numeric.IntegerType;
-import org.bson.codecs.Codec;
 
 import java.io.IOException;
 import java.util.function.LongFunction;
@@ -48,111 +46,67 @@
  * A service to easily access a load/save functionality for BSON-based labeling data files.
  * Basic support for primitive types and BSON standard types is already included. For non-primitive types,
  * a codec must be set and the class must be given as an argument to the methods.
- * Examples for Codecs can be found at {@link LabelingMappingCodec}.
  *
  * @author Tom Burke
  */
 public interface LabelingIOService extends ImageJService {
 
-    <T, I extends IntegerType<I>> ImgLabeling<T,I> load(String file) throws IOException;
-
-    <T, I extends IntegerType<I>> ImgLabeling<T,I> load(String file, Class<T> clazz, Codec<T>... codecs) throws IOException;
-
-    <T, I extends IntegerType<I>> void save(ImgLabeling<T,I> imgLabeling, String file) throws IOException;
-
-    <T, I extends IntegerType<I>> void save(ImgLabeling<T,I> imgLabeling, String file, Class<T> clazz, Codec<T>... codecs) throws IOException;
+    <T, I extends IntegerType<I>> ImgLabeling<T, I> load(String file, Class<T> labelType, Class<I> backingType) throws IOException;
 
+    <T, I extends IntegerType<I>> void save(ImgLabeling<T, I> imgLabeling, String file) throws IOException;
 
     /**
      * Load a labeling container from the given file path as string.
      * The file path must point to the bson file containing the labeling data.
      *
-     * @param file   The path to the file
-     * @param codecs One or more codecs necessary to convert the data to clazz.
-     * @param metadataClazz the metadata class
-     * @param <T>    the label value
-     * @param <I>    IntegerType for the pixel value
-     * @param <S>    Class of the meta data
-     * @throws IOException on file read fail
+     * @param file          The path to the file
+     * @param metadataType the metadata class
+     * @param <T>           the label value
+     * @param <I>           IntegerType for the pixel value
+     * @param <S>           Class of the meta data
      * @return a container object holding the ImgLabeling (as well as an optional source mapping)
-     */
-    <S, T, I extends IntegerType<I>> Container<S, T, I> loadWithMetadata(String file, Class<S> metadataClazz, Codec<?>... codecs) throws IOException;
-
-
-    /**
-     * Load a labeling container from the given file path as string.
-     * The file path must point to the bson file containing the labeling data.
-     *
-     * @param file   The path to the file
-     * @param clazz  The class to convert the contains of the file to
-     * @param metadataClazz the metadata class
-     * @param codecs One or more codecs necessary to convert the data to clazz.
-     * @param <T>    the label value
-     * @param <I>    IntegerType for the pixel value
-     * @param <S>    Class of the meta data
      * @throws IOException on file read fail
-     * @return a container object holding the ImgLabeling (as well as an optional source mapping)
      */
-    <S, T, I extends IntegerType<I>> Container<S, T, I> loadWithMetadata(String file, Class<T> clazz, Class<S> metadataClazz, Codec<?>... codecs) throws IOException;
+    <S, T, I extends IntegerType<I>> Container<S, T, I> loadWithMetadata(String file, Class<S> metadataType, Class<T> labelType, Class<I> backingType) throws IOException;
 
     /**
      * Load a labeling container from the given file path as string.
      * The file path must point to the bson file containing the labeling data.
      *
-     * @param file      The path to the file
-     * @param idToLabel a function transforming the label of type T into something else
+     * @param file          The path to the file
+     * @param idToLabel     a function transforming the label of type T into something else
      * @param metadataClazz the metadata class
-     * @param codecs One or more codecs necessary to convert the data to clazz.
-     * @param <T>       the label value
-     * @param <I>       IntegerType for the pixel value
-     * @param <S>    Class of the meta data
-     * @throws IOException on file read fail
+     * @param <T>           the label value
+     * @param <I>           IntegerType for the pixel value
+     * @param <S>           Class of the meta data
      * @return a container object holding the ImgLabeling (as well as an optional source mapping)
+     * @throws IOException on file read fail
      */
-    <S, T, I extends IntegerType<I>> Container<S, T, I> loadWithMetadata(String file, LongFunction<T> idToLabel, Class<S> metadataClazz, Codec<?>... codecs) throws IOException;
-
-    /**
-     * Save an ImgLabelingContainer in the file-path, transforming it into a bson file and an image.
-     * The path must contain the filename (ending does not matter).
-     *
-     * @param codecs               one or more codecs to convert clazz into something bsonifyable
-     * @param container            the container with the ImgLabeling and a metadata object
-     * @param file                 the path pointing to the file, including the filename
-     * @param metadataClazz        the metadata class
-     * @param <T>                  the label value
-     * @param <I>                  IntegerType for the pixel value
-     * @param <S>                  Class of the meta data
-     */
-    <S, T, I extends IntegerType<I>> void saveWithMetaData(Container<S, T, I> container, String file, Class<S> metadataClazz, Codec<?>... codecs);
+    <S, T, I extends IntegerType<I>> Container<S, T, I> loadWithMetadata(String file, LongFunction<T> idToLabel, Class<S> metadataClazz) throws IOException;
 
     /**
      * Save an ImgLabelingContainer in the file-path, transforming it into a bson file and an image.
      * The path must contain the filename (ending does not matter).
      *
-     * @param clazz                the class of the type T that is contained in the labeling
-     * @param codecs               one or more codecs to convert clazz into something bsonifyable
-     * @param container            the container with the ImgLabeling and a metadata object
-     * @param file                 the path pointing to the file, including the filename
-     * @param metadataClazz        the metadata class
-     * @param <T>                  the label value
-     * @param <I>                  IntegerType for the pixel value
-     * @param <S>                  Class of the meta data
+     * @param imgLabeling the imglabeling object that needs to be serialized
+     * @param file        the path pointing to the file, including the filename
+     * @param <T>         the label value
+     * @param <I>         IntegerType for the pixel value
+     * @param <S>         Class of the meta data
      */
-   <S, T, I extends IntegerType<I>> void saveWithMetaData(Container<S, T, I> container, String file, Class<T> clazz, Class<S> metadataClazz, Codec<?>... codecs);
+    <S, T, I extends IntegerType<I>> void saveWithMetaData(ImgLabeling<T, I> imgLabeling, String file, S metadata) throws IOException;
 
     /**
      * Save an ImgLabelingContainer in the file-path, transforming it into a bson file and an image.
      * The path must contain the filename (ending does not matter).
      *
-     * @param labelToId            a function to convert the type T to a long value.
-     * @param container            the container with the ImgLabeling and a metadata object
-     * @param codecs               one or more codecs to convert clazz into something bsonifyable
-     * @param file                 the path pointing to the file, including the filename
-     * @param metadataClazz        the metadata class
-     * @param <T>                  the label value
-     * @param <I>                  IntegerType for the pixel value
-     * @param <S>                  Class of the meta data
+     * @param imgLabeling the imglabeling object that needs to be serialized
+     * @param labelToId   a function to convert the type T to a long value.
+     * @param file        the path pointing to the file, including the filename
+     * @param <T>         the label value
+     * @param <I>         IntegerType for the pixel value
+     * @param <S>         Class of the meta data
      */
-    <S, T, I extends IntegerType<I>> void saveWithMetaData(Container<S, T, I> container, String file, ToLongFunction<T> labelToId, Class<S> metadataClazz, Codec<?>... codecs);
+    <S, T, I extends IntegerType<I>> void saveWithMetaData(ImgLabeling<T, I> imgLabeling, String file, ToLongFunction<T> labelToId, S metadata) throws IOException;
 
 }