Fix javadoc

README.md

@@ -1,5 +1,3 @@
-[![Java CI with Maven](https://github.com/Labelings/Labeling/actions/workflows/maven.yml/badge.svg)](https://github.com/Labelings/Labeling/actions/workflows/maven.yml)
-
 [![](https://github.com/Labelings/Labeling/actions/workflows/build-main.yml/badge.svg)](https://github.com/Labelings/Labeling/actions/workflows/build-main.yml)
 
 # Labeling

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

@@ -69,8 +69,11 @@ public interface LabelingIOService extends ImageJService {
      *
      * @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
      * @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;
@@ -82,9 +85,12 @@ public interface LabelingIOService extends ImageJService {
      *
      * @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;
@@ -94,9 +100,13 @@ public interface LabelingIOService extends ImageJService {
      * 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 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
      * @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, LongFunction<T> idToLabel, Class<S> metadataClazz, Codec<?>... codecs) throws IOException;
@@ -108,8 +118,10 @@ public interface LabelingIOService extends ImageJService {
      * @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);
 
@@ -121,8 +133,10 @@ public interface LabelingIOService extends ImageJService {
      * @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<T> clazz, Class<S> metadataClazz, Codec<?>... codecs);
 
@@ -132,9 +146,12 @@ public interface LabelingIOService extends ImageJService {
      *
      * @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
      */
     <S, T, I extends IntegerType<I>> void saveWithMetaData(Container<S, T, I> container, String file, ToLongFunction<T> labelToId, Class<S> metadataClazz, Codec<?>... codecs);
 

src/main/java/net/imglib2/labeling/codecs/ImgLabelingCodec.java

@@ -384,6 +384,7 @@ public Builder<T, I> setLabelToId(final ToLongFunction<T> labelToId) {
         /**
          *
          * @param file the fully qualified path to the file
+         * @return a Builder for a LabelingMappingCodec
          */
         public Builder<T, I> setFile(Path file) {
             this.file = file;
@@ -392,7 +393,8 @@ public Builder<T, I> setFile(Path file) {
 
         /**
          * Set the datasetIO Service to use. Can be accessed through the current context.
-         * @param datasetIOService
+         * @param datasetIOService  a scijava dataetIOService gotten through the context
+         * @return a Builder for a LabelingMappingCodec
          */
         public Builder<T, I> setDatasetIOService(DatasetIOService datasetIOService) {
             this.datasetIOService = datasetIOService;

src/main/java/net/imglib2/labeling/codecs/LabelingMappingCodec.java

@@ -388,6 +388,7 @@ public Builder<S, T, I> setLabelToId(final ToLongFunction<T> labelToId) {
         /**
          *
          * @param file the fully qualified path to the file
+         * @return a Builder for a LabelingMappingCodec
          */
         public Builder<S, T, I> setFile(Path file) {
             this.file = file;
@@ -396,7 +397,8 @@ public Builder<S, T, I> setFile(Path file) {
 
         /**
          * Set the datasetIO Service to use. Can be accessed through the current context.
-         * @param datasetIOService
+         * @param datasetIOService  the datasetIO Service to use
+         * @return a Builder for a LabelingMappingCodec
          */
         public Builder<S, T, I> setDatasetIOService(DatasetIOService datasetIOService) {
             this.datasetIOService = datasetIOService;
@@ -405,8 +407,8 @@ public Builder<S, T, I> setDatasetIOService(DatasetIOService datasetIOService) {
 
         /**
          * the class of the metadata that is contained in the file. also needs a codec to decode
-         * @param metadataClazz
-         * @return
+         * @param metadataClazz     the metadata class to use
+         * @return a Builder for a LabelingMappingCodec
          */
         public Builder<S, T, I> setMetadataClazz(Class<S> metadataClazz) {
             this.metadataClazz = metadataClazz;

src/main/java/net/imglib2/labeling/utils/LabelingUtil.java

@@ -55,6 +55,7 @@ public class LabelingUtil {
     public static final String TIF_ENDING = ".tif";
 
     /**
+     * @param context the scijava context used in the project
      * @param filename  the filename of the Img to save
      * @param rai   the img
      * @param <T>   the pixel value