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Rewrite to json from bson #3

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merged 7 commits into from
Apr 20, 2022
Merged

Rewrite to json from bson #3

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116c70e
Rewrite to json from bson
tomburke-rse Apr 6, 2022
04802ec
Do some DRY cleanup
tomburke-rse Apr 6, 2022
3648413
Add Type token as an argument
tomburke-rse Apr 11, 2022
8bf32b6
Extract list instantiation
gselzer Apr 18, 2022
b94719c
Replace NotImplementedException
gselzer Apr 20, 2022
693788a
Replace Types with Classes for TypeVariables
gselzer Apr 20, 2022
b658367
Ensure empty label sets don't throw exceptions
gselzer Apr 20, 2022
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2 changes: 1 addition & 1 deletion labeling.iml
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Expand Up @@ -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" />
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15 changes: 10 additions & 5 deletions pom.xml
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@@ -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>
Expand Down Expand Up @@ -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>
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326 changes: 129 additions & 197 deletions src/main/java/net/imglib2/labeling/DefaultLabelingIOService.java
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106 changes: 30 additions & 76 deletions src/main/java/net/imglib2/labeling/LabelingIOService.java
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Expand Up @@ -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
Expand All @@ -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;
Expand All @@ -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;

}
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