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ppouchinppouchin
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Merge pull request #1 from GReD-Clermont/fix-crop
Fix crop and improve library
2 parents d752973 + 1b271d7 commit 269bb5a

16 files changed

Lines changed: 2818 additions & 3324 deletions

‎.omeroci/test-data‎

Lines changed: 26 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -39,12 +39,32 @@ omero obj new ProjectDatasetLink parent=$PROJECT1 child=$DATASET2
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omero obj new ProjectDatasetLink parent=$PROJECT2 child=$DATASET3
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42-
touch "$WORKDIR/8bit-unsigned&pixelType=uint8&sizeZ=3&sizeC=5&sizeT=7&sizeX=512&sizeY=512.fake"
43-
IMAGE1=$(omero import --output=ids "$WORKDIR/8bit-unsigned&pixelType=uint8&sizeZ=3&sizeC=5&sizeT=7&sizeX=512&sizeY=512.fake" -T Dataset:id:1)
44-
IMAGE2=$(omero import --output=ids "$WORKDIR/8bit-unsigned&pixelType=uint8&sizeZ=3&sizeC=5&sizeT=7&sizeX=512&sizeY=512.fake" -T Dataset:id:1)
45-
touch "$WORKDIR/8bit-unsigned&pixelType=uint8&sizeZ=2&sizeC=5&sizeT=7&sizeX=512&sizeY=512.fake"
46-
IMAGE3=$(omero import --output=ids "$WORKDIR/8bit-unsigned&pixelType=uint8&sizeZ=2&sizeC=5&sizeT=7&sizeX=512&sizeY=512.fake" -T Dataset:id:1)
47-
IMAGE4=$(omero import --output=ids "$WORKDIR/8bit-unsigned&pixelType=uint8&sizeZ=3&sizeC=5&sizeT=7&sizeX=512&sizeY=512.fake" -T Dataset:id:3)
42+
touch "$WORKDIR/image1.fake"
43+
echo "pixelType=uint8" >> $WORKDIR/image1.fake.ini
44+
echo "sizeX=512" >> $WORKDIR/image1.fake.ini
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echo "sizeY=512" >> $WORKDIR/image1.fake.ini
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echo "sizeZ=3" >> $WORKDIR/image1.fake.ini
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echo "sizeC=5" >> $WORKDIR/image1.fake.ini
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echo "sizeT=7" >> $WORKDIR/image1.fake.ini
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echo "physicalSizeX=0.5µm" >> $WORKDIR/image1.fake.ini
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echo "physicalSizeY=0.5µm" >> $WORKDIR/image1.fake.ini
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echo "physicalSizeZ=1µm" >> $WORKDIR/image1.fake.ini
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53+
touch "$WORKDIR/image2.fake"
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echo "pixelType=uint8" >> $WORKDIR/image2.fake.ini
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echo "sizeX=512" >> $WORKDIR/image2.fake.ini
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echo "sizeY=512" >> $WORKDIR/image2.fake.ini
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echo "sizeZ=2" >> $WORKDIR/image2.fake.ini
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echo "sizeC=5" >> $WORKDIR/image2.fake.ini
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echo "sizeT=7" >> $WORKDIR/image2.fake.ini
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echo "physicalSizeX=1µm" >> $WORKDIR/image2.fake.ini
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echo "physicalSizeY=1µm" >> $WORKDIR/image2.fake.ini
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echo "physicalSizeZ=2µm" >> $WORKDIR/image2.fake.ini
63+
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IMAGE1=$(omero import --output=ids "$WORKDIR/image1.fake" -T Dataset:id:1)
65+
IMAGE2=$(omero import --output=ids "$WORKDIR/image1.fake" -T Dataset:id:1)
66+
IMAGE3=$(omero import --output=ids "$WORKDIR/image2.fake" -T Dataset:id:1)
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IMAGE4=$(omero import --output=ids "$WORKDIR/image1.fake" -T Dataset:id:3)
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TAG1=$(omero obj new TagAnnotation textValue=tag1 description=description)
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TAG2=$(omero obj new TagAnnotation textValue=tag2)

‎.travis.yml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,7 @@ before_install:
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- git clone --recurse-submodules git://github.com/openmicroscopy/omero-test-infra .omero
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- export DOCKER_ARGS="-v $HOME/.m2:/root/.m2 -v $(pwd)/target:/src/target"
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- cp .travis.settings.xml $HOME/.m2/settings.xml
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- echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
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after_success:
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- bash <(curl -s https://codecov.io/bash)

‎pom.xml‎

Lines changed: 192 additions & 134 deletions
Original file line numberDiff line numberDiff line change
@@ -1,140 +1,198 @@
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>fr.igred</groupId>
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<artifactId>simple-omero-client</artifactId>
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<packaging>jar</packaging>
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<version>5.6.1</version>
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<name>omero</name>
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>fr.igred</groupId>
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<artifactId>simple-omero-client</artifactId>
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<packaging>jar</packaging>
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<version>5.6.2</version>
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<name>omero</name>
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<dependencies>
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<!-- https://mvnrepository.com/artifact/junit/junit -->
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>4.13</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.openmicroscopy</groupId>
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<artifactId>omero-gateway</artifactId>
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<version>5.6.5</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/ome/pom-bio-formats -->
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<dependency>
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<groupId>ome</groupId>
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<artifactId>pom-bio-formats</artifactId>
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<version>6.6.0</version>
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<type>pom</type>
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</dependency>
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<dependency>
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<groupId>net.imagej</groupId>
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<artifactId>ij</artifactId>
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<version>1.51n</version>
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<optional>true</optional>
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</dependency>
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</dependencies>
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<dependencies>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>4.13</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.openmicroscopy</groupId>
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<artifactId>omero-gateway</artifactId>
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<version>5.6.5</version>
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</dependency>
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<dependency>
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<groupId>org.openmicroscopy</groupId>
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<artifactId>omero-blitz</artifactId>
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<version>5.5.8</version>
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<exclusions>
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<exclusion>
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<groupId>org.springframework</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.springframework.security</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.pdfbox</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.postgresql</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.hibernate</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>com.codahale.metrics</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>org.openmicroscopy</groupId>
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<artifactId>ome-common</artifactId>
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<version>6.0.6</version>
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</dependency>
66+
<dependency>
67+
<groupId>ome</groupId>
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<artifactId>formats-api</artifactId>
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<version>6.6.0</version>
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</dependency>
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<dependency>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>1.4</version>
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</dependency>
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<dependency>
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<groupId>ome</groupId>
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<artifactId>bio-formats_plugins</artifactId>
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<version>6.6.0</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>net.imagej</groupId>
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<artifactId>ij</artifactId>
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<version>1.51n</version>
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<optional>true</optional>
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</dependency>
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</dependencies>
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<repositories>
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<repository>
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<id>ome.maven</id>
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<url>https://artifacts.openmicroscopy.org/artifactory/maven/</url>
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</repository>
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<repository>
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<id>imagej.public</id>
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<url>http://maven.imagej.net/content/groups/public</url>
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</repository>
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</repositories>
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<repositories>
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<repository>
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<id>ome.maven</id>
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<url>https://artifacts.openmicroscopy.org/artifactory/maven/</url>
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</repository>
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<repository>
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<id>imagej.public</id>
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<url>http://maven.imagej.net/content/groups/public</url>
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</repository>
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</repositories>
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<build>
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<plugins>
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<plugin>
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<artifactId>maven-assembly-plugin</artifactId>
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<executions>
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<execution>
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<phase>package</phase>
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<goals>
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<goal>single</goal>
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</goals>
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</execution>
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</executions>
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<configuration>
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<descriptorRefs>
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<descriptorRef>jar-with-dependencies</descriptorRef>
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</descriptorRefs>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.jacoco</groupId>
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<artifactId>jacoco-maven-plugin</artifactId>
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<version>0.8.6</version>
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<executions>
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<execution>
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<goals>
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<goal>prepare-agent</goal>
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</goals>
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</execution>
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<execution>
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<id>report</id>
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<phase>test</phase>
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<goals>
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<goal>report</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-site-plugin</artifactId>
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<version>3.7.1</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-project-info-reports-plugin</artifactId>
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<version>3.0.0</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-source-plugin</artifactId>
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<executions>
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<execution>
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<id>attach-sources</id>
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<goals>
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<goal>jar</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-javadoc-plugin</artifactId>
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<executions>
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<execution>
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<id>attach-javadocs</id>
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<goals>
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<goal>jar</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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<build>
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<plugins>
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<plugin>
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<artifactId>maven-assembly-plugin</artifactId>
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<executions>
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<execution>
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<phase>package</phase>
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<goals>
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<goal>single</goal>
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</goals>
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</execution>
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</executions>
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<configuration>
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<descriptorRefs>
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<descriptorRef>jar-with-dependencies</descriptorRef>
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</descriptorRefs>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.jacoco</groupId>
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<artifactId>jacoco-maven-plugin</artifactId>
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<version>0.8.6</version>
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<executions>
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<execution>
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<goals>
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<goal>prepare-agent</goal>
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</goals>
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</execution>
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<execution>
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<id>report</id>
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<phase>test</phase>
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<goals>
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<goal>report</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-site-plugin</artifactId>
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<version>3.7.1</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-project-info-reports-plugin</artifactId>
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<version>3.0.0</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-source-plugin</artifactId>
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<version>3.2.1</version>
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<executions>
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<execution>
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<id>attach-sources</id>
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<goals>
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<goal>jar</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-javadoc-plugin</artifactId>
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<version>3.2.0</version>
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<executions>
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<execution>
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<id>attach-javadocs</id>
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<goals>
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<goal>jar</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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<reporting>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-javadoc-plugin</artifactId>
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<version>3.2.0</version>
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<configuration></configuration>
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</plugin>
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</plugins>
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</reporting>
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<distributionManagement>
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<repository>
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<id>github</id>
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<name>GitHub GReD-Clermont Apache Maven Packages</name>
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<url>https://maven.pkg.github.com/GReD-Clermont/simple-omero-client</url>
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</repository>
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</distributionManagement>
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<reporting>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-javadoc-plugin</artifactId>
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<version>3.2.0</version>
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</plugin>
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</plugins>
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</reporting>
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<distributionManagement>
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<repository>
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<id>github</id>
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<name>GitHub GReD-Clermont Apache Maven Packages</name>
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<url>https://maven.pkg.github.com/GReD-Clermont/simple-omero-client</url>
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</repository>
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</distributionManagement>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<maven.compiler.source>8</maven.compiler.source>
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<maven.compiler.target>8</maven.compiler.target>
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</properties>
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</project>

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