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Merge branch 'master' into release
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‎.gitignore‎

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sandbox/
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**/target/
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**/tmp/
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/.bsp/

‎.travis.yml‎

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language: scala
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scala:
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- 2.12.10
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- 2.13.1
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- 2.12.13
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- 2.13.4
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jdk:
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- openjdk8
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- oraclejdk11
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- openjdk11
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script:

‎Changes.md‎

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ij-plugins Toolkit Changelog
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============================
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Version 2.3.0
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-------------
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This release contains mostly change to API:
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* Root package renamed from `net.sf.ij_plugins` to `ij_plugins.toolkit` [#14]
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Version 2.2.0
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-------------
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### API Changes
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* Remove duplicate implementation of Progress classes: in `net.sf.ij_plugins.util.progress` and `net.sf.ij_plugins.ui.progress` [#16]
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* Use 'master" branch for development and 'release' branch for stable releases [#9]
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* Remove duplicate implementation of Progress classes: in `net.sf.ij_plugins.util.progress`
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and `net.sf.ij_plugins.ui.progress` [#16]
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* Use 'master" branch for development and 'release' branch for stable releases [#9]
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### Documentation Enhancements
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[#10]: https://github.com/ij-plugins/ijp-toolkit/issues/10
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[#11]: https://github.com/ij-plugins/ijp-toolkit/issues/11
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[#12]: https://github.com/ij-plugins/ijp-toolkit/issues/12
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[#13]: https://github.com/ij-plugins/ijp-toolkit/issues/13
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[#15]: https://github.com/ij-plugins/ijp-toolkit/issues/14
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[#15]: https://github.com/ij-plugins/ijp-toolkit/issues/15
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[#16]: https://github.com/ij-plugins/ijp-toolkit/issues/16
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* Rename AutoClipVolume to AutoCropVolume.
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Developer visible:
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* SRG Tools is now using standard overlays provided in newer versions of
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ImageJ.
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* Signature of net.sf.ij_plugins.io.metaimage.MiDecoder.open changed to support
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multi-channel MetaImage files.
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* SRG Tools is now using standard overlays provided in newer versions of ImageJ.
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* Signature of MiDecoder.open changed to support multi-channel MetaImage files.
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* Improvements to JavaDoc.
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* Separate distribution building Ant script into separate file for simpler
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dependency.

‎ReadMe.md‎

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==================
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[![Build Status](https://travis-ci.org/ij-plugins/ijp-toolkit.svg?branch=develop)](https://travis-ci.org/ij-plugins/ijp-toolkit)
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[![Maven Central](https://maven-badges.herokuapp.com/maven-central/net.sf.ij-plugins/ijp-toolkit_2.13/badge.svg)](https://maven-badges.herokuapp.com/maven-central/net.sf.ij-plugins/ijp-toolkit_2.13)
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[![Scaladoc](http://javadoc-badge.appspot.com/net.sf.ij-plugins/ijp-toolkit_2.13.svg?label=scaladoc)](http://javadoc-badge.appspot.com/net.sf.ij-plugins/ijp-toolkit_2.13)
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[![Maven Central](https://maven-badges.herokuapp.com/maven-central/net.sf.ij-plugins/ijp-toolkit_2.13/badge.svg)](https://maven-badges.herokuapp.com/maven-central/net.sf.ij-plugins/ijp-toolkit_2.13)
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[![Scaladoc](http://javadoc-badge.appspot.com/net.sf.ij-plugins/ijp-toolkit_2.13.svg?label=scaladoc)](http://javadoc-badge.appspot.com/net.sf.ij-plugins/ijp-toolkit_2.13)
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![logo](src/main/resources/net/sf/ij_plugins/IJP-48.png) **IJ-Plugins Toolkit** is a set of plugins for [ImageJ]. The plugins are grouped into:
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![logo](src/main/resources/ij_plugins/toolkit/IJP-48.png) **IJ-Plugins Toolkit** is a set of plugins for [ImageJ]. The
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plugins are grouped into:
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* **[3D IO]** - import and export of data in 3D formats.
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* **[3D Toolkit]** - operations on stacks interpreted as 3D images, including
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morphological operations.
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* **[Color]** - color space conversion, color edge detection (color and
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multi-band images).
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* **[Color]** - color space conversion, color edge detection (color and multi-band images).
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* **[Filters]** - fast median filters, coherence enhancing diffusion, and various anisotropic diffusion filters.
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* **Graphics** > **[Image Quilter]** - A plugin to perform texture synthesis
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using the image quilting algorithm of Efros and Freeman.
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* **Graphics** > **[Image Quilter]** - A plugin to perform texture synthesis using the image quilting algorithm of Efros
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and Freeman.
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* **[Segmentation]** - image segmentation through clustering, thresholding, and region growing.
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* **[Segmentation]** - image segmentation through clustering, thresholding, and
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region growing.
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See the the [Wiki] for mode details on the plugins.
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ImageJ Plugins Installation
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---------------------------
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### Automatic Installation Through Update Center
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For [ImageJ 2] or [Fiji] you can install IJ-Plugins Toolkit using the update center. See [Fiji Managed Installation] for more details.
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For [ImageJ 2] or [Fiji] you can install IJ-Plugins Toolkit using the update center. See [Fiji Managed Installation] for
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more details.
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### Manual Installation
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Using as a Stand-alone Library
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------------------------------
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There are some examples of using IJ-Plugins Toolkit as a stand-alone library in the [examples] folder. You will need to add dependency on:
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There are some examples of using IJ-Plugins Toolkit as a stand-alone library in the [examples](examples) folder. You
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will need to add dependency on:
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```
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groupId : net.sf.ij-plugins
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[ImageJ 2]: http://imagej.net
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[Fiji]: http://imagej.net/Fiji
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[sbt-imagej]: https://github.com/jpsacha/sbt-imagej
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[SBT]: http://www.scala-sbt.org/
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[Wiki]: https://github.com/ij-plugins/ijp-toolkit/wiki
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[Release]: https://github.com/ij-plugins/ijp-toolkit/releases
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[Fiji Managed Installation]: https://github.com/ij-plugins/ijp-toolkit/wiki/Fiji-Managed-Installation
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[Manual Installation]: https://github.com/ij-plugins/ijp-toolkit/wiki/Manual-Installation

‎build.sbt‎

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name := "ijp-toolkit"
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organization := "net.sf.ij-plugins"
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version := "2.2.0"
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version := "2.2.1-SNAPSHOT"
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homepage := Some(new URL("https://github.com/ij-plugins/ijp-toolkit"))
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startYear := Some(2002)
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"</ul>" +
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"</html>"
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crossScalaVersions := Seq("2.13.1", "2.12.10")
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crossScalaVersions := Seq("2.13.4", "2.12.13")
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scalaVersion := crossScalaVersions.value.head
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def isScala2_13plus(scalaVersion: String): Boolean = {
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libraryDependencies ++= Seq(
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"org.apache.commons" % "commons-math3" % "3.6.1",
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"com.jgoodies" % "jgoodies-binding" % "2.13.0",
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"net.imagej" % "ij" % "1.52s",
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"net.imagej" % "ij" % "1.53g",
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// Test
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"junit" % "junit" % "4.13" % "test",
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"org.scalatest" %% "scalatest" % "3.1.0" % "test",
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"junit" % "junit" % "4.13.2" % "test",
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"org.scalatest" %% "scalatest" % "3.2.3" % "test",
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// JUnit runner SBT plugin
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"com.novocode" % "junit-interface" % "0.11" % "test->default"
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)

examples/java/net/sf/ij_plugins/concurrent/BlitterSP.java renamed to examples/java/ij_plugins/toolkit/concurrent/BlitterSP.java

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/*
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* IJ-Plugins
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* Copyright (C) 2002-2020 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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* IJ-Plugins
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* Copyright (C) 2002-2021 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* Latest release available at https://github.com/ij-plugins/ijp-toolkit/
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*/
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package net.sf.ij_plugins.concurrent;
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package ij_plugins.toolkit.concurrent;
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import ij.process.Blitter;
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import ij.process.ImageProcessor;
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import net.sf.ij_plugins.ui.progress.ProgressReporter4J;
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import ij_plugins.toolkit.ui.progress.ProgressReporter4J;
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examples/java/net/sf/ij_plugins/concurrent/ParallelSliceProcessingExample.java renamed to examples/java/ij_plugins/toolkit/concurrent/ParallelSliceProcessingExample.java

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/*
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* IJ-Plugins
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* Copyright (C) 2002-2020 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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* IJ-Plugins
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* Copyright (C) 2002-2021 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* Latest release available at https://github.com/ij-plugins/ijp-toolkit/
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*/
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package net.sf.ij_plugins.concurrent;
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package ij_plugins.toolkit.concurrent;
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import ij.ImagePlus;
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import ij.ImageStack;
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import ij.Prefs;
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import ij.process.ImageProcessor;
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import net.sf.ij_plugins.ui.progress.IJProgressBarAdapter;
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import net.sf.ij_plugins.ui.progress.ProgressAccumulator;
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import net.sf.ij_plugins.ui.progress.ProgressReporter4J;
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import ij_plugins.toolkit.ui.progress.IJProgressBarAdapter;
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import ij_plugins.toolkit.ui.progress.ProgressAccumulator;
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import ij_plugins.toolkit.ui.progress.ProgressReporter4J;
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import java.util.ArrayList;
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import java.util.List;

examples/java/net/sf/ij_plugins/concurrent/ProcessSlicesInParallel.java renamed to examples/java/ij_plugins/toolkit/concurrent/ProcessSlicesInParallel.java

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/*
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* IJ-Plugins
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* Copyright (C) 2002-2020 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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* IJ-Plugins
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* Copyright (C) 2002-2021 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* Latest release available at https://github.com/ij-plugins/ijp-toolkit/
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*/
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package net.sf.ij_plugins.concurrent;
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package ij_plugins.toolkit.concurrent;
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import ij.process.ImageProcessor;
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import net.sf.ij_plugins.ui.progress.ProgressReporter4J;
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import ij_plugins.toolkit.ui.progress.ProgressReporter4J;
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import java.util.concurrent.Callable;
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examples/java/net/sf/ij_plugins/concurrent/SliceProducer.java renamed to examples/java/ij_plugins/toolkit/concurrent/SliceProducer.java

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/*
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* IJ-Plugins
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* Copyright (C) 2002-2020 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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* IJ-Plugins
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* Copyright (C) 2002-2021 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* Latest release available at https://github.com/ij-plugins/ijp-toolkit/
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*/
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package net.sf.ij_plugins.concurrent;
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package ij_plugins.toolkit.concurrent;
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import ij.process.ImageProcessor;
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import net.sf.ij_plugins.ui.progress.ProgressReporter;
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import ij_plugins.toolkit.ui.progress.ProgressReporter;
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/**

examples/java/net/sf/ij_plugins/concurrent/SliceProducerFactory.java renamed to examples/java/ij_plugins/toolkit/concurrent/SliceProducerFactory.java

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/*
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* IJ-Plugins
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* Copyright (C) 2002-2020 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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* IJ-Plugins
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* Copyright (C) 2002-2021 Jarek Sacha
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* Author's email: jpsacha at gmail dot com
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* Latest release available at https://github.com/ij-plugins/ijp-toolkit/
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*/
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package net.sf.ij_plugins.concurrent;
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package ij_plugins.toolkit.concurrent;
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import ij.ImagePlus;
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