Tidy up

- Switch to mvn - Add README - Add LICENSE - Update command names

Tidy up
- Switch to mvn - Add README - Add LICENSE - Update command names
66dec817 · Keith Schulze · e6e14466 · 66dec817 · 66dec817 · 66dec817
Commit 66dec817 authored Nov 22, 2018 by Keith Schulze
--- a/.gitignore
+++ b/.gitignore
-### SBT ###
-# Simple Build Tool
-# http://www.scala-sbt.org/release/docs/Getting-Started/Directories.html#configuring-version-control
+# Created by https://www.gitignore.io/api/java,maven,visualstudiocode
+# Edit at https://www.gitignore.io/?templates=java,maven,visualstudiocode

-dist/*
+### Java ###
+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+### Maven ###
 target/
-lib_managed/
-src_managed/
-project/boot/
-project/plugins/project/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+dependency-reduced-pom.xml
+buildNumber.properties
+.mvn/timing.properties
+.mvn/wrapper/maven-wrapper.jar
+
+### VisualStudioCode ###
+.vscode/*
+# !.vscode/settings.json
+# !.vscode/tasks.json
+# !.vscode/launch.json
+# !.vscode/extensions.json
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
 .history
-.cache
-.lib/

-### Scala ###
-*.class
-*.log
+# Vscode Java extension
+.settings/
+.project
+.classpath
+.factorypath

-.idea/
+# End of https://www.gitignore.io/api/java,maven,visualstudiocode
\ No newline at end of file
--- a/LICENSE
+++ b/LICENSE
+Copyright 2018 Keith Schulze, Monash University
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
--- a/README.md
+++ b/README.md
+# Aggregate
+Aggregate is an ImageJ plugin that semi-automates the process of detecting protein aggregates in 3D images of BAG3-GFP expressing Zebrafish muscle.
+
+## Installing the Aggregate plugin
+
+
+## Using the Aggregate plugin
+
+The aggregate plugin was built to detect aggregates in single channel 3D confocal image stacks of DAG3-GFP experessing fish muscle; however, it should work for any single channel 3D image stack where one wants to quantify the density of aggregates in a tissue.
+
+Table 1: Common parameters
+| Parameter | Description
+| :-------- | :---------- |
+| Estimated radius | Estimated radius of the aggregates in uM |
+| Min aggregate intensity | Minimum peak aggregate intensity |
+| Smooth input | Performance median filtering on raw image prior to processing|
+
+The plugin features 2 ImageJ commands (Plugins -> Aggregate):
+* Dectect Aggregates - processes a single 3D image stack that is already open in ImageJ/Fiji.
+* Batch... - Processes a series of 3D image stacks from a directory.
+
+### Processing a single image volume
+
+1. Open a 3D image stack using the File -> Open... command.
+2. Select Plugins -> Aggregrate -> Detect Aggregates
+3. Specify the parameters described in Table 1.
+4. Click OK.
+
+### Processing a batch of image volumes
+
+1. Select Plugins -> Aggregrate -> Batch...
+2. Specify an input directory containing 3D image stacks.
+3. Specify an output directory where intermediate processing stages will be saved.
+4. Specify the parameters described in Table 1.
+5. Click OK.
+
+Note: the table of results is not automatically saved, so please save it or copy/paste results into a spreadsheet.
\ No newline at end of file
--- a/build.sbt
+++ b/build.sbt
-name := "Aggregate"
-
-organization := "edu.monash"
-
-version := "0.1-SNAPSHOT"
-
-scalaVersion := "2.12.0-M4"
-
-resolvers ++= Seq(
-  "imagej.releases" at "http://maven.imagej.net/content/repositories/releases",
-  "imagej.snapshots" at "http://maven.imagej.net/content/repositories/snapshots",
-  "imagej.public" at "http://maven.imagej.net/content/groups/public"
-)
-
-libraryDependencies ++= Seq (
-  "net.imagej" % "imagej" % "2.0.0-rc-49",
-  "net.imagej" % "imagej-legacy" % "0.20.1",
-  "net.imagej" % "imagej-scripting" % "0.4.0",
-  "io.scif" % "scifio" % "0.27.2",
-  "io.scif" % "scifio-bf-compat" % "2.0.0",
-  "ome" % "formats-gpl" % "5.1.9",
-  "ome" % "bio-formats_plugins" % "5.1.8"
-)
-
-mainClass in (Compile, run) := Some("net.imagej.Main")
-
-fork in run := true
-
-javaOptions += "-Xmx12G"
--- a/pom.xml
+++ b/pom.xml
+<?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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>org.scijava</groupId>
+		<artifactId>pom-scijava</artifactId>
+		<version>23.2.0</version>
+		<relativePath />
+	</parent>
+
+	<groupId>edu.monash.aggregate</groupId>
+	<artifactId>Aggregate</artifactId>
+	<version>0.1.0-SNAPSHOT</version>
+
+	<name>Aggregate</name>
+  <description>An ImageJ plugin for aggregate counting in Zebrafish muscle</description>
+	<inceptionYear>2018</inceptionYear>
+	<organization>
+		<name>Monash University</name>
+		<url>http://monash.edu/</url>
+	</organization>
+	<url>https://gitlab.erc.monash.edu.au/mmi/aggregate</url>
+	<licenses>
+		<license>
+			<name>MIT</name>
+			<distribution>repo</distribution>
+		</license>
+	</licenses>
+
+	<developers>
+		<!-- See https://imagej.net/Team -->
+		<developer>
+			<id>keithschulze</id>
+			<name>Keith Schulze</name>
+			<url>https://platforms.monash.edu/mmi/</url>
+			<roles>
+				<role>developer</role>
+			</roles>
+		</developer>
+	</developers>
+	<contributors>
+		<contributor>
+			<name>Robert Bryson-Richardson</name>
+			<url>http://imagej.net/User:Robertbr</url>
+			<roles><role>founder</role></roles>
+			<properties><id>Robertbr</id></properties>
+		</contributor>
+	</contributors>
+	<mailingLists>
+		<mailingList>
+			<name>Image.sc Forum</name>
+			<archive>https://forum.image.sc/</archive>
+		</mailingList>
+	</mailingLists>
+
+	<scm>
+		<connection>scm:git:git://gitlab.erc.monash.edu.au/mmi/aggregate.git</connection>
+		<developerConnection>scm:git:git@gitlab.erc.monash.edu.au:mmi/aggregate.git</developerConnection>
+		<tag>HEAD</tag>
+		<url>https://gitlab.erc.monash.edu.au/mmi/aggregate</url>
+	</scm>
+	<issueManagement>
+		<system>GitLab Issues</system>
+		<url>https://gitlab.erc.monash.edu.au/mmi/aggregate/issues</url>
+	</issueManagement>
+	<ciManagement>
+		<system>None</system>
+	</ciManagement>
+
+	<properties>
+		<package-name>edu.monash.aggregate</package-name>
+    	<main-class>edu.monash.aggregate.AggregateMulti</main-class>
+		<license.licenseName>mit</license.licenseName>
+		<license.copyrightOwners>Monash University</license.copyrightOwners>
+	</properties>
+
+	<repositories>
+		<repository>
+			<id>imagej.public</id>
+			<url>http://maven.imagej.net/content/groups/public</url>
+		</repository>
+	</repositories>
+
+	<dependencies>
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>imagej</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>imagej-legacy</artifactId>
+		</dependency>
+	</dependencies>
+</project>
--- a/src/main/java/edu/monash/aggregate/AggregateMulti.java
+++ b/src/main/java/edu/monash/aggregate/AggregateMulti.java
@@ -26,7 +26,7 @@ import java.nio.file.Paths;
 *
 * @author Keith Schulze
 */
-@Plugin(type = Command.class, headless = true, menuPath = "Plugins>Aggregate>Batch Aggregate")
+@Plugin(type = Command.class, headless = true, menuPath = "Plugins>Aggregate>Batch...")
 public class AggregateMulti implements Command {

    @Parameter(type = ItemIO.INPUT, style = "directory")
@@ -38,13 +38,13 @@ public class AggregateMulti implements Command {
    @Parameter(type = ItemIO.OUTPUT)
    private GenericTable gt;

-    @Parameter
+    @Parameter(label="Estimated radius")
    private double radius;

-    @Parameter
+    @Parameter(label="Min aggregate intensity")
    private double minPeakThreshold;

-    @Parameter
+    @Parameter(label="Smooth input")
    private boolean doMedian;

    @Parameter

--- a/src/main/java/edu/monash/aggregate/AggregateSingle.java
+++ b/src/main/java/edu/monash/aggregate/AggregateSingle.java
@@ -17,19 +17,19 @@ import org.scijava.plugin.Plugin;
 *
 * @author Keith Schulze
 */
-@Plugin(type = Command.class, headless = true, menuPath = "Plugins>Aggregate>Aggregate")
+@Plugin(type = Command.class, headless = true, menuPath = "Plugins>Aggregate> Detect Aggregates")
 public class AggregateSingle implements Command {

    @Parameter
    private Dataset in;

-    @Parameter
+    @Parameter(label="Estimated radius")
    private double radius;

-    @Parameter
+    @Parameter(label="Min aggregate intensity")
    private double minPeakThreshold;

-    @Parameter
+    @Parameter(label="Smooth input")
    private boolean doMedian;

    @Parameter