Merge branch 'release/v2.2.3'

README.md

+# Well Plate Reader - Read well plates on Icy
+
+## Description
+
+This project contains the code necessary to import and show well plates from Opera machines.
+
+This project has been developed as a _Gradle_ project and can be opened with _Eclipse_ IDE.
+
+### Available plugins
+
+In danyfel.bigimage.io:
+
+- WellPlateImporter
+
+  This plugin reads the information of a well plate and then shows an interface with the available plates and their corresponding fields.
+
+
+## Installation
+
+### Requirements
+
+In order to be able to work with this project you must have installed the following software:
+
+- **Icy**, version 1.9.5.1 or above. ( [Available here](http://icy.bioimageanalysis.org) )
+  - The following plugins should be already installed in order to execute BigImageTools:
+    - EzPlug SDK
+    - Protocols SDK
+- **Eclipse**, version _Neon_ or above. Make sure to have the _Buildship_ plugin installed. ([Available here](http://www.eclipse.org/downloads/))
+- **Icy4Eclipse** plugin for Eclipse, the latest version available. Follow [these](http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy) instructions.
+
+### Setup
+
+1. Use your *Git* repository manager of preference to download this repository (you can use Eclipse Git perspective to do this). The repository URL is [https://gitlab.pasteur.fr/bia/wellPlateReader.git](https://gitlab.pasteur.fr/bia/wellPlateReader.git).
+2. Make sure the environment variable **ICY_HOME** is set to the location of your Icy installation. _**Note**: This could be tricky on Mac so make sure to follow [these](https://stackoverflow.com/questions/829749/launch-mac-eclipse-with-environment-variables-set) instructions._
+3. Open Eclipse and select the menu *File > Import...* Then select *Gradle > Existing Gradle Project*. Click *Next* the project root directory is demanded select the folder **WellPlateReader** inside the folder you downloaded the at. Finally, click *Finish* to create the project in eclipse.
+
+Eclipse will download the dependencies specified in the *gradle.build* file. When it finishes you should see the project without any problem on the project explorer of Eclipse. *If this is not the case, check that the environment variable ICY_HOME is correctly defined.*
\ No newline at end of file

WellPlateReader/.gitignore

+.gradle/
+.settings/
+bin/
+build/
+.project
+.classpath
\ No newline at end of file

WellPlateReader/build.gradle

+apply plugin: 'java-library'
+apply plugin: 'eclipse'
+
+version = '2.2.3'
+task wrapper(type: Wrapper) {
+	gradleVersion = '4.3'
+}
+
+configurations {
+	extraLibs // configuration that holds jars to include in the jar
+}
+
+repositories {
+	jcenter()
+}
+
+println "ICY_HOME=${System.env.ICY_HOME}"
+dependencies {
+	configurations.implementation.extendsFrom(configurations.extraLibs)
+	// 1. External libraries
+	// 2. Icy libraries
+	implementation files("${System.env.ICY_HOME}/icy.jar") // Icy core
+	implementation files("${System.env.ICY_HOME}/plugins/adufour/ezplug/EzPlug.jar") // EzPlug
+	implementation files("${System.env.ICY_HOME}/plugins/adufour/protocols/Protocols.jar") // Protocols
+	implementation files("${System.env.ICY_HOME}/plugins/adufour/blocks/Blocks.jar") // Blocks
+	implementation files("${System.env.ICY_HOME}/lib/bioformats.jar") // Bioformats
+	implementation files("${System.env.ICY_HOME}/lib/flamingo.jar") // Flamingo
+	implementation files("${System.env.ICY_HOME}/lib/jai_core.jar") // JAI
+	implementation files("${System.env.ICY_HOME}/lib/jai_codec.jar") // JAI
+	
+	// 3. Test libraries
+	testImplementation 'org.hamcrest:hamcrest-all:1.3'
+	testImplementation 'junit:junit:4.12'
+}
+
+// Eclipse project creation
+eclipse {
+	classpath.downloadJavadoc = true
+
+	project {
+		buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+		
+		natures += ['icy.icy4eclipse.core.icynature']
+		natures += ['org.eclipse.buildship.core.gradleprojectnature']
+	}
+}
+
+// Jar task to include external libraries
+jar {
+	from configurations.extraLibs.collect { it.isDirectory() ? it : zipTree(it) }
+}
+
+// Jar task to include external libraries and source files in the same zip file
+task sourcesJar(type: Jar) {
+	classifier = 'sources'
+	from sourceSets.main.output
+	from sourceSets.main.java
+	from configurations.extraLibs.collect { it.isDirectory() ? it : zipTree(it) }
+}
+
+// Artifacts created when build
+artifacts {
+	archives sourcesJar
+}
\ No newline at end of file

WellPlateReader/gradle/wrapper/gradle-wrapper.properties

+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.3-bin.zip

WellPlateReader/gradlew

+#!/usr/bin/env sh
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn () {
+    echo "$*"
+}
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    JAVACMD=`cygpath --unix "$JAVACMD"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Escape application args
+save () {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
+}
+APP_ARGS=$(save "$@")
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
+  cd "$(dirname "$0")"
+fi
+
+exec "$JAVACMD" "$@"

WellPlateReader/gradlew.bat

+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

WellPlateReader/settings.gradle

+rootProject.name = 'WellPlateReader'
\ No newline at end of file

WellPlateReader/src/main/java/plugins/adufour/hcs/WellPlateImporter.java

+package plugins.adufour.hcs;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Optional;
+import java.util.Set;
+
+import javax.swing.JFileChooser;
+import javax.swing.filechooser.FileFilter;
+
+import icy.gui.frame.progress.CancelableProgressFrame;
+import icy.main.Icy;
+import icy.plugin.PluginDescriptor;
+import icy.plugin.PluginLoader;
+import icy.plugin.abstract_.PluginActionable;
+import icy.system.IcyHandledException;
+import icy.system.thread.ThreadUtil;
+import plugins.adufour.hcs.data.WellPlate;
+import plugins.adufour.hcs.gui.WellPlateViewer;
+import plugins.adufour.hcs.io.WellPlateReader;
+import plugins.adufour.hcs.io.WellPlateReader_Opera;
+
+public class WellPlateImporter extends PluginActionable {
+	private static final Set<WellPlateReader> availableReaders = new HashSet<WellPlateReader>();
+
+	@SuppressWarnings("unchecked")
+	private static void loadImporters() {
+		availableReaders.clear();
+
+		ArrayList<Class<WellPlateReader>> importers = new ArrayList<>();
+		for (PluginDescriptor pd : PluginLoader.getPlugins(WellPlateReader.class)) {
+			importers.add((Class<WellPlateReader>) pd.getPluginClass());
+		}
+		if (importers.isEmpty()) {
+			// Probably debugging within Eclipse => add one (known) entry manually
+			importers.add((Class<WellPlateReader>) WellPlateReader_Opera.class.asSubclass(WellPlateReader.class));
+		}
+
+		// Add available file filters
+		for (Class<WellPlateReader> importerClass : importers)
+			try {
+				availableReaders.add(importerClass.newInstance());
+			} catch (Exception e) {
+				throw new RuntimeException(e);
+			}
+	}
+
+	@Override
+	public void run() {
+		loadImporters();
+
+		String lastUsedDirectory = getPreferencesRoot().get("lastUsedDirectory", null);
+
+		JFileChooser jfc = new JFileChooser(lastUsedDirectory);
+
+		// Build a descriptor for the file filter
+		String tmpFilterName = "Plate folders (";
+		for (WellPlateReader reader : availableReaders)
+			tmpFilterName += reader.getSystemName() + ", ";
+		// Replace the trailing comma with a closing parenthesis
+		final String filterName = tmpFilterName.substring(0, tmpFilterName.length() - 2) + ")";
+
+		jfc.setFileFilter(new FileFilter() {
+			@Override
+			public String getDescription() {
+				return filterName;
+			}
+
+			@Override
+			public boolean accept(File f) {
+				return f.isDirectory();
+			}
+		});
+		jfc.setAcceptAllFileFilterUsed(false);
+		jfc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+
+		int result = jfc.showOpenDialog(Icy.getMainInterface().getMainFrame());
+
+		if (result == JFileChooser.APPROVE_OPTION)
+			new Thread(() -> {
+				try {
+					File selection = jfc.getSelectedFile();
+
+					CancelableProgressFrame loadingProgress = new CancelableProgressFrame("Loading plate " + selection.getName());
+
+					getPreferencesRoot().put("lastUsedDirectory", selection.getPath());
+
+					WellPlateReader importer = getReaderFor(selection);
+					WellPlate wellPlate = importer.loadPlateFromFolder(selection, Optional.of(loadingProgress));
+
+					loadingProgress.close();
+
+					ThreadUtil.invokeLater(() -> {
+						WellPlateViewer wellPlateViewer = new WellPlateViewer(wellPlate);
+						wellPlateViewer.pack();
+						wellPlateViewer.addToDesktopPane();
+						wellPlateViewer.setVisible(true);
+					});
+				} catch (IOException ioE) {
+					throw new IcyHandledException(
+							"Cannot load folder " + jfc.getSelectedFile().getName() + "\nReason: " + ioE.getMessage());
+				}
+			}).start();
+	}
+
+	/**
+	 * @param path
+	 *          Path to check.
+	 * @return <code>true</code> if at least one reader accepts the given file
+	 */
+	public static boolean isValid(File path) {
+		loadImporters();
+
+		for (WellPlateReader reader : availableReaders)
+			if (reader.isValidPlate(path))
+				return true;
+
+		return false;
+	}
+
+	/**
+	 * Looks for an appropriate readed of the files contained in the provided
+	 * path.
+	 * 
+	 * @param file
+	 *          Path of the folder containing the files to read.
+	 * @return The appropriate reader for the files.
+	 */
+	public static WellPlateReader getReaderFor(File file) {
+		for (WellPlateReader reader : availableReaders)
+			if (reader.isValidPlate(file))
+				return reader;
+		return null;
+	}
+}

WellPlateReader/src/main/java/plugins/adufour/hcs/blocks/WellPlateBatch.java

+package plugins.adufour.hcs.blocks;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Optional;
+
+import icy.gui.frame.progress.CancelableProgressFrame;
+import icy.sequence.Sequence;
+import icy.system.IcyHandledException;
+import icy.system.SystemUtil;
+import plugins.adufour.blocks.lang.Batch;
+import plugins.adufour.blocks.lang.FileBatch;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.hcs.WellPlateImporter;
+import plugins.adufour.hcs.data.Field;
+import plugins.adufour.hcs.data.WellPlate;
+import plugins.adufour.hcs.io.WellPlateReader;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeModel;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.lang.VarString;
+import plugins.adufour.vars.util.VarListener;
+
+/**
+ * A well plate batch is a work-flow that will process every image of every well
+ * in a given well plate (or a selection thereof). Supported plate formats are
+ * the same as those supported by the {@link WellPlateImporter} plug-in.
+ * 
+ * @author Alexandre Dufour
+ */
+public class WellPlateBatch extends Batch {
+	// INTERFACE //
+
+	/**
+	 * The folder containing the well plate. Although we could have extended
+	 * {@link FileBatch}, we choose to extend just {@link Batch} since we don't
+	 * need extension filters or recursive sub-folder analysis
+	 */
+	private VarFile plateFolder;
+
+	private VarSequence element;
+
+	private VarString wellFilter;
+
+	private VarString plateID;
+
+	private VarString wellID;
+
+	private VarInteger fieldID;
+
+	// LOCAL STUFF //
+
+	private WellPlateReader reader;
+
+	private WellPlate currentWellPlate;
+
+	/**
+	 * Indicates whether the current well plate is loaded (avoids reloading it
+	 * every time the protocol is run)
+	 */
+	private boolean wellPlateLoaded = false;
+
+	private Iterator<Field> fieldIterator;
+
+	@Override
+	public Var<?> getBatchSource() {
+		if (plateFolder == null) {
+			// Make sure the well plate is reloaded only when this parameter changes
+			plateFolder = new VarFile("Plate folder", null, new VarListener<File>() {
+				@Override
+				public void valueChanged(Var<File> source, File oldValue, File newValue) {
+					wellPlateLoaded = false;
+				}
+
+				@Override
+				public void referenceChanged(Var<File> source, Var<? extends File> oldReference,
+						Var<? extends File> newReference) {
+					wellPlateLoaded = false;