Commit 5e07458f authored by danyfel80's avatar danyfel80
Browse files

Base implementation added

parent 9ee516c0
# 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
.gradle/
.settings/
bin/
build/
.project
.classpath
\ No newline at end of file
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
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
#!/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" "$@"
@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
rootProject.name = 'WellPlateReader'
\ No newline at end of file
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;
}
}
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) {