Commit d7e443d6 authored by danyfel80's avatar danyfel80
Browse files

Mavenization 1

parent 181af089
.gradle/
.settings/
bin/
build/
.project
.classpath
/ecbuild/
apply plugin: 'java-library'
apply plugin: 'eclipse'
version = '2.2.3.1'
println "ICY_HOME=${System.env.ICY_HOME}"
println project.name + " " + version
configurations {
extraLibs // configuration that holds jars to include in the jar
implementation.extendsFrom(extraLibs)
}
repositories {
jcenter()
}
dependencies {
// 1. External libraries
// 2. Icy libraries
implementation files("${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("${System.env.ICY_HOME}/lib/jai_codec.jar") // JAI
implementation files("${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
// 3. Test libraries
testImplementation 'org.hamcrest:hamcrest-all:1.3'
testImplementation 'junit:junit:4.12'
}
// Eclipse project creation
eclipse {
classpath.downloadJavadoc = true
project.natures += ['icy.icy4eclipse.core.icynature']
}
// 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
distributionUrl=https\://services.gradle.org/distributions/gradle-4.2.1-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
#!/usr/bin/env sh
#
# Copyright 2015 the original author or authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
##############################################################################
##
## 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 "$0"`
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
# Use the maximum available, or set MAX_FD != -1 to use that value.
MAX_FD="maximum"
warn () {
echo "$*"
}
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 or MSYS, switch paths to Windows format before running java
if [ "$cygwin" = "true" -o "$msys" = "true" ] ; 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" "$@"
@rem
@rem Copyright 2015 the original author or authors.
@rem
@rem Licensed under the Apache License, Version 2.0 (the "License");
@rem you may not use this file except in compliance with the License.
@rem You may obtain a copy of the License at
@rem
@rem https://www.apache.org/licenses/LICENSE-2.0
@rem
@rem Unless required by applicable law or agreed to in writing, software
@rem distributed under the License is distributed on an "AS IS" BASIS,
@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@rem See the License for the specific language governing permissions and
@rem limitations under the License.
@rem
@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="-Xmx64m" "-Xms64m"
@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
<?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.bioimageanalysis.icy</groupId>
<artifactId>parent-pom-plugin</artifactId>
<version>1.0.1</version>
</parent>
<artifactId>well-plate-reader</artifactId>
<version>3.0.0-SNAPSHOT</version>
<name>Well Plate Reader</name>
<description/>
<build>
<plugins>
<!--<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.3.2</version>
<executions>
<execution>
<phase>install</phase>
<goals>
<goal>java</goal>
</goals>
</execution>
</executions>
<configuration>
<mainClass>icy.main.Icy</mainClass>
</configuration>
</plugin>-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<configuration>
<additionalOptions>
<additionalOption>-Xdoclint:none</additionalOption>
</additionalOptions>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>ezplug</artifactId>
</dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>protocols</artifactId>
</dependency>
</dependencies>
<repositories>
<repository>
<id>icy</id>
<url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
</repository>
</repositories>
</project>
\ No newline at end of file
rootProject.name = 'WellPlateReader'
\ No newline at end of file
......@@ -5,6 +5,8 @@ import java.util.Iterator;
import org.xml.sax.SAXException;
import com.drew.imaging.tiff.TiffProcessingException;
import icy.sequence.Sequence;
import ome.xml.meta.OMEXMLMetadata;
import plugins.adufour.hcs.io.WellPlateReader;
......@@ -80,7 +82,7 @@ public class WellPlate
return plateID + " (" + plateType + ")";
}
public Sequence loadField(Field field) throws IOException, SAXException
public Sequence loadField(Field field) throws IOException, SAXException, TiffProcessingException
{
wellPlateReader.loadField(field, sequence);
if (field != null) sequence.setName(field.getWell().getAlphanumericID());
......
......@@ -6,6 +6,8 @@ import java.util.Optional;
import org.xml.sax.SAXException;
import com.drew.imaging.tiff.TiffProcessingException;
import icy.gui.frame.progress.CancelableProgressFrame;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginLibrary;
......@@ -53,5 +55,5 @@ public abstract class WellPlateReader extends Plugin implements PluginLibrary {
* @throws SAXException
* If the metadata cannot be correctly read.
*/
public abstract void loadField(Field field, Sequence sequence) throws IOException, SAXException;
public abstract void loadField(Field field, Sequence sequence) throws IOException, SAXException, TiffProcessingException;
}
......@@ -30,6 +30,7 @@ import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import com.drew.imaging.tiff.TiffMetadataReader;
import com.drew.imaging.tiff.TiffProcessingException;
import com.drew.metadata.Directory;
import com.drew.metadata.Metadata;
import com.drew.metadata.exif.ExifIFD0Directory;
......@@ -116,7 +117,7 @@ public class WellPlateReader_Opera extends WellPlateReader {
public Void call() throws Exception {
Metadata flexMetadata = TiffMetadataReader.readMetadata(new File(filePath));
Thread.yield();
Directory flexDirectory = flexMetadata.getDirectory(ExifIFD0Directory.class);
Directory flexDirectory = flexMetadata.getFirstDirectoryOfType(ExifIFD0Directory.class);
// 0xfeb0 is the Tag containing the metadata xml.
Document flexDocument = XMLUtil.createDocument(flexDirectory.getDescription(0xfeb0));
......@@ -415,7 +416,7 @@ public class WellPlateReader_Opera extends WellPlateReader {
}
@Override
public void loadField(Field field, Sequence sequence) throws IOException, SAXException {
public void loadField(Field field, Sequence sequence) throws IOException, SAXException, TiffProcessingException {
sequence.setName("Well " + field.getWell().getAlphanumericID() + ", Field #" + field.getID());
// The field is stored in a single image
String path = field.getFilePaths()[0];
......
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