update to gradle

build.gradle

@@ -1,13 +1,13 @@
 apply plugin: 'java'
-apply plugin: 'maven'
+//apply plugin: 'maven'
 
 group = 'ch.psi'
-version = '0.11.0'
+version = '0.12.0'
 
 description = """"""
 
-sourceCompatibility = 1.7
+sourceCompatibility = 1.8
-targetCompatibility = 1.7
+targetCompatibility = 1.8
 
 
 
@@ -15,16 +15,102 @@ repositories {
      mavenCentral()
      maven { url "http://artifacts.psi.ch/artifactory/libs-releases" }
 }
+
+// define a provided scope
+configurations {
+    provided
+    compile.extendsFrom provided
+}
+
 dependencies {
+
     compile group: 'hdf5', name: 'hdf', version:'2.10.0'
     compile group: 'hdf5', name: 'hdfobj', version:'2.10.0'
     compile group: 'hdf5', name: 'hdf5', version:'2.10.0'
     compile group: 'hdf5', name: 'hdf5obj', version:'2.10.0'
     compile group: 'org.slf4j', name: 'slf4j-api', version:'1.7.6'
     testCompile group: 'junit', name: 'junit', version:'4.11'
-    compile(group: 'gov.nih.imagej', name: 'imagej', version:'1.46') {
+
-       /* This dependency was originally in the Maven provided scope, but the project was not of type war.
+    provided group: 'net.imagej', name: 'ij', version:'1.53e'
-       This behavior is not yet supported by Gradle, so this dependency has been converted to a compile dependency.
-       Please review and delete this closure when resolved. */
 }
+
+task fatJar(type: Jar) {
+//    manifest {
+//        attributes 'Implementation-Title': 'CaView',
+//                'Implementation-Version': version,
+//                'Main-Class': 'ch.psi.caview.CaView'
+//    }
+    archiveBaseName = 'HDF5_Viewer'
+    from { (configurations.compile- configurations.provided).collect { it.isDirectory() ? it : zipTree(it) } }
+    with jar
+//    { exclude group: "net.imagej", name:'ij'}
 }
+//
+//task distributionZip(type: Zip, dependsOn: [jar]) {
+//    baseName "${project.group}-jhdf5"
+//
+//    from('targets/dist') {
+//        into "${project.group}-jhdf5"
+//        include 'version.txt'
+//        include 'build.txt'
+//    }
+//
+//    from ("$buildDir/output/dist") {
+//        into "${project.group}-jhdf5"
+//        include '*'
+//    }
+//
+//    from ("$buildDir/output/dist") {
+//        into "${project.group}-jhdf5"
+//        include 'bin/*'
+//    }
+//
+//    from ("$buildDir/output/dist") {
+//        into "${project.group}-jhdf5"
+//        include 'doc/*'
+//    }
+//
+//    from (javadocJar.archivePath) {
+//        into "${project.group}-jhdf5/doc"
+//    }
+//
+//    from (exampleJar.archivePath) {
+//        into "${project.group}-jhdf5/doc"
+//    }
+//
+//    from (configurations.runtime) {
+//        include '*-sources*'
+//        into "${project.group}-jhdf5/sources"
+//    }
+//
+//    from (sourcesJar.archivePath) {
+//        into "${project.group}-jhdf5/sources"
+//    }
+//
+//    from (jar.archivePath) {
+//        into "${project.group}-jhdf5/lib"
+//    }
+//
+//    from (h5arCLIJar.archivePath) {
+//        into "${project.group}-jhdf5/lib"
+//    }
+//
+//    from (configurations.runtime) {
+//        exclude '*restriction*'
+//        exclude '*bcel*'
+//        exclude '*-sources*'
+//        into "${project.group}-jhdf5/lib"
+//    }
+//
+//    from ("libs") {
+//        into "${project.group}-jhdf5/lib"
+//        include 'native/**'
+//    }
+//
+//    from (configurations.runtime.collect {zipTree(it)}) {
+//        into "${project.group}-jhdf5/lib"
+//        include 'native/**/*'
+//    }
+//
+//}
+

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,5 @@
-#Tue Apr 14 08:25:23 CEST 2015
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-5.2.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-2.3-bin.zip

gradlew

@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 
 ##############################################################################
 ##
@@ -6,12 +6,30 @@
 ##
 ##############################################################################
 
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+# Attempt to set APP_HOME
-DEFAULT_JVM_OPTS=""
+# 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"'
+
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
 
@@ -30,6 +48,7 @@ die ( ) {
 cygwin=false
 msys=false
 darwin=false
+nonstop=false
 case "`uname`" in
   CYGWIN* )
     cygwin=true
@@ -40,31 +59,11 @@ case "`uname`" in
   MINGW* )
     msys=true
     ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
 esac
 
-# For Cygwin, ensure paths are in UNIX format before anything is touched.
-if $cygwin ; then
-    [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
-fi
-
-# 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\"`/" >&-
-APP_HOME="`pwd -P`"
-cd "$SAVED" >&-
-
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
 # Determine the Java command to use to start the JVM.
@@ -90,7 +89,7 @@ location of your Java installation."
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
+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
@@ -114,6 +113,7 @@ fi
 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`
@@ -154,11 +154,19 @@ if $cygwin ; then
     esac
 fi
 
-# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
+# Escape application args
-function splitJvmOpts() {
+save () {
-    JVM_OPTS=("$@")
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
 }
-eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
+APP_ARGS=$(save "$@")
-JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
 
-exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
+# 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" "$@"

gradlew.bat

@@ -8,14 +8,14 @@
 @rem Set local scope for the variables with windows NT shell
 if "%OS%"=="Windows_NT" setlocal
 
-@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=
-
 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"
+
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome
 
@@ -46,10 +46,9 @@ echo location of your Java installation.
 goto fail
 
 :init
-@rem Get command-line arguments, handling Windowz variants
+@rem Get command-line arguments, handling Windows variants
 
 if not "%OS%" == "Windows_NT" goto win9xME_args
-if "%@eval[2+2]" == "4" goto 4NT_args
 
 :win9xME_args
 @rem Slurp the command line arguments.
@@ -60,11 +59,6 @@ set _SKIP=2
 if "x%~1" == "x" goto execute
 
 set CMD_LINE_ARGS=%*
-goto execute
-
-:4NT_args
-@rem Get arguments from the 4NT Shell from JP Software
-set CMD_LINE_ARGS=%$
 
 :execute
 @rem Setup the command line

src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java

@@ -29,7 +29,7 @@ public class HDF5Reader implements PlugIn {
 	public static void main(String[] args){
 		HDF5Reader r = new HDF5Reader();
 //		r.run("");
-		r.open("",false, "/Users/ebner/Desktop/A8_d_400N030_.h5", "/exchange/data", true);
+		r.open("",false, "/Users/ebner/Desktop/pollen.h5", "/t0/channel0", true);
 	}
 
 	public void run(String arg) {