diff --git a/org.knime.knip.imagej3d.base/.classpath b/org.knime.knip.imagej3d.base/.classpath index 59ced13..6589f25 100644 --- a/org.knime.knip.imagej3d.base/.classpath +++ b/org.knime.knip.imagej3d.base/.classpath @@ -1,6 +1,6 @@ - + diff --git a/org.knime.knip.imagej3d.base/.settings/org.eclipse.jdt.core.prefs b/org.knime.knip.imagej3d.base/.settings/org.eclipse.jdt.core.prefs index 812fbdb..38b8619 100644 --- a/org.knime.knip.imagej3d.base/.settings/org.eclipse.jdt.core.prefs +++ b/org.knime.knip.imagej3d.base/.settings/org.eclipse.jdt.core.prefs @@ -6,9 +6,9 @@ org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annota org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled -org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve -org.eclipse.jdt.core.compiler.compliance=1.6 +org.eclipse.jdt.core.compiler.compliance=1.7 org.eclipse.jdt.core.compiler.debug.lineNumber=generate org.eclipse.jdt.core.compiler.debug.localVariable=generate org.eclipse.jdt.core.compiler.debug.sourceFile=generate @@ -96,4 +96,4 @@ org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning -org.eclipse.jdt.core.compiler.source=1.6 +org.eclipse.jdt.core.compiler.source=1.7 diff --git a/org.knime.knip.imagej3d.base/META-INF/MANIFEST.MF b/org.knime.knip.imagej3d.base/META-INF/MANIFEST.MF index d43c131..c5d0382 100644 --- a/org.knime.knip.imagej3d.base/META-INF/MANIFEST.MF +++ b/org.knime.knip.imagej3d.base/META-INF/MANIFEST.MF @@ -2,18 +2,18 @@ Manifest-Version: 1.0 Bundle-Name: KNIME ImageJ 3D Viewer Integration Bundle-SymbolicName: org.knime.knip.imagej3d.base;singleton:=true Bundle-ManifestVersion: 2 -Bundle-Version: 1.0.0.qualifier +Bundle-Version: 1.0.1.qualifier Eclipse-RegisterBuddy: org.knime.knip.imagej2.core Bundle-Vendor: University of Konstanz / FIJI (http://3dviewer.neurofly.de/) -Require-Bundle: org.knime.workbench.repository;bundle-version="[2.8.0,3.0.0)", +Require-Bundle: org.knime.workbench.repository;bundle-version="[2.10.0,3.0.0)", org.apache.log4j;bundle-version="1.2.15", org.eclipse.core.runtime, org.eclipse.ui, - org.knime.knip.base;bundle-version="[1.1.0,2.0.0)", - org.knime.knip.core;bundle-version="[1.1.0,2.0.0)", - org.knime.knip.imagej2.core;bundle-version="[0.8.0,0.9.0)", - org.knime.core;bundle-version="[2.8.2,3.0.0)" -Bundle-RequiredExecutionEnvironment: JavaSE-1.6 + org.knime.knip.base;bundle-version="[1.2.0,2.0.0)", + org.knime.knip.core;bundle-version="[1.2.0,2.0.0)", + org.knime.knip.imagej2.core;bundle-version="[0.9.0,0.10.0)", + org.knime.core;bundle-version="[2.10.0,3.0.0)" +Bundle-RequiredExecutionEnvironment: JavaSE-1.7 Bundle-ClassPath: ., lib/ij3d_knip_build.jar, lib/j3dcore.jar, diff --git a/org.knime.knip.imagej3d.base/src/org/knime/knip/imagej3d/ImageJ3DTableCellView.java b/org.knime.knip.imagej3d.base/src/org/knime/knip/imagej3d/ImageJ3DTableCellView.java index 6dc5b20..4f46aa7 100644 --- a/org.knime.knip.imagej3d.base/src/org/knime/knip/imagej3d/ImageJ3DTableCellView.java +++ b/org.knime.knip.imagej3d.base/src/org/knime/knip/imagej3d/ImageJ3DTableCellView.java @@ -50,10 +50,12 @@ package org.knime.knip.imagej3d; import ij.ImagePlus; -import ij.process.StackConverter; +import ij.process.ByteProcessor; +import ij.process.ImageProcessor; import ij3d.Content; import ij3d.ContentConstants; import ij3d.Image3DUniverse; +import ij3d.ImageWindow3D; import java.awt.BorderLayout; import java.awt.Color; @@ -65,6 +67,7 @@ import java.awt.Rectangle; import java.awt.RenderingHints; +import javax.media.j3d.Canvas3D; import javax.swing.JComponent; import javax.swing.JLabel; import javax.swing.JPanel; @@ -72,16 +75,16 @@ import javax.swing.SwingWorker; import javax.swing.ToolTipManager; -import net.imglib2.converter.read.ConvertedRandomAccessibleInterval; -import net.imglib2.exception.IncompatibleTypeException; -import net.imglib2.img.ImgView; +import net.imglib2.converter.Converter; import net.imglib2.meta.ImgPlus; import net.imglib2.ops.operation.Operations; -import net.imglib2.ops.operation.real.unary.Convert; -import net.imglib2.ops.operation.real.unary.Convert.TypeConversionTypes; +import net.imglib2.ops.operation.iterableinterval.unary.MinMax; +import net.imglib2.ops.operation.real.unary.Normalize; +import net.imglib2.type.Type; import net.imglib2.type.numeric.RealType; -import net.imglib2.type.numeric.integer.ByteType; import net.imglib2.type.numeric.real.DoubleType; +import net.imglib2.type.numeric.real.FloatType; +import net.imglib2.util.ValuePair; import org.knime.core.data.DataValue; import org.knime.core.node.NodeLogger; @@ -91,15 +94,15 @@ import org.knime.knip.base.nodes.view.TableCellView; import org.knime.knip.core.util.waitingindicator.WaitingIndicatorUtils; import org.knime.knip.core.util.waitingindicator.libs.WaitIndicator; +import org.knime.knip.imagej2.core.util.ImageProcessorFactory; import org.knime.knip.imagej2.core.util.ImgToIJ; -import org.knime.knip.imagej2.core.util.UntransformableIJTypeException; import view4d.Timeline; import view4d.TimelineGUI; /** * Helper class for the ImageJ 3D Viewer, which provides the TableCellView. - * + * * @author Gabriel Einsdorf */ public class ImageJ3DTableCellView> implements @@ -121,7 +124,7 @@ public class ImageJ3DTableCellView> implements // rendering Universe private Image3DUniverse m_universe; - private Component m_universePanel; + private Canvas3D m_universePanel; // Container for the converted picture, private ImagePlus m_ijImagePlus; @@ -133,7 +136,7 @@ public class ImageJ3DTableCellView> implements private DataValue m_dataValue; /** - * + * * @return the immage the viewer is displaying */ @@ -160,7 +163,7 @@ public final Component getViewComponent() { /** * flushes the cache and updates the Component. - * + * * @param valueToView * TheImgPlus that is to be displayed by the viewer. */ @@ -173,7 +176,7 @@ protected final void fullReload(final DataValue valueToView) { /** * updates the Component, called whenever a new picture is selected, or the * view is reset. - * + * * @param valueToView * The ImgPlus that is to be displayed by the viewer. */ @@ -190,7 +193,7 @@ public final void updateComponent(final DataValue valueToView) { showError(m_rootPanel, null, false); WaitingIndicatorUtils.setWaiting(m_rootPanel, true); - SwingWorker, Integer> worker = new SwingWorker, Integer>() { + final SwingWorker, Integer> worker = new SwingWorker, Integer>() { @Override protected ImgPlus doInBackground() throws Exception { @@ -200,7 +203,7 @@ protected ImgPlus doInBackground() throws Exception { m_timeline = m_universe.getTimeline(); // Menubar - ImageJ3DMenubar ij3dbar = new ImageJ3DMenubar( + final ImageJ3DMenubar ij3dbar = new ImageJ3DMenubar( m_universe, context); // add menubar and 3Duniverse to the panel @@ -211,7 +214,7 @@ protected ImgPlus doInBackground() throws Exception { m_universe.removeAllContents(); // cleanup universe m_dataValue = valueToView; - ImgPlus in = ((ImgPlusValue) valueToView) + final ImgPlus in = ((ImgPlusValue) valueToView) .getImgPlus(); // abort if input image has to few dimensions. @@ -233,14 +236,8 @@ protected ImgPlus doInBackground() throws Exception { return null; } - final T firstElement = in.firstElement(); - - // wrap for compatibility - ImgPlus imgPlus = (ImgPlus) in; - // abort if unsuported type - if (firstElement instanceof DoubleType) { - // TODO Add normalisation + if (in.firstElement() instanceof DoubleType) { showError( m_rootPanel, new String[] { @@ -250,62 +247,18 @@ protected ImgPlus doInBackground() throws Exception { return null; } - // initalize ImgToIJ converter. - ImgToIJ imgToIJ = new ImgToIJ(); - // validate if mapping can be inferred automatically - if (!imgToIJ.validateMapping(imgPlus)) { - if (!imgToIJ.inferMapping(imgPlus)) { - showError( - m_rootPanel, - new String[] { "Warning: Couldn't match dimensions of input image." }, - true); - return null; - } - } - // convert to ijImagePlus. - try { - m_ijImagePlus = Operations.compute(imgToIJ, imgPlus); - } catch (UntransformableIJTypeException f) { - try { - // convert to ByteType if imgToIJ fails to - // convert, - // fixes most untransformable IJType errors. - ImgPlus imgPlusConverted = null; - ConvertedRandomAccessibleInterval converted = new ConvertedRandomAccessibleInterval( - in, new Convert(firstElement, - new ByteType(), - TypeConversionTypes.SCALE), - new ByteType()); - - imgPlusConverted = new ImgPlus( - new ImgView(converted, in - .factory().imgFactory( - new ByteType())), in); - // second attempt at imgToIJ conversion. - m_ijImagePlus = Operations.compute(imgToIJ, - imgPlusConverted); - } catch (IncompatibleTypeException f1) { - - showError( - m_rootPanel, - new String[] { "Can't convert ImgPlus to ImageJ ImagePlus." }, - true); - return null; - } - } - - // convert into 8-Bit gray values image. - try { - new StackConverter(m_ijImagePlus).convertToGray8(); - } catch (java.lang.IllegalArgumentException e) { + if (!ImgToIJ.validateMapping(in)) { showError( m_rootPanel, - new String[] { "Can't convert ImgPlus to ImageJ ImagePlus." }, + new String[] { "Warning: The input image contains unknown dimensions. Currently we only support 'X','Y','Channel,'Z' and 'Time'!" }, true); return null; } + // here we create an converted ImagePlus + m_ijImagePlus = createImagePlus(in); + try { // select the rendertype switch (m_renderType) { @@ -327,7 +280,7 @@ protected ImgPlus doInBackground() throws Exception { default: break; } - } catch (Exception e) { + } catch (final Exception e) { WaitingIndicatorUtils.setWaiting(m_rootPanel, false); showError(m_rootPanel, new String[] { "error adding picture to universe:", @@ -336,7 +289,43 @@ protected ImgPlus doInBackground() throws Exception { } m_universe.updateTimeline(); - return imgPlus; + return in; + } + + /** + * @param firstElement + * @param imgPlus + * @param factor + */ + private ImagePlus createImagePlus(final ImgPlus in) { + + final double minValue = in.firstElement().getMinValue(); + final double maxValue = in.firstElement().getMaxValue(); + + final ValuePair oldMinMax = Operations.compute( + new MinMax(), in); + + final double factor = (((maxValue - minValue) / 255)) + / Normalize.normalizationFactor( + oldMinMax.a.getRealDouble(), + oldMinMax.b.getRealDouble(), minValue, + maxValue); + + return ImgToIJ.wrap(in, new ImageProcessorFactory() { + + @Override + public > ImageProcessor createProcessor( + final int width, final int height, final V type) { + return new ByteProcessor(width, height); + } + }, new Converter() { + + @Override + public void convert(final T input, + final FloatType output) { + output.setReal(((input.getRealDouble() - minValue) / factor)); + } + }); } @Override @@ -345,7 +334,7 @@ protected void done() { ImgPlus imgPlus = null; try { imgPlus = get(); - } catch (Exception e) { + } catch (final Exception e) { e.printStackTrace(); return; } @@ -356,10 +345,12 @@ protected void done() { } // + + m_universe.init(new ImageWindow3D("abc", m_universe)); m_universePanel = m_universe.getCanvas(0); try { m_rootPanel.add(m_universePanel, BorderLayout.CENTER); - } catch (IllegalArgumentException e) { + } catch (final IllegalArgumentException e) { // TEMPORARY error handling: openen the 3D view // on different monitors doesn't work so far, at // least with linux @@ -373,6 +364,7 @@ protected void done() { } } + WaitingIndicatorUtils.setWaiting(m_rootPanel, false); // enables the timeline gui if picture has 4 or 5 @@ -388,6 +380,8 @@ protected void done() { } else { m_panel4D.setVisible(false); } + + m_rootPanel.updateUI(); } }; @@ -409,7 +403,7 @@ public ImageJ3DErrorIndicator(final JComponent target, @Override public void paint(Graphics g) { - Rectangle r = getDecorationBounds(); + final Rectangle r = getDecorationBounds(); g = g.create(); g.setColor(new Color(211, 211, 211, 255)); g.fillRect(r.x, r.y, r.width, r.height); @@ -428,9 +422,9 @@ public void paint(Graphics g) { // Error message g.setFont(new Font("TimesRoman", Font.BOLD, 14)); - int newline = g.getFontMetrics().getHeight() + 5; + final int newline = g.getFontMetrics().getHeight() + 5; int y = 200; - for (String s : m_errorText) { + for (final String s : m_errorText) { g.drawString(s, 10, y += newline); } g.dispose(); @@ -446,7 +440,7 @@ private void showError(final JComponent jc, final String[] message, if (w == null) { if (on) { String loggerMessage = ""; - for (String s : message) { + for (final String s : message) { loggerMessage += " " + s; } m_logger.warn(loggerMessage); @@ -461,7 +455,18 @@ private void showError(final JComponent jc, final String[] message, @Override public final void onClose() { + + if (m_universe != null) + m_universe.cleanup(); + m_dataValue = null; + m_ijImagePlus = null; + m_c = null; + m_panel4D = null; + m_universe = null; + m_timeline = null; + m_timelineGUI = null; + m_logger = null; } @Override diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/META-INF/MANIFEST.MF b/org.knime.knip.imagej3d.bin.linux.amd64/META-INF/MANIFEST.MF index 92542b6..65426e3 100644 --- a/org.knime.knip.imagej3d.bin.linux.amd64/META-INF/MANIFEST.MF +++ b/org.knime.knip.imagej3d.bin.linux.amd64/META-INF/MANIFEST.MF @@ -2,19 +2,9 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: ImageJ 3D Viewer Libraries for Linux x86_64 Bundle-SymbolicName: org.knime.knip.imagej3d.bin.linux.amd64;singleton:=true -Bundle-Version: 1.0.0.qualifier -Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.0" -Bundle-RequiredExecutionEnvironment: JavaSE-1.6 -Eclipse-PlatformFilter: (&(osgi.os=linux)(osgi.arch=x86_64)) +Bundle-Version: 1.0.1.qualifier +Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.1" +Bundle-RequiredExecutionEnvironment: JavaSE-1.7 Bundle-Vendor: University of Konstanz -Bundle-NativeCode: - lib/linux/amd64/libgluegen-rt.so; - lib/linux/amd64/libjoal.so; - lib/linux/amd64/libjocl.so; - lib/linux/amd64/libjogl_desktop.so; - lib/linux/amd64/libnativewindow_awt.so; - lib/linux/amd64/libnativewindow_x11.so; - lib/linux/amd64/libnewt.so; - lib/linux/amd64/libopenal.so; - osname=Linux; - processor=x86_64 +Eclipse-PlatformFilter: (&(osgi.os=linux)(osgi.arch=x86_64)) + diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/build.properties b/org.knime.knip.imagej3d.bin.linux.amd64/build.properties index 1b2df26..9d4ce15 100644 --- a/org.knime.knip.imagej3d.bin.linux.amd64/build.properties +++ b/org.knime.knip.imagej3d.bin.linux.amd64/build.properties @@ -1,2 +1,2 @@ bin.includes = META-INF/,\ - lib/ \ No newline at end of file + os/ diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libgluegen-rt.so b/org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libgluegen-rt.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libgluegen-rt.so rename to org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libgluegen-rt.so diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libjoal.so b/org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libjoal.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libjoal.so rename to org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libjoal.so diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libjocl.so b/org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libjocl.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libjocl.so rename to org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libjocl.so diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libjogl_desktop.so b/org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libjogl_desktop.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libjogl_desktop.so rename to org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libjogl_desktop.so diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libnativewindow_awt.so b/org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libnativewindow_awt.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libnativewindow_awt.so rename to org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libnativewindow_awt.so diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libnativewindow_x11.so b/org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libnativewindow_x11.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libnativewindow_x11.so rename to org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libnativewindow_x11.so diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libnewt.so b/org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libnewt.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libnewt.so rename to org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libnewt.so diff --git a/org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libopenal.so b/org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libopenal.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.amd64/lib/linux/amd64/libopenal.so rename to org.knime.knip.imagej3d.bin.linux.amd64/os/linux/x86_64/libopenal.so diff --git a/org.knime.knip.imagej3d.bin.linux.x86/META-INF/MANIFEST.MF b/org.knime.knip.imagej3d.bin.linux.x86/META-INF/MANIFEST.MF index 81be374..be72b5b 100644 --- a/org.knime.knip.imagej3d.bin.linux.x86/META-INF/MANIFEST.MF +++ b/org.knime.knip.imagej3d.bin.linux.x86/META-INF/MANIFEST.MF @@ -2,20 +2,8 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: ImageJ 3D Viewer Libraries for Linux x86 Bundle-SymbolicName: org.knime.knip.imagej3d.bin.linux.x86 -Bundle-Version: 1.0.0.qualifier +Bundle-Version: 1.0.1.qualifier Bundle-Vendor: University of Konstanz -Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.0" -Bundle-RequiredExecutionEnvironment: JavaSE-1.6 +Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.1" +Bundle-RequiredExecutionEnvironment: JavaSE-1.7 Eclipse-PlatformFilter: (&(osgi.os=linux)(osgi.arch=x86)) -Bundle-NativeCode: - lib/linux/x86/libgluegen-rt.so; - lib/linux/x86/libjoal.so; - lib/linux/x86/libjocl.so; - lib/linux/x86/libjogl_desktop.so; - lib/linux/x86/libnativewindow_awt.so; - lib/linux/x86/libnativewindow_x11.so; - lib/linux/x86/libnewt.so; - lib/linux/x86/libopenal.so; - osname=Linux; - processor=x86 - diff --git a/org.knime.knip.imagej3d.bin.linux.x86/build.properties b/org.knime.knip.imagej3d.bin.linux.x86/build.properties index 5e583be..9d4ce15 100644 --- a/org.knime.knip.imagej3d.bin.linux.x86/build.properties +++ b/org.knime.knip.imagej3d.bin.linux.x86/build.properties @@ -1,2 +1,2 @@ bin.includes = META-INF/,\ - lib/ + os/ diff --git a/org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libgluegen-rt.so b/org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libgluegen-rt.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libgluegen-rt.so rename to org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libgluegen-rt.so diff --git a/org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libjoal.so b/org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libjoal.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libjoal.so rename to org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libjoal.so diff --git a/org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libjocl.so b/org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libjocl.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libjocl.so rename to org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libjocl.so diff --git a/org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libjogl_desktop.so b/org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libjogl_desktop.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libjogl_desktop.so rename to org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libjogl_desktop.so diff --git a/org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libnativewindow_awt.so b/org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libnativewindow_awt.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libnativewindow_awt.so rename to org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libnativewindow_awt.so diff --git a/org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libnativewindow_x11.so b/org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libnativewindow_x11.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libnativewindow_x11.so rename to org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libnativewindow_x11.so diff --git a/org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libnewt.so b/org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libnewt.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libnewt.so rename to org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libnewt.so diff --git a/org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libopenal.so b/org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libopenal.so similarity index 100% rename from org.knime.knip.imagej3d.bin.linux.x86/lib/linux/x86/libopenal.so rename to org.knime.knip.imagej3d.bin.linux.x86/os/linux/x86/libopenal.so diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/META-INF/MANIFEST.MF b/org.knime.knip.imagej3d.bin.macosx.amd64/META-INF/MANIFEST.MF index 5c01546..b53c9f8 100644 --- a/org.knime.knip.imagej3d.bin.macosx.amd64/META-INF/MANIFEST.MF +++ b/org.knime.knip.imagej3d.bin.macosx.amd64/META-INF/MANIFEST.MF @@ -2,28 +2,11 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: ImageJ 3D Viewer Libraries for OSX Bundle-SymbolicName: org.knime.knip.imagej3d.bin.macosx.amd64;singleton:=true -Bundle-Version: 1.0.0.qualifier +Bundle-Version: 1.0.1.qualifier Bundle-Vendor: University of Konstanz -Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.0" -Bundle-RequiredExecutionEnvironment: JavaSE-1.6 +Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.1" +Bundle-RequiredExecutionEnvironment: JavaSE-1.7 Eclipse-PlatformFilter: (&(osgi.os=macosx)(osgi.arch=x86_64)) -Bundle-NativeCode: lib/macosx/amd64/libgluegen-rt.jnilib; - lib/macosx/amd64/libgluegen-rt.dylib; - lib/macosx/amd64/libjoal.jnilib; - lib/macosx/amd64/libjocl.jnilib; - lib/macosx/amd64/libjogl_desktop.jnilib; - lib/macosx/amd64/libnativewindow_awt.jnilib; - lib/macosx/amd64/libnativewindow_macosx.jnilib; - lib/macosx/amd64/libnewt.jnilib; - lib/macosx/amd64/libjoal.dylib; - lib/macosx/amd64/libjocl.dylib; - lib/macosx/amd64/libjogl_desktop.dylib; - lib/macosx/amd64/libnativewindow_awt.dylib; - lib/macosx/amd64/libnativewindow_macosx.dylib; - lib/macosx/amd64/libnewt.dylib; - osname=macosx; - osname=mac os x; - processor=x86-64 Bundle-ClassPath: . diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/build.properties b/org.knime.knip.imagej3d.bin.macosx.amd64/build.properties index 65f335d..d81b56a 100644 --- a/org.knime.knip.imagej3d.bin.macosx.amd64/build.properties +++ b/org.knime.knip.imagej3d.bin.macosx.amd64/build.properties @@ -1,5 +1,5 @@ bin.includes = META-INF/,\ .,\ - lib/ + os/ jars.compile.order = . source.. = diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libgluegen-rt.dylib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libgluegen-rt.dylib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libgluegen-rt.dylib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libgluegen-rt.dylib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libgluegen-rt.jnilib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libgluegen-rt.jnilib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libgluegen-rt.jnilib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libgluegen-rt.jnilib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjoal.dylib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjoal.dylib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjoal.dylib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjoal.dylib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjoal.jnilib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjoal.jnilib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjoal.jnilib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjoal.jnilib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjocl.dylib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjocl.dylib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjocl.dylib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjocl.dylib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjocl.jnilib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjocl.jnilib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjocl.jnilib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjocl.jnilib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjogl_desktop.dylib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjogl_desktop.dylib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjogl_desktop.dylib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjogl_desktop.dylib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjogl_desktop.jnilib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjogl_desktop.jnilib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libjogl_desktop.jnilib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libjogl_desktop.jnilib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnativewindow_awt.dylib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnativewindow_awt.dylib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnativewindow_awt.dylib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnativewindow_awt.dylib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnativewindow_awt.jnilib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnativewindow_awt.jnilib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnativewindow_awt.jnilib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnativewindow_awt.jnilib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnativewindow_macosx.dylib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnativewindow_macosx.dylib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnativewindow_macosx.dylib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnativewindow_macosx.dylib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnativewindow_macosx.jnilib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnativewindow_macosx.jnilib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnativewindow_macosx.jnilib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnativewindow_macosx.jnilib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnewt.dylib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnewt.dylib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnewt.dylib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnewt.dylib diff --git a/org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnewt.jnilib b/org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnewt.jnilib similarity index 100% rename from org.knime.knip.imagej3d.bin.macosx.amd64/lib/macosx/amd64/libnewt.jnilib rename to org.knime.knip.imagej3d.bin.macosx.amd64/os/macosx/x86_64/libnewt.jnilib diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/META-INF/MANIFEST.MF b/org.knime.knip.imagej3d.bin.windows.amd64/META-INF/MANIFEST.MF index 8f0fcff..87f0b51 100644 --- a/org.knime.knip.imagej3d.bin.windows.amd64/META-INF/MANIFEST.MF +++ b/org.knime.knip.imagej3d.bin.windows.amd64/META-INF/MANIFEST.MF @@ -2,22 +2,8 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: ImageJ 3D Viewer Libraries for Windows x86_64 Bundle-SymbolicName: org.knime.knip.imagej3d.bin.windows.amd64 -Bundle-Version: 1.0.0.qualifier +Bundle-Version: 1.0.1.qualifier Bundle-Vendor: University of Konstanz -Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.0" -Bundle-RequiredExecutionEnvironment: JavaSE-1.6 +Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.1" +Bundle-RequiredExecutionEnvironment: JavaSE-1.7 Eclipse-PlatformFilter: (&(osgi.os=win32)(osgi.arch=x86_64)) -Bundle-NativeCode: - lib/windows/amd64/gluegen-rt.dll; - lib/windows/amd64/joal.dll; - lib/windows/amd64/jocl.dll; - lib/windows/amd64/jogl_desktop.dll; - lib/windows/amd64/nativewindow_awt.dll; - lib/windows/amd64/nativewindow_win32.dll; - lib/windows/amd64/newt.dll; - lib/windows/amd64/soft_oal.dll; - osname=win32; - osname=Windows 8; - osname=Windows8; - osname=Win 8; - processor=x86_64 diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/build.properties b/org.knime.knip.imagej3d.bin.windows.amd64/build.properties index 5e583be..9d4ce15 100644 --- a/org.knime.knip.imagej3d.bin.windows.amd64/build.properties +++ b/org.knime.knip.imagej3d.bin.windows.amd64/build.properties @@ -1,2 +1,2 @@ bin.includes = META-INF/,\ - lib/ + os/ diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/gluegen-rt.dll b/org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/gluegen-rt.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/gluegen-rt.dll rename to org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/gluegen-rt.dll diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/joal.dll b/org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/joal.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/joal.dll rename to org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/joal.dll diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/jocl.dll b/org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/jocl.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/jocl.dll rename to org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/jocl.dll diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/jogl_desktop.dll b/org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/jogl_desktop.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/jogl_desktop.dll rename to org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/jogl_desktop.dll diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/nativewindow_awt.dll b/org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/nativewindow_awt.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/nativewindow_awt.dll rename to org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/nativewindow_awt.dll diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/nativewindow_win32.dll b/org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/nativewindow_win32.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/nativewindow_win32.dll rename to org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/nativewindow_win32.dll diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/newt.dll b/org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/newt.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/newt.dll rename to org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/newt.dll diff --git a/org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/soft_oal.dll b/org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/soft_oal.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.amd64/lib/windows/amd64/soft_oal.dll rename to org.knime.knip.imagej3d.bin.windows.amd64/os/win32/x86_64/soft_oal.dll diff --git a/org.knime.knip.imagej3d.bin.windows.x86/META-INF/MANIFEST.MF b/org.knime.knip.imagej3d.bin.windows.x86/META-INF/MANIFEST.MF index 7851f06..19b5dbd 100644 --- a/org.knime.knip.imagej3d.bin.windows.x86/META-INF/MANIFEST.MF +++ b/org.knime.knip.imagej3d.bin.windows.x86/META-INF/MANIFEST.MF @@ -2,22 +2,8 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: ImageJ 3D Viewer Libraries for Linux x86 Bundle-SymbolicName: org.knime.knip.imagej3d.bin.windows.x86 -Bundle-Version: 1.0.0.qualifier +Bundle-Version: 1.0.1.qualifier Bundle-Vendor: University of Konstanz -Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.0" -Bundle-RequiredExecutionEnvironment: JavaSE-1.6 +Fragment-Host: org.knime.knip.imagej3d.base;bundle-version="1.0.1" +Bundle-RequiredExecutionEnvironment: JavaSE-1.7 Eclipse-PlatformFilter: (&(osgi.os=win32)(osgi.arch=x86)) -Bundle-NativeCode: - lib/windows/x86/gluegen-rt.dll; - lib/windows/x86/joal.dll; - lib/windows/x86/jocl.dll; - lib/windows/x86/jogl_desktop.dll; - lib/windows/x86/nativewindow_awt.dll; - lib/windows/x86/nativewindow_win32.dll; - lib/windows/x86/newt.dll; - lib/windows/x86/soft_oal.dll; - osname=win32; - osname=Windows 8; - osname=Windows8; - osname=Win 8; - processor=x86 diff --git a/org.knime.knip.imagej3d.bin.windows.x86/build.properties b/org.knime.knip.imagej3d.bin.windows.x86/build.properties index 5e583be..9d4ce15 100644 --- a/org.knime.knip.imagej3d.bin.windows.x86/build.properties +++ b/org.knime.knip.imagej3d.bin.windows.x86/build.properties @@ -1,2 +1,2 @@ bin.includes = META-INF/,\ - lib/ + os/ diff --git a/org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/gluegen-rt.dll b/org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/gluegen-rt.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/gluegen-rt.dll rename to org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/gluegen-rt.dll diff --git a/org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/joal.dll b/org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/joal.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/joal.dll rename to org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/joal.dll diff --git a/org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/jocl.dll b/org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/jocl.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/jocl.dll rename to org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/jocl.dll diff --git a/org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/jogl_desktop.dll b/org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/jogl_desktop.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/jogl_desktop.dll rename to org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/jogl_desktop.dll diff --git a/org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/nativewindow_awt.dll b/org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/nativewindow_awt.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/nativewindow_awt.dll rename to org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/nativewindow_awt.dll diff --git a/org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/nativewindow_win32.dll b/org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/nativewindow_win32.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/nativewindow_win32.dll rename to org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/nativewindow_win32.dll diff --git a/org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/newt.dll b/org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/newt.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/newt.dll rename to org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/newt.dll diff --git a/org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/soft_oal.dll b/org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/soft_oal.dll similarity index 100% rename from org.knime.knip.imagej3d.bin.windows.x86/lib/windows/x86/soft_oal.dll rename to org.knime.knip.imagej3d.bin.windows.x86/os/win32/x86/soft_oal.dll diff --git a/org.knime.knip.imagej3d.feature/feature.xml b/org.knime.knip.imagej3d.feature/feature.xml index 86c7389..8c41dd8 100644 --- a/org.knime.knip.imagej3d.feature/feature.xml +++ b/org.knime.knip.imagej3d.feature/feature.xml @@ -2,7 +2,7 @@ diff --git a/org.knime.knip.imagej3d.update/buckminster.cspex b/org.knime.knip.imagej3d.update/buckminster.cspex index 946167b..c1feacb 100644 --- a/org.knime.knip.imagej3d.update/buckminster.cspex +++ b/org.knime.knip.imagej3d.update/buckminster.cspex @@ -6,6 +6,11 @@ + + + + + @@ -17,4 +22,4 @@ - \ No newline at end of file + diff --git a/org.knime.knip.imagej3d.update/feature.xml b/org.knime.knip.imagej3d.update/feature.xml index 77638f0..0348264 100644 --- a/org.knime.knip.imagej3d.update/feature.xml +++ b/org.knime.knip.imagej3d.update/feature.xml @@ -2,7 +2,7 @@ + version="1.0.1.qualifier">