Initial commit from Eclipse project

Initial commit from Eclipse project.
Need to be mavenized

.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="var" path="ICY_PLUGINS/tprovoost/sequenceblocks/SequenceBlocks.jar"/>
+	<classpathentry kind="var" path="ICY_PLUGINS/adufour/blocks/Blocks.jar"/>
+	<classpathentry kind="var" path="ICY_PLUGINS/adufour/ezplug/EzPlug.jar"/>
+	<classpathentry kind="var" path="ICY_JAR"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

.gitignore

+bin
+pluginfile-roi-blocks*.jar

.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>RoiBlocks</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.jdt.core.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.6

export.jardesc

+<?xml version="1.0" encoding="WINDOWS-1252" standalone="no"?>
+<jardesc>
+    <jar path="RoiBlocks/RoiBlocks.jar"/>
+    <options buildIfNeeded="true" compress="true" descriptionLocation="/RoiBlocks/export.jardesc" exportErrors="false" exportWarnings="true" includeDirectoryEntries="true" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
+    <storedRefactorings deprecationInfo="true" structuralOnly="false"/>
+    <selectedProjects/>
+    <manifest generateManifest="true" manifestLocation="/Icy-Kernel/META-INF/MANIFEST.MF" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
+        <sealing sealJar="false">
+            <packagesToSeal/>
+            <packagesToUnSeal/>
+        </sealing>
+    </manifest>
+    <selectedElements exportClassFiles="true" exportJavaFiles="true" exportOutputFolder="false">
+        <javaElement handleIdentifier="=RoiBlocks/src"/>
+    </selectedElements>
+</jardesc>

src/plugins/stef/roi/bloc/RoiBlocks.java

+package plugins.stef.roi.bloc;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginLibrary;
+
+/**
+ * Bundle of blocks (Protocols) to perform different operations on ROI (Region Of Interest).<br>
+ * <br>
+ * Supported operations:<br>
+ * <li>Create rectangular ROI (2D, 3D, 4D or 5D)</li><br>
+ * <li>Filter by size</li><br>
+ * <li>Perform boolean operation between two set of ROI</li><br>
+ * <li>Get / set ROI position</li><br>
+ * <li>Get / set ROI size</li><br>
+ * <li>Get / set ROI properties (name, color)</li><br>
+ * <br>
+ * 
+ * @author stephane
+ */
+public class RoiBlocks extends Plugin implements PluginLibrary
+{
+    //
+}

src/plugins/stef/roi/bloc/convert/ROITo3DStack.java

+package plugins.stef.roi.bloc.convert;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginBundled;
+import icy.plugin.interface_.PluginLibrary;
+import icy.roi.ROI;
+import icy.roi.ROI2D;
+import icy.roi.ROIUtil;
+import plugins.adufour.blocks.tools.roi.ROIBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.util.VarException;
+import plugins.stef.roi.bloc.RoiBlocks;
+
+/**
+ * Block to convert input 2D ROIs to 3D stack ROI by stacking them along the Z axis.
+ * 
+ * @author Stephane
+ */
+public class ROITo3DStack extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
+{
+    protected final VarROIArray input;
+    protected final VarInteger sizeZ;
+    protected final VarROIArray output;
+
+    public ROITo3DStack()
+    {
+        super();
+
+        input = new VarROIArray("Roi(s)");
+        sizeZ = new VarInteger("Size Z", 10);
+        output = new VarROIArray("3D stack roi(s)");
+    }
+
+    @Override
+    public void run()
+    {
+        final ROI[] rois = input.getValue();
+        final List<ROI> result = new ArrayList<ROI>();
+
+        if (rois != null)
+        {
+            final int maxZ = sizeZ.getValue().intValue() - 1;
+            if (maxZ < 0)
+                throw new VarException(sizeZ, "Size Z field should be > 0");
+
+            for (ROI roi : rois)
+            {
+                // only convert 2D roi
+                if (roi instanceof ROI2D)
+                    result.add(ROIUtil.convertToStack((ROI2D) roi, 0, maxZ));
+                else
+                    // otherwise we add them directly to the result
+                    result.add(roi);
+            }
+        }
+
+        output.setValue(result.toArray(new ROI[result.size()]));
+    }
+
+    @Override
+    public void declareInput(VarList inputMap)
+    {
+        inputMap.add("input", input);
+        inputMap.add("sizeZ", sizeZ);
+    }
+
+    @Override
+    public void declareOutput(VarList outputMap)
+    {
+        outputMap.add("output", output);
+    }
+
+    @Override
+    public String getMainPluginClassName()
+    {
+        return RoiBlocks.class.getName();
+    }
+}
\ No newline at end of file

src/plugins/stef/roi/bloc/convert/ROIToEllipse.java

+/**
+ * 
+ */
+package plugins.stef.roi.bloc.convert;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginBundled;
+import icy.plugin.interface_.PluginLibrary;
+import icy.roi.ROI;
+import icy.roi.ROIUtil;
+import plugins.adufour.blocks.tools.roi.ROIBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarDouble;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.stef.roi.bloc.RoiBlocks;
+
+/**
+ * Block to convert input ROI(s) to 2D ellipse type ROI(s) centered on the mass center.<br>
+ * 
+ * @author Stephane
+ */
+public class ROIToEllipse extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
+{
+    protected final VarROIArray input;
+    protected final VarDouble radiusX;
+    protected final VarDouble radiusY;
+    protected final VarROIArray output;
+
+    public ROIToEllipse()
+    {
+        super();
+
+        input = new VarROIArray("Roi(s)");
+        radiusX = new VarDouble("Radius X", 1d);
+        radiusY = new VarDouble("Radius Y", 1d);
+        output = new VarROIArray("Ellipse roi(s)");
+    }
+
+    @Override
+    public void run()
+    {
+        final ROI[] rois = input.getValue();
+        final ROI[] result = new ROI[(rois != null) ? rois.length : 0];
+        final double rx = radiusX.getValue().doubleValue();
+        final double ry = radiusY.getValue().doubleValue();
+
+        if (rois != null)
+        {
+            for (int r = 0; r < rois.length; r++)
+                result[r] = ROIUtil.convertToEllipse(rois[r], rx, ry);
+        }
+
+        output.setValue(result);
+    }
+
+    @Override
+    public void declareInput(VarList inputMap)
+    {
+        inputMap.add("input", input);
+        inputMap.add("radiusX", radiusX);
+        inputMap.add("radiuxY", radiusY);
+    }
+
+    @Override
+    public void declareOutput(VarList outputMap)
+    {
+        outputMap.add("output", output);
+    }
+
+    @Override
+    public String getMainPluginClassName()
+    {
+        return RoiBlocks.class.getName();
+    }
+}

src/plugins/stef/roi/bloc/convert/ROIToMask.java

+/**
+ * 
+ */
+package plugins.stef.roi.bloc.convert;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginBundled;
+import icy.plugin.interface_.PluginLibrary;
+import icy.roi.ROI;
+import icy.roi.ROIUtil;
+import plugins.adufour.blocks.tools.roi.ROIBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.stef.roi.bloc.RoiBlocks;
+
+/**
+ * Block to convert input ROI(s) to (boolean) mask type ROI(s).<br>
+ * Only 2D ROI(s) are supported and conversion is done only if needed.
+ * 
+ * @author Stephane
+ */
+public class ROIToMask extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
+{
+    protected final VarROIArray input;
+    protected final VarROIArray output;
+
+    public ROIToMask()
+    {
+        super();
+
+        input = new VarROIArray("Roi(s)");
+        output = new VarROIArray("Mask roi(s)");
+    }
+
+    @Override
+    public void run()
+    {
+        final ROI[] rois = input.getValue();
+        final List<ROI> result = new ArrayList<ROI>();
+
+        if (rois != null)
+        {
+            for (ROI roi : rois)
+                result.add(ROIUtil.convertToMask(roi));
+        }
+
+        output.setValue(result.toArray(new ROI[result.size()]));
+    }
+
+    @Override
+    public void declareInput(VarList inputMap)
+    {
+        inputMap.add("input", input);
+    }
+
+    @Override
+    public void declareOutput(VarList outputMap)
+    {
+        outputMap.add("output", output);
+    }
+
+    @Override
+    public String getMainPluginClassName()
+    {
+        return RoiBlocks.class.getName();
+    }
+}

src/plugins/stef/roi/bloc/convert/ROIToPoint.java

+/**
+ * 
+ */
+package plugins.stef.roi.bloc.convert;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginBundled;
+import icy.plugin.interface_.PluginLibrary;
+import icy.roi.ROI;
+import icy.roi.ROIUtil;
+import plugins.adufour.blocks.tools.roi.ROIBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.stef.roi.bloc.RoiBlocks;
+
+/**
+ * Block to convert input ROI(s) to single point type ROI(s) representing the mass center.
+ * 
+ * @author Stephane
+ */
+public class ROIToPoint extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
+{
+    protected final VarROIArray input;
+    protected final VarROIArray output;
+
+    public ROIToPoint()
+    {
+        super();
+
+        input = new VarROIArray("Roi(s)");
+        output = new VarROIArray("Point roi(s)");
+    }
+
+    @Override
+    public void run()
+    {
+        final ROI[] rois = input.getValue();
+        final List<ROI> result = new ArrayList<ROI>();
+
+        if (rois != null)
+        {
+            for (ROI roi : rois)
+                result.add(ROIUtil.convertToPoint(roi));
+        }
+
+        output.setValue(result.toArray(new ROI[result.size()]));
+    }
+
+    @Override
+    public void declareInput(VarList inputMap)
+    {
+        inputMap.add("input", input);
+    }
+
+    @Override
+    public void declareOutput(VarList outputMap)
+    {
+        outputMap.add("output", output);
+    }
+
+    @Override
+    public String getMainPluginClassName()
+    {
+        return RoiBlocks.class.getName();
+    }
+}

src/plugins/stef/roi/bloc/convert/ROIToRectangle.java

+/**
+ * 
+ */
+package plugins.stef.roi.bloc.convert;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginBundled;
+import icy.plugin.interface_.PluginLibrary;
+import icy.roi.ROI;
+import icy.roi.ROIUtil;
+import plugins.adufour.blocks.tools.roi.ROIBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarDouble;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.stef.roi.bloc.RoiBlocks;
+
+/**
+ * Block to convert input ROI(s) to 2D rectangle type ROI(s) centered on the mass center.<br>
+ * 
+ * @author Stephane
+ */
+public class ROIToRectangle extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
+{
+    protected final VarROIArray input;
+    protected final VarDouble width;
+    protected final VarDouble height;
+    protected final VarROIArray output;
+
+    public ROIToRectangle()
+    {
+        super();
+
+        input = new VarROIArray("Roi(s)");
+        width = new VarDouble("Width", 1d);
+        height = new VarDouble("Height", 1d);
+        output = new VarROIArray("Rectangle roi(s)");
+    }
+
+    @Override
+    public void run()
+    {
+        final ROI[] rois = input.getValue();
+        final ROI[] result = new ROI[(rois != null) ? rois.length : 0];
+        final double w = width.getValue().doubleValue();
+        final double h = height.getValue().doubleValue();
+
+        if (rois != null)
+        {
+            for (int r = 0; r < rois.length; r++)
+                result[r] = ROIUtil.convertToRectangle(rois[r], w, h);
+        }
+
+        output.setValue(result);
+    }
+
+    @Override
+    public void declareInput(VarList inputMap)
+    {
+        inputMap.add("input", input);
+        inputMap.add("width", width);
+        inputMap.add("height", height);
+    }
+
+    @Override
+    public void declareOutput(VarList outputMap)
+    {
+        outputMap.add("output", output);
+    }
+
+    @Override
+    public String getMainPluginClassName()
+    {
+        return RoiBlocks.class.getName();
+    }
+}

src/plugins/stef/roi/bloc/convert/ROIToShape.java

+package plugins.stef.roi.bloc.convert;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginBundled;
+import icy.plugin.interface_.PluginLibrary;
+import icy.roi.ROI;
+import icy.roi.ROIUtil;
+import plugins.adufour.blocks.tools.roi.ROIBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.stef.roi.bloc.RoiBlocks;
+
+/**
+ * Block to convert input ROI(s) to shape type ROI(s).<br>
+ * Only 2D ROI(s) are supported and conversion is done only if needed.
+ * 
+ * @author Stephane
+ */
+public class ROIToShape extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
+{
+    protected final VarROIArray input;
+    protected final VarROIArray output;
+
+    public ROIToShape()
+    {
+        super();
+
+        input = new VarROIArray("Roi(s)");
+        output = new VarROIArray("Shape roi(s)");
+    }
+
+    @Override
+    public void run()
+    {
+        final ROI[] rois = input.getValue();
+        final List<ROI> result = new ArrayList<ROI>();
+
+        if (rois != null)
+        {
+            for (ROI roi : rois)
+                result.add(ROIUtil.convertToShape(roi, -1));
+        }
+
+        output.setValue(result.toArray(new ROI[result.size()]));
+    }
+
+    @Override
+    public void declareInput(VarList inputMap)
+    {
+        inputMap.add("input", input);
+    }
+
+    @Override
+    public void declareOutput(VarList outputMap)
+    {
+        outputMap.add("output", output);
+    }
+
+    @Override
+    public String getMainPluginClassName()
+    {
+        return RoiBlocks.class.getName();
+    }
+}

src/plugins/stef/roi/bloc/convert/RoiToSequence.java

+package plugins.stef.roi.bloc.convert;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginBundled;
+import icy.plugin.interface_.PluginLibrary;
+import icy.roi.ROIUtil;
+import icy.type.DataType;
+import icy.type.collection.CollectionUtil;
+import plugins.adufour.blocks.tools.roi.ROIBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarBoolean;
+import plugins.adufour.vars.lang.VarDouble;
+import plugins.adufour.vars.lang.VarEnum;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.lang.VarSequence;
+import plugins.stef.roi.bloc.RoiBlocks;
+
+/**
+ * Block (Protocols) to convert ROI(s) (Region Of Interest) into a binary image / sequence.<br>
+ * <br>
+ * It takes a ROI (or a list of ROI) as input and generate a binary sequence from it.<br/>
+ * The content of the ROI area is filled with the specified value while background remains at 0.<br/>
+ * Size informations are used to define the dimension of the output sequence, a value of 0 indicate
+ * to use the ROI dimension instead.
+ * 
+ * @author Stephane
+ */
+public class RoiToSequence extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
+{
+    final VarROIArray inputROI;
+    final VarInteger sizeX;
+    final VarInteger sizeY;
+    final VarInteger sizeC;
+    final VarInteger sizeZ;
+    final VarInteger sizeT;
+    final VarEnum<DataType> dataType;
+    final VarDouble fillValue;
+    final VarBoolean labeled;
+    final VarSequence varOut;
+
+    public RoiToSequence()
+    {
+        super();
+
+        inputROI = new VarROIArray("ROI(s)");
+        sizeX = new VarInteger("Size X", 0);
+        sizeY = new VarInteger("Size Y", 0);
+        sizeC = new VarInteger("Size C", 1);
+        sizeZ = new VarInteger("Size Z", 1);
+        sizeT = new VarInteger("Size T", 1);
+        dataType = new VarEnum<DataType>("Data type", DataType.UBYTE);
+        fillValue = new VarDouble("Fill value", 255.0);
+        labeled = new VarBoolean("Labeled", Boolean.FALSE);
+        varOut = new VarSequence("Sequence", null);
+    }
+
+    @Override
+    public void declareInput(VarList inputMap)
+    {
+        inputMap.add("rois", inputROI);
+        inputMap.add("sizeX", sizeX);
+        inputMap.add("sizeY", sizeY);
+        inputMap.add("sizeC", sizeC);
+        inputMap.add("sizeZ", sizeZ);
+        inputMap.add("sizeT", sizeT);
+        inputMap.add("dataType", dataType);
+        // inputMap.add("fillValue", fillValue);
+        inputMap.add("labeled", labeled);