Merge origin/tuananh into new-feature

Conflicts:
	src/main/java/ijfx/plugins/ImageJ1PluginAdapter.java
	src/main/java/ijfx/service/preview/PreviewService.java
	src/main/resources/ijfx/ui/main/flatterfx.css
	src/main/resources/ijfx/ui/menutoolbar/toolbarSettings.json

.gitignore

@@ -3,4 +3,5 @@ log-*.txt.lck
 *.log
 *.gz
 package.sh
-target/*
+target/*
+/nbproject/

src/main/java/ijfx/bridge/FxUserInterfaceBridge.java

@@ -25,6 +25,7 @@
 import ijfx.ui.datadisplay.image.ImageWindow;
 import ijfx.ui.main.ImageJFX;
 import ijfx.ui.datadisplay.table.TableWindow;
+import ijfx.ui.datadisplay.text.TextWindow;
 import java.io.File;
 import java.util.concurrent.ExecutionException;
 import java.util.logging.Level;
@@ -47,6 +48,7 @@
 import org.scijava.ui.UserInterface;
 import org.scijava.ui.viewer.DisplayWindow;
 import mongis.utils.FXUtilities;
+import org.scijava.display.TextDisplay;
 
 /**
  * UI bridge between ImageJFX and ImageJ
@@ -204,7 +206,15 @@ public void show(final Display<?> dspl) {
                 ImageWindowContainer.getInstance().getChildren().add(new TableWindow((TableDisplay) dspl));
             });
 
-        } else {
+        } 
+        else if (dspl instanceof TextDisplay) {
+            Platform.runLater(() -> {
+
+                ImageWindowContainer.getInstance().getChildren().add(new TextWindow((TextDisplay) dspl));
+            });
+
+        }
+        else {
             logger.warning("Cannot show display type :" + dspl.getClass().getSimpleName());
         }
     }

src/main/java/ijfx/plugins/AbstractImageJ1PluginAdapter.java

@@ -0,0 +1,172 @@
+/*
+ * /*
+ *     This file is part of ImageJ FX.
+ *
+ *     ImageJ FX is free software: you can redistribute it and/or modify
+ *     it under the terms of the GNU General Public License as published by
+ *     the Free Software Foundation, either version 3 of the License, or
+ *     (at your option) any later version.
+ *
+ *     ImageJ FX is distributed in the hope that it will be useful,
+ *     but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *     GNU General Public License for more details.
+ *
+ *     You should have received a copy of the GNU General Public License
+ *     along with ImageJ FX.  If not, see <http://www.gnu.org/licenses/>. 
+ *
+ * 	Copyright 2015,2016 Cyril MONGIS, Michael Knop
+ *
+ */
+package ijfx.plugins;
+
+import ij.ImagePlus;
+import static java.lang.Math.toIntExact;
+import java.util.stream.IntStream;
+import net.imagej.Dataset;
+import net.imagej.DatasetService;
+import net.imagej.axis.Axes;
+import net.imagej.axis.AxisType;
+import net.imagej.axis.CalibratedAxis;
+import net.imagej.display.ImageDisplay;
+import net.imagej.display.ImageDisplayService;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.Img;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.event.EventService;
+import org.scijava.plugin.Parameter;
+
+/**
+ *
+ * @author Cyril MONGIS, 2015
+ * @author Tuan anh TRINH
+ */
+public abstract class AbstractImageJ1PluginAdapter implements Command {
+
+    @Parameter
+    DatasetService service;
+
+    @Parameter
+    ImageDisplayService imageDisplayService;
+
+    @Parameter
+    EventService eventService;
+
+    @Parameter
+    boolean createCopy;
+
+    boolean wholeWrap = false;
+
+    public abstract ImagePlus processImagePlus(ImagePlus input);
+
+    public ImagePlus getInput(Dataset dataset) {
+        return unwrapDataset(dataset);
+    }
+
+    public Dataset setOutput(ImagePlus imp, Dataset dataset) {
+        if (!wholeWrap) {
+            dataset = wrapDataset(imp);
+        } else {
+            ImagePlus resultCopy = imp.duplicate();
+            if (createCopy) {
+                dataset = emptyDataset(dataset, dataset.numDimensions());
+            }
+            Dataset dataset2 = wrapDataset(resultCopy);
+            for (int i = 0; i < getNumberOfSlices(dataset); i++) {
+                dataset.setPlane(i, dataset2.getPlane(i));
+            }
+
+        }
+        return dataset;
+    }
+
+    public static ImagePlus unwrapDataset(Dataset dataset) {
+        RandomAccessibleInterval<UnsignedShortType> r = (RandomAccessibleInterval<UnsignedShortType>) dataset.getImgPlus();
+        ImagePlus wrapImage = ImageJFunctions.wrap(r, "");
+        return wrapImage;
+    }
+
+    public Dataset wrapDataset(ImagePlus imp) {
+        Img img = ImageJFunctions.wrap(imp.duplicate());
+        return service.create(img);
+    }
+
+    public static void configureImagePlus(ImagePlus imp, ImageDisplay imageDisplay) {
+
+        imp.setC(imageDisplay.getIntPosition(Axes.CHANNEL));
+        imp.setZ(imageDisplay.getIntPosition(Axes.Z));
+        imp.setT(imageDisplay.getIntPosition(Axes.TIME));
+
+    }
+
+    private Dataset emptyDataset(Dataset input, int sizeDims) {
+        AxisType[] axisType = new AxisType[input.numDimensions()];
+        CalibratedAxis[] axeArray = new CalibratedAxis[input.numDimensions()];
+        input.axes(axeArray);
+
+        long[] dims = new long[sizeDims];
+        for (int i = 0; i < sizeDims; i++) {
+            axisType[i] = axeArray[i].type();
+            dims[i] = toIntExact(input.max(i) + 1);
+        }
+        return service.create(dims, input.getName(), axisType, input.getValidBits(), input.isSigned(), false);
+    }
+
+    private Dataset chooseDataset(Dataset dataset) {
+        if (createCopy) {
+            return dataset.duplicateBlank();
+        }
+        return dataset;
+    }
+
+    public int getNumberOfSlices(Dataset dataset) {
+
+        return (int) (dataset.getImgPlus().size() / (dataset.dimension(0) * dataset.dimension(1)));
+
+    }
+
+    public Dataset processDataset(Dataset dataset) {
+        Dataset datasetToModify = chooseDataset(dataset);
+
+        for (int i = 0; i < getNumberOfSlices(dataset); i++) {
+            Dataset datasetOnePlane = emptyDataset(dataset, 2);
+            datasetOnePlane.setPlane(0, dataset.getPlane(i));
+            ImagePlus result = processImagePlus(getInput(datasetOnePlane));
+            setOutput(result.duplicate(), datasetOnePlane);
+            datasetToModify.setPlane(i, datasetOnePlane.getPlane(0));
+        }
+        dataset = datasetToModify;
+        return dataset;
+    }
+//
+//    /**
+//     * Wrap the whole Dataset. Use more memory
+//     *
+//     * @param dataset
+//     * @return
+//     */
+//    public Dataset processDatasetWholeWrap(Dataset dataset) {
+//        ImagePlus result = processImagePlus(getInput(dataset));
+//        ImagePlus resultCopy = result.duplicate();
+//        if (createCopy) {
+//            dataset = emptyDataset(dataset, dataset.numDimensions());
+//        }
+//        Dataset dataset2 = wrapDataset(resultCopy);
+//        for (int i = 0; i < getNumberOfSlices(dataset); i++) {
+//            dataset.setPlane(i, dataset2.getPlane(i));
+//        }
+//        return dataset;
+//    }
+
+    public boolean isWholeWrap() {
+        return wholeWrap;
+    }
+
+    public void setWholeWrap(boolean wholeWrap) {
+        this.wholeWrap = wholeWrap;
+    }
+}

src/main/java/ijfx/plugins/DefaultImageJ1PluginAdapter.java

@@ -0,0 +1,49 @@
+/*
+    This file is part of ImageJ FX.
+
+    ImageJ FX is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    ImageJ FX is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with ImageJ FX.  If not, see <http://www.gnu.org/licenses/>. 
+    
+     Copyright 2015,2016 Cyril MONGIS, Michael Knop
+	
+ */
+package ijfx.plugins;
+
+import ij.ImagePlus;
+import net.imagej.Dataset;
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.plugin.Attr;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+/**
+ * 
+ * @author Tuan anh TRINH
+ */
+@Plugin(type = Command.class, menuPath = "Plugins>DefaultAdapter")
+public class DefaultImageJ1PluginAdapter extends AbstractImageJ1PluginAdapter {
+   @Parameter(type = ItemIO.BOTH)
+    protected Dataset dataset;
+    @Override
+    public ImagePlus processImagePlus(ImagePlus input) {
+        return input;
+    }
+
+    @Override
+    public void run() {
+        dataset = processDataset(dataset);
+    }
+
+
+
+}

src/main/java/ijfx/plugins/DefaultWholeWrapper.java

@@ -0,0 +1,51 @@
+/*
+    This file is part of ImageJ FX.
+
+    ImageJ FX is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    ImageJ FX is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with ImageJ FX.  If not, see <http://www.gnu.org/licenses/>. 
+    
+     Copyright 2015,2016 Cyril MONGIS, Michael Knop
+	
+ */
+package ijfx.plugins;
+
+import ij.ImagePlus;
+import java.io.File;
+import net.imagej.Dataset;
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.plugin.Attr;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+/**
+ * 
+ * @author Tuan anh TRINH
+ */
+@Plugin(type = Command.class, menuPath = "Plugins>DefaultWholeAdapter")
+public class DefaultWholeWrapper extends AbstractImageJ1PluginAdapter {
+   @Parameter(type = ItemIO.BOTH)
+    protected Dataset dataset;
+   @Parameter
+   File f;
+    @Override
+    public ImagePlus processImagePlus(ImagePlus input) {
+        return input;
+    }
+
+    @Override
+    public void run() {
+        setWholeWrap(true);
+        dataset = setOutput(getInput(dataset), dataset);
+    }
+
+}