/*
 * #%L
 * ImageJ software for multidimensional image processing and analysis.
 * %%
 * Copyright (C) 2009 - 2012 Board of Regents of the University of
 * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
 * Institute of Molecular Cell Biology and Genetics.
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 * 
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 * 
 * The views and conclusions contained in the software and documentation are
 * those of the authors and should not be interpreted as representing official
 * policies, either expressed or implied, of any organization.
 * #L%
 */

package imagej.core.plugins.assign;

import imagej.core.options.OptionsMisc;
import imagej.data.Dataset;
import imagej.data.display.DatasetView;
import imagej.data.display.ImageDisplay;
import imagej.data.display.ImageDisplayService;
import imagej.data.display.OverlayService;
import imagej.data.overlay.Overlay;
import imagej.ext.plugin.RunnablePlugin;
import imagej.ext.plugin.Menu;
import imagej.ext.plugin.Parameter;
import imagej.ext.plugin.Plugin;
import imagej.menu.MenuConstants;
import imagej.module.ItemIO;
import imagej.options.OptionsService;
import net.imglib2.Cursor;
import net.imglib2.ops.operation.real.unary.RealInvert;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.real.DoubleType;

/**
 * Fills an output Dataset by applying an inversion to an input Dataset's data
 * values. The inversion is relative to the minimum and maximum data values
 * present in the input Dataset. However in IJ1 inversion for 8-bit data is
 * relative to 0 & 255 and that behavior is mirrored here as well.
 * 
 * @author Barry DeZonia
 */
@Plugin(menu = {
	@Menu(label = MenuConstants.EDIT_LABEL, weight = MenuConstants.EDIT_WEIGHT,
		mnemonic = MenuConstants.EDIT_MNEMONIC),
	@Menu(label = "Invert...", weight = 30, accelerator = "shift control I") },
	headless = true)
public class InvertDataValues<T extends RealType<T>> implements RunnablePlugin {

	// -- instance variables that are Parameters --

	@Parameter
	private OverlayService overlayService;

	@Parameter
	private ImageDisplayService imgDispService;

	@Parameter
	private OptionsService optionsService;

	@Parameter(type = ItemIO.BOTH)
	private ImageDisplay display;

	@Parameter(label = "Apply to all planes")
	private boolean allPlanes;

	// -- other instance variables --
	
	private double min, max;

	// -- public interface --

	@Override
	public void run() {
		Dataset dataset = imgDispService.getActiveDataset(display);
		Overlay overlay = overlayService.getActiveOverlay(display);
		DatasetView view = imgDispService.getActiveDatasetView(display);
		OptionsMisc options = optionsService.getOptions(OptionsMisc.class);
		
		if (options.isLegacyMode() && dataset.isInteger() && !dataset.isSigned() &&
			dataset.getType().getBitsPerPixel() == 8)
		{
			min = 0;
			max = 255;
		}
		else calcValueRange(dataset);
		final RealInvert<DoubleType, DoubleType> op =
			new RealInvert<DoubleType, DoubleType>(min, max);
		
		final InplaceUnaryTransform<T, DoubleType> transform;
		
		if (allPlanes)
			transform = 
				new InplaceUnaryTransform<T, DoubleType>(
					op, new DoubleType(), dataset, overlay);
		else
			transform = 
				new InplaceUnaryTransform<T, DoubleType>(
					op, new DoubleType(), dataset, overlay,
					view.getPlanePosition());
		
		transform.run();
	}

	public ImageDisplay getDisplay() {
		return display;
	}

	public void setDisplay(ImageDisplay display) {
		this.display = display;
	}

	public boolean isAllPlanes() {
		return allPlanes;
	}
	
	public void setAllPlanes(boolean value) {
		this.allPlanes = value;
	}

	// -- private interface --

	/**
	 * Finds the smallest and largest data values actually present in the input
	 * image
	 */
	private void calcValueRange(Dataset dataset) {
		min = Double.MAX_VALUE;
		max = -Double.MAX_VALUE;

		final Cursor<? extends RealType<?>> cursor = dataset.getImgPlus().cursor();

		while (cursor.hasNext()) {
			final double value = cursor.next().getRealDouble();

			if (value < min) min = value;
			if (value > max) max = value;
		}
	}

}

@@ -2753,108 +2753,110 @@
 ver 
-in IJ1 inversion for 8-bit data is%0A * relative to 0 & 255 and that behavior is mirrored here as well
+when legacy compatibility mode is%0A * enabled an unsigned 8-bit dataset is inverted relative to 0 & 255
 .%0A *

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