Initial version

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>

.gitignore

+/target/

pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+		http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>org.scijava</groupId>
+		<artifactId>pom-scijava</artifactId>
+		<version>1.19</version>
+	</parent>
+
+	<groupId>sc.fiji</groupId>
+	<artifactId>Process_Pixels</artifactId>
+	<version>1.0.0</version>
+
+	<name>plugins/Process_Pixels.jar</name>
+	<description>A Maven project implementing an ImageJ 1.x plugin</description>
+
+	<dependencies>
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>ij</artifactId>
+			<version>${imagej1.version}</version>
+		</dependency>
+	</dependencies>
+
+</project>

src/main/java/Process_Pixels.java

+import ij.IJ;
+import ij.ImagePlus;
+import ij.gui.GenericDialog;
+import ij.plugin.filter.PlugInFilter;
+import ij.process.ImageProcessor;
+
+/**
+ * ProcessPixels
+ *
+ * A template for processing each pixel of either
+ * GRAY8, GRAY16, GRAY32 or COLOR_RGB images.
+ *
+ * @author The Fiji Team
+ */
+public class Process_Pixels implements PlugInFilter {
+	protected ImagePlus image;
+
+	// image property members
+	private int width;
+	private int height;
+
+	// plugin parameters
+	public double value;
+	public String name;
+
+	/**
+	 * @see ij.plugin.filter.PlugInFilter#setup(java.lang.String, ij.ImagePlus)
+	 */
+	@Override
+	public int setup(String arg, ImagePlus imp) {
+		if (arg.equals("about")) {
+			showAbout();
+			return DONE;
+		}
+
+		image = imp;
+		return DOES_8G | DOES_16 | DOES_32 | DOES_RGB;
+	}
+
+	/**
+	 * @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
+	 */
+	@Override
+	public void run(ImageProcessor ip) {
+		// get width and height
+		width = ip.getWidth();
+		height = ip.getHeight();
+
+		if (showDialog()) {
+			process(ip);
+			image.updateAndDraw();
+		}
+	}
+
+	private boolean showDialog() {
+		GenericDialog gd = new GenericDialog("Process pixels");
+
+		// default value is 0.00, 2 digits right of the decimal point
+		gd.addNumericField("value", 0.00, 2);
+		gd.addStringField("name", "John");
+
+		gd.showDialog();
+		if (gd.wasCanceled())
+			return false;
+
+		// get entered values
+		value = gd.getNextNumber();
+		name = gd.getNextString();
+
+		return true;
+	}
+
+	/**
+	 * Process an image.
+	 *
+	 * Please provide this method even if {@link ij.plugin.filter.PlugInFilter} does require it;
+	 * the method {@link ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)} can only
+	 * handle 2-dimensional data.
+	 *
+	 * If your plugin does not change the pixels in-place, make this method return the results and
+	 * change the {@link #setup(java.lang.String, ij.ImagePlus)} method to return also the
+	 * <i>DOES_NOTHING</i> flag.
+	 *
+	 * @param image the image (possible multi-dimensional)
+	 */
+	public void process(ImagePlus image) {
+		// slice numbers start with 1 for historical reasons
+		for (int i = 1; i <= image.getStackSize(); i++)
+			process(image.getStack().getProcessor(i));
+	}
+
+	// Select processing method depending on image type
+	public void process(ImageProcessor ip) {
+		int type = image.getType();
+		if (type == ImagePlus.GRAY8)
+			process( (byte[]) ip.getPixels() );
+		else if (type == ImagePlus.GRAY16)
+			process( (short[]) ip.getPixels() );
+		else if (type == ImagePlus.GRAY32)
+			process( (float[]) ip.getPixels() );
+		else if (type == ImagePlus.COLOR_RGB)
+			process( (int[]) ip.getPixels() );
+		else {
+			throw new RuntimeException("not supported");
+		}
+	}
+
+	// processing of GRAY8 images
+	public void process(byte[] pixels) {
+		for (int y=0; y < height; y++) {
+			for (int x=0; x < width; x++) {
+				// process each pixel of the line
+				// example: add 'number' to each pixel
+				pixels[x + y * width] += (byte)value;
+			}
+		}
+	}
+
+	// processing of GRAY16 images
+	public void process(short[] pixels) {
+		for (int y=0; y < height; y++) {
+			for (int x=0; x < width; x++) {
+				// process each pixel of the line
+				// example: add 'number' to each pixel
+				pixels[x + y * width] += (short)value;
+			}
+		}
+	}
+
+	// processing of GRAY32 images
+	public void process(float[] pixels) {
+		for (int y=0; y < height; y++) {
+			for (int x=0; x < width; x++) {
+				// process each pixel of the line
+				// example: add 'number' to each pixel
+				pixels[x + y * width] += (float)value;
+			}
+		}
+	}
+
+	// processing of COLOR_RGB images
+	public void process(int[] pixels) {
+		for (int y=0; y < height; y++) {
+			for (int x=0; x < width; x++) {
+				// process each pixel of the line
+				// example: add 'number' to each pixel
+				pixels[x + y * width] += (int)value;
+			}
+		}
+	}
+
+	void showAbout() {
+		IJ.showMessage("ProcessPixels",
+			"a template for processing each pixel of an image"
+		);
+	}
+}

src/main/resources/plugins.config

+# Name: Process Pixels
+# Author: The Fiji Team
+# Version: 1.0.0
+
+# A single .jar file can contain multiple plugins, specified in separate lines.
+#
+# The format is: <menu>, "<menu label>", <class name>
+#
+# If something like ("<arg>") is appended to the class name, the setup() method
+# will get that as arg parameter; otherwise arg is simply the empty string.
+
+Process, "Process Pixels", Process_Pixels