Added SRM

build/classes/filtro_chido/Filtrado.form

@@ -64,6 +64,7 @@
                               <Component id="jButton1" max="32767" attributes="0"/>
                               <Component id="jButton2" max="32767" attributes="0"/>
                               <Component id="jButton3" max="32767" attributes="0"/>
+                              <Component id="jButton4" max="32767" attributes="0"/>
                           </Group>
                       </Group>
                       <Component id="jPanel2" alignment="0" min="-2" max="-2" attributes="0"/>
@@ -83,6 +84,8 @@
                           <Component id="jButton2" min="-2" pref="36" max="-2" attributes="0"/>
                           <EmptySpace type="separate" max="-2" attributes="0"/>
                           <Component id="jButton1" min="-2" pref="33" max="-2" attributes="0"/>
+                          <EmptySpace max="-2" attributes="0"/>
+                          <Component id="jButton4" min="-2" pref="34" max="-2" attributes="0"/>
                       </Group>
                   </Group>
                   <EmptySpace pref="27" max="32767" attributes="0"/>
@@ -172,6 +175,14 @@
             <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButton3ActionPerformed"/>
           </Events>
         </Component>
+        <Component class="javax.swing.JButton" name="jButton4">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="SRM"/>
+          </Properties>
+          <Events>
+            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButton4ActionPerformed"/>
+          </Events>
+        </Component>
       </SubComponents>
     </Container>
   </SubComponents>

src/filtro_chido/Filtrado.form

@@ -64,6 +64,7 @@
                               <Component id="jButton1" max="32767" attributes="0"/>
                               <Component id="jButton2" max="32767" attributes="0"/>
                               <Component id="jButton3" max="32767" attributes="0"/>
+                              <Component id="jButton4" max="32767" attributes="0"/>
                           </Group>
                       </Group>
                       <Component id="jPanel2" alignment="0" min="-2" max="-2" attributes="0"/>
@@ -83,6 +84,8 @@
                           <Component id="jButton2" min="-2" pref="36" max="-2" attributes="0"/>
                           <EmptySpace type="separate" max="-2" attributes="0"/>
                           <Component id="jButton1" min="-2" pref="33" max="-2" attributes="0"/>
+                          <EmptySpace max="-2" attributes="0"/>
+                          <Component id="jButton4" min="-2" pref="34" max="-2" attributes="0"/>
                       </Group>
                   </Group>
                   <EmptySpace pref="27" max="32767" attributes="0"/>
@@ -172,6 +175,14 @@
             <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButton3ActionPerformed"/>
           </Events>
         </Component>
+        <Component class="javax.swing.JButton" name="jButton4">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="SRM"/>
+          </Properties>
+          <Events>
+            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButton4ActionPerformed"/>
+          </Events>
+        </Component>
       </SubComponents>
     </Container>
   </SubComponents>

src/filtro_chido/Filtrado.java

@@ -36,6 +36,7 @@ public class Filtrado extends javax.swing.JFrame {
         jButton1 = new javax.swing.JButton();
         jButton2 = new javax.swing.JButton();
         jButton3 = new javax.swing.JButton();
+        jButton4 = new javax.swing.JButton();
 
         setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
         setName("Panel_Principal"); // NOI18N
@@ -91,6 +92,13 @@ public class Filtrado extends javax.swing.JFrame {
             }
         });
 
+        jButton4.setText("SRM");
+        jButton4.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                jButton4ActionPerformed(evt);
+            }
+        });
+
         javax.swing.GroupLayout jPanel1Layout = new javax.swing.GroupLayout(jPanel1);
         jPanel1.setLayout(jPanel1Layout);
         jPanel1Layout.setHorizontalGroup(
@@ -107,7 +115,8 @@ public class Filtrado extends javax.swing.JFrame {
                         .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
                             .addComponent(jButton1, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                             .addComponent(jButton2, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
-                            .addComponent(jButton3, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)))
+                            .addComponent(jButton3, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                            .addComponent(jButton4, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)))
                     .addComponent(jPanel2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                 .addGap(0, 176, Short.MAX_VALUE))
         );
@@ -121,7 +130,9 @@ public class Filtrado extends javax.swing.JFrame {
                         .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                         .addComponent(jButton2, javax.swing.GroupLayout.PREFERRED_SIZE, 36, javax.swing.GroupLayout.PREFERRED_SIZE)
                         .addGap(18, 18, 18)
-                        .addComponent(jButton1, javax.swing.GroupLayout.PREFERRED_SIZE, 33, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                        .addComponent(jButton1, javax.swing.GroupLayout.PREFERRED_SIZE, 33, javax.swing.GroupLayout.PREFERRED_SIZE)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(jButton4, javax.swing.GroupLayout.PREFERRED_SIZE, 34, javax.swing.GroupLayout.PREFERRED_SIZE)))
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 27, Short.MAX_VALUE)
                 .addComponent(jLabel1)
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
@@ -157,6 +168,10 @@ public class Filtrado extends javax.swing.JFrame {
         
     }//GEN-LAST:event_jButton3ActionPerformed
 
+    private void jButton4ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButton4ActionPerformed
+        SRM();
+    }//GEN-LAST:event_jButton4ActionPerformed
+
     /**
      * @param args the command line arguments
      */
@@ -196,6 +211,7 @@ public class Filtrado extends javax.swing.JFrame {
     private javax.swing.JButton jButton1;
     private javax.swing.JButton jButton2;
     private javax.swing.JButton jButton3;
+    private javax.swing.JButton jButton4;
     private javax.swing.JLabel jLabel1;
     private javax.swing.JPanel jPanel1;
     private javax.swing.JPanel jPanel2;
@@ -206,4 +222,8 @@ public class Filtrado extends javax.swing.JFrame {
         AdaptiveMedian mediana =new AdaptiveMedian();
         mediana.showDialog(null, null, null);
     }
+    private void SRM (){
+        SRM srm1 = new SRM();
+        
+    }
 }

src/filtro_chido/Filtro_Chido.java

@@ -15,6 +15,7 @@ public class Filtro_Chido {
     public static void main(String[] args) {
         Filtrado fl = new Filtrado();
         fl.show();
+        
     }
     
 }

src/filtro_chido/SRM.java

@@ -0,0 +1,378 @@
+
+package filtro_chido;
+
+import ij.IJ;
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.gui.GenericDialog;
+import ij.plugin.filter.PlugInFilter;
+import static ij.plugin.filter.PlugInFilter.DOES_8G;
+import static ij.plugin.filter.PlugInFilter.NO_CHANGES;
+import ij.process.ByteProcessor;
+import ij.process.FloatProcessor;
+import ij.process.ImageProcessor;
+import ij.process.ShortProcessor;
+
+import java.util.Arrays;
+
+
+public class SRM implements PlugInFilter {
+	ImagePlus image;
+
+	public int setup(String arg, ImagePlus image) {
+		this.image = image;
+		return DOES_8G | NO_CHANGES;
+	}
+
+	public void run(ImageProcessor ip) {
+		boolean isStack = image.getStackSize() > 1;
+
+		GenericDialog gd = new GenericDialog("SRM");
+		gd.addNumericField("Q", Q, 2);
+		gd.addCheckbox("showAverages", true);
+		if (isStack)
+			gd.addCheckbox("3d", true);
+		gd.showDialog();
+
+		if (gd.wasCanceled())
+			return;
+
+		Q = (float)gd.getNextNumber();
+		boolean showAverages = gd.getNextBoolean();
+		boolean do3D = isStack ? gd.getNextBoolean() : false;
+		if (do3D)
+			srm3D(showAverages).show();
+		else
+			srm2D(ip, showAverages).show();
+	}
+
+	final float g = 256; // number of different intensity values
+	protected float Q = 25; //25; // complexity of the assumed distributions
+	protected float delta;
+
+	protected float factor, logDelta;
+
+	float[] average;
+	int[] count;
+	int[] regionIndex; // if < 0, it is -1 - actual_regionIndex
+
+	int[] nextNeighbor, neighborBucket;
+
+	protected ImagePlus srm3D(boolean showAverages) {
+		int w = image.getWidth(), h = image.getHeight();
+		int d = image.getStackSize();
+
+		delta = 1f / (6 * w * h * d);
+		
+		factor = g * g / 2 / Q;
+		logDelta = 2f * (float)Math.log(6 * w * h * d);
+
+		IJ.showStatus("Initializing regions");
+		initializeRegions3D(w, h, d);
+		IJ.showStatus("Initializing neighbors");
+		initializeNeighbors3D(w, h, d);
+		IJ.showStatus("Merging neighbors");
+		mergeAllNeighbors3D(w, h);
+		IJ.showStatus("Making stack");
+
+		ImageStack stack = new ImageStack(w, h);
+		if (showAverages)
+			for (int k = 0; k < d; k++) {
+				int off = k * w * h;
+				float[] p = new float[w * h];
+				for (int i = 0; i < w * h; i++)
+					p[i] = average[getRegionIndex(i + off)];
+				stack.addSlice(null, new FloatProcessor(w, h,
+							p, null));
+			}
+		else {
+			int regionCount = consolidateRegions();
+
+			if (regionCount > 1<<16)
+				IJ.showMessage("Found " + regionCount
+					+ " regions, which does not fit"
+					+ " in 16-bit.");
+
+			for (int k = 0; k < d; k++) {
+				ImageProcessor ip;
+
+				int off = k * w * h;
+
+				if (regionCount > 1<<8) {
+					short[] p = new short[w * h];
+					for (int i = 0; i < p.length; i++)
+						p[i] = (short)regionIndex[i
+							+ off];
+					ip = new ShortProcessor(w, h, p, null);
+				}
+				else {
+					byte[] p = new byte[w * h];
+					for (int i = 0; i < p.length; i++)
+						p[i] = (byte)regionIndex[i
+							+ off];
+					ip = new ByteProcessor(w, h, p, null);
+				}
+				stack.addSlice(null, ip);
+			}
+		}
+
+		IJ.showStatus("");
+		String title = image.getTitle() + " (SRM3D Q=" + Q + ")";
+		return new ImagePlus(title, stack);
+	}
+
+	protected ImagePlus srm2D(ImageProcessor ip, boolean showAverages) {
+		int w = ip.getWidth(), h = ip.getHeight();
+
+		delta = 1f / (6 * w * h);
+		
+		factor = g * g / 2 / Q;
+		logDelta = 2f * (float)Math.log(6 * w * h);
+
+		byte[] pixel = (byte[])ip.getPixels();
+		initializeRegions2D(pixel, ip.getWidth(), ip.getHeight());
+		initializeNeighbors2D(pixel, w, h);
+		mergeAllNeighbors2D(w);
+
+		if (showAverages) {
+			for (int i = 0; i < average.length; i++)
+				average[i] = average[getRegionIndex(i)];
+			ip = new FloatProcessor(w, h, average, null);
+		}
+		else {
+			int regionCount = consolidateRegions();
+
+			if (regionCount > 1<<8) {
+				if (regionCount > 1<<16)
+					IJ.showMessage("Found " + regionCount
+						+ " regions, which does not fit"
+						+ " in 16-bit.");
+				short[] pixel16 = new short[w * h];
+				for (int i = 0; i < pixel16.length; i++)
+					pixel16[i] = (short)regionIndex[i];
+				ip = new ShortProcessor(w, h, pixel16, null);
+			}
+			else {
+				pixel = new byte[w * h];
+				for (int i = 0; i < pixel.length; i++)
+					pixel[i] = (byte)regionIndex[i];
+				ip = new ByteProcessor(w, h, pixel, null);
+			}
+		}
+
+		String title = image.getTitle() + " (SRM Q=" + Q + ")";
+		return new ImagePlus(title, ip);
+	}
+
+	void initializeRegions2D(byte[] pixel, int w, int h) {
+		average = new float[w * h];
+		count = new int[w * h];
+		regionIndex = new int[w * h];
+
+		for (int i = 0; i < average.length; i++) {
+			average[i] = pixel[i] & 0xff;
+			count[i] = 1;
+			regionIndex[i] = i;
+		}
+	}
+
+	void initializeRegions3D(int w, int h, int d) {
+		average = new float[w * h * d];
+		count = new int[w * h * d];
+		regionIndex = new int[w * h * d];
+
+		for (int j = 0; j < d; j++) {
+			byte[] pixel =
+				(byte[])image.getStack().getProcessor(j
+						+ 1).getPixels();
+			int offset = j * w * h;
+			for (int i = 0; i < w * h; i++) {
+				average[offset + i] = pixel[i] & 0xff;
+				count[offset + i] = 1;
+				regionIndex[offset + i] = offset + i;
+			}
+		}
+	}
+
+	protected void addNeighborPair(int neighborIndex,
+			byte[] pixel, int i1, int i2) {
+		int difference = Math.abs((pixel[i1] & 0xff)
+				- (pixel[i2] & 0xff));
+		nextNeighbor[neighborIndex] = neighborBucket[difference];
+		neighborBucket[difference] = neighborIndex;
+	}
+
+	void initializeNeighbors2D(byte[] pixel, int w, int h) {
+		nextNeighbor = new int[2 * w * h];
+
+		// bucket sort
+		neighborBucket = new int[256];
+		Arrays.fill(neighborBucket, -1);
+
+		for (int j = h - 1; j >= 0; j--)
+			for (int i = w - 1; i >= 0; i--) {
+				int index = i + w * j;
+				int neighborIndex = 2 * index;
+
+				// vertical
+				if (j < h - 1)
+					addNeighborPair(neighborIndex + 1,
+						pixel, index, index + w);
+
+				// horizontal
+				if (i < w - 1)
+					addNeighborPair(neighborIndex,
+						pixel, index, index + 1);
+			}
+	}
+
+	protected void addNeighborPair(int neighborIndex,
+			byte[] pixel, byte[] nextPixel, int i) {
+		int difference = Math.abs((pixel[i] & 0xff)
+				- (nextPixel[i] & 0xff));
+		nextNeighbor[neighborIndex] = neighborBucket[difference];
+		neighborBucket[difference] = neighborIndex;
+	}
+
+	void initializeNeighbors3D(int w, int h, int d) {
+		nextNeighbor = new int[3 * w * h * d];
+
+		// bucket sort
+		neighborBucket = new int[256];
+		Arrays.fill(neighborBucket, -1);
+
+		byte[] nextPixel = null;
+		for (int k = d - 1; k >= 0; k--) {
+			byte[] pixel =
+				(byte[])image.getStack().getProcessor(k
+						+ 1).getPixels();
+			for (int j = h - 1; j >= 0; j--)
+				for (int i = w - 1; i >= 0; i--) {
+					int index = i + w * j;
+					int neighborIndex =
+						3 * (index + k * w * h);
+
+					// depth
+					if (nextPixel != null)
+						addNeighborPair(neighborIndex
+								+ 2, pixel,
+							nextPixel, index);
+
+					// vertical
+					if (j < h - 1)
+						addNeighborPair(neighborIndex
+								+ 1, pixel,
+							index, index + w);
+
+					// horizontal
+					if (i < w - 1)
+						addNeighborPair(neighborIndex,
+							pixel,
+							index, index + 1);
+				}
+			nextPixel = pixel;
+		}
+	}
+
+	// recursively find out the region index for this pixel
+	int getRegionIndex(int i) {
+		i = regionIndex[i];
+		while (i < 0)
+			i = regionIndex[-1 - i];
+		return i;
+	}
+
+	// should regions i1 and i2 be merged?
+	boolean predicate(int i1, int i2) {
+		float difference = average[i1] - average[i2];
+		/*
+		 * This would be the non-relaxed predicate mentioned in the
+		 * paper.
+		 *
+		 * return difference * difference <
+			factor * (1f / count[i1] + 1f / count[i2]);
+		 *
+		 */
+		float log1 = (float)Math.log(1 + count[i1])
+			* (g < count[i1] ? g : count[i1]);
+		float log2 = (float)Math.log(1 + count[i2])
+			* (g < count[i2] ? g : count[i2]);
+		return difference * difference <
+			.1f * factor * ((log1 + logDelta) / count[i1]
+				+ ((log2 + logDelta) / count[i2]));
+	}
+
+	void mergeAllNeighbors2D(int w) {
+		for (int i = 0; i < neighborBucket.length; i++) {
+			int neighborIndex = neighborBucket[i];
+			while (neighborIndex >= 0) {
+				int i1 = neighborIndex / 2;
+				int i2 = i1
+					+ (0 == (neighborIndex & 1) ? 1 : w);
+
+				i1 = getRegionIndex(i1);
+				i2 = getRegionIndex(i2);
+
+				if (predicate(i1, i2))
+					mergeRegions(i1, i2);
+
+				neighborIndex = nextNeighbor[neighborIndex];
+			}
+		}
+	}
+
+	void mergeAllNeighbors3D(int w, int h) {
+		for (int i = 0; i < neighborBucket.length; i++) {
+			int neighborIndex = neighborBucket[i];
+			IJ.showProgress(i, neighborBucket.length);
+			while (neighborIndex >= 0) {
+				int i1 = neighborIndex / 3;
+				int i2 = i1
+					+ (0 == (neighborIndex % 3) ? 1 :
+					  (1 == (neighborIndex % 3) ? w :
+					   w * h));
+
+				i1 = getRegionIndex(i1);
+				i2 = getRegionIndex(i2);
+
+				if (i1 != i2 && predicate(i1, i2))
+					mergeRegions(i1, i2);
+
+				neighborIndex = nextNeighbor[neighborIndex];
+			}
+		}
+		IJ.showProgress(neighborBucket.length, neighborBucket.length);
+	}
+
+	void mergeRegions(int i1, int i2) {
+		if (i1 == i2)
+			return;
+		int mergedCount = count[i1] + count[i2];
+		float mergedAverage = (average[i1] * count[i1]
+				+ average[i2] * count[i2]) / mergedCount;
+
+		// merge larger index into smaller index
+		if (i1 > i2) {
+			average[i2] = mergedAverage;
+			count[i2] = mergedCount;
+			regionIndex[i1] = -1 - i2;
+		}
+		else {
+			average[i1] = mergedAverage;
+			count[i1] = mergedCount;
+			regionIndex[i2] = -1 - i1;
+		}
+	}
+
+	int consolidateRegions() {
+	
+		int count = 0;
+		for (int i = 0; i < regionIndex.length; i++)
+			if (regionIndex[i] < 0)
+				regionIndex[i] =
+					regionIndex[-1 - regionIndex[i]];
+			else
+				regionIndex[i] = count++;
+		return count;
+	}
+}