Hadoop pipeline complete

extract_detect/Hadoop/Convert.java

@@ -51,6 +51,12 @@ public static double[][] convertImageCompress(String name, int scale) throws IOE
 		return out;
 	}
 
+	/**
+	 * Returns a double array of an image with each cell representing a pixel
+	 * 
+	 * @param image
+	 * @return the 2D double array representing the image
+	 */
 	public static double[][] convertByte(byte[][] image) {
 		double[][] out = new double[image.length][image[0].length];
 		for (int x = 0; x < image.length; x++) {

extract_detect/Hadoop/Extract.java

@@ -6,7 +6,7 @@
 import java.util.Arrays;
 
 /**
- * Hadoop with MapReduce, image only version
+ * Extracts image and metadata from MSTIFF 
  *
  */
 public class Extract { 
@@ -63,7 +63,8 @@ public class Extract {
 	private static long[] Fatho_timestamp_sec;
 
 	// Save
-	public static byte[][] imTemp;
+	public static byte[][] imTempR;
+	public static byte[][] imTempL;
 	public static String[][] metaTemp;
 	private static String lastFile;
 
@@ -98,7 +99,8 @@ public static boolean init() {
 		fileHeader[0][6] = "WaterDepth";
 		fileHeader[0][7] = "TowfishDepth";
 
-		imTemp = new byte[0][0];
+		imTempR = new byte[0][0];
+		imTempL = new byte[0][0];
 		metaTemp = new String[0][0];
 		lastFile = "empty";
 		count = 0;
@@ -225,7 +227,7 @@ public static boolean fileProcess(String x) throws IOException {
 		Extract.metaInit();
 
 		// Check if first
-		if (imTemp == null)
+		if (imTempR == null)
 			init();
 
 		// Save if last of mission
@@ -254,14 +256,15 @@ public static boolean fileProcess(String x) throws IOException {
 		}
 
 		// Combine left and right channels, previous image
-		if (imTemp.length != 0) {
-			imTemp = Util.combineVertically(imTemp, Util.combineHorizontally(left, right));
+		if (imTempR.length != 0) {
+			imTempR = Util.combineVertically(imTempR, right);
+			imTempL = Util.combineVertically(imTempL, left);
 			saveIm();
-			System.out.println("saveIm should have ran");
-			imTemp = Util.combineHorizontally(left, right);
+			imTempR = right;
+			imTempL = left;
 		} else {
-			System.out.println("saveIm should have ran");
-			imTemp = Util.combineHorizontally(left, right);
+			imTempR = right;
+			imTempL = left;
 		}
 
 		// Add metadata to growing table
@@ -278,17 +281,17 @@ public static boolean fileProcess(String x) throws IOException {
 	 * Save image
 	 */
 	public static void saveIm() {
-		Util.saveIm(imTemp, "im" + count, false);
-		System.out.println("saveIm" + count);
+		Util.saveIm(Util.combineHorizontally(imTempL, imTempR), "im" + count, false);
 		count++;
 	}
 
 	/**
 	 * Save metadata as CSV
 	 */
 	public static void saveMeta() throws IOException {
-//		Util.saveIm(imTemp, "im" + count);
-		imTemp = new byte[0][0];
+//		Util.saveIm(imTempR, "im" + count);
+		imTempR = new byte[0][0];
+		imTempL = new byte[0][0];
 		String tempLabel = Util.remPath(lastFile);
 		Util.save(metaTemp, tempLabel + "META");
 		metaTemp = new String[0][0];

extract_detect/Hadoop/MacroMaster.java

@@ -5,56 +5,51 @@
  *
  */
 public class MacroMaster {
-
-	static byte[][] im;
-	static String name;
-	static int dim = 200;
 
-	static boolean lastVal = false;
-
-	public static byte[][] findMine(byte[][] imTemp, String nameSet) throws IOException {
-		init(imTemp, nameSet);
+	static byte[][] imL;
+	static byte[][] imR;
+	static byte[][] im;
+	static int dim = 150;
 
+	public static boolean findMine(byte[][] imTemp, char side) throws IOException {
+		im = imTemp;
 		boolean[][][] layers;
 		boolean[][] bmap;
 
+		// find dark spots
 		Slide.init(im, dim, true);
 		layers = new boolean[2][Slide.bmap.length][Slide.bmap[0].length];
-
 		Slide.process();
 		layers[0] = Slide.bmap;
 
+		// find light spots
 		Slide.init(im, dim, false);
 		Slide.process();
 		layers[1] = Slide.bmap;
 
 		byte[][] imOut = new byte[imTemp.length][imTemp[0].length];
 
+		// find overlapping areas
 		bmap = new boolean[layers[0].length][layers[0][0].length];
 		for (int r = 0; r < bmap.length; r++) {
 			for (int c = 0; c < bmap[0].length; c++) {
 				bmap[r][c] = layers[0][r][c] && layers[1][r][c];
+				if(bmap[r][c]) System.out.println(r + ", " + c);
+
+				// identify bounds of frame on original image and highlight if needed
 				int[] temp = Util.refitRect(r, c, bmap[0].length, bmap.length, imTemp[0].length, imTemp.length);
 				for (int x = temp[1]; x < (temp[3] < imTemp.length ? temp[3] : imTemp.length); x++) {
 					for (int y = temp[0]; y < (temp[2] < imTemp[0].length ? temp[2] : imTemp[0].length); y++) {
-						if (bmap[r][c]) imOut[x][y] = (byte)(Util.getByteVal(imTemp[x][y]) > 150 ? 255 : Util.getByteVal(imTemp[x][y]) + 100);
+						if (bmap[r][c]) { imOut[x][y] = (byte)(Util.getByteVal(imTemp[x][y]) > 150 ? 255 : Util.getByteVal(imTemp[x][y]) + 100); }
 						else imOut[x][y] = imTemp[x][y];
-//						System.out.println(x + " " + y);
-					}
+					}						
 				}
 			}
 		}
 
-		Util.saveIm(imOut, nameSet, false);
+		if (side == 'L') imL = imOut;
+		else imR = imOut;
 
-		lastVal = Calc.containsTrue(bmap);
-
-		return imOut;
-	}
-
-	public static void init(byte[][] imSet, String nameSet) {
-
-		im = imSet;
-		name = nameSet;
+		return Calc.containsTrue(bmap);
 	}
 }

extract_detect/Hadoop/Master.java

@@ -1,5 +1,3 @@
-import java.io.FileNotFoundException;
-
 import java.io.IOException;
 
 /**
@@ -49,7 +47,7 @@ public static boolean process(double[][] vals) {
 		int cenN;
 
 		tmap = Converter.convert(vals);
-		double minP = dark ? 28.3 : 20;
+		double minP = dark ? 28.1 : 22.5;
 		rmap = Scan(tmap, 3, minP);
 		rmap = ColorReduce(rmap, Scan.cenN);
 		bmap = Converter.convert(rmap);