Refactoring, incompatible data file

src/main/java/com/elphel/imagej/orthomosaic/FloatImageData.java

 package com.elphel.imagej.orthomosaic;
 
 import java.awt.Rectangle;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+import java.time.LocalDateTime;
 import java.util.Arrays;
+import java.util.Properties;
 import java.util.concurrent.atomic.AtomicInteger;
 
 import com.elphel.imagej.common.PolynomialApproximation;
+import com.elphel.imagej.readers.ElphelTiffReader;
 import com.elphel.imagej.tileprocessor.ImageDtt;
 
-public class FloatImageData {
-	public int       width;
-	public int       height;
-	public int       zoom_lev;
-	private double [] vert = new double[2]; // x,y offset (in meters) of the point under the camera
-	public float[]   data;
+import ij.ImagePlus;
+
+public class FloatImageData implements Serializable  {
+	private static final long                serialVersionUID = 1L;
+	public static      boolean               FIX_VERT_Y = false; // true; // temporarily fix vertical Y coordinate bug (use -GCORR in the filename?)
+	public             int                   width;
+	public             int                   height;
+	public             int                   zoom_lev;
+	private            boolean               zoom_valid;
+	public             String                path;
+	public             Properties            properties; // serializable
+	private            double []             lla;      // lat/long/alt
+	public             LocalDateTime         dt;
+	private            double []             vert = new double[2]; // x,y offset (in meters) of the point under the camera
+	private            double                pix_meters;
+	private            double                averagePixel=Double.NaN;
+	private transient  float[]               data; // make transient
+	
 	public FloatImageData (
-			int       width,
-			int       height,
-			int       zoom_lev,
-			double [] vert, // x,y pixel offset of the point under the camera
-			float[]   data) {
-		this.width = width;
-		this.height = height;
-		this.zoom_lev = zoom_lev;
-		this.vert = vert.clone();
-		this.data = data;
+			String path) {
+		this.path = path;
+		try {
+			properties = ElphelTiffReader.getTiffMeta(path);				
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		try {
+			lla = ElphelTiffReader.getLLA(properties);
+		} catch (NullPointerException e) {
+			System.out.println("No GPS data in "+path);
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		dt = ElphelTiffReader.getLocalDateTime(properties);
+		vert =      ElphelTiffReader.getXYOffsetMeters(properties);
+		pix_meters = ElphelTiffReader.getPixelSize(properties)[0];
+		if (FIX_VERT_Y) {
+			int height_pix =   ElphelTiffReader.getHeight(properties);
+			double height_meters = height_pix * pix_meters;
+			vert[1] = height_meters-vert[1];
+		}
+		width =  ElphelTiffReader.getWidth(properties);
+		height = ElphelTiffReader.getHeight(properties);
+		zoom_lev = getZoomLevel(pix_meters);
+		zoom_valid = isZoomValid(pix_meters);
 	}
-
-	public int getWidth() {
-		return width;
+	
+	private void writeObject(ObjectOutputStream oos) throws IOException {
+		oos.defaultWriteObject();
 	}
-	public int getHeight() {
-		return height;
+	
+	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
+		ois.defaultReadObject();
+		data = null;
+	}	
+	
+	public void updateLLA() {
+		try {
+			properties = ElphelTiffReader.getTiffMeta(path);				
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		try {
+			lla = ElphelTiffReader.getLLA(properties);
+		} catch (NullPointerException e) {
+			System.out.println("No GPS data in "+path);
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
 	}
 	
-	public double[]  getVertMeters() {
-		return vert;
+	float [] readFData() {
+		if (data == null) {
+			ImagePlus imp = new ImagePlus(path);
+			int width = imp.getWidth();
+			int height = imp.getHeight();
+			if ((width != this.width) || (height != this.height)) {
+				throw new IllegalArgumentException (String.format("IJ image size does not match Exif one: (%d,%d) != (%d,%d)",
+						width,height, this.width,this.height));
+			}
+			data = (float[]) (imp.getProcessor().getPixels());
+		}
+		return data;
 	}
+	
 	public double [] getDData() {
+		if (data==null) {
+			readFData();
+			if (data== null) {
+				return null;
+			}
+		}
 		final double [] ddata = new double [data.length];
 		final Thread[] threads = ImageDtt.newThreadArray();
 		final AtomicInteger ai = new AtomicInteger(0);
@@ -53,6 +124,103 @@ public class FloatImageData {
 		return ddata;
 	}
 	
+
+	public double [] getLLA() {
+		return lla; // null if does not exist, saved with data file 
+	}
+	
+	public LocalDateTime getDT() {
+		return dt;
+	}
+	
+	public boolean isZoomValid() {
+		if (!zoom_valid) {
+			System.out.println("Original zoom level is invalid, need_extra_zoom = "+needZoomIn(pix_meters));
+		}
+		return zoom_valid;
+	}
+	
+	/**
+	 * Get vertical point offset from the top-left corner of the original orthoimage in pixels
+	 * of the original resolution
+	 * @return vertical point X,Y offset in pixels from the top-left image corner in original resolution
+	 */
+	public int [] getVertPixels() {
+		double [] vm = getVertMeters();
+		return new int [] {
+				(int) Math.round(vm[0]/pix_meters),
+				(int) Math.round(vm[1]/pix_meters)};
+	}
+	
+	public double getPixMeters() {
+		return pix_meters;
+	}
+	public FloatImageData (
+			FloatImageData master,
+			int       zoom_level,
+			float[]   data) {
+		this.width =        master.width;
+		this.height =       master.height;
+		this.zoom_valid =   master.zoom_valid;
+		this.path =         master.path;
+		this.properties =   master.properties;
+		this.lla =          master.lla;
+		this.dt =           master.dt;
+		this.vert =         master.vert;
+		this.pix_meters =   master.pix_meters;
+		this.averagePixel = master.averagePixel;
+
+		this.zoom_lev =     zoom_level;
+		this.data =         data;
+	}	
+
+	public double getAveragePixel() {
+		if (Double.isNaN(averagePixel)) {
+			final float [] pixels =  readFData();
+			final Thread[] threads = ImageDtt.newThreadArray();
+			final AtomicInteger ai = new AtomicInteger(0);
+			final AtomicInteger ati = new AtomicInteger(0);
+			final double [] avg_arr =  new double [threads.length];
+			final double [] npix_arr = new double [threads.length];
+			for (int ithread = 0; ithread < threads.length; ithread++) {
+				threads[ithread] = new Thread() {
+					public void run() {
+						int thread_num = ati.getAndIncrement();
+						for (int ipix = ai.getAndIncrement(); ipix < pixels.length; ipix = ai.getAndIncrement()) {
+							float p = pixels[ipix];
+							if (!Float.isNaN(p)) {
+								avg_arr[thread_num] += p;
+								npix_arr[thread_num] +=1;
+							}
+						}
+					}
+				};
+			}		      
+			ImageDtt.startAndJoin(threads);
+			double avg=0, num=0;
+			for (int i = 0; i < avg_arr.length; i++) {
+				avg+=avg_arr[i]; // *npix_arr[i];
+				num+=npix_arr[i];
+			}
+			averagePixel = avg/num; 
+		}
+		return averagePixel;
+	}
+
+	
+	
+	
+	public int getWidth() {
+		return width;
+	}
+	public int getHeight() {
+		return height;
+	}
+	
+	public double[]  getVertMeters() {
+		return vert;
+	}
+	
 	public static int getZoomLevel(
 			double pix_in_meters) {
 		return getZoomLevel (pix_in_meters, null, null);
@@ -70,6 +238,10 @@ public class FloatImageData {
 		return extra_zoom[0];
 	}
 	
+	public int getZoomLevel() {
+		return zoom_lev;
+	}
+	
 	/**
 	 * Find scale level (0: 1pix/cm, 1 - 2pix/cm, -1 - 0.5 pix/cm) from pixel size in meters
 	 * If scale does not match, provide false in optional valid_zoom[0]

src/main/java/com/elphel/imagej/orthomosaic/ObjectLocation.java

@@ -49,7 +49,7 @@ public class ObjectLocation {
 		OrthoMap [] ortho_maps=maps_collection.getMaps();
 		final int width =     ortho_maps[nmap].getImageData().width;
 		final int height =    ortho_maps[nmap].getImageData().height;
-		final float [] src_img =  ortho_maps[nmap].getImageData().data;
+		final float [] src_img =  ortho_maps[nmap].getImageData().readFData();
 		double [] dcrop = new double [size*size];
 		Arrays.fill(dcrop, Double.NaN);
 		int hsize = size/2;

src/main/java/com/elphel/imagej/orthomosaic/OrthoMapsCollection.java

@@ -845,7 +845,7 @@ public class OrthoMapsCollection  implements Serializable{
 						scaled_out_center[0], // double px0, // in render pixels
 						scaled_out_center[1]); // // double py0);
 			}
-			final float [] src_img = use_alt? ortho_maps[nmap].getAltData().data : ortho_maps[nmap].getImageData().data;
+			final float [] src_img = use_alt? ortho_maps[nmap].getAltData().readFData() : ortho_maps[nmap].getImageData().readFData();
 			final Rectangle warp_woi =((indx==1) && (warp != null))? warp.getRenderWOI():null; 
 			final Thread[] threads = ImageDtt.newThreadArray();
 			final AtomicInteger ai = new AtomicInteger(0);
@@ -1011,8 +1011,8 @@ public class OrthoMapsCollection  implements Serializable{
 			}
 			boolean tilt_alt = (ground_planes != null) && (ground_planes[indx] != null);
 			final float [] src_img = use_alt?
-					(tilt_alt? ortho_maps[nmap].getAltData().data.clone(): ortho_maps[nmap].getAltData().data) :
-						ortho_maps[nmap].getImageData().data;
+					(tilt_alt? ortho_maps[nmap].getAltData().readFData().clone(): ortho_maps[nmap].getAltData().readFData()) :
+						ortho_maps[nmap].getImageData().readFData();
 			
 			final Rectangle warp_woi =((indx==1) && (warp != null))? warp.getRenderWOI():null; 
 			final Thread[] threads = ImageDtt.newThreadArray();