Refactoring, incompatible data file (c5431a27) · Commits · Elphel / imagej-elphel

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

+195 −23

Original line number	Original line	Diff line number	Diff line
	package com.elphel.imagej.orthomosaic;		package com.elphel.imagej.orthomosaic;

	import java.awt.Rectangle;		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.Arrays;
			import java.util.Properties;
	import java.util.concurrent.atomic.AtomicInteger;		import java.util.concurrent.atomic.AtomicInteger;

	import com.elphel.imagej.common.PolynomialApproximation;		import com.elphel.imagej.common.PolynomialApproximation;
			import com.elphel.imagej.readers.ElphelTiffReader;
	import com.elphel.imagej.tileprocessor.ImageDtt;		import com.elphel.imagej.tileprocessor.ImageDtt;

	public class FloatImageData {		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 width;
	public int height;		public int height;
	public int zoom_lev;		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 [] vert = new double[2]; // x,y offset (in meters) of the point under the camera
	public float[] data;		private double pix_meters;
			private double averagePixel=Double.NaN;
			private transient float[] data; // make transient

	public FloatImageData (		public FloatImageData (
	int width,		String path) {
	int height,		this.path = path;
	int zoom_lev,		try {
	double [] vert, // x,y pixel offset of the point under the camera		properties = ElphelTiffReader.getTiffMeta(path);
	float[] data) {		} catch (IOException e) {
	this.width = width;		// TODO Auto-generated catch block
	this.height = height;		e.printStackTrace();
	this.zoom_lev = zoom_lev;		}
	this.vert = vert.clone();		try {
	this.data = data;		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() {		private void writeObject(ObjectOutputStream oos) throws IOException {
	return width;		oos.defaultWriteObject();
	}		}
	public int getHeight() {
	return height;		private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
			ois.defaultReadObject();
			data = null;
	}		}

	public double[] getVertMeters() {		public void updateLLA() {
	return vert;		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();
			}
			}

			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() {		public double [] getDData() {
			if (data==null) {
			readFData();
			if (data== null) {
			return null;
			}
			}
	final double [] ddata = new double [data.length];		final double [] ddata = new double [data.length];
	final Thread[] threads = ImageDtt.newThreadArray();		final Thread[] threads = ImageDtt.newThreadArray();
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	@@ -53,6 +124,103 @@ public class FloatImageData {
	return ddata;		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(		public static int getZoomLevel(
	double pix_in_meters) {		double pix_in_meters) {
	return getZoomLevel (pix_in_meters, null, null);		return getZoomLevel (pix_in_meters, null, null);
	@@ -70,6 +238,10 @@ public class FloatImageData {
	return extra_zoom[0];		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		* 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]		* If scale does not match, provide false in optional valid_zoom[0]

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

+1 −1

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

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