Commit 8a9605a5 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

Adding memory saving and loading from a file list

parent 6845c018

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

+138 −9
Original line number Diff line number Diff line 
package com.elphel.imagej.orthomosaic;



import java.io.File;

import java.io.IOException;

import java.nio.charset.StandardCharsets;

import java.nio.file.Files;

import java.nio.file.Path;

import java.nio.file.Paths;

import java.time.LocalDateTime;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashMap;

import java.util.List;

import java.util.Properties;

import java.util.concurrent.atomic.AtomicInteger;
@@ -24,6 +31,8 @@ public class ComboMap { 
	public static boolean FIX_VERT_Y = false; // true; // temporarily fix vertical Y coordinate bug (use -GCORR in the filename?)

	public static int gpu_width =  4096;

	public static int gpu_height =  4096;

	public static final String [] KEY_DIRS= {"rootDirectory", // from EyesisCorrectionParameters

			"sourceDirectory","linkedModels","videoDirectory","x3dDirectory","resultsDirectory"};

	public static final String ALT_SUFFIX = "-ALT";

	public final String               name;  // timestamp

	public String                     path;        // full path to the model directory (including /vXX?)
@@ -41,7 +50,7 @@ public class ComboMap { 
	public double                     need_extra_zoom;

	HashMap <Integer, FloatImageData> images;

	

	public static void setGPUWIdthHeight(

	public static void setGPUWidthHeight(

			int width,

			int height) {

		gpu_width = width;
@@ -87,6 +96,83 @@ public class ComboMap { 
		need_extra_zoom = FloatImageData.needZoomIn(orig_pix_meters);

		images = new HashMap <Integer, FloatImageData>();

	}

	

	public static ComboMap[] initializeComboMaps(

			String [] image_paths) { // full paths, including ext

		double [][] affine = {{1,0,0},{0,1,0}}; // maybe later calculate from mage_enuatr

		ComboMap[] combo_maps = new ComboMap[image_paths.length];

		for (int n = 0; n < combo_maps.length; n++) { 

			combo_maps[n] = new ComboMap(image_paths[n]);

			combo_maps[n].setAffine(affine);

		}

		return combo_maps;

	}

	

	public static ComboMap[] initializeComboMaps(

			String files_list) {

        List<String> lines;

        List<String> rel_files = new ArrayList<String>(); 

		Path seq_path = Paths.get(files_list);

		try {

			lines = Files.readAllLines(seq_path, StandardCharsets.UTF_8);

			//                lines.stream().forEach(System.out::println);

		} catch (IOException e) {

			e.printStackTrace();

			return null;

		}

		Path base_path = seq_path.getParent();

		HashMap<String,String> dir_map = new HashMap<String,String>();

		for (String line:lines){

			if (line.split("#").length > 0) {

				String[] tokens = line.split("#")[0].trim().split("[\\s,;=]+");

				if ((tokens.length > 2) && (tokens[0].toUpperCase().equals("SET"))) {

					parse_set:

					{

						for (String dir_name:KEY_DIRS) if (dir_name.equals(tokens[1])) {

							dir_map.put(dir_name,tokens[2]);

							System.out.println("Parsed SET: "+tokens[1]+" in line: "+line);

							break parse_set;

						}

						System.out.println("*********** Unknown SET: "+tokens[1]+" in line: "+line);

					}

				} else if ((tokens.length == 1) && (tokens[0].length() > 0)) {

					rel_files.add(tokens[0]);

				}

			}

		}

        if (dir_map.containsKey("rootDirectory")) {

        	base_path=base_path.resolve(Paths.get(dir_map.get("rootDirectory")));

			File base_dir = new File(base_path.toString());

//			if (!base_dir.exists()) {

//				base_dir.mkdirs();

//			}

        }

        String sourceDirectory = base_path.toString();

        // set sourceDirectory: 

        if (dir_map.containsKey("sourceDirectory")) {

        	sourceDirectory=(base_path.resolve(Paths.get(dir_map.get("sourceDirectory")))).toString();

        }

		Path source_path = Paths.get(sourceDirectory);

		File source_dir = new File(source_path.toString());

		String [] paths = new String[rel_files.size()];

		for (int i = 0; i < paths.length; i++) {

			paths[i] = (source_path.resolve(Paths.get(rel_files.get(i)))).toString();

		}

		return initializeComboMaps(paths);

	}

	

	

	

	public static String[] getNames(

			ComboMap[] maps) {

		String [] names = new String [maps.length];

		for (int n = 0; n < maps.length; n++) {

			names[n] = maps[n].getName();

		}

		return names;

	}



	

	public String getName() {

		return name;

	}
@@ -96,7 +182,50 @@ public class ComboMap { 
	public double [][] getAffine(){

		return affine;

	}

	public boolean readImageData() {



	public void removeImageData() { // to save memory

		orig_image=null;

	}

	

	public void removeAltData() { // to save memory

		alt_image = null;

	}

	

	public void removeZoomLevel(int zoom_level) { // either to save memory or remove to later replace

		images.remove(zoom_level);

	}

	

	public int [] getZoomLevels() {

		Integer [] ks = (Integer[]) images.keySet().toArray();

		int [] zoom_levels = new int[ks.length];

		for (int i = 0; i < ks.length; i++) {

			zoom_levels[i] = ks[i];

		}

		return zoom_levels;

	}

	

	public void removeAllButZoomLevel(int zoom_level) { // either to save memory or remove to later replace

		int [] zoom_levels = getZoomLevels();

		for (int zl:zoom_levels) if (zl !=zoom_level) {

			images.remove(zl);

		}

	}



	

	public FloatImageData getImageData() {

		if (orig_image == null) {

			readImageData();

		}

		return orig_image;

	}

	public FloatImageData getAltData() {

		if (alt_image == null) {

			readAltData();

		}

		return alt_image;

	}

	

	private boolean readImageData() {

		ImagePlus imp = new ImagePlus(path);

		int width = imp.getWidth();

		int height = imp.getHeight();
@@ -115,7 +244,7 @@ public class ComboMap { 
		return true;

	}



	public boolean readAltData() { // assuming the same scale as main image

	private boolean readAltData() { // assuming the same scale as main image

		ImagePlus imp = new ImagePlus(getAltPath(path));

		int width = imp.getWidth();

		int height = imp.getHeight();
@@ -129,6 +258,7 @@ public class ComboMap { 
	}

	

	public ImagePlus getOriginalImage(boolean show_markers) {

		FloatImageData orig_image = getImageData();

		if (orig_image != null) {

			String full_name = path.substring(path.lastIndexOf(Prefs.getFileSeparator()) + 1);

			ImagePlus imp = ShowDoubleFloatArrays.makeArrays(
@@ -174,6 +304,7 @@ public class ComboMap { 
	 * @return double [4][2] array [corner number]{x,y} 

	 */

	public double [][] get4SourceCornersMeters(){

		FloatImageData orig_image = getImageData();

		double width_meters = orig_image.width * orig_pix_meters;

		double height_meters = orig_image.height * orig_pix_meters;

		return new double[][] { // CW from TL
@@ -323,10 +454,8 @@ public class ComboMap { 
		return iaffine;

	}

	

	public void removeZoomLevel(int zoom_level) { // either to save memory or remove to later replace

		images.remove(zoom_level);

	}

	public boolean downScaleForGPU (int zoom_level){

		FloatImageData orig_image = getImageData();

		if (orig_image == null) {

			System.out.println("Original image is null");

			return false;
@@ -546,9 +675,9 @@ public class ComboMap { 
			double [][] src_bounds=maps[nmap].getBoundsMeters (true);

			final double [] src_center = {-src_bounds[0][0],-src_bounds[1][0]}; // x,y center offset in the source image

			final double [][] affine = maps[nmap].affine;

			final int src_width = use_alt? maps[nmap].alt_image.width: maps[nmap].orig_image.width;

			final int src_height = use_alt? maps[nmap].alt_image.height : maps[nmap].orig_image.height;

			final float [] src_img = use_alt? maps[nmap].alt_image.data : maps[nmap].orig_image.data;

			final int src_width = use_alt? maps[nmap].getAltData().width: maps[nmap].getImageData().width;

			final int src_height = use_alt? maps[nmap].getAltData().height : maps[nmap].getImageData().height;

			final float [] src_img = use_alt? maps[nmap].getAltData().data : maps[nmap].getImageData().data;

			final Thread[] threads = ImageDtt.newThreadArray();

			final AtomicInteger ai = new AtomicInteger(0);

			for (int ithread = 0; ithread < threads.length; ithread++) {

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

+32 −87
Original line number Diff line number Diff line
@@ -43,35 +43,6 @@ public class ComboMatch { 
			 GPUTileProcessor gpu_tile_processor, // initialized by the caller

			 final int        debugLevel) {

		GPU_TILE_PROCESSOR = gpu_tile_processor;

		/*

/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877409_353265/1697877409_353265-RECT-PIX0.01-FLAT_CLN-VERT-GEO.tiff

/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877409_353265/1697877409_353265-RECT-PIX0.01-FLAT_CLN-VERT-GEO-ALT.tiff



/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877410_420287/1697877410_420287-RECT-PIX0.01-FLAT_CLN-VERT-GEO.tiff

/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877410_420287/1697877410_420287-RECT-PIX0.01-FLAT_CLN-VERT-GEO-ALT.tiff





/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877412_004148/1697877412_004148-RECT-PIX0.01-FLAT_CLN-VERT-GEO.tiff

/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877412_004148/1697877412_004148-RECT-PIX0.01-FLAT_CLN-VERT-GEO-ALT.tiff





/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877413_137859/1697877413_137859-RECT-PIX0.01-FLAT_CLN-VERT-GEO.tiff

/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877413_137859/1697877413_137859-RECT-PIX0.01-FLAT_CLN-VERT-GEO-ALT.tiff





/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877414_404948/1697877414_404948-RECT-PIX0.01-FLAT_CLN-VERT-GEO.tiff

/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877414_404948/1697877414_404948-RECT-PIX0.01-FLAT_CLN-VERT-GEO-ALT.tiff



/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877415_521986/1697877415_521986-RECT-PIX0.01-FLAT_CLN-VERT-GEO.tiff

/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877415_521986/1697877415_521986-RECT-PIX0.01-FLAT_CLN-VERT-GEO-ALT.tiff



		 */

		/*

		String [] image_paths_pre = {

				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877410_420287/1697877410_420287-RECT-PIX0.01-FLAT_CLN-VERT-GEO",

				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877412_004148/1697877412_004148-RECT-PIX0.01-FLAT_CLN-VERT-GEO"

		};

		*/

		String [] image_paths_pre_0 = {

//				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877410_420287/1697877410_420287-RECT-PIX0.01-FLAT_CLN-VERT-GEO",

//				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877412_004148/1697877412_004148-RECT-PIX0.01-FLAT_CLN-VERT-GEO",
@@ -92,7 +63,9 @@ public class ComboMatch { 
				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877414_404948/1697877414_404948-RECT-PIX0.01-FLAT_CLN-VERT-GCORR-GEO",

				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877415_521986/1697877415_521986-RECT-PIX0.01-FLAT_CLN-VERT-GCORR-GEO"

		};

		// find -L /media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/ -type f -name "*-GCORR-GEO.tiff" | sort  > GCORR-GEO.list



		String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/maps_01.list";

		

		double [][][] image_enuatr = {{{0,0,0},{0,0,0}},{{0,0,0},{0,0,0}}};

		int gpu_width=  clt_parameters.imp.rln_gpu_width; // 3008;
@@ -101,9 +74,10 @@ public class ComboMatch { 
		boolean use_alt = false;

		boolean show_centers = true;

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,800);

		for (int n = 0; n < image_paths_pre.length; n++) {

			gd.addStringField ("Image path "+n,  image_paths_pre[n], 180, "Image "+n+" full path w/o ext");		

		}

		gd.addStringField ("Image list full path ",  files_list_path, 180, "Image listfull path.");

//		for (int n = 0; n < image_paths_pre.length; n++) {

//			gd.addStringField ("Image path "+n,  image_paths_pre[n], 180, "Image "+n+" full path w/o ext");		

//		}

//		gd.addStringField ("First image path",  image_paths_pre[0], 180, "First image full path w/o ext");		

//		gd.addStringField ("Second image path", image_paths_pre[1], 180, "Second image full path w/o ext");		

		for (int n = 0; n < image_enuatr.length; n++) {
@@ -126,9 +100,10 @@ public class ComboMatch { 


		gd.showDialog();

		if (gd.wasCanceled()) return false;

		for (int n = 0; n < image_paths_pre.length; n++) {

			image_paths_pre[n] = gd.getNextString();

		}		

		files_list_path = gd.getNextString();

//		for (int n = 0; n < image_paths_pre.length; n++) {

//			image_paths_pre[n] = gd.getNextString();

//		}		

//		image_paths_pre[0] = gd.getNextString();

//		image_paths_pre[1] = gd.getNextString();

		for (int n = 0; n < image_enuatr.length; n++) {
@@ -143,23 +118,19 @@ public class ComboMatch { 
		gpu_width =           (int) gd.getNextNumber();

		gpu_height =          (int) gd.getNextNumber();



		ComboMap.setGPUWIdthHeight(gpu_width,gpu_height);

		ComboMap.setGPUWidthHeight(gpu_width,gpu_height);

		

		show_centers =              gd.getNextBoolean();

		use_alt =                   gd.getNextBoolean();

		

		ComboMap[] combo_maps = new ComboMap[image_paths_pre.length];

		String [] map_names = new String[combo_maps.length];

		for (int n = 0; n < combo_maps.length; n++) { 

			combo_maps[n] = new ComboMap(image_paths_pre[n]+".tiff");

			combo_maps[n].readImageData();

			if (use_alt) {

				combo_maps[n].readAltData();

			}

			double [][] affine = {{1,0,0},{0,1,0}}; // maybe later calculate from mage_enuatr

			combo_maps[n].setAffine(affine);

			map_names[n] = combo_maps[n].getName();

		String [] full_paths = new String[image_paths_pre.length];

		for (int n = 0; n < full_paths.length; n++) { 

			full_paths[n] = image_paths_pre[n]+".tiff";

		}		

//		ComboMap[] combo_maps = ComboMap.initializeComboMaps(

//				full_paths); // String [] image_paths);

		ComboMap[] combo_maps = ComboMap.initializeComboMaps(

				files_list_path); // String [] image_paths);

		String [] map_names = ComboMap.getNames(combo_maps);

		

		int [] origin = new int[2];

		ImagePlus imp_img = 	ComboMap.renderMulti (
@@ -170,44 +141,18 @@ public class ComboMatch { 
				zoom_lev,          // int         zoom_level,

				origin);           // int []      origin){

		imp_img.show();



		/*

		int []     wh = new int[2];

		double [][] centers = new double [combo_maps.length][];



		float [][] multi = ComboMap.renderMulti (

				false,      // boolean     use_alt,

				combo_maps, // ComboMap [] maps,

				zoom_lev,   // int         zoom_level,

				wh,         // int []      wh,

				origin,    // int []      origin){ // maps[0] as a reference

				centers); // double [][] centers)

		

        ShowDoubleFloatArrays.showArrays( 

        		multi,

        		wh[0],

        		wh[1],

        		true,

        		"multi_"+zoom_lev,

        		map_names);

		ImagePlus imp_alt = null;

        if (use_alt) {

        	float [][] multi_alt = ComboMap.renderMulti (

        	imp_alt =ComboMap.renderMulti (

    				"multi_alt_"+zoom_lev, // String      title,

    				true,             // boolean     use_alt,

    				show_centers,      // boolean     show_centers,

    				combo_maps,        // ComboMap [] maps,

    				zoom_lev,          // int         zoom_level,

        			wh,         // int []      wh,

    				origin,    // int []      origin){ // maps[0] as a reference

    				centers); // double [][] centers)

        	ShowDoubleFloatArrays.showArrays( 

        			multi_alt,

        			wh[0],

        			wh[1],

        			true,

        			"multi_alt_"+zoom_lev,

        			map_names);

    				origin);           // int []      origin){

    		imp_alt.show();

        }

        */

        // which piar to compare

        // which pair to compare

		int [] gpu_pair = {1,2};

        

		float [][] gpu_pair_img = new  float [2][];