Adding memory saving and loading from a file list

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

 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

@@ -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][];