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imagej-elphel
Commit 8a9605a5 authored by Andrey Filippov's avatar Andrey Filippov
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Adding memory saving and loading from a file list

parent 6845c018
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Showing with 170 additions and 96 deletions
src/main/java/com/elphel/imagej/orthomosaic/ComboMap.java
View file @ 8a9605a5
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
View file @ 8a9605a5
......@@ -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();
}
use_alt = gd.getNextBoolean();
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 (
true, // 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_alt,
wh[0],
wh[1],
true,
"multi_alt_"+zoom_lev,
map_names);
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,
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][];
......
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