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Commit da579ebb authored by Andrey Filippov's avatar Andrey Filippov
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Enhancing moving targets

parent 4e5e1f22
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Showing with 1890 additions and 175 deletions
src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java
View file @ da579ebb
package com.elphel.imagej.common;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Map;
import java.util.Properties;
......@@ -216,6 +217,111 @@ import ij.process.ImageProcessor;
show); // boolean show
}
public static ImagePlus showArraysHyperstack(
float[][][] pixels,
int width,
String title,
String [] titles, // all slices*frames titles or just slice titles or null
String [] frame_titles, // frame titles or null
boolean show) {
int num_frames = pixels.length;
int num_slices = pixels[0].length;
float [][] fpixels = new float [num_frames*num_slices][];
for (int f = 0; f < num_frames; f++) {
for (int s = 0; s < num_slices; s ++) {
int indx = s + f * num_slices;
fpixels[indx] = pixels[f][s];
}
}
String [] combo_titles;
if ((titles != null) && (titles.length == fpixels.length)) {
combo_titles = titles;
} else {
combo_titles = new String[fpixels.length];
if (titles == null) {
titles = new String [pixels[0].length];
for (int i = 0; i < titles.length; i++) {
titles[i] = ""+i;
}
}
if (frame_titles == null) {
frame_titles = new String [pixels.length];
for (int i = 0; i < titles.length; i++) {
frame_titles[i] = ""+i;
}
}
for (int f = 0; f < frame_titles.length; f++) {
for (int s = 0; s < titles.length; s++) {
combo_titles[s + f * titles.length] = frame_titles[f]+":"+titles[s];
}
}
}
int height = -1;
for (int slic = 0; slic < fpixels.length; slic++) {
if (fpixels[slic] != null) {
height = fpixels[slic].length/width;
break;
}
}
return showArraysHyperstack(
fpixels, // double[][] pixels,
width, // int width,
height, // int height,
pixels[0].length, // int slices,
title, // String title,
combo_titles, // String [] titles);
show); // boolean show
}
public static ImagePlus showArraysHyperstack(
float[][] pixels,
int width,
int height,
int slices,
String title,
String [] titles,
boolean show) {
int i,j;
if (pixels==null) {
System.out.println("showDoubleFloatArrays.showArrays(): - pixel array is null");
}
float [] fpixels;
ImageStack array_stack=new ImageStack(width,height);
boolean not_empty = false;
for (i=0;i<pixels.length;i++) if (pixels[i]!=null) {
not_empty = true;
fpixels=new float[pixels[i].length];
for (j=0;j<fpixels.length;j++) fpixels[j]=(float)pixels[i][j];
if (i < titles.length) {
array_stack.addSlice(titles[i], fpixels);
} else {
array_stack.addSlice("slice-"+i, fpixels);
}
}
ImagePlus imp_stack = null;
if (not_empty) {
imp_stack = IJ.createImage(
title, // String title,
"32-bit,grayscale-mode", // ,label", // String type,
width, // int width,
height, // int height,
1, // int channels,
slices, // int slices,
pixels.length / slices); // frames)
imp_stack.setStack(array_stack);
imp_stack.getProcessor().resetMinAndMax();
if (show) {
imp_stack.show();
}
}
return imp_stack;
}
public static void showComplex(double[][][] cpixels, String title) {
......@@ -857,6 +963,123 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
return imp;
}
public static double [][] readDoubleArray(
ImagePlus imp,
int num_slices, // (0 - all)
int [] wh) {
float [][] fdata = readFloatArray(
imp, // ImagePlus imp,
num_slices, // int num_slices, // (0 - all)
wh); // int [] wh)
if (fdata == null) {
return null;
}
double [][] result = new double [fdata.length][];
for (int n = 0; n < fdata.length; n++) if (fdata[n]!=null) {
result[n] = new double [fdata[n].length];
for (int i = 0; i < fdata[n].length; i++) {
result[n][i] = fdata[n][i];
}
}
return result;
}
public static float [][] readFloatArray(
ImagePlus imp,
int num_slices, // (0 - all)
int [] wh) {
if ((imp == null) || (imp.getTitle() == null) || (imp.getTitle().equals(""))) {
return null;
}
ImageStack imageStack = imp.getStack();
int nChn=imageStack.getSize();
if ((num_slices > 0) && (num_slices < nChn)) {
nChn = num_slices;
}
float [][] result = new float [nChn][];
for (int n = 0; n < nChn; n++) {
result[n] = (float[]) imageStack.getPixels(n + 1);
}
if (wh != null) {
wh[0] = imp.getWidth();
wh[1] = imp.getHeight();
}
return result;
}
public static float [][] readFloatArray(
String file_path,
int num_slices, // (0 - all)
int [] wh) {
ImagePlus imp = null;
try {
imp = new ImagePlus(file_path);
} catch (Exception e) {
System.out.println ("Failed to open "+file_path+", maybe will generate it");
}
if ((imp == null) || (imp.getTitle() == null) || (imp.getTitle().equals(""))) {
return null;
}
System.out.println ("Read "+(imp.getStack().getSize())+" slices from "+file_path);
return readFloatArray(
imp, // ImagePlus imp,
num_slices, //int num_slices, // (0 - all)
wh); // int [] wh)
}
public static double [][][] readDoubleHyperstack(
String path,
int [] wh, // should be null or int[2]
String [][] ptop_titles, // should be null or String [1][]
String [][] pslice_titles){// should be null or String [1][]
ImagePlus imp = new ImagePlus(path);
if (imp.getWidth() == 0) {
System.out.println("testSynthetic(): Failed reading Vector field from: " + path);
return null;
}
int num_slices = imp.getStackSize();
String [] slice_labels = imp.getStack().getSliceLabels();
ArrayList<String> top_titles = new ArrayList<String>();
ArrayList<String> slice_titles = new ArrayList<String>();
for (int i = 0; i < num_slices; i++) {
String [] label = slice_labels[i].split(":");
if (label.length>1) {
if (!top_titles.contains(label[0])) {
top_titles.add(label[0]);
}
if (!slice_titles.contains(label[1])) {
slice_titles.add(label[1]);
}
} else if (label.length>0) {
if (!slice_titles.contains(label[0])) {
slice_titles.add(label[0]);
}
}
}
String [] top_l = top_titles.toArray(new String[0]);
String [] slice_l = slice_titles.toArray(new String[0]);
if (ptop_titles != null) {
ptop_titles[0] = top_l;
}
if (pslice_titles != null) {
pslice_titles[0] = slice_l;
}
double [][] file_data = ShowDoubleFloatArrays.readDoubleArray(
imp, // ImagePlus imp,
0, // int num_slices, // (0 - all)
wh); // int [] wh); // int [] wh)
int num_top_slices = num_slices/slice_titles.size();
double [][][] out_data = new double [num_top_slices][num_slices/num_top_slices][];
for (int t = 0; t < out_data.length; t++) {
for (int s = 0; s < out_data[t].length; s++) {
out_data[t][s] = file_data[t * out_data[t].length + s];
}
}
return out_data;
}
}
src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java
View file @ da579ebb
......@@ -109,6 +109,7 @@ import com.elphel.imagej.common.DoubleGaussianBlur;
import com.elphel.imagej.common.GenericJTabbedDialog;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.common.WindowTools;
import com.elphel.imagej.cuas.CuasMotion;
import com.elphel.imagej.dct.FactorConvKernel;
import com.elphel.imagej.gpu.GPUTileProcessor;
import com.elphel.imagej.gpu.GpuQuad;
......@@ -905,6 +906,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
addJButton("UAS log", jpanelOrange, color_process);
addJButton("DJI SRT", jpanelOrange, color_process);
addJButton("SRT to KML", jpanelOrange, color_process);
addJButton("Motion_CUAS", jpanelOrange, color_stop);
addJButton("Motion_scan", jpanelOrange, color_stop);
//
plugInJFrame.add(jpanelOrange);
}
......@@ -1484,6 +1487,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
}
b.addActionListener(this);
b.addKeyListener(IJ.getInstance());
b.setToolTipText(label);
panel.add(b);
}
......@@ -6285,6 +6289,26 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
testDjiSrt();
} else if (label.equals("SRT to KML")) {
djiSrtToKml();
} else if (label.equals("Motion_CUAS")) {
DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
ImagePlus imp_sel = WindowManager.getCurrentImage();
if (imp_sel != null) {
motion_cuas(
imp_sel,
0); // int mode));
} else {
System.out.println("No image selected");
}
} else if (label.equals("Motion_scan")) {
DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
ImagePlus imp_sel = WindowManager.getCurrentImage();
if (imp_sel != null) {
motion_cuas(
imp_sel,
1); // int mode));
} else {
System.out.println("No image selected");
}
}
}
......@@ -6329,6 +6353,77 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
return true;
}
public static boolean motion_cuas(
ImagePlus imp_sel,
int mode) {
// long startTime = System.nanoTime();
// load needed sensor and kernels files
setAllProperties(PROPERTIES); // batchRig may save properties with the model. Extrinsics will be updated,
if (GPU_TILE_PROCESSOR == null) {
try {
GPU_TILE_PROCESSOR = new GPUTileProcessor(CORRECTION_PARAMETERS.tile_processor_gpu);
} catch (Exception e) {
System.out.println("Failed to initialize GPU class");
// TODO Auto-generated catch block
e.printStackTrace();
return false;
} // final int debugLevel);
}
EYESIS_CORRECTIONS_AUX.initSensorFiles(DEBUG_LEVEL);
if (!QUAD_CLT_AUX.CLTKernelsAvailable()) {
if (DEBUG_LEVEL > 0) {
System.out.println("Reading AUX CLT kernels");
}
QUAD_CLT_AUX.readCLTKernels(CLT_PARAMETERS, THREADS_MAX, UPDATE_STATUS, // update status info
DEBUG_LEVEL);
if (DEBUG_LEVEL > 1) {
QUAD_CLT_AUX.showCLTKernels(THREADS_MAX, UPDATE_STATUS, // update status info
DEBUG_LEVEL);
}
}
if (!QUAD_CLT_AUX.geometryCorrectionAvailable()) {
if (DEBUG_LEVEL > 0) {
System.out.println("Calculating geometryCorrection");
}
if (!QUAD_CLT_AUX.initGeometryCorrection(DEBUG_LEVEL + 2)) {
return false;
}
}
if (CLT_PARAMETERS.useGPU(true) && (QUAD_CLT_AUX != null) && (GPU_QUAD_AUX == null)) { // if GPU AUX is
// needed
try {
GPU_QUAD_AUX = new GpuQuad(//
GPU_TILE_PROCESSOR, QUAD_CLT_AUX, CLT_PARAMETERS.gpu_debug_level);
} catch (Exception e) {
System.out.println("Failed to initialize GpuQuad class");
// TODO Auto-generated catch block
e.printStackTrace();
return false;
} // final int debugLevel);
QUAD_CLT_AUX.setGPU(GPU_QUAD_AUX);
}
switch (mode) {
case 0:
CuasMotion.testCuasMotion(
imp_sel, // ImagePlus imp_sel,
CLT_PARAMETERS, // CLTParameters clt_parameters,
QUAD_CLT_AUX, // QuadCLT parentCLT)
DEBUG_LEVEL); // //int debugLevel)
break;
case 1:
CuasMotion.testCuasScanMotion(
imp_sel, // ImagePlus imp_sel,
CLT_PARAMETERS, // CLTParameters clt_parameters,
QUAD_CLT_AUX, // QuadCLT parentCLT)
DEBUG_LEVEL); // //int debugLevel)
break;
}
return true;
}
public static boolean djiSrtToKml() {
String srt_path= "/home/elphel/Documents/dji/images/DJI_001-02/DJI_20250515122524_0007_D.SRT";
String kml_path= "/home/elphel/Documents/dji/images/DJI_001-02/DJI_20250515122524_0007_D.kml";
......
src/main/java/com/elphel/imagej/cuas/CorrectionFPN.java
View file @ da579ebb
......@@ -492,7 +492,7 @@ public class CorrectionFPN {
return null;
}
ImagejJp4Tiff.decodeProperiesFromInfo(imp);
double [][] rowcol_data2 = QuadCLT.readDoubleArray(
double [][] rowcol_data2 = ShowDoubleFloatArrays.readDoubleArray(
imp, // ImagePlus imp,
0, // int num_slices, // (0 - all)
wh); // int [] wh); // int [] wh)
......
src/main/java/com/elphel/imagej/cuas/CuasData.java
View file @ da579ebb
......@@ -123,7 +123,7 @@ public class CuasData implements Serializable {
int [] wh = new int[2];
float [][] fclt_w;
String cuas_old_path = full_path+Prefs.getFileSeparator() + name+ QuadCLTCPU.CENTER_CLT_SUFFIX+ ".tiff";
fclt_w = QuadCLT.readFloatArray(
fclt_w = ShowDoubleFloatArrays.readFloatArray(
cuas_old_path, // String file_path,
0, // int num_slices, // (0 - all)
wh); // int [] wh) {
......
src/main/java/com/elphel/imagej/cuas/CuasMotion.java 0 → 100644
View file @ da579ebb
This diff is collapsed.
src/main/java/com/elphel/imagej/gpu/GpuQuad.java
View file @ da579ebb
......@@ -245,6 +245,11 @@ public class GpuQuad{ // quad camera description
return this.quadCLT;
}
public GPUTileProcessor getGpuTileProcessor() {
return this.gpuTileProcessor;
}
public int getTaskSize() {
if (rectilinear) return TpTask.getSize(1);
return TpTask.getSize(quadCLT.getNumSensors());
......@@ -265,8 +270,8 @@ public class GpuQuad{ // quad camera description
this.num_cams = quadCLT.getNumSensors();
this.num_all_pairs = Correlation2d.getNumPairs(num_cams);
this.num_colors = quadCLT.isMonochrome()?1:3; //num_colors; // maybe should always be 3?
this.kernels_hor = quadCLT.getCLTKernels()[0][0][0].length; // kernels_hor;
this.kernels_vert = quadCLT.getCLTKernels()[0][0].length; // kernels_vert;
this.kernels_hor = (quadCLT.getCLTKernels() == null) ? 0 : quadCLT.getCLTKernels()[0][0][0].length; // kernels_hor;
this.kernels_vert = (quadCLT.getCLTKernels() == null) ? 0 : quadCLT.getCLTKernels()[0][0].length; // kernels_vert;
this.kern_tiles = kernels_hor * kernels_vert * num_colors;
this.kern_size = kern_tiles * 4 * 64;
if (debug_level >= 100) {
......@@ -4713,12 +4718,79 @@ public class GpuQuad{ // quad camera description
return tp_tasks_out;
}
/**
* Prepare tasks for accumulation of multiple images, shifted proportionally to the vector field
* and temporal distance from the middle frame. Accumulation uses the feature developed for the
* thermal camera motion blur correction that allows accumulation in the transform domain. It only
* works with the negative scales, so the result will be a negative image in the TD.
* @param vector_field sparse array of motion vectors (may be longer, only Vx and Vy used). Null elements
* are allowed, they will be skipped, resultin in null TpTask elements.
* @param offset_scale multiply all vectors by this value when calculatingpixel offsets
* @param magnitude_scale Scale data for accumulation (here positive, will be negated
* @param image_width image width in tiles (80 for 640-wide images).
* @return condensed array of TpTask
*/
public static TpTask [] setRectilinearMovingTasks(
final double [][] vector_field,
final double offset_scale,
final double magnitude_scale,
final int tilesX) {
final float fmagnitude_scale = (float) -magnitude_scale;
final int tiles = vector_field.length;
final TpTask [] tp_tasks_full = new TpTask [tiles];
final Thread[] threads = ImageDtt.newThreadArray();
final AtomicInteger ai = new AtomicInteger(00);
final AtomicInteger aTiles = new AtomicInteger(0);
// Not sure which bits are needed to enable GPU processing
final int task_code = (1 << GPUTileProcessor.TASK_TEXT_EN) | (1 << GPUTileProcessor.TASK_CORR_EN) | (1 << GPUTileProcessor.TASK_INTER_EN);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
@Override
public void run() {
for (int nTile = ai.getAndIncrement(); nTile < tiles; nTile = ai.getAndIncrement()) if (vector_field[nTile] != null){
int tileY = nTile / tilesX;
int tileX = nTile % tilesX;;
double dx = vector_field[nTile][0]*offset_scale;
double dy = vector_field[nTile][1]*offset_scale;
double [] cxy0 = { // uniform coordinates for the center scene
(tileX + 0.5) * GPUTileProcessor.DTT_SIZE,
(tileY + 0.5) * GPUTileProcessor.DTT_SIZE};
// check just
TpTask tp_task = new TpTask(1, tileX, tileY); // single "sensor"
tp_task.task = task_code;
tp_task.scale = fmagnitude_scale;
tp_task.setCenterXY(cxy0); // this pair of coordinates will be used by GPU... not yet
tp_task.xy=new float [1][2];
// see where task.disp_dist is used - only in GeometryCorrection, when calculating .xy
tp_task.xy[0][0] = (float) (cxy0[0] + dx);
tp_task.xy[0][1] = (float) (cxy0[1] + dy);
int iTile = aTiles.getAndIncrement();
tp_tasks_full[iTile] = tp_task;
}
}
};
}
ImageDtt.startAndJoin(threads);
final TpTask[] tp_tasks = new TpTask[aTiles.get()];
System.arraycopy(tp_tasks_full, 0, tp_tasks, 0, tp_tasks.length);
return tp_tasks;
}
/**
*
* @param fpixels
* @param img_width
* @param woi
* @param affine
* @return
*/
public static TpTask[][] setRectilinearInterTasks(
final float [][] fpixels, // to check for empty
final int img_width,
Rectangle woi,
final double [][][] affine // [2][2][3] affine coefficients to translate common to 2 images
){
final double [][][] affine_in){ // [2][2][3] affine coefficients to translate common to 2 images
final double [][][] affine = (affine_in != null) ? affine_in : new double [][][] {{{1,0,0},{0,1,0}},{{1,0,0},{0,1,0}}};
final int img_height = fpixels[0].length/img_width;
if (woi == null) {
woi = new Rectangle(0,0,img_width,img_height);
......
src/main/java/com/elphel/imagej/orthomosaic/ComboMatch.java
View file @ da579ebb
......@@ -1995,17 +1995,17 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
/**
*
* @param clt_parameters
* @param fpixels
* @param img_width
* @param woi
* @param affine
* @param tp_tasks_o
* @param batch_mode
* @param dbg_suffix
* @param debugLevel
* @return [2][tilesX*tilesY][3]
* Calculate single-tile and neighbors vector fields
* @param clt_parameters meta parameters
* @param fpixels {reference, other}, each img_width * img_height(calculated)
* @param img_width image width
* @param woi image window to process, if null, use full GPU window
* @param affine [2][2][3] affine coefficients to translate common to 2 images
* @param tp_tasks_o null or TpTask [2][] - will get copy of tasks for both images (different, centers, same tasks)
* @param batch_mode avoid graphics debug in batch mode
* @param dbg_suffix for image_names, such as batch_mode? null: String.format("_%02d", ntry);
* @param debugLevel debug level
* @return [2:neibs/single][tilesX*tilesY][3:x,y,str]
*/
public static double [][][] rectilinearVectorField( // scene0/scene1
final CLTParameters clt_parameters,
......@@ -2019,7 +2019,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
final int debugLevel) {
int [] wh = {img_width, fpixels[0].length/img_width};
TpTask [][] tp_tasks = GpuQuad.setRectilinearInterTasks(
fpixels, // final float [][] fpixels, // to check for empty
fpixels, // final float [][] fpixels, // to check for empty (no processing where it images have NaN
img_width, // final int img_width,
woi, // Rectangle woi,
affine); // final double [][][] affine // [2][2][3] affine coefficients to translate common to 2 images
......@@ -2139,13 +2139,15 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
corr_tiles_pd[0], // final double[][] tiles,
rln_sngl_rstr, // double rmax,
rln_cent_radius, // final double centroid_radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
rln_n_recenter); // final int n_recenter); // re-center window around new maximum. 0 -no refines (single-pass)
rln_n_recenter, // final int n_recenter); // re-center window around new maximum. 0 -no refines (single-pass)
false); // final boolean calc_fraction ){ // calculate fraction inside center circle
if (corr_tiles_pd.length > 1) {
vector_field[1] = TDCorrTile.getMismatchVector(
corr_tiles_pd[1], // final double[][] tiles,
rln_neib_rstr, // double rmax,
rln_cent_radius, // final double centroid_radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
rln_n_recenter); // final int n_recenter); // re-center window around new maximum. 0 -no refines (single-pass)
rln_n_recenter, // final int n_recenter); // re-center window around new maximum. 0 -no refines (single-pass)
false); // final boolean calc_fraction ){ // calculate fraction inside center circle
}
boolean show_vector_field = (debugLevel>100); // true;
boolean show_2d_correlations = (debugLevel>0); // true;
......
src/main/java/com/elphel/imagej/tileprocessor/Correlation2d.java
View file @ da579ebb
......@@ -2412,15 +2412,20 @@ public class Correlation2d {
return rslt;
}
public static double [] getMaxXYCm(
double [] data, // will be modified if fpn_mask != null;
int data_width, // = 2 * transform_size - 1;
int data_width, // = 2 * transform_size - 1; // negative - calculate fraction
double radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
int refine, // re-center window around new maximum. 0 -no refines (single-pass)
boolean [] fpn_mask,
boolean ignore_border, // only if fpn_mask != null - ignore tile if maximum touches fpn_mask
boolean debug)
{
boolean calc_fraction = data_width < 0;
if (calc_fraction) {
data_width = -data_width;
}
int data_height = data.length/data_width;
int center_xy = (data_width - 1)/2; // = transform_size - 1;
double x0 = center_xy, y0 = center_xy;
......@@ -2455,6 +2460,7 @@ public class Correlation2d {
}
}
//calculate as "center of mass"
double frac = 0;
if (radius == 0) {
double s0 = 0, sx=0,sy = 0;
for (int iy = 0; iy < data_height; iy++) {
......@@ -2474,9 +2480,11 @@ public class Correlation2d {
}
x0 += sx / s0;
y0 += sy / s0;
// s00 = s0;
} else {
double radius2 = radius*radius;
for (int nref = 0; nref <= refine; nref++) {
double s_other = 0;
double s0 = 0, sx=0,sy = 0;
for (int iy = 0; iy < data_height; iy++) {
double y = iy - y0;
......@@ -2492,19 +2500,33 @@ public class Correlation2d {
sx += d * x;
sy += d * y;
}
} else if (calc_fraction) {
double d = data[iy * data_width + ix];
if (d > 0) { // ignore negative
s_other += d;
}
}
}
}
x0 += sx / s0;
y0 += sy / s0;
frac = s0 / (s0 + s_other);
}
}
if (calc_fraction) {
double [] rslt = {x0 - center_xy, y0 - center_xy, mx, frac};
if (debug){
System.out.println("getMaxXYCm() -> "+rslt[0]+":"+rslt[1] +" ("+rslt[2]+"), frac = " + rslt[3]);
}
return rslt;
} else {
double [] rslt = {x0 - center_xy, y0 - center_xy, mx};
if (debug){
System.out.println("getMaxXYCm() -> "+rslt[0]+":"+rslt[1]);
System.out.println("getMaxXYCm() -> "+rslt[0]+":"+rslt[1] +" ("+rslt[2]+")");
}
return rslt;
}
}
/**
......
src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java
View file @ da579ebb
......@@ -699,6 +699,19 @@ min_str_neib_fpn 0.35
public double cuas_multi_strength = 0.45; // maximal strength to use multi-tile DSI
public double cuas_reliable_str = 0.8; // use for relaible tiles if INTER-INTRA-LMA is available, not just DSI_MAIN
public double cuas_fat_zero = 1000.0; // phase correlation fat zero
public double cuas_cent_radius = 4.0; // centroids center radius
public int cuas_n_recenter = 2; // when cosine window, re-center window these many times
public double cuas_rstr = 0.001; // minimal phase correlation maximums relative to max str
public boolean cuas_smooth = true; // used cosine window when averaging correlations
public int cuas_corr_pairs = 50; // number of correlation pairs to accumulate
public int cuas_corr_offset = 20; // offset between motion detection pairs
public boolean cuas_half_step = false; // half step (=cuas_corr_offset/2) when scanning for motion
public int cuas_max_range = 2; // how far to extend local max: 1 3x3 neighbors, 2 - 5x5 neighbs
// boosting weight of moving targets
public double cuas_speed_min = 0.2; // minimal pixels per range (per cuas_corr_offset)
public double cuas_speed_pref = 0.5; // preferable speed (boost weights for faster targets)
public double cuas_speed_boost = 2.5; // speed boost limit
public boolean cuas_debug = false; // save debug images (and show them if not in batch mode)
public boolean cuas_step_debug = false; // save debug images during per-step cuas recalculation (and show them if not in batch mode)
......@@ -2106,6 +2119,32 @@ min_str_neib_fpn 0.35
gd.addNumericField("Reliable strength", this.cuas_reliable_str, 5,7,"",
"Reliable tile strength when combo-dsi is available.");
gd.addMessage("=== CUAS motion detection ===");
gd.addNumericField("Phase correlation fat zero", this.cuas_fat_zero, 5,8,"",
"Phase correlation fat zero for motion detection.");
gd.addNumericField("Centroids radius", this.cuas_cent_radius, 5,8,"",
"Centroids radius for maximums isolation.");
gd.addNumericField("Recenter centroid", this.cuas_n_recenter, 0,3,"",
"when cosine window, re-center window these many times");
gd.addNumericField("Minimal correlation strength", this.cuas_rstr, 5,8,"",
"Minimal phase correlation maximums (negative value - relative to the maximal strength of the whole images correlations).");
gd.addCheckbox ("Smooth weights", this.cuas_smooth,
"Apply cosine weights when averaging a sequence of correlation pairs.");
gd.addNumericField("Number of pairs", this.cuas_corr_pairs, 0,3,"",
"The number of correlation pairs to accumulate.");
gd.addNumericField("Pairs offset", this.cuas_corr_offset, 0,3,"",
"Offset between the correlation pairs");
gd.addCheckbox ("Half scan step", this.cuas_half_step,
"Reduce step for motion detection = offset/2, if false = offset.");
gd.addNumericField("Local max range", this.cuas_max_range, 0,3,"",
"While filtering local correlation maximums: 1 - 3x3 neighbors, 2 - 5x5 ones.");
gd.addNumericField("Minimal speed", this.cuas_speed_min, 5,8,"ppr",
"Minimal target speed in pixels per range (per cuas_corr_offset).");
gd.addNumericField("Preferable speed", this.cuas_speed_pref, 5,8,"ppr",
"Boost effective strength when speed is above this.");
gd.addNumericField("Maximal speed boost", this.cuas_speed_boost, 5,8,"",
"Maximal speed-caused effective strength boost.");
gd.addMessage("=== Debug ===");
gd.addCheckbox ("Save/show debug images", this.cuas_debug,
......@@ -3058,6 +3097,19 @@ min_str_neib_fpn 0.35
this.cuas_multi_strength = gd.getNextNumber();
this.cuas_reliable_str = gd.getNextNumber();
this.cuas_fat_zero = gd.getNextNumber();
this.cuas_cent_radius = gd.getNextNumber();
this.cuas_n_recenter = (int) gd.getNextNumber();
this.cuas_rstr = gd.getNextNumber();
this.cuas_smooth = gd.getNextBoolean();
this.cuas_corr_pairs = (int) gd.getNextNumber();
this.cuas_corr_offset = (int) gd.getNextNumber();
this.cuas_half_step = gd.getNextBoolean();
this.cuas_max_range = (int) gd.getNextNumber();
this.cuas_speed_min = gd.getNextNumber();
this.cuas_speed_pref = gd.getNextNumber();
this.cuas_speed_boost = gd.getNextNumber();
this.cuas_debug = gd.getNextBoolean();
this.cuas_step_debug = gd.getNextBoolean();
......@@ -3933,6 +3985,20 @@ min_str_neib_fpn 0.35
properties.setProperty(prefix+"cuas_multi_strength", this.cuas_multi_strength+""); // double
properties.setProperty(prefix+"cuas_reliable_str", this.cuas_reliable_str+""); // double
properties.setProperty(prefix+"cuas_fat_zero", this.cuas_fat_zero+""); // double
properties.setProperty(prefix+"cuas_cent_radius", this.cuas_cent_radius+""); // double
properties.setProperty(prefix+"cuas_n_recenter", this.cuas_n_recenter+""); // int
properties.setProperty(prefix+"cuas_rstr", this.cuas_rstr+""); // double
properties.setProperty(prefix+"cuas_smooth", this.cuas_smooth+""); // boolean
properties.setProperty(prefix+"cuas_corr_pairs", this.cuas_corr_pairs+""); // int
properties.setProperty(prefix+"cuas_corr_offset", this.cuas_corr_offset+""); // int
properties.setProperty(prefix+"cuas_half_step", this.cuas_half_step+""); // boolean
properties.setProperty(prefix+"cuas_max_range", this.cuas_max_range+""); // int
properties.setProperty(prefix+"cuas_speed_min", this.cuas_speed_min+""); // double
properties.setProperty(prefix+"cuas_speed_pref", this.cuas_speed_pref+""); // double
properties.setProperty(prefix+"cuas_speed_boost", this.cuas_speed_boost+""); // double
properties.setProperty(prefix+"cuas_debug", this.cuas_debug+""); // boolean
properties.setProperty(prefix+"cuas_step_debug", this.cuas_step_debug+""); // boolean
......@@ -4780,6 +4846,22 @@ min_str_neib_fpn 0.35
if (properties.getProperty(prefix+"cuas_multi_strength")!=null) this.cuas_multi_strength=Double.parseDouble(properties.getProperty(prefix+"cuas_multi_strength"));
if (properties.getProperty(prefix+"cuas_reliable_str")!=null) this.cuas_reliable_str=Double.parseDouble(properties.getProperty(prefix+"cuas_reliable_str"));
if (properties.getProperty(prefix+"cuas_fat_zero")!=null) this.cuas_fat_zero=Double.parseDouble(properties.getProperty(prefix+"cuas_fat_zero"));
if (properties.getProperty(prefix+"cuas_cent_radius")!=null) this.cuas_cent_radius=Double.parseDouble(properties.getProperty(prefix+"cuas_cent_radius"));
if (properties.getProperty(prefix+"cuas_n_recenter")!=null) this.cuas_n_recenter=Integer.parseInt(properties.getProperty(prefix+"cuas_n_recenter"));
if (properties.getProperty(prefix+"cuas_rstr")!=null) this.cuas_rstr=Double.parseDouble(properties.getProperty(prefix+"cuas_rstr"));
if (properties.getProperty(prefix+"cuas_smooth")!=null) this.cuas_smooth=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_smooth"));
if (properties.getProperty(prefix+"cuas_corr_pairs")!=null) this.cuas_corr_pairs=Integer.parseInt(properties.getProperty(prefix+"cuas_corr_pairs"));
if (properties.getProperty(prefix+"cuas_corr_offset")!=null) this.cuas_corr_offset=Integer.parseInt(properties.getProperty(prefix+"cuas_corr_offset"));
if (properties.getProperty(prefix+"cuas_half_step")!=null) this.cuas_half_step=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_half_step"));
if (properties.getProperty(prefix+"cuas_max_range")!=null) this.cuas_max_range=Integer.parseInt(properties.getProperty(prefix+"cuas_max_range"));
if (properties.getProperty(prefix+"cuas_speed_min")!=null) this.cuas_speed_min=Double.parseDouble(properties.getProperty(prefix+"cuas_speed_min"));
if (properties.getProperty(prefix+"cuas_speed_pref")!=null) this.cuas_speed_pref=Double.parseDouble(properties.getProperty(prefix+"cuas_speed_pref"));
if (properties.getProperty(prefix+"cuas_speed_boost")!=null) this.cuas_speed_boost=Double.parseDouble(properties.getProperty(prefix+"cuas_speed_boost"));
if (properties.getProperty(prefix+"cuas_debug")!=null) this.cuas_debug=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_debug"));
if (properties.getProperty(prefix+"cuas_step_debug")!=null) this.cuas_step_debug=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_step_debug"));
......@@ -5628,6 +5710,19 @@ min_str_neib_fpn 0.35
imp.cuas_multi_strength = this.cuas_multi_strength;
imp.cuas_reliable_str = this.cuas_reliable_str;
imp.cuas_fat_zero = this.cuas_fat_zero;
imp.cuas_cent_radius = this.cuas_cent_radius;
imp.cuas_n_recenter = this.cuas_n_recenter;
imp.cuas_rstr = this.cuas_rstr;
imp.cuas_smooth = this.cuas_smooth;
imp.cuas_corr_pairs = this.cuas_corr_pairs;
imp.cuas_corr_offset = this.cuas_corr_offset;
imp.cuas_half_step = this.cuas_half_step;
imp.cuas_max_range = this.cuas_max_range;
imp.cuas_speed_min = this.cuas_speed_min;
imp.cuas_speed_pref = this.cuas_speed_pref;
imp.cuas_speed_boost = this.cuas_speed_boost;
imp.cuas_debug = this.cuas_debug;
imp.cuas_step_debug = this.cuas_step_debug;
......
src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java
View file @ da579ebb
......@@ -244,6 +244,14 @@ public class QuadCLTCPU {
public ImagePlus imp_center_average = null;
public CorrectionFPN correctionFPN = null;
public int getWidth() {
return tp.getTilesX()*tp.getTileSize();
}
public int getHeight() {
return tp.getTilesY()*tp.getTileSize();
}
public boolean dsiIsFromCombo() {
return dsi_from_combo;
}
......@@ -5943,99 +5951,12 @@ public class QuadCLTCPU {
readX3dDirectory(correctionsParameters.getModelName(image_name));
String file_name = image_name + suffix;
String file_path = x3d_path + Prefs.getFileSeparator() + file_name + ".tiff";
return readFloatArray(
return ShowDoubleFloatArrays.readFloatArray(
file_path, // String file_path,
num_slices, // int num_slices, // (0 - all)
wh); // int [] wh)
}
public static float [][] readFloatArray(
String file_path,
int num_slices, // (0 - all)
int [] wh) {
ImagePlus imp = null;
try {
imp = new ImagePlus(file_path);
} catch (Exception e) {
System.out.println ("Failed to open "+file_path+", maybe will generate it");
}
if ((imp == null) || (imp.getTitle() == null) || (imp.getTitle().equals(""))) {
return null;
}
System.out.println ("Read "+(imp.getStack().getSize())+" slices from "+file_path);
return readFloatArray(
imp, // ImagePlus imp,
num_slices, //int num_slices, // (0 - all)
wh); // int [] wh)
/*
ImageStack imageStack = imp.getStack();
int nChn=imageStack.getSize();
if ((num_slices > 0) && (num_slices < nChn)) {
nChn = num_slices;
}
float [][] result = new float [nChn][];
for (int n = 0; n < nChn; n++) {
result[n] = (float[]) imageStack.getPixels(n + 1);
}
if (wh != null) {
wh[0] = imp.getWidth();
wh[1] = imp.getHeight();
}
return result;
*/
}
public static double [][] readDoubleArray(
ImagePlus imp,
int num_slices, // (0 - all)
int [] wh) {
float [][] fdata = readFloatArray(
imp, // ImagePlus imp,
num_slices, // int num_slices, // (0 - all)
wh); // int [] wh)
if (fdata == null) {
return null;
}
double [][] result = new double [fdata.length][];
for (int n = 0; n < fdata.length; n++) if (fdata[n]!=null) {
result[n] = new double [fdata[n].length];
for (int i = 0; i < fdata[n].length; i++) {
result[n][i] = fdata[n][i];
}
}
return result;
}
public static float [][] readFloatArray(
ImagePlus imp,
int num_slices, // (0 - all)
int [] wh) {
if ((imp == null) || (imp.getTitle() == null) || (imp.getTitle().equals(""))) {
return null;
}
ImageStack imageStack = imp.getStack();
int nChn=imageStack.getSize();
if ((num_slices > 0) && (num_slices < nChn)) {
nChn = num_slices;
}
float [][] result = new float [nChn][];
for (int n = 0; n < nChn; n++) {
result[n] = (float[]) imageStack.getPixels(n + 1);
}
if (wh != null) {
wh[0] = imp.getWidth();
wh[1] = imp.getHeight();
}
return result;
}
public ImagePlus readImagePlusFromModelDirectory(
......
src/main/java/com/elphel/imagej/tileprocessor/TDCorrTile.java
View file @ da579ebb
......@@ -208,7 +208,7 @@ public class TDCorrTile {
* Get number of defined (non-null) tiles
* @param tiles sparse array of tiles
* @param indices - null or int [tiles.length] that will be set to have unique
* indices for non-null tiles. Indices for non-null tiles will not be modified
* indices for non-null tiles. Indices for null tiles will be set to -1
* @return number of non-null tiles
*/
public static int getNumTiles(
......@@ -223,6 +223,8 @@ public class TDCorrTile {
public void run() {
for (int iTile = ai.getAndIncrement(); iTile < tiles.length; iTile = ai.getAndIncrement()) if (tiles[iTile] != null) {
indices[iTile] = anum_tiles.getAndIncrement();
} else {
indices[iTile] = -1;
}
}
};
......@@ -458,16 +460,27 @@ public class TDCorrTile {
return mapped_corrs;
}
/**
* Calculate per-tile motion vectors {x,y,strength_over_min) using centroid approach
* @param tiles sparse array of correlation tiles (now 15*15=255 pix)
* @param rmax minimal tile strength relative to the absolute maximum strength. if negative - use absolute, not relative
* @param centroid_radius 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
* @param n_recenter re-center window around new maximum. 0 -no refines (single-pass)
* @return per-tile array of triplets (x,y,strength-min_strength)
*/
public static double [][] getMismatchVector(
final double [][] tiles,
double rmax,
double rmax, // minimal tile strength relative to the absolute maximum strength.
final double centroid_radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
final int n_recenter){ // re-center window around new maximum. 0 -no refines (single-pass)
final int n_recenter, // re-center window around new maximum. 0 -no refines (single-pass)
final boolean calc_fraction ){ // calculate fraction inside center circle
double [][] vector_field = new double [tiles.length][];
final int corr_size = 2 * GPUTileProcessor.DTT_SIZE - 1;
final int corr_size = (calc_fraction? -1 : 1) * (2 * GPUTileProcessor.DTT_SIZE - 1); // negate to force fraction calculation
final Thread[] threads = ImageDtt.newThreadArray();
final AtomicInteger ai = new AtomicInteger(0);
final AtomicInteger ati = new AtomicInteger(0);
double amax = 0;
if (rmax > 0) {
final double [] th_max = new double [threads.length];
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
......@@ -484,28 +497,33 @@ public class TDCorrTile {
};
}
ImageDtt.startAndJoin(threads);
double amax = th_max[0];
amax = th_max[0];
for (int i = 1; i < th_max.length; i++) {
if (th_max[i] > amax) {
amax = th_max[i];
}
}
final double min_str = rmax * amax;
}
final double min_str = (rmax > 0 ) ?rmax * amax : (-rmax);
ai.set(0);
final int dbg_tile = -(33+35*80);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int iTile = ai.getAndIncrement(); iTile < tiles.length; iTile = ai.getAndIncrement()) if (tiles[iTile] != null) {
if (iTile == dbg_tile) {
System.out.println("getMismatchVector(): iTile="+iTile);
}
double [] mv = Correlation2d.getMaxXYCm( // last, average
tiles[iTile], // corrs.length-1], // double [] data,
corr_size, // int data_width, // = 2 * transform_size - 1;
corr_size, // int data_width, // = 2 * transform_size - 1; // negative - will return center fraction
centroid_radius, // double radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
n_recenter, // int refine, // re-center window around new maximum. 0 -no refines (single-pass)
null, // boolean [] fpn_mask,
false, // boolean ignore_border, // only if fpn_mask != null - ignore tile if maximum touches fpn_mask
false); // boolean debug)
if (mv[2] > min_str) {
vector_field[iTile] = new double [] {mv[0], mv[1], mv[2]-min_str};
vector_field[iTile] = new double [] {mv[0], mv[1], mv[2]-min_str, mv[3]};
}
}
}
......
src/main/java/com/elphel/imagej/vegetation/VegetationSynthesis.java
View file @ da579ebb
......@@ -111,7 +111,7 @@ public class VegetationSynthesis {
int [] wh = new int [2];
int model_slices = imp_model.getStackSize();
System.out.println("testSynthetic(): read model from: " + path_model+", got "+model_slices+" slices");
double [][] model_data = QuadCLT.readDoubleArray(
double [][] model_data = ShowDoubleFloatArrays.readDoubleArray(
imp_model, // ImagePlus imp,
0, // int num_slices, // (0 - all)
wh); // int [] wh); // int [] wh)
......@@ -156,7 +156,7 @@ public class VegetationSynthesis {
} else {
int scene_offs_slices = imp_scene_offs.getStackSize();
System.out.println("testSynthetic(): read scene offsets from: " + path_scene_offs +", got "+scene_offs_slices+" slices, will add them to the rendered images");
scene_offs = QuadCLT.readDoubleArray(
scene_offs = ShowDoubleFloatArrays.readDoubleArray(
imp_scene_offs, // ImagePlus imp,
0, // int num_slices, // (0 - all)
wh); // int [] wh); // int [] wh)
......
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