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Commit 411beb9e authored by Andrey Filippov's avatar Andrey Filippov
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Reimplemented/tested pairwise GPU correlation

parent f97f3155
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Showing with 305 additions and 19 deletions
src/main/java/com/elphel/imagej/gpu/GpuQuad.java
View file @ 411beb9e
......@@ -4473,12 +4473,29 @@ public class GpuQuad{ // quad camera description
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 int img_height = fpixels[0].length/img_width;
final int tilesX = img_width / GPUTileProcessor.DTT_SIZE;
final int tilesY = img_height / GPUTileProcessor.DTT_SIZE;
final int tiles = tilesX*tilesY;
if (woi == null) {
woi = new Rectangle(0,0,img_width,img_height);
} else {
int x0 = ((int) Math.floor(1.0*woi.x/GPUTileProcessor.DTT_SIZE))*GPUTileProcessor.DTT_SIZE;
int y0 = ((int) Math.floor(1.0*woi.y/GPUTileProcessor.DTT_SIZE))*GPUTileProcessor.DTT_SIZE;
woi.width += woi.x-x0;
woi.height += woi.y-y0;
woi.width = ((int) Math.ceil(1.0*woi.width / GPUTileProcessor.DTT_SIZE)) * GPUTileProcessor.DTT_SIZE;
woi.height = ((int) Math.ceil(1.0*woi.height/ GPUTileProcessor.DTT_SIZE)) * GPUTileProcessor.DTT_SIZE;
woi.x = x0;
woi.y = y0;
}
final Rectangle tiles_woi = new Rectangle (
woi.x / GPUTileProcessor.DTT_SIZE,
woi.y / GPUTileProcessor.DTT_SIZE,
woi.width / GPUTileProcessor.DTT_SIZE,
woi.height / GPUTileProcessor.DTT_SIZE);
final int tiles = tiles_woi.width*tiles_woi.height;
final int task_code = (1 << GPUTileProcessor.TASK_CORR_EN) | (1 << GPUTileProcessor.TASK_INTER_EN);
final TpTask[][] tp_tasks_full = new TpTask[2][tiles]; // sparse, rfirst index - image #
final Thread[] threads = ImageDtt.newThreadArray();
......@@ -4492,8 +4509,8 @@ public class GpuQuad{ // quad camera description
double [][] cxy = new double [2][2]; // image number, {x,y}
int [][] icxy = new int [2][2];
for (int nTile = ai.getAndIncrement(); nTile < tiles; nTile = ai.getAndIncrement()) {
int tileY = nTile / tilesX;
int tileX = nTile % tilesX;
int tileY = nTile / tiles_woi.width + tiles_woi.x;
int tileX = nTile % tiles_woi.width + tiles_woi.y;
double [] cxy0 = {
(tileX + 0.5) * GPUTileProcessor.DTT_SIZE,
(tileY + 0.5) * GPUTileProcessor.DTT_SIZE};
......
src/main/java/com/elphel/imagej/orthomosaic/ComboMatch.java
View file @ 411beb9e
package com.elphel.imagej.orthomosaic;
import java.awt.Rectangle;
import java.io.IOException;
import java.time.LocalDateTime;
import java.util.Arrays;
......@@ -142,17 +143,32 @@ public class ComboMatch {
imp_alt.show();
}
float [][] gpu_pair_img = maps_collection.getPaddedPairGPU(
gpu_spair, // String [] spair,
zoom_lev); // int zoom_lev);
System.out.println("Setting up GPU");
if (GPU_QUAD_AFFINE == null) {
try {
GPU_QUAD_AFFINE = new GpuQuad(//
GPU_TILE_PROCESSOR, // GPUTileProcessor gpuTileProcessor,
gpu_max_width, // final int max_width,
gpu_max_height, // final int max_height,
1, // final int num_colors, // normally 1?
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);
}
ShowDoubleFloatArrays.showArrays(
gpu_pair_img,
gpu_width,
gpu_height,
true,
"gpu_pair-zoom"+zoom_lev+"-"+gpu_spair[0]+"-"+gpu_spair[1],
gpu_spair);
double [][] affine0 = {{1,0,0},{0,1,0}}; // will always stay the same
double [][] affine1 = {{1,0,0},{0,1,0}}; // will be variable // here in meters, relative to vertical point
double [][][] affines = {affine0,affine1};
double [][] corr_pair_rslt = maps_collection.correlateOrthoPair(
clt_parameters, // CLTParameters clt_parameters,
gpu_spair, // String [] gpu_spair,
affines, // double [][][] affines, // on top of GPS offsets
zoom_lev, // int zoom_lev,
debugLevel); // final int debugLevel)
if (save_collection) {
try {
maps_collection.writeOrthoMapsCollection(orthoMapsCollection_path);
......@@ -166,6 +182,28 @@ public class ComboMatch {
if (debugLevel <1000) {
return true;
}
/*
double [] offset_xy_second = {0,0};
double [][] corr_pair_rslt = maps_collection. correlateOrthoPair(
clt_parameters, // CLTParameters clt_parameters,
gpu_spair[0], // String first_name,
gpu_spair[1], // String second_name,
zoom_lev, // int zoom_lev,
offset_xy_second, //double [] offset_xy_second, // on top of affine and GPS
debugLevel); // final int debugLevel)
float [][] gpu_pair_img = maps_collection.getPaddedPairGPU(
gpu_spair, // String [] spair,
zoom_lev); // int zoom_lev);
ShowDoubleFloatArrays.showArrays(
gpu_pair_img,
gpu_width,
gpu_height,
true,
"gpu_pair-zoom"+zoom_lev+"-"+gpu_spair[0]+"-"+gpu_spair[1],
gpu_spair);
*/
/* */
OrthoMap [] ortho_maps = maps_collection.getMaps(); // just temporarily
......@@ -322,10 +360,12 @@ public class ComboMatch {
affine[1][1][2] = -0.5*pix_shift[1]*zoom_scale;
TDCorrTile [] td_corr_tiles = rectilinearCorrelate_TD( // scene0/scene1
// TDCorrTile [] td_corr_tiles =
rectilinearVectorField( // rectilinearCorrelate_TD( // scene0/scene1
clt_parameters, // final CLTParameters clt_parameters,
gpu_pix, // final float [][] fpixels, // to check for empty
gpu_width, // final int img_width,
null, // Rectangle woi, // if null, use full GPU window
affine, // final double [][][] affine, // [2][2][3] affine coefficients to translate common to 2 images
false, // final boolean batch_mode,
debugLevel); // final int debugLevel);
......@@ -337,11 +377,23 @@ public class ComboMatch {
return true;
}
/*
public static TDCorrTile [] rectilinearCorrelate_TD( // scene0/scene1
final CLTParameters clt_parameters,
final float [][] fpixels, // to check for empty
final int img_width,
Rectangle woi, // if null, use full GPU window
final double [][][] affine, // [2][2][3] affine coefficients to translate common to 2 images
final boolean batch_mode,
final int debugLevel) {
*/
public static double [][][] rectilinearVectorField( // scene0/scene1
final CLTParameters clt_parameters,
final float [][] fpixels, // to check for empty
final int img_width,
Rectangle woi, // if null, use full GPU window
final double [][][] affine, // [2][2][3] affine coefficients to translate common to 2 images
final boolean batch_mode,
final int debugLevel) {
......@@ -349,6 +401,7 @@ public class ComboMatch {
TpTask [][] tp_tasks = GpuQuad.setRectilinearInterTasks(
fpixels, // final float [][] fpixels, // to check for empty
img_width, // final int img_width,
woi, // Rectangle woi,
affine); // final double [][][] affine // [2][2][3] affine coefficients to translate common to 2 images
boolean is_aux = true;
boolean is_mono = true;
......@@ -509,7 +562,7 @@ public class ComboMatch {
}
return corr_tiles;
return vector_field; // corr_tiles;
}
......
src/main/java/com/elphel/imagej/orthomosaic/OrthoMap.java
View file @ 411beb9e
......@@ -306,11 +306,24 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
}
/**
* Get metric bounds of this image (zero point at vert_meters)
* Get metric bounds of this image (zero point at vert_meters) with the affine transform
* stored with this image.
* @param rectified if true, use rectified (inverse-transformed) image, false - original
* @return rectified {{x_min, x_max},{y_min,y_max}}
*/
public double [][] getBoundsMeters (boolean rectified){
return getBoundsMeters (rectified, affine);
}
/**
* Get metric bounds of this image (zero point at vert_meters) with specified affine transform
* @param rectified if true, use rectified (inverse-transformed) image, false - original
* @param affine - 6-element affine transform
* @return rectified {{x_min, x_max},{y_min,y_max}}
*/
public double [][] getBoundsMeters (
boolean rectified,
double [][] affine){
double [][] corners = get4SourceCornersMeters();
if (rectified) {
double [][] inv_aff = invertAffine(affine);
......@@ -333,6 +346,9 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
return bounds;
}
/**
* Get pixel bounds of this image (zero point at vert_meters) as doubles (to be able to
* offset before converting to int.
......
src/main/java/com/elphel/imagej/orthomosaic/OrthoMapsCollection.java
View file @ 411beb9e
package com.elphel.imagej.orthomosaic;
import java.awt.Rectangle;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
......@@ -20,6 +21,7 @@ import java.util.concurrent.atomic.AtomicInteger;
import com.elphel.imagej.cameras.CLTParameters;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.tileprocessor.ImageDtt;
import com.elphel.imagej.tileprocessor.TDCorrTile;
import ij.ImagePlus;
import ij.ImageStack;
......@@ -173,6 +175,38 @@ public class OrthoMapsCollection implements Serializable{
return bounds;
}
/**
* Get rectified overlap bounds of two provided ortho images relative to the origin (vertical
* point) of the first one in meters. Use specified affine transforms, not saved with the orto map
* @param ref_index - index of the first (reference) map
* @param other_index - index of the second (other) map
* @param ref_affine - specified affine transform of the reference image (referenced to its vertical_point)
* @param other_affine - specified affine transform of the other image (referenced to its vertical_point)
* @return {{min_x,max_x},{min_y,max_y}} bounds that include an overlap of the two provided maps
* relative to the origin (vertical point) of the first image.
* Returns null if there is no overlap
*/
private double [][] getOverlapMeters(
int ref_index,
int other_index,
double [][] ref_affine,
double [][] other_affine){
double [][] bounds = ortho_maps[ref_index].getBoundsMeters(true,ref_affine);
double [][] bounds_other = ortho_maps[other_index].getBoundsMeters(true,other_affine);
double [] enuOffset = ortho_maps[ref_index].enuOffsetTo(ortho_maps[other_index]);
double [] rd = {enuOffset[0], -enuOffset[1]}; // {right,down} of the image
for (int n = 0; n < bounds.length; n++) {
bounds[n][0] = Math.max(bounds[n][0],bounds_other[n][0]+ rd[n]);
bounds[n][1] = Math.min(bounds[n][1],bounds_other[n][1]+ rd[n]);
if (bounds[n][0] > bounds[n][1]) {
return null;
}
}
return bounds;
}
public ImagePlus renderMulti (
String title,
boolean use_alt,
......@@ -336,6 +370,7 @@ public class OrthoMapsCollection implements Serializable{
return gpu_pair_img;
}
/*
public double [][] correlateOrthoPair(
CLTParameters clt_parameters,
String first_name,
......@@ -379,8 +414,173 @@ public class OrthoMapsCollection implements Serializable{
map_names);
}
return null;
} */
public double [][] correlateOrthoPair(
CLTParameters clt_parameters,
String [] gpu_spair,
double [][][] affines, // here in meters, relative to vertical points
int zoom_lev,
final int debugLevel){
int [] gpu_pair = new int[gpu_spair.length];
for (int i = 0; i < gpu_pair.length; i++) {
gpu_pair[i] = map_index_string.get(gpu_spair[i]);
}
return correlateOrthoPair(
clt_parameters, // CLTParameters clt_parameters,
gpu_pair, // int [] gpu_pair,
affines, // double [][][] affines, // here in meters, relative to vertical points
zoom_lev, // int zoom_lev,
debugLevel); // final int debugLevel)
}
private double [][] correlateOrthoPair(
CLTParameters clt_parameters,
int [] gpu_pair,
double [][][] affines, // here in meters, relative to vertical points
int zoom_lev,
final int debugLevel){
double [][] bounds_overlap_meters = getOverlapMeters(
gpu_pair[0], // int ref_index,
gpu_pair[1], // int other_index)
affines[0], // double [][] ref_affine,
affines[1]); // double [][] other_affine
if (bounds_overlap_meters == null) {
if (debugLevel > -3) {
System.out.println("correlateOrthoPair(): no overlap");
return null;
}
}
double pix_size = OrthoMap.getPixelSizeMeters (zoom_lev);
int [] overlap_wh_pixel = new int [2];
for (int i = 0; i < 2; i++) {
overlap_wh_pixel[i] = ((int) Math.ceil(bounds_overlap_meters[i][1]/pix_size)) - ((int) Math.floor(bounds_overlap_meters[i][0]/pix_size));
}
// double [][] bounds_overlap_pixels = new double[2][2];
// convert to pixels,shift top-left to [0,0] (remember offsets, limit w,h,
// change to pixels last, remember TL in meters?
// keep center where it was
// {bounds_overlap_meters[0][0],bounds_overlap_meters[1][0],
double [] enuOffset = ortho_maps[gpu_pair[0]].enuOffsetTo(ortho_maps[gpu_pair[1]]);
double [] rd = {enuOffset[0], -enuOffset[1]}; // {right,down} of the image
double [][] tlo_rect_metric = new double [2][2]; // top-left of overlap referenced to it's own vertical point (subtract!)
tlo_rect_metric[0][0] = bounds_overlap_meters[0][0]; // relative to ref vert_meters
tlo_rect_metric[0][1] = bounds_overlap_meters[1][0]; // vert_meters
tlo_rect_metric[1][0] = bounds_overlap_meters[0][0] // relative to other vert_meters
- rd[0] + ortho_maps[gpu_pair[1]].vert_meters[0]- ortho_maps[gpu_pair[0]].vert_meters[0];
tlo_rect_metric[1][1] = bounds_overlap_meters[1][0]
- rd[1] + ortho_maps[gpu_pair[1]].vert_meters[1]- ortho_maps[gpu_pair[0]].vert_meters[1];
double [][] tlo_src_metric = new double[tlo_rect_metric.length][2]; // relative to it's own vert_meters
for (int n=0; n <tlo_src_metric.length; n++) {
for (int i = 0; i < 2; i++) { // subtracting tl_rect_metric[n] (-1)
tlo_src_metric[n][i] =
tlo_rect_metric[n][0] * affines[n][i][0] +
tlo_rect_metric[n][1] * affines[n][i][1] + affines[n][i][2]; // -
// tl_rect_metric[n][i];
}
}
/// referenced to top-left pixel of the gpu image
double [][] tlo_source_pixel = new double[tlo_src_metric.length][2];
for (int n=0; n <tlo_source_pixel.length; n++) {
for (int i = 0; i < 2; i++) {
tlo_source_pixel[n][i] = (tlo_src_metric[n][i] + ortho_maps[gpu_pair[n]].vert_meters[i])/pix_size;
}
}
double [][][] affines_gpu = new double [affines.length][2][3]; // relative to top left corners, in pixels
float [][] gpu_pair_img = new float [2][];
for (int n = 0; n < gpu_pair.length; n++) {
for (int i = 0; i < 2; i++) {
for (int j = 0; j < 2; j++) {
affines_gpu[n][i][j] = affines[n][i][j];
}
affines_gpu[n][i][2] = tlo_source_pixel[n][i];
}
gpu_pair_img[n] = ortho_maps[gpu_pair[n]].getPaddedGPU (zoom_lev); // int zoom_level,
}
Rectangle woi = new Rectangle(0, 0, overlap_wh_pixel[0], overlap_wh_pixel[1]);
if (woi.width > OrthoMap.gpu_width) {
if (debugLevel > -3) {
System.out.println("correlateOrthoPair() correlation woi.width="+woi.width+" > gpu_width="+OrthoMap.gpu_width+". Truncating.");
}
woi.width = OrthoMap.gpu_width;
}
if (woi.height > OrthoMap.gpu_height) {
if (debugLevel > -3) {
System.out.println("correlateOrthoPair() correlation woi.height="+woi.height+" > gpu_height="+OrthoMap.gpu_height+". Truncating.");
}
woi.height = OrthoMap.gpu_height;
}
final int gpu_width = OrthoMap.gpu_width; // static
// uses fixed_size gpu image size
// TDCorrTile [] td_corr_tiles =
double [][][] vector_field =
ComboMatch.rectilinearVectorField(//rectilinearCorrelate_TD( // scene0/scene1
clt_parameters, // final CLTParameters clt_parameters,
gpu_pair_img, // final float [][] fpixels, // to check for empty
gpu_width, // final int img_width,
woi, // Rectangle woi, // if null, use full GPU window
affines_gpu, // final double [][][] affine, // [2][2][3] affine coefficients to translate common to 2 images
false, // final boolean batch_mode,
debugLevel); // final int debugLevel);
// may use tl_rect_metric to remap to the original image
/*
if (show_vector_field) {
double [][] dbg_vf = new double [3 * vector_field.length][tilesX * tilesY];
String [] dbg_titles = new String[dbg_vf.length];
String [] prefix= {"single","neibs"};
for (int n = 0; n < vector_field.length; n++) {
dbg_titles [3*n+0] = prefix[n]+"-vx";
dbg_titles [3*n+1] = prefix[n]+"-vy";
dbg_titles [3*n+2] = prefix[n]+"-str";
}
for (int i = 0; i < dbg_vf.length; i++) {
Arrays.fill(dbg_vf[i], Double.NaN);
}
for (int t=0; t<dbg_vf[0].length; t++) {
for (int n = 0; n < vector_field.length; n++) {
if (vector_field[n][t] != null) {
for (int k = 0; k < 3; k++) {
dbg_vf[n*3 + k][t] = vector_field[n][t][k];
}
}
}
}
ShowDoubleFloatArrays.showArrays(
dbg_vf,
tilesX,
tilesY,
true,
"vector_field",
dbg_titles);
}
*/
if (debugLevel > 1) {
String [] map_names = {ortho_maps[gpu_pair[0]].getName(),ortho_maps[gpu_pair[1]].getName()};
ShowDoubleFloatArrays.showArrays(
gpu_pair_img,
OrthoMap.gpu_width,
OrthoMap.gpu_height,
true,
"gpu_pair-zoom"+zoom_lev+"-"+ortho_maps[gpu_pair[0]].getName()+"-"+ortho_maps[gpu_pair[1]].getName(),
map_names);
}
return null;
}
public static OrthoMapsCollection readOrthoMapsCollection (
String path) throws IOException, ClassNotFoundException {
FileInputStream fileInputStream = new FileInputStream(path);
......
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