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Commit df789de8 authored by Andrey Filippov's avatar Andrey Filippov
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added multi-cluster backdrop

parent 6315c513
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Showing with 487 additions and 65 deletions
src/main/java/com/elphel/imagej/cameras/CLTParameters.java
View file @ df789de8
......@@ -520,6 +520,7 @@ public class CLTParameters {
public boolean lre_show_textures_slice = false; //true;
public boolean lre_show_textures_combo = false; //true;
public boolean lre_show_textures_tiles = false; //true;
public boolean lre_show_sky_textures = false; //true;
public double pt_super_trust = 1.6; // If strength exceeds ex_strength * super_trust, do not apply ex_nstrength and plate_ds
public boolean pt_keep_raw_fg = true; // Do not replace raw tiles by the plates, if raw is closer (like poles)
......@@ -1626,6 +1627,8 @@ public class CLTParameters {
properties.setProperty(prefix+"lre_show_textures_combo", this.lre_show_textures_combo+""); // boolean
properties.setProperty(prefix+"lre_show_textures_tiles", this.lre_show_textures_tiles+""); // boolean
properties.setProperty(prefix+"lre_show_sky_textures", this.lre_show_sky_textures+""); // boolean
properties.setProperty(prefix+"pt_super_trust", this.pt_super_trust +"");
properties.setProperty(prefix+"pt_keep_raw_fg", this.pt_keep_raw_fg+"");
properties.setProperty(prefix+"pt_scale_pre", this.pt_scale_pre +"");
......@@ -2607,6 +2610,7 @@ public class CLTParameters {
if (properties.getProperty(prefix+"lre_show_textures_combo")!=null) this.lre_show_textures_combo=Boolean.parseBoolean(properties.getProperty(prefix+"lre_show_textures_combo"));// boolean
if (properties.getProperty(prefix+"lre_show_textures_tiles")!=null) this.lre_show_textures_tiles=Boolean.parseBoolean(properties.getProperty(prefix+"lre_show_textures_tiles"));// boolean
if (properties.getProperty(prefix+"lre_show_sky_textures")!=null) this.lre_show_sky_textures=Boolean.parseBoolean(properties.getProperty(prefix+"lre_show_sky_textures"));// boolean
if (properties.getProperty(prefix+"pt_super_trust")!=null) this.pt_super_trust=Double.parseDouble(properties.getProperty(prefix+"pt_super_trust"));
if (properties.getProperty(prefix+"pt_keep_raw_fg")!=null) this.pt_keep_raw_fg=Boolean.parseBoolean(properties.getProperty(prefix+"pt_keep_raw_fg"));
......@@ -3857,6 +3861,8 @@ public class CLTParameters {
"Show all-slice combined images for textures calculation.");
gd.addCheckbox ("Show tile-resolution images", this.lre_show_textures_tiles, // false;
"Show all-slices texture debug images with tile resolution (80x64 for Boson 640).");
gd.addCheckbox ("Show sky/backdrop texture expanding", this.lre_show_sky_textures, // false;
"Show how sky/backdrop texture is cut and extrapolated.");
gd.addTab ("Plates", "Plates filtering when building initial z-map");
gd.addMessage ("********* Plates filtering when building initial z-map *********");
......@@ -4971,8 +4977,9 @@ public class CLTParameters {
this.lre_show_textures_slice= gd.getNextBoolean(); // boolean
this.lre_show_textures_combo= gd.getNextBoolean(); // boolean
this.lre_show_textures_tiles= gd.getNextBoolean(); // boolean
// end of gd.addtab ("Lateral resolution enhancement");
this.lre_show_sky_textures= gd.getNextBoolean(); // boolean
// end of gd.addtab ("Lateral resolution enhancement");
this.pt_super_trust= gd.getNextNumber();
this.pt_keep_raw_fg= gd.getNextBoolean();
......
src/main/java/com/elphel/imagej/tileprocessor/TexturedModel.java
View file @ df789de8
......@@ -326,6 +326,143 @@ public class TexturedModel {
return new int [] {best_tile, best_layer};
}
/**
* Create a "blue sky" tile cluster with flaps, may be disconnected. Should be ran before
* all other clusters are created
* @param disparity_layers [layers][tiles] multi-layer disparity array with NaN
* for non-existing tiles
* @param blue_sky per-tile array of the "blue sky" boolean array
* @param blue_sky_layer layer for the "blue sky" data (should be on a single layer)
* @param blue_sky_below (only if is_sky_cluster) if >=0 - extend bounds, if <0 treat blue_sky bounds
* same as regular ones.
* @param max_neib_lev maximal neighbor level of borders used to generate internal int [] neib_lev
* array. Neighbor level 0 corresponds to internal tiles that uses original
* disparity, level 1 - neighbors of level 0 on the border or in conflict with
* level 0. Level 2 - neighbors of 1 or in conflict with level 0, and so all.
* @param tilesX horizontal array dimension
* @param debugLevel debug level - controls generation of images
* @return TileCluster instance generated from the initial source_disparity[] array.
*/
public static TileCluster buildSkyCluster(
final double [][] disparity_layers, // should not have same tile disparity on multiple layers
final boolean [] blue_sky, // Do not mix bs/no_bs in the same cluster
final int blue_sky_layer,
final int blue_sky_below,
final int max_neib_lev,
final int tilesX,
final int debugLevel){
final int tiles = disparity_layers[0].length;
final int tilesY = tiles/tilesX;
final int [] borders_int = new int[tiles];
Arrays.fill(borders_int, -1);
final TileNeibs tn = new TileNeibs(tilesX, tilesY);
final Thread[] threads = ImageDtt.newThreadArray(THREADS_MAX);
final AtomicInteger ai = new AtomicInteger(0);
final AtomicInteger anum = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int tile = ai.getAndIncrement(); tile < tiles; tile = ai.getAndIncrement()) {
if (blue_sky[tile]) {
int tileX = tile % tilesX;
int tileY = tile / tilesX;
anum.getAndIncrement();
borders_int[tile] = 0;
disparity_layers[blue_sky_layer][tile] = Double.NaN;
}
}
}
};
}
ImageDtt.startAndJoin(threads);
if (anum.get() == 0) {
return null; // no blue sky tiles exist
}
final boolean [] selection = blue_sky.clone();
for (int nlev = 1; nlev <= max_neib_lev; nlev++) {
final int fnlev = nlev;
tn.growSelection(
2, // int grow, // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
selection, // final boolean [] tiles,
null); // null); // final boolean [] prohibit)
ai.set(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int tile = ai.getAndIncrement(); tile < tiles; tile = ai.getAndIncrement()) {
if (selection[tile] && (borders_int[tile] < 0)) {
borders_int[tile] = fnlev;
}
}
}
};
}
ImageDtt.startAndJoin(threads);
}
AtomicInteger min_y = new AtomicInteger(tilesY);
AtomicInteger max_y = new AtomicInteger(0);
AtomicInteger min_x = new AtomicInteger(tilesX);
AtomicInteger max_x = new AtomicInteger(0);
ai.set(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int tile = ai.getAndIncrement(); tile < tiles; tile = ai.getAndIncrement()) {
if (selection[tile]) {
int tileY = tile / tilesX;
int tileX = tile % tilesX;
min_y.getAndAccumulate(tileY, Math::min);
max_y.getAndAccumulate(tileY, Math::max);
min_x.getAndAccumulate(tileX, Math::min);
max_x.getAndAccumulate(tileX, Math::max);
}
}
}
};
}
ImageDtt.startAndJoin(threads);
if (blue_sky_below >= 0) { // increase bounding box for sky cluster
min_y.set(0);
max_y.addAndGet(blue_sky_below);
if (max_y.get() >= tilesY) {
max_y.set(tilesY-1);
}
min_x.set(0);
max_x.set(tilesX -1);
}
final int width = max_x.get() - min_x.get() + 1;
final int height = max_y.get() - min_y.get() + 1;
final Rectangle bounds = new Rectangle(min_x.get(), min_y.get(), width, height);
final double [] disparity_crop = new double [width * height]; //
final int [] border_int_crop = new int [disparity_crop.length];
ai.set(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int tile_crop = ai.getAndIncrement(); tile_crop < disparity_crop.length; tile_crop = ai.getAndIncrement()) {
int tileY = tile_crop / width + bounds.y ;
int tileX = tile_crop % width + bounds.x;
int tile = tileX + tileY * tilesX;
disparity_crop[tile_crop] = (borders_int[tile] >=0) ? 0.0 : Double.NaN;
border_int_crop[tile_crop] = borders_int[tile];
}
}
};
}
ImageDtt.startAndJoin(threads);
TileCluster tileCluster = (new TileCluster(
bounds,
0, // (debug_index? cluster_list.size(): -1),
null, // border_crop, // will create from border_int_crop
border_int_crop, // int [] border_int, // will replace border? Provide on-the-fly?
max_neib_lev, // int border_int_max, // outer border value
disparity_crop,
true)); // boolean is_sky));
return tileCluster;
}
/**
* Create initial cluster of connected tiles without provisions for overlap resolution
* @param disparity_layers [layers][tiles] multi-layer disparity array with NaN
......@@ -573,7 +710,7 @@ public class TexturedModel {
int debugLevel_in)
{
if ((debugLevel_in > -2) && is_sky_cluster) {
System.out.println("buildTileCluster(): processing sky clusterm cluster_list.size()="+cluster_list.size());
System.out.println("buildTileCluster(): processing sky cluster, cluster_list.size()="+cluster_list.size());
}
final int dbg_tile = -2410; // 858; // -3868; // 28+48*80;
......@@ -1368,6 +1505,24 @@ public class TexturedModel {
}
// maybe ncluster[][] will not be used at all - disparity_layers will be modified to NaN used tiles
// Before initial updateSeeds() - may be simplified as BS is already processed
final ArrayList <TileCluster> cluster_list = new ArrayList<TileCluster>();
// build blue sky first
TileCluster blueSkyCluster = buildSkyCluster(
disparity_layers, // final double [][] disparity_layers, // should not have same tile disparity on multiple layers
blue_sky, // final boolean [] blue_sky, // use to expand background by blurring available data?
blue_sky_layer, // final int blue_sky_layer,
blue_sky_below, // final int blue_sky_below, // >=0 this is a blue sky cluster, mark as such and extend bounds
max_neib_lev, // final int max_neib_lev,
tilesX, // final int tilesX,
debugLevel); // final int debugLevel)
if (blueSkyCluster != null) {
cluster_list.add(blueSkyCluster);
if (debugLevel > -2) {
System.out.println("clusterizeFgBg(): processed sky cluster");
}
}
// calculate initial num_neibs_dir
updateSeeds( // and update num_neibs_dir
num_neibs_dir, // final int [][] num_neibs_dir, // [tile][layer]
......@@ -1384,8 +1539,9 @@ public class TexturedModel {
debugLevel); // final int debugLevel)
if (debugLevel > -1) { // was > 0
String [] dbg_titles = {"FG","BG"};
String [] dbg_titles0 = {"FG","BG"};
double [][] dbg_img = new double[layers][tiles];
for (int i = 0; i < tiles;i++) {
for (int j = 0; j < dbg_img.length; j++) {
dbg_img[j][i] = NUM_NEIBS_FROM_BITS[num_neibs_dir[i][j]];
......@@ -1397,19 +1553,26 @@ public class TexturedModel {
tilesY,
true,
"num_neibs",
dbg_titles);
dbg_titles0);
String [] dbg_titles1 = {"FG","BG", "sky"};
double [][] dbg_disp = new double [dbg_titles1.length][];
dbg_disp[0] = disparity_layers[0];
dbg_disp[1] = disparity_layers[1];
dbg_disp[2] = new double[tiles];
for (int i = 0; i < tiles;i++) {
dbg_disp[2][i] = blue_sky[i] ? 20:0;
}
ShowDoubleFloatArrays.showArrays(
disparity_layers,
dbg_disp, // disparity_layers,
tilesX,
tilesY,
true,
"disparity_layers",
dbg_titles);
dbg_titles1);
}
final ArrayList <TileCluster> cluster_list = new ArrayList<TileCluster>();
// build all clusters
int tile_start = 2820; // 0; // change to debug tile to start with the largest one
int tile_start = 0; // 2820; // 0; // change to debug tile to start with the largest one
while (true) {
int [] next_seed_tile_layer = getNextSeed(
disparity_layers, // final double [][] disparity_layers, //
......@@ -1422,7 +1585,7 @@ public class TexturedModel {
// next_seed_tile_layer is now {tile, layer}
final boolean is_sky_cluster = (next_seed_tile_layer[1] == blue_sky_layer) && blue_sky[next_seed_tile_layer[0]];
if ((debugLevel > -2) && is_sky_cluster) {
System.out.println("clusterizeFgBg(): processing sky clusterm cluster_list.size()="+cluster_list.size());
System.out.println("clusterizeFgBg(): processing sky cluster, cluster_list.size()="+cluster_list.size());
}
double [] cluster_initial_disparity = buildInitialCluster(
disparity_layers, // final double [][] disparity_layers, // should not have same tile disparity on multiple layers
......@@ -1663,7 +1826,7 @@ public class TexturedModel {
final boolean disp_hires_tri = !batch_mode && clt_parameters.tex_disp_hires_tri;
final int dbg_scale_mesh = clt_parameters.tex_dbg_scale_mesh; // 4; // <=0 - do not show
/// final double min_non_inf = 0.01; // relative to infinity disparity
final boolean show_bs_debug = !batch_mode && clt_parameters.lre_show_sky_textures; // add parameter
final int sky_layer = 0; // source disparity layer that contains "blue sky"
......@@ -1754,9 +1917,12 @@ public class TexturedModel {
}
}
if (debugLevel > -2) { // was > 0
if (show_bs_debug) {
String [] dbg_titles = {"FG","BG","BS"};
double [][] dbg_img = {ds_fg_bg[0], ds_fg_bg[1],combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_BLUE_SKY]};
double [][] dbg_img = {ds_fg_bg[0], ds_fg_bg[1],combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_BLUE_SKY].clone()};
for (int i = 0; i < dbg_img.length; i++) {
dbg_img[2][i] *= 20;
}
ShowDoubleFloatArrays.showArrays(
dbg_img,
tilesX,
......@@ -3615,13 +3781,15 @@ public class TexturedModel {
* undefined pixels
* @param width image width (640 for Flir Boson)
* @param transform_size CLT transform size (==8)
* @param dbg_prefix null or debug image name prefix
*/
public static void extendBlueSKy(
final TileCluster [] tileClusters,
final double [][][] faded_textures,
final int shrink_sky_tiles,
final int width,
final int transform_size) {
final int transform_size,
final String dbg_prefix) {
final Thread[] threads = ImageDtt.newThreadArray(THREADS_MAX);
final AtomicInteger ai = new AtomicInteger(0);
int sky_slice = -1;
......@@ -3641,7 +3809,7 @@ public class TexturedModel {
sky_tiles_bounds.width * transform_size,
sky_tiles_bounds.height * transform_size
);
final double [] sky_disparity = tileClusters[sky_slice].getSubDisparity(sky_subindex);
final double [] sky_disparity = tileClusters[sky_slice].getSubDisparity(sky_subindex); // window
final int num_sky_tiles = sky_disparity.length;
final TileNeibs tn_sky_tiles = new TileNeibs(sky_tiles_bounds.width, sky_tiles_bounds.height);
final boolean [] sky_sel = new boolean [sky_disparity.length];
......@@ -3653,6 +3821,11 @@ public class TexturedModel {
sky_pixels_bounds, // Rectangle window,
faded_textures[sky_slice][0], // double [] data,
width); // int data_width)
final String [] dbg_titles = {"source","shrank", "hinted", "filled"};
final String [] dbg_tile_titles = {"start", "filled"};
final double [][] dbg_img = (dbg_prefix != null) ? new double [dbg_titles.length][]:null;
final double [][] dbg_timg = (dbg_prefix != null) ? new double [dbg_tile_titles.length][]:null;
if (dbg_img != null) dbg_img[0] = sky_pixels.clone();
if (shrink_sky_tiles > 0) {
tn_sky_tiles.shrinkSelection(
shrink_sky_tiles,
......@@ -3688,6 +3861,8 @@ public class TexturedModel {
}
ImageDtt.startAndJoin(threads);
}
if (dbg_img != null) dbg_img[1] = sky_pixels.clone();
// now fill gaps in disparity and pixels
double []sky_disparity_filled = TileProcessor.fillNaNs( // multithreaded
sky_disparity, // final double [] data,
......@@ -3699,17 +3874,60 @@ public class TexturedModel {
0.01, // final double max_rchange, // = 0.01
THREADS_MAX); // final int threadsMax) // maximal number of threads to launch
tileClusters[sky_slice].setSubDisparity(sky_subindex,sky_disparity_filled);
// downscale texture
int tile_size = transform_size * 1;
int lores_width = width / tile_size;
double [] sky_lores = TileProcessor.fillNaNsScaleDown(
sky_pixels, // final double [] data,
null, // final boolean [] prohibit,
tile_size, // final int tile_size,
width, // int width,
THREADS_MAX); // final int threadsMax) // maximal number of threads to launch
if (dbg_timg != null) dbg_timg[0] = sky_lores;
double [] sky_lores_filled = TileProcessor.fillNaNs( // multithreaded
sky_lores, // final double [] data,
null, // final boolean [] prohibit,
lores_width, // int width,
2 * Math.max(sky_tiles_bounds.width, sky_tiles_bounds.height), // 16, // final int grow,
0.7, // double diagonal_weight, // relative to ortho
100, // int num_passes,
0.001, // final double max_rchange, // = 0.01
THREADS_MAX); // final int threadsMax) // maximal number of threads to launch
if (dbg_timg != null) dbg_timg[1] = sky_lores_filled;
if ((dbg_prefix != null) && (dbg_timg != null)) {
ShowDoubleFloatArrays.showArrays(
dbg_timg,
sky_tiles_bounds.width,
sky_tiles_bounds.height,
true,
dbg_prefix+"-extended-sky-lowres",
dbg_tile_titles);
}
double [] sky_pixels_nan = sky_pixels.clone(); // original data with NaN to be replaced
TileProcessor.fillNaNsScaleUp( // replace gaps with low-res data
sky_pixels, // final double [] data, // will be replaced
sky_lores_filled, // final double [] data_scaled,
null, // final boolean [] prohibit,
tile_size, // final int tile_size,
width, // int width,
THREADS_MAX); // final int threadsMax) // maximal number of threads to launch
if (dbg_img != null) dbg_img[2] = sky_pixels.clone();
double[] sky_pixels_filled = TileProcessor.fillNaNs( // multithreaded
sky_pixels, // final double [] data,
sky_pixels, // final double [] data, hinted (NaN replaced from low-res )
sky_pixels_nan, // final double [] data_nan, origina with NaN
null, // final boolean [] prohibit,
sky_pixels_bounds.width, // int width,
// 3 * Math.min(sky_pixels_bounds.width,sky_pixels_bounds.height) / 2, // 16, // final int grow,
2 * Math.max(sky_pixels_bounds.width,sky_pixels_bounds.height), // 16, // final int grow,
0.7, // double diagonal_weight, // relative to ortho
100, // int num_passes,
0.01, // final double max_rchange, // = 0.01
THREADS_MAX); // final int threadsMax) // maximal number of threads to launch
if (dbg_img != null) dbg_img[3] = sky_pixels_filled.clone();
TileNeibs.setDoubleWindow(
sky_pixels_bounds, // Rectangle window,
......@@ -3723,6 +3941,16 @@ public class TexturedModel {
sky_alpha, // double [] window_data,
faded_textures[sky_slice][1], // double [] data,
width); // int data_width)
if ((dbg_prefix != null) && (dbg_img != null)) {
ShowDoubleFloatArrays.showArrays(
dbg_img,
sky_pixels_bounds.width,
sky_pixels_bounds.height,
true,
dbg_prefix+"-extended-sky",
dbg_titles);
//dbg_tile_titles
}
}
return;
}
......@@ -5734,6 +5962,8 @@ public class TexturedModel {
final double tex_hist_amount = clt_parameters.tex_hist_amount; // clt_parameters. 0.7;
final int tex_hist_bins = clt_parameters.tex_hist_bins; // 1024 ;
final int tex_hist_segments = clt_parameters.tex_hist_segments; // 32 ;
final boolean show_sky_textures = clt_parameters.lre_show_sky_textures && !clt_parameters.multiseq_run;
final int shrink_sky_tiles = 4; // 2; sum of 2 +bg extend
final boolean grow_sky = true;
final boolean alphaOverlapFix = true; // if multiple tiles have the same (+/-?) disparity, make alpha max of them
......@@ -6021,12 +6251,15 @@ public class TexturedModel {
}
// Grow sky
if (grow_sky) {
String dbg_prefix = show_sky_textures ? ref_scene.getImageName() : null;
extendBlueSKy(
tileClusters, // final TileCluster [] tileClusters,
faded_textures, // final double [][][] faded_textures,
shrink_sky_tiles, // final int shrink_sky_tiles,
width, // final int width,
transform_size); // final int transform_size);
transform_size, // final int transform_size);
dbg_prefix); // dbg_prefix); // final String dbg_prefix)
}
// fix alpha
if (alphaOverlapFix) {
......
src/main/java/com/elphel/imagej/tileprocessor/TileProcessor.java
View file @ df789de8
......@@ -8635,7 +8635,141 @@ ImageDtt.startAndJoin(threads);
return -1;
}
/**
* Helper method for fillNaNs() - scaling down input data to first fill low-res array
* of tiles as initial approximation for filling large NaN areas.
* @param data data with NaN-s to be replaced
* @param prohibit optional (may be null) array that discards data pixels from processing
* @param tile_size tile size - reciprocal to the scale
* @param width input data[] width in pixels (height = data.length/width)
* @param threadsMax maximal number of threads to use
* @return scaled down data[]. Each item (tile) is average of the corresponding data[] pixels
* or NaN if it has no non-NaN pixels in a tile.
*/
public static double [] fillNaNsScaleDown(
final double [] data,
final boolean [] prohibit,
final int tile_size,
int width,
final int threadsMax) { // maximal number of threads to launch
int height = data.length/width;
int tilesX = (width + tile_size - 1) / tile_size; // round up
int tilesY = (height + tile_size - 1) / tile_size; // round up
double [] data_scaled = new double [tilesX * tilesY];
Arrays.fill(data_scaled, Double.NaN);
final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int tile = ai.getAndIncrement(); tile < data_scaled.length; tile = ai.getAndIncrement()) {
int npix = 0;
double sum_pix = 0.0;
int tileX = tile % tilesX;
int tileY = tile / tilesX;
int indx0 = (tileX + tileY * width) * tile_size;
int lim_dy = Math.min(tile_size, height - tileY * tile_size);
int lim_dx = Math.min(tile_size, width - tileX * tile_size);
for (int dy = 0; dy < lim_dy; dy++) {
int indx1 = indx0 + dy * width;
for (int dx = 0; dx < lim_dx; dx++) {
int indx = indx1 + dx;
double d = data[indx];
if (!Double.isNaN(d) && ((prohibit == null) || !prohibit[indx])) {
npix++;
sum_pix += d;
}
}
}
if (npix > 0) {
data_scaled[tile] = sum_pix/npix;
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return data_scaled;
}
/**
* Generate a hint for a final replacing NaN with averaging neighbors (Laplassian). Replace all
* NaN in input data[] with the corresponding values from the matching low-res data_scaled[].
* @param data full resolution input data containing NaN values to be replaced. This array
* is MODIFIED by this method
* @param data_scaled low-resolution data with NaN already filled with fillNaNs() for scaled
* down data (tiles)
* @param prohibit optional (may be null) array indicating which data[] pixels to be ignored
* @param tile_size tile size - reciprocal to the scale down of data_scaled
* @param width input data[] width in pixels (height = data.length/width)
* @param threadsMax maximal number of threads to use
*/
public static void fillNaNsScaleUp(
final double [] data, // will be replaced
final double [] data_scaled,
final boolean [] prohibit,
final int tile_size,
int width,
final int threadsMax) { // maximal number of threads to launch
int tilesX = (width + tile_size - 1) / tile_size; // round up
final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int pix = ai.getAndIncrement(); pix < data.length; pix = ai.getAndIncrement()) {
if (Double.isNaN(data[pix]) && ((prohibit == null) || !prohibit[pix])) {
int px = pix % width;
int py = pix / width;
int tileX = px / tile_size;
int tileY = py / tile_size;
data[pix] = data_scaled[tileX + tileY * tilesX];
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return;
}
public static boolean [] fillNaNsGetFixed(
final double [] data,
final boolean [] prohibit,
final int threadsMax) { // maximal number of threads to launch
final boolean [] fixed = new boolean [data.length];
final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
final AtomicInteger ai = new AtomicInteger(0);
if (prohibit == null) {
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int pix = ai.getAndIncrement(); pix < data.length; pix = ai.getAndIncrement()) {
if (!Double.isNaN(data[pix])) {
fixed[pix] = true;
}
}
}
};
}
ImageDtt.startAndJoin(threads);
} else {
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int pix = ai.getAndIncrement(); pix < data.length; pix = ai.getAndIncrement()) {
if (!Double.isNaN(data[pix]) && !prohibit[pix]) {
fixed[pix] = true;
}
}
}
};
}
ImageDtt.startAndJoin(threads);
}
return fixed;
}
/**
* Fill NaN values in 2D array from neighbors using Laplassian==0
......@@ -8661,16 +8795,57 @@ ImageDtt.startAndJoin(threads);
int num_passes,
final double max_rchange, // = 0.01
final int threadsMax) // maximal number of threads to launch
{
return fillNaNs(
data, // final double [] data,
null, // final double [] data_nan,
prohibit, // final boolean [] prohibit_in,
width, // int width,
grow, // final int grow,
diagonal_weight, //double diagonal_weight, // relative to ortho
num_passes, // int num_passes,
max_rchange, // final double max_rchange, // = 0.01
threadsMax); // final int threadsMax)
}
/**
* Fill NaN values in 2D array from neighbors using Laplassian==0
* @param data data array (in line-scan order) with NaN values to be filled,
* non-NaN values will not be modified.
* @param data_nan optional "original" data with NaN values to be replaced. If null,
* (single-pass) the data[] array will be used
* @param prohibit_in optional (may be null) boolean array of the same size specifying
* prohibited pixels.
* @param width data width (height = data.length/width)
* @param grow limit area to process by expanding defined pixel area.
* @param diagonal_weight weight of 4 diagonal neighbors relative to 4 ortho ones.
* @param num_passes maximal number of iterations.
* @param max_rchange max relative (to data RMS) step change to exit iterations.
* @param threadsMax maximal number of concurrent threads to launch.
* @return data array made of input data with replaced NaN limited by
* optional prohibit array and amount of growth.
*/
public static double [] fillNaNs(
final double [] data,
final double [] data_nan, // only modify tiles that are not fixed
final boolean [] prohibit,
int width,
final int grow,
double diagonal_weight, // relative to ortho
int num_passes,
final double max_rchange, // = 0.01
final int threadsMax) // maximal number of threads to launch
{
int height = data.length/width;
double wdiag = 0.25 *diagonal_weight / (diagonal_weight + 1.0);
double wortho = 0.25 / (diagonal_weight + 1.0);
final double [] neibw = {wortho, wdiag, wortho, wdiag, wortho, wdiag, wortho, wdiag};
final int tiles = width * height;
final boolean [] fixed = new boolean [tiles]; // Original non-NaN, will not be modified
final boolean [] fixed = new boolean [tiles];
int num_fixed = 0;
double davg = 0.0; // average of all fixed samples
double davg2 = 0.0; // average of all fixed samples
if (data_nan == null) {
for (int i = 0; i < tiles; i++) {
if (!Double.isNaN(data[i])) {
fixed[i] = true;
......@@ -8679,6 +8854,16 @@ ImageDtt.startAndJoin(threads);
davg2 += data[i] * data[i];
}
}
} else {
for (int i = 0; i < tiles; i++) {
if (!Double.isNaN(data[i]) && !Double.isNaN(data_nan[i])) {
fixed[i] = true;
num_fixed ++;
davg += data[i];
davg2 += data[i] * data[i];
}
}
}
if (num_fixed > 0) {
davg /= num_fixed;
davg2 = Math.sqrt(davg2/num_fixed - davg*davg);
......@@ -8721,7 +8906,8 @@ ImageDtt.startAndJoin(threads);
final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
final AtomicInteger ai = new AtomicInteger(0);
final AtomicInteger ati = new AtomicInteger(0);
//Set initial values
//Set initial values - only if fixed[] was not provided
if (data_nan == null) {
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
......@@ -8748,9 +8934,10 @@ ImageDtt.startAndJoin(threads);
};
}
ImageDtt.startAndJoin(threads);
} else {
data_io[0] = data.clone(); // just use original "hint" data
}
data_io[1] = data_io[0].clone();
final double [] last_change = new double [threads.length];
for (int pass = 0; pass < num_passes; pass ++) {
ai.set(0);
......@@ -8769,12 +8956,6 @@ ImageDtt.startAndJoin(threads);
if ((nt1 >=0) && grown[nt1]) {
s += data_io[0][nt1] * neibw[dir];
/* if (fixed[nt1]) {
s += data[nt1] * neibw[dir];
} else {
s += data_io[0][nt1] * neibw[dir];
}
*/
sw += neibw[dir];
}
}
......@@ -8792,7 +8973,9 @@ ImageDtt.startAndJoin(threads);
multi_change = Math.max(multi_change, last_change[i]);
}
boolean done = (pass >= (num_passes - 1)) || (multi_change < max_change);
// System.out.println("fillNaNs(): pass="+pass+" change="+multi_change+" done="+done);
if (data_nan != null) {
System.out.println("fillNaNs(): pass="+pass+" change="+multi_change+" done="+done);
}
if (done) {
break;
} else { // swap data_io[0] <--> data_io[1]
......@@ -8807,7 +8990,6 @@ ImageDtt.startAndJoin(threads);
/* Create a Thread[] array as large as the number of processors available.
* From Stephan Preibisch's Multithreading.java class. See:
* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
......
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