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imagej-elphel
Commit ce1b3a18 authored by Andrey Filippov's avatar Andrey Filippov
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Added documentation

parent cc453673
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Showing with 196 additions and 131 deletions
src/main/java/com/elphel/imagej/tileprocessor/TexturedModel.java
View file @ ce1b3a18
......@@ -547,7 +547,34 @@ public class TexturedModel {
}
// generate/update number of neighbors to select clusters' seeds
// public static int [] getSeedTile( // and update num_neibs_dir
/**
* Generate and later update array on number of neighbors to find candidates for the next
* texture meshes. Initially calculated for all tiles, then updated by after each cluster
* extraction in the area possibly affected by the cluster (cluster bounds extended by one
* in each direction).
*
* @param num_neibs_dir [layers][tiles] - array of connections (defined by close disparities)
* per layer, per tile. Undefined tile has 0, isolated tile - 1, maximal
* (with all 8 neighbors present) - 9. Should be initialized to
* [layers][tiles].
* @param bounds Rectangle instance specifying the new cluster bounds. If null (used
* during first run), all tiles are processed
* @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 disp_adiffo absolute disparity difference for connecting tiles in ortho
* directions (used for initial connections estimations)
* @param disp_rdiffo relative disparity difference (added to absolute being multiplied
* by the tile disparity)
* @param disp_adiffd absolute disparity difference for diagonal tiles.
* @param disp_rdiffd relative disparity difference for diagonal tiles.
* @param disp_fof >=1.0 - increased inter-tile tolerance for a friend-of-a-friend.
* In current code just scales calculated (absolute+relative) tolerance
* for all steps after initial connections.
* @param tilesX horizontal array dimension
* @param debugLevel debug level - controls generation of images
*/
public static void updateSeeds( // and update num_neibs_dir
final int [][] num_neibs_dir, // [tile][layer]
final Rectangle bounds, // null - all
......@@ -560,11 +587,9 @@ public class TexturedModel {
final double disp_rdiffd,
final double disp_fof, // enable higher difference (scale) for fried of a friend
final int tilesX,
// final int transform_size,
final int debugLevel) {
final int tiles = disparity_layers[0].length;
final int tiles_wnd = (bounds == null) ? tiles : (bounds.width * bounds.height);
// final Rectanle ext_bounds
final int tilesY = tiles/tilesX;
final int layers = disparity_layers.length;
final Thread[] threads = ImageDtt.newThreadArray(THREADS_MAX);
......@@ -648,28 +673,6 @@ public class TexturedModel {
if (tile==dbg_tile) {
System.out.println("clusterizeFgBg().2: tile="+tile);
}
/*
if (connections[tile] != null) {
for (int dir0 = 0; dir0 < TileNeibs.DIRS/2; dir0++) {
int tile1 = tn.getNeibIndex(tile, dir0);
if ((tile1 >= 0) && (connections[tile1] != null)) {
int dir = TileNeibs.reverseDir(dir0);
for (int layer = 0; layer < layers; layer++) if (connections[tile1][layer] != null){
if (connections[tile1][layer][dir] == null) {
connections[tile1][layer][dir] = new double[layers];
Arrays.fill(connections[tile1][layer][dir],Double.NaN);
}
for (int layer1 = 0; layer1 < layers; layer1++) {
if ( (connections[tile][layer1] != null) &&
(connections[tile][layer1][dir0] != null)) {
connections[tile1][layer][dir][layer1] = connections[tile][layer1][dir0][layer];
}
}
}
}
}
}
*/
for (int layer = 0; layer < layers; layer++) if (!Double.isNaN(disparity_layers[layer][tile])) {
if ((connections[tile] != null) && (connections[tile][layer] != null)) {
for (int dir0 = 0; dir0 < TileNeibs.DIRS/2; dir0++) {
......@@ -737,12 +740,20 @@ public class TexturedModel {
}
/**
* Find the next seed tile to build a new mesh (tile cluster). Search concludes with the maximal
* Number of neighbors tile or the first encountered 9 neighbors (self plus 8 around) as it is the
* maximal possible number.
*
* @param disparity_layers
* @param num_neibs_dir
* @param tile_start
* @param tilesX
* @return {tile, layer} or null
* @param disparity_layers [layers][tiles] multi-layer disparity array with NaN
* for non-existing tiles
* @param num_neibs_dir [layers][tiles] - array of connections (defined by close disparities)
* per layer, per tile. Undefined tile has 0, isolated tile - 1, maximal
* (with all 8 neighbors present) - 9. Should be initialized to
* [layers][tiles].
* @param tile_start tile index to begin search. Provide tile where the last search ended,
* the search will wrap over the full array size and start from 0.
* @param tilesX horizontal array dimension.
* @return a pair {tile, layer} or null if there are no tiles left
*/
public static int [] getNextSeed(
final double [][] disparity_layers, //
......@@ -782,6 +793,33 @@ public class TexturedModel {
return new int [] {best_tile, best_layer};
}
/**
* Create initial cluster of connected tiles without provisions for overlap resolution
* @param disparity_layers [layers][tiles] multi-layer disparity array with NaN
* for non-existing tiles
* @param start_layer seed layer to start growing a cluster
* @param start_tile seed tile to start growing a cluster
* @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 disp_adiffo absolute disparity difference for connecting tiles in ortho
* directions (used for initial connections estimations)
* @param disp_rdiffo relative disparity difference (added to absolute being multiplied
* by the tile disparity)
* @param disp_adiffd absolute disparity difference for diagonal tiles.
* @param disp_rdiffd relative disparity difference for diagonal tiles.
* @param disp_fof >=1.0 - increased inter-tile tolerance for a friend-of-a-friend.
* In current code just scales calculated (absolute+relative) tolerance
* for all steps after initial connections.
* @param jump_r "jump" over small gaps when building initial clusters. jump_r == 2
* allows jumping to other tiles in 5x5 square around the defined tile,
* jump_r == 3 - inside 7x7 square. The jump destination should not have
* any already defined tiles among 8 neighbors (in a 3x3 square).
* @param disp_adiffj maximal absolute disparity difference for the "jumps".
* @param disp_rdiffj maximal relative disparity difference for the "jumps".
* @param tilesX horizontal array dimension
* @param debugLevel debug level - controls generation of images
* @return [tiles] disparity array of the selected tiles. NaN for unselected
*/
public static double[] buildInitialCluster(
final double [][] disparity_layers, // should not have same tile disparity on multiple layers
final int start_layer,
......@@ -937,7 +975,40 @@ public class TexturedModel {
return disparity;
}
/**
* Use initial cluster (source_disparity) to output cluster with appropriate border tiles (currently
* trying with two border layers around the selected disparity tiles). Foreground has higher priority,
* so if higher disparity conflicts with lower disparity it pushes lower disparity tiles until higher
* disparity with specified (now 2) layers of extrapolated (not from disparity_layers array /
* source_disparity). After "pushing away" conflicting tiles, additional layers (same number) over
* defined (in source_disparity) tiles are removed from source_disparity. Only remaining (not
* marked as borders) tiles from the original source_disparity are removed from disparity_layers
* used to generate next clusters. Each extracted tileCluster preserves Rectangle bounds later used
* to combine multiple clusters in the same full frame array, disparity and bounds arrays are defined
* in rectangular arrays corresponding to bounds.
*
* @param cluster_list ArrayList of previously defined tileCluster instances. Used to get this
* tileCluster index, the new tileCluster is added to the list.
* @param is_sky_cluster if this cluster is a special type cluster - "blue sky". This property is
* saved in the tileCluster instance. If, additionally, the next parameter
* is >=0 the cluster bounds are extended: left, right and top bounds - to the
* frame edges, and the bottom one - blue_sky_below below the highest tile Y.
* @param blue_sky_below (only if is_sky_cluster) if >=0 - extend bounds, if <0 treat blue_sky bounds
* same as regular ones.
* @param disparity_layers [layers][tiles] multi-layer disparity array with NaN for non-existing tiles
* @param source_disparity [tiles] continuous tiles used to generate this tileCluster that uses only
* of source_disparity and extrapolated borders.
* @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 disp_adiff absolute disparity difference for connecting tiles in any direction,
* should include disp_fof used for initial cluster generation
* @param disp_rdiff relative disparity difference for connecting tiles in any direction.
* @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 buildTileCluster(
// used disparity_layers will be set to Double.NaN
// make it in a separate method?
......@@ -1291,9 +1362,12 @@ public class TexturedModel {
}
ImageDtt.startAndJoin(threads);
// final boolean sky_cluster = blue_sky_below >=0;
if (is_sky_cluster) { // increase bounding box for sky cluster
if (is_sky_cluster && (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);
}
......@@ -1359,14 +1433,49 @@ public class TexturedModel {
return tileCluster;
}
/**
* Create texture clusters collectively covering the depth map from multi-layer
* disparity arrays and optional "blue sky" binary array
* @param tilesX horizontal array dimension
* @param disparity_layers_src [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 if >=0, specifies how low to extend blue sky backdrop below
* the lowest defined blue sky tile. In that case bounds are
* also extended to the top of frame, right and left margins.
* If (blue_sky_below <0) cluster its bounds are treated the same
* as regular ones.
* @param max_neib_lev Maximal level of additional (to defined in disparity_layers)
* tiles. Currently max_neib_lev=2 adding 2 border layers. So
* a single isolated tile results in total 5x5 area with level 2,
* center 3x3 - level 1, and the center tile(defined) - level 0.
* Other (undefined) tiles are assigned level of -1.
* @param disp_adiffo absolute disparity difference for connecting tiles in ortho
* directions (used for initial connections estimations)
* @param disp_rdiffo relative disparity difference (added to absolute being multiplied
* by the tile disparity)
* @param disp_adiffd absolute disparity difference for diagonal tiles.
* @param disp_rdiffd relative disparity difference for diagonal tiles.
* @param disp_fof >=1.0 - increased inter-tile tolerance for a friend-of-a-friend.
* In current code just scales calculated (absolute+relative) tolerance
* for all steps after initial connections.
* @param jump_r "jump" over small gaps when building initial clusters. jump_r == 2
* allows jumping to other tiles in 5x5 square around the defined tile,
* jump_r == 3 - inside 7x7 square. The jump destination should not have
* any already defined tiles among 8 neighbors (in a 3x3 square).
* @param disp_adiffj maximal absolute disparity difference for the "jumps".
* @param disp_rdiffj maximal relative disparity difference for the "jumps".
* @param debugLevel debug level - controls generation of images
* @return array of consolidated (multiple non-overlapping clusters) clusters,
* each having the full frame bounds.
*/
public static TileCluster [] clusterizeFgBg( //
final int tilesX,
final double [][] disparity_layers_src, // may have more layers
final boolean [] blue_sky, // use to expand background by blurring available data?
final int blue_sky_layer,
final int blue_sky_below,
// final boolean [] selected, // to remove sky (pre-filter by caller, like for ML?)
final int max_neib_lev,
final double disp_adiffo,
final double disp_rdiffo,
......@@ -1725,7 +1834,6 @@ public class TexturedModel {
sky_tiles, // final boolean blue_sky, // use to expand background by blurring available data?
sky_layer, // final int sky_layer,
sky_below, // final int blue_sky_below,
// null, // sky_invert, // final boolean [] selected, // to remove sky (pre-filter by caller, like for ML?)
max_neib_lev, // final int max_neib_lev,
tex_disp_adiffo, // final double disp_adiffo,
tex_disp_rdiffo, // final double disp_rdiffo,
......@@ -1735,24 +1843,7 @@ public class TexturedModel {
jump_r, // final int jump_r,
disp_adiffj, // final double disp_adiffj,
disp_rdiffj, // final double disp_rdiffj,
// tex_cluster_gap, // final int cluster_gap, // gap between clusters
debugLevel); //1); // 2); // final int debugLevel)
/*
TileCluster [] tileClusters = clusterizeFgBg( // wrong result type, not decided
tilesX, // final int tilesX,
ds_fg_bg, // final double [][] disparities, // may have more layers
sky_tiles, // final boolean blue_sky, // use to expand background by blurring available data?
sky_layer, // final int sky_layer,
sky_below, // final int blue_sky_below,
null, // sky_invert, // final boolean [] selected, // to remove sky (pre-filter by caller, like for ML?)
tex_disp_adiffo, // final double disp_adiffo,
tex_disp_rdiffo, // final double disp_rdiffo,
tex_disp_adiffd, // final double disp_adiffd,
tex_disp_rdiffd, // final double disp_rdiffd,
tex_disp_fof, // final double disp_fof, // enable higher difference (scale) for friend of a friend
tex_cluster_gap, // final int cluster_gap, // gap between clusters
debugLevel); //1); // 2); // final int debugLevel)
*/
// Debugging up to here:
// if (debugLevel > -1000) {
// return false;
......@@ -1769,8 +1860,7 @@ public class TexturedModel {
scenes_sel[i] = true;
}
// If there is gap between clusters, add extra row of background tiles
int add_bg_tiles = 1;
int add_bg_tiles = 0; // 1;
while ((add_bg_tiles--) > 0) {
extendClustersBackground(
tileClusters, // final TileCluster[] tileClusters,
......@@ -1781,18 +1871,16 @@ public class TexturedModel {
}
boolean renormalize = true;// false - use normalizations from previous scenes to keep consistent colors
ImagePlus[] combined_textures = getInterCombinedTextures( // return ImagePlus[] matching tileClusters[], with alpha
clt_parameters, // final CLTParameters clt_parameters,
colorProcParameters, // ColorProcParameters colorProcParameters,
rgbParameters, // EyesisCorrectionParameters.RGBParameters rgbParameters,
parameter_scene, // final QuadCLT parameter_scene, // to use for rendering parameters in multi-series sequences
// if null - use reference scene
ref_index, // final int ref_index,
scenes, // final QuadCLT [] scenes,
scenes_sel, // final boolean [] scenes_sel, // null or which scenes to process
null, // final boolean [] selection, // may be null, if not null do not process unselected tiles
tileClusters, // final TileCluster [] tileClusters, // disparities, borders, selections for texture passes
// final int margin,
renormalize, // final boolean renormalize, // false - use normalizations from previous scenes to keep consistent colors
max_disparity_lim, // final double max_disparity_lim, // 100.0; // do not allow stray disparities above this
min_trim_disparity, //final double min_trim_disparity, // 2.0; // do not try to trim texture outlines with lower disparities
......@@ -3878,16 +3966,15 @@ public class TexturedModel {
return textures_alphas; // What about colors?
}
public static ImagePlus[] getInterCombinedTextures( // return ImagePlus[] matching tileClusters[], with alpha
final CLTParameters clt_parameters,
ColorProcParameters colorProcParameters,
EyesisCorrectionParameters.RGBParameters rgbParameters,
QuadCLT parameter_scene, // to use for rendering parameters in multi-series sequences
// if null - use reference scene
final int ref_index,
final QuadCLT [] scenes,
final boolean [] scenes_sel, // null or which scenes to process
final boolean [] selection, // may be null, if not null do not process unselected tiles
final TileCluster [] tileClusters, // disparities, borders, selections for texture passes
final boolean renormalize, // false - use normalizations from previous scenes to keep consistent colors
final double max_disparity_lim, // 100.0; // do not allow stray disparities above this
......@@ -3895,7 +3982,6 @@ public class TexturedModel {
final int debug_level)
{
// TODO: ***** scenes with high motion blur also have high ERS to be corrected ! *****
final int ref_index = scenes.length -1;
final QuadCLT ref_scene = scenes[ref_index];
if (parameter_scene == null) {
parameter_scene = ref_scene;
......@@ -3907,8 +3993,6 @@ public class TexturedModel {
final int tiles = tilesX * tilesY;
final int transform_size= ref_scene.getTileProcessor().getTileSize();
final int tile_len = transform_size * transform_size;
// final int num_channels = ref_scene.isMonochrome()?2:4; //
final boolean filter_bg = true; // make a clt parameter?
final boolean mb_en = clt_parameters.imp.mb_en;
final double mb_tau = clt_parameters.imp.mb_tau; // 0.008;// time constant, sec
......@@ -3916,31 +4000,26 @@ public class TexturedModel {
final double max_distortion = clt_parameters.tex_distort; // 0.5; // Maximal texture distortion to accumulate multiple scenes (0 - any)
final double tex_mb = clt_parameters.tex_mb; // 1.0; // Reduce texture weight if motion blur exceeds this (as square of MB length)
final boolean sharp_alpha = clt_parameters.sharp_alpha;
// final boolean sharp_alpha = clt_parameters.sharp_alpha;
final boolean is_lwir = ref_scene.isLwir();
final boolean tex_um = clt_parameters.tex_um; // imp.um_mono; // TODO: add own parameter
final double tex_um_sigma = clt_parameters.tex_um_sigma; // imp.um_sigma;
final double tex_um_weight = clt_parameters.tex_um_weight; // imp.um_weight;
// TODO: - make texture variants, tex_um_fixed/tex_um_range apply only to unsharp mask, regardless of colors
final boolean lwir_autorange = is_lwir && clt_parameters.tex_lwir_autorange; // colorProcParameters.lwir_autorange;
final boolean tex_um_fixed = clt_parameters.tex_um_fixed; // imp.mono_fixed; // true; // normalize to fixed range when converting to 8 bits
final double tex_um_range = clt_parameters.tex_um_range; // imp.mono_range; // 500.0; // monochrome full-scale range (+/- half)
final boolean tex_hist_norm = clt_parameters.tex_hist_norm; // true;
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 int tex_hist_segments = clt_parameters.tex_hist_segments; // 32 ;
final boolean tex_color = clt_parameters.tex_color; // true;
final int tex_palette = clt_parameters.tex_palette; // 2 ;
// final boolean extend_sky = true;
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
final double alphaOverlapTolerance = 0.0; // compare same disparity with tolerance (relative to disparity? make absolute meters?)
ImageDtt image_dtt;
image_dtt = new ImageDtt(
ref_scene.getNumSensors(), // numSens,
......@@ -3960,7 +4039,6 @@ public class TexturedModel {
// weighted sum
double [][][][][] inter_textures_wd= new double [num_slices][tilesY][tilesX][][]; // [channel][64] - overlapping textures
// weighted sum of squares
/// double [][][][][] inter_textures_wd2= new double [num_slices][tilesY][tilesX][][]; // [channel][64] - overlapping textures
double [][][] ref_pXpYDs = new double [num_slices][][]; // individual for each slice
int [][] cluster_indices = (max_distortion > 0.0) ? (new int [num_slices][]): null;
boolean [][] borders = new boolean [num_slices][];
......@@ -4009,8 +4087,6 @@ public class TexturedModel {
}
scenes[nscene].saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU)
//parameter_scene
// boolean keep_channels = false;
for (int nslice = 0; nslice < num_slices; nslice++) { // prepare and measure textures for each combo textures
final double [] disparity_ref = tileClusters[nslice].getDisparity(); // disparity in the reference view tiles (Double.NaN - invalid)
// Motion blur vectors are individual per-slice
......@@ -4029,8 +4105,6 @@ public class TexturedModel {
System.out.println("nscene="+nscene+", nslice="+nslice+" will run texturesGPUFromDSI() that needs debug >2");
System.out.print("");
}
double [][][][] slice_texture88 = QuadCLT.texturesNoOverlapGPUFromDSI(
clt_parameters, // CLTParameters clt_parameters,
disparity_ref, // double [] disparity_ref,
......@@ -4052,7 +4126,6 @@ public class TexturedModel {
1, // final int keep_frame_tiles, // do not discard pixels for border tiles in reference frame
true, // keep_channels, // final boolean keep_channels,
debug_level); // final int debugLevel);
if (slice_texture88 != null) { // will just accumulate
// Use MB vectors for texture weights
final Thread[] threads = ImageDtt.newThreadArray(THREADS_MAX);
......@@ -4187,12 +4260,9 @@ public class TexturedModel {
sensor_textures, // final double [][] sensor_texture, // per-sensor texture value
null, // combo_textures, // null, // final double [] combo_texture_in, // average texture value
tileClusters, // final TileCluster[] tileClusters, // to process blue_sky?
// extend_sky, // final boolean extend_sky,
// shrink_sky_tiles, // final int shrink_sky_tiles,
max_disparity_lim, // final double max_disparity_lim, // do not allow stray disparities above this
min_trim_disparity, // final double min_trim_disparity, // do not try to trim texture outlines with lower disparities
ref_scene.getImageName()); // null); // ref_scene.getImageName()); // final String dbg_prefix);
if (debug_level > -1) {
double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];
String [] dbg_titles = new String[dbg_textures.length];
......@@ -4200,7 +4270,6 @@ public class TexturedModel {
for (int i = 0; i < dbg_subtitles.length; i++) {
dbg_subtitles[i] = (i < (dbg_subtitles.length -1)) ? ("Y"+i):"alpha";
}
for (int i = 0; i < dbg_textures.length; i++) {
dbg_textures[i] = faded_textures[i / faded_textures[0].length][i % faded_textures[0].length];
dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
......@@ -4215,9 +4284,6 @@ public class TexturedModel {
dbg_titles);
}
// boolean grow_sky = true;
//int shrink_sky_tiles = 2;
// Grow sky
if (grow_sky) {
extendBlueSKy(
......@@ -4227,7 +4293,6 @@ public class TexturedModel {
width, // final int width,
transform_size); // final int transform_size);
}
// fix alpha
if (alphaOverlapFix) {
fixAlphaSameDisparity(
......
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