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imagej-elphel
Commit 9d1a83ef authored by Andrey Filippov's avatar Andrey Filippov
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added limits on zoom change, multi-color preview images - working state

parent 97109dcb
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Showing with 272 additions and 92 deletions
src/main/java/com/elphel/imagej/cameras/CLTParameters.java
View file @ 9d1a83ef
......@@ -426,6 +426,9 @@ public class CLTParameters {
public boolean tex_debug_disp_tri = false; // !batch_mode && (debugLevel > 0); // TODO: use clt_parameters
public int tex_add_bg_tiles = 0; // If there is gap between clusters, add extra row of background tiles
public boolean tex_save_full_textures = true; // false; // true;
public boolean tex_save_interm_textures = false; // Save intermediate texture
public boolean tex_save_um_texture0 = true; // Save full-res texture (only first slice) after unsharp mask filter
public boolean tex_save_preview = true; // Save normalized texture0 as a scene sequence preview
public double tex_alpha_threshold = 0.5;
public boolean tex_renormalize = true; // false - use normalizations from previous scenes to keep consistent colors
public boolean tex_alpha = false; // also - use jpeg?
......@@ -438,9 +441,9 @@ public class CLTParameters {
public boolean tex_um_fixed = false; // Use fixed range after unsharp mask instead of autorange
public double tex_um_range = 500; // Full range after unsharp mask
public boolean tex_hist_norm = true; // Normalize texture histogram
public double tex_hist_amount = 0.7; // Texture histogram normalization amount (0.0 - no normalization, 1.0 - full normalization)
public double tex_hist_amount = 0.5; // Texture histogram normalization amount (0.0 - no normalization, 1.0 - full normalization)
public int tex_hist_bins = 1024; // Number of histogram bins to use for texture histograms
public int tex_hist_segments = 32; // Number of evenly-spaced percentiles to use for histogram normalization
public int tex_hist_segments = 128; // Number of evenly-spaced percentiles to use for histogram normalization
public boolean tex_color = true; // Use pseudo-colored textures
public int tex_palette = 1; // Palette number for pseudo colors
......@@ -1548,6 +1551,9 @@ public class CLTParameters {
properties.setProperty(prefix+"tex_debug_disp_tri", this.tex_debug_disp_tri+""); // boolean
properties.setProperty(prefix+"tex_add_bg_tiles", this.tex_add_bg_tiles+""); // int
properties.setProperty(prefix+"tex_save_full_textures", this.tex_save_full_textures+""); // boolean
properties.setProperty(prefix+"tex_save_interm_textures", this.tex_save_interm_textures+"");// boolean
properties.setProperty(prefix+"tex_save_um_texture0", this.tex_save_um_texture0+""); // boolean
properties.setProperty(prefix+"tex_save_preview", this.tex_save_preview+""); // boolean
properties.setProperty(prefix+"tex_alpha_threshold", this.tex_alpha_threshold+""); // double
properties.setProperty(prefix+"tex_renormalize", this.tex_renormalize+""); // boolean
properties.setProperty(prefix+"tex_alpha", this.tex_alpha+""); // boolean
......@@ -2547,6 +2553,9 @@ public class CLTParameters {
if (properties.getProperty(prefix+"tex_debug_disp_tri")!=null) this.tex_debug_disp_tri=Boolean.parseBoolean(properties.getProperty(prefix+"tex_debug_disp_tri"));
if (properties.getProperty(prefix+"tex_add_bg_tiles")!=null) this.tex_add_bg_tiles=Integer.parseInt(properties.getProperty(prefix+"tex_add_bg_tiles"));
if (properties.getProperty(prefix+"tex_save_full_textures")!=null)this.tex_save_full_textures=Boolean.parseBoolean(properties.getProperty(prefix+"tex_save_full_textures"));
if (properties.getProperty(prefix+"tex_save_interm_textures")!=null)this.tex_save_interm_textures=Boolean.parseBoolean(properties.getProperty(prefix+"tex_save_interm_textures"));
if (properties.getProperty(prefix+"tex_save_um_texture0")!=null) this.tex_save_um_texture0=Boolean.parseBoolean(properties.getProperty(prefix+"tex_save_um_texture0"));
if (properties.getProperty(prefix+"tex_save_preview")!=null) this.tex_save_preview=Boolean.parseBoolean(properties.getProperty(prefix+"tex_save_preview"));
if (properties.getProperty(prefix+"tex_alpha_threshold")!=null) this.tex_alpha_threshold=Double.parseDouble(properties.getProperty(prefix+"tex_alpha_threshold"));
if (properties.getProperty(prefix+"tex_renormalize")!=null) this.tex_renormalize=Boolean.parseBoolean(properties.getProperty(prefix+"tex_renormalize"));
if (properties.getProperty(prefix+"tex_alpha")!=null) this.tex_alpha=Boolean.parseBoolean(properties.getProperty(prefix+"tex_alpha"));
......@@ -3740,6 +3749,13 @@ public class CLTParameters {
gd.addCheckbox ("Save full textures", this.tex_save_full_textures,
"Will save anyway if !tex_split_textures.");
gd.addCheckbox ("Save intermediate textures", this.tex_save_interm_textures,
"Save intermediate textures - all slices as floating-point TIFFs.");
gd.addCheckbox ("Save texture slice0", this.tex_save_um_texture0,
"Save full-res texture (only first slice) after unsharp mask filter. Used for flat down-views from UAS.");
gd.addCheckbox ("Save texture as preview", this.tex_save_preview,
"Save full-res texture (first slice) after unsharp mask and histogram normalilzationas a scene sequence preview image.");
gd.addNumericField("Alpha threshold", this.tex_alpha_threshold, 5,7,"",
"Alpha threshold to consider it opaque.");
gd.addCheckbox ("Re-normalize photometric range", this.tex_renormalize,
......@@ -4969,6 +4985,9 @@ public class CLTParameters {
this.tex_debug_disp_tri = gd.getNextBoolean();
this.tex_add_bg_tiles = (int) gd.getNextNumber();
this.tex_save_full_textures = gd.getNextBoolean();
this.tex_save_interm_textures = gd.getNextBoolean();
this.tex_save_um_texture0 = gd.getNextBoolean();
this.tex_save_preview = gd.getNextBoolean();
this.tex_alpha_threshold = gd.getNextNumber();
this.tex_renormalize = gd.getNextBoolean();
this.tex_alpha = gd.getNextBoolean();
......
src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java
View file @ 9d1a83ef
......@@ -264,7 +264,8 @@ public class IntersceneMatchParameters {
public double min_offset = 1.5; // pixels - minimal average pixel offset between images to consider interscene matching
public double max_rel_offset = 0.5; // maximal interscene offset as a fraction of image width
public double max_roll_deg = 10.0; // maximal interscene roll to consider matching
public double max_roll_deg = 5.0; // maximal interscene roll to consider matching
public double max_zoom_diff = 0; // for down-views when changing altitude (0 - ignore)
public boolean fpn_skip = true; // skip too close scenes (false - abort, previous behavior)
public boolean fpn_rematch = true; // match fpn-failed scenes to later scenes with larger difference
......@@ -809,6 +810,8 @@ public class IntersceneMatchParameters {
"Maximal interscene offset as a fraction of image width to handle low overlap");
gd.addNumericField("Maximal interscene roll", this.max_roll_deg, 6,7,"degrees",
"Maximal interscene roll to consider matching");
gd.addNumericField("Maximal interscene relative zoom difference", this.max_zoom_diff, 6,7,"",
"Applicable for the down views from a drone. Saet to 0 to ignore.");
gd.addCheckbox ("Skip too close to reference scenes", this.fpn_skip,
"Skip too close to reference scenes (false - abort, previous behavior)");
gd.addCheckbox ("Match FPN-failed with other scenes", this.fpn_rematch,
......@@ -1193,6 +1196,8 @@ public class IntersceneMatchParameters {
this.min_offset = gd.getNextNumber();
this.max_rel_offset = gd.getNextNumber();
this.max_roll_deg = gd.getNextNumber();
this.max_zoom_diff = gd.getNextNumber();
this.fpn_skip = gd.getNextBoolean();
this.fpn_rematch = gd.getNextBoolean();
......@@ -1528,6 +1533,7 @@ public class IntersceneMatchParameters {
properties.setProperty(prefix+"min_offset", this.min_offset+""); // double
properties.setProperty(prefix+"max_rel_offset", this.max_rel_offset+""); // double
properties.setProperty(prefix+"max_roll_deg", this.max_roll_deg+""); // double
properties.setProperty(prefix+"max_zoom_diff", this.max_zoom_diff+""); // double
properties.setProperty(prefix+"fpn_skip", this.fpn_skip+""); // boolean
properties.setProperty(prefix+"fpn_rematch", this.fpn_rematch+""); // boolean
......@@ -1821,6 +1827,7 @@ public class IntersceneMatchParameters {
if (properties.getProperty(prefix+"min_offset")!=null) this.min_offset=Double.parseDouble(properties.getProperty(prefix+"min_offset"));
if (properties.getProperty(prefix+"max_rel_offset")!=null) this.max_rel_offset=Double.parseDouble(properties.getProperty(prefix+"max_rel_offset"));
if (properties.getProperty(prefix+"max_roll_deg")!=null) this.max_roll_deg=Double.parseDouble(properties.getProperty(prefix+"max_roll_deg"));
if (properties.getProperty(prefix+"max_zoom_diff")!=null) this.max_zoom_diff=Double.parseDouble(properties.getProperty(prefix+"max_zoom_diff"));
if (properties.getProperty(prefix+"fpn_skip")!=null) this.fpn_skip=Boolean.parseBoolean(properties.getProperty(prefix+"fpn_skip"));
if (properties.getProperty(prefix+"fpn_rematch")!=null) this.fpn_rematch=Boolean.parseBoolean(properties.getProperty(prefix+"fpn_rematch"));
......@@ -2125,6 +2132,7 @@ public class IntersceneMatchParameters {
imp.min_offset = this.min_offset;
imp.max_rel_offset = this.max_rel_offset;
imp.max_roll_deg = this.max_roll_deg;
imp.max_zoom_diff = this.max_zoom_diff;
imp.fpn_skip = this.fpn_skip;
imp.fpn_rematch = this.fpn_rematch;
......
src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java
View file @ 9d1a83ef
......@@ -203,6 +203,21 @@ public class QuadCLTCPU {
}
public double getAverageZ(boolean use_lma) {
double [][] dls = getDLS();
if (dls==null) {
return Double.NaN;
}
double [][] ds = new double [][] {dls[use_lma?1:0], dls[2]};
double sw=0, swd=0;
for (int i = 0; i < ds[0].length; i++) if (!Double.isNaN(ds[0][i])){
sw += ds[1][i];
swd += ds[0][i] * ds[1][i];
}
double disp_avg = swd/sw;
double z_avg = getGeometryCorrection().getZFromDisparity(disp_avg);
return z_avg;
}
public double [][] getDLS(){ // get disparity, disparity_lma, strength
if (dsi == null) {
......@@ -2205,6 +2220,25 @@ public class QuadCLTCPU {
return imp;
}
public ImagePlus saveDoubleArrayInModelDirectory(
String suffix,
double [] data,
int width,
int height)
{
double [][] data2= new double[][] {data};
String x3d_path = getX3dDirectory();
String file_name = image_name + suffix;
String file_path = x3d_path + Prefs.getFileSeparator() + file_name + ".tiff";
ImageStack imageStack = ShowDoubleFloatArrays.makeStack(data2, width, height, null);
ImagePlus imp = new ImagePlus( file_name, imageStack);
FileSaver fs=new FileSaver(imp);
fs.saveAsTiff(file_path);
System.out.println("saveDoubleArrayInModelDirectory(): saved "+file_path);
return imp;
}
public String saveImagePlusInModelDirectory(
String suffix, // null - use title from the imp
ImagePlus imp)
......@@ -15115,6 +15149,65 @@ public class QuadCLTCPU {
return true;
}
public boolean writeLwirPreview(
final CLTParameters clt_parameters,
double [] data,
QuadCLT scene,
int tex_palette,
String suffix,
int debugLevel) {
if (scene == null) {
scene = (QuadCLT) this;
}
double [][] rendered_texture = new double[][] {data, new double[data.length]};
for (int i = 0; i < rendered_texture[0].length; i++) {
rendered_texture[1][i] = Double.isNaN(rendered_texture[0][i])? 0.0: 1.0;
}
double [] minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
int width = getTileProcessor().getTilesX() *getTileProcessor().getTileSize();
int height = data.length/width;
String set_name = getImageName();
if (set_name == null ) {
QuadCLTCPU.SetChannels [] set_channels = setChannels(debugLevel);
set_name = set_channels[0].set_name;
}
String model_dir= correctionsParameters.selectX3dDirectory(
set_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
null,
true, // smart,
true); //newAllowed, // save\
String title = getImageName()+suffix+"-preview";
ImagePlus imp = QuadCLTCPU.linearStackToColorLWIR(
clt_parameters, // CLTParameters clt_parameters,
tex_palette, // int lwir_palette, // <0 - do not convert
minmax, // double [] minmax,
title, // String name,
"", // String suffix, // such as disparity=...
true, // boolean toRGB,
rendered_texture, // faded_textures[nslice], // double [][] texture_data,
width, // int width, // int tilesX,
height, // int height, // int tilesY,
debugLevel); // int debugLevel )
String preview_path = model_dir + Prefs.getFileSeparator() + title+".jpeg";
if (new File(preview_path).exists() && !correctionsParameters.thumb_overwrite) {
System.out.println("file "+preview_path+" exists, skipping preview generation");
return false;
}
if (debugLevel > -2) {
System.out.println("Saving preview image to "+preview_path);
}
EyesisCorrections.saveAndShow(
imp,
model_dir,
false,
false,
correctionsParameters.JPEG_quality, // jpegQuality); // jpegQuality){// <0 - keep current, 0 - force Tiff, >0 use for JPEG
(debugLevel > -2) ? debugLevel : 1); // int debugLevel (print what it saves)
return true;
}
public boolean writeRatingFile( // USED in lwir
int debugLevel
)
......
src/main/java/com/elphel/imagej/tileprocessor/TexturedModel.java
View file @ 9d1a83ef
......@@ -2478,7 +2478,7 @@ public class TexturedModel {
// If there is gap between clusters, add extra row of background tiles
// int add_bg_tiles = clt_parameters.tex_add_bg_tiles; // 0; // 1;
final boolean save_full_textures=clt_parameters.tex_save_full_textures || !clt_parameters.tex_split_textures; //true; // false; // true;
final boolean save_full_textures= clt_parameters.tex_save_full_textures || !clt_parameters.tex_split_textures; //true; // false; // true;
final double alpha_threshold = clt_parameters.tex_alpha_threshold; // 0.5;
final boolean renormalize = clt_parameters.tex_renormalize; // true; // false - use normalizations from previous scenes to keep consistent colors
final boolean no_alpha = !clt_parameters.tex_alpha; // true; // also - use jpeg?
......@@ -7026,6 +7026,9 @@ 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 save_interm_textures= clt_parameters.tex_save_interm_textures;
final boolean save_um_texture0= clt_parameters.tex_save_um_texture0;
final boolean save_preview= clt_parameters.tex_save_preview;
// final boolean show_sky_textures = clt_parameters.lre_show_sky_textures && !clt_parameters.multiseq_run;
// final int show_slice_bitmap = clt_parameters.lre_show_slice_bitmap;
......@@ -7297,7 +7300,7 @@ public class TexturedModel {
min_trim_disparity, // final double min_trim_disparity, // do not try to trim texture outlines with lower disparities
tp_tasks_ref, // final TpTask[][][] tp_tasks_ref, // reference tasks for each slice to get offsets
ref_scene.getImageName()); // null); // ref_scene.getImageName()); // final String dbg_prefix);
if (debugLevel > -20) {
if (save_interm_textures) {
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];
String [] dbg_subtitles = new String [faded_textures[0].length];
......@@ -7309,19 +7312,7 @@ public class TexturedModel {
dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
}
ref_scene.writePreview(
dbg_textures[0], // double [] data,
debugLevel); // int debugLevel
String suffix = "-combined_textures-prenorm-pre_UM";
if (!batch_run && (debugLevel > -1)) {
ShowDoubleFloatArrays.showArrays(
dbg_textures,
tilesX * transform_size,
tilesY * transform_size,
true,
ref_scene.getImageName()+suffix,
dbg_titles);
}
ref_scene.saveDoubleArrayInModelDirectory(
suffix, // String suffix,
null, // String [] labels, // or null
......@@ -7353,7 +7344,7 @@ public class TexturedModel {
THREADS_MAX); // final int threadsMax) // maximal number of threads to launch
}
if (debugLevel > -20) {
if (save_interm_textures) {
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];
String [] dbg_subtitles = new String [faded_textures[0].length];
......@@ -7396,7 +7387,7 @@ public class TexturedModel {
tex_um_weight); // final double um_weight)
}
if (debugLevel > -20) {
if (save_interm_textures || save_um_texture0) {
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];
String [] dbg_subtitles = new String [faded_textures[0].length];
......@@ -7410,6 +7401,7 @@ public class TexturedModel {
}
String suffix = "-combined_textures-prenorm";
if (save_interm_textures) {
if (!batch_run && (debugLevel > -1)) {
ShowDoubleFloatArrays.showArrays(
dbg_textures,
......@@ -7419,6 +7411,7 @@ public class TexturedModel {
ref_scene.getImageName()+suffix,
dbg_titles);
}
ref_scene.saveDoubleArrayInModelDirectory(
suffix, // String suffix,
null, // String [] labels, // or null
......@@ -7444,6 +7437,19 @@ public class TexturedModel {
tilesY * transform_size); // int height, // int tilesY,
}
}
// here is the best full-range texture. For UAS just use slice 0
if (save_um_texture0) {
suffix = "-texture";
if (tex_um) {
suffix+= "-UM"+tex_um_sigma+"_"+tex_um_weight;
}
ref_scene.saveDoubleArrayInModelDirectory(
suffix, // String suffix,
dbg_textures[0], // double [][] data,
tilesX * transform_size, // int width, // int tilesX,
tilesY * transform_size); // int height, // int tilesY,
}
}
//renormalize
......@@ -7508,9 +7514,7 @@ public class TexturedModel {
cold_hot, // final double [] min_max,
inverted_table); // final double [] inv_table)
}
if (debugLevel > -20) { // always
if (save_interm_textures || save_preview) {
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];
String [] dbg_subtitles = new String [faded_textures[0].length];
......@@ -7521,12 +7525,23 @@ public class TexturedModel {
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);
}
// ref_scene.writePreview( // may movbe to different (earlier) stage of processing, (search for "-combined_textures")
// dbg_textures[0], // double [] data,
// debugLevel); // int debugLevel
if (save_preview) {
ref_scene.writePreview( // may movbe to different (earlier) stage of processing, (search for "-combined_textures")
dbg_textures[0], // double [] data,
debugLevel); // int debugLevel
// Trying different palettes
int tex_palette = 2; // regular color
ref_scene.writeLwirPreview(
clt_parameters, // final CLTParameters clt_parameters,
dbg_textures[0], // double [] data,
null, // QuadCLT scene,
tex_palette, // int tex_palette,
"-color", // +tex_palette, // String suffix,
debugLevel); // int debugLevel)
}
if (save_interm_textures) {
String suffix = "-combined_textures";
if (!batch_run && (debugLevel > -1)) {
ShowDoubleFloatArrays.showArrays(
......@@ -7543,27 +7558,7 @@ public class TexturedModel {
dbg_textures, // double [][] data,
tilesX * transform_size, // int width, // int tilesX,
tilesY * transform_size); // int height, // int tilesY,
if (dbg_weights != null) {
suffix = "-texture_weights";
if (!batch_run && (debugLevel > -1)) {
ShowDoubleFloatArrays.showArrays(
dbg_weights,
tilesX * transform_size,
tilesY * transform_size,
true,
ref_scene.getImageName()+suffix,
dbg_titles);
}
ref_scene.saveDoubleArrayInModelDirectory(
suffix, // String suffix,
null, // String [] labels, // or null
dbg_weights, // double [][] data,
tilesX * transform_size, // int width, // int tilesX,
tilesY * transform_size); // int height, // int tilesY,
}
}
return faded_textures;
}
......@@ -7593,7 +7588,8 @@ public class TexturedModel {
int transform_size,
int debugLevel)
{
boolean save_tiff_texture = true;
final boolean save_interm_textures= clt_parameters.tex_save_interm_textures;
boolean save_tiff_texture = save_interm_textures;
if (debugLevel > -2) {
System.out.println("getInterCombinedTextures(): no_alpha=" + no_alpha); // true
}
......
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