Commit 5f08ad84 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

Update ij macros

parent 849b916d

ij_macros/cross_offset.ijm

+54 −9
Original line number Original line Diff line number Diff line
@@ -18,21 +18,25 @@ macro "cross_offset" { 
  thresh1 =     0.7;

  thresh1 =     0.7;

  sigma =       10.0;

  sigma =       10.0;

  min_height= -0.1;

  min_height= -0.1;

  max_height=  0.25;

  max_height=  0.18; // 0.25;

  maxmin_min = 82.0; //difference between local maximum and local minimum (norm_radius) should be not less than this

  maxmin_min = 75;  // 82.0; //difference between local maximum and local minimum (norm_radius) should be not less than this

  maxmin_max = 150; //difference between local maximum and local minimum (norm_radius) should be not more than this

  maxmin_max = 150; //difference between local maximum and local minimum (norm_radius) should be not more than this

  maxmin_rad = 15.0

  maxmin_rad = 15.0

  // for illustrations - run for one pair with disabled close() in the end

  // for illustrations - run for one pair with disabled close() in the end

  // scale_prod=-40000 to get meters of height (depends on image offset), negative if first image is taken from higher point on the image map

  // scale_prod=-40000 to get meters of height (depends on image offset), negative if first image is taken from higher point on the image map

  //>>> dx,dy (-59, 985) pixels, l = 987 pixels = 19.7m





  File.makeDirectory(results_directory);   

  // negative disparity

  // negative disparity

  getCrossOffset("L3-1691017293_032075-7285_82.jpeg", "L3-1691017285_820540.jpeg", -0.060, 0.998, 300, norm_radius, thresh0, sigma,  thresh1, min_height, max_height, scoremaps_directory, scoremaps_suffix, jpeg_directory, results_directory, maxmin_min, maxmin_max, maxmin_rad);

  getCrossOffset("L3-1691017293_032075-7285_82.jpeg", "L3-1691017285_820540.jpeg", -0.060, 0.998, 150, norm_radius, thresh0, sigma,  thresh1, min_height, max_height, scoremaps_directory, scoremaps_suffix, jpeg_directory, results_directory, maxmin_min, maxmin_max, maxmin_rad);





  getCrossOffset("L3-1691017285_820540.jpeg","L3-1691017293_032075-7285_82.jpeg",  0.060, -0.998, 300, norm_radius, thresh0, sigma,  thresh1, min_height, max_height,  scoremaps_directory, scoremaps_suffix, jpeg_directory, results_directory, maxmin_min, maxmin_max, maxmin_rad);

  getCrossOffset("L3-1691017285_820540.jpeg","L3-1691017293_032075-7285_82.jpeg",  0.060, -0.998, 150, norm_radius, thresh0, sigma,  thresh1, min_height, max_height,  scoremaps_directory, scoremaps_suffix, jpeg_directory, results_directory, maxmin_min, maxmin_max, maxmin_rad);

  

  

  

  

  

  

  function getCrossOffset(src1_basename, src2_basename, kx, ky, scale_prod, nrad, thresh0, sigma,  thresh1, min_height, max_height, scoremaps_directory, scoremaps_suffix, jpeg_directory, results_directory, maxmin_min, maxmin_max, maxmin_rad) {

  function getCrossOffset(src1_basename, src2_basename, kx, ky, scale_prod, nrad, thresh0, sigma,  thresh1, min_height, max_height, scoremaps_directory, scoremaps_suffix, jpeg_directory, results_directory, maxmin_min, maxmin_max, maxmin_rad) {

    nrad_dd = 10; // normalization for directional derivative

    min_dd = 0.3; // do not boost dd if scoremap less than this

    score1_file = src1_basename+scoremaps_suffix+".tiff";

    score1_file = src1_basename+scoremaps_suffix+".tiff";

    score2_file = src2_basename+scoremaps_suffix+".tiff";

    score2_file = src2_basename+scoremaps_suffix+".tiff";

    open(scoremaps_directory+"/"+score1_file); // use for derivative

    open(scoremaps_directory+"/"+score1_file); // use for derivative
@@ -50,8 +54,28 @@ macro "cross_offset" { 
    

    

    // put src1_dup aside, continue with score1_file - directional derivative

    // put src1_dup aside, continue with score1_file - directional derivative

    selectImage(score1_file);

    selectImage(score1_file);

    src1_dd = src1_basename+"-directional_derivative.tiff";

    run("Duplicate...", "title="+src1_dd);

    selectImage(src1_dd);

    print("operation=[Directional derivative] multiply_d/dx_by="+kx+" multiply_d/dy_by="+ky+" normalization_radius="+nrad);

    print("operation=[Directional derivative] multiply_d/dx_by="+kx+" multiply_d/dy_by="+ky+" normalization_radius="+nrad);

    run("Differentials ", "operation=[Directional derivative] multiply_d/dx_by="+kx+" multiply_d/dy_by="+ky+" normalization_radius="+nrad);

    run("Differentials ", "operation=[Directional derivative] multiply_d/dx_by="+kx+" multiply_d/dy_by="+ky+" normalization_radius="+nrad);

    saveAs("Tiff", results_directory + "/"+src1_dd);  

    src1_dd = src1_basename+"-directional_derivative_normalized.tiff";

    rename(src1_dd);

    // normalize directional derivative by the limited by min local maximum of the scoremap

    selectImage(score1_file); // original scoremap

    src1_dd_norm = "src1_dd_norm"; // no need to save

    run("Duplicate...", "title="+src1_dd_norm);

    selectImage(src1_dd_norm);

    run("Differentials ", "operation=[Local max] multiply_d/dx_by="+kx+" multiply_d/dy_by="+ky+" normalization_radius="+nrad_dd);

    run("Min...", "value="+min_dd);

    imageCalculator("Divide", src1_dd, src1_dd_norm);

    saveAs("Tiff", results_directory + "/"+src1_dd);  // now src1_dd is normalized directiona derivative 

    

//run("Window/Level...");

//setMinAndMax(-0.50, 0.50);

    selectImage(src1_dd_norm);

    close(); // src1_dd_norm is not needed anymore

    open(scoremaps_directory+"/"+score2_file); // use for derivative

    open(scoremaps_directory+"/"+score2_file); // use for derivative

    selectImage(score2_file);

    selectImage(score2_file);

    src2_dup = "src2_dup";

    src2_dup = "src2_dup";
@@ -61,13 +85,30 @@ macro "cross_offset" { 
    run("Min...", "value=0");

    run("Min...", "value=0");

    run("Differentials ", "operation=[Normalize by local maximum] multiply_d/dx_by="+kx+" multiply_d/dy_by="+ky+" normalization_radius="+nrad);

    run("Differentials ", "operation=[Normalize by local maximum] multiply_d/dx_by="+kx+" multiply_d/dy_by="+ky+" normalization_radius="+nrad);

    

    

    imageCalculator("Multiply create", score1_file,score2_file);

    // save normalized score2 as intermediate result

    img_prod = "Result of "+score1_file;

    score2_norm_file = src2_basename+scoremaps_suffix+"-norm.tiff";

    rename(score2_norm_file);

    saveAs("Tiff", results_directory + "/"+score2_norm_file);  

    

    // create same-size sampling, not just same max value

    run("Differentials ", "operation=[Local ismax] multiply_d/dx_by="+kx+" multiply_d/dy_by="+ky+" normalization_radius="+nrad);

    run("Gaussian Blur...", "sigma=2.0");

    run("Differentials ", "operation=[Normalize by local maximum] multiply_d/dx_by="+kx+" multiply_d/dy_by="+ky+" normalization_radius="+nrad);

    score2_normsize_file = src2_basename+scoremaps_suffix+"-normsize.tiff";

    rename(score2_normsize_file);

    saveAs("Tiff", results_directory + "/"+score2_normsize_file);  

    

    imageCalculator("Multiply create", src1_dd,score2_normsize_file); // score1_file was directional derivative, now src1_dd

    img_prod = "Result of "+src1_dd;

    selectImage(img_prod); 

    selectImage(img_prod); 

    run("Gaussian Blur...", "sigma="+sigma); // max= 0.000541

    run("Gaussian Blur...", "sigma="+sigma); // max= 0.000541

    run("Multiply...", "value="+(-scale_prod));

    run("Multiply...", "value="+(-scale_prod));

    setMinAndMax(-0.50, 0.50);

    setMinAndMax(-0.50, 0.50);

    img_rslt=src1_basename+"-"+src2_basename+"-GB"+sigma+"-scale"+(scale_prod)+".tiff";

    img_rslt=src1_basename+"-"+src2_basename+"-GB"+sigma+"-scale"+(scale_prod)+".tiff";

// 2180, 2429    0.2046-> 0.1269 0.2227??     old: 0.1183  -> 0.2136 (-0.02405 / 0.7425)  -0.03189 + -> 0.2832 (0.1123) 120/300 -> .0113 150/300 -> .14

// 2172 3350     0.1131->0.09811 * 1.2 0.1134 old: 0.09811 -> 0.1131 (-0.01059 / 0.7407)  -0.01423 + -> 0.1524                  -> .061  150/300 -> .076

// 131.44, 250.05

// 2008 3164 0.008551 -> 0.2039                                      (-0.01463 / 0.03470) -0.02909 -0.01443->0.0290-9 ->0.4082  -> 0.2014

// save as intermediate result  

// save as intermediate result  

    saveAs("Tiff", results_directory + "/"+img_rslt);

    saveAs("Tiff", results_directory + "/"+img_rslt);

    print(results_directory + "/"+img_rslt);

    print(results_directory + "/"+img_rslt);
@@ -88,6 +129,9 @@ macro "cross_offset" { 
        run("Multiply...", "value=10000");

        run("Multiply...", "value=10000");

        run("Max...", "value=1");

        run("Max...", "value=1");

    }

    }

   img_rslt=src1_basename+"-"+src2_basename+"-GB"+sigma+"-scale"+(scale_prod)+"-height-mask.tiff";

   rename(img_rslt); 

   saveAs("Tiff", results_directory + "/"+img_rslt); // now it is height mask

// Multiply mask by src1_dup

// Multiply mask by src1_dup

   imageCalculator("Multiply create", img_rslt, src1_dup);

   imageCalculator("Multiply create", img_rslt, src1_dup);

   img_mask2 = "Result of "+img_rslt; // combined mask - has src1 maximum, not too high

   img_mask2 = "Result of "+img_rslt; // combined mask - has src1 maximum, not too high
@@ -132,7 +176,8 @@ macro "cross_offset" { 
//src2_basename    

//src2_basename    

    saveAs("Tiff", results_directory + "/"+img_result_score);

    saveAs("Tiff", results_directory + "/"+img_result_score);

/* */

/* */

//now open are 9 images

//now open are 10 images

    close();

    close();

    close();

    close();

    close();

    close();

    close();

ij_macros/fiji_scoremaps.ijm

+5 −3
Original line number Original line Diff line number Diff line
@@ -2,15 +2,17 @@ macro "fiji_scoremaps" { 
  saveSettings;

  saveSettings;

  template_dir="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching";

  template_dir="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching";

//template_file= "object3_black_half_7-24x24.tiff"; // blurred

//template_file= "object3_black_half_7-24x24.tiff"; // blurred

  template_file="object3_black_48_gb5-0.33_32x32.tiff"; // sharper circle

//  template_file="object3_black_48_gb5-0.33_32x32.tiff"; // sharper circle

// template_file="object3_black_48-0.33_32x32.tiff"; // sharp circle

// template_file="object3_black_48-0.33_32x32.tiff"; // sharp circle

  template_file="object4_black_48_gb8-0.333-UM5-0.9-48x48.tiff"; // with unsharp mask

  

  

  soure_dir="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/exported_layers_on_grey";

  soure_dir="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/exported_layers_on_grey";

//  scoremaps_directory="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/scoremaps";

//  scoremaps_directory="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/scoremaps";

  scoremaps_directory="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/scoremaps_medium";

//  scoremaps_directory="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/scoremaps_medium";

//  scoremaps_directory="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/scoremaps_sharp";

//  scoremaps_directory="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/scoremaps_sharp";

   scoremaps_directory="/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/scoremaps_UM5-0.9

  suffix="-scoremap";

  suffix="-scoremap";

  

  File.makeDirectory(scoremaps_directory); 





  create_scoremap("L3-1691017293_032075-7285_82.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017293_032075-7285_82.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017293_032075-7285_82-rot-shift.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017293_032075-7285_82-rot-shift.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);