Commit 849b916d authored by Andrey Filippov's avatar Andrey Filippov
Browse files

added imagej macros

parent a602300e

ij_macros/cross_offset.ijm

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macro "cross_offset" {

  saveSettings;

  jpeg_directory = "/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";

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

// scoremaps_blurred

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

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

  // used old files for now

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

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

  

//L3-1691017293_032075-7285_82.jpeg



  scoremaps_suffix="-scoremap";

  norm_radius = 20;

  thresh0 =     0.6; 

  thresh1 =     0.7;

  sigma =       10.0;

  min_height= -0.1;

  max_height=  0.25;

  maxmin_min = 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_rad = 15.0

  // 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

  

  // 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("L3-1691017285_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);

  

  

  

  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) {

    score1_file = src1_basename+scoremaps_suffix+".tiff";

    score2_file = src2_basename+scoremaps_suffix+".tiff";

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

    selectImage(score1_file);



    // save normalized src1 to be used for mask to disable points far from src1

    src1_dup = "src1_dup"; // will have grown, normalized candidates from the first image

    run("Duplicate...", "title="+src1_dup);

    selectImage(src1_dup);  // just in case - duplicate changes selection

    run("Subtract...", "value=" + thresh0);

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

    // grow with GB, then re-normalize

    run("Gaussian Blur...", "sigma="+sigma); // Maybe different sigma?

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

    

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

    selectImage(score1_file);

    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);

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

    selectImage(score2_file);

    src2_dup = "src2_dup";

    run("Duplicate...", "title="+src2_dup);    

    selectImage(score2_file);

    run("Subtract...", "value=" + thresh0);

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

    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);

    img_prod = "Result of "+score1_file;

    selectImage(img_prod); 

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

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

    setMinAndMax(-0.50, 0.50);

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

// save as intermediate result  

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

    print(results_directory + "/"+img_rslt);

    grow_gb=0; // 3.0;

    grow_gb_thresh=0.8;

// create mask

    run("Subtract...", "value="+((min_height+ max_height)/2)); // average

    run("Abs");

    run("Subtract...", "value="+((max_height-min_height)/2));  // half range

    run("Multiply...", "value=-10000.000"); // just a big number and inverse, so good are inside the [min_height,max_height] range

    run("Min...", "value=0");  // limit to [0,1] range

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

// grow it with GB filter

    if (grow_gb>0) {

        run("Gaussian Blur...", "sigma="+grow_gb);

        run("Subtract...", "value="+grow_gb_thresh);

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

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

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

    }

// Multiply mask by src1_dup

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

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

// measure difference between local maximum and local minimum for the input image2 and mask out to little and too much

    jpeg2_file = src2_basename; // +".jpeg" is already included

    print ("opening: '"+jpeg_directory+"/"+jpeg2_file+"'");

    open(jpeg_directory+"/"+jpeg2_file);

    selectImage(jpeg2_file);

    run("32-bit");

    run("Subtract...", "value=128");

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

    // save intermediate result

    img_minmax2 = src2_basename+"-minmax_diff"+"-r"+maxmin_rad+".tiff";

    saveAs("Tiff", results_directory + "/"+img_minmax2);

    run("Subtract...", "value="+((maxmin_max+ maxmin_min)/2)); // average

    run("Abs");

    run("Subtract...", "value="+((maxmin_max-maxmin_min)/2));  // half range

    run("Multiply...", "value=-10000.000"); // just a big number and inverse, , so good are inside the [maxmin_min,maxmin_max] range

    run("Min...", "value=0");  // limit to [0,1] range

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

    img_minmax2_mask = src2_basename+"-minmax_mask"+"-r"+maxmin_rad+"_"+maxmin_min+"-"+maxmin_max+".tiff";

    saveAs("Tiff", results_directory + "/"+img_minmax2_mask);

// combine masks - multiply existing by the new for object contrast    

   imageCalculator("Multiply create", img_mask2, img_minmax2_mask);

   img_mask3 = "Result of "+img_mask2; // combined mask - has src1 maximum, not too high

   selectImage(img_mask3);

//

// save mask file    

    img_mask="mask_"+src1_basename+"-"+src2_basename+"-GB"+sigma+"-scale"+scale_prod+"-min"+min_height+"-max"+max_height+"-grow"+grow_gb+".tiff";

// save as intermediate result  

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

// create pessimistic scoremap (higher threshold) and multiply by the mask    

    selectImage(src2_dup);

    run("Subtract...", "value=" + thresh1);

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

    run("Multiply...", "value=" + (1.0/(1.0-thresh1))); //  will still be much less than 1.0, just expanding [thersh1,1.0] to [0,1]

    imageCalculator("Multiply create", src2_dup, img_mask);

    img_prod = "Result of "+src2_dup;

    selectImage(img_prod); 

    run("Find Maxima...", "prominence=0.01 output=[Point Selection]");    

    img_result_score = src2_basename+"-rslt_score.tiff";

//src2_basename    

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

/* */

//now open are 9 images

    close();

    close();

    close();

    close();

    close();

    close();

    close();

    close();

    close();

/* */    

  } // end of function

  restoreSettings;

} // end of macro



/*

//#6 -  2180, 2428    0.12

//#7 -  2172, 3350    0.1

//#12 - 2295, 3238 - new? 0.06

//

// 2291, 3241



(-0.05979131273315754, 0.998210899019664)



open("/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/test_macros/L3-1691017285_820540.jpeg-scoremap.tiff");

selectImage("L3-1691017285_820540.jpeg-scoremap.tiff");

run("Subtract...", "value=0.7");

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

run("Differentials ", "operation=[Normalize by local maximum] multiply=0.000 multiply_0=1.000 normalization=20");

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

saveAs("Tiff", "/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/test_macros/L3-1691017285_820540.jpeg-scoremap_lm20.tif");

open("/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/test_macros/L3-1691017285_820540.jpeg-scoremap.tiff");

selectImage("L3-1691017285_820540.jpeg-scoremap.tiff");

selectImage("L3-1691017285_820540.jpeg-scoremap_lm20.tif");

selectImage("L3-1691017285_820540.jpeg-scoremap.tiff");

run("Subtract...", "value=0.500");

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

run("Differentials ", "operation=[Normalize by local maximum] multiply=0.000 multiply_0=1.000 normalization=20.000");

selectImage("L3-1691017285_820540.jpeg-scoremap_lm20.tif");

selectImage("L3-1691017285_820540.jpeg-scoremap.tiff");

open("/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/test_macros/L3-1691017293_032075.jpeg-scoremap.tiff");

selectImage("L3-1691017293_032075.jpeg-scoremap.tiff");

run("Differentials ", "operation=[Directional derivative] multiply=-0.0598 multiply_0=0.998 normalization=20.000");



selectImage("L3-1691017285_820540.jpeg-scoremap_lm20.tif");

selectImage("Result of L3-1691017293_032075.jpeg-scoremap.tiff");

close();

selectImage("1691017283_609002-RECT-UM10.0_0.97-PIX0.02-CROP-PAL0-RANGE250.0-preview.jpeg");

close();

selectImage("1691017285_262848-RECT-UM10.0_0.97-PIX0.02-CROP-PAL0-RANGE250.0-preview.jpeg");

close();

imageCalculator("Multiply create", "L3-1691017293_032075.jpeg-scoremap.tiff","L3-1691017285_820540.jpeg-scoremap_lm20.tif");

selectImage("Result of L3-1691017293_032075.jpeg-scoremap.tiff");

setMinAndMax(-5.000E-3, 5.000E-3);selectImage("L3-1691017285_820540.jpeg-scoremap_lm20.tif");

selectImage("Result of L3-1691017293_032075.jpeg-scoremap.tiff");

saveAs("Tiff", "/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/test_macros/Result of L3-1691017293_032075.jpeg-scoremap_prod.tif");

run("Gaussian Blur...", "sigma=5");

run("Save");

saveAs("Tiff", "/media/elphel/SSD3-4GB/lwir16-proc/berdich/annotations/collages/pattern-matching/test_macros/Result of L3-1691017293_032075.jpeg-scoremap_prod_gb5.tif");



run("Close All");



*/

ij_macros/fiji_scoremaps.ijm

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macro "fiji_scoremaps" {

  saveSettings;

  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_48_gb5-0.33_32x32.tiff"; // sharper circle

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

  

  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_medium";

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

  suffix="-scoremap";

  



  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("L3-1691017288_801308.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

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

  create_scoremap("L3-1691017286_416693.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017285_820540.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017285_262848.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017284_609002.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017284_070541.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017283_609002.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  function create_scoremap (src_file, template, template_dir, src_dir, score_dir, suffix) {

    open(template_dir+"/"+template);

    selectImage(template);

    open(src_dir+"/"+src_file);

    selectImage(src_file);

    source_width=getWidth();

    source_height=getHeight();

    run("32-bit");

    run("Subtract...", "value=128");

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

    run("Enhance Contrast", "saturated=0.35");

    run("Compute ScoreMap", "template="+template+" image=" + src_file+" method=[Normalised cross-correlation] score_threshold=0.9");

    close(); // thresholded result

    run("Canvas Size...", "width="+source_width+" height="+source_height+" position=Center zero");

    saveAs("Tiff", score_dir + "/"+src_file+suffix+".tiff");

    close(); // saved result

    close(); // source file

    close(); // template file

  }

  

  restoreSettings;

}

// /home/elphel/git/imagej-elphel/ij_macros/fiji_scoremaps.txt

ij_macros/get_points.ijm

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macro "fiji_get_points" {

  saveSettings;

  s = selectionType();

    if ( s == -1 ) {

        exit("There was no selection.");

    } else if( s != 10 ) {

        exit("The selection wasn't a point selection.");

    } else {

        getSelectionCoordinates(xPoints,yPoints);

        x = xPoints[0];

        y = yPoints[0];

        showMessage("Got coordinates ("+x+","+y+")");

        showMessage("Got points:" + xPoints.length);

        for (i = 0; i < xPoints.length; i++){

          print (i, xPoints[i], yPoints[i]); 

        }

        

    }



  /*

  

  2180, 2428 -16: 2164, 2412

  3441, 2561

  6: 2185, 2431 ( 2180, 2427 - offsest by 5?

  7: 2175, 3351

  2299, 3241

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

  template_file="object3_black_half_7-24x24.tiff";

  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";

  suffix="-scoremap";

  

  create_scoremap("L3-1691017288_801308.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

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

  create_scoremap("L3-1691017286_416693.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017285_820540.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017285_262848.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017284_609002.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017284_070541.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  create_scoremap("L3-1691017283_609002.jpeg", template_file, template_dir, soure_dir, scoremaps_directory, suffix);

  function create_scoremap (src_file, template, template_dir, src_dir, score_dir, suffix) {

    open(template_dir+"/"+template);

    selectImage(template);

    open(src_dir+"/"+src_file);

    selectImage(src_file);

    source_width=getWidth();

    source_height=getHeight();

    run("32-bit");

    run("Subtract...", "value=128");

    run("Wi8dow/Level...");

    run("Enhance Contrast", "saturated=0.35");

    run("Compute ScoreMap", "template="+template+" image=" + src_file+" method=[Normalised cross-correlation] score_threshold=0.9");

    close(); // thresholded result

    run("Canvas Size...", "width="+source_width+" height="+source_height+" position=Center zero");

    saveAs("Tiff", score_dir + "/"+src_file+suffix+".tiff");

    close(); // saved result

    close(); // source file

    close(); // template file

  }

  */

  restoreSettings;

}

// /home/elphel/git/imagej-elphel/ij_macros/fiji_scoremaps.txt

ij_macros/goto_coordinates.ijm

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macro "goto_coordinates" {

    saveSettings;

    width=300;

    height=200;

    xc=0; yc=0;

    Dialog.create("My dialog"); // ("Go to selected coordinates. Creates rectangular selection" );

    Dialog.addNumber("Selection center X",xc);

    Dialog.addNumber("Selection center Y",yc);

    Dialog.addNumber("Selection width", width);

    Dialog.addNumber("Selection height", height);

    Dialog.show();

    xc = Dialog.getNumber();

    yc = Dialog.getNumber();

    width = Dialog.getNumber();

    height = Dialog.getNumber();

    print("xc="+xc+", yc="+yc+", width="+width+", height="+height);

    makeRectangle(xc-width/2, yc-height/2, width, height);

    run("To Selection");

    restoreSettings;

}

ij_macros/make_objects_snapshots.ijm

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macro "make_snapshots" {

  saveSettings;

  // copy lines to match required objects and put actual coordinates/names

  // (no spaces) below using kate's  <cntrl><shift>b mode

  // To run - open file in imagej, go to Plugins->Macros->Run and select this file (should have .txt extension)

  //

  subdir = "objects"

  Dialog.create("objects snapshots "); // ("Go to selected coordinates. Creates rectangular selection" );

  Dialog.addString("Subdirectory name",subdir);

  Dialog.show();

  subdir = Dialog.getString();

  

  makeSnapshot( 2456, 6458 , 150, 150, "_M", subdir);

  makeSnapshot( 4790, 9484 , 150, 150, "01", subdir);

  makeSnapshot( 4624, 10291, 150, 150, "02", subdir);

  makeSnapshot( 4642, 12968, 150, 150, "03", subdir);

  makeSnapshot( 4734, 11946, 150, 150, "04", subdir);

  makeSnapshot( 5266, 11618, 150, 150, "05", subdir);

  makeSnapshot( 4865, 5362 , 150, 150, "06", subdir);

  makeSnapshot( 4805, 7027 , 150, 150, "07", subdir);

  makeSnapshot( 4791, 8698 , 150, 150, "08", subdir);

  makeSnapshot( 4358, 5972 , 150, 150, "09", subdir);

  makeSnapshot( 4785, 12213, 150, 150, "10", subdir);

  makeSnapshot( 5620, 11280, 150, 150, "11", subdir);



    function makeSnapshot(xc, yc, width, height, suffix, subdir) {

        base_directory=getInfo("image.directory");

        directory = base_directory+"/"+subdir;

        filename=getInfo("image.filename")+"-"+suffix;

        makeRectangle(xc-width/2, yc-height/2, width, height);

        run("Duplicate...", " ");

        print("saving object snapshot to: "+  directory+"/"+filename+"-"+xc+"_"+yc+"_"+width+"_"+height+".tiff");

        File.makeDirectory(directory); 

        saveAs("Tiff", directory+"/"+filename+"-"+xc+"_"+yc+"_"+width+"_"+height+".tiff");

        saveAs("Jpeg", directory+"/"+filename+"-"+xc+"_"+yc+"_"+width+"_"+height+".jpeg");

        close();

    }

  restoreSettings;

}