IJ macro course codes

IJ macro course codes

//variables
a = 1;
b = 2;
c = a + b;
print("\\Clear");
print( c );
print(a, "+", b, "=", c);

//variables, exercise, an example answer
a = 1;
b = 2;
c = a + b * 2 + a/0.1 - 2;
print("\\Clear");
print( c );
//print(a, "+", b, "=", c);

//user input, numerical variable
a = getNumber("a?", 10);
b = getNumber("b?", 5);
c = a * b;
print("\\Clear");
print(c);

//user input, String variable
a = getString("a?", 10);
b = getString("b?", 5);
c = a + b;
print("\\Clear");
print(c);

//script parameters
#@ String(label="Word1") text1
#@ String(label="Word2") text2

text3 = text1 + text2;
print( text3 ); 



//*** recording ImageJ macro and modifying the macro
newImage("Untitled", "8-bit Black", 300, 300, 1);
run("Salt and Pepper");
run("Gaussian Blur...", "sigma=3");
setAutoThreshold("Default dark");
setOption("BlackBackground", true);
run("Convert to Mask");

// extract variables
width = 300;
title = "Noisy_Image"
newImage(title, "8-bit Black", width, 300, 1);
run("Salt and Pepper");
run("Gaussian Blur...", "sigma=3");
setAutoThreshold("Default dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Erode");


// for-looping 
width = 300;
title = "Noisy_Image"
newImage(title, "8-bit Black", width, 300, 1);
run("Salt and Pepper");
run("Gaussian Blur...", "sigma=3");
setAutoThreshold("Default dark");
setOption("BlackBackground", true);
run("Convert to Mask");
for (i = 0; i < 3; i+=1){
    run("Erode");
} 

//****** for-looping, scanning through image

// measure single pixel
val = getPixel( 10, 10);
print( val );

// parameterizing measurements
x = 10;
y = 10;
val = getPixel( x, y);
print( val );

// for-looping to measure more pixels
for (i = 0; i < 50; i++) {
    x = i;
    y = 10;
    val = getPixel( x, y);
    print( val );
}

//// counting, with "if"
c255 = 0;
for (i = 0; i < 50; i++) {
    x = i;
    y = 10;
    val = getPixel( x, y);
    if ( val == 0) {
        c255 +=1;
    }
}
print( "255 counts:", c255 );

// scanning through full image to count pixels with a specific value
c255 = 0;
for (j = 0; j < getHeight(); j++){
	for (i = 0; i < getWidth(); i++){
		val = getPixel( i,  j);
		if (val == 255){
			c255 += 1;
		}
	}
}
print("255 counts:", c255);

//*** user defined function
a = 4;
b = a * a * a * a;
print(b);

// step 2
a = 4;
b = compute( a );
print(b);

function compute( num ){
    p4 = num * num * num * num;
    return p4;
}


// step 3

a = 4;
b = differentone( a );
print(b);

function compute( num ){
    p4 = num * num * num * num;
    return p4;
}

function differentone( num ){
    p4 = num * num * num * num * num;
    return p4;
}

//step 4
a = 4;
c = 2;
b = compute( a, c );
print(b);

function compute( num1, num2 ){
    p4 = num1 * num2 * num1 * num2;
    return p4;
}

//*** Stack Management

frames = nSlices;
run("Set Measurements...", "  mean redirect=None decimal=3");
run("Clear Results");
for(i=0; i<frames; i++) {
    currentslice = i+1;
    setSlice(currentslice);
    run("Measure");
}

//Stack Management, exercise answer example

frames = nSlices;
run("Set Measurements...", "  mean min centroid redirect=None decimal=3");
run("Clear Results");
for(i=0; i<frames; i++) {
    currentslice = i+1;
    setSlice(currentslice);
    run("Measure");
}

//multiple ROIs
run("Clear Results");
roinum = roiManager("count");
for (index = 0; index < roinum; index++) {
    roiManager("select", index);
    run("Measure");
}



// stack management * multiple ROIs
run("Clear Results");
roinum = roiManager("count");
for (index = 0; index < roinum; index++) {
    roiManager("select", index);
    measureStack();
}

function measureStack(){
    frames = nSlices;
    run("Set Measurements...", "  mean min centroid redirect=None decimal=3");
    //run("Clear Results");
    for(i=0; i<frames; i++) {
        currentslice = i+1;
        setSlice(currentslice);
        run("Measure");
    }
}


//*** array, accessing Results Table
aa = newArray(nResults);
for (i = 0; i < aa.length; i++){
	aa[i] = getResult("Min", i);
}
Array.getStatistics(aa, min, max, mean, stdDev);
print("Average of Min = ", min);

//exercise: prep 1 to 10 array, get the average
aa = newArray(10);
for ( i = 0; i < aa.length; i++){
    aa[i] = i + 1;
}
Array.getStatistics(aa, min, max, mean, stdDev);
print("Mean of the array", mean);


// array and setting results table
if (selectionType() != 5) {
    exit("selection type must be a straight line ROI");
}
lineProfile = getProfile();
run("Clear Results");
for(i = 0; i < lineProfile.length; i++) { 
    setResult("n", i, i);
    setResult("intensity", i, lineProfile[i]);
}
updateResults();

//User interface, Dialog
Dialog.create("add two numbers");
Dialog.addMessage("Computes x + y");
Dialog.addNumber("x", 10);
Dialog.addNumber("y", 20);
Dialog.show();
n1 = Dialog.getNumber();
n2 = Dialog.getNumber();
print("Results:", n1 + n2);

//UI exercies
Dialog.create("Distance Calculator");
Dialog.addMessage("Please put two point coordinates");
Dialog.addNumber("p1 x", 0);
Dialog.addNumber("p1 y", 0);
Dialog.addNumber("p2 x", 10);
Dialog.addNumber("p2 y", 20);
Dialog.show();
p1x = Dialog.getNumber();
p1y = Dialog.getNumber();
p2x = Dialog.getNumber();
p2y = Dialog.getNumber();
print("P1(", p1x, ",", p1y, ")");
print("P2(", p2x, ",", p2y, ")");
dist = sqrSumSquared(p1x, p1y, p2x, p2y);
print("Distance:", dist);

function sqrSumSquared(x1, y1, x2, y2){
    sumsquared = pow(x1-x2, 2) + pow(y1-y2, 2);
    return pow(sumsquared, 0.5);     
}


//***  dot animation

newImage("dot", "8-bit Black", 200, 50, 2);
setForegroundColor(255, 255, 255);
setBackgroundColor(0, 0, 0);
makeOval( 100, 25, 10, 10);
run("Fill", "slice");


// dot animation with variables

stackname = "dot";
w = 250;
h = 50;
frames = 2;
int = 255
x_position = 100;
y_position = 25;
sizenum = 10;
newImage(stackname, "8-bit Black", w, h, frames);
setForegroundColor(int, int, int);
setBackgroundColor(0, 0, 0);
makeOval(x_position, y_position, sizenum, sizenum);
run("Fill", "slice");

// dot animation, no bouncing case
stackname = "dot";
w = 250;
h = 50;
frames = 50;
sizenum = 10;
int = 255
x_position = sizenum;
y_position = (h/2)-(sizenum/2);
newImage(stackname, "8-bit Black", w, h, frames);
setForegroundColor(int, int, int);
setBackgroundColor(0, 0, 0);
speed = 10;
for (i = 0; i < frames; i++){
    setSlice( i + 1);
    makeOval(x_position, y_position, sizenum, sizenum);
    x_position += speed;
    run("Fill", "slice");
}

// boucing dot animation
stackname = "dot";
w = 250;
h = 50;
frames = 50;
sizenum = 10;
int = 255
x_position = sizenum;
y_position = (h/2)-(sizenum/2);
newImage(stackname, "8-bit Black", w, h, frames);
setForegroundColor(int, int, int);
setBackgroundColor(0, 0, 0);
speed = 10;
for (i = 0; i < frames; i++){
    setSlice( i + 1);
    if ((x_position > (w-sizenum)) || (x_position < 0) ) { 
        speed*=-1;
        x_position += speed*2;  //avoids penetrating boundary
    }    
    makeOval(x_position, y_position, sizenum, sizenum);
    x_position += speed;
    run("Fill", "slice");
}
run("Select None");


// exercise, vertical movement
stackname = "dot";
w = 250;
h = 250;
frames = 50;
sizenum = 10;
int = 255
x_position = sizenum;
y_position = (h/2)-(sizenum/2);
newImage(stackname, "8-bit Black", w, h, frames);
setForegroundColor(int, int, int);
setBackgroundColor(0, 0, 0);
speed = 10;
for (i = 0; i < frames; i++){
    setSlice( i + 1);
    if ((y_position > (h-sizenum)) || (y_position < 0) ) { 
        speed*=-1;
        y_position += speed*2;  //avoids penetrating boundary
    }    
    makeOval(x_position, y_position, sizenum, sizenum);
    y_position += speed;
    run("Fill", "slice");
}
run("Select None");

// another way of looping, do while

counter=0;
while ( counter <= 90 ){
	print( counter );
	counter = counter + 10;
}


// do -while, evaluation that comes after. 
counter=0;
do {
	print( counter );
	counter += 10;
} while (counter < 0)	 


// File I/O

// code component, get directory

Ddir = getDirectory("Choose Destination Directory");
print(Ddir);

// code component, get threshold

getThreshold(lower, upper);
if ( ( lower == -1 ) && ( upper == -1 ) ) {
    exit("Image must be thresholded");
}
setThreshold(lower, 255);

// code component, save results

Ddir = getDirectory("Choose Destination Directory");
print(Ddir);
img_title = getTitle();
run("Measure");

dest_filename = img_title + "_measure.xls";
fullpath = Ddir + dest_filename;
saveAs("Measurements", fullpath);

//code 21, auto save results 
Ddir = getDirectory("Choose Destination Directory");
print(Ddir);
getThreshold(lower, upper);
if ((lower==-1) && (upper==-1)) {
    exit("Image must be thresholded");
}
setThreshold(lower, 255);
img_title=getTitle();
run("Set Measurements...", 
    "area mean centroid circularity slice limit redirect=None decimal=2");
run("Analyze Particles...", 
    "size=10-Infinity circularity=0.50-1.00 show=Outlines display exclude clear stack");
dest_filename = img_title+"_measure.xls";
fullpath = Ddir + dest_filename;
saveAs("Measurements", fullpath);

//batch analysis - list files
source_dir = getDirectory("Choose the Directory where the file is");
list = getFileList(source_dir);
for(i=0; i<list.length; i++) {
    print(list[i]);
} 

// filename extension cleaner
imgtitle = getTitle();
print( imgtitle );
print(  indexOf( imgtitle, ".tif") );
imgtitleNoext = substring(imgtitle, 0, indexOf( imgtitle, ".tif"));
print( imgtitleNoext ); 
resultsfilename = imgtitleNoext + "_measurements.csv";
print( resultsfilename );

// code 23, batch analysis
//batch analysis Code 23 ---------------------------------------------

source_dir = getDirectory("Choose the Directory where the file is");
out_dir = getDirectory("Choose the Directory to save files");
list = getFileList(source_dir);
for(i=0; i<list.length; i++) {
    NucAnalysis(list[i]);
}   

function NucAnalysis(img_filename) {
	fullpath_image = source_dir + img_filename;
	open(fullpath_image);
	sourceID = getImageID();		
	setAutoThreshold("Li dark");
	img_title = getTitle();

	run("Set Measurements...", 
	    "area mean centroid circularity slice limit redirect=None decimal=2");
	run("Analyze Particles...", 
	    "size=10-Infinity circularity=0.50-1.00 show=Outlines display exclude clear stack");
	selectImage(sourceID);
	close();
	
	dest_outlinename = img_title+"_outline.tif";
	fullpath = out_dir + dest_outlinename;
	saveAs("tiff", fullpath);
	close();

	dest_filename = img_title+"_measure.xls";
	fullpath = out_dir + dest_filename;
	print(fullpath );
	saveAs("Measurements", fullpath);
}

/////// Trainable Weka Segmentation

// single
//Step 1:  create path variables
inputdir = "/Users/miura/Dropbox/Courses/IJMacro/IJmacro_samples/CellsDividing";
outputdir = "/Users/miura/Downloads/out";
themodel = "/Users/miura/Dropbox/Courses/IJMacro/exampleWekaSegModel/classifier.model";

//Step 2  Launch Trainable Segmentation Plugin
open(inputdir + File.separator + "Nucseq0010000.tif");
imgid = getImageID();
run("Trainable Weka Segmentation");
wait(3000);

//Step 3 Load the classifier model
call("trainableSegmentation.Weka_Segmentation.loadClassifier", themodel);

//Step 4 Apply classifier to an image

image = "Nucseq0010021.tif";
call("trainableSegmentation.Weka_Segmentation.applyClassifier",
	inputdir, 
	image, 
	"showResults=false", 
	"storeResults=true", 
	"probabilityMaps=false", 
	outputdir);


// batch
//Step 1:  create path variables
inputdir = "/Users/miura/Dropbox/Courses/IJMacro/IJmacro_samples/CellsDividing";
outputdir = "/Users/miura/Downloads/out";
themodel = "/Users/miura/Dropbox/Courses/IJMacro/exampleWekaSegModel/classifier.model";

//Step 2  Launch Trainable Segmentation Plugin
open(inputdir + File.separator + "Nucseq0010000.tif");
imgid = getImageID();
run("Trainable Weka Segmentation");
wait(3000);

//Step 3 Load the classifier model
call("trainableSegmentation.Weka_Segmentation.loadClassifier", themodel);

//Step 4 Batch processing
// get file list
files = getFileList(inputdir);
// looping for each file
for (i = 0; i < files.length; i++){
	if ( endsWith( files[i], ".tif")){
		call("trainableSegmentation.Weka_Segmentation.applyClassifier",
			inputdir, 
			files[i], 
			"showResults=false", 
			"storeResults=true", 
			"probabilityMaps=false", 
			outputdir);
		//clear memory, just be on the safe side
		run("Collect Garbage");
	}
}

//cleanup
selectImage(imgid);
close();
selectWindow("Trainable Weka Segmentation v3.2.32");
close();



/////// colocalization - pixel based

//use JaCOP recorder

run("Bio-Formats Importer", "open=/Users/miura/Dropbox/20190225_Stuttgart/IJmacro/samples/Stephan/S467D_1.czi autoscale color_mode=Default open_all_series rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");

run("Split Channels");

run("JACoP ", "imga=C3-S467D_1.czi imgb=C4-S467D_1.czi thra=6068 thrb=8495 pearson mm cytofluo");

//use JaCOP modified

path = "/Users/miura/" +
    "Dropbox/20190225_Stuttgart/Coloc/colocExample/S467D_1.czi";
run("Bio-Formats Importer", "open=" + path + 
    " color_mode=Default view=Hyperstack stack_order=XYCZT");
srcImgName = getTitle();
run("Split Channels");
c1name = "C1-" + srcImgName;
c2name = "C2-" + srcImgName;
c3name = "C3-" + srcImgName;
c4name = "C4-" + srcImgName;
imga_th = 6068;
imgb_th = 8495;
run("JACoP ", "imga=" + c3name + " imgb=" + c4name +
        " thra=" + imga_th + " thrb=" + imgb_th + " pearson mm");

// list files
dirpath = getDirectory("Choose a Directory");
filelist = getFileList(dirpath);
for (i = 0; i < filelist.length; i++) {
    if (endsWith( filelist[ i ], "czi") ){
        print( filelist[ i ] );
    }
}

//JaCop Batch
dirpath = getDirectory("Choose a Directory");
filelist = getFileList(dirpath);
for (i = 0; i < filelist.length; i++) {
    if (endsWith( filelist[ i ], "czi") ){
        print( filelist[ i ] );
        doJacop( dirpath + filelist[ i ] );
    }
}

function doJacop( czipath ){
    path = czipath;
    run("Bio-Formats Importer", "open=" + path + 
        " color_mode=Default view=Hyperstack stack_order=XYCZT");
    srcImgName = getTitle();
    run("Split Channels");
    c1name = "C1-" + srcImgName;
    c2name = "C2-" + srcImgName;
    c3name = "C3-" + srcImgName;
    c4name = "C4-" + srcImgName;
    imga_th = 6000;
    imga_th = 8000;
    run("JACoP ", "imga=" + c3name + " imgb=" + c4name +
            " thra=" + imga_th + " thrb=93 pearson mm");
    selectWindow(c1name);
    close();
    selectWindow(c2name);
    close();
    selectWindow(c3name);
    close();
    selectWindow(c4name);
    close();
}



//colocalzation - object based

//outline
// splitting and grab ImageIDs

// segmentation

// divide ch1 image by 2

// get average of two segmented channels

// count each area

//output results


//fullcode
// splitting and grab ImageIDs
run("Duplicate...", "duplicate"); //keep the original
srcImageName = getTitle();
run("Split Channels");
c1name = "C1-" + srcImageName;
c2name = "C2-" + srcImageName;
selectWindow(c1name);
c1ID = getImageID();
selectWindow(c2name);
c2ID = getImageID();

// segmentation
selectImage( c1ID );
run("Auto Threshold", "method=Otsu white");
selectImage( c2ID );
run("Auto Threshold", "method=Otsu white");

// divide ch1 image by 2
selectImage( c1ID );
run("Divide...", "value=2.000");

// get average of two segmented channels
//imageCalculator("Average create", "C1-PlusTIPs_z16.tif","C2-PlusTIPs_z16.tif");
imageCalculator("Average create", c1ID, c2ID);
averageID = getImageID();

// count each area
c1only = countPixels( 64 );
c2only = countPixels( 127 );
overlap = countPixels( 191 );

//output results
print("Ch1 ratio: ", overlap / (overlap + c1only));
print("Ch2 ratio: ", overlap / (overlap + c2only));

//clean up
selectImage( c1ID );
close();
selectImage( c2ID );
close();
selectImage( averageID );
close();

// count the number of pixels with specific value
function countPixels( pixelvalue ){
    count = 0;
    for (j = 0; j < getHeight(); j++){
        for (i = 0; i < getWidth(); i++){
            val = getPixel( i,  j);
            if (val == pixelvalue){
                count += 1;
            }
        }
    }
    print(pixelvalue, "counts:", count);
    return count;
}

// complex dialogue
Dialog.create("Calculate Distance");
Dialog.addMessage("Calculates distance between two points");
Dialog.addNumber("point1 x:", 0);		//number 1
Dialog.addNumber("point1 y:", 0);		//number 2
Dialog.addNumber("point2 x:", 2);		//number 3
Dialog.addNumber("point2 y:", 2);		//number 4
Dialog.addNumber("Scale [um/pixel]:", 0.1);	//number 5
Dialog.addCheckbox("scale?", true);		//check 1
Dialog.show();
p1x = Dialog.getNumber();	//1
p1y = Dialog.getNumber();	//2
p2x = Dialog.getNumber();	//3
p2y = Dialog.getNumber();	//4
scale = Dialog.getNumber();	//5
scaleswitch = Dialog.getCheckbox();
distance = CalcDistance(p1x, p1y, p2x, p2y);
if (scaleswitch) 
	distance *= scale;
print("p1:", p1x, ",", p1y);
print("p2:", p2x, ",", p2y);
if (scaleswitch) {
	print("distance:" + distance + " [um]");
} else {
	print("distance:" + distance + " [pixels]");
}

function CalcDistance(p1x, p1y, p2x, p2y) {
	sum_difference_squared = pow((p2x - p1x),2) + pow((p2y - p1y),2);
	distance = pow(sum_difference_squared, 0.5);
	return distance;
}

// homework
grid( 400, 400);
diagonalLattice();
gridDiagonal_byWhileLoop();


function grid( ww, hh){
    //y = 1000;
    //x = 400;	
    newImage("grid", "8-bit Black", ww, hh, 1);
    setColor(100);
    setLineWidth(2);
    for(i = 20; i < ww; i += 20)
        drawLine( i, 0, i, hh - 1);
        
    for(j = 20; j < hh; j += 20)
        drawLine( 0, j, ww - 1, j);   
}

function diagonalLattice(){
    size = 400
    newImage("grid", "8-bit Black", size, size, 1);
    ww = size;
    hh = size;
    for (i = 0; i < size; i += 20){
        drawLine(i, 0, 0, i);
        drawLine(i, hh-1, ww-1, i);
    }
    for (i = 0; i < size; i += 20){
        drawLine(i, hh-1, 0, ww - 1 - i);
        drawLine(i, 0, ww-1, ww - 1 - i);   
    }
    
}

function gridDiagonal_byWhileLoop(){
    ww = 300;
    hh = 500;
    newImage("diagonal grid", "8-bit black", ww, hh, 1);
    
    cursor = 0;
    
    gspacing = 10;
    
    while (cursor < ww + hh){
        px1 = 0;
        py1 = cursor;
        px2 = cursor;
        py2 = 0;
        if (py1 > hh){
            py1 = hh;
            px1 = cursor - hh;; 
        }
        if (px2 > ww){
            px2 = ww;
            py2 = cursor - ww;  
        }
        drawLine(px1, py1, px2, py2);
        cursor += gspacing;
    }
    
}