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Jazy_ACF.ijm
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Jazy_ACF.ijm
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//Version 0.0.6a
//-----------------------------------------------------------------------------------------
//----------------------------------------ACF-related-macros-for---------------------------
//---------------------------------------------ImageJ--------------------------------------
//todo - fix LUT - where?
//14.3.14 add threshold to size (thresholded ACF will have a certain size in units related to image)
macro "make grid overlay [o]"{
grid_size = 256;
xinit = 0;
yinit = 0;
Dialog.create("x-start");
Dialog.addMessage("x-start coordinates");
Dialog.addNumber("", xinit);
Dialog.show();
xinit = Dialog.getNumber();
Dialog.create("y-start");
Dialog.addMessage("y-start coordinates");
Dialog.addNumber("", yinit);
Dialog.show();
yinit = Dialog.getNumber();
Dialog.create("grid size");
Dialog.addMessage("grid size");
Dialog.addNumber("", grid_size);
Dialog.show();
grid_size = Dialog.getNumber();
xwidth = getWidth();
yheight = getHeight();
nx =floor((xwidth-xinit)/grid_size);
ny =floor((yheight-yinit)/grid_size);
setForegroundColor(0 ,0 , 0);
setLineWidth(1);
for (i=0; i <= nx; i++){
x = (i * grid_size) + xinit;
y = yinit;
Overlay.moveTo(x,y);
Overlay.lineTo(x,(ny*grid_size)+yinit); //Overlay.drawLine(x, y, x, yheight)
Overlay.add;
Overlay.show;
}
for (i = 0; i <= ny; i++ ){
x = xinit;
y = (i * grid_size) + yinit;
Overlay.moveTo(x,y);
Overlay.lineTo((nx*grid_size)+xinit,y); //Overlay.drawLine(x, y, xwidth, y)
Overlay.add;
Overlay.show;
}
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "make grid [g]"{
run("Remove Overlay");
grid_size = 256;
xinit = 0;
yinit = 0;
Dialog.create("x-start");
Dialog.addMessage("x-start coordinates");
Dialog.addNumber("", xinit);
Dialog.show();
xinit = Dialog.getNumber();
Dialog.create("y-start");
Dialog.addMessage("y-start coordinates");
Dialog.addNumber("", yinit);
Dialog.show();
yinit = Dialog.getNumber();
Dialog.create("grid size");
Dialog.addMessage("grid size");
Dialog.addNumber("", grid_size);
Dialog.show();
grid_size = Dialog.getNumber();
xwidth = getWidth();
yheight = getHeight();
nx =floor((xwidth-xinit)/grid_size);
ny =floor((yheight-yinit)/grid_size);
setForegroundColor(0 ,0 , 0);
setLineWidth(1);
for (i=0; i <= nx; i++){
x = (i * grid_size) + xinit;
y = yinit;
moveTo(x,y);
lineTo(x,(ny*grid_size)+yinit);
}
for (i = 0; i <= (ny); i++ ){
x = xinit;
y = (i * grid_size) + yinit;
moveTo(x,y);
lineTo((nx*grid_size)+xinit,y);
}
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "make 2n*2n ROI [1]"{
//roiManager("reset");
grid_size = 256;
Dialog.create("grid size");
Dialog.addMessage("Enter grid size (2^n)");
Dialog.addNumber("Pixels ", grid_size);
Dialog.show();
grid_size = Dialog.getNumber();
makeRectangle(0,0,grid_size,grid_size);
//roiManager("Add");
//roiManager("select",0);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "make ROI there [2]"{
getCursorLoc(x, y, z, flags);
xwidth = getWidth();
yheight = getHeight();
xinit = x;
yinit = y;
roi_size = 256;
Dialog.create("x-start");
Dialog.addMessage("x-start coordinates");
Dialog.addNumber("", xinit);
Dialog.show();
xinit = Dialog.getNumber();
Dialog.create("y-start");
Dialog.addMessage("y-start coordinates");
Dialog.addNumber("", yinit);
Dialog.show();
yinit = Dialog.getNumber();
Dialog.create("roi size");
Dialog.addMessage("roi size");
Dialog.addNumber("", roi_size);
Dialog.show();
roi_size = Dialog.getNumber();
makeRectangle(xinit,yinit,roi_size,roi_size);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "single ACF of ROI in 2-layer stack [3]"{
function doACFsingle(fname){
run("FD Math...", "image1="+fname+" operation=Correlate image2="+fname+" result=temp do");
run("Invert");}
//do ACF in ROI in Image
fname = getTitle();
autoUpdate(false);
setBatchMode(true);
run("Add Slice");
Stack.setSlice(1);
selectWindow(fname);
run("Copy");
getSelectionBounds(x, y, width, height)
newImage("temp", "8-bit white", width, height, 1);
selectWindow("temp");
run("Paste");
doACFsingle("temp");
run("Copy");
selectWindow(fname);
Stack.setSlice(2);
run("Paste");
close("\\Others");
autoUpdate(true);
setBatchMode(false);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "single ACFcenter of ROI in 2-layer stack [4]"{
function doACFsingle(fname){
run("FD Math...", "image1="+fname+" operation=Correlate image2="+fname+" result=Result do");
run("Invert");}
//do ACF in ROI in Image
fname = getTitle();
autoUpdate(false);
setBatchMode(true);
run("Add Slice");
Stack.setSlice(1);
selectWindow(fname);
//roiManager("select",0);
run("Copy");
getSelectionBounds(x, y, width, height)
xc = x;
yc = y;
center = width/2;
corner = center/2;
newImage("temp", "8-bit white", width, height, 1);
selectWindow("temp");
run("Paste");
doACFsingle("temp");
makeRectangle(corner,corner,center,center);
run("Copy");
run("Select None");
selectWindow(fname);
Stack.setSlice(2);
makeRectangle(x+corner,y+corner,center,center);
run("Paste");
close("\\Others");
autoUpdate(true);
setBatchMode(false);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "tiling of ACFs in 2-layer stack [5]"{
function doACFsingle(fname){
run("FD Math...", "image1="+fname+" operation=Correlate image2="+fname+" result=Result do");
}
fname = getTitle();
selectWindow(fname);
run("Add Slice");
Stack.setSlice(1);
//query start point and size
grid_size = 256;
xinit = 0;
yinit = 0;
Dialog.create("x-start");
Dialog.addMessage("x-start coordinates");
Dialog.addNumber("", xinit);
Dialog.show();
xinit = Dialog.getNumber();
Dialog.create("y-start");
Dialog.addMessage("y-start coordinates");
Dialog.addNumber("", yinit);
Dialog.show();
yinit = Dialog.getNumber();
Dialog.create("grid size");
Dialog.addMessage("grid size");
Dialog.addNumber("", grid_size);
Dialog.show();
grid_size = Dialog.getNumber();
xwidth = getWidth();
yheight = getHeight();
nx =floor((xwidth-xinit)/grid_size);
ny =floor((yheight-yinit)/grid_size);
Dialog.create("grids in x direction");
Dialog.addMessage("#y");
Dialog.addNumber("", nx);
Dialog.show();
nx = Dialog.getNumber();
Dialog.create("grids in y direction");
Dialog.addMessage("#y");
Dialog.addNumber("", ny);
Dialog.show();
ny = Dialog.getNumber();
t1=getTime();
selectWindow(fname);
Stack.setSlice(1);
autoUpdate(false);
setBatchMode(true);
newImage("temp", "8-bit white", grid_size, grid_size, 1);
for (i=1; i<=nx; i++){
for (j=1; j<=ny; j++){
selectWindow(fname);
Stack.setSlice(1);
makeRectangle(xinit+(i-1)*grid_size,yinit+(j-1)*grid_size,grid_size,grid_size);
run("Copy");
selectWindow("temp");
run("Paste");
doACFsingle("temp");
run("Copy");
selectWindow(fname);
Stack.setSlice(2);
run("Paste");
close("Result");
}}
close("temp");
selectWindow(fname);
Stack.setSlice(2);
run("Select All")
//run("Invert", "slice");
print(getTime()-t1);
autoUpdate(true);
setBatchMode(false);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "tiling of ACFcenters in 2-layer stack [6]"{
function doACFsingle(fname){
run("FD Math...", "image1="+fname+" operation=Correlate image2="+fname+" result=Result do");
}
fname = getTitle();
selectWindow(fname);
run("Add Slice");
Stack.setSlice(1);
//query start point and size
grid_size = 256;
xinit = 0;
yinit = 0;
Dialog.create("x-start");
Dialog.addMessage("x-start coordinates");
Dialog.addNumber("", xinit);
Dialog.show();
xinit = Dialog.getNumber();
Dialog.create("y-start");
Dialog.addMessage("y-start coordinates");
Dialog.addNumber("", yinit);
Dialog.show();
yinit = Dialog.getNumber();
Dialog.create("grid size");
Dialog.addMessage("grid size");
Dialog.addNumber("", grid_size);
Dialog.show();
grid_size = Dialog.getNumber();
xwidth = getWidth();
yheight = getHeight();
nx =floor((2*(xwidth-xinit)/grid_size)-1);
ny =floor((2*(yheight-yinit)/grid_size)-1);
center = grid_size/2;
corner = center/2;
Dialog.create("grids in x direction");
Dialog.addMessage("#y");
Dialog.addNumber("", nx);
Dialog.show();
nx = Dialog.getNumber();
Dialog.create("grids in y direction");
Dialog.addMessage("#y");
Dialog.addNumber("", ny);
Dialog.show();
ny = Dialog.getNumber();
t1=getTime();
selectWindow(fname);
Stack.setSlice(1);
autoUpdate(false);
setBatchMode(true);
newImage("temp", "8-bit white", grid_size, grid_size, 1);
for (i=1; i<=nx; i++){
for (j=1; j<=ny; j++){
selectWindow(fname);
Stack.setSlice(1);
makeRectangle(xinit+(i-1)*center,yinit+(j-1)*center,grid_size,grid_size);
run("Copy");
selectWindow("temp");
run("Paste");
doACFsingle("temp");
makeRectangle(corner, corner, center, center);
run("Copy");
selectWindow(fname);
Stack.setSlice(2);
makeRectangle(corner+xinit+(i-1)*center,corner+yinit+(j-1)*center,center,center);
run("Paste");
close("Result");
}}
close("temp");
//selectWindow(fname);
//Stack.setSlice(2);
//run("Select All")
//run("Invert", "slice");
print(getTime()-t1);
autoUpdate(true);
setBatchMode(false);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "tiling of ACFcenters in 3-layer stack (scaled) [7]"{
function doACFsingle(fname){
run("FD Math...", "image1="+fname+" operation=Correlate image2="+fname+" result=Result do");
}
//silly thing to get the scaling
info = getInfo();
index1 = indexOf(info, "Resolution: ");
if (index1==-1)
{scale=1; unit = "pixel"; return;}
index2 = indexOf(info, "\n", index1);
line = substring(info, index1+12, index2);
words = split(line, "");
scale = 0+words[0];
unit = words[3];
run("Set Scale...", "distance=1 known=1 pixel=1 unit=pixel");
print("scale="+scale);
fname = getTitle();
selectWindow(fname);
run("Add Slice");
run("Add Slice");
Stack.setSlice(1);
//query start point and size
grid_size = 256;
xinit = 0;
yinit = 0;
Dialog.create("x-start");
Dialog.addMessage("x-start coordinates");
Dialog.addNumber("", xinit);
Dialog.show();
xinit = Dialog.getNumber();
Dialog.create("y-start");
Dialog.addMessage("y-start coordinates");
Dialog.addNumber("", yinit);
Dialog.show();
yinit = Dialog.getNumber();
Dialog.create("grid size");
Dialog.addMessage("grid size");
Dialog.addNumber("", grid_size);
Dialog.show();
grid_size = Dialog.getNumber();
xwidth = getWidth();
yheight = getHeight();
nx =floor((2*(xwidth-xinit)/grid_size)-1);
ny =floor((2*(yheight-yinit)/grid_size)-1);
center = grid_size/2;
corner = center/2;
darea = (center*center)/50;
darea = darea * scale * scale;
Dialog.create("Thresholded ACF size");
Dialog.addMessage("Size of thresholded ACF? \n You can use image units \n default 2% of image area =");
Dialog.addNumber("", darea);
Dialog.show();
darea = Dialog.getNumber();
threshold = (center*center)-darea;
Dialog.create("grids in x direction");
Dialog.addMessage("#y");
Dialog.addNumber("", nx);
Dialog.show();
nx = Dialog.getNumber();
Dialog.create("grids in y direction");
Dialog.addMessage("#y");
Dialog.addNumber("", ny);
Dialog.show();
ny = Dialog.getNumber();
t1=getTime();
selectWindow(fname);
Stack.setSlice(1);
autoUpdate(false);
setBatchMode(true);
newImage("temp", "8-bit white", grid_size, grid_size, 1);
newImage("temp2", "8-bit white", center, center, 1);
for (i=1; i<=nx; i++){
for (j=1; j<=ny; j++){
selectWindow(fname);
Stack.setSlice(1);
makeRectangle(xinit+(i-1)*center,yinit+(j-1)*center,grid_size,grid_size);
run("Copy");
selectWindow("temp");
run("Paste");
doACFsingle("temp");
makeRectangle(corner, corner, center, center);
run("Copy");
selectWindow(fname);
Stack.setSlice(2);
makeRectangle(corner+xinit+(i-1)*center,corner+yinit+(j-1)*center,center,center);
run("Paste");
selectWindow("temp2");
run("Paste");
getHistogram(values, counts, 256);
sum = 0;
index = 0;
for (k =1; k <= 255; k++){
sum = sum+counts[k];
if (sum > threshold && index == 0){
index = k;
}
}
print("index="+index);
setThreshold(0, index);
run("Make Binary", "thresholded remaining black");
run("Select All");
run("Copy");
selectWindow(fname);
Stack.setSlice(3);
makeRectangle(corner+xinit+(i-1)*center,corner+yinit+(j-1)*center,center,center);
run("Paste");
close("Result");
}
}
close("temp");
close("temp2");
run("Set Scale...", "distance="+scale+" known=1 pixel=1 unit="+unit+"");
//selectWindow(fname);
//Stack.setSlice(2);
//run("Select All")
//run("Invert", "slice");
//Stack.setSlice(3);
//run("Select All")
//run("Invert", "slice");
print(getTime()-t1);
autoUpdate(true);
setBatchMode(false);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "tiling of ACFcenters in 3-layer stack (unscaled)"{
function doACFsingle(fname){
run("FD Math...", "image1="+fname+" operation=Correlate image2="+fname+" result=Result do");
}
fname = getTitle();
selectWindow(fname);
run("Add Slice");
run("Add Slice");
Stack.setSlice(1);
//query start point and size
grid_size = 256;
xinit = 0;
yinit = 0;
Dialog.create("x-start");
Dialog.addMessage("x-start coordinates");
Dialog.addNumber("", xinit);
Dialog.show();
xinit = Dialog.getNumber();
Dialog.create("y-start");
Dialog.addMessage("y-start coordinates");
Dialog.addNumber("", yinit);
Dialog.show();
yinit = Dialog.getNumber();
Dialog.create("grid size");
Dialog.addMessage("grid size");
Dialog.addNumber("", grid_size);
Dialog.show();
grid_size = Dialog.getNumber();
xwidth = getWidth();
yheight = getHeight();
nx =floor((2*(xwidth-xinit)/grid_size)-1);
ny =floor((2*(yheight-yinit)/grid_size)-1);
center = grid_size/2;
corner = center/2;
darea = (center*center)/50;
Dialog.create("Thresholded ACF size");
Dialog.addMessage("Size of thresholded ACF? \n You can use pixel units \n default 2% of image area =");
Dialog.addNumber("", darea);
Dialog.show();
darea = Dialog.getNumber();
threshold = (center*center)-darea;
Dialog.create("grids in x direction");
Dialog.addMessage("#y");
Dialog.addNumber("", nx);
Dialog.show();
nx = Dialog.getNumber();
Dialog.create("grids in y direction");
Dialog.addMessage("#y");
Dialog.addNumber("", ny);
Dialog.show();
ny = Dialog.getNumber();
t1=getTime();
selectWindow(fname);
Stack.setSlice(1);
autoUpdate(false);
setBatchMode(true);
newImage("temp", "8-bit white", grid_size, grid_size, 1);
newImage("temp2", "8-bit white", center, center, 1);
for (i=1; i<=nx; i++){
for (j=1; j<=ny; j++){
selectWindow(fname);
Stack.setSlice(1);
makeRectangle(xinit+(i-1)*center,yinit+(j-1)*center,grid_size,grid_size);
run("Copy");
selectWindow("temp");
run("Paste");
doACFsingle("temp");
makeRectangle(corner, corner, center, center);
run("Copy");
selectWindow(fname);
Stack.setSlice(2);
makeRectangle(corner+xinit+(i-1)*center,corner+yinit+(j-1)*center,center,center);
run("Paste");
selectWindow("temp2");
run("Paste");
getHistogram(values, counts, 256);
sum = 0;
index = 0;
for (k =1; k <= 255; k++){
sum = sum+counts[k];
if (sum > threshold && index == 0){
index = k;
}
}
print("index="+index);
setThreshold(0, index);
run("Make Binary", "thresholded remaining black");
run("Select All");
run("Copy");
selectWindow(fname);
Stack.setSlice(3);
makeRectangle(corner+xinit+(i-1)*center,corner+yinit+(j-1)*center,center,center);
run("Paste");
close("Result");
}
}
close("temp");
close("temp2");
//selectWindow(fname);
//Stack.setSlice(2);
//run("Select All")
//run("Invert", "slice");
//Stack.setSlice(3);
//run("Select All")
//run("Invert", "slice");
print(getTime()-t1);
autoUpdate(true);
setBatchMode(false);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "threshold ACF at area (scaled) [s] "{
fname = getTitle();
//silly thing to get the scaling
info = getInfo();
index1 = indexOf(info, "Resolution: ");
if (index1==-1)
{scale=1; unit = "pixel"; return;}
index2 = indexOf(info, "\n", index1);
line = substring(info, index1+12, index2);
words = split(line, "");
scale = 0+words[0];
unit = words[3];
print(scale);
run("Set Scale...", "distance=1 known=1 pixel=1 unit=pixel");
selectWindow(fname);
run("Add Slice");
Stack.setSlice(1);
xwidth = getWidth();
yheight = getHeight();
area = xwidth*yheight;
darea = 21;
Dialog.create("Thresholded ACF size");
Dialog.addMessage("Thresholded ACF size? \n area =");
Dialog.addNumber("", darea);
Dialog.show();
darea = Dialog.getNumber();
print("beforescaling"+darea);
darea = darea * scale * scale;
print("afterscaling"+darea);
threshold = area-darea;
selectWindow(fname);
Stack.setSlice(1);
autoUpdate(false);
setBatchMode(true);
newImage("temp", "8-bit white", xwidth, yheight, 1);
selectWindow(fname);
Stack.setSlice(1);
run("Copy");
selectWindow("temp");
run("Paste");
getHistogram(values, counts, 256);
sum = 0;
index = 0;
for (k =1; k <= 255; k++)
{
sum = sum+counts[k];
if (sum >= threshold && index == 0)
{
index = k;
}
}
setThreshold(0, index);
run("Make Binary", "thresholded remaining black");
selectWindow("temp");
run("Copy");
selectWindow(fname);
Stack.setSlice(2);
run("Paste");
run("Set Scale...", "distance="+scale+" known=1 pixel=1 unit="+unit+"");
close("Result");
}
}
close("temp");
autoUpdate(true);
setBatchMode(false);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "threshold ACF at area (unscaled) [S]"{
fname = getTitle();
selectWindow(fname);
run("Add Slice");
Stack.setSlice(1);
xwidth = getWidth();
yheight = getHeight();
area = xwidth*yheight;
darea = 21;
Dialog.create("Thresholded ACF size");
Dialog.addMessage("Thresholded ACF size? \n area =");
Dialog.addNumber("", darea);
Dialog.show();
darea = Dialog.getNumber();
threshold = area-darea;
selectWindow(fname);
Stack.setSlice(1);
autoUpdate(false);
setBatchMode(true);
newImage("temp", "8-bit white", xwidth, yheight, 1);
selectWindow(fname);
Stack.setSlice(1);
run("Copy");
selectWindow("temp");
run("Paste");
getHistogram(values, counts, 256);
sum = 0;
index = 0;
for (k =1; k <= 255; k++)
{
sum = sum+counts[k];
if (sum >= threshold && index == 0)
{
index = k;
}
}
setThreshold(0, index);
run("Make Binary", "thresholded remaining black");
selectWindow("temp");
run("Copy");
selectWindow(fname);
Stack.setSlice(2);
run("Paste");
close("Result");
}
}
close("temp");
autoUpdate(true);
setBatchMode(false);
}
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------
macro "individual ACFcenters to stack [8]" {
function doACFsingle(fname){
run("FD Math...", "image1="+fname+" operation=Correlate image2="+fname+" result=Result do");
}
fname = getTitle();
selectWindow(fname);
//query start point and size
grid_size = 256;
xinit = 0;
yinit = 0;
Dialog.create("x-start");
Dialog.addMessage("x-start coordinates");
Dialog.addNumber("", xinit);
Dialog.show();
xinit = Dialog.getNumber();
Dialog.create("y-start");
Dialog.addMessage("y-start coordinates");
Dialog.addNumber("", yinit);
Dialog.show();
yinit = Dialog.getNumber();
Dialog.create("grid size");
Dialog.addMessage("grid size");
Dialog.addNumber("", grid_size);
Dialog.show();
grid_size = Dialog.getNumber();
xwidth = getWidth();
yheight = getHeight();
nx =floor((2*(xwidth-xinit)/grid_size)-1);
ny =floor((2*(yheight-yinit)/grid_size)-1);
center = grid_size/2;
corner = center/2;
Dialog.create("grids in x direction");
Dialog.addMessage("#y");
Dialog.addNumber("", nx);
Dialog.show();
nx = Dialog.getNumber();
Dialog.create("grids in y direction");
Dialog.addMessage("#y");
Dialog.addNumber("", ny);
Dialog.show();
ny = Dialog.getNumber();
t1=getTime();
selectWindow(fname);
autoUpdate(false);
setBatchMode(true);
newImage("ACF_stack", "8-bit white", center, center, nx*ny);
newImage("temp", "8-bit white", grid_size, grid_size, 1);
lc = 0;
for (i=1; i<=nx; i++){
for (j=1; j<=ny; j++){
lc = lc+1; //counter
selectWindow(fname);
makeRectangle(xinit+(i-1)*center,yinit+(j-1)*center,grid_size,grid_size);
run("Copy");
selectWindow("temp");
run("Paste");
doACFsingle("temp");
makeRectangle(corner, corner, center, center);
run("Copy");