RGB Profiles Tool

[Kolb, Thorsten]

Hello,

I am using the RGB Profiles Tool (attached at the end) to plot line profiles of microscope Images. The tool works great, but I would like to be able to get the profiles updated when I draw a new line without having to load the macro again.

Unfortunately I am not very familiar with coding macros for ImageJ...

Could somebody please help me with adding the code required for adding this function?


Thanks in advance!

Thorsten


---

// RGB Profiles Tool
//
// This is a tool macro that draws red, green and blue
// line profiles from an RGB image on the same plot.

var listResults=true;

macro "RGB Profiles Tool  - Cf00D02D13D14D24D25D26D27D38D46D47D56D65D75D85D95Da5Db5Dc5Dc6Dd6Dd7Dd8De7De8Df6Df7C00fD09D1aD1bD2cD2dD2eD3eD3fD4dD4eD5cD6bD7bD7cD8bD9aDabDbaDcaDdbDdcDddDecDedDfbC0f0D06D07D17D18D29D2aD2bD3bD3cD4aD4bD59D5aD68D69D79D88D89D98Da8Db8Dc7Dc8Dd9DdaDeaDebDf9"{
if (bitDepth!=24)
exit("RGB image required");
getCursorLoc(x, y, z, flags);
xstart = x; ystart = y;
x2=x; y2=y;
while (true) {
getCursorLoc(x, y, z, flags);
if (flags&16==0) {
setRGBWeights(1,0,0);r=getProfile();
setRGBWeights(0,1,0);g=getProfile();
setRGBWeights(0,0,1);b=getProfile();
Plot.create("RGB Profiles","distance","value");
Plot.setLimits(0,r.length-1,0,getMax(r,g,b));
Plot.setColor("red");
Plot.add("line",r);
Plot.setColor("green");
Plot.add("line",g);
Plot.setColor("blue");
Plot.add("line",b);
Plot.update();
if (listResults==true) list(r,g,b);
exit;
}
if (x!=x2 || y!=y2) makeLine(xstart, ystart, x, y);
x2=x; y2=y;
wait(10);
}
}


//Plot.update();

macro "RGB Profiles Tool Options" {
Dialog.create("RGB Profiles Options");
Dialog.addCheckbox("List Results",listResults);
Dialog.show();
listResults=Dialog.getCheckbox();
}

function getMax(a,b,c) {
// returns the maximum value of three arrays of the same size
max=a[0];
for (i=0;i<a.length;i++) {
max=maxOf(max,a[i]);
max=maxOf(max,b[i]);
max=maxOf(max,c[i]);
}
return max;
}

function list(a,b,c) {
if (isOpen("Results")) {selectWindow("Results"); run("Close");}
for (i=0; i<a.length; i++){
setResult("Red", i, a[i]);
setResult("Green", i, b[i]);
setResult("Blue", i, c[i]);
}
function updateResults() {};

}

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[Tiago Ferreira-2]

Hi Thorsten,

On Jun 4, 2015, at 08:56, Kolb, Thorsten <[hidden email]> wrote:
> I am using the RGB Profiles Tool (attached at the end) to plot line profiles of microscope
> Images. The tool works great, but I would like to be able to get the profiles updated when
> I draw a newline without having to load the macro again.

You could use Multichannel_Plot_Profile.bsh, a BAR[1] script:

In Fiji, subscribe to the BAR update site[2], then use BAR>Analysis>Multichannel
Plot Profile in e.g., the confocal-series image (File>Open Samples>).
If you are not using Fiji, you can download it directly from its documentation
page[3].

BARs are a collection of scripts that extend IJ built-in commands. Typically,
they are designed to accomplish one task only, so you will find variants of
the above script that perform multichannel live analysis of Z/T axis, or smooth
sampled data. You will find those in the respective menu[4].

-tiago

[1] https://github.com/tferr/Scripts#ij-bar
[2] http://fiji.sc/BAR#Installation
[3] https://github.com/tferr/Scripts/tree/master/Analysis#multichannel-plot-profile
[4] https://github.com/tferr/Scripts#analysis

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