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148 changes: 148 additions & 0 deletions AutoInstall/Line Profile Action Tool.ijm
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macro "Line Profile Action Tool - 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"{
// macro to make line plots
// will select different colours to plot
// handles 8, 16 and 32 bit images as well as maximal 7 channels

// version 4.1; Solved problem with x-coordinates in scaled images.
// version 4.2; Thanks to Michael Epping (mailinglist 15-05-2013) the X-scale on
// the scaled plot is also drawn corectly.
// version 4.3; The plot is now scaled depending on the channels selected by the user.
// The colour for each channel is first detected followed by selection of the
// colours by the user instead of the user has to select channel numbers.

// Kees Straatman, University of Leicester, 19 January 2014

setTool("line");
if (isOpen("ROI Manager")) {
selectWindow("ROI Manager");
run("Close");
}
inv = false; // To check if LUT is inverted
p = 0; //Counter for presence of plot
intensityBottom=0;
color = "black";
getVoxelSize(vw, vh, vd, unit);

// Check that there is a line selection
do{
type = selectionType();
if (type!=5){
title="Warning";
msg="The macro needs a line selection.\nMake a line selection and click \"OK\"";
waitForUser(title, msg);
}
wait(100);
}while(type!=5);
getLine(x1, y1, x2, y2, lineWidth);

// Parameters for the plot
dx = (x2-x1)*vw;
dy = (y2-y1)*vh;
maxT=0;
minT=100000000;
Stack.getDimensions(width, height, channels, slices, frames);

if (bitDepth==24){
if (nSlices>1){
roiManager("Add");
run("Make Composite");
wait(100); // Line is sometimes not transfered to the new image
setVoxelSize(vw, vh, vd, unit);
roiManager("select", 0);
//wait(100);
selectWindow("ROI Manager");
run("Close");
}else{
run("Make Composite");
}
}

Stack.getDimensions(width, height, channels, slices, frames); // need to repeat because of creation of new composite
channel = newArray(channels);
color=newArray(channels+1);

// to allow single channel profile in color
for (i=0; i<channels;i++)
channel[i]=true;

for (i=1; i<=channels; i++){
// Solve problem with inverted images (blobs)
if (is("Inverting LUT")){
run("Invert LUT");
inv=true;
}
if (channels>1) Stack.setChannel(i);
getLut(reds, greens, blues);
if ((reds[i]==i)&&(greens[i]==0)&&(blues[i]==0)) color[i] = "red";
if ((reds[i]==0)&&(greens[i]==i)&&(blues[i]==0)) color[i] = "green";
if ((reds[i]==0)&&(greens[i]==0)&&(blues[i]==i)) color[i] = "blue";
if ((reds[i]==0)&&(greens[i]==i)&&(blues[i]==i)) color[i] = "cyan";
if ((reds[i]==i)&&(greens[i]==0)&&(blues[i]==i)) color[i] = "magenta";
if ((reds[i]==i)&&(greens[i]==1)&&(blues[i]==0)) color[i] = "yellow";
if ((reds[i]==i)&&(greens[i]==i)&&(blues[i]==i)) color[i] = "black";
}
if (inv) run("Invert LUT"); // reset inverted image

// Select channels to plot
if (channels > 1){
Dialog.create("channels");
Dialog.addMessage("Which channels do you want to plot?");
for (i=0; i<channels;i++){
Dialog.addCheckbox(color[i+1], true);
}
Dialog.show();
setBatchMode(true);
for (i=0; i<channels;i++){
channel[i] = Dialog.getCheckbox();

}
}

// Collect data for minimal and maximal values of the selected channels for the plot
if ((Stack.isHyperstack)||(is("composite"))){
Stack.getDimensions(width, height, channels, slices, frames); // need to repeat because of creation of new composite
for (i=1; i<=channels;i++){
if(channel[i-1]==true){
Stack.setChannel(i);
profile = getProfile();
for (j=0; j<profile.length; j++){
if (maxT<profile[j]) maxT=profile[j];
if(profile[j]<minT) minT=profile[j];
}
}
}
}else{
channels = 1;
profile = getProfile();
for (j=0; j<profile.length; j++){
if (maxT<profile[j]) maxT=profile[j];
if(profile[j]<minT) minT=profile[j];
}
}
intensityTop=maxT;
intensityBottom=minT;

// Check if channel is selected.
for (i=1; i<=channels; i++){
if (channels>1) Stack.setChannel(i);
if(channel[i-1]==true){

// Plot different colours
if (p==0){
profile=getProfile();
Plot.create("multi Channel Plot", "Distance("+unit+")", "Intensity");
Plot.setLimits(0,sqrt(dx*dx+dy*dy),intensityBottom,intensityTop);
p=1;
}

// Scale the profiles for correct x-coordinates
run("Plot Profile");
Plot.getValues(x, y);
close();
Plot.setColor(color[i]);
Plot.add("line",x,y);
}
}

}

148 changes: 148 additions & 0 deletions AutoInstall/Plot_Multicolor4.3.ijm
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Original file line number Diff line number Diff line change
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// macro to make line plots
// will select different colours to plot
// handles 8, 16 and 32 bit images as well as maximal 7 channels

// version 4.1; Solved problem with x-coordinates in scaled images.
// version 4.2; Thanks to Michael Epping (mailinglist 15-05-2013) the X-scale on
// the scaled plot is also drawn correctly.
// version 4.3; The plot is now scaled depending on the channels selected by the user.
// The colour for each channel is first detected followed by selection of the
// colours by the user instead of the user has to select channel numbers.

// Kees Straatman, University of Leicester, 19 January 2014

macro plot_multicolor{
setTool("line");
if (isOpen("ROI Manager")) {
selectWindow("ROI Manager");
run("Close");
}
inv = false; // To check if LUT is inverted
p = 0; //Counter for presence of plot
intensityBottom=0;
color = "black";
getVoxelSize(vw, vh, vd, unit);

// Check that there is a line selection
do{
type = selectionType();
if (type!=5){
title="Warning";
msg="The macro needs a line selection.\nMake a line selection and click \"OK\"";
waitForUser(title, msg);
}
wait(100);
}while(type!=5);
getLine(x1, y1, x2, y2, lineWidth);

// Parameters for the plot
dx = (x2-x1)*vw;
dy = (y2-y1)*vh;
maxT=0;
minT=100000000;
Stack.getDimensions(width, height, channels, slices, frames);

if (bitDepth==24){
if (nSlices>1){
roiManager("Add");
run("Make Composite");
wait(100); // Line is sometimes not transfered to the new image
setVoxelSize(vw, vh, vd, unit);
roiManager("select", 0);
//wait(100);
selectWindow("ROI Manager");
run("Close");
}else{
run("Make Composite");
}
}

Stack.getDimensions(width, height, channels, slices, frames); // need to repeat because of creation of new composite
channel = newArray(channels);
color=newArray(channels+1);

// to allow single channel profile in color
for (i=0; i<channels;i++)
channel[i]=true;

for (i=1; i<=channels; i++){
// Solve problem with inverted images (blobs)
if (is("Inverting LUT")){
run("Invert LUT");
inv=true;
}
if (channels>1) Stack.setChannel(i);
getLut(reds, greens, blues);
if ((reds[i]==i)&&(greens[i]==0)&&(blues[i]==0)) color[i] = "red";
if ((reds[i]==0)&&(greens[i]==i)&&(blues[i]==0)) color[i] = "green";
if ((reds[i]==0)&&(greens[i]==0)&&(blues[i]==i)) color[i] = "blue";
if ((reds[i]==0)&&(greens[i]==i)&&(blues[i]==i)) color[i] = "cyan";
if ((reds[i]==i)&&(greens[i]==0)&&(blues[i]==i)) color[i] = "magenta";
if ((reds[i]==i)&&(greens[i]==1)&&(blues[i]==0)) color[i] = "yellow";
if ((reds[i]==i)&&(greens[i]==i)&&(blues[i]==i)) color[i] = "gray";
}
if (inv) run("Invert LUT"); // reset inverted image

// Select channels to plot
if (channels > 1){
Dialog.create("channels");
Dialog.addMessage("Which channels do you want to plot?");
for (i=0; i<channels;i++){
Dialog.addCheckbox(color[i+1], true);
}
Dialog.show();
setBatchMode(true);
for (i=0; i<channels;i++){
channel[i] = Dialog.getCheckbox();

}
}

// Collect data for minimal and maximal values of the selected channels for the plot
if ((Stack.isHyperstack)||(is("composite"))){
Stack.getDimensions(width, height, channels, slices, frames); // need to repeat because of creation of new composite
for (i=1; i<=channels;i++){
if(channel[i-1]==true){
Stack.setChannel(i);
profile = getProfile();
for (j=0; j<profile.length; j++){
if (maxT<profile[j]) maxT=profile[j];
if(profile[j]<minT) minT=profile[j];
}
}
}
}else{
channels = 1;
profile = getProfile();
for (j=0; j<profile.length; j++){
if (maxT<profile[j]) maxT=profile[j];
if(profile[j]<minT) minT=profile[j];
}
}
intensityTop=maxT;
intensityBottom=minT;

// Check if channel is selected.
for (i=1; i<=channels; i++){
if (channels>1) Stack.setChannel(i);
if(channel[i-1]==true){

// Plot different colours
if (p==0){
profile=getProfile();
Plot.create("multi Channel Plot", "Distance("+unit+")", "Intensity");
Plot.setLimits(0,sqrt(dx*dx+dy*dy),intensityBottom,intensityTop);
p=1;
}

// Scale the profiles for correct x-coordinates
run("Plot Profile");
Plot.getValues(x, y);
close();
Plot.setColor(color[i]);
Plot.add("line",x,y);
}
}

}

64 changes: 64 additions & 0 deletions README.md
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Expand Up @@ -18,6 +18,70 @@ To run the macro a single time open an image and via Plugins > Macros > Run... s

Download and save the "Line Profile Action Tool" as described above using the name Line Profile Action Tool.txt. When you install this tool via Plugins > Macros > Install .. an icon will be added to the ImageJ/Fiji tool bar. Clicking this icon will execute the macro code.

## Auto installation of the tool during Fiji startup.
Clone repository or download code.
Copy the AutoInstall folder to the Fiji/macro directory.
Modify the StartupMacros.fiji.ijm script in the macro directory in the following way:

Originally the sctipt contain this autostart past:
```
macro "AutoRun" {
// run all the .ijm scripts provided in macros/AutoRun/
autoRunDirectory = getDirectory("imagej") + "/macros/AutoRun/";
if (File.isDirectory(autoRunDirectory)) {
list = getFileList(autoRunDirectory);
// make sure startup order is consistent
Array.sort(list);
for (i = 0; i < list.length; i++) {
if (endsWith(list[i], ".ijm")) {
runMacro(autoRunDirectory + list[i]);
}
}
}
}
```
You can comment or delere it and replace it with this:

```
macro "AutoRun" {
// ----- 1) Run all .ijm scripts from macros/AutoRun/ -----
autoRunDirectory = getDirectory("imagej")
+ "macros" + File.separator
+ "AutoRun" + File.separator;

if (File.isDirectory(autoRunDirectory)) {
list = getFileList(autoRunDirectory);
Array.sort(list); // consistent order

for (i = 0; i < list.length; i++) {
if (endsWith(list[i], ".ijm")) {
runMacro(autoRunDirectory + list[i]);
}
}
}

// ----- 2) Install all .ijm macros from macros/AutoInstall/ -----
autoInstallDirectory = getDirectory("imagej")
+ "macros" + File.separator
+ "AutoInstall" + File.separator;

if (File.isDirectory(autoInstallDirectory)) {
installList = getFileList(autoInstallDirectory);
Array.sort(installList);

for (i = 0; i < installList.length; i++) {
if (endsWith(installList[i], ".ijm")) {
// Only install, do NOT run
fullPath = autoInstallDirectory + installList[i];
run("Install...", "install=[" + fullPath + "]");
}
}
}
}
```
Then the tool shall load on the startup.


## Disclaimer

All the macros published on this repository can be used at your own risk. Although I did my best to ensure that they run as intended, there may be bugs, not expected use or changes to the ImageJ code that results in unexpected behaviour. If you notice a problem with any of the macros please let me know and I can try to solve the problem.
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