diff --git a/BIOP_Channel_Tools.ijm b/BIOP_Channel_Tools.ijm
index daa8f2c..f9c0964 100644
--- a/BIOP_Channel_Tools.ijm
+++ b/BIOP_Channel_Tools.ijm
@@ -1,774 +1,775 @@
// Install the BIOP Library
call("BIOP_LibInstaller.installLibrary", "BIOP"+File.separator+"BIOPLib.ijm");
// Name ActionBar
bar_name = "BIOP Channel Tools";
bar_file = replace(bar_name, " ", "_")+".ijm";
bar_jar = replace(bar_name, " ", "_")+".jar";
runFrom = "jar:file:BIOP/"+bar_jar+"!/"+bar_file;
//////////////////////////////////////////////////////////////////////////////////////////////
// The line below is for debugging. Place this VSI file in the ActionBar folder within Plugins
//////////////////////////////////////////////////////////////////////////////////////////////
//runFrom = "/plugins/ActionBar/Debug/"+bar_file;
if(isOpen(bar_name)) {
run("Close AB", bar_name);
}
run("Action Bar",runFrom);
exit();
//Start of ActionBar
<codeLibrary>
function toolName() {
return "Channel Tools";
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// specific library
function channelsLUTSelection(){
run("Make Composite", "display=Color");
getDimensions(width, height, channels, slices, frames);
defaultsArray = newArray("Red","Green","Blue","Grays","Cyan","Magenta","Yellow","Fire");
names = newArray(0);
types = newArray(0);
defaults = newArray(0);
for (i=0;i<channels;i++){
names = Array.concat(names, "color channel "+(i+1)+" using LUT");
types = Array.concat(types,"lut");
defaults = Array.concat(defaults, defaultsArray[i]);
}
promptParameters(names, types, defaults);
}
function channelsLUTApply(){
run("Make Composite", "display=Color");
+ Stack.setDisplayMode("color");
getDimensions(width, height, channels, slices, frames);
colorFirstChannel = getData("color channel 1 using LUT");
if (colorFirstChannel ==""){
noLutRecorded = true;
}else{
noLutRecorded = false;
}
if( noLutRecorded ){ //if no LUT slected
showMessage("Please select LUT for channels");
}else{ //get from the record
for (i=0;i<channels;i++){
chNbr=(i+1);
recColorTemp = getData("color channel "+chNbr+" using LUT");
if(nSlices>1) {
Stack.setChannel(chNbr);
}
run(recColorTemp);
}
}
}
function brightnessAndContrastSetting(){
getDimensions(width, height, channels, slices, frames);
for (i=0;i<channels;i++){
chNbr=(i+1);
if(nSlices>1) {
Stack.setChannel(chNbr);
}
run("Brightness/Contrast...");
waitForUser(" Set B&C for channel "+chNbr+"\n Please set Min and Max \n and press Ok");
getMinAndMax(min, max);
setData("min ch"+chNbr,min);
setData("max ch"+chNbr,max);
}
}
function brightnessAndContrastSettingApply(){
getDimensions(width, height, channels, slices, frames);
for (i=0;i<channels;i++){
chNbr=(i+1);
if(nSlices>1) {
Stack.setChannel(chNbr);
}
min = getData("min ch"+chNbr);
max = getData("max ch"+chNbr);
setMinAndMax(min, max);
}
}
//montage options
function montageOptions(){
// Get dimensions
getDimensions(x,y,c,z,t);
// Check if ROIS
nRois = roiManager("Count");
useScale = getBoolD("Use Scalebar", true);
// Scale bar position
scalePos = getDataD("ScaleBar Position", "Lower Right");
// scale bar size
scaleLength = getDataD("ScaleBar Length", 100);
// scalebar height
scaleHeight = getDataD("ScaleBar height", 5);
// Which Position gets the scalebar
atImage = getDataD("Scalebar At", "");
// nrows ncols
mRows = getDataD("Montage Rows", "As Row");
mCols = getDataD("Montage Cols", 1);
// position of composite
cPos = getDataD("Channel Merge Position", "First");
isIgnore = getBoolD("Ignore LUTs except for Merged", false);
advMon = getDataD("Advanced Montage", "");
// border size
bSize = getDataD("Montage Border", 0);
zSlices = getDataD("Z Slices", "");
// Image Legend
fontSize = getDataD("Font Size", 14);
chanNames = getDataD("Channel Names", "");
position = getDataD("Legend Position", "bottom left");
slice = getDataD("Legend Montage Position", 1);
// ROIs
isShowRois = getBoolD("Display ROIs", false);
roiOrder = getDataD("ROI Order","");
roiColors = getDataD("ROI Colors","");
// border color
rowChoice= newArray("As Row", "1","2", "3", "4", "5", "6");
colChoice= newArray("As Column","1", "2", "3", "4", "5", "6");
scalePoses=newArray("Lower Right", "Lower Left", "Upper Right", "Upper Left");
imgPos=newArray("First", "Last");
positions = newArray("top left", "top right", "bottom left", "bottom right");
Dialog.create("Montage Options");
Dialog.addCheckbox("Use Scalebar", useScale);
Dialog.addChoice("Scalebar Position", scalePoses, scalePos);
Dialog.addNumber("Scalebar Length", scaleLength, 0, 5, "um");
Dialog.addNumber("Scalebar Height", scaleHeight, 0, 5, "px");
Dialog.addString("Scalebar At Image", atImage);
Dialog.addChoice("Montage Rows", rowChoice, mRows);
Dialog.addChoice("Montage Columns", colChoice, mCols);
Dialog.addChoice("Merged Image Position", imgPos, cPos);
Dialog.addCheckbox("Ignore LUTs except for Merged", isIgnore);
Dialog.addString("Advanced Montage", advMon);
Dialog.addNumber("Montage Border", bSize,0,5,"px");
if (z > 1) {
Dialog.addMessage("Image is Z Stack (nZ = "+z+")\nLeave blank to do all slices");
Dialog.addString("Choose slice range for MIP", zSlices);
}
Dialog.addMessage("Montage Lengend");
Dialog.addString("Names for the Channels", chanNames);
Dialog.addNumber("Font Size", fontSize);
Dialog.addChoice("Legend Position", positions, position);
Dialog.addNumber("Legend At Image", slice);
//ROIS
if(nRois > 0) {
Dialog.addMessage("There are "+nRois+" ROIs");
Dialog.addCheckbox("Show ROIs on Montage?", isShowRois);
Dialog.addString("ROI Order", roiOrder);
Dialog.addString("ROI Colors", roiColors);
}
Dialog.show();
// Scale bar position
useScale = Dialog.getCheckbox();
scalePos = Dialog.getChoice();
scaleLen = Dialog.getNumber();
scaleHei = Dialog.getNumber();
atImage = Dialog.getString();
mRows = Dialog.getChoice();
mCols = Dialog.getChoice();
cPos = Dialog.getChoice();
isIgnore = Dialog.getCheckbox();
advMon = Dialog.getString();
bSize = Dialog.getNumber();
if (z > 1) {
zSlices = Dialog.getString();
} else {
zSlices = "None";
}
chanNames= Dialog.getString();
fontSize = Dialog.getNumber();
position = Dialog.getChoice();
slice = Dialog.getNumber();
//ROIS
if(nRois > 0) {
isShowRois = Dialog.getCheckbox();
roiOrder = Dialog.getString();
roiColors = Dialog.getString();
}
setBool("Use Scalebar", useScale);
setData("ScaleBar Position", scalePos);
setData("ScaleBar Length", scaleLen);
setData("ScaleBar Height", scaleHei);
setData("Scalebar At", atImage);
setData("Montage Rows", mRows);
setData("Montage Cols", mCols);
setData("Channel Merge Position", cPos);
setBool("Ignore LUTs except for Merged", isIgnore);
setData("Advanced Montage", advMon);
setData("Montage Border", bSize);
setData("Z Slices", zSlices);
setData("Font Size", fontSize);
setData("Channel Names", chanNames);
setData("Legend Position", position);
setData("Legend Montage Position", slice);
setBool("Display ROIs",isShowRois);
setData("ROI Order",roiOrder);
setData("ROI Colors",roiColors);
}
function montageApply(){
// Use scalebar
useScale = getBoolD("Use Scalebar", true);
// Scale bar position
scalePos = getData("ScaleBar Position");
// scale bar size
scaleLength = getData("ScaleBar Length");
// scalebar height
scaleHeight = getData("ScaleBar Height");
// nrows ncols
mRows = getData("Montage Rows");
mCols = getData("Montage Cols");
// position of composite
cPos = getData("Channel Merge Position");
// border size
bSize = getData("Montage Border");
//Ignore LUT colors and keep gray
isIgnore = getBoolD("Ignore LUTs except for Merged", false);
// border color
bColor = getData("Montage Border Color");
advMon = getData("Advanced Montage");
atImage = getData("Scalebar At");
zSlices = getData("Z Slices");
if(scalePos == "") {
showMessage("Montage Settings not set.");
exit();
}
ori = getTitle();
// Get LUTS
Stack.getDimensions(dx,dy,dc,dz,dt);
r = newArray(dc);
g = newArray(dc);
b = newArray(dc);
for(ch=0; ch<dc;ch++) {
Stack.setPosition(ch+1,1,1);
getLut(reds, greens, blues);
r[ch] = reds[255];
g[ch] = greens[255];
b[ch] = blues[255];
}
if(zSlices != "None" && zSlices != "") {
zds = split(zSlices,"-");
if ( lengthOf(zds) == 2) {
zStart = parseInt(zds[0]);
zStop = parseInt(zds[1]);
} else {
zStart = parseInt(zSlices);
zStop = zStart;
}
run("Z Project...", "start="+zStart+" stop="+zStop+" projection=[Max Intensity]");
rename(ori+" Slice_"+zSlices);
} else if (zSlices == "") {
run("Z Project...", "projection=[Max Intensity]");
rename(ori+" Slice_All");
}
ori = getTitle();
if (advMon != "") {
run("Make Composite", "display=Composite");
run("Duplicate...", " duplicate channels");
name = getTitle();
run("Split Channels");
// Get the number of separate images we need to create
monImages = split(advMon, ", ");
finalImages = newArray(lengthOf(monImages));
c = monImages.length-1;
for(i=0; i< monImages.length; i++) {
channels = split(monImages[i], "+");
str = "";
for (ch=0; ch<channels.length; ch++) {
str += "c"+(ch+1)+"=[C"+channels[ch]+"-"+name+"] ";
}
for (k=ch-1;k<7;k++) {
str += "c"+(k+1)+"=[*None*] ";
}
//print("Position "+(i+1)+"String: "+str);
if(channels.length>1) {
run("Merge Channels...", str+"create keep");
} else {
selectImage("C"+monImages[i]+"-"+name);
run("Duplicate...", "title=[temp]");
}
run("RGB Color");
rename("Position "+(i+1));
finalImages[i] = "Position "+(i+1);
}
for(i=1; i< monImages.length; i++) {
// Make Montage
selectImage(finalImages[i]);
run("Copy");
close();
selectImage(finalImages[0]);
run("Add Slice");
run("Paste");
}
} else {
getDimensions(x,y,c,z,t);
Stack.setDisplayMode("composite");
name = getTitle();
run("Duplicate...", " duplicate channels");
name2 = getTitle();
// Make RGB
run("Stack to RGB");
rgbName = getTitle();
//Split the other images
selectImage(name2);
run("Split Channels");
//Make each an RGB image
RGBnames = newArray(c);
for (i=1;i<=c; i++) {
if (cPos == "First") {
k = i;
} else {
k=c-i+1;
}
selectImage("C"+k+"-"+name2);
if(isIgnore) {
getMinAndMax(min, max);
run ("Grays");
setMinAndMax(min, max);
}
run("RGB Color");
run("Copy");
close();
selectImage(rgbName);
run("Add Slice");
run("Paste");
}
// Make the RGB first or last
if (cPos == "Last") {
run("Reverse");
}
}
//Set the scale
if (useScale) {
if (atImage=="") {
run("Scale Bar...", "width="+scaleLength+" height="+scaleHeight+" font=9 color=White background=None location=["+scalePos+"] bold hide");
} else {
setSlice(parseInt(atImage));
run("Scale Bar...", "width="+scaleLength+" height="+scaleHeight+" font=9 color=White background=None location=["+scalePos+"] bold hide");
}
}
// If there are channel names, add them
channelNames = getData("Channel Names");
fontSize = parseInt(getData("Font Size"));
position = getData("Legend Position");
slice = getData("Legend Montage Position");
if(channelNames != "") {
nameChannels(channelNames, fontSize, r,g,b, slice, position);
}
// Here we have a stack and maybe some ROIs exist in the ROI manager
dealWithRois();
if(nSlices >1) {
if (mRows == "As Row") {
run("Make Montage...", "columns="+(c+1)+" rows=1 scale=1.0 border="+bSize+" use");
} else if (mCols == "As Column") {
run("Make Montage...", "columns=1 rows="+(c+1)+" scale=1.0 border="+bSize+" use");
} else {
// Assemble the stack for
run("Make Montage...", "columns="+mCols+" rows="+mRows+" scale=1.0 border="+bSize+" use");
}
}
rename(ori+"_Montage");
selectWindow(ori+"_Montage");
}
function dealWithRois() {
name = getTitle();
// Right now we have the montage and we want to see if we put some ROIs in there
isShowRois = getBoolD("Display ROIs", false);
if (!isShowRois) return;
getDimensions(x,y,c,z,t);
// Work on the Rois
roiOrder = split(getDataD("ROI Order" ,""),",");
roiColors = split(getDataD("ROI Colors",""),",");
roiWidth = getDataD("ROI Width" ,2);
roiIdx = 0;
for(i=0; i<roiOrder.length; i++) {
selectImage(name);
if(roiOrder[i] != "") {
roiManager("Select", roiOrder[i]);
Roi.setStrokeWidth(roiWidth);
Roi.setStrokeColor(roiColors[i]);
setSlice(i+1);
run("Add Selection...");
roiIdx++;
}
}
run("Flatten", "stack");
}
function getLargestString(stringArray) {
maxLen = -1;
for(i=0; i<stringArray.length; i++) {
if(lengthOf(stringArray[i]) > maxLen) {
maxLen = lengthOf(stringArray[i]);
largest = stringArray[i];
}
}
return largest;
}
function nameChannels(channelNames, fontSize, r,g,b, slice, position) {
padding=5;
// work in the right position
setSlice(slice);
// Width and height of the image
height = getHeight();
width = getWidth();
// Find dimensions of legend
// Split Channel names
channels = split(channelNames, ",");
setFont("SansSerif", fontSize, "bold");
largestS = getLargestString(channels);
boxWidth = getStringWidth(largestS)+2*padding;
boxHeight = (fontSize+1)*channels.length+2*padding;
// Get the position of the legend
thePos = split(position, " ");
if (thePos[0] == "top") {
posy = 0;
} else {
posy = height - boxHeight;
}
if (thePos[1] == "left") {
posx = 0;
} else {
posx = width - boxWidth;
}
// Create a box around the fonts
setColor(128,128,128);
fillRect(posx, posy, boxWidth, boxHeight);
// Make the text the right color
textString = channels[0];
for(i=0; i<channels.length;i++) {
setColor(r[i]-25,g[i]-25,b[i]-25);
textString= channels[i];
posy += fontSize+1;
drawString(textString, posx+padding, posy+padding);
}
}
</codeLibrary>
<text><html><font size=1 color=#66666f>
<text><html><font size=3 color=#66666f> Parameters
<line>
<button>
label=Save Parameters
icon=noicon
arg=<macro>
saveParameters();
</macro>
<button>
label=Load Parameters
icon=noicon
arg=<macro>
loadParameters();
</macro>
</line>
<text><html><font size=1 color=#66666f>
<text><html><font size=3 color=#66666f> Lookup Table Modification
<line>
<button>
label= Channels LUT Selection
icon=noicon
arg=<macro>
channelsLUTSelection();
</macro>
</line>
<line>
<button>
label= Apply to Image
icon=noicon
arg=<macro>
channelsLUTApply();
</macro>
<button>
label= Apply To Folder...
icon=noicon
arg=<macro>
dir = getDirectory("Please , select a folder containing images"); //get the folder
file = getFileList(dir);
savingDir = dir+"saving_selectedLUT"+File.separator;
File.makeDirectory(savingDir);
for (i=0; i<lengthOf(file); i++) {
if (isImage(file[i])){
open(dir+file[i]); // open the image
fileNameNoExt = File.nameWithoutExtension; // get the file name without the extension
channelsLUTApply();
saveAs("Tiff", savingDir+fileNameNoExt+"_LUT.tif"); // save the file
run("Close All"); // Close the image before going to the next one
}
}
</macro>
</line>
<text><html><font size=1 color=#66666f>
<text><html><font size=3 color=#66666f> Brightness & Contrast Modification
<line>
<button>
label= B&C Selection
icon=noicon
arg=<macro>
brightnessAndContrastSetting();
</macro>
</line>
<line>
<button>
label= Apply to Image
icon=noicon
arg=<macro>
brightnessAndContrastSettingApply();
</macro>
<button>
label= Apply To Folder...
icon=noicon
arg=<macro>
dir = getDirectory("Please , select a folder containing images"); //get the folder
file = getFileList(dir);
savingDir = dir+"saving_selectedBC"+File.separator;
File.makeDirectory(savingDir);
for (i=0; i<lengthOf(file); i++) {
if (isImage(file[i])){
open(dir+file[i]); // open the image
fileNameNoExt = File.nameWithoutExtension; // get the file name without the extension
brightnessAndContrastSettingApply();
saveAs("Tiff", savingDir+fileNameNoExt+"_BC.tif"); // save the file
run("Close All"); // Close the image before going to the next one
}
}
</macro>
</line>
<text><html><font size=1 color=#66666f>
<text><html><font size=3 color=#66666f> Montage Settings
<line>
<button>
label= Montage Options
icon=noicon
arg=<macro>
montageOptions();
</macro>
</line>
<line>
<button>
label= Apply to Image
icon=noicon
arg=<macro>
setBatchMode(true);
montageApply();
setBatchMode(false);
</macro>
<button>
label= Apply To Folder...
icon=noicon
arg=<macro>
dir = getDirectory("Please , select a folder containing images"); //get the folder
file = getFileList(dir);
savingDir = dir+"saving_montage"+File.separator;
File.makeDirectory(savingDir);
for (i=0; i<lengthOf(file); i++) {
if (isImage(file[i])){
open(dir+file[i]); // open the image
fileNameNoExt = File.nameWithoutExtension; // get the file name without the extension
montageApply();
saveAs("Tiff", savingDir+fileNameNoExt+"_Montage.tif"); // save the file
run("Close All"); // Close the image before going to the next one
}
}
</macro>
</line>
<text><html><font size=1 color=#66666f>
<text><html><font size=2.5 color=#66666f>All at once...
<line>
<button>
label= ... on the current image
icon=noicon
arg=<macro>
setBatchMode(true);
checkLUT = getData("color channel 1 using LUT");
checkBC = getData("min ch1");
checkMontage = getData("Channel Merge Position");
//Check process to do
if(checkLUT!="") {
channelsLUTApply(); // action to perform, HERE!
}
if(checkBC!="") {
brightnessAndContrastSettingApply();
}
if(checkMontage!="") {
montageApply();
}
setBatchMode(false);
</macro>
<button>
label= ... on a folder
icon=noicon
arg=<macro>
dir = getDirectory("Please , select a folder containing images"); //get the folder
setBatchMode(true);
file = getFileList(dir);
savingDir = dir+"Processed"+File.separator;
File.makeDirectory(savingDir);
checkLUT = getData("color channel 1 using LUT");
checkBC = getData("min ch1");
checkMontage = getData("Channel Merge Position");
for (i=0; i<lengthOf(file); i++) {
if (isImage(file[i])){
open(dir+file[i]); // open the image
fileNameNoExt = File.nameWithoutExtension; // get the file name without the extension
process="";
//Check process to do
if(checkLUT!="") {
process+="_LUT";
channelsLUTApply(); // action to perform, HERE!
}
if(checkBC!="") {
process+="_BC";
brightnessAndContrastSettingApply();
}
if(checkMontage!="") {
process+="_Montage";
montageApply();
}
//print(savingDir+fileNameNoExt+process+".tif");
saveAs("Tiff", savingDir+fileNameNoExt+process+".tif"); // save the file
run("Close All"); // Close the image before going to the next one
}
setBatchMode(false);
}
</macro>
</line>
<text><html><font size=2.5 color=#66666f>Help
<line>
<button>
label=Infos & Contact
icon=noicon
arg=<macro>
theUrl = "https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/imagej_tools/ijab-biop_channel_tools/";
run("URL...", "url="+theUrl);
</macro>
</line>
\ No newline at end of file
diff --git a/BIOP_Channel_Tools.jar b/BIOP_Channel_Tools.jar
index d8882b7..fe61e2b 100644
Binary files a/BIOP_Channel_Tools.jar and b/BIOP_Channel_Tools.jar differ