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Copy pathMUSCLEMOTION v1.0.ijm
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MUSCLEMOTION v1.0.ijm
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//BJ van Meer//L Sala
//F Burton//
//Leiden University Medical Center - 2017
macro "MUSCLEMOTION Action Tool - C1422444T0c10MTac10M;" {
//STATIC PARAMETERS
showStatus("Initialization...");
run("Input/Output...", "jpeg=100");
var versionNumber="1.0";
var referenceFrameSlice=1; //if nothing is set somehow, the reference frame will be set to 1
var hideIntermediateResults=true;
//this speeds up calculations by hiding some result windows
var checkClip=true;
//simple tool to check clipping in the plot
var checkSpeedlinearity=true;
//displays the final window to compare the measured speed and speed calculated from the measured contraction
var manualReferenceFrame = false; //will be changed to true if selected
var drawPeaks=true; //if transients are analyzed, the peaks are drawn
//DEFAULT VALUES - you might want to change this to have your custom defaults selected once you select 'Yes, but keep it simple'.
var default_recordedFramerate = 100; //frames per second
var default_speedWindow = 2; //frames; see UserManual
var default_MPstartRange = 1; //frame number
var default_MPendRange = -1; //frame number; -1 is infinite
var default_autoDetectStart = 1; //frame number; estimation at least 2 contraction periods between autoDetectStart and autoDetectStop
var default_autoDetectStop = 300; //frame number; estimation at least 2 contraction periods between autoDetectStart and autoDetectStop
var default_lowValueN = 20; //frames; see UserManual
var default_unitySelectionN = 10; //frames; see UserManual
var default_PeakDetectionWindow = 20; //frames; estimation around 0.75*[contraction period]
var default_peakThreshold = 30; //percentage
var default_baselineThreshold = 2; //percentage
var default_baselineNumberOfPoints = 5; //frames; averaging baseline
var default_highFreqBaselineDetection = "Yes"; //"Yes" or "No"; overrules baselineThreshold and baselineNumberOfPoints
var default_binaryFormatPercentages = "100010001"; // binary format, order is 10-20-...-80-90
var default_tiffImSequence = "No"; //"Yes" or "No"
var default_guassianBlur10 = "No"; //"Yes" or "No"
//DO NOT CHANGE
var simpleAnswers = newArray("Yes", "No");
var complexAnswers = newArray("Yes, but keep it simple", "Yes & show me advanced options", "No");
var percentageOptions = newArray("10", "20","30","40","50","60","70","80","90");
var percentagesDefaults=newArray(percentageOptions.length);
//Let's start
showStatus("Get analysis parameters");
//load stored settings or iniate defaults
var batchAnalysis = readSettingValue("c1.batchAnalysis", "No");
var recordedFramerate = readSettingValue("c1.recordedFramerate", default_recordedFramerate);
var speedWindow = readSettingValue("c1.speedWindow", default_speedWindow);
var SNRimprovement = readSettingValue("c1.SNRimprovement", "Yes, but keep it simple");
var autodetectReferenceFrame = readSettingValue("c1.autodetectReferenceFrame", "Yes, but keep it simple");
var automaticTransientDetection = readSettingValue("c1.automaticTransientDetection", "Yes, but keep it simple");
var MPstartRange = readSettingValue("c1.MPstartRange", default_MPstartRange);
var MPendRange = readSettingValue("c1.MPendRange", default_MPendRange);
var autoDetectStart = readSettingValue("c1.autoDetectStart", default_autoDetectStart);
var autoDetectStop = readSettingValue("c1.autoDetectStop", default_autoDetectStop);
var lowValueN = readSettingValue("c1.lowValueN", default_lowValueN);
var unitySelectionN = readSettingValue("c1.unitySelectionN", default_unitySelectionN);
var PeakDetectionWindow = readSettingValue("c1.PeakDetectionWindow", default_PeakDetectionWindow);
var peakThreshold = readSettingValue("c1.peakThreshold", default_peakThreshold);
var baselineThreshold = readSettingValue("c1.baselineThreshold", default_baselineThreshold);
var baselineNumberOfPoints = readSettingValue("c1.baselineNumberOfPoints", default_baselineNumberOfPoints);
var highFreqBaselineDetection = readSettingValue("c1.highFreqBaselineDetection", default_highFreqBaselineDetection);
var binaryFormatPercentages = readSettingValue("c1.binaryFormatPercentages", default_binaryFormatPercentages);
var tiffImSequence = readSettingValue("c1.tiffImSequence", default_tiffImSequence);
var guassianBlur10 = readSettingValue("c1.guassianBlur10", default_guassianBlur10);
//get array from string save format
countOnes=0;
for(findOne=0;findOne<lengthOf(binaryFormatPercentages);findOne++){
if(substring(binaryFormatPercentages,findOne,findOne+1)=="1"){
countOnes=countOnes+1;
percentagesDefaults[findOne]=true;
}
else{
percentagesDefaults[findOne]=false;
}
}
percentages=newArray(countOnes);
countOnes=0;
for(findOne=0;findOne<lengthOf(binaryFormatPercentages);findOne++){
if(substring(binaryFormatPercentages,findOne,findOne+1)=="1"){
percentages[countOnes]=(findOne+1)*10;
countOnes=countOnes+1;
}
}
//Dialog #1
Dialog.create("Analysis parameter wizard");
Dialog.addRadioButtonGroup(" A. Do you want to analyze a directory containing multiple TIFFs or subdirectories (batch)?\n", simpleAnswers, 0, 2, batchAnalysis);
Dialog.addRadioButtonGroup(" B. Do you want to analyze a TIFF image sequence instead of a stack?\n", simpleAnswers, 0, 2, tiffImSequence);
Dialog.addRadioButtonGroup(" C. Do you want to add a Gaussian blur to cancel out repetitive patterns?\n", simpleAnswers, 0, 2, guassianBlur10);
Dialog.addMessage("D. What is the frame rate of your recording(s)?");
Dialog.addNumber(" ", recordedFramerate, 0, 5, "frames/second");
Dialog.addMessage("E. What speedWindow would you like to use?");
Dialog.addNumber(" ", speedWindow, 0, 5, "frames");
Dialog.addMessage("Please refer to the UserManual for an instruction how to choose the correct reference frame.");
Dialog.addRadioButtonGroup(" F. Do you want to decrease noise in your output?\n", complexAnswers, 0, 2, SNRimprovement);
Dialog.addMessage("Please refer to the UserManual for more information. Computational time will increase.");
Dialog.addRadioButtonGroup(" G. Do want MUSCLEMOTION to detect your reference frame?\n", complexAnswers, 0, 2, autodetectReferenceFrame);
Dialog.addMessage("The default is YES, but in some situations the program might fail to detect the correct reference \nframe. This is setup dependent, be careful to check your output carefully. Please refer to the \nUserManual for more information.");
Dialog.addRadioButtonGroup(" H. Do you want MUSCLEMOTION to analyze your transients?\n", complexAnswers, 0, 2, automaticTransientDetection);
Dialog.show();
//grab data
batchAnalysis = Dialog.getRadioButton();
tiffImSequence = Dialog.getRadioButton();
guassianBlur10 = Dialog.getRadioButton();
recordedFramerate = Dialog.getNumber();
speedWindow = Dialog.getNumber();
SNRimprovement = Dialog.getRadioButton();
autodetectReferenceFrame = Dialog.getRadioButton();
automaticTransientDetection = Dialog.getRadioButton();
//write data from dialog 1
writeSettingOption("c1.batchAnalysis", batchAnalysis);
writeSettingOption("c1.tiffImSequence", tiffImSequence);
writeSettingOption("c1.guassianBlur10", guassianBlur10);
writeSettingValue("c1.recordedFramerate", recordedFramerate, 0);
writeSettingValue("c1.speedWindow", speedWindow, 0);
writeSettingOption("c1.SNRimprovement", SNRimprovement);
writeSettingOption("c1.autodetectReferenceFrame", autodetectReferenceFrame);
writeSettingOption("c1.automaticTransientDetection", automaticTransientDetection);
//Do something with the values given. Load default settings if simple option is chosen
var samplingTime=(1/recordedFramerate)*1000;
secondDialogSNR = false;
secondDialogARF = false;
secondDialogTA = false;
if(batchAnalysis=="Yes"){
batchDirLoad=true;
}
else{
batchDirLoad=false;
}
if(SNRimprovement=="Yes & show me advanced options"){
secondDialogSNR = true;
var maxProject = true;
}
else if(SNRimprovement=="Yes, but keep it simple"){
var maxProject = true;
MPstartRange = default_MPstartRange;
MPendRange = default_MPendRange;
}
else{
var maxProject = false;
}
if(autodetectReferenceFrame=="Yes & show me advanced options"){
secondDialogARF = true;
autodetectReferenceFrame = true;
}
else if(autodetectReferenceFrame=="Yes, but keep it simple"){
autodetectReferenceFrame = true;
lowValueN=default_lowValueN;
unitySelectionN=default_unitySelectionN;
autoDetectStart=default_autoDetectStart;
autoDetectStop=default_autoDetectStop;
}
else{
autodetectReferenceFrame = false;
manualReferenceFrame = true;
}
if(automaticTransientDetection=="Yes & show me advanced options"){
secondDialogTA = true;
automaticTransientDetection = true;
}
else if(automaticTransientDetection=="Yes, but keep it simple"){
automaticTransientDetection = true;
PeakDetectionWindow=default_PeakDetectionWindow;
peakThreshold=default_peakThreshold;
percentages=percentages;
baselineThreshold=default_baselineThreshold;
baselineNumberOfPoints=default_baselineNumberOfPoints;
highFreqBaselineDetection=default_highFreqBaselineDetection;
}
else{
automaticTransientDetection = false;
}
//Dialog #2
if(secondDialogSNR || secondDialogARF){
Dialog.create("Analysis parameter wizard");
Dialog.addMessage("Please check the UserManual for detailed instructions per option.");
if(secondDialogSNR){
Dialog.addMessage("----------------------------- SNR -----------------------------");
Dialog.addMessage("What is the starting frame for SNR improvement?");
Dialog.addNumber(" ", MPstartRange, 0, 5, "(default = 1)");
Dialog.addMessage("What is the end frame for SNR improvement?");
Dialog.addNumber(" ", MPendRange, 0, 5, "(default = -1 = infinite)");
Dialog.addMessage(" ");
}
if(secondDialogARF){
Dialog.addMessage("----- Automatic Reference Frame (ARF) Detection ------");
Dialog.addMessage("What is the starting frame for ARF Detection?");
Dialog.addNumber(" ", autoDetectStart, 0, 5, "(default = 1)");
Dialog.addMessage("What is the end frame for ARF Detection?");
Dialog.addNumber(" ", autoDetectStop, 0, 5, "(default = 300)");
Dialog.addMessage("What is the number of low points for ARF Detection?");
Dialog.addNumber(" ", lowValueN, 0, 5, "frames (default = 20)");
Dialog.addMessage("What is the number of points near the unity line?");
Dialog.addNumber(" ", unitySelectionN, 0, 5, "frames (default = 10)");
}
Dialog.show();
if(secondDialogSNR){
MPstartRange = Dialog.getNumber();
MPendRange = Dialog.getNumber();
}
if(secondDialogARF){
autoDetectStart = Dialog.getNumber();
autoDetectStop = Dialog.getNumber();
lowValueN = Dialog.getNumber();
unitySelectionN = Dialog.getNumber();
}
}
if(secondDialogTA){
Dialog.create("Analysis parameter wizard");
Dialog.addMessage("Please check the UserManual for detailed instructions per option.");
Dialog.addMessage("--------- Automatic Transient Analysis ----------");
Dialog.addMessage("What do you estimate as peak width?");
Dialog.addNumber(" ", PeakDetectionWindow, 0, 5, "frames (~0.75*frames per period, default = 20)");
Dialog.addMessage("What is the minimum amplitude compared to all values in the plot to be considered a peak?");
Dialog.addNumber(" ", peakThreshold, 0, 5, "% (default = 30%)");
Dialog.addMessage("What percentages of the transient do you want in your output?");
Dialog.addCheckboxGroup(1, 9, percentageOptions, percentagesDefaults);
Dialog.addMessage("What is percentage around baseline that you consider noise?");
Dialog.addNumber(" ", baselineThreshold, 0, 5, "% (default = 2)");
Dialog.addMessage("What is number of points you would like to average in the baseline?");
Dialog.addNumber(" ", baselineNumberOfPoints, 0, 5, "frames (default = 5)");
Dialog.addRadioButtonGroup(" Would you like to optimize for high frequencies and select the minimum before each peak?\n", simpleAnswers, 0, 2, highFreqBaselineDetection);
Dialog.show();
PeakDetectionWindow = Dialog.getNumber();
peakThreshold = Dialog.getNumber();
baselineThreshold = Dialog.getNumber();
baselineNumberOfPoints = Dialog.getNumber();
highFreqBaselineDetection = Dialog.getRadioButton();
countNumberPercentages=0;
binaryFormatPercentages="";
for(opt=0;opt<percentageOptions.length;opt++){
if(Dialog.getCheckbox()==true){
binaryFormatPercentages=binaryFormatPercentages+"1";
countNumberPercentages=countNumberPercentages+1;
}
else{
binaryFormatPercentages=binaryFormatPercentages+"0";
}
}
percentages = newArray(countNumberPercentages);
countOnes=0;
for(findOne=0;findOne<lengthOf(binaryFormatPercentages);findOne++){
if(substring(binaryFormatPercentages,findOne,findOne+1)=="1"){
percentages[countOnes]=(findOne+1)*10;
countOnes=countOnes+1;
}
}
}
//write data from dialog 2 & 3
writeSettingValue("c1.MPstartRange", MPstartRange, 0);
writeSettingValue("c1.MPendRange", MPendRange, 0);
writeSettingValue("c1.autoDetectStart", autoDetectStart, 0);
writeSettingValue("c1.autoDetectStop", autoDetectStop, 0);
writeSettingValue("c1.lowValueN", lowValueN, 0);
writeSettingValue("c1.unitySelectionN", unitySelectionN, 0);
writeSettingValue("c1.PeakDetectionWindow", PeakDetectionWindow, 0);
writeSettingValue("c1.peakThreshold", peakThreshold, 0);
writeSettingValue("c1.baselineThreshold", baselineThreshold, 0);
writeSettingValue("c1.baselineNumberOfPoints", baselineNumberOfPoints, 0);
writeSettingOption("c1.highFreqBaselineDetection", highFreqBaselineDetection);
writeSettingValue("c1.binaryFormatPercentages", binaryFormatPercentages, 0);
//Convert some values
if(highFreqBaselineDetection=="Yes"){
highFreqBaselineDetection=true;
}
else{
highFreqBaselineDetection=false;
}
//Get user input for saveDir
saveDir = getDirectory("Select a directory to save your outputfiles");
//select folder or file
//batch mode
if(batchDirLoad==true){
startDir = getDirectory("Choose a directory to analyze");
dirList1=getDirsInDir(startDir);
fileList1=getFilesInDir(startDir);
for(cDir=0;cDir<fileList1.length;cDir++){
fileList1[cDir]=startDir+fileList1[cDir];
}
//Get dirs in startDir and subfolders deeper
if(dirList1[0]!=0){
for(addDir=0;addDir<dirList1.length;addDir++){
dirList2=getDirsInDir(startDir+dirList1[addDir]);
if(dirList2[0]!=0){
for(y=0;y<dirList2.length;y++){
dirList2[y]=dirList1[addDir]+dirList2[y];
}
dirList1=Array.concat(dirList1,dirList2);
}
}
}
//Get files in startDir en subfolders
for(y=0;y<dirList1.length;y++){
fileList2=getFilesInDir(startDir+dirList1[y]);
if(fileList2[0]!=0){
for(cDir=0;cDir<fileList2.length;cDir++){
fileList2[cDir]=startDir+dirList1[y]+fileList2[cDir];
}
if(fileList1[0]==0){
fileList1=fileList2;
}
else{
fileList1=Array.concat(fileList1,fileList2);
}
}
}
Array.sort(fileList1);
Array.print(fileList1);
fileList=newArray(1);
for(checkExt=0;checkExt<fileList1.length;checkExt++){
if(endsWith(fileList1[checkExt],"tif") || endsWith(fileList1[checkExt],"png") || endsWith(fileList1[checkExt],"avi")){
if(fileList[0]==0){
fileList[0]=fileList1[checkExt];
}
else{
fileList=Array.concat(fileList,fileList1[checkExt]);
}
}
}
Array.print(fileList);
if(fileList[0]==0){exit("No images found");}
numberOfFiles=fileList.length;
}
//single file mode
else{
path = File.openDialog("Choose a file to analyze");
numberOfFiles=1;
}
//loop through the files to analyze
for(fileCounter=0;fileCounter<numberOfFiles;fileCounter++){
//CLEANUP and start log
close("*");
run("Clear Results");
print("\\Clear");
print("Log started...");
getDateAndTime(year, month, week, day, hour, min, sec, msec);
print("Date: "+day+"-"+month+"-"+year);
print("Time: "+hour+":"+min+":"+sec);
print("***");
//Print parameters to Log
print("Algorithm tool version number: "+versionNumber);
print("recordedFramerate: "+recordedFramerate);
print("speedWindow: "+speedWindow);
print("referenceFrameSlice: "+referenceFrameSlice);
print("maxProject: "+maxProject);
if(maxProject==true){
print("MPstartRange: "+MPstartRange);
print("MPendRange: "+MPendRange);
}
print("hideIntermediateResults: "+hideIntermediateResults);
print("checkClip: "+checkClip);
print("checkSpeedlinearity: "+true);
print("autodetectReferenceFrame: "+autodetectReferenceFrame);
if(autodetectReferenceFrame==true){
print("***autodetectReferenceFrame parameters");
print("*lowValueN: "+lowValueN);
print("*unitySelectionN: "+unitySelectionN);
print("*autoDetectStart: "+autoDetectStart);
print("*autoDetectStop: "+autoDetectStop);
print("***");
}
print("manualReferenceFrame: "+manualReferenceFrame+ " NOTE:overruled if autodetectReferenceFrame is true");
print("automaticTransientDetection: "+automaticTransientDetection);
if(automaticTransientDetection==true){
print("***automaticTransientDetection parameters");
print("*PeakDetectionWindow: "+PeakDetectionWindow);
print("*peakThreshold: "+peakThreshold);
print("*drawPeaks: "+drawPeaks);
print("*percentages: ");Array.print(percentages);
print("*baselineThreshold: "+baselineThreshold);
print("*baselineNumberOfPoints: "+baselineNumberOfPoints);
print("*highFreqBaselineDetection: "+highFreqBaselineDetection);
print("*guassianBlur10: "+guassianBlur10);
print("*tiffImSequence: "+tiffImSequence);
print("***");
}
print("batchDirLoad: "+batchDirLoad);
if(batchDirLoad==true){
print("BatchDir path="+fileList[fileCounter]);
}
//specify path if batchDirLoad is turned on
if(batchDirLoad==true){
path=fileList[fileCounter];
}
fileDir=File.getParent(path);
//check what kind of file we are going to analyze and open it
var LoadingAvi=false;
var LoadingImageSequence=false;
if(endsWith(path, "avi")){
LoadingAvi=true;
run("AVI...", "select=["+path+"] use");
}
else if(endsWith(path, "png") || tiffImSequence=="Yes"){
LoadingImageSequence=getImageSequence(path);
}
else{
run("TIFF Virtual Stack...", "open=["+path+"]");
}
rename("orginal-stack");
print(" ");
print("----------------- Evaluating file:"+File.nameWithoutExtension+" -----------------");
showStatus("Analyzing stack...");
Stack.getDimensions(width, height, channels, slices, frames);
if(frames>slices){
slices=frames;
}
//Run some basic tests:
if(recordedFramerate<50){
print("WARNING: Recorded framerate is low");
}
//check if file is a stack or a sequence
if(slices<2){
LoadingImageSequence=getImageSequence(path);
}
//if it is still not a stack, stop the macro
if(slices<2){
close("*");
run("Clear Results");
exit("Image was not a stack. \nStack required for this macro, please try again.");
}
//some more checks regarding reference frame autodetection
if(autodetectReferenceFrame==true){
if(autoDetectStop<=autoDetectStart){
autoDetectStart=(autoDetectStop-1);
print("WARNING: autoDetectStart set to "+autoDetectStart+" since it should be smaller than autoDetectStop ("+autoDetectStop+").");
}
if(autoDetectStop>=slices){
autoDetectStop=(slices-speedWindow-1);
print("WARNING: autoDetectStop set to "+autoDetectStop+" since it should be smaller than stack number ("+slices+") minus speedWindow ("+speedWindow+") minus 1 (Reference frame).");
}
if(lowValueN>=autoDetectStop){
lowValueN=(autoDetectStop-1);
print("WARNING: lowValueN set to "+lowValueN+" since it should be smaller than autoDetectStop ("+autoDetectStop+").");
}
if(lowValueN<=unitySelectionN){
unitySelectionN=(lowValueN-1);
print("WARNING: unitySelectionN set to "+unitySelectionN+" since it should be smaller than lowValueN ("+lowValueN+").");
}
}
//Speed measurement
startTime=getTime();
//enable batchmode
if(hideIntermediateResults==true){
setBatchMode(true);
}
//preperation of names and output folders
showStatus("Preparing output folders and names...");
var outputName=File.getName(path);
outputName=replace(outputName, ".png", "");
outputName=replace(outputName, ".tif", "");
outputName=replace(outputName, ".avi", "");
dirMakeName=saveDir+File.separator+outputName+"-Contr-Results";
if (!File.isDirectory(dirMakeName)){
File.makeDirectory(dirMakeName);
}
else {
dirVersion=1;
dirMakeName=saveDir+File.separator+outputName+"-Contr-Results-"+dirVersion;
while (File.isDirectory(dirMakeName)){
dirMakeName=saveDir+File.separator+outputName+"-Contr-Results-"+dirVersion;
dirVersion=dirVersion+1;
}
File.makeDirectory(dirMakeName);
}
var savePath=dirMakeName;
resultFile=getFileName("Overview-results");
logFile=getFileName("Log_file");
//MAIN SCRIPT
showStatus("Reference frame selection...");
referenceFrameSlice=getReferenceFrame();
showStatus("Calculating contraction...");
//OPTIONAL: use maximum projection masking to improve SNR, var declared in initialization
if(maxProject==true){
pixelsOfInterest();
}
//Calculate contraction
lfhMeanArray=getContractionData();
customPlotZaxis("Contraction", lfhMeanArray);
//saving data
contractionFile=getFileName("contraction");
writeFile(contractionFile);
//calculate speed of contraction
lfhMeanArraySpeed=getSpeedData();
customPlotZaxis("Speed of contraction", lfhMeanArraySpeed);
//saving data
speedFile=getFileName("speed-of-contraction");
writeFile(speedFile);
//check whether the calculated speed and measured speed are similar in terms of ratio
if(checkSpeedlinearity==true){
speedLinCompare(lfhMeanArraySpeed, lfhMeanArray);
}
//save results
updateResults();
//REACHING END OF MACRO
//Show timing and save results
print("Elapsed time (ms): "+(getTime()-startTime));
print("----------------- Evaluation finished -----------------");
saveAs("Results", resultFile);
selectWindow("Log");
run("Text...", "save=["+logFile+"]");
setBatchMode(false);
} //end of for loop dirCounter
} //end of macro
//Function library
function getImageSequence(imPath){
countTrim=0;
close("orginal-stack");
run("Image Sequence...", "open=["+imPath+"] sort use");
rename("orginal-stack");
Stack.getDimensions(width, height, channels, slices, frames);
if(frames>slices){
slices=frames;
}
print(slices+" and name: "+imPath);
return true
}
function getDirsInDir(dir){
list = getFileList(dir);
var dirList=newArray(1);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/")){
if (dirList[0]==0){
dirList[0]=list[i];
}
else{
dirList = Array.concat(dirList,list[i]);
}
}
}
return dirList;
}
function getFilesInDir(dir){
list = getFileList(dir);
fileListT=newArray(1);
for (i=0; i<list.length; i++) {
if (!endsWith(list[i], "/")){
if (fileListT[0]==0){
fileListT[0]=list[i];
}
else{
fileListT = Array.concat(fileListT,list[i]);
}
}
}
if(endsWith(fileListT[0], "png") || tiffImSequence=="Yes"){
fileListB=newArray(1);
fileListB[0]=fileListT[0];
}
else{
fileListB=fileListT;
}
return fileListB;
}
function openVirtualStack(VirtualStackName, deleteReferenceFrame){
if(hideIntermediateResults==true){
setBatchMode(true);
}
if(LoadingImageSequence){
run("Image Sequence...", "open=["+path+"] sort use");
}
else if(LoadingAvi){
run("AVI...", "select=["+path+"] use");
}
else{
run("TIFF Virtual Stack...", "open=["+path+"]");
}
rename(VirtualStackName);
if(deleteReferenceFrame==true){
setSlice(referenceFrameSlice);
run("Delete Slice");
setSlice(1);
}
}
function pixelsOfInterest() {
//identify pixels of interest in speed stack by masking with a threshold based on standard deviation
showStatus("Improving Signal to Noise Ratio (SNR)...");
openVirtualStack("original-stack-small", true);
newImage("maxProjectStack", "32-bit black", width, height, 1);
setBatchMode(true);
if(MPendRange==-1){MPendRange=slices;}
else if(MPendRange>slices){MPendRange=slices;}
for(lfhIndex=MPstartRange;lfhIndex<MPendRange;lfhIndex++){
selectWindow("original-stack-small");
setSlice(lfhIndex);
run("Duplicate...", "title=subtractTemp");
if(guassianBlur10=="Yes"){
run("Gaussian Blur...", "sigma=10");
}
imageCalculator("Difference create 32-bit stack", "subtractTemp","reference-frame");
run("Concatenate...", " title=[maxProjectStack] image1=maxProjectStack image2=[Result of subtractTemp] image3=[-- None --]");
selectWindow("maxProjectStack");
run("Z Project...", "projection=[Max Intensity]");
rename("maxProjectStackTemp");
close("maxProjectStack");
selectWindow("maxProjectStackTemp");
rename("maxProjectStack");
close("subtractTemp");
}
close("original-stack-small");
setBatchMode("show");
selectWindow("maxProjectStack");
getStatistics(nothing, mean, min, max, stdDev);
var lucaVar = (mean + stdDev);
setThreshold(lucaVar, max);
run("Make Binary");
}
function getContractionData(){
//routine to calculate image[i]-image[ref]
showStatus("Calculating contraction...");
if(hideIntermediateResults==true){
setBatchMode(true);
}
openVirtualStack("original-stack-small", true);
lfhMeanArray=newArray(slices-1);
setBatchMode(true);
for(lfhIndex=1;lfhIndex<slices;lfhIndex++){
selectWindow("original-stack-small");
setSlice(lfhIndex);
run("Duplicate...", "title=subtractTemp");
if(guassianBlur10=="Yes"){
run("Gaussian Blur...", "sigma=10");
}
imageCalculator("Difference create 32-bit stack", "subtractTemp","reference-frame");
if(maxProject==true){
imageCalculator("Multiply create 32-bit stack", "Result of subtractTemp","maxProjectStack");
}
getStatistics(LFHnothing, LFHmean, LFHmin, LFHmax, LFHstdDev);
lfhMeanArray[lfhIndex-1]=LFHmean;
close("Result of subtractTemp");
close("subtractTemp");
}
close("Result of Result of subtractTemp");
close("original-stack-small");
if(hideIntermediateResults==false){
setBatchMode(false);
}
return lfhMeanArray;
}
function getSpeedData(){
//routine to calculate image[i]-image[i-1]
showStatus("Calculating speed of contraction...");
if(hideIntermediateResults==true){
setBatchMode(true);
}
openVirtualStack("original-stack-small", true);
openVirtualStack("second-stack", true);
for(shift=0;shift<speedWindow;shift++){
run("Delete Slice"); //-1 because reference frame is removed
}
selectWindow("original-stack-small");
setSlice(slices-1);
for(shift=0;shift<speedWindow;shift++){
run("Delete Slice");
}
lfhMeanArraySpeed=newArray(slices-speedWindow-1);
setBatchMode(true);
for(lfhIndex=1;lfhIndex<(slices-speedWindow);lfhIndex++){
selectWindow("original-stack-small");
setSlice(lfhIndex);
run("Duplicate...", "title=OriginalSubtractTemp");
if(guassianBlur10=="Yes"){
run("Gaussian Blur...", "sigma=10");
}
selectWindow("second-stack");
setSlice(lfhIndex);
run("Duplicate...", "title=SecondSubtractTemp");
if(guassianBlur10=="Yes"){
run("Gaussian Blur...", "sigma=10");
}
imageCalculator("Difference create 32-bit stack", "OriginalSubtractTemp","SecondSubtractTemp");
if(maxProject==true){
imageCalculator("Multiply create 32-bit stack", "Result of OriginalSubtractTemp","maxProjectStack");
}
getStatistics(LFHnothing, LFHmean, LFHmin, LFHmax, LFHstdDev);
lfhMeanArraySpeed[lfhIndex-1]=LFHmean;
close("Result of OriginalSubtractTemp");
close("OriginalSubtractTemp");
close("SecondSubtractTemp");
}
close("Result of Result of OriginalSubtractTemp");
close("original-stack-small");
close("second-stack");
if(hideIntermediateResults==false){
setBatchMode(false);
}
return lfhMeanArraySpeed;
}
function customPlotZaxis(parameter, yArrayMean) {
//plot z-profile function that can cope with arrays that have only the same value
if(hideIntermediateResults==true){
setBatchMode(true);
}
Stack.getDimensions(Zwidth, Zheight, Zchannels, Zslices, Zframes);
yConstant=false;
sortedArray=Array.copy(yArrayMean);
Array.sort(sortedArray);
if(sortedArray[0]==sortedArray[sortedArray.length-1]){
yArrayMean[0]=yArrayMean[0]-0.01;
yConstant=true;
print("Warning: Array of "+parameter+" was constant. In order to plot, 0.01 has been removed from the first value");
}
//create the actual plot
xTimeArray=newArray(yArrayMean.length);
xTimeArray[0]=0;
for(xTimeIndex=1;xTimeIndex<yArrayMean.length;xTimeIndex++){
xTimeArray[xTimeIndex]=xTimeArray[xTimeIndex-1]+samplingTime;
}
Plot.create("Z-Plot of "+parameter, "Time (ms)", parameter+ " (a.u.)", xTimeArray, yArrayMean);
if(automaticTransientDetection==true && parameter=="Contraction"){
transientAnalysis(yArrayMean);
}
Plot.setColor("black");
Plot.show();
rename(parameter+"-profileData");
if(hideIntermediateResults==true){
setBatchMode(false);
setBatchMode(true);
}
Plot.makeHighResolution(parameter+"-profile",4.0);
saveAs("Jpeg", savePath+File.separator+parameter);
if(hideIntermediateResults==true){
setBatchMode(false);
setBatchMode(true);
}
selectWindow(parameter+"-profileData");
//warning flag for clipping
if(checkClip==true){
if(sortedArray[sortedArray.length-1]==sortedArray[sortedArray.length-2] && sortedArray[sortedArray.length-1]==sortedArray[sortedArray.length-3]){
if (yConstant==false){
print("Warning: it seems like your "+parameter+" plot is clipping!");
}
}
}
return yArrayMean;
}
function getFileName(parameter) {
//check if file exists and else add/change version number
version=1;
fileName=savePath+File.separator+parameter+".txt";
while (File.exists(fileName)){
fileName=savePath+File.separator+parameter+version+".txt";
version=version+1;
}
return fileName;
}
function writeFile(filename) {
//save plot values
Plot.getValues(xvalues, yvalues);
f = File.open(filename);
for (i=0; i<xvalues.length; i++){
print(f, xvalues[i]+"\t"+yvalues[i]);
}
File.close(f);
}
function getReferenceFrame(){
if(autodetectReferenceFrame==true){
showStatus("Autodetecting reference frame...");
//prepare stacks
openVirtualStack("second-stack", false);
setSlice(1);
for(shift=0;shift<speedWindow;shift++){
run("Delete Slice");
}
openVirtualStack("original-stack-small", false);
setSlice(slices-1);
for(shift=0;shift<speedWindow;shift++){
run("Delete Slice");
}
speedY=newArray(autoDetectStop-autoDetectStart+1);
setBatchMode(true);
for(lfhIndex=1;lfhIndex<speedY.length+1;lfhIndex++){
selectWindow("original-stack-small");
setSlice(lfhIndex);
run("Duplicate...", "title=OriginalSubtractTemp");
if(guassianBlur10=="Yes"){
run("Gaussian Blur...", "sigma=10");
}
selectWindow("second-stack");
setSlice(lfhIndex);
run("Duplicate...", "title=SecondSubtractTemp");
if(guassianBlur10=="Yes"){
run("Gaussian Blur...", "sigma=10");
}
imageCalculator("Difference create 32-bit stack", "OriginalSubtractTemp","SecondSubtractTemp");
getStatistics(LFHnothing, LFHmean, LFHmin, LFHmax, LFHstdDev);
speedY[lfhIndex-1]=LFHmean;
close("Result of OriginalSubtractTemp");
close("OriginalSubtractTemp");
close("SecondSubtractTemp");
}
setBatchMode(false);
//close stacks
close("second-stack");
close("original-stack-small");
//prepare arrays
speedY=Array.slice(speedY,autoDetectStart,autoDetectStop);
speedYshift=Array.copy(speedY);
speedYshift=Array.slice(speedYshift,1);
speedY=Array.trim(speedY,speedY.length-1);
radianPoints=newArray(speedY.length);
for(d=0;d<speedY.length;d++){
radianPoints[d]=sqrt((speedY[d]*speedY[d])+(speedYshift[d]*speedYshift[d]));
}
indicesVal=Array.rankPositions(radianPoints);
low=0;
unitySelection=newArray(lowValueN);
for(d=0;d<lowValueN-1;d++){
index=indicesVal[d];
unitySelection[d]=abs((speedY[index]/speedYshift[index])-1);
}
//check which [unitySelectionN] of the unitySelection is smallest
indicesUni=Array.rankPositions(unitySelection);
for(d=0;d<unitySelectionN-1;d++){
indexTrans=indicesUni[d];
index=indicesVal[indexTrans];
lowValue=(speedY[index]*speedYshift[index])*unitySelection[indexTrans];
if(d==0){
low=lowValue;
lowIndex=index;
}
else if(low>lowValue){
low=lowValue;
lowIndex=index;
}
}
selectWindow("orginal-stack");
setSlice((lowIndex+1));
run("Duplicate...", "title=reference-frame");
if(guassianBlur10=="Yes"){
run("Gaussian Blur...", "sigma=10");
}
print("Automatic detected reference frame: frame "+lowIndex+1);
referenceFrameSlice=lowIndex+1;
}
else if(manualReferenceFrame==true){
setSlice(1);
waitForUser( "Pause","Manual reference frame selection.\nSelect the reference frame and press 'OK'.");
getSliceNumber();
referenceFrameSlice=getSliceNumber();
print("Manual selected reference frame: frame "+getSliceNumber());
run("Duplicate...", "title=reference-frame");
if(guassianBlur10=="Yes"){
run("Gaussian Blur...", "sigma=10");
}
}
else {
//set frame 1 to be the reference frame
setSlice(1);
run("Duplicate...", "title=reference-frame");
if(guassianBlur10=="Yes"){
run("Gaussian Blur...", "sigma=10");
}
print("No selection reference frame: frame 1");
referenceFrameSlice=1;
}
selectWindow("orginal-stack");
run("Delete Slice");
return referenceFrameSlice;
}
function speedLinCompare(speedY, contractionY) {
calculatedSpeed=newArray(speedY.length);
for(j=0;j<speedY.length;j++){
calculatedSpeed[j]=abs(contractionY[j+1]-contractionY[j]);
}
//normalize both speed arrays
calculatedSpeedNorm=newArray(speedY.length-1);
measuredSpeedNorm=newArray(speedY.length-1);
Array.getStatistics(calculatedSpeed, calculatedSpeedMin, calculatedSpeedMax, calculatedSpeedMean, calculatedSpeedStd);
Array.getStatistics(speedY, speedYMin, speedYMax, speedYMean, speedYStd);
for(j=0;j<calculatedSpeedNorm.length-1;j++){
calculatedSpeedNorm[j]=(calculatedSpeed[j]-calculatedSpeedMin)/(calculatedSpeedMax-calculatedSpeedMin);
measuredSpeedNorm[j]=(speedY[j]-speedYMin)/(speedYMax-speedYMin);
}
xTimeArray=newArray(measuredSpeedNorm.length);
xTimeArray[0]=0;
for(xTimeIndex=1;xTimeIndex<measuredSpeedNorm.length;xTimeIndex++){
xTimeArray[xTimeIndex]=xTimeArray[xTimeIndex-1]+samplingTime;
}
//create plot for visual inspection
Plot.create("Comparison calculated (red) and measured (black) speed-lowRes", "Time (ms)", "Normalized contraction speed (a.u.)", xTimeArray, measuredSpeedNorm);
Plot.setColor("red");
Plot.add("line", xTimeArray, calculatedSpeedNorm);
Plot.setColor("black");
Plot.show();
Plot.makeHighResolution("Comparison calculated (red) and measured (black) speed",4.0);
saveAs("Jpeg", savePath+File.separator+"Comparison calculated (red) and measured (black) speed.jpg");
if(hideIntermediateResults==true){
setBatchMode(false);
setBatchMode(true);
}
}
function transientAnalysis(yValues){
//initialization
print("automaticTransientDetection starting..");
Plot.setColor("red");
//go foward
maxMin=Array.rankPositions(yValues);