//CV7000-Z-Projection macroName = "CV7000-Z-Projection"; macroShortDescription = "This macro opens CV7000 images of a well-field-channel and does a z projection."; macroDescription = "This macro reads single CV7000 images of a well as .tif ." + "
The chosen folder will be searched for images including subfolders." + "
All images of a unique well, field and channel are opened and projected." + "
All z-projection methods selectable."; macroRelease = "fifth.2 release 06-11-2018/16-03-2022"; macroAuthor = "by Martin Stöter (stoeter(at)mpi-cbg.de)"; generalHelpURL = "https://github.com/stoeter/Fiji-Tools-for-HCS/wiki"; macroHelpURL = generalHelpURL + "/" + macroName; macroHtml = "" +"" + macroName + "\n" + macroRelease + " " + macroAuthor + "

" +"" + macroDescription + "

" +"Check for more help on this web page:
" +"" + macroHelpURL + "
" +"General info:
" +"" + generalHelpURL + "
" +"...get these URLs from Log window!
" +""; //print macro name and current time to Log window getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec); month++; print("\\Clear"); print(macroName, "(" + macroRelease + ")", "\nStart:",year + "-" + month + "-" + dayOfMonth + ", h" + hour + "-m" + minute + "-s" + second); print(macroHelpURL); print(generalHelpURL); //start macro Dialog.create("Fiji macro: " + macroName); Dialog.addMessage("Fiji macro: " + macroName + " (Fiji-Tools-for-HCS by TDS@MPI-CBG)\n \n" + macroShortDescription + "\n \nClick 'OK' to go on, 'Cancel' to quit or 'Help' for online description."); Dialog.addHelp(macroHtml); Dialog.show; //choose folders inputPath = getDirectory("Choose image folder... "); outputPath = getDirectory("Choose result image folder... or create a folder"); printPaths = "inputPath = \"" + inputPath + "\";\noutputPath = \"" + outputPath + "\";"; print(printPaths); //set log file number tempLogFileNumber = 1; if(outputPath != "not available") while (File.exists(outputPath + "Log_temp_" + tempLogFileNumber +".txt")) tempLogFileNumber ++; //find last tempLog file to prevent overwriting of log //initialize => default settings run("Set Measurements...", "area mean standard min centroid center shape integrated median display redirect=None decimal=3"); run("Input/Output...", "jpeg=95 gif=-1 file=.txt copy_column copy_row save_column save_row"); run("Close All"); //run("Color Balance..."); //////////////////////////////// M A C R O C O D E /////////////////////////////// //set variables batchMode = true; availableProjectionTerms = newArray("Max Intensity", "Sum Slices", "Average Intensity", "Min Intensity", "Standard Deviation", "Median"); availableProjectionFileTags = newArray("00", "all", "max", "min", "avg", "put my own tag"); defaultFilterStrings = newArray("DC_sCMOS #","SC_BP",""); print("Files containing these strings will be automatically filtered out:"); Array.print(defaultFilterStrings); saveStack = false; //set array variables var fileExtension = ".tif"; //pre-definition of extension var filterStrings = newArray("","",""); //pre-definition of strings to filter var availableFilterTerms = newArray("no filtering", "include", "exclude"); //dont change this var filterTerms = newArray("no filtering", "no filtering", "no filtering"); //pre-definition of filter types var displayFileList = false; //shall array window be shown? setDialogImageFileFilter(); print("Image file filter:", filterTerms[0],filterStrings[0] + ";",filterTerms[1],filterStrings[1] + ";",filterTerms[2],filterStrings[2]); displayMetaData = false; Dialog.create("Find meta data"); Dialog.addCheckbox("Display unique values of meta data:", displayMetaData); Dialog.show(); displayMetaData = Dialog.getCheckbox(); print("Processing file list..."); //get file list ALL fileList = getFileListSubfolder(inputPath, displayFileList); //read all files in subfolders fileList = getFileType(fileList, fileExtension, displayFileList); fileList = getFilteredFileList(fileList, false, displayFileList); //filter for strings if (fileList.length == 0) exit("No files to process"); filterStrings = newArray("DC_sCMOS #","SC_BP",""); filterTerms = newArray("exclude", "exclude", "no filtering"); print("removing correction files from file list containing text", filterStrings[0], filterStrings[1], filterStrings[2]); fileList = getFilteredFileList(fileList, false, false); if (fileList.length == 0) exit("No files to process"); wellList = getUniqueWellListCV7000(fileList, displayMetaData); wellFieldList = getUniqueWellFieldListCV7000(fileList, displayMetaData); fieldList = getUniqueFieldListCV7000(fileList, displayMetaData); channelList = getUniqueChannelListCV7000(fileList, displayMetaData); print(wellList.length, "wells found\n", wellFieldList.length, "well x fields found\n", fieldList.length, "fields found\n", channelList.length, "channels found\n"); stackSize = fileList.length / wellFieldList.length / channelList.length; print("Assuming stacks with ", stackSize, "planes. Please check if this is correct!"); if(displayFileList || displayMetaData) waitForUser("Take a look at the list windows..."); //give user time to analyse the lists //set projection type Dialog.create("Set projection type"); Dialog.addChoice("Projection:", availableProjectionTerms); //set number of images in one row Dialog.addNumber("Lowest plane:", 1); Dialog.addNumber("Highest plane:", stackSize); Dialog.addChoice("Projection file tag:", availableProjectionFileTags); Dialog.addCheckbox("Save Z-stack instead of projection?", saveStack); //if checked no projection will be done and image will be saves as stack Dialog.addCheckbox("Set batch mode (hide images)?", batchMode); //if checked no images will be displayed Dialog.show(); projectionType = Dialog.getChoice(); Zstart = Dialog.getNumber(); Zstop = Dialog.getNumber(); projectionFileTag = Dialog.getChoice(); saveStack = Dialog.getCheckbox(); batchMode = Dialog.getCheckbox(); if (projectionFileTag == "put my own tag") { // user defined file tag Dialog.create("Set projection tag"); Dialog.addString("Projection file tag:", availableProjectionFileTags[1]); Dialog.show(); projectionFileTag = Dialog.getString(); } print("Selected projection type:", projectionType, "starting from plane", Zstart, "until plane",Zstop); print("Saving the stack instead of projection (0=false, 1=true):", saveStack, "using file tag", projectionFileTag); print("===== starting processing.... ====="); setBatchMode(batchMode); //go through all files for (currentWellField = 0; currentWellField < wellFieldList.length; currentWellField++) { // well by well print("well-field (" + (currentWellField + 1) + "/" + wellFieldList.length + ") ..."); //to log window for (currentChannel = 0; currentChannel < channelList.length; currentChannel++) { // channel by channel per well //define new filters and filter file list for currentWell and currentChannel filterStrings = newArray(wellFieldList[currentWellField],channelList[currentChannel] + ".tif",""); //pre-definition of strings to filter, add "_" because well strings e.g. A03, L01, C02 can be in file name at other places, e.g ..._A06_T0001F001L01A03Z01C02.tif and ".tif" to excluse well C02 instead of channel C02 filterTerms = newArray("include", "include", "no filtering"); //pre-definition of filter types wellChannelFileList = getFilteredFileList(fileList, false, false); //now open all files (wellChannelFileList) that belong to one wellField in one channel for (currentFile = 0; currentFile < wellChannelFileList.length; currentFile++) { //image sequence & regEx would be possible, but it seems to be slow: run("Image Sequence...", "open=Y:\\correctedimages\\Martin\\150716-wormEmbryo-Gunar-test2x3-lowLaser_20150716_143710\\150716-wormEmbryo-6half-days-old\\ file=(_B03_.*C01) sort"); IJ.redirectErrorMessages(); if (File.exists(wellChannelFileList[currentFile])) { open(wellChannelFileList[currentFile]); currentImage = getTitle(); print("opened (" + (currentFile + 1) + "/" + wellChannelFileList.length + "):", wellChannelFileList[currentFile]); //to log window } else { print("file not found (" + (currentFile + 1) + "/" + wellChannelFileList.length + "):", wellChannelFileList[currentFile]); //to log window } showProgress(currentFile / wellChannelFileList.length); showStatus("processing" + fileList[currentFile]); } //end for all images per channel //waitForUser("done"); if (nImages > 1) { run("Images to Stack", "name=Stack title=[] use"); if (!saveStack) run("Z Project...", "start=" + Zstart + " stop=" + Zstop + " projection=[" + projectionType + "]"); outputFileName = substring(currentImage,0,lengthOf(currentImage)-9) + projectionFileTag + substring(currentImage,lengthOf(currentImage)-7,lengthOf(currentImage)); saveAs("Tiff", outputPath + outputFileName); close(); //Z projection if (!saveStack) { print("saved projection as " + outputPath + outputFileName); //to log window selectWindow("Stack"); //stack close(); } else { print("saved image stack as " + outputPath + outputFileName); //to log window } } else { //end if images are open run("Close All"); } } //end for all channels in well saveLog(outputPath + "Log_temp_" + tempLogFileNumber + ".txt"); } //end for all wells //print current time to Log window and save log getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec); month++; print("Macro executed successfully.\nEnd:",year+"-"+month+"-"+dayOfMonth+", h"+hour+"-m"+minute+"-s"+second); selectWindow("Log"); if(outputPath != "not available") { saveAs("Text", outputPath + "Log_"+year+"-"+month+"-"+dayOfMonth+", h"+hour+"-m"+minute+"-s"+second+".txt"); if (File.exists(outputPath + "Log_temp_" + tempLogFileNumber +".txt")) File.delete(outputPath + "Log_temp_" + tempLogFileNumber + ".txt"); //delete current tempLog file } ///////////////////////////////////////////////////////////////////////////////////////////// //////// F U N C T I O N S ///////////// ///////////////////////////////////////////////////////////////////////////////////////////// //function opens a dialog to set text list for filtering a list //example: setDialogImageFileFilter(); //this function set interactively the global variables used by the function getFilteredFileList //this function needs global variables! (see below) /* var fileExtension = ".tif"; //default definition of extension var filterStrings = newArray("","",""); //default definition of strings to filter var availableFilterTerms = newArray("no filtering", "include", "exclude"); //dont change this var filterTerms = newArray(filterStrings.length); for (i = 0; i < filterStrings.length; i++) {filterTerms[i] = "no filtering";} //default definition of filter types (automatic) //var filterTerms = newArray("no filtering", "no filtering", "no filtering"); //default definition of filter types (manual) var displayFileList = false; //shall array window be shown? */ function setDialogImageFileFilter() { Dialog.create("Image file filter..."); //enable use inveractivity Dialog.addMessage("Define the files to be processed:"); Dialog.addString("Files should have this extension:", fileExtension); //add extension Dialog.addMessage("Define filter for files:"); for (i = 0; i < filterStrings.length; i++) { Dialog.addString((i + 1) + ") Filter this text from file list: ", filterStrings[i]); Dialog.addChoice((i + 1) + ") Files with text are included/excluded?", availableFilterTerms, filterTerms[i]); } Dialog.addCheckbox("Display the file lists?", displayFileList); //if check file lists will be displayed Dialog.show(); fileExtension = Dialog.getString(); for (i = 0; i < filterStrings.length; i++) { filterStrings[i] = Dialog.getString(); filterTerms[i] = Dialog.getChoice(); } displayFileList = Dialog.getCheckbox(); } //function filters a file list for a certain strings //example: myFileList = getFilteredFileList(myFileList, false, true); //if filterOnInputList = true, then additional filtering is possible (e.g. file names containing "H08" and "D04" => H08 and D04 in list) //if filterOnInputList = false, then subsequent filtering is possible (e.g. file names containing "controls" and "positive" => positive controls, but not negative controls in list!) //this function needs global variables (see function setDialogImageFileFilter) //var filterStrings = newArray("","",""); //pre-definition of strings to filter //var availableFilterTerms = newArray("no filtering", "include", "exclude"); //dont change this //var filterTerms = newArray("no filtering", "no filtering", "no filtering"); function getFilteredFileList(fileListFunction, filterOnInputList, displayList) { skippedFilter = 0; for (i = 0; i < filterStrings.length; i++) { if (filterTerms[i] != availableFilterTerms[0]) { returnedFileList = newArray(0); //this list stores all files found to have the extension and is returned at the end of the function for (j = 0; j < fileListFunction.length; j++) { if (filterTerms[i] == "include" && indexOf(fileListFunction[j],filterStrings[i]) != -1) returnedFileList = Array.concat(returnedFileList,fileListFunction[j]); if (filterTerms[i] == "exclude" && indexOf(fileListFunction[j],filterStrings[i]) <= 0) returnedFileList = Array.concat(returnedFileList,fileListFunction[j]); } print(returnedFileList.length + " file(s) found after filter: " + filterTerms[i] + " text " + filterStrings[i] + "."); if (displayList) {Array.show("List of files - after filtering for " + filterStrings[i], returnedFileList);} //see description above! default: filterOnInputList = false if(!filterOnInputList) fileListFunction = returnedFileList; } else skippedFilter++; } if (skippedFilter == filterStrings.length) returnedFileList = fileListFunction; //if no filter condition is selected return returnedFileList; } //function gets all files from folders and subfolders //example: myFileList = getFileListSubfolder("/home/myFolder/", true); function getFileListSubfolder(inputPathFunction, displayList) { fileListFunction = getFileList(inputPathFunction); //read file list Array.sort(fileListFunction); returnedFileList = newArray(0); //this list stores all found files and is returned at the end of the function for (i=0; i < fileListFunction.length; i++) { if ((File.separator == "\\") && (endsWith(fileListFunction[i], "/"))) fileListFunction[i] = replace(fileListFunction[i],"/",File.separator); //fix windows/Fiji File.separator bug if (endsWith(fileListFunction[i], File.separator)) { //if it is a folder returnedFileListTemp = newArray(0); returnedFileListTemp = getFileListSubfolder(inputPathFunction + fileListFunction[i], displayList); returnedFileList = Array.concat(returnedFileList, returnedFileListTemp); } else { //if it is a file returnedFileList = Array.concat(returnedFileList, inputPathFunction + fileListFunction[i]); //print(i, inputPath + fileList[i]); //to log window } } if(inputPathFunction == inputPath) { //if local variable is equal to global path variable = if path is folder and NOT subfolder print(returnedFileList.length + " file(s) found in selected folder and subfolders."); if (displayList) {Array.show("All files - all",returnedFileList);} } return returnedFileList; } //function filters all files with certain extension //example: myFileList = getFileType(myFileList, ".tif", true); function getFileType(fileListFunction, fileExtension, displayList) { returnedFileList = newArray(0); //this list stores all files found to have the extension and is returned at the end of the function if(lengthOf(fileExtension) > 0) { for (i = 0; i < fileListFunction.length; i++) { if (endsWith(fileListFunction[i],fileExtension)) returnedFileList = Array.concat(returnedFileList,fileListFunction[i]); } print(returnedFileList.length + " file(s) found with extension " + fileExtension + "."); if (displayList) {Array.show("All files - filtered for " + fileExtension, returnedFileList);} } else { returnedFileList = fileListFunction; } return returnedFileList; } //function filters a list for a certain string (filter) //example: myList = getFilteredList(myList, "myText", true); function getFilteredList(inputList, filterStringFunction, displayList { skippedFilter = 0; returnedList = newArray(0); //this list stores all items of the input list that were found to contain the filter string and is returned at the end of the function for (i = 0; i < inputList.length; i++) { if (indexOf(inputList[i],filterStringFunction) != -1) returnedList = Array.concat(returnedList,inputList[i]); } print(returnedList.length + " file(s) found after filtering: " + filterStringFunction); if (displayList) {Array.show("List after filtering for " + filterStringFunction, returnedFileList);} return returnedList; } //function returnes the unique wells of an array of CV7000 files //example: myUniqueWells = getUniqueWellListCV7000(myList, true); function getUniqueWellListCV7000(inputArray, displayList) { if (lastIndexOf(inputArray[0],"_T0") > 0) { //check first well currentWell = substring(inputArray[0],lastIndexOf(inputArray[0],"_T0")-3,lastIndexOf(inputArray[0],"_T0")); //first well found } else { print("no well found in path:", inputArray[i]); exit("No well information found in file name. Please double-check the file filtering..."); } returnedWellList = newArray(currentWell); //this list stores all unique wells found and is returned at the end of the function for (i = 1; i < inputArray.length; i++) { j = 0; //counter for returned well list valueUnique = true; //as long as value was not found in array of unique values if (lastIndexOf(inputArray[i],"_T0") > 0) { // if CV7000 file names are recognized while (valueUnique && (returnedWellList.length > j)) { //as long as value was not found in array of unique values and end of array is not reached currentWell = substring(inputArray[i],lastIndexOf(inputArray[i],"_T0")-3,lastIndexOf(inputArray[i],"_T0")); if (returnedWellList[j] == currentWell) { valueUnique = false; //if value was found in array of unique values stop while loop } else { j++; } } //end while } else { print("no well found in path:", inputArray[i]); } if (valueUnique) returnedWellList = Array.concat(returnedWellList, currentWell); //if value was not found in array of unique values add it to the end of the array of unique values } print(returnedWellList.length + " well(s) found."); Array.sort(returnedWellList); if (displayList) {Array.show("List of " + returnedWellList.length + " unique wells", returnedWellList);} return returnedWellList; } //function returnes the unique well files (all fields of all wells, e.g. G10_T0001F001) of an array of CV7000 files //example: myUniqueWellFileds = getUniqueWellFieldListCV7000(myList, true); function getUniqueWellFieldListCV7000(inputArray, displayList) { if (lastIndexOf(inputArray[0],"_T0") > 0) { //check first well field currentWellField = substring(inputArray[0],lastIndexOf(inputArray[0],"_T0")-3,lastIndexOf(inputArray[0],"_T0")+10); //first well field found } else { print("no well found in path:", inputArray[i]); exit("No well field information found in file name. Please double-check the file filtering..."); } returnedWellFieldList = newArray(currentWellField); //this list stores all unique wells fields found and is returned at the end of the function //print("start:", currentWellField, returnedWellFieldList.length); for (i = 0; i < inputArray.length; i++) { j = 0; //counter for returned well field list valueUnique = true; //as long as value was not found in array of unique values if (lastIndexOf(inputArray[i],"_T0") > 0) { // if CV7000 file names are recognized while (valueUnique && (returnedWellFieldList.length > j)) { //as long as value was not found in array of unique values and end of array is not reached currentWellField = substring(inputArray[i],lastIndexOf(inputArray[i],"_T0")-3,lastIndexOf(inputArray[i],"_T0")+10); //print(i,j,currentWellField, returnedWellFieldList[j]); if(returnedWellFieldList[j] == currentWellField) { valueUnique = false; //if value was found in array of unique values stop while loop } else { j++; } } //end while } else { print("no well field found in path:", inputArray[i]); } //print("final:", currentWellField, valueUnique, returnedWellFieldList.length); if (valueUnique) returnedWellFieldList = Array.concat(returnedWellFieldList, currentWellField); //if value was not found in array of unique values add it to the end of the array of unique values } print(returnedWellFieldList.length + " well field(s) found."); Array.sort(returnedWellFieldList); if (displayList) {Array.show("List of " + returnedWellFieldList.length + " unique well fields", returnedWellFieldList);} return returnedWellFieldList; } //function returnes the unique fields (all fields of all wells, e.g. F001, F002,...) of an array of CV7000 files //example: myUniqueFields = getUniqueFieldListCV7000(myList, true); function getUniqueFieldListCV7000(inputArray, displayList) { currentField = substring(inputArray[0],lastIndexOf(inputArray[0],"_T0")+6,lastIndexOf(inputArray[0],"_T0")+10); //first field found returnedFieldList = newArray(currentField); //this list stores all unique fields found and is returned at the end of the function for (i = 0; i < inputArray.length; i++) { j = 0; //counter for returned field list valueUnique = true; //as long as value was not found in array of unique values while (valueUnique && (returnedFieldList.length > j)) { //as long as value was not found in array of unique values and end of array is not reached currentField = substring(inputArray[i], lastIndexOf(inputArray[i],"_T0")+6, lastIndexOf(inputArray[i],"_T0")+10); if(returnedFieldList[j] == currentField) { valueUnique = false; //if value was found in array of unique values stop while loop } else { j++; } } //end while if (valueUnique) returnedFieldList = Array.concat(returnedFieldList, currentField); //if value was not found in array of unique values add it to the end of the array of unique values } print(returnedFieldList.length + " field(s) found."); Array.sort(returnedFieldList); if (displayList) {Array.show("List of " + returnedFieldList.length + " unique fields", returnedFieldList);} return returnedFieldList; } //function returnes the unique channels (e.g. C01) of an array of CV7000 files //example: myUniqueChannels = getUniqueChannelListCV7000(myList, true); function getUniqueChannelListCV7000(inputArray, displayList) { currentChannel = substring(inputArray[0],lastIndexOf(inputArray[0],".tif")-3,lastIndexOf(inputArray[0],".tif")); //first channel found returnedChannelList = newArray(currentChannel); //this list stores all unique channels found and is returned at the end of the function for (i = 1; i < inputArray.length; i++) { j = 0; //counter for returned channel list valueUnique = true; //as long as value was not found in array of unique values while (valueUnique && (returnedChannelList.length > j)) { //as long as value was not found in array of unique values and end of array is not reached currentChannel = substring(inputArray[i],lastIndexOf(inputArray[i],".tif")-3,lastIndexOf(inputArray[i],".tif")); if(returnedChannelList[j] == currentChannel) { valueUnique = false; //if value was found in array of unique values stop while loop } else { j++; } } //end while if (valueUnique) returnedChannelList = Array.concat(returnedChannelList, currentChannel); //if value was not found in array of unique values add it to the end of the array of unique values } print(returnedChannelList.length + " channel(s) found."); Array.sort(returnedChannelList); if (displayList) {Array.show("List of " + returnedChannelList.length + " unique channels", returnedChannelList);} return returnedChannelList; } //function saves the log window in the given path //example: saveLog("C:\\Temp\\Log_temp.txt"); function saveLog(logPath) { if (nImages > 0) currentWindow = getTitle(); selectWindow("Log"); saveAs("Text", logPath); if (nImages > 0) selectWindow(currentWindow); } //function returns a number in specific string format, e.g 2.5 => 02.500 //example: myStringNumber = getNumberToString(2.5, 3, 6); function getNumberToString(number, decimalPlaces, lengthNumberString) { numberString = "000000000000" + toString(number, decimalPlaces); //convert to number to string and add zeros in the front numberString = substring(numberString, lengthOf(numberString) - lengthNumberString, lengthOf(numberString)); //shorten string to lengthNumberString return numberString; } //////////////////////////////////////// E N D O F M A C R O ////////////////////////////