//CV7000-Z-Projection macroName = "CV7000-Image-Crop"; macroShortDescription = "This macro opens CV7000 images of a well-field-channel and does cropping based on a defined ROI."; macroDescription = "This macro reads single CV7000 images of a well as .tif ." + "\nThe chosen folder will be searched for images including subfolders." + "\nOption to select several input folders for batch processing at end of GUI." + "\nAll images of a unique well, field and channel are opened and cropped for a given ROI." + "\nROI dimension and position can be adjusted. Pixel size can be automatically corrected." + "\nCropped images can automatically overwrite and replace the input (raw) data, be saved in a separate folder 'Cropped', or saved with file tag (to be specified)." + "\nOption to copy CV7000 meta data files to output folder."; macroRelease = "2.0.0_260226"; macroAuthor = "by Martin Stöter (stoeter(at)mpi-cbg.de)"; generalHelpURL = "https://github.com/stoeter/Fiji-Tools-for-HCS/wiki"; macroHelpURL = generalHelpURL + "/" + macroName; //===== Script Parameters ===== #@ String spMacroTitle (label="===== Macro CV7000 Image crop =====", visibility=MESSAGE, required=false, description="This macro opens CV7000 images of a well-field-channel and does crops a defined ROI.\nFiji-Tools-for-HCS by TDS@MPI-CBG, Version 2.0.4_260203") #@ String spMacroSubTitle (label="----- use mouse-roll-over for help ----- ", visibility=MESSAGE, required=false, description="Essential configuration in orange. Non-persistent default values in dark blue.
For further help and hints see also in Log window...") // image input and output #@ String spInput (label="Select one or multiple CV7000 folders:", visibility=MESSAGE, required=false, description="Select CV7000 measurement folder, subfolders are included.\nOutput folder does not need to be specified") #@ File[] inputPaths (label="Input folders:", style="both", description="For multiple folders hold SHIFT / STRG ...") #@ File outputPath (label="Specific output folder?", style="directory", required=false, persist=false, description="Not essential. Per default projections will be saved in subfolder 'Cropped' of selected input folder.\nChange default output folder name selection 'Crop tag' as 'customize own tag'") //set crop secific settings #@ String spCrop (label="Cropping - Define settings ...", visibility=MESSAGE, required=false, description="Customize ROI cropping settings ...") #@ Integer cropWidth (label="Crop ROI width (x-dim.):", min=0, max=10000, value=1200, description="Specify width of crop ROI = dimension in x") #@ Integer cropHeight (label="Crop ROI height (y-dim.):", min=0, max=10000, value=1200, description="Specify height of crop ROI = dimension in y") #@ Integer cropXpos (label="Crop ROI x-position (x-pos.):", min=0, max=10000, value=680, description="Specify position of crop ROI = x-coordinate of top left corner of crop ROI") #@ Integer cropYpos (label="Crop ROI y-position (y-pos.):", min=0, max=10000, value=480, description="Specify position of crop ROI = y-coordinate of top left corner of crop ROI") #@ String cropFileTag (label="Crop tag:", choices={"*NONE*", "_cropped", "_small", "customize own tag"}, style="listBox", description="Customize file tag for cropped image, e.g. *NONE* = as input file, ..._cropped.tif, or _200x200..., or ... customize default output folder name (customize own tag)") #@ Boolean overwriteImage (label="Overwrite input image in same folder?", value=false, persist=false, description="If checked the input files and raw data will be overwritten in same folder. When unchecked (default) cropped images are saved in a subfolder (Cropped).") // image file filter #@ String spImageFileFilter (label="Image file filter - Define the files to be processed ...", visibility=MESSAGE, required=false, description="This feature helps to shape and filter the file list to obtain a specific set of image files") #@ String fileExtension (label="Files should have this extension:", value=".tif", persist=false, description="Enter an image extension (like '.tif') to e.g. exclude file types other than CV7000 meta data files") #@ String spDefineFilter (label="Define filter for files:", visibility=MESSAGE, required=false, description="Below three consecutive filters can be configured to include or exclude files based on a specific text tags") #@ String filterStrings0 (label="1) Filter this text from file list:", value="", description="Enter text to specify file names (1), e.g for channel: C01.tif") #@ String filterTerms0 (label="1) Files with text are included/excluded?", choices={"no filtering", "include", "exclude"}, persist=false, style="radioButtonHorizontal", description="Choose to include or exclude files with specific text (1)") #@ String filterStrings1 (label="2) Filter this text from file list:", value="", description="Enter text to specify file names (2), e.g. for well: _C05_") #@ String filterTerms1 (label="2) Files with text are included/excluded?", choices={"no filtering", "include", "exclude"}, persist=false, style="radioButtonHorizontal", description="Choose to include or exclude files with specific text (2)") #@ String filterStrings2 (label="3) Filter this text from file list:", value="", description="Enter text to specify file names (3), ...") #@ String filterTerms2 (label="3) Files with text are included/excluded?", choices={"no filtering", "include", "exclude"}, persist=false, style="radioButtonHorizontal", description="Choose to include or exclude files with specific text (3)") #@ Boolean displayFileList (label="Display the file lists?", value=false, persist=false, description="If checked the file lists are displyed at each step of the Image file filter") //if check file lists will be displayed #@ Boolean displayMetaData (label="Display unique values of meta data?", value=false, persist=false, description="If checked unique values of meta data from file names (like wells, fields, channel, etc.) are displyed in separate windows") //if check file lists will be displayed //set general settings #@ String spGeneral (label="General settings ...", visibility=MESSAGE, required=false, description="Select other general features of the script") #@ Boolean doPixelSizeCorr (label="Automatically correct pixel size?", value=true, persist=false, description="If checked .mrf file will be read and the pixel size will be corrected") #@ Boolean copyMetaDataFiles (label="Copy CV7000 meta data files?", value=false, persist=false, description="If checked meta data files from CV7000, such as .mrf, .mes, correction files, etc., will be copied to the output path") #@ Boolean batchMode (label="Set batch mode (hide images)?", value=true, persist=false, description="If checked no images will be displayed while processing") //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(macroDescription); print(macroHelpURL); print(generalHelpURL); // ===== organize oupput folder stttings ===== print("\n=== Input / Output settings ===\nInput path(s):"); for (i = 0; i < inputPaths.length; i++) { inputPaths[i] = inputPaths[i] + File.separator; print(inputPaths[i]); } //Array.show(inputPaths); print("In total", inputPaths.length, "folder(s) will be processed..."); // ===== organize output (folder) settings ===== defaultOutputfolderName = "Cropped"; // if no selection in script parameters, then it is output path is ImageJ path!?? Set variavle outputPathSelected then to 0, it is 1 when an outputPath was selected //print((replace(outputPath + File.separator, File.separator, "/") == replace(getDir("imagej") , File.separator, "/"))); //outputPathSelected = !( replace(outputPath + File.separator, File.separator, "/") == replace(getDir("imagej") , File.separator, "/") ); // cannot compare strings with backslash!??? //if (outputPath == 0) outputPathSelected = false; // if nothing is selected in GUI then the return value will be 0, not NA or null (see here: https://forum.image.sc/t/issue-with-script-parameter-file-in-fiji-when-not-selected-and-the-getdir-imagej-function/91420) //print(outputPathSelected); //set output crop folder name if (cropFileTag == "customize own tag") { // user defined output folder name Dialog.create("Set specific crop file tag options (*NONE*=as input file)"); Dialog.addString("Crop file tag:", "_cropped"); Dialog.addString("Change default output folder name?", defaultOutputfolderName); Dialog.show(); cropFileTag = Dialog.getString(); defaultOutputfolderName = Dialog.getString(); print("Default output folder was set to:", defaultOutputfolderName); } if (cropFileTag == "*NONE*") cropFileTag = ""; if ( (inputPaths.length > 1) || outputPath == 0 ) { // if nothing is selected in GUI then the return value of outpuPath will be 0 (see above) print("Selected output path will be ignored and output folders will be generated automatically in each input folder"); outputPathSelected = false; } else { outputPath = outputPath + File.separator; print("Output path:", outputPath, ""); outputPathSelected = true; } //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 save copy_column copy_row save_column save_row"); // set byte order to little-Endian / Intel -> 'save' run("Close All"); //run("Color Balance..."); //////////////////////////////// M A C R O C O D E /////////////////////////////// //set variables var CV7000metadataFileList = newArray(0); //initialize - list of files (metadata forom CV7000) that will be copied to outoutPath doubleCheckOverwriting = 1; //set array variables var defaultFilterStrings = newArray("DC_sCMOS #","SC_BP",""); print("\nFiles (images) containing these strings will be automatically filtered out:"); Array.print(defaultFilterStrings); //pre-definition of extension var filterStrings = newArray(filterStrings0, filterStrings1, filterStrings2); // get variable settings from script parameter GUI var availableFilterTerms = newArray("no filtering", "include", "exclude"); //dont change this var filterTerms = newArray(filterTerms0, filterTerms1, filterTerms2); // get variable settings from script parameter GUI //setDialogImageFileFilter(); //replaced by scrip parameters filterStringsUserGUI = filterStrings; //store strings that user enterd in "backup variable" filterTermsUserGUI = filterTerms; //store terms that user enterd in "backup variable" print("Image file filter:", filterTerms[0],filterStrings[0] + ";",filterTerms[1],filterStrings[1] + ";",filterTerms[2],filterStrings[2]); // start looping over all folders for (currentFolder = 0; currentFolder < inputPaths.length; currentFolder++) { // folder by folder inputPath = inputPaths[currentFolder]; // need to create static variable here from current array value, because a funtion (getFileListSubfolder) need to check against this global variable print("\n================== starting processing folder #" + (currentFolder + 1) + "... ===================="); print("Preparation for folder #" + (currentFolder + 1) + ":", inputPaths[currentFolder]); //to log window // if multiple folders are selected or no outputPath was selected (see above) then make default output folder in input folder if (!outputPathSelected) { if (overwriteImage) { print("Output folder = input folder -> possible overwriting of files (!) ... "); //to log window outputPath = 0; // outputPath not know at this stage (only later when tif is opened), therefore set it o 0, if nothing is selected in GUI then the return value of outpuPath will be 0 (see above) } else { //outputPath = substring(inputPaths[currentFolder], 0, lastIndexOf(inputPaths[currentFolder], File.separator)) + File.separator + "Zprojection" + File.separator; outputPath = inputPath + defaultOutputfolderName + File.separator; File.makeDirectory(outputPath); print("New output folder -> made folder for cropped files: " + outputPath); //to log window } } //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 saveLog(outputPath + "Log_temp_" + tempLogFileNumber + ".txt"); print("Processing file list..."); // for multiple folders from second iteration on the several lists need to be updated/reseted for next iteration, like fileList, CV7000metadataFileList, well/field/channelList, filterStrings/Terms(user/GUI variables) if (currentFolder > 0) { // dont do on first iteration: from second iteration on, get file list from new folder CV7000metadataFileList = newArray(0); // reset the meta data file list filterStrings = filterStringsUserGUI; //restore user enterd strings from "backup variable" filterTerms = filterTermsUserGUI; displayFileList = false; // dont display lists after the first iteration displayMetaData = false; } //get file list ALL fileList = getFileListSubfolder(inputPaths[currentFolder], displayFileList); //read all files in subfolders fileList = getFileTypeAndCV7000metaDataFiles(fileList, fileExtension, displayFileList); // new funtion to store the CV7000 meta data files in separate list (CV7000metadataFileList) filterStrings = filterStringsUserGUI; //restore user enterd strings from "backup variable" filterTerms = filterTermsUserGUI; //restore user enterd terms from "backup variable" fileList = getFilteredFileList(fileList, false, displayFileList); //filter for strings if (fileList.length == 0) { print("No files to process, folder is skipped..."); //print current time to Log window and save log getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec); month++; if ((currentFolder + 1 ) < inputPaths.length) { print("Macro executed successfully for this folder.\nFinished folder:", inputPaths[currentFolder],"at", year+"-"+month+"-"+dayOfMonth+", h"+hour+"-m"+minute+"-s"+second); } else { print("Macro executed successfully.\nEnd:",year+"-"+month+"-"+dayOfMonth+", h"+hour+"-m"+minute+"-s"+second); } saveLogFinal(logPath, tempLogFileNumber); continue; } //print("removing correction files from file list containing text", defaultFilterStrings[0], defaultFilterStrings[1], defaultFilterStrings[2]); wellList = getUniqueWellListCV7000(fileList, displayMetaData); wellFieldList = getUniqueWellFieldListCV7000(fileList, displayMetaData); fieldList = getUniqueFieldListCV7000(fileList, displayMetaData); zPlaneList = getUniqueZplaneListCV7000(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"); if (currentFolder == 0) { // in first iteration check stack size and options //print("fileList.length, wellFieldList.length, channelList.length", fileList.length, wellFieldList.length, channelList.length); if (displayFileList || displayMetaData) waitForUser("Take a look at the list windows..."); //give user time to analyse the lists } print("Overwriting input images (0=false, 1=true):", overwriteImage, "copy CV700 meta data files:", copyMetaDataFiles, "using file tag:", cropFileTag); //print(outputPath); //saveLog(outputPath + "Log_temp_" + tempLogFileNumber + ".txt"); if (doPixelSizeCorr) pixelSizeMrf = readMRFfile(inputPaths[currentFolder]); // get pixel size from .mrf file print("\n===== starting processing files... ====="); setBatchMode(batchMode); print("Input path is:", inputPaths[currentFolder]); if (copyMetaDataFiles) copyFiles(CV7000metadataFileList, outputPath); //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); if (currentWellField == 0) updateMRFfile(inputPath, cropWidth, cropHeight, channelList[currentChannel]); //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 if (!outputPathSelected & overwriteImage) { //print(File.directory); outputPath = File.directory; } outputFileName = substring(currentImage, 0, lengthOf(currentImage) - 4) + cropFileTag + ".tif"; // if cropFileTag == "*NONE*" => cropFileTag = "" means like input file name if (doPixelSizeCorr) correctPixelSize(pixelSizeMrf); // do pixel size / unit correction run("Specify...", "width=" + cropWidth + " height=" + cropHeight + " x=" + cropXpos+ " y=" + cropYpos); run("Crop"); if (doubleCheckOverwriting) { // default and intiallysed as 1 = true; safety rule, before overwriting for the first time, as the user for confirmation on all subsequent files and folders if (File.exists(outputPath + outputFileName)) { print("\n === WARNING!!! ===\n This file exists:\n", outputPath + outputFileName); print("If you ckeck the box and continue, then ALL the files with the same name will be OVERWRITTEN from here on !!!"); Dialog.create("=== WARNING! ==="); Dialog.addMessage(" === WARNING! ===\nDo you really want to overwrite files?", 18, "#ff0000"); Dialog.addMessage("Please check also log file...."); Dialog.addCheckbox("Confirm overwriting files (tick for 'yes')?", false); Dialog.show(); doubleCheckOverwriting = !(Dialog.getCheckbox()); // is !true => false if overwriting is confirmed print("Overwriting confirmation was set to:", !doubleCheckOverwriting); //here if checked !!true => true if (doubleCheckOverwriting) { print("EXIT: overwriting was not confirmed!\n Please select not to overwrite in the GUI upon scipt launch or select other than *NONE* file tag."); saveLogFinal(outputPath, tempLogFileNumber); exit("EXIT: overwriting was not confirmed!\nPlease see log..."); } } // file exists } // double checking overwriting saveAs("Tiff", outputPath + outputFileName); print("saved cropped image as " + outputPath + outputFileName); //to log window close(); } else { print("file not found (" + (currentFile + 1) + "/" + wellChannelFileList.length + "):", wellChannelFileList[currentFile]); //to log window } //end for all images per wellField showProgress(currentFile / wellChannelFileList.length); showStatus("processing" + fileList[currentFile]); } //end for all images per channel //waitForUser("done"); run("Close All"); } //end for all channels in well // clear memory print("current memory:", parseInt(IJ.currentMemory())/(1024*1024*1024), "GB"); run("Collect Garbage"); print("memory after clearing:", parseInt(IJ.currentMemory())/(1024*1024*1024), "GB"); 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++; if ((currentFolder + 1 ) < inputPaths.length) { print("Macro executed successfully for this folder.\nFinished folder:", inputPaths[currentFolder],"at", year+"-"+month+"-"+dayOfMonth+", h"+hour+"-m"+minute+"-s"+second); } else { print("Macro executed successfully.\nEnd:",year+"-"+month+"-"+dayOfMonth+", h"+hour+"-m"+minute+"-s"+second); } // set byte order again to standard run("Input/Output...", "jpeg=95 gif=-1 file=.txt copy_column copy_row save_column save_row"); saveLogFinal(outputPath, tempLogFileNumber); } // unitl here processing of multiple folders ///////////////////////////////////////////////////////////////////////////////////////////// //////// F U N C T I O N S ///////////// ///////////////////////////////////////////////////////////////////////////////////////////// //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++) { //print(i, inputPathFunction + fileListFunction[i]); if ((File.separator == "\\") && (endsWith(fileListFunction[i], "/"))) fileListFunction[i] = replace(fileListFunction[i],"/",File.separator); //fix windows/Fiji File.separator bug //print("fixed", i, inputPathFunction + fileListFunction[i]); 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, inputPathFunction + fileListFunction[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 = getFileTypeAndCV7000metaDataFiles(myFileList, ".tif", true); function getFileTypeAndCV7000metaDataFiles(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 defaultCV7000metadataFileExtensionList = newArray(".icr", ".mes", ".mlf", ".mrf", ".wpi", ".wpp", ".xml"); if (lengthOf(fileExtension) > 0) { for (i = 0; i < fileListFunction.length; i++) { if (endsWith(fileListFunction[i], fileExtension)) { // if this is e.g. .tif if (indexOf(fileListFunction[i], defaultFilterStrings[0]) > 0 || // is "DC_sCMOS #" indexOf(fileListFunction[i], defaultFilterStrings[1]) > 0) { // is "SC_BP" CV7000metadataFileList = Array.concat(CV7000metadataFileList, fileListFunction[i]); print("Added " + fileListFunction[i] + " to CV7000 meta data file list"); } else { returnedFileList = Array.concat(returnedFileList, fileListFunction[i]); } } else { // if this file has other file extension if (endsWith(fileListFunction[i], defaultCV7000metadataFileExtensionList[0]) || endsWith(fileListFunction[i], defaultCV7000metadataFileExtensionList[1]) || endsWith(fileListFunction[i], defaultCV7000metadataFileExtensionList[2]) || endsWith(fileListFunction[i], defaultCV7000metadataFileExtensionList[3]) || endsWith(fileListFunction[i], defaultCV7000metadataFileExtensionList[4]) || endsWith(fileListFunction[i], defaultCV7000metadataFileExtensionList[5]) || endsWith(fileListFunction[i], defaultCV7000metadataFileExtensionList[6]) //endsWith(fileListFunction[i], defaultCV7000metadataFileExtensionList[7]) // see definition of array defaultCV7000metadataFileExtensionList in the beginning ) { CV7000metadataFileList = Array.concat(CV7000metadataFileList, fileListFunction[i]); print("Added " + fileListFunction[i] + " to CV7000 meta data file list"); } } } print(returnedFileList.length + " file(s) found with extension " + fileExtension + "."); print(CV7000metadataFileList.length + " file(s) of CV7000 meta data found"); if (displayList) {Array.show("All files - filtered for " + fileExtension, returnedFileList);Array.show("CV7000 meta data files", CV7000metadataFileList);} } else { returnedFileList = fileListFunction; } return returnedFileList; // note: metadataFileList is globel variable (var) and does not need to be returned } //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); Array.print(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); Array.print(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); Array.print(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); Array.print(returnedChannelList); if (displayList) {Array.show("List of " + returnedChannelList.length + " unique channels", returnedChannelList);} return returnedChannelList; } //function returnes the unique z-planes (e.g. Z01) of an array of CV7000 files //example: myUniqueZplanes = getUniqueZplaneListCV7000(myList, true); function getUniqueZplaneListCV7000(inputArray, displayList) { currentZplane = substring(inputArray[0],lastIndexOf(inputArray[0],".tif")-6,lastIndexOf(inputArray[0],".tif")-3); //first Zplane found returnedZplaneList = newArray(currentZplane); //this list stores all unique Zplanes found and is returned at the end of the function for (i = 1; i < inputArray.length; i++) { j = 0; //counter for returned Zplane list valueUnique = true; //as long as value was not found in array of unique values while (valueUnique && (returnedZplaneList.length > j)) { //as long as value was not found in array of unique values and end of array is not reached currentZplane = substring(inputArray[i],lastIndexOf(inputArray[i],".tif")-6,lastIndexOf(inputArray[i],".tif")-3); if(returnedZplaneList[j] == currentZplane) { valueUnique = false; //if value was found in array of unique values stop while loop } else { j++; } } //end while if (valueUnique) returnedZplaneList = Array.concat(returnedZplaneList, currentZplane); //if value was not found in array of unique values add it to the end of the array of unique values } print(returnedZplaneList.length + " Zplane(s) found."); Array.sort(returnedZplaneList); Array.print(returnedZplaneList); if (displayList) {Array.show("List of " + returnedZplaneList.length + " unique Zplanes", returnedZplaneList);} return returnedZplaneList; } //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 saves the log window in the given folder and deleted tempLofFile //example: saveLogFinal("C:\\Temp\\"); function saveLogFinal(logPath, tempLogFileNumber) { getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec); month++; if (nImages > 0) currentWindow = getTitle(); 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 } 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; } //function detemins the current pixel size and unit of an image and corrects it this the given parameter // if pixel size paramweter is <= 0 no correction of pixel size will be done //example: correctPixelSize(pixelSizeMrf) function correctPixelSize(pixelSizeMrf) { if (pixelSizeMrf <= 0) return; getPixelSize(pixelUnit, pixelWidth, pixelHeight); if (pixelUnit == "inches") { // default, but wrong in CV7000 images print("Pixel units:", pixelUnit, "; pixel size and unit will be corrected."); Stack.setXUnit("um"); Stack.setYUnit("um"); run("Properties...", "channels=1 slices=1 frames=1 pixel_width=" + pixelSizeMrf + " pixel_height=" + pixelSizeMrf + " voxel_depth=1"); } else { print("Pixel size was already adapted. No correction will be done. Pixel units and sizes are:", pixelUnit, pixelWidth, pixelHeight); } } //function reads the CV7000 .mrf file and detemins the pixel size //example: pixelSizeMrf = readMRFfile(inputPath) function readMRFfile(inputPath) { mrfFilePath = inputPath + "MeasurementDetail.mrf"; for (i = 0; i < CV7000metadataFileList.length; i++) { // try to find .mrf file in CV7000metadataFileList if (endsWith(CV7000metadataFileList[i], ".mrf")) { print("found .mrf file in meta data file list:", CV7000metadataFileList[i]); mrfFilePath = CV7000metadataFileList[i]; } } pixelSizeMrf = 0; // by default initialize value that is given back by this function doPixelSizeCorr = true; // function variable that checks it pixel sizes are unique in .mrf, otherwise funtion will return -1 // open .mrf file and split into line array if (!File.exists(mrfFilePath)) { print("Could not find .mrf file:", mrfFilePath, "\nPixel size could not be determined and is not automatically corrected!"); return -1; } else { mrfFile = File.openAsString(mrfFilePath); lines = split(mrfFile,"\n"); print("Reading .mrf file... length:", mrfFile.length, "; lines:", lines.length); // go through each line and fine dimension for each channel for (line = 0; line < lines.length; line++) { if (matches(lines[line], "(.*Dimension.*)") ) { splitLines = split(lines[line], "\""); channelMrf = splitLines[1]; if (pixelSizeMrf == 0) { // on first iteration pixelSizeMrf = splitLines[3]; } else { if (pixelSizeMrf != splitLines[3] && doPixelSizeCorr) { // if multiple pixel sizes or no correction print("Multiple pixel sizes in .mrf file. No correction of pixel sizes will be applied, because this could lead to mistakes..."); doPixelSizeCorr = false; pixelSizeMrf = splitLines[3]; } else { // if all is normal pixelSizeMrf = splitLines[3]; } } print("Channel", channelMrf, "has pixel size of", pixelSizeMrf, "um/px"); } // line matches } // for each line if (doPixelSizeCorr == false) { return -1; // if multiple pixel sizes in .mrf, then return -1 as pixel size } else { return pixelSizeMrf; } } // if exists } // function //function changes the CV7000 .mrf file and updates the image dimension for the cropped image and channel //example: updateMRFfile(inputPath, cropWidth, cropHeight, channel); function updateMRFfile(inputPath, cropWidth, cropHeight, channel) { mrfFilePath = inputPath + "MeasurementDetail.mrf"; channelNumber = substring(channel, 2, 3); for (i = 0; i < CV7000metadataFileList.length; i++) { // try to find .mrf file in CV7000metadataFileList if (endsWith(CV7000metadataFileList[i], ".mrf") & !(endsWith(CV7000metadataFileList[i], "_original.mrf"))) { print("found .mrf file in meta data file list:", CV7000metadataFileList[i]); mrfFilePath = CV7000metadataFileList[i]; } } // open .mrf file and split into line array if (!File.exists(mrfFilePath)) { print("Could not find .mrf file:", mrfFilePath, "\n.mrf file could not be updated!"); return -1; } else { mrfFilePathOriginal = substring(mrfFilePath, 0, lengthOf(mrfFilePath) - 4) + "_original.mrf"; if (!File.exists(mrfFilePathOriginal)) { print("Saving original .mrf file under new name:", mrfFilePathOriginal); File.copy(mrfFilePath, mrfFilePathOriginal); } else { print("Original .mrf file was already saved under new name:", mrfFilePathOriginal); } mrfFile = File.openAsString(mrfFilePath); lines = split(mrfFile,"\n"); //Array.show("MRF file", lines); print("Reading .mrf file... length:", mrfFile.length, "; lines:", lines.length); //for (i = 0; i < lines.length; i++) print(lines[i]); // go through each line and fine dimension for each channel for (line = 0; line < lines.length; line++) { if (matches(lines[line], "(.*bts:Ch=\"" + channelNumber + "\".*)") ) { //print(lines[line]); splitLines = split(lines[line], "\""); //for (i = 0; i < splitLines.length; i++) print(i, splitLines[i]); print("Original .mrf dimensions for channel", splitLines[1], "are:", splitLines[12] + splitLines[13], "; and", splitLines[14] + splitLines[15]); print("Croping reduces file size to", d2s((cropWidth * cropHeight) / (splitLines[13] * splitLines[15]) / 100, 2), "%."; splitLines[13] = cropWidth; splitLines[15] = cropHeight; print("Updated .mrf dimensions for channel", splitLines[1], "are:", splitLines[12] + splitLines[13], "; and", splitLines[14] + splitLines[15]); lines[line] = String.join(splitLines, "\""); //print(lines[line]); } // line matches } // for each line mrfFile = String.join(lines,"\n"); File.saveString(mrfFile, mrfFilePath); print("Updaed and saved the .mrf file ..."); } // if exists } // function //function copies files (the metadata files from CV7000) to destination folder //example: copyFiles(metadataFileList, outputPath); function copyFiles(listOfFilePaths, outputPath) { // go through the list of file path, get file name and copy to destination folder for (i = 0; i < listOfFilePaths.length; i++) { currentFile = substring(listOfFilePaths[i], lastIndexOf(listOfFilePaths[i], File.separator) + 1); File.copy(listOfFilePaths[i], outputPath + currentFile); print("copied:", currentFile); } //end for } // function //////////////////////////////////////// E N D O F M A C R O ////////////////////////////