//Show-Help-and-Functions
macroName = "Show-Help-and-Functions";
macroShortDescription = "This macro writes links (URLs) to the documentation to the log window.";
macroDescription = "This macro writes links (URLs) to the documentation to the log window." +
"
Copy/paste into web browser to access the function of choise." +
"
Check box to open this macro containing all available function now.";
macroRelease = "first release 21-012015 by Martin Stöter (stoeter(at)mpi-cbg.de)";
macroHelpURL = "https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Macro-" + macroName;
macroHtml = ""
+"" + macroName + "\n" + macroRelease + "
"
+"" + macroDescription + "
"
+"Check for more help on this web page:
"
+"" + macroHelpURL + "
"
+"...get this URL from Log window!"
+"";
//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;
//////////////////////////////// M A C R O C O D E ///////////////////////////////
listedFunctions = newArray("no URL","getFileListSubfolder", "getFolderList", "getFileType", "getFilteredFileList", "setDialogImageFileFilter", "getFilteredList", "getUniqueArrayValues", "getUniqueWellListCV7000");
Dialog.create("Print web links to log window...");
Dialog.addCheckbox("Open all functions as macro?" false);
Dialog.addChoice("URLs to functions", listedFunctions, "no URL");
Dialog.show;
openMacro = Dialog.getCheckbox;
chosenFunction = Dialog.getChoice;
if(chosenFunction == "getFileListSubfolder") {
print("https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Useful-Functions-for-Fiji-Macros#Find_all_files_from_folders_and_subfolders_getFileListSubfolder");
}
if(chosenFunction == "getFolderList") {
print("https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Useful-Functions-for-Fiji-Macros#Find_all_folders_from_a_folder_getFolderList");
}
if(chosenFunction == "getFileType") {
print("https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Useful-Functions-for-Fiji-Macros#Filter_a_list_of_filespaths_for_a_certain_file_extension_getFileType");
}
if(chosenFunction == "getFilteredFileList") {
print("https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Useful-Functions-for-Fiji-Macros#Filter_a_list_of_filespaths_for_a_certain_stringtext_inside_the_path_getFilteredFileList");
}
if(chosenFunction == "setDialogImageFileFilter") {
print("https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Useful-Functions-for-Fiji-Macros#Opens_a_dialog_window_to_user_define_the_test_filters_setDialogImageFileFilter");
}
if(chosenFunction == "getFilteredList") {
print("https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Useful-Functions-for-Fiji-Macros#Filter_a_list_for_a_certain_stringtext_getFilteredList");
}
if(chosenFunction == "getUniqueArrayValues") {
print("https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Useful-Functions-for-Fiji-Macros#Find_unique_values_in_list_getUniqueArrayValues");
}
if(chosenFunction == "getUniqueWellListCV7000") {
print("https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Useful-Functions-for-Fiji-Macros#Find_unique_wells_in_file_list_of_CV7000getUniqueWellListCV7000");
}
if(openMacro) open(getDirectory("macros") + "Scripts" + File.separator + "Plugins" + File.separator + "TDS macros" + File.separator + "Development" + File.separator + "Macro_Show_Help_And_Functions.ijm");
/*
s1 = "This macro demonstrates how to display text in a text window.\n"
s2 = "It uses the Plugins>New>Text Window commad to open the window\n"
s3 = "if it is not already open. Note that newline characters (backslash-n) \n"
s4 = "https://github.com/stoeter/Fiji-Tools-for-HCS/wiki/Useful-Functions-for-Fiji-Macros#Find_unique_wells_in_file_list_of_CV7000getUniqueWellListCV7000\n"
requires("1.38m");
title1 = "Text Window";
title2 = "["+title1+"]";
f = title2;
if (isOpen(title1))
print(f, "\\Update:"); // clears the window
else
run("Text Window...", "name="+title2+" width=72 height=8 menu");
print(f, s1);
print(f, s2);
print(f, s3+s4);
*/
//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;
/////////////////////////////////////////////////////////////////////////////////////////////
//////// F U N C T I O N S /////////////
/////////////////////////////////////////////////////////////////////////////////////////////
var displayFileList = false; //shall array window be shown?
//function get all files from folders and subfolders
function getFileListSubfolder(inputPathFunction) {
fileList = getFileList(inputPathFunction); //read file list
Array.sort(fileList);
returnedFileList = newArray(0); //this list stores all found files and is returned at the end of the function
for (i=0; i < fileList.length; i++) {
if ((File.separator == "\\") && (endsWith(fileList[i], "/"))) fileList[i] = replace(fileList[i],"/",File.separator); //fix windows/Fiji File.separator bug
if (endsWith(fileList[i], File.separator)) { //if it is a folder
returnedFileListTemp = newArray(0);
returnedFileListTemp = getFileListSubfolder(inputPathFunction + fileList[i]);
returnedFileList = Array.concat(returnedFileList, returnedFileListTemp);
} else { //if it is a file
returnedFileList = Array.concat(returnedFileList, inputPathFunction + fileList[i]);
//print(i, inputPath + fileList[i]);
}
}
if(inputPathFunction == inputPath) { //if local variable is equal to global path variable = if path is folder and NOT subfolder
print(returnedFileList.length + " files found in selected folder and subfolders.");
if (displayFileList) {Array.show("All files - all",returnedFileList);}
}
return returnedFileList;
}
var displayFileList = false; //shall array window be shown?
//function get all folders from a folder
function getFolderList(inputPathFunction) {
fileListFunction = getFileList(inputPathFunction); //read file list
Array.sort(fileList);
returnedFileList = newArray(0); //this list stores all found files and is returned at the end of the function
for (i=0; i < fileList.length; i++) {
if ((File.separator == "\\") && (endsWith(fileList[i], "/"))) fileList[i] = replace(fileList[i],"/",File.separator); //fix windows/Fiji File.separator bug
if (endsWith(fileList[i], File.separator)) returnedFileList = Array.concat(returnedFileList,fileList[i]);//if it is a folder
}
print(returnedFileList.length + " folders were found.");
if (displayFileList) {Array.show("Found folders",returnedFileList);}
return returnedFileList;
}
var fileExtension = ".tif"; //pre-definition of extension
var displayFileList = false; //shall array window be shown?
//function finds all files with certain extension
function getFileType(fileListFunction) {
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 + " files found with extension " + fileExtension + ".");
if (displayFileList) {Array.show("All files - filtered for " + fileExtension, returnedFileList);}
} else {
returnedFileList = fileListFunction;
}
return returnedFileList;
}
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?
//function filter a file list for a certain string
function getFilteredFileList(fileListFunction) {
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 < fileList.length; j++) {
if (filterTerms[i] == "include" && indexOf(fileList[j],filterStrings[i]) != -1) returnedFileList = Array.concat(returnedFileList,fileListFunction[j]);
if (filterTerms[i] == "exclude" && indexOf(fileList[j],filterStrings[i]) <= 0) returnedFileList = Array.concat(returnedFileList,fileListFunction[j]);
}
print(returnedFileList.length + " files found after filter: " + filterTerms[i] + " text " + filterStrings[i] + ".");
if (displayFileList) {Array.show("List of files - after filtering for " + filterStrings[i], returnedFileList);}
fileListFunction = returnedFileList;
} else skippedFilter++;
}
if (skippedFilter == filterStrings.length) returnedFileList = fileListFunction; //if no filter condition is selected
return returnedFileList;
}
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?
//function open dialog to set image file list filter
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("Check 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();
}
var displayList = false; //shall array window be shown?
//function filter a list for a certain string (filter)
function getFilteredList(inputList, filterStringFunction) {
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 + " files found after filtering: " + filterStringFunction);
if (displayList) {Array.show("List after filtering for " + filterStringFunction, returnedFileList);}
return returnedList;
}
var displayList = false; //shall array window be shown?
//function returnes the unique values of an array
function getUniqueArrayValues(inputArray) {
outputArray = newArray(inputArray[0]); //outputArray stores unique values, here initioalitaion with first element of inputArray
for (i = 1; i < inputArray.length; i++) {
j = 0; //counter for outputArray
valueUnique = true; //as long as value was not found in array of unique values
while (valueUnique && (outputArray.length > j)) { //as long as value was not found in array of unique values and end of array is not reached
if(outputArray[j] == inputArray[i]) {
valueUnique = false; //if value was found in array of unique values stop while loop
} else {
j++;
}
} //end while
if (valueUnique) outputArray = Array.concat(outputArray,inputArray[i]); //if value was not found in array of unique values add it to the end of the array of unique values
}
print(outputArray.length + " unique values found.");
if (displayList) {Array.show("List of " + outputArray.length + " unique values", outputArray);}
return outputArray;
}
var displayList = false; //shall array window be shown?
//function returnes the unique wells of an array of CV7000 files
function getUniqueWellListCV7000(inputArray) {
currentWell = substring(inputArray[0],lastIndexOf(inputArray[0],"_T00")-3,lastIndexOf(inputArray[0],"_T00")); //first well found
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
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],"_T00")-3,lastIndexOf(inputArray[i],"_T00"));
if(returnedWellList[j] == currentWell) {
valueUnique = false; //if value was found in array of unique values stop while loop
} else {
j++;
}
} //end while
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 + " wells found.");
if (displayList) {Array.show("List of " + returnedWellList.length + " unique wells", returnedWellList);}
return returnedWellList;
}
//////////////////////////////////////// E N D O F M A C R O ////////////////////////////