Useful Functions for Fiji Macros - stoeter/Fiji-Tools-for-HCS GitHub Wiki

Table of Contents Useful Functions for Fiji Macros Fiji functions for files/data input Find all files from folders and subfolders (getFileListSubfolder) Find all folders from a folder (getFolderList) Filter a list of files/paths for a certain file extension (getFileType) Filter a list of files/paths for a certain string/text inside the path (getFilteredFileList) Opens a dialog window to user define the test filters (setDialogImageFileFilter) Fiji functions for lists/arrays Filter a list for a certain string/text (getFilteredList) Find unique values in list (getUniqueArrayValues) Find unique wells in file list of CV7000 (getUniqueWellListCV7000) Find unique well fields in file list of CV7000 (getUniqueWellFieldListCV7000) Find unique channels in file list of CV7000 (getUniqueChannelListCV7000) Issues Latest changes

• This section lists some useful functions for development of new Fiji macros
• So far these function are helpful for:
  • handling and listing file/folder lists
  • filtering lists (in Fiji = arrays)
  • finding unique values in lists
• All function here start with the name 'get' if the function returns a value or array
• Copy & paste these functions at the and of your macro code and call them within your code
• For questions, bugs, requests... please contact stoeter at mpi-cbg.de

• Input:
  • a path that will be searched for files
• Output:
  • an array with all found files
• Reports:
  • Log window: number of found files
  • Array window: all files with complete paths that were found
• Dependencies:
  • directory name (string)
  • display array window (boolean)
• Example:

myFileList = getFileListSubfolder("/home/myFolder/", true);

• The function: .ijm here

• Input:
  • a path that will be searched for folders
• Output:
  • an array with all found folders
• Reports:
  • Log window: number of found folders
  • Array window: all folders with complete paths that were found
• Dependencies:
  • directory name (string)
  • display array window (boolean)
• Example:

myFolderList = getFolderList("/home/myFolder/", true);

• The function: .ijm here

• Input:
  • a list/array of files/paths
• Output:
  • a list/array of files with certain extension
• Reports:
  • Log window: number of found files with certain extension
  • Array window: all files with complete paths with certain extension
• Dependencies:
  • list of files/paths (array)
  • file extension (string)
  • display array window (boolean)
• Example:

myFileList = getFileType(myFileList, ".tif", true);

• The function: .ijm here

• Input:
  • a list/array of files/paths
• Output:
  • a filtered list/array of files with/without certain string/text
• Reports:
  • Log window: number of found files with certain strings/text
  • Array window: filtered files/paths for certain strings/text
• Dependencies:
  • list of files/paths (array)
  • additive(AND)/subsequent(OR) filtering (boolean)
    • hint: if true (= OR), then e.g. file names containing "H08" or "D04" are in the filtered list
    • hint: if false (= AND), then e.g. file names containing "controls" and "positive" are in the list (but not the negative controls)
  • display array window (boolean)
• Dependencies (global variables):
  • hints:
    • define text to be filtered in array filterStrings (default = 3, but can be extended)
    • define filter type in array filterTerms ("include" = files containing this string will be kept in the list, "exclude" = files not containing this string will be filtered out of the list, "no filtering" = for this string filter is not applied)
    • possible filter types are: "no filtering", "no filtering", "no filtering" (availableFilterTerms)
    • to create a dialog/user interactivity use the this function in combination with the setDialogImageFileFilter
  • e.g. copy/paste this at the beginning of the macro:

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 

• Example:

  myFileList = getFilteredFileList(myFileList, false, true);

• The function: .ijm here

• Input:
  • none
• Output:
  • none (changes variables)
• Reports:
  • none
• Dependencies (global variables):
  • hints:
    • set global variables to have default values
    • see explanation of variables and filter here
  • copy/paste this at the beginning of the macro:

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? 

• Example:

  setDialogImageFileFilter();

• The function: .ijm here

• Input:
  • a list/array
  • string to be found in list values
• Output:
  • a filtered list/array with certain extension
• Reports:
  • Log window: number of values in list after filtering
  • Array window: all list values after filtering
• Dependencies:
  • list of strings (array)
  • filter string (string)
  • display array window (boolean)
• Example:

myList = getFilteredList(myList, "myText", true);

• The function: .ijm here

• Input:
  • a list/array
• Output:
  • a list/array of unique values
• Reports:
  • Log window: number of unique values found in list
  • Array window: all unique values
• Dependencies:
  • list of strings (array)
  • display array window (boolean)
• Example:

  myUniqueValues = getUniqueArrayValues(myList, true);

• The function: .ijm here

• Input:
  • a list/array of files/paths from CV7000
• Output:
  • a list/array of unique wells
• Reports:
  • Log window: number of unique values found in list
  • Array window: all unique values
• Dependencies:
  • list of files/paths from CV7000 (array)
  • display array window (boolean)
• Example:

myUniqueWells = getUniqueWellListCV7000(myList, true);

• The function: .ijm here

• Input:
  • a list/array of files/paths from CV7000
• Output:
  • a list/array of unique well fields (e.g. G10_T0001F001)
• Reports:
  • Log window: number of unique values found in list
  • Array window: all unique values
• Dependencies:
  • list of files/paths from CV7000 (array)
  • display array window (boolean)
• Example:

  myUniqueWellFileds = getUniqueWellFieldListCV7000(myList, true);

• The function: .ijm here

• Input:
  • a list/array of files/paths from CV7000
• Output:
  • a list/array of unique channels (e.g. C01)
• Reports:
  • Log window: number of unique values found in list
  • Array window: all unique values
• Dependencies:
  • list of files/paths from CV7000 (array)
  • display array window (boolean)
• Example:

  myUniqueChannels = getUniqueChannelListCV7000(myList, true);

• The function: .ijm here

• make them available in Fiji by writing selected function of log or test window for copy paste
• re-write funtions in java and packages as .jar, then functions can be called easily within the macro and copy/paste becomes obsolete

• second release 16-03-2015: re-writing functions as individual file that are concatenated by script
  • re-writing of wiki documentation
• first release 20-01-2015: release of all developed functions so far