extract_slices.template

// extract_slices.template version 1.0 (June 2019)
// CAUTION: This is a *template file* which contains invalid ImageJ characters.
// Therefore you cannot run it directly. R analyse_actin.sh instead.

setBatchMode(true);

// Retrieve the name of a TIFF file received as argument, loads it and returns 
// its parameters (width and height, number of channels, slices and frames). 
inputPath = getArgument();
open(inputPath);
getDimensions(width, height, channels, slices, frames);

// Here we define some useful file aliases that will help us to create 
// output file names. For more details see online ImageJ macro documentation.
fileName = File.getName(inputPath);
fileBase = File.nameWithoutExtension;
filePath = File.getParent(inputPath);
// File.getParent returns 0 when the file is located in the current folder.
// In that case we redefine filePath as "." (standard name for current folder). 
if (filePath == 0) {filePath = ".";};

// Here we create folders for confocal slices and pixel data (= matrices).
sliceDir = fileBase + "_slices";
pixelDir = fileBase + "_pixels";
File.makeDirectory(filePath + File.separator + sliceDir);
File.makeDirectory(filePath + File.separator + pixelDir);

// Now we can tell ImageJ to convert the TIFF stack to individual images.
run("Stack to Images");

// Here we allow the user to define the upper limit for the slices to keep.
// This is because photobleaching occurs over time and the latest slices from a 
// given stack may be of poor quality.
maxSlices = <max_slices>;
if (slices < maxSlices) {upperLimit = slices;} else {upperLimit = maxSlices;};

for(i = 1; i <= upperLimit; i++) {
  // There is no printf-like formatter in ImageJ macros.
  // To achieve 0001, ..., 0010, ..., 0100 we calculate the number of zeroes to
  // add in front of the number fo maintain a constant length of 4 (znum) and 
  // later extract the corresponding substring from a template (zpad).
  znum = floor(log(i) / log(10)) + 1;
  zpad = substring("000000000000", 0, 4 - znum);
  // This is the name of the current slice we are working with.
  curSlice = fileBase + "-" + zpad + i;
  selectWindow(curSlice);
  // We save the slice as a matrix and as a TIFF image.
  saveAs("Text Image", filePath + File.separator 
                     + pixelDir + File.separator 
                     + curSlice + ".txt");
  saveAs("Tiff", filePath + File.separator 
               + sliceDir + File.separator 
               + curSlice + ".tif");
  // Not mandatory but this will also free some memory...
  close();
}

// We print width, height and matrix directory for use by the next script!
print(width, height, pixelDir);
setBatchMode(false);