ImageJ/Fiji plugin: Extracts frames from a multi-frame TIFF file and saves them into a new multi-frame TIFF

extract_z_slices_from_sequence_into_one_tiff.py

import os
import os.path
import glob
from loci.plugins.util import BFVirtualStack
from loci.formats import ImageReader
from ij import ImagePlus, ImageStack
from ij import IJ
from ij.io import DirectoryChooser
from ij.gui import GenericDialog


def getOptions():
    gd = GenericDialog("Options")
    # show 2 decimals
    gd.addStringField("Z indices to extract (comma separated)", "1,2")
    gd.showDialog()
    #
    if gd.wasCanceled():
        print "User canceled dialog!"
        return
    # Read out the options
    z_to_extract = gd.getNextString()
    return z_to_extract


def run():
    # Choose a file to open
    srcDir = DirectoryChooser("Choose source directory").getDirectory()
    if srcDir is None:
        # User canceled the dialog
        return

    # Choose a directory to store each slice as a file
    targetDir = DirectoryChooser("Choose target directory").getDirectory()
    if targetDir is None:
        # User canceled the dialog
        return

    # Open each tif stack as a virtual BFVirtualStack
    # then, extract the nth z slice and save it as a tif file in the out dir
    z_to_extract = getOptions()
    out_stack = False

    dirlist = glob.glob(srcDir + '*.tif')
    file_map = {}
    for filename in dirlist:
        fn, fext = os.path.splitext(filename)
        nr = fn.split('X')[-1]
        print nr
        file_map[int(nr)] = filename
    #file_map_ordered = collections.OrderedDict(sorted(file_map.items()))

    for i in sorted(file_map):
        for z in z_to_extract.split(','):
            filename = file_map[i]
            print "Reading metadata from", filename
            fn, fext = os.path.splitext(filename)
            ir = ImageReader()
            ir.setId(filename)
            bfvs = BFVirtualStack(filename, ir, False, False, False)
            print z
            ipr = bfvs.getProcessor(int(z))
            if not out_stack:
                out_stack = ImageStack(ipr.getWidth(), ipr.getHeight())
            out_stack.addSlice(ipr)
    print out_stack, out_stack.getSize()
    print "Saving to ",  targetDir + os.path.basename(fn) + '.tif'
    IJ.save(ImagePlus('Concatenated stack', out_stack),
            targetDir + os.path.basename(fn) + '_extracted' + '.tif')

run()