spooookyghost.py

# Open a stack
# get number of slices in stack (s)
# ask for window size (w)
# ask for directory (d_a) for substack sequence
# ask for directory (d_b) for z-projection sequence
# iterate (i) from (w) to (s-w)
#     Things to do here:
#     -make a substack from (i-(w/2)) to (i+(w/2))
#     -save substack in (d_a)
# iterate (i) on sequence of substacks (w) to (s-w) in (d)
#     -do a z projection on each substack
#     -save z projection in (d_b)
#
# Or, if stack is already split into images:
# Ask for directory containing images (d_a)
# Ask for directory (d_b) for z-projection sequence
# Determine number of images (s) in (d_a)
# ask for window size (w)
# ask for directory (d_b) for z-projection sequence
# iterate (i) from (w) to (s-w)
#     Things to do here:
#     -make a substack from (i-(w/2)) to (i+(w/2))
#     -do a z projection on substack
#     -save z projection in (d_b)

import os
from ij.io import OpenDialog
from ij.io import DirectoryChooser
from ij.plugin import ZProjector
from ij import IJ, ImagePlus, VirtualStack, ImageStack, WindowManager
from ij import Menus
from ij.gui import GenericDialog
from java.awt import FileDialog

def run():
    # Choose a source directory
    srcDir = DirectoryChooser("Choose source directory").getDirectory()
    if srcDir is None:
        #if this is true, indicates that cancel was clicked, returns from function
        return
    # Prints source directory to log
    IJ.log("Directory: " + srcDir)
    # Prompts user to choose target directory
    targetdir = DirectoryChooser("Choose target dictionary").getDirectory()
    if targetdir is None:
        #returns, same as for source directory
        return

    # Make a preferences dialog box
    gd = GenericDialog('Preferences')
    #initialize window
    window = 0
    #add a numeric field for the window
    gd.addNumericField('Window: ', window, 0)
    #initialize z_proj_choice
    z_proj_choice = ''
    # make a list of Z projection types
    z_proj_types = ['projection=[Average Intensity]','projection=[Max Intensity]','projection=[Min Intensity]','projection=[Sum Slices]','projection=[Standard Deviation]','projection=[Median]']
    # add menu item for z projection types
    gd.addChoice('Z-projection type: ', z_proj_types, 'Average')
    #show dialog box
    gd.showDialog()
    #if user cancels dialog, return
    if gd.wasCanceled():
        IJ.log('User canceled dialog.')
        return
    #put interger form of user input in numeric field into window variable
    window = int(gd.getNextNumber())
    #put z projection choice into z_proj_choice variable
    z_proj_choice = gd.getNextChoice()
    #display window in log box
    IJ.log("Window: " + str(window))
    # display z projection choice in IJ log
    IJ.log("Z projection type: " + z_proj_choice)

    #walks through source directory: determines number of files, makes list of files
    walk_result = os.walk(srcDir)
    lst_walk_result = list(walk_result)
    files = lst_walk_result[0][2]
    number_of_files = len(lst_walk_result[0][2])
    IJ.log("Number of files in source directory: " + str(number_of_files))

    #iterate over range (window/2), number of files-(window/2):
    for i in range(window, (number_of_files - window + 1)):
        #for each i, open files (i-(w/2)) to (i+(w/2)) indexed in files list
        for n in range((i - window), (i + window)):
            path = os.path.join(srcDir, files[n])
            img = IJ.openImage(path)
            img.show()
        IJ.run("Images to Stack", "stack")
        IJ.run("Z Project...", z_proj_choice)
        imp = IJ.getImage()
        IJ.saveAs(imp, "PNG", targetdir + str(i-(window/2)))
        IJ.run("Close All")

run()