a script for group1 2_EVA data. (MultipleFileTracking.py)

ptaScriptV5_G1_2eva.py

from ij import IJ, Prefs
from ij.gui import Roi
from ij.io import DirectoryChooser
from ij.plugin.frame import ThresholdAdjuster
from ij.process import ImageProcessor
from ij.plugin.filter import BackgroundSubtracter
from fiji.threshold import Auto_Threshold
from loci.plugins import BF
from pta import PTA
from pta.gui import ShowPdata
from pta.track import DetectParticle
from pta.data import PtaParam
from java.util import ArrayList

import os, csv

def CSVwrite(srcpath, msddata):
    parentdirectory = os.path.dirname(srcpath)
    filename = os.path.basename(srcpath)
    basename = os.path.splitext(filename)[0]
    for msd in msddata:
        thisid = msd.getID()
        coordsPath = os.path.join(parentdirectory, basename + "_" + str(int(thisid)) +"_coords.csv")
        msdPath = os.path.join(parentdirectory, basename + "_" + str(int(thisid)) + "_msd.csv")
        print coordsPath
        print msdPath
        f1 = open(coordsPath, 'wb')
        writer = csv.writer(f1)
        track = msd.getTrack()
        for node in track:
            writer.writerow([node.getCx(), node.getCy(), node.getParam()[1],node.getParam()[2]])
        f1.close()

        f2 = open(msdPath, 'wb')
        writer = csv.writer(f2)
        dtA = msd.getFullDFrames()
        msdA = msd.getFullMSD()
        for i in range(len(dtA)):
            writer.writerow([dtA[i], msdA[i]])
        f2.close()


def core(datafilepath):
    # load data as an ImagePlus object
    #imp = IJ.openImage(datafilepath)
    imp = BF.openImagePlus(datafilepath)[0]

    # default ROI = full frame
    scanAreaRoi = Roi(0,0,imp.getWidth(),imp.getHeight())

    IJ.run(imp,"Subtract Background...", "rolling=10 stack")
    #bs = BackgroundSubtracter()
    #for frame in range(imp.getStackSize()):
    #	ip = imp.getStack().getProcessor(frame + 1)
    #	bs.rollingBallBackground(ip, 10.0, False, False, False, False, False) 
    ip = imp.getProcessor()
    #ht = ip.getAutoThreshold()
    Prefs.blackBackground = True
    iphist = imp.getProcessor().getHistogram()
    #lt = Auto_Threshold.Intermodes(iphist)
    #lt = Auto_Threshold.Triangle(iphist)
    lt = Auto_Threshold.Moments(iphist) 
    ip.setThreshold(lt, ip.getMax(), ImageProcessor.RED_LUT)
    #ip.setThreshold(0, 111, ImageProcessor.RED_LUT)

    PTA.setDetectionState(True)
    #PTA.setDebugMode()
    # set no GUI mode
    PTA.setNoGUI(True)

    # set Detection Parameters
    ptap = PtaParam.Builder(16,16, False).build()

    ### paramter customizations
    #ptap.setDo2dGaussfit(False)
    ptap.setDo2dGaussfit(True) 
    #ptap.setMinIntensity(100.0)
    ptap.setSearchPointIncrement(2)

    # instantiate a DetectParticle object
    dp = DetectParticle(ptap,imp,scanAreaRoi, True)

    # set range of frames to analyze
    dp.setStackRange(1, imp.getStackSize())

    # start threads. 
    dp.start()
    # wait till the processing finishes
    dp.join()
    # stop the thread. 
    dp.interrupt()

    PTA.setDetectionState(False)

    # show detection results
    imp.show()

    # Particle lists
    #ll = dp.getalldplist()
    #print ll



    # track lists
    tracks = dp.getLinkedPointList()
    for t in tracks: 
       print t

    # MSD analysis
    msds = dp.getMSDres(5.0, True)
    print "msd data size", msds.size()
    for msd in msds:
       print msd.getID(), msd.getA(), msd.getB(), msd.getR()

    CSVwrite(datafilepath, msds)

    # discard the DetextParticle Object
    dp = None

    ##Back to the GUI mode: without this line, PTA GUI will not showup from next time. 
    PTA.setNoGUI(False)

srcDir = DirectoryChooser("Choose!").getDirectory()
IJ.log("directory: "+srcDir)
for root, directories, filenames in os.walk(srcDir):
    for filename in filenames:
        if filename.endswith(".tif"):
            path = os.path.join(root, filename)
            IJ.log(path)
            core(path)