SingleFileTrackingAdv.py

ptaScriptV3_5.py

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

'''
a function for writing CSV files, 
1. XY coordinates and sigma_x, sigma_y for each track
2. timescale and MSD for each track. 
''' 
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()

datafilepath = "/Users/miura/Dropbox/20130805_Osaka/data/transferrin-movement/tconc10_16.tif"
#datafilepath = "/Users/araiyoshiyuki/Desktop/spool-tub_2-2.tif"

# 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())

# ip = imp.getProcessor()
IJ.run(imp,"Subtract Background...", "rolling=10 stack")
# above IJ.run method could be written in a lower way like the following. 
#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()
iphist = ip.getHistogram()
Prefs.blackBackground = True
# **** Auto Threshold Algorithm should be examined before running the script. 
#lt = Auto_Threshold.Intermodes(iphist)
#lt = Auto_Threshold.Triangle(iphist)
lt = Auto_Threshold.Moments(iphist)
ip.setThreshold(lt, ip.getMax(), ImageProcessor.RED_LUT)

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

# set Detection Parameters
ptap = PtaParam.Builder(12,12, False).build()

### paramter customizations
#ptap.setDo2dGaussfit(False)
#ptap.setDo2dGaussfit(True) 
#ptap.setMinIntensity(100.0)
#ptap.setSearchPointIncrement(1)

# 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()

# TODO: write MSD values in a csv file. 
# http://cmci.embl.de/documents/120206pyip_cooking/python_imagej_cookbook#saving_csv_file_data_table

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)