Single molecule tracking using PTAj. - input: line 12-13, image stack. - output: track file (CSV) per track, MSD file (CSV) per track

PTAjScriptV2.py

from ij import IJ
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
 
#datafilepath = "/Users/miura/Dropbox/20130805_Osaka/data/transferrin-movement/tconc1_3.tif"
datafilepath = "/Users/araiyoshiyuki/Desktop/spool-tub_2-2.tif"
 
# load data as an ImagePlus object
imp = IJ.openImage(datafilepath)
 
# 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()
ip.setThreshold(0, ht, 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

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()
	

# 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)