PTAscriptV4.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
from fiji.threshold import Auto_Threshold

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)
	
	# 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()
	iphist = imp.getProcessor().getHistogram()
	lt = Auto_Threshold.Intermodes(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(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)

#datafilepath = "/Users/miura/Dropbox/20130805_Osaka/data/transferrin-movement/tconc1_3.tif"
#datafilepath = "/Users/tsubasa/Desktop/minority/130730/MSD/Data57-crop.tif"
#datafilepath = "/Users/tsubasa/Desktop/Data57-crop-1.tif"

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)