miura

// matrix algebra functions
//Kota Miura (miura@embl.de)
//050131 2D matrix to 1D arary and vice versa
//	matrix transpose, multiplication
//050201 Pivot, Gauss-Jordan (half done)

//  matrix format: m[0] contains number of rows in matrix. In the order of a11(=m[1]), a21(=m[2]), a31, a21,a22.....
// vector format: no info on length. starts from v[0]

//****************************** Global variables ***************************************** 

miura

//generating random steps
for(i =0; i<10; i++){
  print(randsteps());
}

function randsteps(){
	direction = "";
	r = random();
	if (r < 0.25)
		direction = "right";

miura

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

miura

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)
            imp = IJ.openImage(path)
            imp.show()
            imp.close()

miura

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

miura

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

miura

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

miura

from fiji.threshold import Auto_Threshold
from pta import PTA
imp = IJ.getImage()
iphist = imp.getProcessor().getHistogram()
print Auto_Threshold.Intermodes(iphist)
PTA.setNoGUI(False)

miura

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

miura

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