miyanari

from fiji.threshold import Auto_Local_Threshold as ALT

# nucleus selection 

#imp = IJ.getImage()
imp = IJ.openImage("/Users/miyanari/Desktop/EMBL_with Kota/FISH_data/DNA-FISH_Demo.tif")
#IJ.run(imp, "Split Channels", "")
imps = ChannelSplitter.split(imp)
nucimp = imps[0]
#nucimp.show()

miyanari

from process3d import MinMaxMedian

imp = IJ.getImage()
#mmm = MinMaxMedian() 
medimp = MinMaxMedian.convolve(imp, MinMaxMedian.MEDIAN) 
medimp.show()

miyanari

from imagescience.image import Image
from imagescience.feature import Laplacian
imp = IJ.getImage()
#fjimp = FJ_Laplacian()
img = Image.wrap(imp)
lap =Laplacian()
lapimg = lap.run(img, 2.0)
lapimp = lapimg.imageplus()
lapimp.show()

miyanari

from process3d import Erode_

imp = IJ.getImage()
#IJ.run(imp, "Erode (3D)", "iso=255")
er = Erode_()
ip = imp.getProcessor()
erimp = er.erode(imp, 255, True)
erimp.show()

miyanari

from process3d import Dilate_

imp = IJ.getImage()
#IJ.run(imp, "Erode (3D)", "iso=255")
dil = Dilate_()
dilimp = dil.dilate(imp, 255, True)
dilimp.show()

miyanari

imp = IJ.getImage()
midslice = int(imp.getStackSize() / 2)
imp.setSlice(midslice)
#IJ.setThreshold(-50, -0.62)
ip.setAutoThreshold(AutoThresholder.Method.Default, False) 
IJ.setThreshold(ip.getMinThreshold(), ip.getMaxThreshold())
print ip.getMaxThreshold()
print ip.getMinThreshold()
#th = ip.getMaxThreshold()
IJ.run("Convert to Mask", "method=Default background=Light black")

miyanari

def stacklistGenerate(imp):
        stk = imp.getStack()
	imglist = []
	print len(imglist)
	for i in range(imp.getStackSize()):
		ip = stk.getProcessor(i+1)
		title = "img" + str(i+1)
		impsingle = ImagePlus(title, ip.duplicate())

miyanari

from fiji.threshold import Auto_Local_Threshold as ALT
from ij.gui import Roi
from imagescience.image import Image
from imagescience.feature import Laplacian
from process3d import Erode_, Dilate_, MinMaxMedian
from process3d import DistanceTransform3D as D3D
from Utilities import Counter3D
from ij.plugin import Thresholder, GaussianBlur3D, ZProjector, Duplicator
from ij.process import ImageProcessor

miyanari

'''
loading multiple tif files and store them in a list. 
'''
import os
from ij import IJ
from ij.io import DirectoryChooser
 
def run():
  srcDir = DirectoryChooser("Choose!").getDirectory()
	IJ.log("directory: "+srcDir)

miyanari

'''
writing data to a csv file. 
'''
import os, csv

# prepare test data to wirte to a csv file
data1 = range(10)
data2 = [x * x for x in data1]
data3 = [pow(x, 3) for x in data1]
print data3