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
import os, csv

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

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

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

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

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

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

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 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 MinMaxMedian

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