miyanari’s gists

miyanari / data2csv.py

Created September 6, 2013 11:46 — forked from miura/data2csv.py

	'''
	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 / tiff_loder.py

Created September 6, 2013 11:46 — forked from miura/tiff_loder.py

	'''
	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 / stack2list.py

Created September 4, 2013 17:26 — forked from miura/stack2list.py



	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 / 32bit autothreshold.py

Created September 3, 2013 17:02 — forked from miura/32bit autothreshold.py

	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 / gist:6412961

Last active December 22, 2015 03:49 — forked from miura/gist:6412898

	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()