ImageJ-plugins/dialog_FRAP.py at master · Oftatkofta/ImageJ-plugins · GitHub

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import java.awt.Color as Color
from ij import WindowManager as WindowManager
from ij.plugin.frame import RoiManager as RoiManager
from ij.process import ImageStatistics as ImageStatistics
from ij.measure import Measurements as Measurements
from ij import IJ as IJ
from ij.measure import CurveFitter as CurveFitter
from ij.gui import Plot as Plot
from ij.gui import PlotWindow as PlotWindow
import math

from ij.gui import GenericDialog
from ij.plugin import ChannelSplitter


def FRAPsetup(imp):

	gd = GenericDialog("FRAP analysis options")
	calibration = imp.getCalibration()
	if calibration.frameInterval is None:
		default_interval=0
		setCalFlag=1
	else:
		default_interval=calibration.frameInterval

	gd.addNumericField("Frame interval (s):", default_interval, 3)  # show 3 decimals
	channels = [str(ch) for ch in range(1, imp.getNChannels()+1)]
	gd.addChoice("Analyze channel:", channels, channels[0])


	gd.addSlider("Number of frames to analyze:", 1, imp.getNFrames(), 30)
	gd.addCheckbox("Automatic FRAP frame detection?", True)
	gd.addNumericField("Manual FRAP frame:", 0, 0)
	gd.addMessage("Automatic FRAP checkbox has to be unchecked for maual selection to work")

	gd.showDialog()

  	if gd.wasCanceled():
		IJ.log("User canceled dialog!")
		return
  	# Read out the options

  	frame_interval = gd.getNextNumber()
  	channel = int(gd.getNextChoice())
  	max_frame = int(gd.getNextNumber())
  	manual_FRAP_frame = int(gd.getNextNumber())
  	autoFRAPflag=gd.getNextBoolean()

	#Set the frame interval in calibration

	calibration.frameInterval = frame_interval
	imp.setCalibration(calibration)

	#Extract the desired channel

  	imp=channelSelector(imp,channel)

  	return imp, max_frame, manual_FRAP_frame, autoFRAPflag

def channelSelector(imp, channelno):
	'''
	arguments imp: imageProcessor, channelno: imteger, channel number
	returns an imp containing the desired channel
	'''
	imps=ChannelSplitter.split(imp)
	return imps[(channelno-1)]


current_imp  = WindowManager.getCurrentImage()
current_imp, max_frame, maual_FRAP_frame, manualFRAPflag = FRAPsetup(current_imp)
print current_imp, max_frame, maual_FRAP_frame, manualFRAPflag