def __mainsettings(self) :
# options :
#We ask if the user wants to import cells from .cell files
# we track the cells in a stack that the user has to choose.
def outputpath(event) :
self.__pathdir=IJ.getDirectory("image")
self.__pathdir=IJ.getDirectory("")
self.__text.setText(self.__pathdir)
panel0=Panel()
pathbutton=Button("Select output path", actionPerformed = outputpath)
#pathbutton.actionPerformed = outputpath
self.__text = TextField(self.__pathdir)
panel0.add(pathbutton)
panel0.add(self.__text)
firstgd=NonBlockingGenericDialog("First choices")
firstgd.addMessage("------------------ WELCOME ----------------------")
firstgd.addMessage("")
firstgd.addMessage("Please fill the following options")
firstgd.addMessage("")
choices=["Already opened images", "Files from hard disk"]
firstgd.addChoice("Images source : ", choices, choices[0]) # 1 choice
firstgd.addCheckbox("Run in batch mode ?", False) # 2 batch
firstgd.addMessage("")
firstgd.addCheckbox("Import a set of cells from hardisk ?", self.__optionImport) # 3 import
firstgd.addMessage("")
firstgd.addNumericField("Size factor (binning)", 2, 0) # 4 number
firstgd.addPanel(panel0)
firstgd.showDialog()
#self.__optionImages=firstgd.getNextBoolean()
choice=firstgd.getNextChoiceIndex() # 1 choice
self.__batch = firstgd.getNextBoolean() # 2 batch
self.__optionImport=firstgd.getNextBoolean() # 3 import
self.__binning = firstgd.getNextNumber() # 4 number
if choice==0 : self.__optionImages=True
else : self.__optionImages=False
if firstgd.wasCanceled() : return False
#IJ.showMessage("Select a working directory to save results")
#self.__pathdir=IJ.getDirectory("image")
#self.__pathdir=IJ.getDirectory("")
#self.__pathdir=self.__pathdir+imp.getShortTitle()+os.path.sep+time.strftime('%d-%m-%y_%Hh%Mm%Ss',time.localtime())+os.path.sep
if self.__pathdir is not None : return True
else : return False
## Opens the options dialog box
gd = NonBlockingGenericDialog("Select channel...")
gd.addChoice("Analysis_channel",["Channel "+str(i) for i in range(1,nChannels+1)],"Channel 1")
gd.addChoice("Bleeding_channel",["Channel "+str(i) for i in range(nChannels+1)],"Channel 0")
gd.addChoice("Refractive_reference_channel",["Channel "+str(i) for i in range(nChannels+1)],"Channel 0")
gd.addNumericField("Intensity_threshold",128,0)
gd.addNumericField("Size_threshold",100,0)
gd.addChoice("Process_filter",["None","Min","Median"],"None")
gd.addCheckbox("Operate_on_tile_subset",False)
gd.addStringField("Which_tile_subset","1-4,9,11",12)
gd.showDialog()
## Parses the information from the dialog box
if (gd.wasOKed()):
analysisChannel = gd.getNextChoiceIndex()+1
bleedingChannel = gd.getNextChoiceIndex()
refChannel = gd.getNextChoiceIndex()
intThreshold = gd.getNextNumber()
sizeThreshold = gd.getNextNumber()
processFilter = gd.getNextChoiceIndex()
doSubset = gd.getNextBoolean()
whichTiles = gd.getNextString()
tileList = []
parsingFailed = False
if doSubset:
try:
whichTilesDespaced = whichTiles.replace(" ","")
tilesListed = whichTilesDespaced.split(",")
for tile in tilesListed:
tilesExpanded = tile.split("-")
calib = calibImage.getCalibration()
calibImage.close()
activeImage.updateAndRepaintWindow()
else:
calib = activeImage.getCalibration()
## Runs interface that allows to correct for bleedthrough and refraction
if activeImage is not None:
gd = NonBlockingGenericDialog("Select channel to operate on...")
gd.addChoice("Select_channel:",["Channel "+str(i) for i in range(1,activeImage.getNChannels()+1)],"Channel 1")
gd.addChoice("Bleeding_channel:",["None"] + ["Channel "+str(i) for i in range(1,activeImage.getNChannels()+1)],"None")
gd.addChoice("Refraction_reference_channel:",["None"] + ["Channel "+str(i) for i in range(1,activeImage.getNChannels()+1)],"None")
gd.showDialog()
if (gd.wasOKed()):
channelImages = ChannelSplitter.split(activeImage)
channel = gd.getNextChoiceIndex()+1
bleedingC = gd.getNextChoiceIndex()
refractRefC = gd.getNextChoiceIndex()
if (bleedingC > 0):
params = ("bleeding_channel=" + str(bleedingC) + " bloodied_channel=" + str(channel) + " " +
"allowable_saturation_percent=1.0 rsquare_threshold=0.50")
IJ.run("Remove Bleedthrough (automatic)", params)
dataImage = WindowManager.getImage("Corrected_ch" + str(channel))
if (refractRefC > 0):
refractCImage = channelImages[refractRefC-1].duplicate()
refractCImage.show()
IJ.run("Merge Channels...", "c1=" + dataImage.getTitle() + " c2=" + refractCImage.getTitle() + " create ignore")
mergedImage = WindowManager.getImage("Composite")
params = ("reference_channel=2 application_channel=1 automatic_operation generate_log " +
"max_slice=43 surface_slice=87")
IJ.run(mergedImage,"Refractive Signal Loss Correction",params)
from ij.gui import WaitForUserDialog
from ij.plugin import ChannelSplitter
from ij.plugin import ImageCalculator
from ij.measure import ResultsTable
from ij.measure import Measurements
from ij.plugin.filter import Analyzer
## Main body of script
theImage = IJ.getImage()
gd = NonBlockingGenericDialog("Pick parameters...")
gd.addChoice("Analysis_channel",["Channel "+str(i+1) for i in range(theImage.getNChannels())],"Channel 1")
gd.addNumericField("Pick_threshold",50,0)
gd.addCheckbox("Apply_min",True)
gd.showDialog()
if (gd.wasOKed()):
analysisChannel = gd.getNextChoiceIndex() + 1
intensityThreshold = gd.getNextNumber()
doMin = gd.getNextBoolean()
splitImage = ChannelSplitter.split(theImage)
dataImage = splitImage[analysisChannel-1].duplicate()
if doMin:
IJ.run(dataImage,"Minimum...", "radius=2 stack")
goRun = True
rt = ResultsTable()
while goRun:
wfud = WaitForUserDialog("Pick freehand ROI, then hit OK to analyze")
wfud.show()
roi = theImage.getRoi()
if roi is None:
goRun = False
else: