Python RoiManager.select方法代码示例

# 需要导入模块: from ij.plugin.frame import RoiManager [as 别名]
# 或者: from ij.plugin.frame.RoiManager import select [as 别名]
	def __displayCells(self, nameimage, methodeleon=False):
		"""
		Displays all the ROIs of the cells with different colors
		
		"""
		# we define a list of colors that will be used.

		colors = []
		ncells= len(self.__dict[nameimage])
		if ncells > 0 :
			step=200/ncells
			if step<1 : step=1
			for i in range(ncells) : 
				r = random.randrange(5,205,step)
				g = random.randrange(10,210,step)
				b = random.randrange(30,230,step)
				#r = int(0+i*step)
				#g = random.randrange(10, 190, 30)
				#b = int(250-i*step)
				
				colors.append(Color(r, g, b))

		else : 	colors=[Color.blue, Color.green, Color.magenta, Color.orange, Color.yellow]
		tempcolors=list(colors)
		# we try to have random and different colors for each cell.
		for cellname in self.__dict[nameimage].keys() :
			if len(tempcolors)>0 : 
				self.__dict[nameimage][cellname].setColor(tempcolors.pop(0))
			else :
				tempcolors=list(colors)
				self.__dict[nameimage][cellname].setColor(tempcolors.pop(0))
		

		self.__SaveCells(nameimage)
		
		rm = RoiManager.getInstance()
		if (rm==None): rm = RoiManager()
		rm.runCommand("reset")

		# if the user wants to save files, .zip for the ROIs are saved.
		#if self.__optionSave == True : 
		#os.mkdir(self.__pathdir+"ROIs/", mode=0777)
		os.makedirs(self.__pathdir+"ROIs/", mode=0777)
		tempimp = IJ.createImage("tempimp", "8-bit Black", self.__dictImages[nameimage].getWidth(), self.__dictImages[nameimage].getHeight(), 1)
		tempimp.show()
		for cellname in self.__dict[nameimage].keys() :
			for numslice in range(self.__dictImages[nameimage].getImageStackSize()) :
				r = self.__dict[nameimage][cellname].getRoi(numslice)
				try : 
					name=r.getName()
				
				except AttributeError : continue

				else :
					s = "%04i" % (numslice+1)
					#name=s+"-"+name.split("-", 1)[1]
					name=s+"-cell"+name.split("cell")[1]
					r.setName(name)
					try :
						rm.addRoi(r)
						rname=rm.getName(rm.getCount()-1)
						#rm.select(self.__dictImages[nameimage], rm.getCount()-1)
						rm.select(tempimp, rm.getCount()-1)
						rm.runCommand("Rename", name)
					except TypeError : continue
					
					
				#if isinstance(self.__dict[nameimage][cellname].getRoi(numslice),Roi) == True :
				#	s = "%04i" % (numslice)
				#	#rm.add(self.__dictImages[nameimage], self.__dict[nameimage][cellname].getRoi(numslice)  ,  numslice)
				#	name=self.__dict[nameimage][cellname].getRoi(numslice).getName()
				#	name=s+name
				#	self.__dict[nameimage][cellname].getRoi(numslice).setName(name)
				#	rm.addRoi(self.__dict[nameimage][cellname].getRoi(numslice))
			rm.runCommand("Save", self.__pathdir+"ROIs/"+cellname+".zip")
			rm.runCommand("reset")
		
		tempimp.close()

# 需要导入模块: from ij.plugin.frame import RoiManager [as 别名]
# 或者: from ij.plugin.frame.RoiManager import select [as 别名]

#.........这里部分代码省略.........
		measureslabels_indep=["MaxFeret","MinFeret","AngleFeret","XFeret","YFeret","Area","Angle","Major","Minor","Solidity","AR","Round","Circ","XC","YC","FerCoord","FerAxis","MidAxis"]
		measureslabels_dep=["Mean","StdDev","IntDen","Kurt","Skew","XM","YM","Fprofil","MidProfil","NFoci","ListFoci","ListAreaFoci","ListPeaksFoci","ListMeanFoci"]
		measureslabels_global=["Latency", "velocity", "cumulatedDist"]
		measureslabels_dep_tabonly=set(["MidAxis","FerCoord","FerAxis","Fprofil","MidProfil","ListFoci","ListAreaFoci","ListPeaksFoci","ListMeanFoci"])
		ens_measures_global=set(measureslabels_global)
		ens_measures_indep=set(measureslabels_indep)
		ens_measures_dep=set(measureslabels_dep)
		measureslabels=[]
		
		for label in measureslabels_indep :
			measureslabels.append(label)

		for label in measureslabels_dep :
			measureslabels.append(label)

		#self.__defaultmeasures=[False for i in range(len(measureslabels))]
		#self.__defaultmeasures_global=[False for i in range(len(measureslabels_global))]

		gdmeasures=NonBlockingGenericDialog("MeasuresChoice")
		gdmeasures.setFont(Font("Courrier", 1, 10))
		gdmeasures.addMessage("*******     TIME SETTINGS     *******")
		gdmeasures.addCheckbox("Only starting at begining  :", self.__onlystart)				# 1 only start
		gdmeasures.addNumericField("Minimal Lifetime  : ",self.__minLife,0)
		gdmeasures.addNumericField("Maximal Lifetime  : ",self.__maxLife,0)
		#gdmeasures.addNumericField("Maximal Lifetime  : ",self.__img.getImageStackSize(),0)
		gdmeasures.addCheckbox("x axis in seconds", self.__useTime)				# 2 use time
		gdmeasures.addMessage("")
		gdmeasures.addMessage("")
		gdmeasures.addMessage("Choose the measures to make on the cells : ")			
		gdmeasures.addMessage("*******     TIME MEASURES     *******")
		gdmeasures.addCheckboxGroup(4,8,measureslabels,self.__defaultmeasures)
		gdmeasures.addMessage("")
		gdmeasures.addMessage("*******     GLOBAL MEASURES     *******")
		gdmeasures.addMessage("PLEASE : If you have selected movement parameters you MUST to select XC and YC !")
		gdmeasures.addCheckboxGroup(3,1,measureslabels_global,self.__defaultmeasures_global)
		gdmeasures.addNumericField("Noise value for maxima finder: ",self.__noise,0)
		gdmeasures.addMessage("")	
		gdmeasures.addMessage("*******     OPTIONS     *******")
		gdmeasures.addCheckbox("Select the cells in next dialog ?", self.__onlyselect)			# 3 only select
		gdmeasures.addCheckbox("Save results to text files ?", self.__savetables)			# 4 save files
		#gdmeasures.addCheckbox("Append mode ?", self.__savemode)					# 5 append mode
		gdmeasures.addCheckbox("Analyse in batch mode ?", self.__batchanalyse)				# 6 analysis batch mode
		gdmeasures.addCheckbox("Update overlay ?", self.__updateoverlay)				# 7 update overlay
		gdmeasures.addMessage("")
		gdmeasures.addMessage("")
		help_panel=Panel()
		helpbutton=Button("HELP")
		helpbutton.actionPerformed = helpbuttonPressed
		help_panel.add(helpbutton)	
		gdmeasures.addPanel(help_panel)	
		gdmeasures.hideCancelButton()

		if not self.__batchanalyse :
			gdmeasures.showDialog()
			self.__onlystart=gdmeasures.getNextBoolean() 						# 1 only start
			self.__minLife=gdmeasures.getNextNumber()
			self.__maxLife=gdmeasures.getNextNumber()
			self.__useTime=gdmeasures.getNextBoolean()						# 2 use time

			self.__measuresparambool=[]
			self.__measuresparambool_global=[]
			for i in range(len(measureslabels)) : 
				self.__measuresparambool.append(gdmeasures.getNextBoolean())
				self.__defaultmeasures[i]=self.__measuresparambool[-1]
			for i in range(len(measureslabels_global)) : 
				self.__measuresparambool_global.append(gdmeasures.getNextBoolean())

# 需要导入模块: from ij.plugin.frame import RoiManager [as 别名]
# 或者: from ij.plugin.frame.RoiManager import select [as 别名]
	def __ImportCells(self, imagesnames) :

		#self.__dictCells[imgName]={}
		
		rm = RoiManager.getInstance()
		if (rm==None): rm = RoiManager()
		rm.runCommand("reset")

		listpaths = []
		listfilescells=[]

		if self.__optionImages :
			IJ.showMessage("Select the folder 'Cells' containing the cells to import")
			selectdir=IJ.getDirectory("image")
			selectdir=IJ.getDirectory("")
			listfilescells.extend(glob.glob(selectdir+os.path.sep+"*"))
			listpaths.append("")

		else : 
			IJ.showMessage("Select the text file containing the list cell paths (listpaths.txt)")
			selectdir=IJ.getDirectory("current")
			frame = Frame("Text file settings ?")
			fd = FileDialog(frame)
			fd.setDirectory(selectdir)
			fd.show()
			selectdir = fd.getDirectory() 
			textfile = fd.getFile()
			fichier = open(selectdir+textfile,"r")
			listpaths=[ glob.glob(f.split("\n")[0]+"Selected-Cells"+os.path.sep+"*") for f in fichier.readlines()]

			#for f in templist : 
			#	listpaths.append(f.split("\n")+"Cells")
				
			listfilescells.append("")

		if listfilescells[0]=="" : importmode = True
		else : importmode = False
		
		for j in range(len(listpaths)) :
			self.__dictCells[imagesnames[j]]={}
			if importmode : listfilescells = listpaths[j]
			pathtemp = []
			for cellfile in listfilescells :
				filetemp = open(cellfile,"r")
				linestemp=filetemp.readlines()
				for line in linestemp :
					params=line.split("=")
					values=params[1].split("\n")
					if params[0] == "NAMECELL" :
						celltemp=Bacteria_Cell(str(values[0]))
						self.__dictCells[imagesnames[j]][values[0]]=celltemp
						self.__dictMeasures[self.__dictCells[imagesnames[j]][values[0]]]={} 


					if params[0] == "PATHROIS" :
						pathtemp.append(str(values[0]))
						
					if params[0] == "NSLICES" : 
						for i in range(int(values[0])) :
							celltemp.getListRoi().append("")
				
					if params[0] == "SLICEINIT" :
						celltemp.setSlideInit(int(values[0]))
						for i in range(int(values[0])-2) :
							celltemp.setRoi("NOT HERE YET",i)
				
					if params[0] == "SLICEEND" :
						celltemp.setSlideEnd(int(values[0]))
						for i in range(int(values[0])) :
							celltemp.setRoi("LOST",i)
				
					if params[0] == "COLOR" :
						colorstemp=values[0].split(";")
						celltemp.setColor(Color(int(colorstemp[0]),int(colorstemp[1]),int(colorstemp[2])))
		
		
			indiceroi=0
			ind=0
			tempimp = WindowManager.getImage(imagesnames[j])
			if tempimp is not None : 
				IJ.selectWindow(imagesnames[j])
				tempimp.show()
			else : 
				if imagesnames[j][-4:]==".tif" : 
					IJ.selectWindow(imagesnames[j][:-4])
					tempimp = IJ.getImage()
				else : 
					IJ.selectWindow(imagesnames[j]+".tif")
					tempimp = IJ.getImage()
					
			rm.runCommand("reset")
			
			for cellname in self.__dictCells[imagesnames[j]].keys() :
				rm.runCommand("Open", pathtemp[ind])
				ind+=1
				nbtemp=self.__dictCells[imagesnames[j]][cellname].getLifeTime()
				for i in range(nbtemp) :
					rm.select(tempimp, indiceroi)
					roi=rm.getSelectedRoisAsArray()[0]
					self.__dictCells[imagesnames[j]][cellname].setRoi(roi,i+self.__dictCells[imagesnames[j]][cellname].getSlideInit()-1)
#.........这里部分代码省略.........

# 需要导入模块: from ij.plugin.frame import RoiManager [as 别名]
# 或者: from ij.plugin.frame.RoiManager import select [as 别名]
from ij import IJ
from ij.gui import OvalRoi
from ij.plugin.frame import RoiManager

imp = IJ.getImage()  
rm = RoiManager()  # instantiate manager # throws exception if it doesn't exist
#rm = RoiManager.getInstance() # if manager exists 
 
roi = OvalRoi(75, 75, 50, 50); # define and add ROI
imp.setRoi(roi)  # make active on image
rm.addRoi(roi)  # add
rm.select(0) # select the zeroth ROI and rename it
rm.runCommand("Rename", "roi");

# 需要导入模块: from ij.plugin.frame import RoiManager [as 别名]
# 或者: from ij.plugin.frame.RoiManager import select [as 别名]
def segmentation(imp, spot_data, channel, diameter_init, ES_tolerance, ES_area_max, ES_ctrl_pts, ES_iteration, repeat_max):
    # Open files
    cal = imp.getCalibration()
    manager = RoiManager.getInstance()
    if manager is None:
        manager = RoiManager()
    # Prepare log files for output
    options = IS.MEDIAN | IS.AREA | IS.MIN_MAX | IS.CENTROID | IS.PERIMETER | IS.ELLIPSE | IS.SKEWNESS
    convergence = []
    Sintensity = []
    for spot in spot_data:
        repeat = 0
        flag = False
        spotID = int(spot[0])
        Xcenter = (float(spot[1]) / cal.pixelWidth)
        Ycenter = (float(spot[2]) / cal.pixelHeight)
        Quality = float(spot[3])
        diameter_init = float(spot[4] / cal.pixelWidth) * 2.0
        while True:
            manager = RoiManager.getInstance()
            if manager is None:
                manager = RoiManager()
            Xcurrent = int(Xcenter - diameter_init / 2.0)
            Ycurrent = int(Ycenter - diameter_init / 2.0)
            Dcurrent1 = int(diameter_init * (1.2 - repeat / 10.0))
            Dcurrent2 = int(diameter_init * (0.8 + repeat / 10.0))
            roi = OvalRoi(Xcurrent, Ycurrent, Dcurrent1, Dcurrent2)
            imp.setPosition(channel)
            imp.setRoi(roi)
            Esnake_options1 = "target_brightness=Bright control_points=" + \
                str(ES_ctrl_pts) + " gaussian_blur=0 "
            Esnake_options2 = "energy_type=Contour alpha=2.0E-5 max_iterations=" + \
                str(ES_iteration) + " immortal=false"
            IJ.run(imp, "E-Snake", Esnake_options1 + Esnake_options2)
            roi_snake = manager.getRoisAsArray()
            roi_ind = len(roi_snake) - 1
            stats = IS.getStatistics(
                imp.getProcessor(), options, imp.getCalibration())
            perimeter = roi_snake[roi_ind].getLength() * cal.pixelWidth
            circularity = 4.0 * 3.1417 * (stats.area / (perimeter * perimeter))
            if stats.area > 17.0 and stats.area < ES_area_max and stats.skewness < -0.01 and circularity > 0.01 and stats.minor > 2.0 and boundaries(Xcenter, Ycenter, stats.xCentroid / cal.pixelWidth, stats.yCentroid / cal.pixelHeight, ES_tolerance):
                Sintensity = stats.median
                convergence.append(True)
                break
            if stats.median > 6000 and stats.area > 17.0 and stats.area < ES_area_max:
                Sintensity = stats.median
                convergence.append(True)
                break
            elif repeat > repeat_max:
                manager.select(imp, roi_ind)
                manager.runCommand(imp, 'Delete')
                roi = OvalRoi(Xcenter + 1.0 - diameter_init / 2.0, Ycenter +
                              1.0 - diameter_init / 2.0, diameter_init, diameter_init)
                imp.setRoi(roi)
                manager.add(imp, roi, spotID)
                roi_snake.append(roi)
                stats = IS.getStatistics(
                    imp.getProcessor(), options, imp.getCalibration())
                Sintensity = stats.median
                convergence.append(False)
                break
            else:
                IJ.log('Area=' + str(stats.area) + '  Skewness=' + str(stats.skewness) +
                       ' circularity=' + str(circularity) + ' Minor=' + str(stats.minor))
                manager.select(imp, roi_ind)
                manager.runCommand(imp, 'Delete')
                repeat += 1
        # End Spot-segmentation
    # End all Spots-segmentation
    manager.runCommand(imp, 'Show All')
    imp.setPosition(channel)
    color = imp.createImagePlus()
    ip = imp.getProcessor().duplicate()
    color.setProcessor("segmentation" + str(channel), ip)
    color.show()
    IJ.selectWindow("segmentation" + str(channel))
    manager.moveRoisToOverlay(color)
    spot_optimal = manager.getRoisAsArray()
    manager.reset()
    for i in xrange(0, len(spot_optimal)):
        spot = spot_optimal[i]
        spot.setStrokeWidth(2)
        if convergence[i]:
            spot.setStrokeColor(Color.GREEN)
        else:
            spot.setStrokeColor(Color.MAGENTA)
        imp.setRoi(spot)
        manager.add(imp, spot, i)
    manager.runCommand(imp, 'Show All')
    imp.setPosition(channel)

# 需要导入模块: from ij.plugin.frame import RoiManager [as 别名]
# 或者: from ij.plugin.frame.RoiManager import select [as 别名]
# addAndDeleteROI_.py
# Add and delete a ROI from an image
#
#  Modifications
#   Date      Who  Ver                       What
# ----------  --- ------  -------------------------------------------------
# 2014-10-21  JRM 0.1.00  Initial prototype

from ij import WindowManager
from ij import IJ
from ij.plugin.frame import RoiManager

raw = IJ.openImage("D:\\Data\\images\\tmp\\sis-efi-sc.png")
raw.show()
IJ.makeRectangle(0, 190, 1600, 260)
wbROI = raw.getRoi()
if (wbROI==None):
  exit("you must draw region first")
print(wbROI)
rm = RoiManager()
rm.select(raw, 0)
rm.runCommand("Show All")
rm.runCommand("Draw")
print("done")