Python ImagePlus.getStack方法代码示例

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import getStack [as 别名]
newfilename = os.path.join(os.path.splitext(filename)[0], '_plotStack.tif')
out.setTitle(os.path.basename(filename)+'_OutStack.tif')

PLOT_ONLY_IN_FRAME1 = False
data = readCSV(filepath)
calib = imp.getCalibration()
xscale = calib.pixelWidth
yscale = calib.pixelHeight
zscale = calib.pixelDepth
cred = Color(255, 0, 0)
cblue = Color(0, 0, 255)
xoffset = imp.getWidth()
yoffset = imp.getHeight()
for d in data:
   frame = int(d[1])
   if frame < out.getStack().getSize():
      x1 = int(round(float(d[2]) / xscale))
      y1 = int(round(float(d[3]) / yscale))
      z1 = int(round(float(d[4]) / zscale))
      x2 = int(round(float(d[5]) / xscale))
      y2 = int(round(float(d[6]) / yscale))
      z2 = int(round(float(d[7]) / zscale))
      direction = float(d[8])
      if PLOT_ONLY_IN_FRAME1:
         ip = out.getStack().getProcessor(1)
      else:
         ip = out.getStack().getProcessor(frame+1)      
      if direction <= 0:
         ip.setColor(Color(255, 100, 100))
      else:
         ip.setColor(Color(100, 100, 255))

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import getStack [as 别名]
yoffset = imp.getHeight()
#ip = out.getStack().getProcessor(1)

for i in range(len(data)-1):
	if i < 1:
		continue
#	if i > 20:
#		break
	frame = float(data.get(i)[2])
	nextframe = float(data.get(i+1)[2])
	if nextframe - frame < 1:
		print str(i), 'trackend'
	else:
		frame = int(frame)
		print str(frame+1), '...plotting'
		ip = out.getStack().getProcessor(frame + 1) 
		x1 = int(round(float(data.get(i)[6]) / xscale))
		y1 = int(round(float(data.get(i)[7]) / xscale))
		z1 = int(round(float(data.get(i)[8]) / xscale))
		x2 = int(round(float(data.get(i+1)[6]) / xscale))
		y2 = int(round(float(data.get(i+1)[7]) / xscale))
		z2 = int(round(float(data.get(i+1)[8]) / xscale))	
		ip.setLineWidth(1)
		ip.setColor(Color(255, 100, 100))
		ip.drawLine(x1, y1, x2, y2)
		ip.drawLine(x1, yoffset+ z1, x2, yoffset+z2)
		ip.drawLine(xoffset+z1, y1, xoffset+z2, y2)
		

#for d in data:
#   frame = int(d[1])

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import getStack [as 别名]
# load data from file
filename = os.path.basename(filepath)
newfilepath = os.path.splitext(filepath)[0] + '_plot.tif'

PLOT_ONLY_IN_FRAME1 = False
data = readCSV(filepath)
calib = imp.getCalibration()
xscale = calib.pixelWidth
yscale = calib.pixelHeight
zscale = calib.pixelDepth
cred = Color(255, 0, 0)
cblue = Color(0, 0, 255)
xoffset = imp.getWidth()
yoffset = imp.getHeight()
ip = out.getStack().getProcessor(1)
for d in data:
   frame = int(d[1])
   x1 = int(round(float(d[2]) / xscale))
   y1 = int(round(float(d[3]) / yscale))
   z1 = int(round(float(d[4]) / xscale**2 * zscale))
   x2 = int(round(float(d[5]) / xscale))
   y2 = int(round(float(d[6]) / yscale))
   z2 = int(round(float(d[7]) / xscale**2 * zscale))
   direction = float(d[8])
   if direction <= 0:
      ip.setColor(Color(255, 100, 100))
   else:
      ip.setColor(Color(100, 100, 255))
   ip.setLineWidth(1)
   ip.drawLine(x1, y1, x2, y2)

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import getStack [as 别名]

#.........这里部分代码省略.........
	def __boxaction5(self, event):
		self.__fire = event.getSource().isSelected()
		#self.__setDisplay(str(event.getSource().text)+" is "+str(event.getSource().isSelected()))

	def __boxaction6(self, event):
		self.__align = event.getSource().isSelected()
		#self.__setDisplay(str(event.getSource().text)+" is "+str(event.getSource().isSelected()))

	def __boxaction7(self, event):
		self.__enlarge = event.getSource().isSelected()
		#self.__setDisplay(str(event.getSource().text)+" is "+str(event.getSource().isSelected()))

	def __boxaction8(self, event):
		self.__measures = event.getSource().isSelected()
		#self.__setDisplay(str(event.getSource().text)+" is "+str(event.getSource().isSelected()))

	def __boxaction9(self, event):
		self.__alignC = event.getSource().isSelected()
		#self.__setDisplay(str(event.getSource().text)+" is "+str(event.getSource().isSelected()))
	
	def __boxaction10(self, event):
		self.__conEllipses = event.getSource().isSelected()
	
	def __favg(self) :
		zp = ZProjector(self.__impRes) 
		zp.setMethod(ZProjector.AVG_METHOD)
		zp.doProjection() 
		imp = zp.getProjection()
		imp.show()
		if self.__fire : IJ.run(imp, "Fire", "")

	def __fmosa(self) :
		mm = MontageMaker()
		imp = mm.makeMontage2(self.__impRes, 1, self.__impRes.getStackSize(), 1, 1, self.__impRes.getStackSize(), 1, 0, False)
		imp.setTitle("MONTAGE"+self.__name)
		imp.show()
		if self.__fire : IJ.run(imp, "Fire", "")

	def __fmaxfinder(self) :
		#stack = self.__impRes.getStack()
		self.__impD.killRoi()
		self.__impF.killRoi()
		stack = self.__impF.getStack()
		n_slices = stack.getSize()
		#newstack=ImageStack(self.__impRes.getWidth(), self.__impRes.getHeight())
		newstack=ImageStack(self.__impF.getWidth(), self.__impF.getHeight())
		noise = self.__display3.text
		for index in range(1,n_slices+1):
			IJ.selectWindow(self.__impF.getTitle())
			self.__impF.setSlice(index)
			ip = self.__impF.getProcessor()
			mf=MaximumFinder()
			ipmax = mf.findMaxima(ip, int(noise), 0, 0, False, False)
			newstack.addSlice("", ipmax)
			

		newimage=ImagePlus("max points"+self.__name, newstack)
		newimage.show()
		newimage.updateAndDraw()
		
		listip = []
		maxh=self.__impRes.getHeight()

		for roi in self.__cellsrois : 
			straightener = Straightener()
			newimage.setSlice(roi[1])

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import getStack [as 别名]
IJ.run(InputImg, "Multiply...", "value=2 stack");       

              

# End of Anscombe transform
elapsed_time = time.time() - start_time
print "Elapsed time:", elapsed_time


Stats = StackStatistics(medianFilteredImage)
print "mean:", Stats.mean, "minimum:", Stats.min, "maximum:", Stats.max




medianFilteredStack = medianFilteredImage.getStack()
InputStack = InputImg.getStack()


# Get the Input and filtered Images as 1D arrays
medfiltArray = array.array('f')
InputImgArray = array.array('f')


for i in xrange(1 , z + 1):
    ip = medianFilteredStack.getProcessor(i).convertToFloat()
    ip2 = InputStack.getProcessor(i).convertToFloat()
    pixels = ip.getPixels()
    pixels2 = ip2.getPixels()
    medfiltArray.extend(pixels)
    InputImgArray.extend(pixels2)

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import getStack [as 别名]
            stack.addSlice(Filter.createDownsampled(
                stackSource.getProcessor(z+1),
    	        xyScale,
    	        0.5,
                0.5))
                
             
        img = ImagePlus("", stack)
    else:
        img = imgSource

    width  = img.getWidth()
    height =  img.getHeight()

    # img.show()
    print img.getWidth(), img.getHeight(), img.getStack().getSize()
    for c in correlationRanges:    
        correlationRange = c
        homeScale = root.rstrip('/') + '/xyScale=%f' % xyScale
        home = homeScale.rstrip('/') + '/range=%d_%s'.rstrip('/')
        home = home % ( correlationRange, str(datetime.datetime.now() ) )
        make_sure_path_exists( home.rstrip('/') + '/' )

        options.comparisonRange = c

        serializationString = '%s/correlations_range=%d.sr' % ( homeScale.rstrip(), correlationRange )

        gitCommitInfoFile = '%s/commitHash' % home.rstrip('/')
        with open( gitCommitInfoFile, 'w' ) as f:
            f.write( '%s\n' % utility.gitcommit.getCommit( thickness_estimation_repo_dir ) )