Python ij.WindowManager类代码示例

def select_images():
    """
    Returns two ImagePlus objects that can be used by the drift correction.
    If more than two images are available a dialog is used for selection.
    """
    if WindowManager.getImageCount() > 0:
        imp = WindowManager.getCurrentImage()
        if imp.getImageStackSize() == 2:
            dup = Duplicator()
            img1 = dup.run(imp, 1, 1)
            img1.setTitle("Slice1")
            img2 = dup.run(imp, 2, 2)
            img2.setTitle("Slice2")
        elif WindowManager.getImageCount() == 2:
            img1, img2 = [WindowManager.getImage(id) for id in WindowManager.getIDList()]
        elif WindowManager.getImageCount() > 2:
            image_ids = WindowManager.getIDList()
            image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
            try:
                sel1, sel2 = dialogs.create_selection_dialog(image_titles, range(2))
            except TypeError:
                return(None, None)
            img1 = WindowManager.getImage(image_ids[sel1])
            img2 = WindowManager.getImage(image_ids[sel2])
        else:
            IJ.error("You need two images to run the script.")
            return(None, None)
    else:
        IJ.error("You need two images to run the script.")
        return(None, None)
    return (img1, img2)

def get_images(ids):
    """
    Returns a list of ImagePlus objects.
    :param ids: The ids of the ImagePlus objects to return.
    """
    image_ids = WindowManager.getIDList()
    return [WindowManager.getImage(image_ids[id]) for id in ids]

def get_image_titles():
    """
    Returns the titles of all open image windows as a list.
    """
    image_ids = WindowManager.getIDList()
    image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
    return image_titles

 def close(self):
     if self.olay != None:
         yncd = YesNoCancelDialog(self.frame, "Save overlay?", "Save overlay?") #frame, title, message
         if yncd.yesPressed():
             self.saveOverlay()
     WindowManager.removeWindow(self.frame)
     self.frame.dispose()

    def __init__(self, p):
        self.cellCounter = 1
        self.olay = Overlay()
        self.position = p
        print p.getRoiPath()
        if p.getRoiPath() != None:         # check if there is an existing overlay file and load it!
            p.loadRois()

        self.frame = JFrame("CellCropper", size=(200,200))
        self.frame.setLocation(20,120)
        self.Panel = JPanel(GridLayout(0,1))
        self.frame.add(self.Panel)
        #self.nameField = JTextField("p" + "_c",15)
        self.nameField = JTextField("p" + str(self.position.getID()) + "_c",15)
        self.Panel.add(self.nameField)
        self.cutoutButton = JButton("Cut out cell",actionPerformed=cut)
        self.Panel.add(self.cutoutButton)
        self.delOlButton = JButton("Delete Overlay",actionPerformed=delOverlay)
        self.Panel.add(self.delOlButton)
        self.saveOlButton = JButton("Save Overlay",actionPerformed=saveOverlay)
        self.Panel.add(self.saveOlButton) 
        self.quitButton = JButton("Quit script",actionPerformed=quit)
        self.Panel.add(self.quitButton)
        self.frame.pack()
        WindowManager.addWindow(self.frame)
        self.show()

def get_setup():
    ''' Returns the drift correction mode and three image.
    The order of return values is drift detection mode, pre-edge 1, pre-edge 2, post-edge.
    '''
    options = drift.get_options()
    modes = drift.get_modes()
    dialog = GenericDialog('3-window-method setup')
    dialog.addMessage('Select the mode  for drift correction\n' +
                      'and the images to process.')
    dialog.addChoice('Mode:', options, options[0])
    image_ids = WindowManager.getIDList()
    if not image_ids or len(image_ids) < 2:
        return [None]*4
    image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
    dialog.addMessage('Post-edge is divided by the pre-edge.')
    dialog.addChoice('Pre-edge 1', image_titles, image_titles[0])
    dialog.addChoice('Pre-edge 2', image_titles, image_titles[1])
    dialog.addChoice('Post-edge', image_titles, image_titles[2])
    dialog.showDialog()
    if dialog.wasCanceled():
        return [None]*4
    mode = modes[dialog.getNextChoiceIndex()]
    img1 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    img2 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    img3 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    return mode, img1, img2, img3

def getImage():
    """Get first open image or open Bio-Formats importer if no image is
	available."""
    imp = WindowManager.getCurrentImage()
    if not imp:
        # Show bio formats open dialog
        IJ.run("Bio-Formats")
        imp = WindowManager.getCurrentImage()
        print("Start")
    if not imp:
        IJ.noImage()
        raise ValueError("Need image")
    return imp

def draw_roi_on_full_res_tile(containing_tiles_dict,subupcoords_dict):
	masterXs = []
	masterYs = []
	for key in containing_tiles_dict.keys():
		if (len(containing_tiles_dict.keys())>1):
			active_image = WindowManager.getImage("Fused")
		else:
			active_image = WindowManager.getImage("tile_"+key+".ome.tif")
		for point in containing_tiles_dict[key]:
			masterXs.append(point[3]+subupcoords_dict["tile_"+str(point[0])][0])
			masterYs.append(point[4]+subupcoords_dict["tile_"+str(point[0])][1])
	proi = PolygonRoi(masterXs,masterYs,Roi.FREEROI)
	active_image.setRoi(proi)
	return active_image

   def __init__(self):
      self.mainDir = ""
   
      self.frame = JFrame("Dots Quality Check", size=(250,300))
      self.frame.setLocation(20,120)
      self.Panel = JPanel(GridLayout(0,1))
      self.frame.add(self.Panel)

      self.openNextButton = JButton('Open Next Random',actionPerformed=openRandom)
      self.Panel.add(self.openNextButton)
      
      self.saveButton = JButton('Save',actionPerformed=save)
      self.saveButton.setEnabled(False)
      self.Panel.add(self.saveButton)

      self.cropButton = JButton('Crop values from here', actionPerformed=cropVals)
      self.Panel.add(self.cropButton)

      self.DiscardButton = JButton('Discard cell', actionPerformed=discardCell)
      self.DiscardButton.setEnabled(True)
      self.Panel.add(self.DiscardButton)

      self.quitButton = JButton('Quit script',actionPerformed=quit)
      self.Panel.add(self.quitButton)

      annoPanel = JPanel()
      #add gridlayout
      wtRButton = JRadioButton("wt", actionCommand="wt")
      defectRButton = JRadioButton("Defect", actionCommand="defect")
      annoPanel.add(wtRButton)
      annoPanel.add(defectRButton)
      self.aButtonGroup = ButtonGroup()
      self.aButtonGroup.add(wtRButton)
      self.aButtonGroup.add(defectRButton)
      
      self.Panel.add(annoPanel)

      self.ProgBar = JProgressBar()
      self.ProgBar.setStringPainted(True)
      self.ProgBar.setValue(0)
      self.Panel.add(self.ProgBar)

      self.pathLabel = JLabel("-- No main directory chosen --")
      self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
      self.Panel.add(self.pathLabel)

      
      WindowManager.addWindow(self.frame)
      self.show()

def bSaveZProject(imp, dstFolder, shortname):
	#bring to front
	impWinStr = imp.getTitle()
	IJ.selectWindow(impWinStr)
	
	bPrintLog('Making Z-Project from ' + impWinStr, 2)
	madez = 0
	z1 = 1
	z2 = imp.getNSlices()
	if z2>1:
		paramStr = 'start=%s stop=%s projection=[Max Intensity]' % (z1, z2)
		IJ.run('Z Project...', paramStr) #makes 'MAX_' window
		zWinStr = 'MAX_' + impWinStr
		zImp = WindowManager.getImage(zWinStr)
		madez = 1
	else:
		zImp = imp
			
	if dstFolder != None:
		dstFile = dstFolder + 'max_' + shortname + '.tif'
		bPrintLog('Saving Z-Project: ' + dstFile, 2)
		bSaveStack(zImp, dstFile)

	if madez:
		zImp.changes = 0
		zImp.close()

    def myrun(self):
        imp = IJ.openImage(self.path) #open imp
        if imp is None:
            print 'ERROR opening file:', self.path
            return 0
        numSlices = imp.getNSlices()
        if numSlices<2:
        	return 0
        
        middleSlice = int(math.floor(imp.getNSlices() / 2)) #int() is necc., python is fucking picky
        
        imp.show()
        imp.setSlice(middleSlice)
        impTitle = imp.getTitle()
        impWin = WindowManager.getWindow(impTitle) #returns java.awt.Window

        transformationFile = os.path.basename(self.path)
        transformationFile = os.path.splitext(transformationFile)[0] + '.txt'
        transformationFile = '/Users/cudmore/Desktop/out/' + transformationFile
        stackRegParams = 'stack_1=[%s] action_1=Align file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save' %(impWin,transformationFile)
        IJ.run('MultiStackReg', stackRegParams)
        
        imp.close()
        
        '''
        #20150723, we just aligned on a cropped copy, apply alignment to original imp
        origImpTitle = imp.getTitle()
        stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(origImpTitle,transformationFile)
        IJ.run('MultiStackReg', stackRegParams)        
        '''
        
        '''

def runPoreDetection():
	'''roiManager=RoiManager(False)
	roiManager.runCommand("open", roiname)
	roiHash=roiManager.getROIs()
	roi=roiHash.get("Right")
	print roi'''
	
	imageList=Utility.GetOpenImageList()

	nbgd=NonBlockingGenericDialog(Messages.AddRoi)
	nbgd.addMessage(Messages.ChooseImage)
	                              
	if (imageList==None):
		IJ.showMessage(Messages.noOpenImages)
		return;
		
	nbgd.addChoice("Image1:", imageList, imageList[0]);
	nbgd.showDialog()

	name = nbgd.getNextChoice()

	inputImp = WindowManager.getImage(name)
	inputDataset=Utility.getDatasetByName(data, name)
	
	detectionParameters=DetectionParameters(10, 200, 0.5, 1.0, 0.3)

	#inputImp.setRoi(roi)

	nbgd2=NonBlockingGenericDialog(Messages.PositionRoi)
	nbgd2.addMessage(Messages.PositionRoiAndPressOK)
	nbgd2.showDialog()

	poreDetectionUV(inputImp, inputDataset, inputImp.getRoi().clone(), ops, data, display, detectionParameters)

def main():
    """Get options and create new image."""
    options = get_options()
    if options is not None:
        bwidth, bheight = options
        img_cur = WindowManager.getCurrentImage()
        img_new = boxed_intensities(img_cur, bwidth, bheight)
        img_new.show()

    def __init__(self):
        self.mainDir = ""

        self.setTitle("Dots Quality Check")
        self.setSize(250, 300)
        self.setLocation(20,120)
        self.addWindowFocusListener(self)
        
        self.Panel = JPanel(GridLayout(0,1))
        self.add(self.Panel)
        self.openNextButton = JButton("Open Next Random", actionPerformed=self.openRandom)
        self.Panel.add(self.openNextButton)
        self.saveButton = JButton("Save", actionPerformed=self.save, enabled=False)
        self.Panel.add(self.saveButton)
        self.cropButton = JButton("Crop values from here", actionPerformed=self.cropVals)
        self.Panel.add(self.cropButton)
        self.DiscardButton = JButton("Discard cell", actionPerformed=self.discardCell)
        self.Panel.add(self.DiscardButton)
        self.quitButton = JButton("Quit script",actionPerformed=self.quit)
        self.Panel.add(self.quitButton)

        annoPanel = JPanel()
        #add gridlayout
        self.wtRButton = JRadioButton("wt", actionCommand="wt")
        self.wtRButton.addActionListener(self)
        self.defectRButton = JRadioButton("Defect", actionCommand="defect")
        self.defectRButton.addActionListener(self)
        annoPanel.add(self.wtRButton)
        annoPanel.add(self.defectRButton)
        self.aButtonGroup = ButtonGroup()
        self.aButtonGroup.add(self.wtRButton)
        self.aButtonGroup.add(self.defectRButton)
      
        self.Panel.add(annoPanel)

        self.ProgBar = JProgressBar()
        self.ProgBar.setStringPainted(True)
        self.ProgBar.setValue(0)
        self.Panel.add(self.ProgBar)

        self.pathLabel = JLabel("-- No main directory chosen --")
        self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
        self.Panel.add(self.pathLabel)
      
        WindowManager.addWindow(self)
        self.show()

def Resize(imp):
	gd = GenericDialog("Image size")
	scales = ["1024","2048","4096"]
	gd.addChoice("Choose image size",scales,scales[1])
	gd.showDialog()
	scale_choice = gd.getNextChoice()
	IJ.run(imp,"Scale...", "x=- y=- z=1.0 width="+scale_choice+" height="+scale_choice+" interpolation=Bilinear average process create title=Scaled")
	scaled_imp = WindowManager.getImage("Scaled")
	return scaled_imp