Python WindowManager.getImage方法代码示例

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
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)

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

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
def get_images(minimum=0, maximum=None, exact=None):
    ''' Returns a list of ImagePlus objects or None if it failed.
    Passing None as parameter will trigger a dialog to show up to enter the exact number of images.
    :param minimum: The minimum number of images to select (default: 0).
    :param maximum: The maximum number of images to select (default: None).
    :param exact: Set this to get an exact number of images (default: None).
    '''
    if not (minimum or maximum or exact):
        exact = int(IJ.getNumber("How many images do you want to process?", 3))
    def check_count(count):
        '''Returns True if the count of images is as required.'''
        # print count, exact, minimum, maximum
        if exact:
            if not count == exact:
                return False
        else:
            if minimum:
                if count < minimum:
                    return False
            if maximum:
                if count > maximum:
                    return False
        return True

    # Option 1: The selected image is a stack and has the demanded size.
    if check_count(WindowManager.getCurrentImage().getStackSize()):
        return stack_to_list_of_imp(WindowManager.getCurrentImage())

    # Option 2: The count of open images matches the demanded number.
    image_ids = WindowManager.getIDList()
    if exact:
        if len(image_ids) < exact:
            return None
        if len(image_ids) == exact:
            return [WindowManager.getImage(img_id) for img_id in image_ids]

    # Option 3: The user can select the images from a list.
    image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
    img_count = len(image_ids)
    if exact:
        img_count = exact
    elif maximum:
        img_count = maximum
        image_titles.append('None')
    images_selected = dialogs.create_selection_dialog(image_titles,
                                                      range(img_count),
                                                      'Select images for drift correction'
                                                     )
    # dialogs.create_selection_dialog() returns None if canceled
    if not images_selected:
        return None
    # This is only true if 'None has been appended to image_titles and the user selected it.
    if len(image_ids) in images_selected:
        images_selected.remove(len(image_ids))
    if not check_count(len(images_selected)):
        return None
    image_list = [WindowManager.getImage(image_ids[selection]) for selection in images_selected]
    return image_list

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

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

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

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
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()

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
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)

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
def ridge_detect(imp, rd_max, rd_min, rd_width, rd_length):
    title = imp.getTitle()
    IJ.run(imp, "8-bit", "");
    IJ.run(imp, "Ridge Detection", "line_width=%s high_contrast=%s low_contrast=%s make_binary method_for_overlap_resolution=NONE minimum_line_length=%s maximum=0" % (rd_width, rd_max, rd_min, rd_length))
    IJ.run(imp, "Remove Overlay", "")
    skel = WindowManager.getImage(title + " Detected segments")
    IJ.run(skel, "Skeletonize (2D/3D)", "")
    skel.hide()
    return(skel)

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

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
def merge_images(_imp1, _imp2, force_same_bit_depth):
  imp1 = _imp1.duplicate()
  imp2 = _imp2.duplicate()
  imp1.show(); imp2.show();
  if(force_same_bit_depth):
    bd = max(imp1.getBitDepth(),imp2.getBitDepth())
    if bd==16:
      convert_to_16bit(imp1)
      convert_to_16bit(imp2)
    if bd==32:
      convert_to_32bit(imp1)
      convert_to_32bit(imp2)
  IJ.run(imp1, "Merge Channels...", "c1=[%s] c2=[%s] create" % (imp1.getTitle(), imp2.getTitle()))
  
  imp_out = WindowManager.getImage("Composite") 
  if not imp_out:
    imp_out = WindowManager.getImage("Merged")
  imp_out.hide()
  imp1.hide(); imp2.hide()
  return imp_out

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
	def __selectMeasureStack(self) : 
		# We allow the user to choose what to measure in the stack, and on which stack.
		gd1=NonBlockingGenericDialog("Stack Choice for measures")
		idimages=WindowManager.getIDList()
		images=[WindowManager.getImage(imgID) for imgID in idimages if WindowManager.getImage(imgID).getImageStackSize()>1 ]
		imagesnames=[img.getTitle() for img in images]

		activindex=0
		
		for i in range(len(imagesnames)) : 
				if imagesnames[i] == self.__activeTitle : 
					activindex=i
				
		gd1.addChoice("Select a stack in the list : ",imagesnames,imagesnames[activindex])
		gd1.showDialog()
		chosenstack=gd1.getNextChoice()
		self.__img=WindowManager.getImage(chosenstack)
		IJ.selectWindow(self.__img.getID())
		if gd1.wasOKed() : return True
		else : 	return False

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
    def overlayImages(self, e):
        impBase = WindowManager.getImage(self.imageIDs[self.baseImageBox.getSelectedIndex()])
        refBase = impBase.getStack().getProcessor(1)
        
        impOverlay = WindowManager.getImage(self.imageIDs[self.overlayImageBox.getSelectedIndex()])
        refOverlay = impOverlay.getStack().getProcessor(1)
        
        print "Overlaying for stack sizes " + str(impBase.getStackSize()) + "/" + str(impOverlay.getStackSize()) + "..."
        
        stack = None
        
        if self.virtualStackCheckbox.isSelected():
            stack = OverlayVirtualStack()
            stack.overlayOpacity = float(self.opacitySpinner.getValue())/100.0
            stack.overlayColor = AWTColorToArray(self.overlayColorPreviewLabel.getBackground())
            stack.base = impBase
            stack.overlay = impOverlay

            ImagePlus("Stack Overlay from " + self.imageNames[self.baseImageBox.getSelectedIndex()] + " and " + self.imageNames[self.overlayImageBox.getSelectedIndex()], stack).show()
        else:
            IJ.error("Not implemented yet", "Using normal stacks is not implemented yet. Please use the Virtual Stack option.")

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
def run_script():
    while WindowManager.getImageCount() < 10:
        create_test_image()
     
    image_titles = [WindowManager.getImage(id).getTitle() for id in WindowManager.getIDList()]
    # range(3) will create the list [0, 1, 2].
    selected_indices = create_selection_dialog(image_titles, range(3))
    # The script stops if the dialog has ben canceld (None was returned from create_selection_dialog).
    if selected_indices is None:
        print('Script was canceld.')
        return
    # We have to get the corresponding IMagePlus objects.
    selected_imps = [WindowManager.getImage(id) for id in [WindowManager.getIDList()[index] for index in selected_indices]]
    # The previous line can be split into 2 lines:
    # selected_ids = [WindowManager.getIDList()[index] for index in selected_indices]
    # selected_imps = [WindowManager.getImage(id) for id in selected_ids]
     
    for imp in selected_imps:
        # Strings can be formated using the % operator:
        # http://www.learnpython.org/en/String_Formatting
        IJ.log('The image \'%s\' has been selected.' % imp.getTitle())

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getImage [as 别名]
def get_setup():
    '''Returns two ImagePlus objects and a dictionary of properties to copy.'''
    dialog = GenericDialog('Copy Properties setup')
    dialog.addMessage('Select the source and target image and the properties to copy.')
    image_ids = WindowManager.getIDList()
    if not image_ids or len(image_ids) < 2:
        IJ.showMessage('Two or more images are necessary to use this plugin.')
        return [None]*3
    image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
    dialog.addChoice('Source', image_titles, image_titles[0])
    dialog.addChoice('Target', image_titles, image_titles[1])
    dialog.addCheckbox('Copy Calibration', True)
    dialog.addCheckbox('Copy Slice Labels', False)
    dialog.showDialog()
    if dialog.wasCanceled():
        return [None]*3
    source = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    target = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    choices = {'cal': dialog.getNextBoolean(),
               'labels': dialog.getNextBoolean()
              }
    return source, target, choices