Python GenericDialog.addCheckbox方法代码示例

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def main():
    properties = ImageProperties(imp)
    # Create a GenericDialog to configure renaming:
    gd = GenericDialog('Gatan Reamer')
    gd.addMessage('Modifying: %s' % (imp.getTitle(),))
    gd.addMessage('Recorded: %s' % (properties.date.toString(),))
    gd.addNumericField('Exposure time', properties.exposure, 4, field_width, 's')
    gd.addNumericField('Magnification:', properties.magnification, 0, field_width, 'x')
    mag_units = ('kx', 'x')
    gd.addChoice('Magnification unit:', mag_units, mag_units[0])
    gd.addMessage('The actual magnification is %.2f times larger.' % (properties.mag_factor,))
    gd.addCheckbox('Use actual magnification:', False)
    gd.addMessage('')
    gd.addNumericField('Energy loss:', properties.energyloss, 1, field_width, 'eV')
    gd.addStringField('Date:', properties.date_string, field_width)
    gd.addStringField('original name:', properties.name, field_width_long)
    gd.addStringField('Filename format', default_format_str, field_width_long)
    gd.showDialog()

    if not gd.wasCanceled():
        # Edit the properties to consiter user choices:
        properties.exposure = gd.getNextNumber()
        mag = gd.getNextNumber()
        properties.mag_unit = gd.getNextChoice()
        if gd.getNextBoolean():
            properties.calc_mag(mag)
        properties.energyloss = gd.getNextNumber()
        properties.date_string = gd.getNextString()
        properties.name = gd.getNextString()
        format_str = gd.getNextString()
        # Chenge the title:
        imp.setTitle(format_str % properties.to_dict())

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def optionsDialog():
	gd = GenericDialog('bPrairie2tif options')

	# label, value, digits
	gd.addNumericField('Median Filter Pixel Size (0 for no filtering)', globalOptions['medianFilter'], 0)
	gd.addCheckbox('Convert to 8 bit', globalOptions['convertToEightBit'])
	
	gd.showDialog()
	if gd.wasCanceled():
		return None

	globalOptions['medianFilter'] = gd.getNextNumber()
	globalOptions['convertToEightBit'] = gd.getNextBoolean()

	return 1

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def getOptions(imp):
  gd = GenericDialog("Correct 3D Drift Options")
  channels = []
  for ch in range(1, imp.getNChannels()+1 ):
    channels.append(str(ch))
  gd.addMessage("Select a channel to be used for the registration.")
  gd.addChoice("     channel:", channels, channels[0])
  gd.addCheckbox("Use virtualstack?", False)
  gd.addMessage("This will store the registered hyperstack as an image sequence and\nshould be used if free RAM is less than 2X the size of the hyperstack. ")
  gd.showDialog()
  if gd.wasCanceled():
    return
  channel = gd.getNextChoiceIndex() + 1  # zero-based
  virtual = gd.getNextBoolean()
  return channel, virtual

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def getOptions():
	global numberOfChannels
	global replaceExisting

	gd = GenericDialog("Options")
	gd.addNumericField("Number of channel", 2, 0) # show 0 decimals
	gd.addCheckbox("Replace Destination .tif files", 0)
	gd.addHelp("http://robertcudmore.org/software_index.html")
	gd.showDialog()

	if gd.wasCanceled():
		print "User cancelled dialog."
		return -1
	#read out options
	numberOfChannels = gd.getNextNumber()
	replaceExisting = gd.getNextBoolean()
	

	return 1 #int(numberOfChannels)

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def getOptions(imp):
  gd = GenericDialog("Correct 3D Drift Options")
  channels = []
  for ch in range(1, imp.getNChannels()+1 ):
    channels.append(str(ch))
  gd.addChoice("Channel for registration:", channels, channels[0])
  gd.addCheckbox("Multi_time_scale computation for enhanced detection of slow drifts?", False)
  gd.addCheckbox("Sub_pixel drift correction (possibly needed for slow drifts)?", False)
  gd.addCheckbox("Edge_enhance images for possibly improved drift detection?", False)
  gd.addCheckbox("Use virtualstack for saving the results to disk to save RAM?", False)
  gd.addCheckbox("Only compute drift vectors?", False)
  gd.addMessage("If you put a ROI, drift will only be computed in this region;\n the ROI will be moved along with the drift to follow your structure of interest.")
  gd.showDialog()
  if gd.wasCanceled():
    return
  channel = gd.getNextChoiceIndex() + 1  # zero-based
  multi_time_scale = gd.getNextBoolean()
  subpixel = gd.getNextBoolean()
  process = gd.getNextBoolean()
  virtual = gd.getNextBoolean()
  only_compute = gd.getNextBoolean()
  return channel, virtual, multi_time_scale, subpixel, process, only_compute

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [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

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def run(title):
    gd = GenericDialog("Record Window")
    gd.addMessage("Maximum number of frames to record.\nZero means infinite, interrupt with ESC key.")
    gd.addNumericField("Max. frames:", 50, 0)
    gd.addNumericField("Milisecond interval:", 300, 0)
    gd.addSlider("Start in (seconds):", 0, 20, 5)
    frames = []
    titles = []
    for f in Frame.getFrames():
        if f.isEnabled() and f.isVisible():
            frames.append(f)
            titles.append(f.getTitle())
    gd.addChoice("Window:", titles, titles[0])
    gd.addCheckbox("To file", False)
    gd.showDialog()
    if gd.wasCanceled():
        return
    n_frames = int(gd.getNextNumber())
    interval = gd.getNextNumber() / 1000.0  # in seconds
    frame = frames[gd.getNextChoiceIndex()]
    delay = int(gd.getNextNumber())
    tofile = gd.getNextBoolean()

    dir = None
    if tofile:
        dc = DirectoryChooser("Directory to store image frames")
        dir = dc.getDirectory()
        if dir is None:
            return  # dialog canceled

    snaps = []
    borders = None
    executors = Executors.newFixedThreadPool(1)
    try:
        while delay > 0:
            IJ.showStatus("Starting in " + str(delay) + "s.")
            time.sleep(1)  # one second
            delay -= 1

        IJ.showStatus("Capturing frame borders...")
        bounds = frame.getBounds()
        robot = Robot()
        frame.toFront()
        time.sleep(0.5)  # half a second
        borders = robot.createScreenCapture(bounds)

        IJ.showStatus("Recording " + frame.getTitle())

        # Set box to the inside borders of the frame
        insets = frame.getInsets()
        box = bounds.clone()
        box.x = insets.left
        box.y = insets.top
        box.width -= insets.left + insets.right
        box.height -= insets.top + insets.bottom

        start = System.currentTimeMillis() / 1000.0  # in seconds
        last = start
        intervals = []
        real_interval = 0
        i = 1
        fus = None
        if tofile:
            fus = []

            # 0 n_frames means continuous acquisition
        while 0 == n_frames or (len(snaps) < n_frames and last - start < n_frames * interval):
            now = System.currentTimeMillis() / 1000.0  # in seconds
            real_interval = now - last
            if real_interval >= interval:
                last = now
                img = snapshot(frame, box)
                if tofile:
                    fus.append(executors.submit(Saver(i, dir, bounds, borders, img, insets)))  # will flush img
                    i += 1
                else:
                    snaps.append(img)
                intervals.append(real_interval)
            else:
                time.sleep(interval / 5)
                # interrupt capturing:
            if IJ.escapePressed():
                IJ.showStatus("Recording user-interrupted")
                break

                # debug:
                # print "insets:", insets
                # print "bounds:", bounds
                # print "box:", box
                # print "snap dimensions:", snaps[0].getWidth(), snaps[0].getHeight()

                # Create stack
        stack = None
        if tofile:
            for fu in snaps:
                fu.get()  # wait on all
            stack = VirtualStack(bounds.width, bounds.height, None, dir)
            files = File(dir).list(TifFilter())
            Arrays.sort(files)
            for f in files:
#.........这里部分代码省略.........

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def open_Octopus_file():

	# set up a file info structure
	fi = FileInfo()
	fi.fileFormat = fi.RAW
	fi.fileType=FileInfo.GRAY16_UNSIGNED
	fi.intelByteOrder = True
	fi.nImages = 1

	op = OpenDialog("Choose Octopus .dth file...", "")
	if not op.getDirectory(): return False

	# get the file extension
	file_extension = re.search('(\.[a-z][a-z][a-z])', op.getFileName()).group(1)
	
	if file_extension != ".dth":
		dlg = GenericDialog("Warning")
		dlg.addMessage("Please select an octopus .dth file")
		dlg.showDialog()
		return False

	# now strip the filename into a stem and index
	file_parse = re.match('([a-zA-z0-9_]*_)([0-9]+)\.dth', op.getFileName())
	file_stem = file_parse.group(1)
	file_index = int( file_parse.group(2) )

	# ok now we need to parse the header info
	header = get_Octopus_header(op.getDirectory(), file_stem, file_index)
	fi.nImages  = len(header['N'])

	# check to see whether we have a bit depth, if not, assume 16-bit
	if 'Bit_Depth' in header:
		print header['Bit_Depth']
		bit_depth = int(header['Bit_Depth'][0])
		if bit_depth == 8: fi.fileType = FileInfo.GRAY8
	else:
		bit_depth = 16

	# will assume that all files have the same size
	fi.width = int( header['W'][0] )
	fi.height = int( header['H'][0] )
	file_timestamp = strftime("%a, %d %b %Y %H:%M:%S", gmtime(float(header['Time'][0])) )
	

	# make a new imagestack to store the data
	stack = ImageStack(fi.width, fi.height)

	# finally, we need to make a list of files to import as sometimes we have
	# non contiguous file numbers
	try:
		files = os.listdir(op.getDirectory())
	except IOError:
		raise IOError( "No files exist in directory: " + op.getDirectory())

	filenums = []
	for f in files:
		# strip off the stem, and get the number
		targetfile = re.match(file_stem+'([0-9]+)\.dth', f)
		# only take thosefiles which match the formatting requirements
		if targetfile:
			filenums.append( int(targetfile.group(1)) )

	# sort the file numbers
	sorted_filenums = sorted(filenums)

	# make a file stats string
	file_stats_str = file_stem + '\n' + str(fi.width) +'x' + str(fi.height) + 'x' + \
		str(len(sorted_filenums)) +' ('+str(bit_depth)+'-bit)\n' + file_timestamp


	# now open a dialog to let the user set options
	dlg = GenericDialog("Load Octopus Stream (v"+__version__+")")
	dlg.addMessage(file_stats_str)
	dlg.addStringField("Title: ", file_stem)
	dlg.addNumericField("Start: ", 1, 0);
	dlg.addNumericField("End: ", len(sorted_filenums), 0)
	dlg.addCheckbox("Open headers", True)
	dlg.addCheckbox("Contiguous stream?", False)
	dlg.addCheckbox("8-bit unsigned", bit_depth==8)
	dlg.showDialog()

	# if we cancel the dialog, exit here
	if dlg.wasCanceled():
		return

	# set some params
	file_title = dlg.getNextString()
	file_start = dlg.getNextNumber()
	file_end = dlg.getNextNumber()
	DISPLAY_HEADER = bool( dlg.getNextBoolean() )

	# check the ranges
	if file_start > file_end: 
		file_start, file_end = file_end, file_start
	if file_start < 1: 
		file_start = 1
	if file_end > len(sorted_filenums): 
		file_end = len(sorted_filenums) 

	# now set these to the actual file numbers in the stream
#.........这里部分代码省略.........

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
from ij.gui import GenericDialog
from ij import IJ
from ij import WindowManager
import os
import glob

dirChooser = DirectoryChooser("Choose directory of images to normalize...")
dirPath = dirChooser.getDirectory()
scaleXs = []
if dirPath is not None:
	if not os.path.exists(dirPath + "resized"):
		os.mkdir(dirPath + "resized")

	gd = GenericDialog("Settings...")
	gd.addNumericField("Final scale factor:",0.5,2)
	gd.addCheckbox("Convert multichannel to RGB:",True)
	gd.showDialog()
	if (gd.wasOKed()):
		common_scale = gd.getNextNumber()
		convert_to_rgb = gd.getNextBoolean()
		filecollection = glob.glob(os.path.join(dirPath, '*.tif'))
		if (len(filecollection) > 0):
			for path in filecollection:
				theImage = IJ.openImage(path)
				calibration = theImage.getCalibration()
				scaleXs.append(calibration.pixelWidth)
				theImage.close()
			lc_scale = max(scaleXs)
			print lc_scale
			for path in filecollection:
				theImage = IJ.openImage(path)

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
	print tiles

	# Copies tiles for stitching into temp directory and stitches, if necessary
	if len(tiles)==1:
		params = "open=["+ imgDir +"tile_"+str(tiles[0])+".ome.tif] color_mode=Default view=Hyperstack stack_order=XYCZT"
		IJ.run("Bio-Formats Importer", params);
		tileImage = WindowManager.getImage("tile_"+str(tiles[0])+".ome.tif")
		tileImage.setSlice(int(tileImage.getNSlices()/2))
	else:
		ind = 1
		tileDiskSize = os.path.getsize(imgDir+"tile_"+str(tiles[0])+".ome.tif")
		totalDiskSize = tileDiskSize * len(tiles)
		totalDiskSizeMB = totalDiskSize / 1048576
		sizeGD = GenericDialog("Warning")
		sizeGD.addMessage("Memory used by selected tiles is " + str(totalDiskSizeMB) + "MB. Continue?")
		sizeGD.addCheckbox("Compute overlap",False)
		sizeGD.addNumericField("Tile overlap percentage",10,0)
		sizeGD.addCheckbox("Write fused image sequence to disk",False)
		sizeGD.showDialog()
		doComputeOverlap = sizeGD.getNextBoolean()
		overlapPctStr = str(sizeGD.getNextNumber())
		doWriteToDisk = sizeGD.getNextBoolean()
		if (doComputeOverlap):
			overlapText = "compute_overlap ignore_z_stage"
		else:
			overlapText = ""
		if (doWriteToDisk):
			outputPath = imgDir + "substitched"
			diskWriteText = "image_output=[Write to disk] output_directory=[" + outputPath + "]"
		else:
			diskWriteText = "image_output=[Fuse and display]"

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def main_interactive():
    """The main routine for running interactively."""
    log.info('Running in interactive mode.')
    (base, fname) = ui_get_input_file()
    if (base is None):
        return
    log.warn("Parsing project file: %s" % (base + fname))
    IJ.showStatus("Parsing experiment file...")
    mosaics = fv.FluoViewMosaic(join(base, fname), runparser=False)
    IJ.showStatus("Parsing mosaics...")
    progress = 0.0
    count = len(mosaics.mosaictrees)
    step = 1.0 / count
    for subtree in mosaics.mosaictrees:
        IJ.showProgress(progress)
        mosaics.add_mosaic(subtree)
        progress += step
    IJ.showProgress(progress)
    IJ.showStatus("Parsed %i mosaics." % len(mosaics))
    dialog = GenericDialog('FluoView OIF / OIB Stitcher')
    if len(mosaics) == 0:
        msg = ("Couldn't find any (valid) mosaics in the project file.\n"
               " \n"
               "Please make sure to have all files available!\n"
               " \n"
               "Will stop now.\n")
        log.warn(msg)
        dialog.addMessage(msg)
        dialog.showDialog()
        return
    msg = "------------------------ EXPORT OPTIONS ------------------------"
    dialog.addMessage(msg)
    formats = ["OME-TIFF", "ICS/IDS"]
    dialog.addChoice("Export Format", formats, formats[0])
    dialog.addCheckbox("separate files by Z slices (OME-TIFF only)?", False)
    msg = "------------------------ EXPORT OPTIONS ------------------------"
    dialog.addMessage(msg)
    dialog.addMessage("")
    dialog.addMessage("")
    msg = gen_mosaic_details(mosaics)
    log.warn(msg)
    msg += "\n \nPress [OK] to write tile configuration files\n"
    msg += "and continue with running the stitcher."
    dialog.addMessage(msg)
    dialog.showDialog()

    opts = {}
    if dialog.getNextChoice() == 'ICS/IDS':
        opts['export_format'] = '".ids"'
    else:
        opts['export_format'] = '".ome.tif"'
        if dialog.getNextBoolean() == True:
            opts['split_z_slices'] = 'true'
    code = imagej.gen_stitching_macro_code(mosaics, 'templates/stitching',
                                           path=base, tplpath=imcftpl, opts=opts)
    log.warn("============= generated macro code =============")
    log.warn(flatten(code))
    log.warn("============= end of generated  macro code =============")

    if dialog.wasOKed():
        log.warn('Writing stitching macro.')
        imagej.write_stitching_macro(code, fname='stitch_all.ijm', dname=base)
        log.warn('Writing tile configuration files.')
        imagej.write_all_tile_configs(mosaics, fixsep=True)
        log.warn('Launching stitching macro.')
        IJ.runMacro(flatten(code))

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
if __name__ == "__main__":



    t0 = time.time()
    print t0 - t0

    imgSource = IJ.getImage()

    root   = '/tier2/saalfeld/hanslovskyp/shan/thickness/'
    c      = imgSource.getWidth()/2
    height = imgSource.getHeight()

    dialog = GenericDialog( "Overlapping thickness estimation" )
    dialog.addStringField( "Root directory for storing results", root )
    dialog.addCheckbox( "Render matrix to image at each iteration.", False )
    dialog.addNumericField( "Start.", 0, 0 )
    dialog.addNumericField( "Stop.", height, 0 )
    dialog.addNumericField( "Interval size.", 1000, 0 )
    dialog.addNumericField( "Overlap.", imgSource.getWidth()/2, 0 )
    dialog.addNumericField( "Range.", c, 0 )

    dialog.showDialog()

    if dialog.wasCanceled():
        raise Exception( "dialog was canceled" )

    root     = dialog.getNextString()
    doRender = dialog.getNextBoolean()
    start    = dialog.getNextNumber()
    stop     = dialog.getNextNumber()

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def uScopeCalDialog(cal):
    ''' Pop up a dialog asking user to choose from the calibration names etc.
    
    CalIdx, SetGlobalScale, AddScaleBar = uScopeCalDialog(cal)
    
    `cal` should be the object containing `names`, `cals`, `units` attributes
    as set in the "user_settings.py" file.
    
    `CalIdx` is the list index to the chosen calibration.  
        Eg., if the options were 
            ['5x', '10x', '20x']
        and the user chose '10x', then 
            CalIdx = 1
        Returns `None` if the user cancelled the dialog.
    
    `SetGlobalScale` is a boolean (True/False) from a checkbox option, if the user wants this calibration set 'globally' to all open images.
    
    `AddScaleBar` is also a boolean (True/False), for a checkbox option, if user would like to run "Scale Bar..." afterwards.
    '''
    
    # The following inspired heavily by Correct_3D_drift.py:
    
    #print "uScopeCalDialog():"
    #print cal.names, [str(x) for x in cal.cals]
    
    gd = GenericDialog("Microscope Calibrations")
    gd.addMessage("Choose the calibration to load:")
    
    
    # generate text to display in list:
    # Radio Buttons:
    CalStr = []
    CalType_IsFunc = []
    
    
    for ii, name in enumerate(cal.names):
        if mc_DEBUG: print( "item #%i: name=" % (ii), name, "\n\t type=", type(name)  )
        if isinstance(name, basestring):
            '''It's just a regular calibration setting'''
            CalStr.append(  name + "      (%s"%cal.cals[ii] + " pixels/%s)"%cal.units[ii]  )
        else:
            ''' Assume we'll be loading a custom function/class '''
            CalStr.append(  name.name  )    # get the name from the Class' .name attribute
        #end if(str)
    #end for(cal.names)

    
    '''if > 20 cals, use dropdown list, otherwise use radio buttons'''
    if len(cal.names) > 20:
        Radio=False
        # Drop-Down list:
        gd.addChoice("     Calibration:", CalStr, CalStr[0]   )   # default = 1st (#0)
    
    else:
        Radio=True
        gd.addRadioButtonGroup("     Calibration:", CalStr, len(CalStr), 1, CalStr[0])
        #addRadioButtonGroup(label, [String items],  rows,  columns,  String:defaultItem)
    #end if(cal>20)
    
    gd.addCheckbox("Apply Scale to all open images?", False)
    gd.addCheckbox("Add Scale Bar to this image?", False)
    gd.addMessage("These calibrations can be altered by editing the file: \nFiji.app/plugins/Scripts/Plugins/Analyze/...\n\tMicroscope Measurement Tools/...\n\tMicroscope_Calibrations_user_settings.py")
    
    gd.showDialog()
    
    
    if gd.wasCanceled():
        return  None, None, None  # return None's if user cancels
    
    if Radio:
        ChosenCal = gd.getNextRadioButton()
        # Find the index to the chosen radio button w/ [list].index():
        CalIdx = CalStr.index(  ChosenCal )
    else:
        ChosenCal = gd.getNextChoiceIndex()
        CalIdx = ChosenCal  # the index to the choice
    
    SetGlobalScale = gd.getNextBoolean()
    AddScaleBar = gd.getNextBoolean()
    
    
    
    #if mc_DEBUG: print( ChosenCal,CalIdx, SetGlobalScale )
    #if mc_DEBUG: print( "end uScopeCalDialog()." )
    return CalIdx, SetGlobalScale, AddScaleBar

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
from ij import IJ
from ij.gui import GenericDialog
from ij.plugin import ChannelSplitter
from ij.plugin import RGBStackMerge
from ij.plugin import ImageCalculator
from ij import WindowManager

theImage = IJ.getImage()
gd = GenericDialog("Options...")
channelText = [("Channel " + str(ch+1)) for ch in range(theImage.getNChannels())]
gd.addChoice("Amplified_channel",channelText,channelText[0])
gd.addChoice("Reference_channel",channelText,channelText[-1])
gd.addNumericField("Amplifying_ratio",1,0)
gd.addCheckbox("Remove_bleedthrough",True)
gd.addCheckbox("Correct_for_refraction",True)
gd.showDialog()
if gd.wasOKed():
	amplifyChannel = gd.getNextChoiceIndex() + 1
	refChannel = gd.getNextChoiceIndex() + 1
	ampFactor = gd.getNextNumber()
	doRemoveBleedthrough = gd.getNextBoolean()
	doCorrectRefraction = gd.getNextBoolean()
	chImages = ChannelSplitter.split(theImage)
	
	## After this step, the image to operate on is "nextStepImage"
	if doRemoveBleedthrough:
		params = ("bleeding_channel=" + str(refChannel) + " bloodied_channel=" + str(amplifyChannel) + " " +
				"allowable_saturation_percent=1.0 rsquare_threshold=0.50")
		IJ.run("Remove Bleedthrough (automatic)", params)
		unbledImage = WindowManager.getImage("Corrected_ch" + str(amplifyChannel))
		mergingImages = [unbledImage,chImages[refChannel-1].duplicate()]

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addCheckbox [as 别名]
def getOptions(imp):
  gd = GenericDialog("Correct 3D Drift Options")
  channels = []
  for ch in range(1, imp.getNChannels()+1 ):
    channels.append(str(ch))
  methods = ["phase_correlation","center_of_mass"]
  gd.addChoice("Channel for registration:", channels, channels[0])
  gd.addChoice("Method for registration:", methods, methods[1])
  gd.addNumericField("Background value:", 0, 0)
  gd.addCheckbox("Multi_time_scale computation for enhanced detection of slow drifts?", False)
  gd.addCheckbox("Sub_pixel drift correction (possibly needed for slow drifts)?", False)
  gd.addCheckbox("Edge_enhance images for possibly improved drift detection?", False)
  gd.addCheckbox("Use virtualstack for saving the results to disk to save RAM?", False)
  gd.addCheckbox("Drift correct only data inside ROI?", False)
  gd.addCheckbox("Only compute drift vectors?", False)
  gd.addMessage("If you put a ROI, drift will only be computed in this region;\n the ROI will be moved along with the drift to follow your structure of interest.")
  gd.addSlider("z_min of ROI", 1, imp.getNSlices(), 1)
  gd.addSlider("z_max of ROI", 1, imp.getNSlices(), imp.getNSlices())
  gd.showDialog()
  if gd.wasCanceled():
    return
  channel = gd.getNextChoiceIndex() + 1  # zero-based
  method = gd.getNextChoiceIndex() + 1  # zero-based
  bg_value = gd.getNextNumber()
  multi_time_scale = gd.getNextBoolean()
  subpixel = gd.getNextBoolean()
  process = gd.getNextBoolean()
  virtual = gd.getNextBoolean()
  only_roi = gd.getNextBoolean()
  only_compute = gd.getNextBoolean()
  roi_z_min = int(gd.getNextNumber())
  roi_z_max = int(gd.getNextNumber())
  return channel, method, bg_value, virtual, multi_time_scale, subpixel, process, only_roi, only_compute, roi_z_min, roi_z_max