Python GenericDialog.addNumericField方法代碼示例

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
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

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
def getSettings(img):
    """This function assesses (by returning a boolean value) if the filter can
    be applied to the image passed as argument. Will ask the user for new values
    if current parameters are undefined."""
    global xradius, yradius, zradius
    canProceed = True

    if not img:
        IJ.error("No images open.")
        canProceed = False

    # Get new values if at least one of the parameters is 'null'
    if canProceed and None in (xradius, yradius, zradius):
        gd = GenericDialog("Median Filter")
        gd.addNumericField("X radius:", 2.0, 1)
        gd.addNumericField("Y radius:", 2.0, 1)
        gd.addNumericField("Z radius:", 2.0, 1)
        gd.showDialog()
        if gd.wasCanceled():
            canProceed = False
        else:
            xradius = gd.getNextNumber()
            yradius = gd.getNextNumber()
            zradius = gd.getNextNumber()
 
    return canProceed

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
def getOptions():
    lowerThreshold = 80;
    upperThreshold = 255;
    stepNumber = 1
    stepThreshold = 5;
    #p3DOCThreshold = 70;
    #p3DOCSlice = 1;
    p3DOCmin = 100;
    p3DOCmax = 2658480;
    gd = GenericDialog( "Parameters" )
    gd.addMessage("Binary mask thresholds")
    gd.addNumericField("Lower Threshold", lowerThreshold, 0)  # show 2 decimals  
    gd.addNumericField("Upper threshold", upperThreshold, 0)  # show 2 decimals  
    gd.addNumericField("Step number", stepNumber, 0)  # show 2 decimals  
    gd.addNumericField("Step threshold", stepThreshold, 0)  # show 2 decimals      
    gd.addMessage("3D Object Counter parameters")
    #gd.addNumericField("threshold", p3DOCThreshold, 0)  # show 2 decimals  
    gd.addNumericField("min.", p3DOCmin, 0)  # show 2 decimals  
    gd.addNumericField("max.", p3DOCmax, 0)  # show 2 decimals  
    gd.showDialog()  
    if gd.wasCanceled():  
        return  
    # Read out the options  
    lowerThreshold = gd.getNextNumber()
    upperThreshold = gd.getNextNumber()
    stepNumber = gd.getNextNumber()
    stepThreshold = gd.getNextNumber()
    #p3DOCThreshold = gd.getNextNumber()
    p3DOCmin = gd.getNextNumber()
    p3DOCmax = gd.getNextNumber()   
    return lowerThreshold, upperThreshold, stepNumber, stepThreshold, p3DOCmin, p3DOCmax      

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
def get_options():
    """Ask user for input values."""
    dlg = GenericDialog("Options for Boxed Heatmap")
    dlg.addMessage("Boxed Heatmap settings")
    dlg.addMessage("Specify box size:")
    dlg.addNumericField("Width", 32, 0)
    dlg.addNumericField("Height", 32, 0)
    dlg.showDialog()
    if dlg.wasCanceled():
        print "User canceled dialog."
        return  None
    # Read out the options
    boxw = int(dlg.getNextNumber())
    boxh = int(dlg.getNextNumber())
    return boxw, boxh

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
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

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
def getOptions(options, image):
	if 'channel' not in options:
		channels = []
		for ch in range(1, image.getNChannels() + 1):
			channels.append("Channel " + "%i" % ch)
		dialog = GenericDialog("Select deconvolution parameters")
		dialog.addChoice("Channel to process", channels, None)
		dialog.addNumericField("Regularization parameter", 0.01, 2)
		dialog.addNumericField("Number of iterations", 50, 0)
		dialog.showDialog()
		if dialog.wasCanceled():
			sys.exit(1)	
		options['channel'] = dialog.getNextChoiceIndex()
		options['regparam'] = dialog.getNextNumber()
		options['iterations'] = dialog.getNextNumber()
	
	return options

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
def get_parameters(p, num_data_sets):
  gd = GenericDialog("Correct 3D Drift Options")

  gd.addMessage("Found "+str(num_data_sets)+" data sets")
  gd.addStringField("analyse", "all");

  gd.addMessage("Image analysis parameters:")
  for k in p.keys():
    gd.addNumericField(k, p[k], 2);
  gd.showDialog()
  if gd.wasCanceled():
    return

  to_be_analyzed = gd.getNextString()
  for k in p.keys():
    p[k] = gd.getNextNumber()
    
  return to_be_analyzed, p

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
def getRefIdDialog():  
  gd = GenericDialog("Reference Image")
  gd.addMessage("Preparing Turboreg(Rigidbody)\nSpecify image for reference")
  gd.addNumericField("Channel (C):", 2, 0)
  gd.addNumericField("Slice (Z):", 1, 0)
  gd.addNumericField("Frame (T):", 1, 0)
  gd.addMessage("Note: All fields start with 1 (not 0)")
  gd.showDialog()
  #  
  if gd.wasCanceled():
    print "User canceled dialog!"  
    return
  # Read out the options  
  c = int(gd.getNextNumber())
  z = int(gd.getNextNumber())
  t = int(gd.getNextNumber())
  refId = [c,z,t]
  return refId

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
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)

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
#
def get_parameters(p, keys, num_data_sets):
  gd = GenericDialog("Please enter parameters")

  gd.addMessage("Found "+str(num_data_sets)+" data sets")
  gd.addStringField("analyse", "all");

  gd.addMessage("Image analysis parameters:")
  gd.addMessage("Please note: the threshold values are inclusive!\nThus, to exlude pixels with value 255 the upper threshold needs to be 254")
  
  
  for k in keys:
    gd.addNumericField(k, p[k], 2);
  gd.showDialog()
  if gd.wasCanceled():
    return

  to_be_analyzed = gd.getNextString()
  for k in keys:
    p[k] = gd.getNextNumber()
    

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
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())

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
def getOptions():  
    gd = GenericDialog("Options") 
    gd.addMessage("Filter Parameters")  
    gd.addNumericField("Smoothing Parameter", 0.1, 2)  # show 2 decimals
    gd.addNumericField("Patch radius", 2 , 1)
    gd.addNumericField("Search volume radius", 3 , 1)  
    gd.showDialog()  
    
    if gd.wasCanceled():  
        print "User canceled dialog!"  
        sys.exit()  
    # Read out the options    
    beta = gd.getNextNumber()
    patchradius = gd.getNextNumber()
    searchradius = gd.getNextNumber()     
    return beta, patchradius, searchradius  

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
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:
#.........這裏部分代碼省略.........

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
dc = DirectoryChooser("Choose directory with OME.TIF files...")
sourceDir = dc.getDirectory()

if not(sourceDir is None):
	if not os.path.exists(sourceDir + "resized"):
		os.mkdir(sourceDir + "resized")

	dirSize = get_directory_size(sourceDir)
	dirSizeMB = dirSize / 1048576
	memoryObj = Memory()
	memFiji = memoryObj.maxMemory()
	memFijiMB = memFiji / 1048576

	gd = GenericDialog("Set Parameters...")
	gd.addNumericField("Sizing_ratio (Final disk space / Initial disk space):",0.25,2)
	gd.addMessage("Directory size: " + str(dirSizeMB) + "MB")
	gd.addMessage("Maximum memory: " + str(memFijiMB) + "MB")
	mem_recs = calculate_memory_recs(dirSize,memFiji)
	print mem_recs
	for i in range(0,len(mem_recs)):
		ratio_rec = float(mem_recs[i]) / dirSizeMB
		if (ratio_rec > 1):
			ratio_rec = 1
		print ratio_rec
		ratio_rec_str = "%.3f" % ratio_rec
		gd.addMessage(str(i+1)+"-channel: " + str(mem_recs[i]) + "MB; Ratio: " + ratio_rec_str)
	gd.showDialog()
	ratioRaw = gd.getNextNumber()
	ratio = math.sqrt(ratioRaw)

# 需要導入模塊: from ij.gui import GenericDialog [as 別名]
# 或者: from ij.gui.GenericDialog import addNumericField [as 別名]
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
#.........這裏部分代碼省略.........