Python GenericDialog.addMessage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 addMessage [as 别名]
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      

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

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addMessage [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.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addMessage [as 别名]
def run():
    ''' If someone tries to run this file by itself, warn them of their error.  Unfortunately, since I was too lazy to make Microscope_Calibrations a full plugin (rather than a script), this accompanying settings file will show up in the Scripts menu.'''
    from ij.gui import GenericDialog
    
    gd = GenericDialog("Microscope_Calibrations_user_settings.py")
    gd.addMessage("This file is only for adding functionality to the plugin 'Microscope Measurement Tools'.\nNothing is done when this settings file is run by itself."  )
    
    gd.showDialog()

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addMessage [as 别名]
def run():
    ''' If someone tries to run this file by itself, warn them of their error.  Unfortunately, since I was too lazy to make Microscope_Calibrations a full plugin (rather than a script), this accompanying settings file will show up in the Scripts menu.'''
    from ij.gui import GenericDialog
    
    gd = GenericDialog("Microscope_Calibrations_user_settings.py")
    gd.addMessage("This file is only for setting the microscope calibrations and settings for the plugins 'Microscope Measurement Tools'.\nNothing is done when this settings file is run by itself.\nPlease open this file in a text editor instead, to edit the calibrations.\n  \n"  +  \
    "The file should reside in a path like the following\n"  +  \
    "Fiji.app/plugins/Scripts/Analyze/Microscope Measurement Tools/Microscope_Calibrations_user_settings.py\n  "  +  "\n" +  \
    "Changes to the settings file are not automatically picked up by Fiji.  The workaround is to\n  1) Quit Fiji.\n  2) Delete the '$py.class' file 'Microscope_Calibrations_user_settings$py.class'\n  3) Open Fiji.  Make sure the new settings show up in 'Choose Microscope Calibration'."  )
    
    gd.showDialog()

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

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

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

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

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addMessage [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.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()
  dt = gd.getNextNumber()
  return channel, virtual, multi_time_scale, subpixel, process

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addMessage [as 别名]
def run():
	bPrintLog(' ', 0)
	bPrintLog('=====================================', 0)
	bPrintLog('Running bAlign_Batch_v7', 0)
	bPrintLog('=====================================', 0)

	if len(sys.argv) < 2:
		print "   We need a hard-drive folder with .tif stacks as input"
		print "	  Usage: ./fiji-macosx bALign_Batch_7 <full-path-to-folder>/"
		# Prompt user for a folder
		sourceFolder = DirectoryChooser("Please Choose A Directory Of .tif Files").getDirectory()
		if not sourceFolder:
			return 0
		strippedFolder = sourceFolder.replace(' ', '')
		if sourceFolder != strippedFolder:
			print 'found a space in specified path. Pease remove spaces and try again.'
			print 'path:', sourceFolder
			errorDialog = GenericDialog('Align Batch 7 Options')
			errorDialog.addMessage('bAlignBatch7 Error !!!')
			errorDialog.addMessage('There can not be any spaces in the path.')
			errorDialog.addMessage('Please remove spaces and try again.')
			errorDialog.addMessage('Offending path is:')
			errorDialog.addMessage(sourceFolder)
			errorDialog.showDialog()
			return 0
	else:
		sourceFolder = sys.argv[1] #assuming it ends in '/'
	
	if not os.path.isdir(sourceFolder):
		bPrintLog('\nERROR: run() did not find folder: ' + sourceFolder + '\n',0)
		return 0

	
	if (Options(sourceFolder)):
		runOneFolder(sourceFolder)

	bPrintLog('=====================================', 0)
	bPrintLog('Done bAlign_Batch_v7', 0)
	bPrintLog('=====================================', 0)
        bPrintLog(' ', 0)

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import addMessage [as 别名]
def get_config_file(folder):
    '''Returns the config file name.'''
    # Get list of files in the selected directory.
    files = os.listdir(folder)

    # Check if a config file is present in folder.
    if default_config in files:
        dialog = GenericDialog('Default config file found!')
        dialog.addMessage('Use this file for the analysis?\n \n%s' % os.path.join(folder, default_config))
        dialog.enableYesNoCancel()
        dialog.showDialog()
        if dialog.wasCanceled():
            return None
        elif dialog.wasOKed():
            return default_config
        else:
            open_dialog = OpenDialog('Select a config file', folder, default_config)
            return open_dialog.getFileName()
    else:
        # Ask user to select a config file.
        open_dialog = OpenDialog('Select a config file', folder, default_config)
        return open_dialog.getFileName()

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