def registerExtenderCallbacks(self, callbacks):
# keep a reference to our callbacks object
self._callbacks = callbacks
# obtain an extension helpers object
self._helpers = callbacks.getHelpers()
# define stdout writer
self._stdout = PrintWriter(callbacks.getStdout(), True)
self._stdout.println(self.EXTENSION_NAME + ' by @luxcupitor')
self._stdout.println('================================')
self._stdout.println('')
self._stdout.println('TIP: Go to "Custom Scanner" tab and click "Execute on Proxy History"')
self._stdout.println('to run the scanner checks on recently imported session files.')
self._stdout.println('')
# set our extension name
callbacks.setExtensionName(self.EXTENSION_NAME)
callbacks.registerScannerCheck(self)
# add the custom tab and button to Burp's UI
self._newpanel = Panel()
self._newpanel.setLayout(FlowLayout())
self._button = JButton("Execute on Proxy History", actionPerformed=self.checkProxyHistory)
self._newpanel.add(self._button)
callbacks.customizeUiComponent(self._newpanel)
callbacks.addSuiteTab(self)
return
def addControl(self, dialog):
if self.control_type==MyControlDefinition.Numeric:
dialog.addNumericField(self.label, self.default_val, 2);
dialog.getNumericFields()[-1].setEnabled(self.enabled);
elif self.control_type==MyControlDefinition.String:
dialog.addStringField(self.label, self.default_val);
dialog.getStringFields()[-1].setEnabled(self.enabled);
elif self.control_type==MyControlDefinition.Choice:
if not self.default_val in self.choices:
raise IndexError("default value isn''t in list of choices");
dialog.addChoice(self.label, self.choices, self.default_val);
dialog.getChoices()[-1].setEnabled(self.enabled);
elif self.control_type==MyControlDefinition.Checkbox:
if not isinstance(self.default_val, bool):
raise TypeError();
dialog.addCheckbox(self.label, self.default_val);
dialog.getCheckboxes()[-1].setEnabled(self.enabled);
elif self.control_type==MyControlDefinition.RadioButtonGroup:
if not self.default_val in self.choices:
raise IndexError("default value isn''t in list of choices");
panel = Panel();
cbg = CheckboxGroup();
for ch in self.choices:
cb = Checkbox(ch, cbg, ch==self.default_val)
cb.setEnabled(self.enabled);
self.checkboxes.append(cb);
panel.add(cb);
dialog.addPanel(panel);
def getUiComponent(self):
panel = Panel()
panel.setBackground(Color.gray)
button = Button('Hello Burp Button!')
panel.add(button)
self.callbacks.customizeUiComponent(
panel) # customize UI components in line with Burp's UI style
return panel
def __init__(self, listCategories): """ listCategories: initial list of categories to fill the fields """ GenericDialogPlus.__init__(self, "Category names") self.addPanel( Panel(GridLayout(0,1)) ) self.panel = self.getComponent(0) for category in listCategories: self.panel.add( TextField(category) ) # Add string input to GUI self.addButton(CategoryDialog.ADD_CATEGORY, self)
def choose_series(filepath, params):
"""if input file contains more than one image series (xy position), prompt user to choose which one to use"""
# todo: if necessary (e.g. if lots of series), can improve thumbnail visuals based loosely on https://github.com/ome/bio-formats-imagej/blob/master/src/main/java/loci/plugins/in/SeriesDialog.java
import_opts = ImporterOptions();
import_opts.setId(filepath);
reader = ImageReader();
ome_meta = MetadataTools.createOMEXMLMetadata();
reader.setMetadataStore(ome_meta);
reader.setId(filepath);
no_series = reader.getSeriesCount();
if no_series == 1:
return import_opts, params;
else:
series_names = [ome_meta.getImageName(idx) for idx in range(no_series)];
dialog = GenericDialog("Select series to load...");
dialog.addMessage("There are multiple series in this file! \n" +
"This is probably because there are multiple XY stage positions. \n " +
"Please choose which series to load: ");
thumbreader = BufferedImageReader(reader);
cbg = CheckboxGroup();
for idx in range(no_series):
p = Panel();
p.add(Box.createRigidArea(Dimension(thumbreader.getThumbSizeX(), thumbreader.getThumbSizeY())));
ThumbLoader.loadThumb(thumbreader, idx, p, True);
dialog.addPanel(p);
cb = Checkbox(series_names[idx], cbg, idx==0);
p.add(cb);
dialog.showDialog();
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled");
if dialog.wasOKed():
selected_item = cbg.getSelectedCheckbox().getLabel();
selected_index = series_names.index(selected_item);
params.setSelectedSeriesIndex(selected_index);
for idx in range(0, no_series):
import_opts.setSeriesOn(idx, True) if (idx==selected_index) else import_opts.setSeriesOn(idx, False);
reader.close();
return import_opts, params
def gui(self):
x = 10 # panel padding
y = 5 # panel padding
self.panel = Panel()
self.panel.setLayout(None)
self.scn_lbl = JLabel("Enable scanning")
self.scn_lbl.setBounds(x, y, 100, 20)
self.panel.add(self.scn_lbl)
self.enable = JCheckBox()
self.enable.setBounds(x + 120, y, 50, 20)
self.panel.add(self.enable)
self.rand_lbl = JLabel("Randomize payloads")
self.rand_lbl.setBounds(x, y + 15, 100, 20)
self.panel.add(self.rand_lbl)
self.randomize = JCheckBox()
self.randomize.setBounds(x + 120, y + 15, 50, 20)
self.panel.add(self.randomize)
self.pyld_lbl = JLabel("Payloads List (Line separated)")
self.pyld_lbl.setBounds(x, y + 30, 180, 20)
self.panel.add(self.pyld_lbl)
self.payloads_list = JTextArea()
self.pyld_scrl = JScrollPane(self.payloads_list)
self.pyld_scrl.setBounds(x, y + 50, 600, 200)
self.panel.add(self.pyld_scrl)
self.save_btn = JButton("Save", actionPerformed=self.save_settings)
self.save_btn.setBounds(x, y + 250, 100, 30)
self.panel.add(self.save_btn)
# Settings loader from [utils/Helpers/load_settings]
self.load_settings()
return self
headers = csvIterator.next() # read first header line
n = len(headers)
dropdowns = [
[] for i in range(n)
] # [[], [], [], [], []] such that dropdowns[i] contains the list of choices for dropdowns i
for row in csvIterator:
for i, entry in enumerate(row): # row is a list
if entry:
dropdowns[i].append(
entry
) # dropdown[i] is the list of choices # if necessary since all columns might not have the same length
# Create horizontal panel for dropdowns
panel = Panel(GridLayout(
0, n)) # as many columns (n) as menus, as many rows as necessary (0)
# First panel row -> dropdown labels
for header in headers:
panel.add(Label(header))
# Second panel row -> dropdown choices
for i in range(n):
label = headers[i]
chooser = Choice()
chooser.setName(label) # not display but easier to recover infos
dropdown = dropdowns[i]
for option in dropdown:
chooser.add(option)
# inherits from the Java ActionListener interface.
#
class TestButtonAction(ActionListener):
def actionPerformed(self, e):
textArea.append("Test Button Clicked!\n")
#
# Create the Frame, Panel, Button,
# TextArea, and TestButtonAction objects.
#
frame = Frame("Hello World")
panel = Panel()
button = Button("Test Button")
buttonAction = TestButtonAction()
textArea = TextArea()
#
# Put everything together and show
# the window.
#
button.addActionListener(buttonAction)
panel.add(button)
panel.add(textArea)
frame.add(panel)
frame.pack()
frame.show()
if nCat <= 12: button.setToolTipText("Keyboard shortcut: F" + str(nCat)) # F shortcut labels are 1-based, ie match the len value
return button
############### GUI - CATEGORY DIALOG - collect N classes names (N define at first line) #############
textFilePath = textFile.getPath() if textFile else ""
listCategories = getCategoriesFrom(categorySource, textFilePath) # initial list, before user-edit
catDialog = CategoryDialog(listCategories)
catDialog.showDialog()
################# After OK clicking ###########
# Recover fields from the formular
if catDialog.wasOKed():
# Loop over categories and add a button to the panel for each
catPanel = Panel(GridLayout(0,4)) # Unlimited number of rows - fix to 4 columns - not possible to use a JPanel, not supported by GenericDialog
listCat = catDialog.getListCategories()
listShortcut = range( 112, 112+len(listCat)
)
for index, category in enumerate(listCat):
# Create a Button
button = JButton(category) # button label
if index<12: button.setToolTipText( "Keyboard shortcut: F" + str(index+1) ) # index is 0-based, F shortcut are 1-based
# Bind action to button
button.addActionListener(categoryAction)
return checkbox
############### GUI - CATEGORY DIALOG #############
textFilePath = textFile.getPath() if textFile else ""
listCategories = getCategoriesFrom(categorySource, textFilePath)
# Initialize a category dialog with list of categories
catDialog = CategoryDialog(listCategories)
catDialog.showDialog()
# Recover fields from the formular
if catDialog.wasOKed():
# Loop over categories, adding a tickbox to the panel for each
catPanel = Panel(GridLayout(
0, 4)) # Unlimited number of rows - fix to 4 columns
for category in catDialog.getListCategories():
# Make a checkbox with the category name
box = Checkbox(category, False)
box.setFocusable(
False) # important to have the keyboard shortcut working
# Add checkbox to the gui for this category
catPanel.add(box)
## Initialize dialog
winButton = MainDialog(catPanel, browse_mode, run_measure)
winButton.showDialog()
def perform_user_qc(in_imp, edges, alt_edges, fixed_anchors_list, params):
"""allow the user to intervene to fix erroneously identified membrane edges"""
n_frames = in_imp.getNFrames();
n_channels = in_imp.getNChannels();
output_folder = params.output_path;
current_edges = edges;
rgbstack = ImageStack(in_imp.getWidth(), in_imp.getHeight());
if n_frames > 1:
for tidx in range(n_frames):
in_imp.setT(tidx+1);
ip = in_imp.getProcessor();
rgbip = ip.convertToRGB();
rgbstack.addSlice(rgbip);
else:
for cidx in range(n_channels):
in_imp.setC(cidx+1);
ip = in_imp.getProcessor();
rgbip = ip.convertToRGB();
rgbstack.addSlice(rgbip);
imp = ImagePlus(("RGB " + in_imp.getTitle()), rgbstack);
IJ.run("Colors...", "foreground=red background=white selection=yellow");
for tidx in range(imp.getNSlices()):
imp.setSlice(tidx+1);
for anchor in params.manual_anchor_positions:
imp.setRoi(PointRoi(anchor[0], anchor[1]));
IJ.run(imp, "Draw", "slice");
imp.show();
autoset_zoom(imp);
imp.setPosition(1);
imp.setRoi(current_edges[0]);
if n_frames > 1:
listener = UpdateRoiImageListener(current_edges);
imp.addImageListener(listener);
IJ.setTool("freeline");
do_flip = True;
while do_flip:
dialog = NonBlockingGenericDialog("User quality control");
dialog.enableYesNoCancel("Continue", "Flip all edges");
dialog.setCancelLabel("Cancel analysis");
dialog.addMessage("Please redraw the membrane edges as necessary, \n" +
"making sure to draw beyond anchor points at either end...\n" +
"Click OK when done. ");
p = Panel();
but = Button("Flip this edge");
al = Listener(edges, alt_edges, imp);
but.addActionListener(al);
p.add(but);
dialog.addPanel(p);
dialog.showDialog();
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled");
elif dialog.wasOKed():
do_flip = False;
else:
print("flip edges");
do_flip = True;
if n_frames > 1:
imp.removeImageListener(listener);
current_edges = alt_edges if (current_edges == edges) else edges;
imp.setPosition(1);
imp.setRoi(current_edges[0]);
if n_frames > 1:
listener = UpdateRoiImageListener(current_edges);
imp.addImageListener(listener);
last_roi = imp.getRoi();
if n_frames > 1:
qcd_edges = listener.getRoiList();
if imp.getNFrames() > imp.getNSlices():
qcd_edges[imp.getT() - 1] = last_roi;
else:
qcd_edges[imp.getZ() - 1] = last_roi;
imp.removeImageListener(listener);
else:
qcd_edges = [last_roi];
mbio.save_qcd_edges2(qcd_edges, output_folder);
# next four lines are a quick and dirty hack...
if n_frames > 1:
nframes = imp.getNFrames() if imp.getNFrames()>imp.getNSlices() else imp.getNSlices();
else:
nframes = n_frames;
for fridx in range(0, nframes):
if (qcd_edges[fridx].getType()==Roi.FREELINE) or (qcd_edges[fridx].getType()==Roi.POLYLINE):
if (fridx == 0) or params.constrain_anchors:
anchors = params.manual_anchor_positions;
else:
anchors = fixed_anchors_list[fridx - 1];
fixed_anchors = mb.fix_anchors_to_membrane(anchors, qcd_edges[fridx], params);
fixed_anchors = mb.order_anchors(fixed_anchors, params.manual_anchor_midpoint);
fixed_anchors_list[fridx] = fixed_anchors;
poly = qcd_edges[fridx].getInterpolatedPolygon(0.25, False);
polypoints = [(x,y) for x,y in zip(poly.xpoints, poly.ypoints)];
idx = [polypoints.index(fixed_anchors[0]), polypoints.index(fixed_anchors[1])];
idx.sort();
polypoints = polypoints[idx[0]:idx[1]];
newedge = PolygonRoi([x for (x,y) in polypoints],
[y for (x,y) in polypoints],
Roi.POLYLINE);
newedge = mb.check_edge_order(anchors, newedge);
imp.setPosition(fridx + 1);
imp.setRoi(newedge);
IJ.run(imp, "Interpolate", "interval=1.0 smooth adjust");
IJ.run(imp, "Fit Spline", "");
qcd_edges[fridx] = imp.getRoi();
mbio.save_qcd_edges2(qcd_edges, output_folder);
imp.changes = False;
imp.close();
return qcd_edges, fixed_anchors_list;
def settings():
""" Settings """
# Calls potential config file to set defaults
# for settings dialog. Sets all defaults to 0
# if no config file exists.
con_path = os.path.join(str(Root), "FRET_params.cfg")
if os.path.exists(con_path):
dflt = config_read()
print type(dflt.get("b_sub", "Rolling ball"))
print (dflt.get("b_sub", "Rolling ball"))
print type(int(dflt.get("b_sub", "Rolling ball")))
print (dflt.get("b_sub", "Rolling ball"))
else:
dflt = {}
feat_model_strings = ["Translation", "Rigid",
"Similarity", "Affine
]
reg_model_strings = ["Translation", "Rigid",
"Similarity", "Affine",
"Elastic", "Least Squares"
]
b_sub_strings = ["Rolling Ball", "Manual Selection"]
# Registration parameters dialog.
gd = GenericDialog("Advanced Settings")
gd.addMessage("REGISTRATION PARAMETERS")
gd.addNumericField("Steps per scale octave: ", float(dflt.get("steps", 6)), 0, 7, "")
gd.addNumericField("Max Octave Size: ", float(dflt.get("max_oct", 1024)), 0, 7, "")
gd.addNumericField("Feature Descriptor Size: ", float(dflt.get("fd_size", 12)), 1, 7, "")
gd.addNumericField("Initial Sigma: ", float(dflt.get("sigma", 1.2)), 2, 7, "")
gd.addNumericField("Max Epsilon: ", float(dflt.get("max_eps", 15)), 1, 7, "")
gd.addNumericField("Min Inlier Ratio: ", float(dflt.get("min_inlier", 0.05)), 3, 7, "")
gd.addCheckbox("Use Shrinkage Constraint", ast.literal_eval(dflt.get("shrinkage", "False")))
gd.addChoice("Feature extraction model", feat_model_strings,
feat_model_strings[int(dflt.get("feat_model", 1))]
)
gd.addChoice("Registration model", reg_model_strings,
reg_model_strings[int(dflt.get("reg_model", 1))]
)
# Background removal parameters dialog.
gd.addPanel(Panel())
gd.addMessage("BACKGROUND REMOVAL")
gd.addChoice("Subtraction method:", b_sub_strings,
b_sub_strings[int(dflt.get("b_sub", 0))]
)
gd.addNumericField("Rolling ball size: ",
float(dflt.get("ballsize", 50)), 1, 7, "px"
)
gd.addCheckbox("Create Background", ast.literal_eval(dflt.get("create_b", "False")))
gd.addCheckbox("Light Background", ast.literal_eval(dflt.get("light_b", "False")))
gd.addCheckbox("Use Parabaloid", ast.literal_eval(dflt.get("parab", "False")))
gd.addCheckbox("Do Pre-smoothing", ast.literal_eval(dflt.get("smooth", "False")))
gd.addCheckbox("Correct Corners", ast.literal_eval(dflt.get("corners", "False")))
# Measumrent parameters dialog.
gd.addPanel(Panel())
gd.addMessage("MEASUREMENT PARAMETERS")
gd.addNumericField("Max Cell Area", float(dflt.get("cell_max", 2200)), 0, 7, "px")
gd.addNumericField("Min Cell Area", float(dflt.get("cell_min", 200)), 0, 7, "px")
gd.addNumericField("Ratio Subtraction", float(dflt.get("subtr_ratio", 0.31)), 3, 7, "")
# Plot parameters dialog.
gd.addPanel(Panel())
gd.addMessage("PLOT PARAMETERS")
gd.addNumericField("Max y, d and aFRET", float(dflt.get("p_max", 0.65)), 2, 7, "")
gd.addNumericField("Min y, d and aFRET", float(dflt.get("p_min", 0.0)), 2, 7, "")
gd.addNumericField("Max y, norm. d and aFRET", float(dflt.get("p_max_n", 1.65)), 2, 7, "")
gd.addNumericField("Min y, norm. d and aFRET", float(dflt.get("p_min_n", 0.5)), 2, 7, "")
# Set location of dialog on screen.
#gd.setLocation(0,1000)
gd.showDialog()
# Checks if cancel was pressed, kills script.
if gd.wasCanceled() is True:
sys.exit("Cancel was pressed, script terminated.")
# Parameters dictionary.
parameters = {"steps" : gd.getNextNumber(),
"max_oct" : gd.getNextNumber(),
"fd_size" : gd.getNextNumber(),
"sigma" : gd.getNextNumber(),
"max_eps" : gd.getNextNumber(),
"min_inlier" : gd.getNextNumber(),
"shrinkage" : gd.getNextBoolean(),
"feat_model" : gd.getNextChoiceIndex(),
"reg_model" : gd.getNextChoiceIndex(),
"b_sub" : gd.getNextChoiceIndex(),
"ballsize" : gd.getNextNumber(),
"create_b" : gd.getNextBoolean(),
"light_b" : gd.getNextBoolean(),
"parab" : gd.getNextBoolean(),
"smooth" : gd.getNextBoolean(),
"corners" : gd.getNextBoolean(),
"cell_max" : gd.getNextNumber(),
"cell_min" : gd.getNextNumber(),
"subtr_ratio" : gd.getNextNumber(),
"p_max" : gd.getNextNumber(),
"p_min" : gd.getNextNumber(),
"p_max_n" : gd.getNextNumber(),
"p_min_n" : gd.getNextNumber()
}
parameters = config_write(parameters)
return parameters
