def __init__(self):
# set up the layout
self.__component = JPanel(GridBagLayout())
self.__image = JLabel()
self.__album = JLabel()
self.__artist = JLabel()
self.__application = None
self.__image.setVerticalAlignment(SwingConstants.TOP)
self.__album.setVerticalAlignment(SwingConstants.TOP)
self.__artist.setVerticalAlignment(SwingConstants.TOP)
gbc = GridBagConstraints()
gbc.fill = GridBagConstraints.VERTICAL
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 0
gbc.gridy = 0
gbc.weighty = 2
gbc.gridheight = 2
self.__component.add(self.__image, gbc)
gbc.fill = GridBagConstraints.HORIZONTAL
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 1
gbc.gridy = 0
gbc.gridheight = 1
gbc.weighty = 0
gbc.insets = Insets(0, 10, 0, 10)
self.__component.add(self.__album, gbc)
gbc.fill = GridBagConstraints.BOTH
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 1
gbc.gridy = 1
gbc.weightx = 2
gbc.weighty = 2
gbc.gridheight = 1
self.__component.add(self.__artist, gbc)
def cachedBPROM(genome, fileName, frame):
"""
genome: Genome as a string.
fileName: File to save the BPROM results in.
swing: A JFrame or None. If this is None then messages will be printed, if it isn't then
they will also be put in a dialog box.
return: Results of the BPROM prediction stored in a list of Promoter objects.
If the file Specified by fileName already exists then this function simply parses the file
already there. Also, if a request is made to BPROM and nothing is returned, no file is
created, the user is warned, and an empty list is returned.
"""
offset = 25 if ".forward.bprom" in fileName else 50
direction = "forward" if offset == 50 else "reverse"
def getPromoters():
input = open(fileName, "r")
results = parseBPROM(input.read())
input.close()
return results
if not os.path.isfile(fileName):
results = urllib.urlopen("http://linux1.softberry.com/cgi-bin/programs/gfindb/bprom.pl",
urllib.urlencode({"DATA" : genome}))
resultString = results.read()
results.close()
resultString = resultString[resultString.find("<pre>"):resultString.find("</pre>")]
resultString = re.sub("<+.+>+", "", resultString).strip()
if resultString:
output = open(fileName, "w")
output.write(resultString)
output.close()
return getPromoters()
else:
if frame:
messageFrame = JFrame("BPROM Error",
defaultCloseOperation = WindowConstants.DISPOSE_ON_CLOSE)
messageFrame.setLocation(frame.location().x + offset, frame.location().y + offset)
messageFrame.contentPane.layout = GridBagLayout()
constraints = GridBagConstraints()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
messageFrame.contentPane.add(JLabel("<html>The pipeline will continue to run but BPROM<br/>did not process the request for promoters on the<br/>" + direction + " strand. Try again tomorrow.</html>"), constraints)
constraints.gridx, constraints.gridy = 0, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 1, 1
constraints.anchor = GridBagConstraints.LINE_END
messageFrame.contentPane.add(JButton("Ok", actionPerformed = lambda e: messageFrame.dispose()), constraints)
messageFrame.pack()
messageFrame.visible = True
print "BPROM Error:", "The pipeline will continue to run but BPROM did not process the request for promoters on the " + direction + " strand. Try again tomorrow"
return []
else:
return getPromoters()
def __createDropDownConstraints(self):
constr = GridBagConstraints()
constr.fill = GridBagConstraints.HORIZONTAL
constr.weighty = 1
constr.gridwidth = 4
constr.gridx = 0
constr.gridy = 0
return constr
def __createRadioConstraints(self, mode):
constr = GridBagConstraints()
constr.fill = GridBagConstraints.HORIZONTAL
constr.weighty = 1
constr.weightx = 1
if mode == 'cases': constr.gridx = 2
elif mode == 'commands': constr.gridx = 3
constr.gridy = 1
return constr
def __createTableConstraints(self):
constr = GridBagConstraints()
constr.fill = GridBagConstraints.BOTH
constr.weighty = 1000
constr.weightx = 2
constr.gridwidth = 4
constr.gridx = 0
constr.gridy = 2
return constr
def __setupLayout(self):
self.setLayout(GridBagLayout())
constr = GridBagConstraints()
constr.weighty = 1
constr.weightx = 1
constr.gridx = 0
constr.gridy = 1
constr.fill = GridBagConstraints.BOTH
return constr
def _new_grid_bag(gridx, gridy, gridwidth=1):
"""Creates a new GridBagConstraints"""
g = GridBagConstraints()
g.gridx = gridx
g.gridy = gridy
g.gridwidth = gridwidth
g.fill = GridBagConstraints.BOTH
g.insets = Insets(2,2,5,5)
return g
def createAndShowGUI():
# Create the GUI and show it. As with all GUI code, this must run
# on the event-dispatching thread.
frame = JFrame("MAE ")
frame.setSize(1024, 768)
panel= JPanel()
panel.setLayout(GridBagLayout())
#Create and set up the content pane.
psimures= SimoutPanel()
psimures.setOpaque(True)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridx = 0
c.gridy = 0
panel.add(psimures, c);
pmeasure= MeasPanel()
pmeasure.setOpaque(True)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridx = 0
c.gridy = 1
panel.add(pmeasure, c);
preport = ReportPanel()
preport.setOpaque(True)
c = GridBagConstraints()
c.fill = GridBagConstraints.VERTICAL
c.weighty = 1
c.gridx = 1
c.gridy = 0
c.gridheight= 2
panel.add(preport,c)
# show the GUI
frame.add(panel)
# frame.add(pmeasure)
# frame.add(preport)
frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE)
frame.setVisible(True)
def __init__(self):
self.setLayout(GridBagLayout())
shrinkX = JButton("shrinkX")
shrinkX.actionPerformed = lambda event : rescaleLayout(0.5, 1)
constr = GridBagConstraints()
constr.gridx = 0
constr.gridy = 0
self.add(shrinkX, constr)
growX = JButton("growX")
growX.actionPerformed = lambda event : rescaleLayout(1.5, 1)
constr = GridBagConstraints()
constr.gridx = 2
constr.gridy = 0
self.add(growX, constr)
shrinkY = JButton("shrinkY")
shrinkY.actionPerformed = lambda event : rescaleLayout(1, 0.5)
constr = GridBagConstraints()
constr.gridx = 0
constr.gridy = 2
self.add(shrinkY, constr)
growY = JButton("growY")
growY.actionPerformed = lambda event : rescaleLayout(1, 1.5)
constr = GridBagConstraints()
constr.gridx = 2
constr.gridy = 2
self.add(growY, constr)
centerB = JButton("center")
centerB.actionPerformed = lambda event : center()
constr = GridBagConstraints()
constr.gridx = 1
constr.gridy = 1
self.add(centerB, constr)
ui.dock(self)
def initComponents(self):
self.setLayout(GridBagLayout())
gbc = GridBagConstraints()
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 0
gbc.gridy = 0
descriptionLabel = JLabel("FEA - BitCoin Validation module")
self.add(descriptionLabel, gbc)
tlHitlist = JLabel("Base list of hashes to analyze: ")
gbc.gridy = 1
self.add(tlHitlist, gbc)
self.tbHitlist = JTextField("testlist", 20)
self.tbHitlist.addActionListener(self.tbHitlistActionPerformed)
gbc.gridx = 1
self.add(self.tbHitlist, gbc)
gbc.gridx = 0
self.cbBlockchainCheck = JCheckBox(
"Query Blockchain.info",
actionPerformed=self.cbBlockchainCheckActionPerformed)
self.cbBlockchainCheck.setSelected(True)
gbc.gridy = 2
self.add(self.cbBlockchainCheck, gbc)
tlBCMaxHits = JLabel(
"Timeout (in seconds) between calls to Blockchain.info: ")
gbc.gridy = 3
self.add(tlBCMaxHits, gbc)
self.tbMaxBCHits = JTextField("5", 5)
self.tbMaxBCHits.addActionListener(self.tbMaxBCHitsActionPerformed)
gbc.gridx = 1
self.add(self.tbMaxBCHits, gbc)
def arrange_plots(regplot, plotm, plotd):
"""
arranges the plots in a certain order,
regplot and plotm in first row next to each other
plotd in second row
"""
from javax.swing import JPanel, JFrame
from java.awt import GridBagLayout, GridBagConstraints
mainPanel = JPanel()
mainPanel.setLayout(GridBagLayout())
c = GridBagConstraints()
c.fill = c.BOTH
c.weightx, c.weighty = 0.5, 1
c.gridx, c.gridy, c.gridwidth, c.gridheight = 0, 0, 10, 4
c.weightx, c.weighty = 0.5, 1
c.gridx, c.gridy, c.gridwidth, c.gridheight = 0, 0, 10, 4
mainPanel.add(regplot)
c.gridx, c.gridy, c.gridwidth, c.gridheight = 0, 0, 10, 4
c.weightx, c.weighty = 1, 1
mainPanel.add(plotm, c)
c.gridx, c.gridy, c.gridwidth, c.gridheight = 0, 4, 10, 6
mainPanel.add(plotd, c)
return mainPanel
def arrange_plots(regplot, plotm, plotd):
"""
arranges the plots in a certain order,
regplot and plotm in first row next to each other
plotd in second row
"""
from javax.swing import JPanel,JFrame
from java.awt import GridBagLayout, GridBagConstraints
mainPanel = JPanel()
mainPanel.setLayout(GridBagLayout())
c=GridBagConstraints()
c.fill=c.BOTH
c.weightx,c.weighty=0.5,1
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
c.weightx,c.weighty=0.5,1
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
mainPanel.add(regplot)
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
c.weightx,c.weighty=1,1
mainPanel.add(plotm,c)
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,4,10,6
mainPanel.add(plotd,c)
return mainPanel
def __init__(self):
self.running = True
menuBar = JMenuBar()
menu = JMenu("File")
menu.add(OpenAction(self))
menu.add(CloseAction(self))
menu.addSeparator()
menu.add(QuitAction(self))
self.addWindowListener(ProfelisWindowAdapter(self))
menuBar.add(menu)
self.setJMenuBar(menuBar)
self.contentPane = JPanel()
self.contentPane.layout = GridBagLayout()
constraints = GridBagConstraints()
self.blastLocation = JTextField(System.getProperty("user.home") + "/blast")
self.databaseLocation = JTextField(System.getProperty("user.home") + "/blast/db")
self.projects = JTabbedPane()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JLabel("Blast Location"), constraints)
constraints.gridx, constraints.gridy = 1, 0
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx, constraints.weighty = 1, 0
self.contentPane.add(self.blastLocation, constraints)
constraints.gridx, constraints.gridy = 2, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JButton(BlastAction(self)), constraints)
constraints.gridx, constraints.gridy = 3, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JLabel("Database Location"), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx, constraints.weighty = 1, 0
self.contentPane.add(self.databaseLocation, constraints)
constraints.gridx, constraints.gridy = 5, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JButton(DatabaseAction(self)), constraints)
constraints.gridx, constraints.gridy = 0, 1
constraints.gridwidth, constraints.gridheight = 6, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.contentPane.add(self.projects, constraints)
def initializeDisplay(self, queries, swing):
"""
queries: A list of the fasts files to be processed.
swing: If true then updates about progress will be displayed in a swing window, otherwise they will be written to stdout.
Initializes the interface for telling the user about progress in the pipeline. Queries is used to count the
number of queries the pipeline will process and to size the swing display(if it is used) so that text
isn't cutoff at the edge of the window. The swing display is setup if swing is true.
"""
self.numJobs = len(queries)
if swing:
self.frame = JFrame("Neofelis")
self.frame.addWindowListener(PipelineWindowAdapter(self))
contentPane = JPanel(GridBagLayout())
self.frame.setContentPane(contentPane)
self.globalLabel = JLabel(max(queries, key = len))
self.globalProgress = JProgressBar(0, self.numJobs)
self.currentLabel = JLabel(max(self.messages, key = len))
self.currentProgress = JProgressBar(0, len(self.messages))
self.doneButton = JButton(DoneAction(self.frame))
self.doneButton.setEnabled(False)
constraints = GridBagConstraints()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.weightx = 1
constraints.fill = GridBagConstraints.HORIZONTAL
contentPane.add(self.globalLabel, constraints)
constraints.gridy = 1
contentPane.add(self.globalProgress, constraints)
constraints.gridy = 2
contentPane.add(self.currentLabel, constraints)
constraints.gridy = 3
contentPane.add(self.currentProgress, constraints)
constraints.gridy = 4
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(self.doneButton, constraints)
self.frame.pack()
self.frame.setResizable(False)
self.globalLabel.setText(" ")
self.currentLabel.setText(" ")
self.frame.setLocationRelativeTo(None)
self.frame.setVisible(True)
def initializeDisplay(self, queries, swing):
"""
queries: A list of the fasts files to be processed.
swing: If true then updates about progress will be displayed in a swing window, otherwise they will be written to stdout.
Initializes the interface for telling the user about progress in the pipeline. Queries is used to count the
number of queries the pipeline will process and to size the swing display(if it is used) so that text
isn't cutoff at the edge of the window. The swing display is setup if swing is true.
"""
self.numJobs = len(queries)
if swing:
self.frame = JFrame("Neofelis")
self.frame.addWindowListener(PipelineWindowAdapter(self))
contentPane = JPanel(GridBagLayout())
self.frame.setContentPane(contentPane)
self.globalLabel = JLabel(max(queries, key=len))
self.globalProgress = JProgressBar(0, self.numJobs)
self.currentLabel = JLabel(max(self.messages, key=len))
self.currentProgress = JProgressBar(0, len(self.messages))
self.doneButton = JButton(DoneAction(self.frame))
self.doneButton.setEnabled(False)
constraints = GridBagConstraints()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.weightx = 1
constraints.fill = GridBagConstraints.HORIZONTAL
contentPane.add(self.globalLabel, constraints)
constraints.gridy = 1
contentPane.add(self.globalProgress, constraints)
constraints.gridy = 2
contentPane.add(self.currentLabel, constraints)
constraints.gridy = 3
contentPane.add(self.currentProgress, constraints)
constraints.gridy = 4
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(self.doneButton, constraints)
self.frame.pack()
self.frame.setResizable(False)
self.globalLabel.setText(" ")
self.currentLabel.setText(" ")
self.frame.setLocationRelativeTo(None)
self.frame.setVisible(True)
def __fillQuestions(self):
panel = JPanel()
panel.setLayout(GridBagLayout())
panel.setBorder(None)
c = GridBagConstraints()
c.gridx = 0
c.gridy = 0
c.weightx = 1.0
c.fill = GridBagConstraints.HORIZONTAL
c.anchor = GridBagConstraints.PAGE_START
line = 0
for question in self.test.getQuestions():
c.gridy = line
panel.add(question.getPanel().asJComponent(),c)
line += 1
scrollPanel = JScrollPane(panel)
scrollPanel.setBorder(None)
self.questionsContainer.setLayout(BorderLayout())
self.questionsContainer.add(scrollPanel, BorderLayout.CENTER)
def getGridBagConstraints(game,node):
c = GridBagConstraints()
for str in node.getAttribute("constraints").split(","):
a = str.split(":")
if a[0]=="fill":
c.fill = int(a[1])
elif a[0]=="gridwidth":
c.gridwidth = int(a[1])
elif a[0]=="gridheight":
c.gridheight = int(a[1])
elif a[0]=="gridx":
c.gridx = int(a[1])
elif a[0]=="gridy":
c.gridy = int(a[1])
elif a[0]=="weightx":
c.weightx = int(a[1])
elif a[0]=="weighty":
c.weighty = int(a[1])
else:
print a[0]+"was not found"
return c
def __init__(self, view, sys):
JDialog.__init__(self, view,
jEdit.getProperty("jython.pathhandler.title"))
self.sys = sys
content = self.contentPane
content.layout = BorderLayout()
upperPanel = JPanel(BorderLayout())
leftPanel = JPanel(BorderLayout(), border = \
BorderFactory.createTitledBorder(jEdit.getProperty("jython.pathhandler.pathborder")))
self.model = DefaultListModel()
for s in sys.path:
self.model.addElement(s)
self.pathlist = JList(
self.model, selectionMode=ListSelectionModel.SINGLE_SELECTION)
leftPanel.add(JScrollPane(self.pathlist))
rightPanel = JPanel(GridBagLayout())
constraints = GridBagConstraints()
constraints.insets = Insets(5, 5, 5, 5)
constraints.gridy = GridBagConstraints.RELATIVE
constraints.gridx = 0
buttons = [("Plus.png", "New...", self.new), \
("ButtonProperties.png", "Edit...", self.edit),
("Minus.png", "Remove", self.remove), \
("ArrowU.png", "Move Up", self.up), \
("ArrowD.png", "Move down", self.down)]
for (i, t, a) in buttons:
rightPanel.add(JButton(icon = GUIUtilities.loadIcon(i), \
toolTipText=t, actionPerformed=a), constraints)
upperPanel.add(leftPanel, BorderLayout.CENTER)
upperPanel.add(rightPanel, BorderLayout.EAST)
content.add(upperPanel, BorderLayout.CENTER)
lowerPanel = JPanel(FlowLayout(FlowLayout.RIGHT))
self.saveAsk = JCheckBox(jEdit.getProperty("options.jython.saveJythonPathTitle"), \
selected = jEdit.getBooleanProperty("options.jython.saveJythonPath"), actionPerformed = self.saveAsk)
ok = JButton("Ok", actionPerformed=self.__ok)
lowerPanel.add(self.saveAsk)
lowerPanel.add(ok)
self.rootPane.defaultButton = ok
lowerPanel.add(JButton("Cancel", actionPerformed=self.__cancel))
content.add(lowerPanel, BorderLayout.SOUTH)
def add(parent, child,
gridx=0, gridy=0,
anchor=GC.NORTHWEST, fill=GC.NONE,
weightx=0.0, weighty=0.0,
gridwidth=1):
c = GC()
c.gridx = gridx
c.gridy = gridy
c.anchor = anchor
c.fill = fill
c.weightx = weightx
c.weighty = weighty
c.gridwidth = gridwidth
"""
# Same, more flexible, less verbose: BUT FAILS at parent, child args
kv = locals() # dict of local variables including the function arguments
c = GC()
for key, value in kv.iteritems():
setattr(c, key, value)
"""
#
parent.getLayout().setConstraints(child, c)
parent.add(child)
def doall(locations, fileobs,filerun1,filerun2,stime,etime,imageDir='d:/temp',weights=None,filter_type="AVE",normalize=False):
obs=HecDss.open(fileobs,True)
obs.setTimeWindow(stime,etime)
run1=HecDss.open(filerun1,True)
run1.setTimeWindow(stime,etime)
if filerun2 != None:
run2=HecDss.open(filerun2,True)
run2.setTimeWindow(stime,etime)
else:
run2=None
rms1=0
rms1_min,rms1_max=0,0
rms2=0
rms2_min,rms2_max=0,0
rmsmap={}
#run2=None
sumwts=0
average_interval=None;
for l in locations:
data1=get_matching(obs,'A=%s C=%s E=15MIN'%(l,type))
if data1 == None:
data1=get_matching(obs,'A=%s C=%s E=1DAY'%(l,type))
if data1 == None:
data1=get_matching(obs,'A=%s C=%s E=IR-DAY'%(l,type))
if data1 == None:
data1=get_matching(obs,'A=%s C=%s E=1HOUR'%(l,type))
drun1=get_matching(run1,'B=%s C=%s'%(l,type))
if run2 != None:
drun2=get_matching(run2, 'B=%s C=%s'%(l,type))
else:
drun2=None
avg_intvl="1DAY"
if data1 != None:
if average_interval != None:
dobsd=TimeSeriesMath(data1).transformTimeSeries(average_interval, None, filter_type, 0)
else:
dobsd=TimeSeriesMath(data1)
if normalize:
dobsd=dobsd.divide(TimeSeriesMath(data1).mean())
dobsm=TimeSeriesMath(data1).transformTimeSeries(avg_intvl, None, filter_type, 0)
dobsm_max=TimeSeriesMath(data1).transformTimeSeries(avg_intvl, None, "MAX", 0)
dobsm_max.data.fullName=dobsm_max.data.fullName+"MAX"
dobsm_min=TimeSeriesMath(data1).transformTimeSeries(avg_intvl, None, "MIN", 0)
dobsm_min.data.fullName=dobsm_min.data.fullName+"MIN"
if normalize:
dobsm=dobsm.divide(TimeSeriesMath(data1).mean())
if drun1==None:
continue;
else:
if average_interval != None:
drun1d=TimeSeriesMath(drun1).transformTimeSeries(average_interval, None, filter_type, 0)
else:
drun1d=TimeSeriesMath(drun1)
if normalize:
drun1d=drun1d.divide(TimeSeriesMath(drun1).mean())
if drun2 != None:
if average_interval != None:
drun2d=TimeSeriesMath(drun2).transformTimeSeries(average_interval, None, filter_type, 0)
else:
drun2d=TimeSeriesMath(drun2)
if normalize:
drun2d=drun2d.divide(TimeSeriesMath(drun2).mean())
drun1m=TimeSeriesMath(drun1).transformTimeSeries(avg_intvl, None, filter_type, 0)
drun1m_max=TimeSeriesMath(drun1).transformTimeSeries(avg_intvl, None, "MAX", 0)
drun1m_min=TimeSeriesMath(drun1).transformTimeSeries(avg_intvl, None, "MIN", 0)
if normalize:
drun1m=drun1m.divide(TimeSeriesMath(drun1).mean())
if drun2 != None:
drun2m=TimeSeriesMath(drun2).transformTimeSeries(avg_intvl, None, filter_type, 0)
drun2m_max=TimeSeriesMath(drun2).transformTimeSeries(avg_intvl, None, "MAX", 0)
drun2m_min=TimeSeriesMath(drun2).transformTimeSeries(avg_intvl, None, "MIN", 0)
if normalize:
drun2m=drun2m.divide(TimeSeriesMath(drun2).mean())
else:
drun2m=None
if weights != None:
sumwts=sumwts+weights[l]
lrms1 = calculate_rms(drun1m.data, dobsm.data)*weights[l]
lrms1_min=calculate_rms(drun1m_min.data,dobsm_min.data)*weights[l]
lrms1_max=calculate_rms(drun1m_max.data,dobsm_max.data)*weights[l]
rms1=rms1+lrms1
rms1_min=rms1_min+lrms1_min
rms1_max=rms1_max+lrms1_max
lrms2 = calculate_rms(drun2m.data,dobsm.data)*weights[l]
lrms2_min=calculate_rms(drun2m_min.data,dobsm_min.data)*weights[l]
lrms2_max=calculate_rms(drun2m_max.data,dobsm_max.data)*weights[l]
rmsmap[l] = lrms1,lrms2,lrms1_min,lrms2_min,lrms1_max,lrms2_max
rms2=rms2+lrms2
rms2_min=rms2_min+lrms2_min
rms2_max=rms2_max+lrms2_max
plotd = newPlot("Hist vs New Geom [%s]"%l)
if data1 != None:
plotd.addData(dobsd.data)
plotd.addData(drun1d.data)
if drun2 != None:
plotd.addData(drun2d.data)
plotd.showPlot()
legend_label = plotd.getLegendLabel(drun1d.data)
legend_label.setText(legend_label.getText()+" ["+str(int(lrms1*100)/100.)+","+str(int(lrms1_min*100)/100.)+","+str(int(lrms1_max*100)/100.)+"]")
legend_label = plotd.getLegendLabel(drun2d.data)
legend_label.setText(legend_label.getText()+" ["+str(int(lrms2*100)/100.)+","+str(int(lrms2_min*100)/100.)+","+str(int(lrms2_max*100)/100.)+"]")
plotd.setVisible(False)
xaxis=plotd.getViewport(0).getAxis("x1")
vmin =xaxis.getViewMin()+261500. # hardwired to around july 1, 2008
xaxis.setViewLimits(vmin,vmin+10000.)
if data1 != None:
pline = plotd.getCurve(dobsd.data)
pline.setLineVisible(1)
pline.setLineColor("blue")
pline.setSymbolType(Symbol.SYMBOL_CIRCLE)
pline.setSymbolsVisible(0)
pline.setSymbolSize(3)
pline.setSymbolSkipCount(0)
pline.setSymbolFillColor(pline.getLineColorString())
pline.setSymbolLineColor(pline.getLineColorString())
g2dPanel = plotd.getPlotpanel()
g2dPanel.revalidate();
g2dPanel.paintGfx();
plotm = newPlot("Hist vs New Geom Monthly [%s]"%l)
plotm.setSize(1800,1200)
if data1 != None:
plotm.addData(dobsm.data)
#plotm.addData(dobsm_max.data)
#plotm.addData(dobsm_min.data)
plotm.addData(drun1m.data)
#plotm.addData(drun1m_max.data)
#plotm.addData(drun1m_min.data)
if drun2 != None:
plotm.addData(drun2m.data)
#plotm.addData(drun2m_max.data)
#plotm.addData(drun2m_min.data)
plotm.showPlot()
if data1 != None:
pline = plotm.getCurve(dobsm.data)
pline.setLineVisible(1)
pline.setLineColor("blue")
pline.setSymbolType(Symbol.SYMBOL_CIRCLE)
pline.setSymbolsVisible(0)
pline.setSymbolSize(3)
pline.setSymbolSkipCount(0)
pline.setSymbolFillColor(pline.getLineColorString())
pline.setSymbolLineColor(pline.getLineColorString())
plotm.setVisible(False)
if data1 != None:
plots=do_regression_plots(dobsm,drun1m,drun2m)
if plots != None:
spanel = plots.getPlotpanel()
removeToolbar(spanel)
mpanel = plotm.getPlotpanel()
removeToolbar(mpanel)
dpanel = plotd.getPlotpanel()
removeToolbar(dpanel)
from javax.swing import JPanel,JFrame
from java.awt import GridBagLayout, GridBagConstraints
mainPanel = JPanel()
mainPanel.setLayout(GridBagLayout())
c=GridBagConstraints()
c.fill=c.BOTH
c.weightx,c.weighty=0.5,1
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
if data1 != None:
if plots != None:
pass
#mainPanel.add(spanel,c)
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,0,10,4
c.weightx,c.weighty=1,1
mainPanel.add(mpanel,c)
c.gridx,c.gridy,c.gridwidth,c.gridheight=0,4,10,6
mainPanel.add(dpanel,c)
fr=JFrame()
fr.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
fr.getContentPane().add(mainPanel)
fr.setSize(1100,850);
fr.show();
mainPanel.setSize(1100,850);
mainPanel.setBackground(Color.WHITE);
#import time; time.sleep(5)
saveToPNG(mainPanel,imageDir+l+".png")
if weights != None:
rms1=(rms1+rms1_min+rms1_max)/sumwts
rms2=(rms2+rms2_min+rms2_max)/sumwts
print 'RMS Run 1: %f'%rms1
print 'RMS Run 2: %f'%rms2
for loc in rmsmap.keys():
print loc, rmsmap[loc]
def show_detectable_objects_dialog(self, e):
parentComponent = SwingUtilities.windowForComponent(self.panel0)
self.detectable_obejcts_dialog = JDialog(
parentComponent, "List of Objects to Detect",
ModalityType.APPLICATION_MODAL)
panel = JPanel()
self.detectable_obejcts_dialog.add(panel)
gbPanel = GridBagLayout()
gbcPanel = GridBagConstraints()
panel.setLayout(gbPanel)
y = 0
x = 0
for line in self.local_settings.getClassesOfInterest():
if y > 15:
y = 0
x = x + 1
class_check_box = JCheckBox(line['name'])
self.classes_of_interest_checkboxes.append(class_check_box)
class_check_box.setEnabled(True)
class_check_box.setSelected(line['enabled'])
class_check_box.addItemListener(self.on_class_checkbox_clicked)
gbcPanel.gridx = x
gbcPanel.gridy = y
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 1
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(class_check_box, gbcPanel)
panel.add(class_check_box)
y = y + 1
blank_1_L = JLabel(" ")
blank_1_L.setEnabled(True)
gbcPanel.gridx = 0
gbcPanel.gridy = y + 1
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 1
gbcPanel.weighty = 0
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(blank_1_L, gbcPanel)
panel.add(blank_1_L)
deselect_all_button = JButton("Deselect all")
deselect_all_button.setEnabled(True)
deselect_all_button.addActionListener(self.on_deselect_all_clicked)
gbcPanel.gridx = 1
gbcPanel.gridy = y + 2
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 2
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(deselect_all_button, gbcPanel)
panel.add(deselect_all_button)
select_all_button = JButton("Select all")
select_all_button.setEnabled(True)
select_all_button.addActionListener(self.on_select_all_clicked)
gbcPanel.gridx = 3
gbcPanel.gridy = y + 2
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 2
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(select_all_button, gbcPanel)
panel.add(select_all_button)
blank_2_L = JLabel(" ")
blank_2_L.setEnabled(True)
gbcPanel.gridx = 0
gbcPanel.gridy = y + 3
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 1
gbcPanel.weighty = 0
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(blank_2_L, gbcPanel)
panel.add(blank_2_L)
cancel_button = JButton("Cancel")
cancel_button.setEnabled(True)
cancel_button.addActionListener(
self.on_cancel_classes_of_interest_click)
gbcPanel.gridx = 1
gbcPanel.gridy = y + 4
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 2
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(cancel_button, gbcPanel)
panel.add(cancel_button)
save_button = JButton("Save")
save_button.setEnabled(True)
save_button.addActionListener(self.on_save_classes_of_interest_click)
gbcPanel.gridx = 3
gbcPanel.gridy = y + 4
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 2
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(save_button, gbcPanel)
panel.add(save_button)
blank_3_L = JLabel(" ")
blank_3_L.setEnabled(True)
gbcPanel.gridx = 0
gbcPanel.gridy = y + 5
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 1
gbcPanel.weighty = 0
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(blank_3_L, gbcPanel)
panel.add(blank_3_L)
self.detectable_obejcts_dialog.pack()
screenSize = Toolkit.getDefaultToolkit().getScreenSize()
self.detectable_obejcts_dialog.setLocation(
int((screenSize.getWidth() / 2) -
(self.detectable_obejcts_dialog.getWidth() / 2)),
int((screenSize.getHeight() / 2) -
(self.detectable_obejcts_dialog.getHeight() / 2)))
self.detectable_obejcts_dialog.setVisible(True)
def registerExtenderCallbacks(self, callbacks):
# keep a reference to our callbacks object
self._callbacks = callbacks
# obtain an extension helpers object
self._helpers = callbacks.getHelpers()
# set our extension name
callbacks.setExtensionName("Response Clusterer")
# create the log and a lock on which to synchronize when adding log entries
self._log = ArrayList()
self._lock = Lock()
# main split pane
self._main_jtabedpane = JTabbedPane()
# The split pane with the log and request/respponse details
self._splitpane = JSplitPane(JSplitPane.VERTICAL_SPLIT)
# table of log entries
logTable = Table(self)
scrollPane = JScrollPane(logTable)
self._splitpane.setLeftComponent(scrollPane)
# List of log entries
self._log_entries = []
# tabs with request/response viewers
tabs = JTabbedPane()
self._requestViewer = callbacks.createMessageEditor(self, False)
self._responseViewer = callbacks.createMessageEditor(self, False)
tabs.addTab("Request", self._requestViewer.getComponent())
tabs.addTab("Response", self._responseViewer.getComponent())
self._splitpane.setRightComponent(tabs)
#Setup the options
self._optionsJPanel = JPanel()
gridBagLayout = GridBagLayout()
gbc = GridBagConstraints()
self._optionsJPanel.setLayout(gridBagLayout)
self.max_clusters = 500
self.JLabel_max_clusters = JLabel("Maximum amount of clusters: ")
gbc.gridy = 0
gbc.gridx = 0
self._optionsJPanel.add(self.JLabel_max_clusters, gbc)
self.JTextField_max_clusters = JTextField(str(self.max_clusters), 5)
self.JTextField_max_clusters.getDocument().addDocumentListener(self)
gbc.gridx = 1
self._optionsJPanel.add(self.JTextField_max_clusters, gbc)
callbacks.customizeUiComponent(self.JLabel_max_clusters)
callbacks.customizeUiComponent(self.JTextField_max_clusters)
self.similarity = 0.95
self.JLabel_similarity = JLabel("Similarity (between 0 and 1)")
gbc.gridy = 1
gbc.gridx = 0
self._optionsJPanel.add(self.JLabel_similarity, gbc)
self.JTextField_similarity = JTextField(str(self.similarity), 5)
self.JTextField_similarity.getDocument().addDocumentListener(self)
gbc.gridx = 1
self._optionsJPanel.add(self.JTextField_similarity, gbc)
callbacks.customizeUiComponent(self.JLabel_similarity)
callbacks.customizeUiComponent(self.JTextField_similarity)
self.use_quick_similar = False
self.JLabel_use_quick_similar = JLabel(
"Use set intersection of space splitted tokens for similarity (default: optimized difflib.SequenceMatcher.quick_ratio)"
)
gbc.gridy = 2
gbc.gridx = 0
self._optionsJPanel.add(self.JLabel_use_quick_similar, gbc)
self.JCheckBox_use_quick_similar = JCheckBox("")
self.JCheckBox_use_quick_similar.addActionListener(self)
gbc.gridx = 1
self._optionsJPanel.add(self.JCheckBox_use_quick_similar, gbc)
callbacks.customizeUiComponent(self.JCheckBox_use_quick_similar)
self.response_max_size = 10 * 1024 #10kb
self.JLabel_response_max_size = JLabel("Response max size (bytes)")
gbc.gridy = 3
gbc.gridx = 0
self._optionsJPanel.add(self.JLabel_response_max_size, gbc)
self.JTextField_response_max_size = JTextField(
str(self.response_max_size), 5)
self.JTextField_response_max_size.getDocument().addDocumentListener(
self)
gbc.gridx = 1
self._optionsJPanel.add(self.JTextField_response_max_size, gbc)
callbacks.customizeUiComponent(self.JLabel_response_max_size)
callbacks.customizeUiComponent(self.JTextField_response_max_size)
self.uninteresting_mime_types = ('JPEG', 'CSS', 'GIF', 'script', 'GIF',
'PNG', 'image')
self.uninteresting_status_codes = ()
self.uninteresting_url_file_extensions = ('js', 'css', 'zip', 'war',
'jar', 'doc', 'docx', 'xls',
'xlsx', 'pdf', 'exe', 'dll',
'png', 'jpeg', 'jpg', 'bmp',
'tif', 'tiff', 'gif', 'webp',
'm3u', 'mp4', 'm4a', 'ogg',
'aac', 'flac', 'mp3', 'wav',
'avi', 'mov', 'mpeg', 'wmv',
'swf', 'woff', 'woff2')
about = "<html>"
about += "Author: floyd, @floyd_ch, http://www.floyd.ch<br>"
about += "modzero AG, http://www.modzero.ch<br>"
about += "<br>"
about += "<h3>Getting an overview of the tested website</h3>"
about += "<p style=\"width:500px\">"
about += "This plugin clusters all response bodies by similarity and shows a summary, one request/response per cluster. "
about += 'Adjust similarity in the options if you get too few or too many entries in the "One member of each cluster" '
about += "tab. The plugin will allow a tester to get an overview of the tested website's responses from all tools (scanner, proxy, etc.). "
about += "As similarity comparison "
about += "can use a lot of ressources, only small, in-scope responses that have interesting response codes, "
about += "file extensions and mime types are processed. "
about += "</p>"
about += "</html>"
self.JLabel_about = JLabel(about)
self.JLabel_about.setLayout(GridBagLayout())
self._aboutJPanel = JScrollPane(self.JLabel_about)
# customize our UI components
callbacks.customizeUiComponent(self._splitpane)
callbacks.customizeUiComponent(logTable)
callbacks.customizeUiComponent(scrollPane)
callbacks.customizeUiComponent(tabs)
# add the splitpane and options to the main jtabedpane
self._main_jtabedpane.addTab("One member of each cluster", None,
self._splitpane, None)
self._main_jtabedpane.addTab("Options", None, self._optionsJPanel,
None)
self._main_jtabedpane.addTab("About & README", None, self._aboutJPanel,
None)
# clusters will grow up to self.max_clusters response bodies...
self._clusters = set()
self.Similarity = Similarity()
# Now load the already stored
with self._lock:
log_entries_from_storage = self.load_project_setting("log_entries")
if log_entries_from_storage:
for toolFlag, req, resp, url in log_entries_from_storage:
try:
self.add_new_log_entry(toolFlag, req, resp, url)
except Exception as e:
print "Exception when deserializing a stored log entry", toolFlag, url
print e
# Important: Do this at the very end (otherwise we could run into troubles locking up entire threads)
# add the custom tab to Burp's UI
callbacks.addSuiteTab(self)
# register ourselves as an HTTP listener
callbacks.registerHttpListener(self)
def __init__(self):
''' Configuration Panel '''
# pconfig = JPanel(GridBagLayout())
# pconfig.setSize(Dimension(500,300))
self.setLayout(GridBagLayout())
# super(self,GridBagLayout())
self.setSize(Dimension(500,300))
''' fila 1 '''
label = JLabel('Configuration panel')
c1 = GridBagConstraints()
c1.fill = GridBagConstraints.HORIZONTAL
c1.weightx = 0.5
c1.gridwidth = 4
c1.gridx = 0
c1.gridy = 0
self.add(label, c1)
''' fila 2 '''
self.radioBtnOMC = JRadioButton('OpenModelica')
c2 = GridBagConstraints()
c2.fill = GridBagConstraints.HORIZONTAL
c2.weightx = 0.5
c2.gridx = 0
c2.gridy = 1
self.add(self.radioBtnOMC, c2)
self.radioBtnJM = JRadioButton('JModelica')
c3 = GridBagConstraints()
c3.fill = GridBagConstraints.HORIZONTAL
c3.weightx = 0.5
c3.gridx = 1
c3.gridy = 1
self.add(self.radioBtnJM, c3)
self.radioBtnDY = JRadioButton('Dymola')
c4 = GridBagConstraints()
c4.fill = GridBagConstraints.HORIZONTAL
c4.weightx = 0.5
c4.gridx = 2
c4.gridy = 1
self.add(self.radioBtnDY, c4)
rbBtnGroup = ButtonGroup()
rbBtnGroup.add(self.radioBtnOMC)
rbBtnGroup.add(self.radioBtnJM)
rbBtnGroup.add(self.radioBtnDY)
''' fila 2 '''
label = JLabel('Start time')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 2
self.add(label, c)
self.txtstart= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 2
self.add(self.txtstart, c)
label = JLabel('Stop time')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 2
c.gridy = 2
self.add(label, c)
self.txtstop= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 3
c.gridy = 2
self.add(self.txtstop, c)
''' fila 3 '''
label = JLabel('Solver')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 3
self.add(label, c)
self.cbsolver= JComboBox(['dassl','rkfix2'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 3
self.add(self.cbsolver, c)
label = JLabel('Algorithm (JM)')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 2
c.gridy = 3
self.add(label, c)
self.cbalgorithm= JComboBox(['AssimuloAlg'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 3
c.gridy = 3
self.add(self.cbalgorithm, c)
''' fila 4 '''
label = JLabel('Interval')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 4
self.add(label, c)
self.txtinterval= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 4
self.add(self.txtinterval, c)
''' fila 5 '''
label = JLabel('Tolerance')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 5
self.add(label, c)
self.txttolerance= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 5
self.add(self.txttolerance, c)
''' fila 6 '''
label = JLabel('Output format')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 6
self.add(label, c)
self.cboutformat= JComboBox(['.mat','.h5','.csv'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 6
self.add(self.cboutformat, c)
label = JLabel('Initialize (JM)')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 2
c.gridy = 6
self.add(label, c)
self.cbinitialize= JComboBox(['True','False'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 3
c.gridy = 6
self.add(self.cbinitialize, c)
''' fila 7 '''
bSaveCfg= JButton('Save Configuration', actionPerformed= self.saveConfiguration)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 0
c.gridy = 7
self.add(bSaveCfg, c)
self.bSimulation= JButton('Load Configuration', actionPerformed= self.loadConfiguration)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 2
c.gridy = 7
self.add(self.bSimulation, c)
''' fila 8 '''
self.bSimulation= JButton('Simulate', actionPerformed= self.startSimlation)
self.bSimulation.enabled= 0
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 8
self.add(self.bSimulation, c)
''' file 9 '''
simProgress= JProgressBar(0, self.getWidth(), value=0, stringPainted=True)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 9
self.add(simProgress, c)
''' fila 10 '''
self.lblResult= JLabel('Simulation information')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 10
self.add(self.lblResult, c)
def __init__(self):
''' Resources Panel '''
# psimures= JPanel(GridBagLayout())
# psimures.setSize(Dimension(500,300))
self.setLayout(GridBagLayout())
# super(self,GridBagLayout())
self.setSize(Dimension(500,300))
''' fila 1 '''
label = JLabel('Resources panel')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 0
self.add(label, c)
''' fila 2 '''
self.dModelFile = []
self.cbMoFile = JComboBox(self.dModelFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 1
self.add(self.cbMoFile, c)
bloadmodel= JButton('Load Model',actionPerformed=self.onOpenFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 1
self.add(bloadmodel, c)
''' fila 3 '''
self.dLibFile = []
self.cbMoLib = JComboBox(self.dLibFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 2
self.add(self.cbMoLib, c)
bloadlib= JButton('Load Library',actionPerformed=self.onOpenFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 2
self.add(bloadlib, c)
''' fila 4 '''
self.dModel = []
self.cbModel = JComboBox(self.dModel)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 3
self.add(self.cbModel, c)
bselectmodel= JButton('Select Model',actionPerformed=self.onOpenModel)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 3
self.add(bselectmodel, c)
''' fila 5 '''
self.dOutPath = []
self.cbOutDir = JComboBox(self.dOutPath)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 4
self.add(self.cbOutDir, c)
bloadoutpath= JButton('Output Path',actionPerformed=self.onOpenFolder)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 4
self.add(bloadoutpath, c)
''' fila 6 '''
bsaveSource= JButton('Save Resources',actionPerformed=self.saveResources)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 0
c.gridy = 5
self.add(bsaveSource, c)
bloadSource= JButton('Load Resources',actionPerformed=self.loadResources)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 2
c.gridy = 5
self.add(bloadSource, c)
def makeRegistrationUI(original_images, original_calibration, coarse_affines, params, images, minC, maxC, cropped, cropped_imp):
"""
Register cropped images either all to all or all to the first one,
and print out a config file with the coarse affines,
the ROI for cropping, and the refined affines post-crop.
original_images: the original, raw images, with original dimensions.
original_calibration: the calibration of the images as they are on disk.
coarse_affines: list of AffineTransform3D, one per image, that specify the translation between images
as manually set using the makeTranslationUI.
params: dictionary with parameters for registering the given cropped images.
This includes a calibration that is likely [1.0, 1.0, 1.0] as the cropped images
are expected to have been scaled to isotropy.
images: the list of near-original images but scaled (by calibration) to isotropy.
(These are really views of the original images, using nearest neighbor interpolation
to scale them to isotropy.)
minC, maxC: the minimum and maximum coordinates of a ROI with which the cropped images were made.
cropped: the list of images that have been scaled to isotropy, translated and cropped by the ROI.
(These are really interval views of the images, the latter using nearest neighbor interpolation.)
cropped_imp: the ImagePlus holding the virtual stack of cropped image views.
The computed registration will merge the scaling to isotropy + first transform (a translation)
+ roi cropping translation + the params["modelclass"] registration transform, to read directly
from the original images using a nearest interpolation, for best performance (piling two nearest
interpolations over one another would result in very slow access to pixel data).
"""
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
calibration = params["calibration"]
params["cal X"] = calibration[0]
params["cal Y"] = calibration[1]
params["cal Z"] = calibration[2]
# Add a label and a text field for every parameter, with titles for every block
strings = [["Calibration",
"cal X", "cal Y", "cal Z"],
["Difference of Gaussian",
"minPeakValue", "sigmaSmaller", "sigmaLarger"],
["Feature extraction",
"radius", "min_angle", "max_per_peak",
"angle_epsilon", "len_epsilon_sq",
"pointmatches_nearby", "pointmatches_search_radius"],
["RANSAC parameters for the model",
"maxEpsilon", "minInlierRatio", "minNumInliers",
"n_iterations", "maxTrust"],
["All to all registration",
"maxAllowedError", "maxPlateauwidth", "maxIterations", "damp"]]
# Insert all as fields, with values populated from the params dictionary
# and updating dynamically the params dictionary
params = dict(params) # copy, will be updated
insertFloatFields(panel, gb, gc, params, strings)
# Identity transforms prior to registration
affines = [affine3D([1, 0, 0, 0,
0, 1, 0, 0,
0, 0, 1, 0]) for img in cropped]
def run():
exe = newFixedThreadPool(min(len(cropped), numCPUs()))
try:
# Dummy for in-RAM reading of isotropic images
img_filenames = [str(i) for i in xrange(len(cropped))]
loader = InRAMLoader(dict(zip(img_filenames, cropped)))
getCalibration = params.get("getCalibration", None)
if not getCalibration:
getCalibration = lambda img: [1.0] * cropped[0].numDimensions()
csv_dir = params["csv_dir"]
modelclass = params["modelclass"]
# Matrices describing the registration on the basis of the cropped images
matrices = computeOptimizedTransforms(img_filenames, loader, getCalibration,
csv_dir, exe, modelclass, params)
# Store outside, so they can be e.g. printed, and used beyond here
for matrix, affine in zip(matrices, affines):
affine.set(*matrix)
# Combine the transforms: scaling (by calibration)
# + the coarse registration (i.e. manual translations)
# + the translation introduced by the ROI cropping
# + the affine matrices computed above over the cropped images.
coarse_matrices = []
for coarse_affine in coarse_affines:
matrix = zeros(12, 'd')
coarse_affine.toArray(matrix)
coarse_matrices.append(matrix)
# NOTE: both coarse_matrices and matrices are from the camera X to camera 0. No need to invert them.
# NOTE: uses identity calibration because the coarse_matrices already include the calibration scaling to isotropy
transforms = mergeTransforms([1.0, 1.0, 1.0], coarse_matrices, [minC, maxC], matrices, invert2=False)
print "calibration:", [1.0, 1.0, 1.0]
print "cmTransforms:\n %s\n %s\n %s\n %s" % tuple(str(m) for m in coarse_matrices)
print "ROI", [minC, maxC]
print "fineTransformsPostROICrop:\n %s\n %s\n %s\n %s" % tuple(str(m) for m in matrices)
print "invert2:", False
# Show registered images
registered = [transformedView(img, transform, interval=cropped[0])
for img, transform in izip(original_images, transforms)]
registered_imp = showAsStack(registered, title="Registered with %s" % params["modelclass"].getSimpleName())
registered_imp.setDisplayRange(cropped_imp.getDisplayRangeMin(), cropped_imp.getDisplayRangeMax())
"""
# TEST: same as above, but without merging the transforms. WORKS, same result
# Copy into ArrayImg, otherwise they are rather slow to browse
def copy(img1, affine):
# Copy in two steps. Otherwise the nearest neighbor interpolation on top of another
# nearest neighbor interpolation takes a huge amount of time
dimensions = Intervals.dimensionsAsLongArray(img1)
aimg1 = ArrayImgs.unsignedShorts(dimensions)
ImgUtil.copy(ImgView.wrap(img1, aimg1.factory()), aimg1)
img2 = transformedView(aimg1, affine)
aimg2 = ArrayImgs.unsignedShorts(dimensions)
ImgUtil.copy(ImgView.wrap(img2, aimg2.factory()), aimg2)
return aimg2
futures = [exe.submit(Task(copy, img, affine)) for img, affine in izip(cropped, affines)]
aimgs = [f.get() for f in futures]
showAsStack(aimgs, title="DEBUG Registered with %s" % params["modelclass"].getSimpleName())
"""
except:
print sys.exc_info()
finally:
exe.shutdown()
SwingUtilities.invokeLater(lambda: run_button.setEnabled(True))
def launchRun(event):
# Runs on the event dispatch thread
run_button.setEnabled(False) # will be re-enabled at the end of run()
# Fork:
Thread(run).start()
def printAffines(event):
for i, affine in enumerate(affines):
matrix = zeros(12, 'd')
affine.toArray(matrix)
msg = "# Refined post-crop affine matrix " + str(i) + ": \n" + \
"affine" + str(i) + ".set(*[%f, %f, %f, %f,\n %f, %f, %f, %f,\n %f, %f, %f, %f])" % tuple(matrix.tolist())
# Print everywhere
print msg
IJ.log(msg)
System.out.println(msg)
def prepareDeconvolutionScriptUI(event):
"""
# DEBUG generateDeconvolutionScriptUI: generate params as a loadable serialized file
with open("/tmp/parameters.pickle", 'w') as f:
import pickle
def asArrays(affines):
arrays = []
for affine in affines:
matrix = zeros(12, 'd')
affine.toArray(matrix)
arrays.append(matrix)
return arrays
pickle.dump([params["srcDir"], params["tgtDir"], calibration,
asArrays(coarse_affines), [minC, maxC], asArrays(affines)], f)
"""
generateDeconvolutionScriptUI(params["srcDir"], params["tgtDir"], calibration,
coarse_affines, [minC, maxC], affines)
# Buttons
panel_buttons = JPanel()
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 2
gb.setConstraints(panel_buttons, gc)
panel.add(panel_buttons)
run_button = JButton("Run")
run_button.addActionListener(launchRun)
gb.setConstraints(run_button, gc)
panel_buttons.add(run_button)
print_button = JButton("Print affines")
print_button.addActionListener(printAffines)
panel_buttons.add(print_button)
prepare_button = JButton("Prepare deconvolution script")
prepare_button.addActionListener(prepareDeconvolutionScriptUI)
panel_buttons.add(prepare_button)
frame = JFrame("Registration")
frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
frame.addWindowListener(CloseControl())
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setVisible(True)
def makeTranslationUI(affines, imp, show=True, print_button_text="Print transforms"):
"""
A GUI to control the translation components of a list of AffineTransform3D instances.
When updated, the ImagePlus is refreshed.
affines: a list (will be read multiple times) of one affine transform per image.
imp: the ImagePlus that hosts the virtual stack with the transformed images.
show: defaults to True, whether to make the GUI visible.
print_button_text: whatever you want the print button to read like, defaults to "Print transforms".
Returns the JFrame, the main JPanel and the lower JButton panel.
"""
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
gc.anchor = GBC.WEST
gc.fill = GBC.NONE
# Column labels
gc.gridy = 0
for i, title in enumerate(["Camera", "translation X", "translation Y", "translation Z"]):
gc.gridx = i
gc.anchor = GBC.CENTER
label = JLabel(title)
gb.setConstraints(label, gc)
panel.add(label)
gc.anchor = GBC.WEST
listeners = []
# One row per affine to control: skip the first
for i, affine in enumerate(affines[1:]):
gc.gridx = 0
gc.gridy += 1
label = JLabel("CM0%i: " % (i + 1))
gb.setConstraints(label, gc)
panel.add(label)
# One JTextField per dimension
for dimension, translation in enumerate(affine.getTranslation()):
tf = JTextField(str(translation), 10)
listener = MatrixTextFieldListener(affine, dimension, tf, imp)
listeners.append(listener)
imp.addImageListener(listener) # to disable the JTextField when closed
tf.addKeyListener(listener)
tf.addMouseWheelListener(listener)
gc.gridx += 1
gb.setConstraints(tf, gc)
panel.add(tf)
# Documentation for the user
help_lines = ["Type a number and push enter,",
"or use the scroll wheel."]
gc.gridx = 0
gc.gridwidth = 4
for line in help_lines:
gc.gridy += 1
help = JLabel(line)
gb.setConstraints(help, gc)
panel.add(help)
# Buttons
printButton = JButton(print_button_text)
def printTransforms(event):
for i, aff in enumerate(affines): # print all, including the first
matrix = zeros(12, 'd')
aff.toArray(matrix)
msg = "# Coarse affine matrix " + str(i) + ": \n" + \
"affine" + str(i) + ".set(*[%f, %f, %f, %f,\n %f, %f, %f, %f,\n %f, %f, %f, %f])" % tuple(matrix.tolist())
# Print everywhere
print msg
IJ.log(msg)
System.out.println(msg)
printButton.addActionListener(printTransforms)
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 4
button_panel = JPanel()
button_panel.add(printButton)
gb.setConstraints(button_panel, gc)
panel.add(button_panel)
frame = JFrame("Translation control")
frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
frame.addWindowListener(CloseControl(destroyables=listeners))
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setVisible(show)
return frame, panel, button_panel
def registerExtenderCallbacks(self, callbacks):
self.callbacks = callbacks
self.helpers = callbacks.getHelpers()
callbacks.setExtensionName("Session Authentication Tool")
self.out = callbacks.getStdout()
# definition of suite tab
self.tab = JPanel(GridBagLayout())
self.tabledata = MappingTableModel(callbacks)
self.table = JTable(self.tabledata)
#self.table.getColumnModel().getColumn(0).setPreferredWidth(50);
#self.table.getColumnModel().getColumn(1).setPreferredWidth(100);
self.tablecont = JScrollPane(self.table)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 0
c.gridy = 0
c.gridheight = 6
c.weightx = 0.3
c.weighty = 0.5
self.tab.add(self.tablecont, c)
c = GridBagConstraints()
c.weightx = 0.1
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 1
c.gridy = 0
label_id = JLabel("Identifier:")
self.tab.add(label_id, c)
self.input_id = JTextField(20)
self.input_id.setToolTipText("Enter the identifier which is used by the application to identifiy a particular test user account, e.g. a numerical user id or a user name.")
c.gridy = 1
self.tab.add(self.input_id, c)
c.gridy = 2
label_content = JLabel("Content:")
self.tab.add(label_content, c)
self.input_content = JTextField(20, actionPerformed=self.btn_add_id)
self.input_content.setToolTipText("Enter some content which is displayed in responses of the application and shows that the current session belongs to a particular user, e.g. the full name of the user.")
c.gridy = 3
self.tab.add(self.input_content, c)
self.btn_add = JButton("Add/Edit Identity", actionPerformed=self.btn_add_id)
c.gridy = 4
self.tab.add(self.btn_add, c)
self.btn_del = JButton("Delete Identity", actionPerformed=self.btn_del_id)
c.gridy = 5
self.tab.add(self.btn_del, c)
callbacks.customizeUiComponent(self.tab)
callbacks.customizeUiComponent(self.table)
callbacks.customizeUiComponent(self.tablecont)
callbacks.customizeUiComponent(self.btn_add)
callbacks.customizeUiComponent(self.btn_del)
callbacks.customizeUiComponent(label_id)
callbacks.customizeUiComponent(self.input_id)
callbacks.addSuiteTab(self)
callbacks.registerScannerCheck(self)
callbacks.registerIntruderPayloadGeneratorFactory(self)
callbacks.registerContextMenuFactory(self)
def registerExtenderCallbacks(self, callbacks):
endianVal = 0
def generateTextBox(defaultTxt, editable):
sample = JTextArea(5, 20)
scrollPane1 = JScrollPane(sample)
sample.setBounds(0, 0, 400, 400)
sample.setEditable(editable)
sample.setLineWrap(True)
sample.setWrapStyleWord(True)
sample.setBorder(BorderFactory.createLineBorder(Color.BLACK))
sample.setText(defaultTxt)
return sample
def decodeData(event):
#Get Base64 token
full_str = base64.b64decode(self._left_tb1.getText())
sha_mac = full_str[44:64].encode('hex')
inflate_data = full_str[76:]
data = zlib.decompress(inflate_data)
user_length = data[20]
loc = 21
tokenDetails = "User name :" + data[
loc:loc + int(user_length.encode('hex'), 16)].replace(
"\x00", "") + "\n"
loc = loc + int(user_length.encode('hex'), 16)
lang_length = data[loc]
loc = loc + 1
tokenDetails += "Lang Code :" + data[
loc:loc + int(lang_length.encode('hex'), 16)].replace(
"\x00", "") + "\n"
tmp1.setText(data[loc:loc +
int(lang_length.encode('hex'), 16)].replace(
"\x00", ""))
loc = loc + int(lang_length.encode('hex'), 16)
node_length = data[loc]
loc = loc + 1
tokenDetails += "Node name :" + data[
loc:loc + int(node_length.encode('hex'), 16)].replace(
"\x00", "") + "\n"
tmp2.setText(data[loc:loc +
int(node_length.encode('hex'), 16)].replace(
"\x00", ""))
loc = loc + int(node_length.encode('hex'), 16)
time_length = data[loc]
loc = loc + 1
tokenDetails += "Creation time :" + data[
loc:loc + int(time_length.encode('hex'), 16)].replace(
"\x00", "")
tmp = data[loc:loc + int(time_length.encode('hex'), 16)].replace(
"\x00", "")
datestamp = tmp[:len(tmp) - 7]
tmp3.setText(datestamp)
# Determine if it's little or big endian
if (data[4:8].encode('hex') == '04030201'):
endianVal = 0
else:
endianVal = 1
tmp4.setText(str(endianVal))
hashcatFormat = sha_mac + ":" + data.encode("hex")
left_tb2.setText(tokenDetails)
left_tb3.setText(hashcatFormat)
def make_field(part, size):
part = chr(len(part) + size) + part
return part
def generateToken(event):
newtoken = ""
endianVal = int(tmp4.getText())
if endianVal == 1:
username = right_tb2.getText().encode('utf_16_be')
nodepw = right_tb1.getText().encode('utf_16_le')
lang = tmp1.getText().encode('utf_16_be')
nodename = tmp2.getText().encode('utf_16_be')
datestamp = (tmp3.getText() + '.164266').encode('utf_16_be')
token_ver = "8.10".encode('utf_16_be')
unknown_field = "N".encode('utf_16_be')
uncompressed_data = '\x01\x02\x03\x04\x00\x01\x00\x00\x00\x00\x02\xbc\x00\x00\x00\x00' + make_field(
username, 0) + make_field(lang, 0) + make_field(
nodename, 0) + make_field(datestamp, 0) + '\x00'
uncompressed_field = '\x00\x00\x00' + make_field(
uncompressed_data, 4)
inflate_data = zlib.compress(uncompressed_field)
sha1_mac = hashlib.sha1(uncompressed_field + nodepw).digest()
uncompressed_length = chr(len(uncompressed_field))
static_headers1 = '\x01\x02\x03\x04\x00\x01\x00\x00\x00\x00\x02\xbc\x00\x00\x00\x00\x00\x00\x00\x2c\x00\x04\x53\x68\x64\x72\x02' + unknown_field + uncompressed_length + '\x08' + token_ver + '\x14'
static_headers2 = '\x00\x05\x53\x64\x61\x74\x61'
body = '\x00\x00\x00' + make_field(
static_headers2 + make_field(inflate_data, 0), 4)
token = '\x00\x00\x00' + make_field(
static_headers1 + sha1_mac + body, 4)
newtoken = base64.b64encode(token)
elif endianVal == 0:
username = right_tb2.getText().encode('utf_16_le')
nodepw = right_tb1.getText().encode('utf_16_le')
lang = tmp1.getText().encode('utf_16_le')
nodename = tmp2.getText().encode('utf_16_le')
datestamp = (tmp3.getText() + '.999543').encode('utf_16_le')
token_ver = "8.10".encode('utf_16_le')
unknown_field = "N".encode('utf_16_le')
uncompressed_data = '\x00\x00\x00\x04\x03\x02\x01\x01\x00\x00\x00\xbc\x02\x00\x00\x00\x00\x00\x00' + make_field(
username, 0) + make_field(lang, 0) + make_field(
nodename, 0) + make_field(datestamp, 0) + '\x00'
uncompressed_field = make_field(uncompressed_data, 1)
inflate_data = zlib.compress(uncompressed_field)
sha1_mac = hashlib.sha1(uncompressed_field + nodepw).digest()
uncompressed_length = chr(len(uncompressed_field))
static_headers1 = '\x00\x00\x00\x04\x03\x02\x01\x01\x00\x00\x00\xbc\x02\x00\x00\x00\x00\x00\x00\x2c\x00\x00\x00\x04\x00\x53\x68\x64\x72\x02' + unknown_field + uncompressed_length + '\x08' + token_ver + '\x14'
static_headers2 = '\x00\x00\x00\x05\x00\x53\x64\x61\x74\x61'
body = make_field(
static_headers2 + make_field(inflate_data, 0), 1)
token = make_field(static_headers1 + sha1_mac + body, 1)
newtoken = base64.b64encode(token)
right_tb3.setText("PS_TOKEN=" + newtoken + ";")
# keep a reference to our callbacks object
self._callbacks = callbacks
# obtain an extension helpers object
self._helpers = callbacks.getHelpers()
# set our extension name
callbacks.setExtensionName("PeopleSoft PSToken Processor")
# main split pane
self._splitpane = JSplitPane(JSplitPane.HORIZONTAL_SPLIT)
self._splitpane.setResizeWeight(0.5)
c = GridBagConstraints()
c.weightx = 1
c.weighty = 1
c.anchor = GridBagConstraints.NORTHWEST
#Temp variables
tmp1 = JLabel("tmp")
tmp2 = JLabel("tmp")
tmp3 = JLabel("tmp")
tmp4 = JLabel("tmp")
# add left panel
panel1 = JPanel(GridBagLayout())
header1 = JLabel("EXTRACTION")
header1.setFont(Font("Myriad Pro", Font.BOLD, 24))
left_t1 = JLabel("PS_TOKEN Cookie")
left_t2 = JLabel("Token Details")
left_t3 = JLabel("Token Hash + Salt (Hashcat Format)")
left_t4 = JLabel(
"Save this into a .hash file and run the following Hashcat command: hashcat -m 13500 <hashfile> <dictionary file>"
)
self._left_tb1 = generateTextBox("Your PS_TOKEN value here", True)
left_tb2 = generateTextBox("Token Details here", False)
left_tb3 = generateTextBox("Hashcat format here", False)
btnDecode = JButton("Decode", actionPerformed=decodeData)
btnGenerate = JButton("Generate", actionPerformed=generateToken)
#add right panel
panel2 = JPanel(GridBagLayout())
header2 = JLabel("GENERATION")
header2.setFont(Font("Myriad Pro", Font.BOLD, 24))
right_t1 = JLabel("Node password")
right_t2 = JLabel("New username")
right_t3 = JLabel("New Base64 PS_TOKEN")
right_t4 = JLabel(
"Match & Replace rule to modify PS_TOKEN (Type: Request Header, enable regex)"
)
right_t5 = JLabel("Match rule: PS_TOKEN=[A-Za-z0-9\/\+]*;")
right_t6 = JLabel("Replace: PS_TOKEN=<new generated PS_TOKEN>;")
right_tb1 = generateTextBox("Password here", True)
right_tb2 = generateTextBox("PSADMIN", True)
right_tb3 = generateTextBox("Your new token here", False)
panel1.add(header1, c)
panel2.add(header2, c)
c.gridx = 0
c.gridy = 1
panel1.add(left_t1, c)
panel2.add(right_t1, c)
c.gridy += 1
panel1.add(self._left_tb1, c)
panel2.add(right_tb1, c)
c.gridy += 1
panel1.add(left_t2, c)
panel2.add(right_t2, c)
c.gridy += 1
panel1.add(left_tb2, c)
panel2.add(right_tb2, c)
c.gridy += 1
panel1.add(left_t3, c)
panel2.add(right_t3, c)
c.gridy += 1
panel1.add(left_t4, c)
panel2.add(right_t4, c)
c.gridy += 1
panel1.add(left_tb3, c)
panel2.add(right_t5, c)
c.gridy += 1
panel2.add(right_t6, c)
c.gridy += 1
panel2.add(right_tb3, c)
c.gridy += 1
panel1.add(btnDecode, c)
panel2.add(btnGenerate, c)
self._splitpane.setLeftComponent(panel1)
self._splitpane.setRightComponent(panel2)
# customize our UI components
callbacks.customizeUiComponent(self._splitpane)
#callbacks.customizeUiComponent(panel1)
#callbacks.customizeUiComponent(scrollPane)
# add the custom tab to Burp's UI
callbacks.addSuiteTab(self)
#add option to do right-click
callbacks.registerContextMenuFactory(self)
return
def getArguments(self):
"""
This function brings up a window to retreive any required arguments. It uses a window with fields for each argument, filled with any arguments already given.
While this window is visible the program will wait, once it is no longer visible all the arguments will be filled with the entries in the fields.
"""
class LocationAction(AbstractAction):
"""
Action to set the text of a text field to a folder or directory.
"""
def __init__(self, field):
AbstractAction.__init__(self, "...")
self.field = field
def actionPerformed(self, event):
fileChooser = JFileChooser()
fileChooser.fileSelectionMode = JFileChooser.FILES_AND_DIRECTORIES
if fileChooser.showOpenDialog(None) == JFileChooser.APPROVE_OPTION:
self.field.text = fileChooser.selectedFile.absolutePath
class HelpAction(AbstractAction):
"""
Displays a help page in a web browser.
"""
def __init__(self):
AbstractAction.__init__(self, "Help")
def actionPerformed(self, event):
browsers = ["google-chrome", "firefox", "opera", "epiphany", "konqueror", "conkeror", "midori", "kazehakase", "mozilla"]
osName = System.getProperty("os.name")
helpHTML = ClassLoader.getSystemResource("help.html").toString()
if osName.find("Mac OS") == 0:
Class.forName("com.apple.eio.FileManager").getDeclaredMethod( "openURL", [String().getClass()]).invoke(None, [helpHTML])
elif osName.find("Windows") == 0:
Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + helpHTML)
else:
browser = None
for b in browsers:
if browser == None and Runtime.getRuntime().exec(["which", b]).getInputStream().read() != -1:
browser = b
Runtime.getRuntime().exec([browser, helpHTML])
class OKAction(AbstractAction):
"""
Action for starting the pipeline. This action will simply make the window invisible.
"""
def __init__(self):
AbstractAction.__init__(self, "Ok")
def actionPerformed(self, event):
frame.setVisible(False)
class CancelAction(AbstractAction):
"""
Action for canceling the pipeline. Exits the program.
"""
def __init__(self):
AbstractAction.__init__(self, "Cancel")
def actionPerformed(self, event):
sys.exit(0)
frame = JFrame("Neofelis")
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
constraints = GridBagConstraints()
contentPane = JPanel(GridBagLayout())
frame.setContentPane(contentPane)
blastField = JTextField(self.blastLocation)
genemarkField = JTextField(self.genemarkLocation)
transtermField = JTextField(self.transtermLocation)
tRNAscanField = JTextField(self.tRNAscanLocation)
databaseLocationField = JTextField(os.path.split(self.database)[0])
databaseField = JTextField(os.path.split(self.database)[1])
matrixField = JTextField(str(self.matrix))
eValueField = JTextField(str(self.eValue))
minLengthField = JTextField(str(self.minLength))
scaffoldingDistanceField = JTextField(str(self.scaffoldingDistance))
promoterScoreField = JTextField(str(self.promoterScoreCutoff))
queryField = JTextField(self.sources[0])
constraints.gridx = 0
constraints.gridy = 0
constraints.gridwidth = 1
constraints.gridheight = 1
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx = 0
constraints.weighty = 0
contentPane.add(JLabel("Blast Location"), constraints)
constraints.gridy = 1
contentPane.add(JLabel("Genemark Location"), constraints)
constraints.gridy = 2
contentPane.add(JLabel("Transterm Location"), constraints)
constraints.gridy = 3
contentPane.add(JLabel("tRNAscan Location"), constraints)
constraints.gridy = 4
contentPane.add(JLabel("Databases Location"), constraints)
constraints.gridy = 5
contentPane.add(JLabel("Database"), constraints)
constraints.gridy = 6
contentPane.add(JLabel("Matrix(Leave blank to use heuristic matrix)"), constraints)
constraints.gridy = 7
contentPane.add(JLabel("E Value"), constraints)
constraints.gridy = 8
contentPane.add(JLabel("Minimum Intergenic Length"), constraints)
constraints.gridy = 9
contentPane.add(JLabel("Scaffold Distance"), constraints)
constraints.gridy = 10
contentPane.add(JLabel("Promoter Score Cutoff"), constraints)
constraints.gridy = 11
contentPane.add(JLabel("Query"), constraints)
constraints.gridx = 1
constraints.gridy = 0
constraints.weightx = 1
contentPane.add(blastField, constraints)
constraints.gridy = 1
contentPane.add(genemarkField, constraints)
constraints.gridy = 2
contentPane.add(transtermField, constraints)
constraints.gridy = 3
contentPane.add(tRNAscanField, constraints)
constraints.gridy = 4
contentPane.add(databaseLocationField, constraints)
constraints.gridy = 5
contentPane.add(databaseField, constraints)
constraints.gridy = 6
contentPane.add(matrixField, constraints)
constraints.gridy = 7
contentPane.add(eValueField, constraints)
constraints.gridy = 8
contentPane.add(minLengthField, constraints)
constraints.gridy = 9
contentPane.add(scaffoldingDistanceField, constraints)
constraints.gridy = 10
contentPane.add(promoterScoreField, constraints)
constraints.gridy = 11
contentPane.add(queryField, constraints)
constraints.gridx = 2
constraints.gridy = 0
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(JButton(LocationAction(blastField)), constraints)
constraints.gridy = 1
contentPane.add(JButton(LocationAction(genemarkField)), constraints)
constraints.gridy = 2
contentPane.add(JButton(LocationAction(transtermField)), constraints)
constraints.gridy = 3
contentPane.add(JButton(LocationAction(tRNAscanField)), constraints)
constraints.gridy = 4
contentPane.add(JButton(LocationAction(databaseLocationField)), constraints)
constraints.gridy = 11
contentPane.add(JButton(LocationAction(queryField)), constraints)
constraints.gridx = 0
constraints.gridy = 12
constraints.anchor = GridBagConstraints.LINE_START
contentPane.add(JButton(HelpAction()), constraints)
constraints.gridx = 1
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(JButton(OKAction()), constraints)
constraints.gridx = 2
contentPane.add(JButton(CancelAction()), constraints)
frame.pack()
frame.setLocationRelativeTo(None)
frame.setVisible(True)
while frame.isVisible():
pass
self.blastLocation = blastField.getText()
self.genemarkLocation = genemarkField.getText()
self.transtermLocation = transtermField.getText()
self.database = databaseLocationField.getText() + "/" + databaseField.getText()
self.matrix = matrixField.getText()
self.eValue = float(eValueField.getText())
self.minLength = int(minLengthField.getText())
self.scaffoldingDistance = int(scaffoldingDistanceField.getText())
self.promoterScoreCutoff = float(promoterScoreField.getText())
self.sources = [queryField.getText()]
def registerExtenderCallbacks(self, callbacks):
Cb(callbacks)
Cb.callbacks.setExtensionName(self.ext_name)
try:
global compuracer_communication_lock
# option picker item objects (for Java compatibility)
item1 = {'key': 'item1', 'name': '2'}
item2 = {'key': 'item2', 'name': '3'}
item3 = {'key': 'item3', 'name': '4'}
item4 = {'key': 'item4', 'name': '5'}
item5 = {'key': 'item5', 'name': '10'}
item6 = {'key': 'item6', 'name': '15'}
item7 = {'key': 'item7', 'name': '20'}
item8 = {'key': 'item8', 'name': '25'}
item9 = {'key': 'item9', 'name': '50'}
item10 = {'key': 'item10', 'name': '100'}
# main splitted pane + top pane
self._main_splitpane = JSplitPane(JSplitPane.VERTICAL_SPLIT)
self._outer_settings_pane = JPanel(BorderLayout())
self._settings_pane = JPanel(GridBagLayout())
c = GridBagConstraints()
self.label_1 = JLabel("Number of parallel requests:")
c.fill = GridBagConstraints.NONE
c.gridx = 0
c.gridy = 0
c.insets = Insets(0, 5, 0, 10)
c.anchor = GridBagConstraints.LINE_START
self._settings_pane.add(self.label_1, c)
self.input_parallel_requests = JComboBox([
Item(item1),
Item(item2),
Item(item3),
Item(item4),
Item(item5),
Item(item6),
Item(item7),
Item(item8),
Item(item9),
Item(item10)
])
self.input_parallel_requests.setSelectedIndex(4)
self.input_parallel_requests.setToolTipText(
"Select the number of parallel requests that will be sent")
self.input_parallel_requests.addActionListener(
self.change_parallel_requests)
c.gridx = 1
c.gridy = 0
c.insets = Insets(0, 5, 0, 10)
self._settings_pane.add(self.input_parallel_requests, c)
self.option_allow_redirects = JCheckBox(
"Allow redirects", actionPerformed=self.check_allow_redirects)
self.option_allow_redirects.setToolTipText(
"Select whether redirect responses are followed")
c.gridx = 2
c.gridy = 0
c.insets = Insets(0, 20, 0, 10)
self._settings_pane.add(self.option_allow_redirects, c)
self.option_sync_last_byte = JCheckBox(
"Sync last byte", actionPerformed=self.check_sync_last_byte)
self.option_sync_last_byte.setToolTipText(
"Select whether last byte synchronisation is enabled")
c.gridx = 2
c.gridy = 1
c.insets = Insets(0, 20, 0, 0)
self._settings_pane.add(self.option_sync_last_byte, c)
self.label_2 = JLabel("Send timeout in seconds:")
c.gridx = 0
c.gridy = 1
c.insets = Insets(0, 5, 0, 0)
self._settings_pane.add(self.label_2, c)
self.input_send_timeout = JComboBox([
Item(item2),
Item(item4),
Item(item5),
Item(item7),
Item(item9),
Item(item10)
])
self.input_send_timeout.setSelectedIndex(3)
self.input_send_timeout.setToolTipText(
"Select the wait-for-response timeout after sending the request(s)"
)
self.input_send_timeout.addActionListener(self.change_send_timeout)
c.gridx = 1
c.gridy = 1
c.insets = Insets(0, 5, 0, 0)
self._settings_pane.add(self.input_send_timeout, c)
self.button_resend_batch = JButton("Resend requests")
self.button_resend_batch.setToolTipText(
"Resend all requests with the current configuration")
self.button_resend_batch.setEnabled(False)
self.button_resend_batch.addActionListener(
MenuFactory.start_request_transmitter_button)
c.gridx = 3
c.gridy = 0
c.insets = Insets(0, 20, 0, 10)
self._settings_pane.add(self.button_resend_batch, c)
immediate_data_ui_elements[
"parallel_requests"] = self.input_parallel_requests
immediate_data_ui_elements[
"allow_redirects"] = self.option_allow_redirects
immediate_data_ui_elements[
"sync_last_byte"] = self.option_sync_last_byte
immediate_data_ui_elements[
"send_timeout"] = self.input_send_timeout
immediate_data_ui_elements[
"resend_batch"] = self.button_resend_batch
c = GridBagConstraints()
c.anchor = GridBagConstraints.WEST
self._outer_settings_pane.add(self._settings_pane,
BorderLayout.WEST)
self._main_splitpane.setTopComponent(self._outer_settings_pane)
self._results_splitpane = JSplitPane(JSplitPane.HORIZONTAL_SPLIT)
self._main_splitpane.setBottomComponent(self._results_splitpane)
# table of log entries
self.tabs_right = JTabbedPane()
global _textEditors, DEFAULT_RESULTS
for i in range(3):
_textEditors.append(Cb.callbacks.createTextEditor())
_textEditors[-1].setText(str.encode("\n" + DEFAULT_RESULTS))
self.tabs_right.add("Summary", _textEditors[0].getComponent())
self.tabs_right.add("Full result", _textEditors[1].getComponent())
self.tabs_right.add("Config", _textEditors[2].getComponent())
self._results_splitpane.setRightComponent(self.tabs_right)
# tabs with request/response viewers
global _requestViewers, _requestPane
_requestPane = JTabbedPane()
_requestViewers.append(
Cb.callbacks.createMessageEditor(None, False))
_requestPane.addTab("Request", _requestViewers[-1].getComponent())
self._results_splitpane.setLeftComponent(_requestPane)
# customize our UI components
Cb.callbacks.customizeUiComponent(self._settings_pane)
Cb.callbacks.customizeUiComponent(self.tabs_right)
Cb.callbacks.customizeUiComponent(_requestPane)
# add the custom tab to Burp's UI
Cb.callbacks.addSuiteTab(self)
except RuntimeException as e:
callbacks.printError(traceback.format_exc())
e = PyException(e)
print("10")
print(str(self))
print("{}\t{}\n{}\n".format(e.type, e.value, e.traceback))
Cb.callbacks.registerContextMenuFactory(MenuFactory())
callbacks.registerExtensionStateListener(self)
self.start_alive_checker()
Cb.callbacks.printOutput('%s v%s extension loaded\n' %
(self.ext_name, self.ext_version))
def __init__(self, extender=None, *rows):
self.extender = extender
self.table = table = JTable(ParameterProcessingRulesTableModel(*rows))
table.setPreferredScrollableViewportSize(Dimension(500, 70))
table.setRowSorter(TableRowSorter(table.getModel()))
table.setFillsViewportHeight(True)
gridBagLayout = GridBagLayout()
gridBagLayout.columnWidths = [0, 0, 25, 0 ]
gridBagLayout.rowHeights = [0, 0, 0, 0]
gridBagLayout.columnWeights = [0.0, 1.0, 1.0, Double.MIN_VALUE]
gridBagLayout.rowWeights = [0.0, 0.0, 0.0, Double.MIN_VALUE]
self.setLayout(gridBagLayout)
addButton = JButton("Add")
addButton.addActionListener(AddRemoveParameterListener(table))
addButtonConstraints = GridBagConstraints()
addButtonConstraints.fill = GridBagConstraints.HORIZONTAL
addButtonConstraints.insets = Insets(0, 0, 5, 5)
addButtonConstraints.gridx = 0
addButtonConstraints.gridy = 0
self.add(addButton, addButtonConstraints)
removeButton = JButton("Remove")
removeButton.addActionListener(AddRemoveParameterListener(table))
removeButtonConstraints = GridBagConstraints()
removeButtonConstraints.fill = GridBagConstraints.HORIZONTAL
removeButtonConstraints.insets = Insets(0, 0, 5, 5)
removeButtonConstraints.gridx = 0
removeButtonConstraints.gridy = 1
self.add(removeButton, removeButtonConstraints)
upButton = JButton("Up")
upButton.addActionListener(AddRemoveParameterListener(table))
upButtonConstraints = GridBagConstraints()
upButtonConstraints.fill = GridBagConstraints.HORIZONTAL
upButtonConstraints.insets = Insets(0, 0, 5, 5)
upButtonConstraints.gridx = 0
upButtonConstraints.gridy = 2
self.add(upButton, upButtonConstraints)
downButton = JButton("Down")
downButton.addActionListener(AddRemoveParameterListener(table))
downButtonConstraints = GridBagConstraints()
downButtonConstraints.fill = GridBagConstraints.HORIZONTAL
downButtonConstraints.anchor = GridBagConstraints.NORTH
downButtonConstraints.insets = Insets(0, 0, 5, 5)
downButtonConstraints.gridx = 0
downButtonConstraints.gridy = 3
self.add(downButton, downButtonConstraints)
scrollPane = JScrollPane(table)
scrollPaneConstraints = GridBagConstraints()
scrollPaneConstraints.gridwidth = 2
scrollPaneConstraints.gridheight = 5
scrollPaneConstraints.insets = Insets(0, 0, 5, 5)
scrollPaneConstraints.anchor = GridBagConstraints.NORTHWEST
scrollPaneConstraints.gridx = 1
scrollPaneConstraints.gridy = 0
self.add(scrollPane, scrollPaneConstraints)
self.initParameterColumn(table)
self.initColumnSizes(table)
def initComponents(self):
self.setLayout(GridBagLayout())
gbc = GridBagConstraints()
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 0
gbc.gridy = 0
descriptionLabel = JLabel("FEA - Forensics Email Analysis")
self.add(descriptionLabel, gbc)
gbc.gridy = 1
self.cbNSLookup = JCheckBox(
"Perform DNS Lookup on email domains",
actionPerformed=self.cbNSLookupActionPerformed)
self.cbNSLookup.setSelected(True)
self.add(self.cbNSLookup, gbc)
# TODO: include option to browse for text file with list of emails to exclude from analysis
numberThreadsLabel = JLabel(
"Maximum number of threads for DNS Lookup task: ")
gbc.gridy = 2
self.add(numberThreadsLabel, gbc)
self.numberThreadsSlider = JSlider(
JSlider.HORIZONTAL,
1,
16,
8,
stateChanged=self.sliderActionPerformed)
self.numberThreadsSlider.setMajorTickSpacing(1)
self.numberThreadsSlider.setPaintLabels(True)
self.numberThreadsSlider.setPaintTicks(True)
self.numberThreadsSlider.setSnapToTicks(True)
self.numberThreadsSlider.setToolTipText(
"set maximum number of concurrent threads when performing DNS lookup on email domains"
)
gbc.gridy = 5
gbc.gridwidth = 15
gbc.gridheight = 1
gbc.fill = GridBagConstraints.BOTH
gbc.weightx = 0
gbc.weighty = 0
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridy = 3
self.add(self.numberThreadsSlider, gbc)
self.cbGenerateExcel = JCheckBox(
"Generate Excel format report (more detailed)",
actionPerformed=self.cbGenerateExcelActionPerformed)
self.cbGenerateExcel.setSelected(True)
gbc.gridy = 4
self.add(self.cbGenerateExcel, gbc)
self.cbGenerateCSV = JCheckBox(
"Generate CSV format report (plaintext)",
actionPerformed=self.cbGenerateCSVActionPerformed)
self.cbGenerateCSV.setSelected(True)
gbc.gridy = 5
self.add(self.cbGenerateCSV, gbc)
gbc.gridy = 6
self.cbWayback = JCheckBox(
"Perform Wayback Machine Lookup on email domains (WARNING: can be a slow process!)",
actionPerformed=self.cbWaybackActionPerformed)
self.cbWayback.setSelected(True)
self.add(self.cbWayback, gbc)
def __init__(self, callbacks, parent):
# Initialze self stuff
self._callbacks = callbacks
self.config = {}
self.ext_stats = {}
self.url_reqs = []
self.parse_files = False
self.tab = JPanel(GridBagLayout())
self.view_port_text = JTextArea("===SpyDir===")
self.delim = JTextField(30)
self.ext_white_list = JTextField(30)
# I'm not sure if these fields are necessary still
# why not just use Burp func to handle this?
# leaving them in case I need it for the HTTP handler later
# self.cookies = JTextField(30)
# self.headers = JTextField(30)
self.url = JTextField(30)
self.parent_window = parent
self.plugins = {}
self.loaded_p_list = set()
self.loaded_plugins = False
self.config['Plugin Folder'] = None
self.double_click = False
self.source_input = ""
self.print_stats = True
self.curr_conf = JLabel()
self.window = JFrame("Select plugins",
preferredSize=(200, 250),
windowClosing=self.p_close)
self.window.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
self.window.setVisible(False)
self.path_vars = JTextField(30)
# Initialize local stuff
tab_constraints = GridBagConstraints()
status_field = JScrollPane(self.view_port_text)
# Configure view port
self.view_port_text.setEditable(False)
labels = self.build_ui()
# Add things to rows
tab_constraints.anchor = GridBagConstraints.FIRST_LINE_END
tab_constraints.gridx = 1
tab_constraints.gridy = 0
tab_constraints.fill = GridBagConstraints.HORIZONTAL
self.tab.add(JButton(
"Resize screen", actionPerformed=self.resize),
tab_constraints)
tab_constraints.gridx = 0
tab_constraints.gridy = 1
tab_constraints.anchor = GridBagConstraints.FIRST_LINE_START
self.tab.add(labels, tab_constraints)
tab_constraints.gridx = 1
tab_constraints.gridy = 1
tab_constraints.fill = GridBagConstraints.BOTH
tab_constraints.weightx = 1.0
tab_constraints.weighty = 1.0
tab_constraints.anchor = GridBagConstraints.FIRST_LINE_END
self.tab.add(status_field, tab_constraints)
try:
self._callbacks.customizeUiComponent(self.tab)
except Exception:
pass
def registerExtenderCallbacks(self, callbacks):
self.callbacks = callbacks
self.helpers = callbacks.getHelpers()
callbacks.setExtensionName("Session Authentication Tool")
self.out = callbacks.getStdout()
# definition of suite tab
self.tab = JPanel(GridBagLayout())
self.tabledata = MappingTableModel(callbacks)
self.table = JTable(self.tabledata)
#self.table.getColumnModel().getColumn(0).setPreferredWidth(50);
#self.table.getColumnModel().getColumn(1).setPreferredWidth(100);
self.tablecont = JScrollPane(self.table)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 0
c.gridy = 0
c.gridheight = 6
c.weightx = 0.3
c.weighty = 0.5
self.tab.add(self.tablecont, c)
c = GridBagConstraints()
c.weightx = 0.1
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 1
c.gridy = 0
label_id = JLabel("Identifier:")
self.tab.add(label_id, c)
self.input_id = JTextField(20)
self.input_id.setToolTipText(
"Enter the identifier which is used by the application to identifiy a particular test user account, e.g. a numerical user id or a user name."
)
c.gridy = 1
self.tab.add(self.input_id, c)
c.gridy = 2
label_content = JLabel("Content:")
self.tab.add(label_content, c)
self.input_content = JTextField(20, actionPerformed=self.btn_add_id)
self.input_content.setToolTipText(
"Enter some content which is displayed in responses of the application and shows that the current session belongs to a particular user, e.g. the full name of the user."
)
c.gridy = 3
self.tab.add(self.input_content, c)
self.btn_add = JButton("Add/Edit Identity",
actionPerformed=self.btn_add_id)
c.gridy = 4
self.tab.add(self.btn_add, c)
self.btn_del = JButton("Delete Identity",
actionPerformed=self.btn_del_id)
c.gridy = 5
self.tab.add(self.btn_del, c)
callbacks.customizeUiComponent(self.tab)
callbacks.customizeUiComponent(self.table)
callbacks.customizeUiComponent(self.tablecont)
callbacks.customizeUiComponent(self.btn_add)
callbacks.customizeUiComponent(self.btn_del)
callbacks.customizeUiComponent(label_id)
callbacks.customizeUiComponent(self.input_id)
callbacks.addSuiteTab(self)
callbacks.registerScannerCheck(self)
callbacks.registerIntruderPayloadGeneratorFactory(self)
callbacks.registerContextMenuFactory(self)
def initComponents(self):
#set the layout and add form components
self.setLayout(GridBagLayout())
gc = GridBagConstraints()
gc.weightx = 1
gc.weighty = 1
# First Row
gc.gridy = 0
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.fill = GridBagConstraints.NONE
gc.anchor = GridBagConstraints.LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.nameLabel, gc)
gc.gridx = 1
gc.anchor = GridBagConstraints.LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.nameField, gc)
# Second Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.anchor = GridBagConstraints.LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.mobLabel, gc)
gc.gridx = 1
gc.anchor = GridBagConstraints.LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.mobField, gc)
#Third Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.anchor = GridBagConstraints.FIRST_LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.emailLabel, gc)
gc.weightx = 1
gc.weighty = 0.2
gc.gridx = 1
gc.anchor = GridBagConstraints.FIRST_LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.emailField, gc)
#Next Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.anchor = GridBagConstraints.FIRST_LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.userNameLabel, gc)
gc.weightx = 1
gc.weighty = 0.2
gc.gridx = 1
gc.anchor = GridBagConstraints.FIRST_LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.userNameField, gc)
# Next Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.anchor = GridBagConstraints.FIRST_LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.passwordLabel, gc)
gc.weightx = 1
gc.weighty = 0.2
gc.gridx = 1
gc.anchor = GridBagConstraints.FIRST_LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.passwordField, gc)
# Next Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.anchor = GridBagConstraints.FIRST_LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.confirmPasswordLabel, gc)
gc.weightx = 1
gc.weighty = 0.2
gc.gridx = 1
gc.anchor = GridBagConstraints.FIRST_LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.confirmPasswordField, gc)
# Next Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.anchor = GridBagConstraints.FIRST_LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.superPassLabel, gc)
gc.weightx = 1
gc.weighty = 0.2
gc.gridx = 1
gc.anchor = GridBagConstraints.FIRST_LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.superPassField, gc)
# Next Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 2.0
gc.gridx = 1
gc.anchor = GridBagConstraints.FIRST_LINE_START
self.add(self.addAdminBtn, gc)
innerBorder = BorderFactory.createTitledBorder('Add Admin')
outerBorder = BorderFactory.createEmptyBorder(5, 5, 5, 5)
self.setBorder(
BorderFactory.createCompoundBorder(outerBorder, innerBorder))
def makeCropUI(imp, images, tgtDir, panel=None, cropContinuationFn=None):
""" imp: the ImagePlus to work on.
images: the list of ImgLib2 images, one per frame, not original but already isotropic.
(These are views that use a nearest neighbor interpolation using the calibration to scale to isotropy.)
tgtDir: the target directory where e.g. CSV files will be stored, for ROI, features, pointmatches.
panel: optional, a JPanel controlled by a GridBagLayout.
cropContinuationFn: optional, a function to execute after cropping,
which is given as arguments the original images,
minC, maxC (both define a ROI), and the cropped images. """
independent = None == panel
if not panel:
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
gc = GBC()
else:
gb = panel.getLayout()
# Constraints of the last component
gc = gb.getConstraints(panel.getComponent(panel.getComponentCount() - 1))
# Horizontal line to separate prior UI components from crop UI
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 4
gc.anchor = GBC.WEST
gc.fill = GBC.HORIZONTAL
sep = JSeparator()
sep.setMinimumSize(Dimension(200, 10))
gb.setConstraints(sep, gc)
panel.add(sep)
# ROI UI header
title = JLabel("ROI controls:")
gc.gridy +=1
gc.anchor = GBC.WEST
gc.gridwidth = 4
gb.setConstraints(title, gc)
panel.add(title)
# Column labels for the min and max coordinates
gc.gridy += 1
gc.gridwidth = 1
for i, title in enumerate(["", "X", "Y", "Z"]):
gc.gridx = i
gc.anchor = GBC.CENTER
label = JLabel(title)
gb.setConstraints(label, gc)
panel.add(label)
textfields = []
rms = []
# Load stored ROI if any
roi_path = path = os.path.join(tgtDir, "crop-roi.csv")
if os.path.exists(roi_path):
with open(roi_path, 'r') as csvfile:
reader = csv.reader(csvfile, delimiter=',', quotechar="\"")
reader.next() # header
minC = map(int, reader.next()[1:])
maxC = map(int, reader.next()[1:])
# Place the ROI over the ImagePlus
imp.setRoi(Roi(minC[0], minC[1], maxC[0] + 1 - minC[0], maxC[1] + 1 - minC[1]))
else:
# Use whole image dimensions
minC = [0, 0, 0]
maxC = [v -1 for v in Intervals.dimensionsAsLongArray(images[0])]
# Text fields for the min and max coordinates
for rowLabel, coords in izip(["min coords: ", "max coords: "],
[minC, maxC]):
gc.gridx = 0
gc.gridy += 1
label = JLabel(rowLabel)
gb.setConstraints(label, gc)
panel.add(label)
for i in xrange(3):
gc.gridx += 1
tf = JTextField(str(coords[i]), 10)
gb.setConstraints(tf, gc)
panel.add(tf)
textfields.append(tf)
listener = RoiMaker(imp, textfields, len(textfields) -1)
rms.append(listener)
tf.addKeyListener(listener)
tf.addMouseWheelListener(listener)
# Listen to changes in the ROI of imp
rfl = RoiFieldListener(imp, textfields)
Roi.addRoiListener(rfl)
# ... and enable cleanup
ImagePlus.addImageListener(FieldDisabler(rfl, rms))
# Functions for cropping images
cropped = None
cropped_imp = None
def storeRoi(minC, maxC):
if os.path.exists(roi_path):
# Load ROI
with open(path, 'r') as csvfile:
reader = csv.reader(csvfile, delimiter=',', quotechar="\"")
reader.next() # header
same = True
for a, b in izip(minC + maxC, map(int, reader.next()[1:] + reader.next()[1:])):
if a != b:
same = False
# Invalidate any CSV files for features and pointmatches: different cropping
for filename in os.listdir(tgtDir):
if filename.endswith("features.csv") or filename.endswith("pointmatches.csv"):
os.remove(os.path.join(tgtDir, filename))
break
if same:
return
# Store the ROI as crop-roi.csv
with open(roi_path, 'w') as csvfile:
w = csv.writer(csvfile, delimiter=',', quotechar="\"", quoting=csv.QUOTE_NONNUMERIC)
w.writerow(["coords", "x", "y", "z"])
w.writerow(["min"] + map(int, minC))
w.writerow(["max"] + map(int, maxC))
def crop(event):
global cropped, cropped_imp
coords = [int(float(tf.getText())) for tf in textfields]
minC = [max(0, c) for c in coords[0:3]]
maxC = [min(d -1, c) for d, c in izip(Intervals.dimensionsAsLongArray(images[0]), coords[3:6])]
storeRoi(minC, maxC)
print "ROI min and max coordinates"
print minC
print maxC
cropped = [Views.zeroMin(Views.interval(img, minC, maxC)) for img in images]
cropped_imp = showAsStack(cropped, title="cropped")
cropped_imp.setDisplayRange(imp.getDisplayRangeMin(), imp.getDisplayRangeMax())
if cropContinuationFn:
cropContinuationFn(images, minC, maxC, cropped, cropped_imp)
# Buttons to create a ROI and to crop to ROI,
# which when activated enables the fine registration buttons
crop_button = JButton("Crop to ROI")
crop_button.addActionListener(crop)
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 4
gc.anchor = GBC.WEST
buttons_panel = JPanel()
buttons_panel.add(crop_button)
gb.setConstraints(buttons_panel, gc)
panel.add(buttons_panel)
if independent:
frame = JFrame("Crop by ROI")
frame.getContentPane().add(panel)
frame.pack()
frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
frame.addWindowListener(CloseControl(destroyables=rms + [rfl]))
frame.setVisible(True)
else:
# Re-pack the JFrame
parent = panel.getParent()
while not isinstance(parent, JFrame) and parent is not None:
parent = parent.getParent()
if parent:
frame = parent
frame.pack()
found = False
for wl in frame.getWindowListeners():
if isinstance(wl, CloseControl):
wl.addDestroyables(rms + [rfl])
found = True
break
if not found:
frame.addWindowListener(CloseControl(destroyables=rms + [rfl]))
frame.setVisible(True)
return panel
def registerExtenderCallbacks(self, this_callbacks): ### IBurpExtender
global callbacks, helpers
global extension_enable, in_scope_only
global remove_csrf_headers, remove_csrf_params, change_method_to_post
global change_ct_to_json, change_ct_to_plain, change_to_get
callbacks = this_callbacks
helpers = callbacks.getHelpers()
callbacks.setExtensionName(NAME)
self.settings = JPanel(GridBagLayout())
c = GridBagConstraints()
self.extension_enable_box = JCheckBox('Enable extension',
extension_enable)
self.setFontBold(self.extension_enable_box)
self.extension_enable_box.setForeground(Color(0, 0, 153))
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 0
c.gridwidth = 1
c.weightx = 1
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.WEST
self.settings.add(self.extension_enable_box, c)
self.in_scope_only_box = JCheckBox('Modify only in-scope requests',
in_scope_only)
self.setFontBold(self.in_scope_only_box)
self.in_scope_only_box.setForeground(Color(0, 0, 153))
c.insets = Insets(40, 5, 5, 5)
c.gridx = 0
c.gridy = 1
self.settings.add(self.in_scope_only_box, c)
self.remove_csrf_headers_box = JCheckBox('Remove CSRF headers',
remove_csrf_params)
self.setFontBold(self.remove_csrf_headers_box)
self.remove_csrf_headers_box.setForeground(Color(0, 0, 153))
c.insets = Insets(40, 5, 5, 5)
c.gridx = 0
c.gridy = 2
self.settings.add(self.remove_csrf_headers_box, c)
remove_csrf_headers_box_lbl = JLabel(
'Check to remove headers with CSRF tokens from all requests.')
self.setFontItalic(remove_csrf_headers_box_lbl)
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 3
self.settings.add(remove_csrf_headers_box_lbl, c)
self.remove_csrf_params_box = JCheckBox('Remove CSRF parameters',
remove_csrf_params)
self.setFontBold(self.remove_csrf_params_box)
self.remove_csrf_params_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 4
self.settings.add(self.remove_csrf_params_box, c)
remove_csrf_params_box_lbl = JLabel(
'Check to remove URL/body parameters with CSRF tokens from all requests. URL-encoded, multipart, JSON parameters are supported.'
)
self.setFontItalic(remove_csrf_params_box_lbl)
c.gridx = 0
c.gridy = 5
self.settings.add(remove_csrf_params_box_lbl, c)
self.change_method_to_post_box = JCheckBox(
'Change HTTP method to POST', change_method_to_post)
self.setFontBold(self.change_method_to_post_box)
self.change_method_to_post_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 6
self.settings.add(self.change_method_to_post_box, c)
change_method_to_post_lbl = JLabel(
'Check to convert PUT/DELETE/PATCH method to POST in all requests.'
)
self.setFontItalic(change_method_to_post_lbl)
c.gridx = 0
c.gridy = 7
self.settings.add(change_method_to_post_lbl, c)
self.change_ct_to_json_box = JCheckBox('Change media type to json',
change_ct_to_json)
self.setFontBold(self.change_ct_to_json_box)
self.change_ct_to_json_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 8
self.settings.add(self.change_ct_to_json_box, c)
change_ct_to_json_lbl = JLabel(
'Check to convert body to json and set Content-Type to application/json in url-encoded requests.'
)
self.setFontItalic(change_ct_to_json_lbl)
c.gridx = 0
c.gridy = 9
self.settings.add(change_ct_to_json_lbl, c)
self.change_ct_to_plain_box = JCheckBox(
'Change Content-Type to text/plain', change_ct_to_plain)
self.setFontBold(self.change_ct_to_plain_box)
self.change_ct_to_plain_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 10
self.settings.add(self.change_ct_to_plain_box, c)
change_ct_to_plain_lbl = JLabel(
'Check to set Content-Type to text/plain in request with non-simple media type. Simple media types - application/application/x-www-form-urlencoded, text/plain, multipart/form-data.'
)
self.setFontItalic(change_ct_to_plain_lbl)
c.gridx = 0
c.gridy = 11
self.settings.add(change_ct_to_plain_lbl, c)
self.change_to_get_box = JCheckBox('Change to GET', change_to_get)
self.setFontBold(self.change_to_get_box)
self.change_to_get_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 12
self.settings.add(self.change_to_get_box, c)
change_to_get_lbl = JLabel(
'Check to convert POST/PUT/DELETE/PATCH url-encoded requests to GET.'
)
self.setFontItalic(change_to_get_lbl)
c.gridx = 0
c.gridy = 13
self.settings.add(change_to_get_lbl, c)
self.csrf_headers_params = JPanel(GridBagLayout())
c = GridBagConstraints()
lblParams = JLabel("CSRF parameters:")
self.setFontBold(lblParams)
lblParams.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 0
c.insets = Insets(5, 5, 5, 5)
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.FIRST_LINE_END
self.csrf_headers_params.add(lblParams, c)
self.csrf_param_text_field = JTextField()
c.fill = GridBagConstraints.BOTH
c.gridx = 1
c.gridy = 0
self.csrf_headers_params.add(self.csrf_param_text_field, c)
lblParamsNote = JLabel(
"Remove parameter from request if name contains")
self.setFontItalic(lblParamsNote)
c.fill = GridBagConstraints.NONE
c.gridx = 0
c.gridy = 1
self.csrf_headers_params.add(lblParamsNote, c)
self.csrf_params_text_area = JTextArea()
self.csrf_params_text_area.setColumns(20)
self.csrf_params_text_area.setRows(10)
self.csrf_params_text_area.setEditable(False)
c.fill = GridBagConstraints.BOTH
self.csrf_params_mouse_listener = TextAreaMouseListener(
self.csrf_params_text_area)
self.csrf_params_text_area.addMouseListener(
self.csrf_params_mouse_listener)
for name in csrf_params_names:
self.csrf_params_text_area.append(name + os.linesep)
c.gridx = 1
c.gridy = 1
sp = JScrollPane(self.csrf_params_text_area)
self.csrf_headers_params.add(sp, c)
buttonsPanel = JPanel(GridBagLayout())
_c = GridBagConstraints()
_c.insets = Insets(3, 3, 3, 3)
_c.gridx = 0
_c.gridy = 0
_c.fill = GridBagConstraints.BOTH
_c.weightx = 1
_c.gridwidth = 1
handlers = ButtonHandlers(self.csrf_param_text_field,
self.csrf_params_text_area,
self.csrf_params_mouse_listener,
csrf_params_names)
self.csrf_param_add_button = JButton(
'Add', actionPerformed=handlers.handler_add)
self.csrf_param_rm_button = JButton(
'Remove', actionPerformed=handlers.handler_rm)
self.csrf_param_restore_button = JButton(
'Restore', actionPerformed=handlers.handler_restore)
buttonsPanel.add(self.csrf_param_add_button, _c)
_c.gridy = 1
buttonsPanel.add(self.csrf_param_rm_button, _c)
_c.gridy = 2
buttonsPanel.add(self.csrf_param_restore_button, _c)
_c.gridy = 3
c.gridx = 2
c.gridy = 1
c.fill = GridBagConstraints.NONE
self.csrf_headers_params.add(buttonsPanel, c)
lblHeaders = JLabel("CSRF headers:")
self.setFontBold(lblHeaders)
lblHeaders.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 2
c.insets = Insets(40, 5, 5, 5)
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.FIRST_LINE_END
self.csrf_headers_params.add(lblHeaders, c)
self.csrf_header_text_field = JTextField()
c.fill = GridBagConstraints.BOTH
c.gridx = 1
c.gridy = 2
self.csrf_headers_params.add(self.csrf_header_text_field, c)
lblHeadersNote = JLabel("Remove header from request if name equals to")
self.setFontItalic(lblHeadersNote)
c.fill = GridBagConstraints.NONE
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 3
self.csrf_headers_params.add(lblHeadersNote, c)
self.csrf_headers_text_area = JTextArea()
self.csrf_headers_text_area.setColumns(20)
self.csrf_headers_text_area.setRows(10)
self.csrf_headers_text_area.setEditable(False)
c.fill = GridBagConstraints.BOTH
self.csrf_headers_mouse_listener = TextAreaMouseListener(
self.csrf_headers_text_area)
self.csrf_headers_text_area.addMouseListener(
self.csrf_headers_mouse_listener)
for name in csrf_headers_names:
self.csrf_headers_text_area.append(name + os.linesep)
c.gridx = 1
c.gridy = 3
sp = JScrollPane(self.csrf_headers_text_area)
self.csrf_headers_params.add(sp, c)
buttonsPanel = JPanel(GridBagLayout())
_c = GridBagConstraints()
_c.insets = Insets(3, 3, 3, 3)
_c.gridx = 0
_c.gridy = 0
_c.fill = GridBagConstraints.BOTH
_c.weightx = 1
_c.gridwidth = 1
handlers = ButtonHandlers(self.csrf_header_text_field,
self.csrf_headers_text_area,
self.csrf_headers_mouse_listener,
csrf_headers_names)
self.csrf_header_add_button = JButton(
'Add', actionPerformed=handlers.handler_add)
self.csrf_header_rm_button = JButton(
'Remove', actionPerformed=handlers.handler_rm)
self.csrf_header_restore_button = JButton(
'Restore', actionPerformed=handlers.handler_restore)
buttonsPanel.add(self.csrf_header_add_button, _c)
_c.gridy = 1
buttonsPanel.add(self.csrf_header_rm_button, _c)
_c.gridy = 2
buttonsPanel.add(self.csrf_header_restore_button, _c)
_c.gridy = 3
c.gridx = 2
c.gridy = 3
c.fill = GridBagConstraints.NONE
self.csrf_headers_params.add(buttonsPanel, c)
self.whitelist = JPanel(GridBagLayout())
c = GridBagConstraints()
lblWhitelist = JLabel("URLs whitelist:")
self.setFontBold(lblWhitelist)
lblWhitelist.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 0
c.insets = Insets(5, 5, 5, 5)
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.FIRST_LINE_END
self.whitelist.add(lblWhitelist, c)
self.whitelist_text_field = JTextField()
c.fill = GridBagConstraints.BOTH
c.gridx = 1
c.gridy = 0
self.whitelist.add(self.whitelist_text_field, c)
lblWhitelistNote = JLabel(
"Do not perform request modification if URL starts with")
self.setFontItalic(lblWhitelistNote)
c.fill = GridBagConstraints.NONE
c.gridx = 0
c.gridy = 1
self.whitelist.add(lblWhitelistNote, c)
self.whitelist_text_area = JTextArea()
self.whitelist_text_area.setColumns(30)
self.whitelist_text_area.setRows(10)
self.whitelist_text_area.setEditable(False)
c.fill = GridBagConstraints.BOTH
self.whitelist_mouse_listener = TextAreaMouseListener(
self.whitelist_text_area)
self.whitelist_text_area.addMouseListener(
self.whitelist_mouse_listener)
c.gridx = 1
c.gridy = 1
sp = JScrollPane(self.whitelist_text_area)
self.whitelist.add(sp, c)
buttonsPanel = JPanel(GridBagLayout())
_c = GridBagConstraints()
_c.insets = Insets(3, 3, 3, 3)
_c.gridx = 0
_c.gridy = 0
_c.fill = GridBagConstraints.BOTH
_c.weightx = 1
_c.gridwidth = 1
handlers = ButtonHandlers(self.whitelist_text_field,
self.whitelist_text_area,
self.whitelist_mouse_listener, [])
self.whitelist_add_button = JButton(
'Add', actionPerformed=handlers.handler_add)
self.whitelist_rm_button = JButton('Remove',
actionPerformed=handlers.handler_rm)
self.whitelist_clear_button = JButton(
'Clear', actionPerformed=handlers.handler_restore)
buttonsPanel.add(self.whitelist_add_button, _c)
_c.gridy = 1
buttonsPanel.add(self.whitelist_rm_button, _c)
_c.gridy = 2
buttonsPanel.add(self.whitelist_clear_button, _c)
_c.gridy = 3
c.gridx = 2
c.gridy = 1
c.fill = GridBagConstraints.NONE
self.whitelist.add(buttonsPanel, c)
self.tabs = JTabbedPane()
self.tabs.addTab('Settings', self.settings)
self.tabs.addTab('CSRF params/headers to remove',
self.csrf_headers_params)
self.tabs.addTab('Requests whitelist', self.whitelist)
callbacks.customizeUiComponent(self.tabs)
callbacks.addSuiteTab(self)
callbacks.registerProxyListener(self)
callbacks.registerContextMenuFactory(
SendToWhitelist(self.whitelist_text_area))
print "Successfully loaded %s v%s by Mikhail Egorov @0ang3el" % (
NAME, VERSION)
def generateDeconvolutionScriptUI(srcDir,
tgtDir,
calibration,
preCropAffines,
ROI,
postCropAffines):
"""
Open an UI to automatically generate a script to:
1. Register the views of each time point TM folder, and deconvolve them.
2. Register deconvolved time points to each other, for a range of consecutive time points.
Will ask for the file path to the kernel file,
and also for the range of time points to process,
and for the deconvolution iterations for CM00-CM01, and CM02-CM03.
"""
template = """
# AUTOMATICALLY GENERATED - %s
import sys, os
sys.path.append("%s")
from lib.isoview import deconvolveTimePoints
from mpicbg.models import RigidModel3D, TranslationModel3D
from net.imglib2.img.display.imagej import ImageJFunctions as IL
# The folder with the sequence of TM\d+ folders, one per time point in the 4D series.
# Each folder should contain 4 KLB files, one per camera view of the IsoView microscope.
srcDir = "%s"
# A folder to save deconvolved images in, and CSV files describing features, point matches and transformations
targetDir = "%s"
# Path to the volume describing the point spread function (PSF)
kernelPath = "%s"
calibration = [%s] # An array with 3 floats (identity--all 1.0--because the coarse affines, that is,
# the camera transformations, already include the scaling to isotropy computed using the original calibration.
# The transformations of each timepoint onto the camera at index zero.
def cameraTransformations(dims0, dims1, dims2, dims3, calibration):
return {
0: [%s],
1: [%s],
2: [%s],
3: [%s]
}
# Deconvolution parameters
paramsDeconvolution = {
"blockSizes": None, # None means the image size + kernel size. Otherwise specify like e.g. [[128, 128, 128]] for img in images]
"CM_0_1_n_iterations": %i,
"CM_2_3_n_iterations": %i,
}
# Joint dictionary of parameters
params = {}
params.update(paramsDeconvolution)
# A region of interest for each camera view, for cropping after registration but prior to deconvolution
roi = ([%s], # array of 3 integers, top-left coordinates
[%s]) # array of 3 integers, bottom-right coordinates
# All 4 cameras relative to CM00
fineTransformsPostROICrop = \
[[1, 0, 0, 0,
0, 1, 0, 0,
0, 0, 1, 0],
[%s],
[%s],
[%s]]
deconvolveTimePoints(srcDir, targetDir, kernelPath, calibration,
cameraTransformations, fineTransformsPostROICrop,
params, roi, fine_fwd=True, subrange=range(%i, %i))
"""
od = OpenDialog("Choose kernel file", srcDir)
kernel_path = od.getPath()
if not kernel_path:
JOptionPane.showMessageDialog(None, "Can't proceed without a filepath to the kernel", "Alert", JOptionPane.ERROR_MESSAGE)
return
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
msg = ["Edit parameters, then push the button",
"to generate a script that, when run,",
"will execute the deconvolution for each time point",
"saving two 3D stacks per time point as ZIP files",
"in the target directory under subfolder 'deconvolved'.",
"Find the script in a new Script Editor window.",
" "]
gc.gridy = -1 # init
for line in msg:
label = JLabel(line)
gc.anchor = GBC.WEST
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 2
gc.gridheight = 1
gb.setConstraints(label, gc)
panel.add(label)
strings = [["Deconvolution iterations",
"CM_0_1_n_iterations", "CM_2_3_n_iterations"],
["Range",
"First time point", "Last time point"]]
params = {"CM_0_1_n_iterations": 5,
"CM_2_3_n_iterations": 7,
"First time point": 0,
"Last time point": -1} # -1 means last
insertFloatFields(panel, gb, gc, params, strings)
def asString(affine):
matrix = zeros(12, 'd')
affine.toArray(matrix)
return ",".join(imap(str, matrix))
def generateScript(event):
script = template % (str(datetime.now()),
filter(lambda path: path.endswith("IsoView-GCaMP"), sys.path)[-1],
srcDir,
tgtDir,
kernel_path,
", ".join(imap(str, calibration)),
asString(preCropAffines[0]),
asString(preCropAffines[1]),
asString(preCropAffines[2]),
asString(preCropAffines[3]),
params["CM_0_1_n_iterations"],
params["CM_2_3_n_iterations"],
", ".join(imap(str, ROI[0])),
", ".join(imap(str, ROI[1])),
asString(postCropAffines[1]),
asString(postCropAffines[2]),
asString(postCropAffines[3]),
params["First time point"],
params["Last time point"])
tab = None
for frame in JFrame.getFrames():
if str(frame).startswith("org.scijava.ui.swing.script.TextEditor["):
try:
tab = frame.newTab(script, "python")
break
except:
print sys.exc_info()
if not tab:
try:
now = datetime.now()
with open(os.path.join(System.getProperty("java.io.tmpdir"),
"script-%i-%i-%i_%i:%i.py" % (now.year, now.month, now.day,
now.hour, now.minute)), 'w') as f:
f.write(script)
except:
print sys.exc_info()
print script
gen = JButton("Generate script")
gen.addActionListener(generateScript)
gc.anchor = GBC.CENTER
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 2
gb.setConstraints(gen, gc)
panel.add(gen)
frame = JFrame("Generate deconvolution script")
frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setVisible(True)
def build_gui(self):
component = JPanel(GridBagLayout())
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.gridwidth = 2
# 1st line
c.gridy = 0
c.gridx = 0
component.add(
JLabel(
'Don\'t forget to create a Session handling rule invoking this Burp extension under Project options > Sessions and to configure the tool and URL scopes.'
), c)
c.gridwidth = 1
# 2nd line
c.gridy = 1
c.gridx = 0
component.add(JLabel(' '), c)
# 3rd line
c.gridy = 2
c.gridx = 0
component.add(
JLabel(
'Name of the anti-CSRF token, can also be a substring of the name of the anti-CSRF token:'
), c)
self._csrf_name_contains_field = JTextField('csrf', 40)
c.gridx = 1
component.add(self._csrf_name_contains_field, c)
# 4th line
c.gridy = 3
c.gridx = 0
component.add(
JLabel(
'Start marker of the anti-CSRF token in the response, #csrf_name# is replaced by the name of the anti-CSRF token:'
), c)
self._csrf_start_marker_field = JTextField(
'name="' + CSRF_NAME_PLACEHOLDER + '" value="', 40)
c.gridx = 1
component.add(self._csrf_start_marker_field, c)
# 5th line
c.gridy = 4
c.gridx = 0
component.add(
JLabel(
'End marker of the anti-CSRF token in the response, #csrf_name# is replaced by the name of the anti-CSRF token:'
), c)
self._csrf_end_marker_field = JTextField('"', 40)
c.gridx = 1
component.add(self._csrf_end_marker_field, c)
# 6th line
c.gridy = 5
c.gridx = 0
component.add(JLabel(' '), c)
# 7th line
c.gridy = 6
c.gridx = 0
component.add(JLabel('HTML decode the anti-CSRF token:'), c)
self._do_html_decode = JCheckBox("", True)
c.gridx = 1
component.add(self._do_html_decode, c)
# 8th line
c.gridy = 7
c.gridx = 0
component.add(JLabel('URL decode the anti-CSRF token:'), c)
self._do_url_decode = JCheckBox("", True)
c.gridx = 1
component.add(self._do_url_decode, c)
# 9th line
c.gridy = 8
c.gridx = 0
component.add(JLabel('URL encode the anti-CSRF token:'), c)
self._do_url_encode = JCheckBox("", True)
c.gridx = 1
component.add(self._do_url_encode, c)
# 10th line
c.gridy = 9
c.gridx = 0
component.add(JLabel(' '), c)
self._callbacks.customizeUiComponent(component)
self._ui_component = component
SwingUtilities.invokeLater(
lambda: table.updateUI()) # executed by the event dispatch thread
except:
print "Malformed regex pattern"
def typingInSearchField(event):
if KeyEvent.VK_ENTER == event.getKeyCode():
filterTable()
elif KeyEvent.VK_ESCAPE == event.getKeyCode():
search_field.setText("")
filterTable() # to restore the full list of rows
# Top-left element: a text field for filtering rows by regular expression match
c.gridx = 0
c.gridy = 0
c.anchor = GridBagConstraints.CENTER
c.fill = GridBagConstraints.HORIZONTAL
search_field = JTextField("", keyPressed=typingInSearchField)
gb.setConstraints(search_field, c)
all.add(search_field)
# Bottom left element: the table, wrapped in a scrollable component
table = JTable(TableModel())
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION)
#table.setCellSelectionEnabled(True)
table.setAutoCreateRowSorter(
True) # to sort the view only, not the data in the underlying TableModel
c.gridx = 0
c.gridy = 1
def __init__(self, frame, name):
self.frame = frame
self.exception = None
self.name = name
self.searchTerm = None
self.searchIndex = -1
self.searchField = JTextField("")
self.searchField.addActionListener(SearchListener(self))
self.newGeneFrom = JTextField("")
self.newGeneTo = JTextField("")
self.newGeneButton = JButton("New Gene")
newGeneActionListener = NewGeneActionListener(self)
self.newGeneFrom.addActionListener(newGeneActionListener)
self.newGeneTo.addActionListener(newGeneActionListener)
self.newGeneButton.addActionListener(newGeneActionListener)
self.markForRemovalButton = JButton("Mark For Removal")
self.markForRemovalButton.addActionListener(MarkForRemovalListener(self))
self.inGenes = JList(DefaultListModel())
self.inGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.inGenes.cellRenderer = ProfelisCellRenderer()
self.markButtonLabelerTimer = Timer(100, MarkButtonLabeler(self))
self.markButtonLabelerTimer.start()
self.loadFile()
self.outGenes = JList(DefaultListModel())
self.outGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.outGenes.cellRenderer = ProfelisCellRenderer()
constraints = GridBagConstraints()
self.layout = GridBagLayout()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes In Artemis File"), constraints)
constraints.gridx, constraints.gridy = 0, 1
self.add(JButton(RemoveAction(self)), constraints)
constraints.gridx, constraints.gridy = 1, 1
self.add(self.markForRemovalButton, constraints)
constraints.gridx, constraints.gridy = 2, 1
self.add(JLabel("Search"), constraints)
constraints.gridx, constraints.gridy = 3, 1
constraints.fill = GridBagConstraints.HORIZONTAL
self.add(self.searchField, constraints)
constraints.gridx, constraints.gridy = 0, 2
constraints.gridwidth, constraints.gridheight = 4, 2
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.inGenes), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes To Add To Artemis File"), constraints)
constraints.gridx, constraints.gridy = 4, 1
self.add(self.newGeneButton, constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 5, 1
self.add(self.newGeneFrom, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 6, 1
self.add(JLabel("To"), constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 7, 1
self.add(self.newGeneTo, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 4, 2
self.add(JButton(AddGenesAction(self)), constraints)
constraints.gridx, constraints.gridy = 4, 3
constraints.gridwidth, constraints.gridheight = 4, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.outGenes), constraints)
# Create the UI: a 3-column table and a text area next to it
# to show the Motivation column of any selected row:
all = JPanel()
gb = GridBagLayout()
all.setLayout(gb)
c = GridBagConstraints()
table = JTable(TableModel())
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION)
table.setAutoCreateRowSorter(True) # to sort the view only, not the data in the underlying TableModel
jsp = JScrollPane(table)
jsp.setPreferredSize(Dimension(200, 500))
c.anchor = GridBagConstraints.NORTHWEST
c.fill = GridBagConstraints.BOTH # resize with the frame
gb.setConstraints(jsp, c)
all.add(jsp)
c.gridx = 1
c.weightx = 1.0 # take any additionally available horizontal space
c.weighty = 1.0
textarea = JTextArea()
textarea.setLineWrap(True)
textarea.setWrapStyleWord(True) # wrap text by cutting at whitespace
textarea.setEditable(False) # avoid changing the text, as any changes wouldn't be persisted to disk
font = textarea.getFont().deriveFont(20.0)
textarea.setFont(font)
textarea.setPreferredSize(Dimension(500, 500))
gb.setConstraints(textarea, c)
all.add(textarea)
frame = JFrame("CSV")
frame.getContentPane().add(all)
frame.pack()
frame.setVisible(True)
def registerExtenderCallbacks(self, this_callbacks): ### IBurpExtender
global callbacks, helpers
global extension_enable, in_scope_only
global change_method_to_post
callbacks = this_callbacks
helpers = callbacks.getHelpers()
callbacks.setExtensionName(NAME)
self.settings = JPanel(GridBagLayout())
c = GridBagConstraints()
self.extension_enable_box = JCheckBox('Enable extension',
extension_enable)
self.setFontBold(self.extension_enable_box)
self.extension_enable_box.setForeground(Color(0, 0, 153))
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 0
c.gridwidth = 1
c.weightx = 1
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.WEST
self.settings.add(self.extension_enable_box, c)
self.in_scope_only_box = JCheckBox('Modify only in-scope requests',
in_scope_only)
self.setFontBold(self.in_scope_only_box)
self.in_scope_only_box.setForeground(Color(0, 0, 153))
c.insets = Insets(40, 5, 5, 5)
c.gridx = 0
c.gridy = 1
self.settings.add(self.in_scope_only_box, c)
self.change_method_to_post_box = JCheckBox(
'Change HTTP method to POST', change_method_to_post)
self.setFontBold(self.change_method_to_post_box)
self.change_method_to_post_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 6
self.settings.add(self.change_method_to_post_box, c)
change_method_to_post_lbl = JLabel(
'Check to convert PUT/DELETE/PATCH method to POST in all requests.'
)
self.setFontItalic(change_method_to_post_lbl)
c.gridx = 0
c.gridy = 7
self.settings.add(change_method_to_post_lbl, c)
self.change_to_get_box = JCheckBox('Change to GET', change_to_get)
self.setFontBold(self.change_to_get_box)
self.change_to_get_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 12
self.settings.add(self.change_to_get_box, c)
change_to_get_lbl = JLabel(
'Check to convert POST/PUT/DELETE/PATCH url-encoded requests to GET.'
)
self.setFontItalic(change_to_get_lbl)
c.gridx = 0
c.gridy = 13
self.settings.add(change_to_get_lbl, c)
self.tabs = JTabbedPane()
self.tabs.addTab('Settings', self.settings)
callbacks.customizeUiComponent(self.tabs)
callbacks.addSuiteTab(self)
callbacks.registerProxyListener(self)
print "Successfully loaded %s v%s by Mohammed alsaggaf " % (NAME,
VERSION)
def create(self):
# Estilo general para todas las sub-tab.
gBC = GridBagConstraints()
gBC.fill = GridBagConstraints.BOTH
gBC.ipadx = 5
gBC.ipady = 5
gBC.insets = Insets(0, 5, 5, 5)
gBC.weightx = 0.5
#gBC.weighty = 0.7
#######################################
### Creamos la primera sub-tab. (MASHUP)
#######################################
tab_1 = JPanel(GridBagLayout())
tab_1_jlabelAyuda = JLabel(
'<html><i>•Tip: This Mashup receive one or more keywords in order to generate a list of possible passwords</i></html>'
)
tab_1_jlabelAyuda.setFont(Font("Serif", 0, 12))
gBC.gridx = 0
gBC.gridy = 0
tab_1.add(
JLabel('<html><font color=green><i>Income:</i></font></html>'),
gBC)
gBC.gridy = 1
tab_1.add(JLabel('<html><b>• Name:</b></html>'), gBC)
gBC.gridy = 2
tab_1.add(self._tab1_nombre, gBC)
gBC.gridy = 3
tab_1.add(JLabel('<html><b>• Surname:</b></html>'), gBC)
gBC.gridy = 4
tab_1.add(self._tab1_apellido, gBC)
gBC.gridy = 5
tab_1.add(JLabel('<html><b>• Birthdate: (DDMMYYYY)</b></html>'),
gBC)
gBC.gridy = 6
tab_1.add(self._tab1_FNacimiento, gBC)
gBC.gridy = 7
tab_1.add(JLabel('<html><b>• Pet:</b></html>'), gBC)
gBC.gridy = 8
tab_1.add(self._tab1_mascota, gBC)
gBC.gridy = 9
tab_1.add(JLabel('<html><b>• Anyother:</b></html>'), gBC)
gBC.gridy = 10
tab_1.add(self._tab1_otro, gBC)
gBC.gridy = 11
tab_1.add(JLabel('<html><b>• Passwd Min Size:</b></html>'), gBC)
gBC.gridy = 12
tab_1.add(self._tab1_minsize, gBC)
gBC.gridy = 13
tab_1.add(JLabel('<html><b>• Passwd Max Size:</b></html>'), gBC)
gBC.gridy = 14
tab_1.add(self._tab1_maxsize, gBC)
gBC.gridy = 15
tab_1.add(
JLabel(
'<html><b>• Especial Chars: (comma separated)</b></html>'
), gBC)
gBC.gridy = 16
tab_1.add(self._tab1_specialchars, gBC)
gBC.gridy = 17
tab_1.add(self._tab1_transformations, gBC)
gBC.gridy = 18
tab_1.add(self._tab1_firstcapital, gBC)
gBC.gridy = 19
tab_1.add(JButton('Mashup!', actionPerformed=self.mashup), gBC)
gBC.gridy = 20
gBC.gridwidth = 3
tab_1.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.gridy = 21
gBC.gridwidth = 3
tab_1.add(tab_1_jlabelAyuda, gBC)
gBC.gridwidth = 1
gBC.gridx = 1
gBC.gridy = 0
gBC.gridheight = 20
gBC.weightx = 0
tab_1.add(JSeparator(SwingConstants.VERTICAL), gBC)
gBC.gridheight = 1
gBC.weightx = 0.5
gBC.gridx = 2
gBC.gridy = 0
tab_1.add(
JLabel('<html><font color=green><i>Outcome:</i></font></html>'),
gBC)
gBC.gridy = 1
gBC.gridwidth = 2
gBC.gridheight = 18
tab_1.add(self._tab1_feedback_sp, gBC)
gBC.gridwidth = 1
gBC.gridheight = 1
gBC.gridy = 19
tab_1.add(
JButton('Copy to clipboard!', actionPerformed=self.cpy_clipboard),
gBC)
#######################################
### Creamos la segunda sub-tab. (REDIRECT)
#######################################
tab_2 = JPanel(GridBagLayout())
tab_2_jlabelAyuda = JLabel(
'<html><i>•Tip: This Redirect receive a pair of hosts x,y in order to redirect from x to y.</i></html>'
)
tab_2_jlabelAyuda.setFont(Font("Serif", 0, 12))
gBC.gridx = 0
gBC.gridy = 0
tab_2.add(
JLabel('<html><b>• From: (i.e. www.facebook.com)</b></html>'),
gBC)
gBC.gridx = 1
gBC.gridy = 0
tab_2.add(self._tab2_JTFa, gBC)
gBC.gridx = 2
gBC.gridy = 0
tab_2.add(
JLabel('<html><b>• To: (i.e. www.myhomepage.es)</b></html>'),
gBC)
gBC.gridx = 3
gBC.gridy = 0
tab_2.add(self._tab2_JTFaa, gBC)
gBC.gridx = 0
gBC.gridy = 1
gBC.gridwidth = 4
tab_2.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.gridx = 0
gBC.gridy = 2
tab_2.add(JLabel('<html><b>• From:</b></html>'), gBC)
gBC.gridx = 1
gBC.gridy = 2
tab_2.add(self._tab2_JTFb, gBC)
gBC.gridx = 2
gBC.gridy = 2
tab_2.add(JLabel('<html><b>• To:</b></html>'), gBC)
gBC.gridx = 3
gBC.gridy = 2
tab_2.add(self._tab2_JTFbb, gBC)
gBC.gridx = 0
gBC.gridy = 3
gBC.gridwidth = 4
tab_2.add(self._tab2_boton, gBC)
gBC.gridwidth = 1
gBC.gridx = 0
gBC.gridy = 4
gBC.gridwidth = 4
gBC.insets = Insets(100, 10, 5, 10)
tab_2.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.insets = Insets(5, 10, 5, 10)
gBC.gridx = 0
gBC.gridy = 5
gBC.gridwidth = 4
tab_2.add(tab_2_jlabelAyuda, gBC)
gBC.gridwidth = 1
#######################################
### Creamos la tercera sub-tab. (LOADER)
#######################################
tab_3 = JPanel(GridBagLayout())
tab_3_jlabelAyuda = JLabel(
'<html><i>•Tip: This Loader receive a list of Hosts or IPs that will be added to the Burp Scope.</i></html>'
)
tab_3_jlabelAyuda.setFont(Font("Serif", 0, 12))
gBC.gridx = 0
gBC.gridy = 0
tab_3.add(
JLabel(
'<html><font color=green><i>List of targets: (i.e. http://www.mytargetweb.com)</i></font></html>'
), gBC)
gBC.gridy = 1
gBC.gridheight = 10
gBC.weighty = 0.5
tab_3.add(self._tab3_urls_sp, gBC)
gBC.gridheight = 1
gBC.weighty = 0
gBC.gridy = 11
tab_3.add(
JButton('Load Into Target => Scope!', actionPerformed=self.loader),
gBC)
gBC.gridy = 12
gBC.gridwidth = 5
gBC.insets = Insets(100, 10, 5, 10)
tab_3.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.insets = Insets(5, 10, 5, 10)
gBC.gridy = 13
tab_3.add(tab_3_jlabelAyuda, gBC)
#######################################
### Creamos la cuarta sub-tab. (HEADERS)
#######################################
tab_4_jlabelAyuda = JLabel(
"<html><i>•Tip: This Headers records all unique headers that appear in every host, check out the security headers.</i></html>"
)
tab_4_jlabelAyuda.setFont(Font("Serif", 0, 12))
tab_4_jLabelRecomendacion = JLabel(
"<html>•<b>Server</b>: Don't give away much information.<br> •<b>Content-Security-Policy</b>: Protect your site from XSS attacks by whitelisting sources of approved content.<br> •<b>Strict-Transport-Security</b>: Enforce the browser to use HTTPS.<br> •<b>Public-Key-Pins</b>: Protect your site from MITM attacks.<br> •<b>X-Content-Type-Options</b>: the valid value is -> nosniff .<br> •<b>X-Frame-Options</b>: tells the browser whether you want to allow your site to be framed or not.<br> •<b>X-XSS-Protection</b>: the best value is -> 1; mode=block .</html>"
)
tab_4_jLabelRecomendacion.setFont(Font("Dialog", 0, 13))
tab_4 = JPanel(GridBagLayout())
splitpane = JSplitPane(JSplitPane.VERTICAL_SPLIT)
tab_4_top = JPanel(GridBagLayout())
tab_4_bottom = JPanel(GridBagLayout())
gBC_table = GridBagConstraints()
gBC_table.fill = GridBagConstraints.BOTH
gBC_table.ipadx = 5
gBC_table.ipady = 5
gBC_table.insets = Insets(5, 10, 5, 10)
gBC_table.weightx = 1
gBC_table.weighty = 1
tabla_datos = []
tabla_headers = ('Severity', 'Header', 'Value', 'Host')
self._tab4_tabla_model = DefaultTableModel(tabla_datos, tabla_headers)
tabla_ej = JTable(self._tab4_tabla_model)
tabla_example = JScrollPane(tabla_ej,
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED)
gBC_table.gridx = 0
gBC_table.gridy = 0
gBC_table.gridheight = 5
tab_4_top.add(tabla_example, gBC_table)
gBC_table.gridheight = 1
gBC_table.weightx = 0.5
gBC_table.weighty = 0
gBC_table.gridwidth = 2
gBC_table.gridx = 0
gBC_table.gridy = 0
tab_4_bottom.add(JSeparator(), gBC_table)
gBC_table.gridy = 1
tab_4_bottom.add(tab_4_jlabelAyuda, gBC_table)
gBC_table.gridy = 2
tab_4_bottom.add(tab_4_jLabelRecomendacion, gBC_table)
splitpane.setTopComponent(tab_4_top)
splitpane.setBottomComponent(tab_4_bottom)
gBC_table.weightx = 1
gBC_table.weighty = 1
gBC_table.gridx = 0
gBC_table.gridy = 0
tab_4.add(splitpane, gBC_table)
#######################################
### Creamos la quinta sub-tab. (ACTIVE SCAN)
#######################################
tab_5 = JPanel(GridBagLayout())
tab_5_jlabelAyuda = JLabel(
'<html><i>•Tip: This Quick Scan receive a list of targets and launch an active scan.</i></html>'
)
tab_5_jlabelAyuda.setFont(Font("Serif", 0, 12))
tab_5_jlabelWarning = JLabel(
'<html><font color=red><i>•Warning: Active scanning generates large numbers of requests which are malicious in form and which may result in compromise of the application. You should use this scanning mode with caution, only with the explicit permission of the application owner. For more information, read the documentation of active scan, Burp Suite.</font></i></html>'
)
tab_5_jlabelWarning.setFont(Font("Dialog", 0, 13))
gBC.gridx = 0
gBC.gridy = 0
tab_5.add(
JLabel(
'<html><font color=green><i>List of targets: (i.e. http://192.168.1.1/index.html)</i></font></html>'
), gBC)
gBC.gridy = 1
gBC.gridheight = 8
gBC.weighty = 0.5
tab_5.add(self._tab5_target_sp, gBC)
gBC.gridheight = 1
gBC.weighty = 0
gBC.gridy = 9
tab_5.add(JButton('Launch Scan!', actionPerformed=self.do_active_scan),
gBC)
gBC.gridy = 10
gBC.gridwidth = 5
gBC.insets = Insets(100, 10, 5, 10)
tab_5.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.insets = Insets(5, 10, 5, 10)
gBC.gridy = 11
tab_5.add(tab_5_jlabelAyuda, gBC)
gBC.gridy = 12
tab_5.add(tab_5_jlabelWarning, gBC)
#######################################
### Creamos la ultima sub-tab.
#######################################
tab_about = JPanel(GridBagLayout())
gBC_about = GridBagConstraints()
gBC_about.fill = GridBagConstraints.HORIZONTAL
gBC_about.ipadx = 5
gBC_about.ipady = 5
gBC_about.insets = Insets(5, 10, 5, 10)
gBC_about.weightx = 1
gBC_about.weighty = 1
Jlabel1 = JLabel('<html><b>Plug-in L-Tools</b></html>')
Jlabel1.setFont(Font("Dialog", 1, 18))
jlabel2 = JLabel(
'<html>This Plug-in provides utilities for pentesters, researchers and developers, in order to support their work.</html>'
)
jlabel3 = JLabel('<html><b>CC-BY 4.0, 2017. Gino Angles</b></html>')
jlabel3.setFont(Font("Dialog", 1, 14))
jlabel4 = JLabel('<html><b>License</b></html>')
jlabel4.setFont(Font("Dialog", 1, 14))
jlabel5 = JLabel(
'<html><img alt="Licensed under a Creative Commons BY" style="border-width:0" src="https://licensebuttons.net/l/by/4.0/88x31.png"></html>'
)
jlabel6 = JLabel(
'<html>This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</html>'
)
jlabel7 = JLabel('<html><b>Dependencies</b></html>')
jlabel7.setFont(Font("Dialog", 1, 14))
jlabel8 = JLabel('Jython +2.7')
jlabel9 = JLabel('http://www.jython.org')
gBC_about.gridx = 0
gBC_about.gridy = 0
tab_about.add(Jlabel1, gBC_about)
gBC_about.gridy = 1
tab_about.add(jlabel2, gBC_about)
gBC_about.gridy = 2
tab_about.add(jlabel3, gBC_about)
gBC_about.gridy = 3
gBC_about.gridwidth = 5
tab_about.add(JSeparator(), gBC_about)
gBC_about.gridwidth = 1
gBC_about.gridy = 4
tab_about.add(jlabel4, gBC_about)
gBC_about.gridy = 5
tab_about.add(jlabel5, gBC_about)
gBC_about.gridy = 6
tab_about.add(jlabel6, gBC_about)
gBC_about.gridy = 7
gBC_about.gridwidth = 5
tab_about.add(JSeparator(), gBC_about)
gBC_about.gridwidth = 1
gBC_about.gridy = 8
tab_about.add(jlabel7, gBC_about)
gBC_about.gridy = 9
tab_about.add(jlabel8, gBC_about)
gBC_about.gridy = 10
tab_about.add(jlabel9, gBC_about)
# Añadimos los sub-tab al contenedor y lo devolvemos.
self.contenedor.addTab('Mashup', tab_1)
self.contenedor.addTab('Redirect', tab_2)
self.contenedor.addTab('Loader', tab_3)
self.contenedor.addTab('Headers', tab_4)
self.contenedor.addTab('Quick Scan', tab_5)
self.contenedor.addTab('About', tab_about)
return self.contenedor
def specifyRoiUI(roi=Roi(0, 0, 0, 0)):
# A panel in which to place UI elements
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
bounds = roi.getBounds() if roi else Rectangle()
textfields = []
roimakers = []
# Basic properties of most UI elements, will edit when needed
gc.gridx = 0 # can be any natural number
gc.gridy = 0 # idem.
gc.gridwidth = 1 # when e.g. 2, the UI element will occupy two horizontally adjacent grid cells
gc.gridheight = 1 # same but vertically
gc.fill = GBC.NONE # can also be BOTH, VERTICAL and HORIZONTAL
for title in ["x", "y", "width", "height"]:
# label
gc.gridx = 0
gc.anchor = GBC.EAST
label = JLabel(title + ": ")
gb.setConstraints(label, gc) # copies the given constraints 'gc',
# so we can modify and reuse gc later.
panel.add(label)
# text field, below the title
gc.gridx = 1
gc.anchor = GBC.WEST
text = str(getattr(bounds,
title)) # same as e.g. bounds.x, bounds.width, ...
textfield = JTextField(text,
10) # 10 is the size of the field, in digits
gb.setConstraints(textfield, gc)
panel.add(textfield)
textfields.append(
textfield) # collect all 4 created textfields for the listeners
# setup ROI and text field listeners
listener = RoiMaker(textfields,
len(textfields) -
1) # second argument is the index of textfield
# in the list of textfields.
roimakers.append(listener)
textfield.addKeyListener(listener)
textfield.addMouseWheelListener(listener)
# Position next ROI property in a new row by increasing the Y coordinate of the layout grid
gc.gridy += 1
# User documentation (uses HTML to define line breaks)
doc = JLabel(
"<html><body><br />Click on a field to activate it, then:<br />" +
"Type in integer numbers<br />" +
"or use arrow keys to increase by 1<br />" +
"or use the scroll wheel on a field.</body></html>")
gc.gridx = 0 # start at the first column
gc.gridwidth = 2 # Spans both columns
gb.setConstraints(doc, gc)
panel.add(doc)
# Listen to changes in the ROI of imp
roilistener = TextFieldUpdater(textfields)
Roi.addRoiListener(roilistener)
# Show window
frame = JFrame("Specify rectangular ROI")
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setDefaultCloseOperation(
JFrame.DO_NOTHING_ON_CLOSE) # prevent closing the window
frame.addWindowListener(
CloseControl(roilistener)) # handles closing the window
frame.setVisible(True)
def _constructAttackPanel(self, insets, messageEditorComponent):
attackPanel = JPanel(GridBagLayout())
targetHeadingLabel = JLabel("<html><b>Target</b></html>")
targetHeadingLabelConstraints = GridBagConstraints()
targetHeadingLabelConstraints.gridx = 0
targetHeadingLabelConstraints.gridy = 0
targetHeadingLabelConstraints.gridwidth = 4
targetHeadingLabelConstraints.anchor = GridBagConstraints.LINE_START
targetHeadingLabelConstraints.insets = insets
attackPanel.add(targetHeadingLabel, targetHeadingLabelConstraints)
startAttackButton = JButton("<html><b>Start Attack</b></html>",
actionPerformed=self._startAttack)
startAttackButtonConstraints = GridBagConstraints()
startAttackButtonConstraints.gridx = 4
startAttackButtonConstraints.gridy = 0
startAttackButtonConstraints.insets = insets
attackPanel.add(startAttackButton, startAttackButtonConstraints)
hostLabel = JLabel("Host:")
hostLabelConstraints = GridBagConstraints()
hostLabelConstraints.gridx = 0
hostLabelConstraints.gridy = 1
hostLabelConstraints.anchor = GridBagConstraints.LINE_START
hostLabelConstraints.insets = insets
attackPanel.add(hostLabel, hostLabelConstraints)
self._hostTextField = JTextField(25)
self._hostTextField.setMinimumSize(
self._hostTextField.getPreferredSize())
hostTextFieldConstraints = GridBagConstraints()
hostTextFieldConstraints.gridx = 1
hostTextFieldConstraints.gridy = 1
hostTextFieldConstraints.weightx = 1
hostTextFieldConstraints.gridwidth = 2
hostTextFieldConstraints.anchor = GridBagConstraints.LINE_START
hostTextFieldConstraints.insets = insets
attackPanel.add(self._hostTextField, hostTextFieldConstraints)
portLabel = JLabel("Port:")
portLabelConstraints = GridBagConstraints()
portLabelConstraints.gridx = 0
portLabelConstraints.gridy = 2
portLabelConstraints.anchor = GridBagConstraints.LINE_START
portLabelConstraints.insets = insets
attackPanel.add(portLabel, portLabelConstraints)
self._portTextField = JTextField(5)
self._portTextField.setMinimumSize(
self._portTextField.getPreferredSize())
portTextFieldConstraints = GridBagConstraints()
portTextFieldConstraints.gridx = 1
portTextFieldConstraints.gridy = 2
portTextFieldConstraints.gridwidth = 2
portTextFieldConstraints.anchor = GridBagConstraints.LINE_START
portTextFieldConstraints.insets = insets
attackPanel.add(self._portTextField, portTextFieldConstraints)
self._protocolCheckBox = JCheckBox("Use HTTPS")
protocolCheckBoxConstraints = GridBagConstraints()
protocolCheckBoxConstraints.gridx = 0
protocolCheckBoxConstraints.gridy = 3
protocolCheckBoxConstraints.gridwidth = 3
protocolCheckBoxConstraints.anchor = GridBagConstraints.LINE_START
protocolCheckBoxConstraints.insets = insets
attackPanel.add(self._protocolCheckBox, protocolCheckBoxConstraints)
requestHeadingLabel = JLabel("<html><b>Request</b></html>")
requestHeadingLabelConstraints = GridBagConstraints()
requestHeadingLabelConstraints.gridx = 0
requestHeadingLabelConstraints.gridy = 4
requestHeadingLabelConstraints.gridwidth = 4
requestHeadingLabelConstraints.anchor = GridBagConstraints.LINE_START
requestHeadingLabelConstraints.insets = insets
attackPanel.add(requestHeadingLabel, requestHeadingLabelConstraints)
messageEditorComponentConstraints = GridBagConstraints()
messageEditorComponentConstraints.gridx = 0
messageEditorComponentConstraints.gridy = 5
messageEditorComponentConstraints.weightx = 1
messageEditorComponentConstraints.weighty = .75
messageEditorComponentConstraints.gridwidth = 4
messageEditorComponentConstraints.gridheight = 2
messageEditorComponentConstraints.fill = GridBagConstraints.BOTH
messageEditorComponentConstraints.insets = insets
attackPanel.add(
messageEditorComponent, messageEditorComponentConstraints)
addPayloadButton = JButton(
"Add \xa7", actionPerformed=self._addPayload)
addPayloadButtonConstraints = GridBagConstraints()
addPayloadButtonConstraints.gridx = 4
addPayloadButtonConstraints.gridy = 5
addPayloadButtonConstraints.fill = GridBagConstraints.HORIZONTAL
addPayloadButtonConstraints.insets = insets
attackPanel.add(addPayloadButton, addPayloadButtonConstraints)
clearPayloadButton = JButton(
"Clear \xa7", actionPerformed=self._clearPayloads)
clearPayloadButtonConstraints = GridBagConstraints()
clearPayloadButtonConstraints.gridx = 4
clearPayloadButtonConstraints.gridy = 6
clearPayloadButtonConstraints.anchor = GridBagConstraints.PAGE_START
clearPayloadButtonConstraints.fill = GridBagConstraints.HORIZONTAL
clearPayloadButtonConstraints.insets = insets
attackPanel.add(clearPayloadButton, clearPayloadButtonConstraints)
payloadHeadingLabel = JLabel("<html><b>Payloads<b></html>")
payloadHeadingLabelConstraints = GridBagConstraints()
payloadHeadingLabelConstraints.gridx = 0
payloadHeadingLabelConstraints.gridy = 7
payloadHeadingLabelConstraints.gridwidth = 4
payloadHeadingLabelConstraints.anchor = GridBagConstraints.LINE_START
payloadHeadingLabelConstraints.insets = insets
attackPanel.add(payloadHeadingLabel, payloadHeadingLabelConstraints)
self._payloadTextArea = JTextArea()
payloadScrollPane = JScrollPane(self._payloadTextArea)
payloadScrollPaneConstraints = GridBagConstraints()
payloadScrollPaneConstraints.gridx = 0
payloadScrollPaneConstraints.gridy = 8
payloadScrollPaneConstraints.weighty = .25
payloadScrollPaneConstraints.gridwidth = 3
payloadScrollPaneConstraints.fill = GridBagConstraints.BOTH
payloadScrollPaneConstraints.insets = insets
attackPanel.add(payloadScrollPane, payloadScrollPaneConstraints)
requestsNumLabel = JLabel("Number of requests for each payload:")
requestsNumLabelConstraints = GridBagConstraints()
requestsNumLabelConstraints.gridx = 0
requestsNumLabelConstraints.gridy = 9
requestsNumLabelConstraints.gridwidth = 2
requestsNumLabelConstraints.anchor = GridBagConstraints.LINE_START
requestsNumLabelConstraints.insets = insets
attackPanel.add(requestsNumLabel, requestsNumLabelConstraints)
self._requestsNumTextField = JTextField("100", 4)
self._requestsNumTextField.setMinimumSize(
self._requestsNumTextField.getPreferredSize())
requestsNumTextFieldConstraints = GridBagConstraints()
requestsNumTextFieldConstraints.gridx = 2
requestsNumTextFieldConstraints.gridy = 9
requestsNumTextFieldConstraints.anchor = GridBagConstraints.LINE_START
requestsNumTextFieldConstraints.insets = insets
attackPanel.add(
self._requestsNumTextField, requestsNumTextFieldConstraints)
return attackPanel
def addSigningKeyFromCmdTextField(self):
c = GridBagConstraints()
c.gridx = 1
c.gridy = 6
self._configurationPanel.add(self._fromCmdTextField, c)
def initComponents(self):
self.setLayout(GridBagLayout())
gc = GridBagConstraints()
gc.weightx = 1
gc.weighty = 1
# First Row
gc.gridy = 0
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.fill = GridBagConstraints.NONE
gc.anchor = GridBagConstraints.LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.nameLabel, gc)
gc.gridx = 1
gc.anchor = GridBagConstraints.LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.nameField, gc)
# Second Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.anchor = GridBagConstraints.LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.mobLabel, gc)
gc.gridx = 1
gc.anchor = GridBagConstraints.LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.mobField, gc)
#Third Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.anchor = GridBagConstraints.FIRST_LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.emailLabel, gc)
gc.weightx = 1
gc.weighty = 0.2
gc.gridx = 1
gc.anchor = GridBagConstraints.FIRST_LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.emailField, gc)
#Next Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 0.1
gc.gridx = 0
gc.anchor = GridBagConstraints.FIRST_LINE_END
gc.insets = Insets(0, 0, 0, 5)
self.add(self.vehicleLabel, gc)
gc.weightx = 1
gc.weighty = 0.2
gc.gridx = 1
gc.anchor = GridBagConstraints.FIRST_LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.vehicleField, gc)
gc.weightx = 1
gc.weighty = 0.2
gc.gridx = 2
gc.anchor = GridBagConstraints.FIRST_LINE_START
gc.insets = Insets(0, 0, 0, 0)
self.add(self.automateRecogBtn, gc)
#Next Row
gc.gridy += 1
gc.weightx = 1
gc.weighty = 2.0
gc.gridx = 1
gc.anchor = GridBagConstraints.FIRST_LINE_START
self.add(self.regBtn, gc)
innerBorder = BorderFactory.createTitledBorder('Register Vehicle')
outerBorder = BorderFactory.createEmptyBorder(5, 5, 5, 5)
self.setBorder(
BorderFactory.createCompoundBorder(outerBorder, innerBorder))
def build_welcome_panel(self):
'''
Construct the welcome panel here.
'''
panel = JPanel(GridBagLayout())
constraints = GridBagConstraints()
constraints.insets = Insets(10, 10, 10, 10)
message = ('<html><body>'
'<h1>Welcome to Nammu</h1>'
'<h2>An editor for the ORACC project<h2>'
'<p>'
'<a href=\'oracc\'>Click here</a> for help with ORACC.'
'</p>'
'<p>Learn more about Nammu <a href=\'nammu\'>here</a>.</p>'
'</body></html>')
# Configure a JEditorPane to display HTML for our welcome message
msg_pane = JEditorPane()
msg_pane.setEditable(False)
kit = HTMLEditorKit()
msg_pane.setEditorKit(kit)
scrollPane = JScrollPane(msg_pane)
# This handles the stylesheet applied to the welcome message
styleSheet = kit.getStyleSheet()
styleSheet.addRule('body {color:black; font-size: 16 pt; }')
styleSheet.addRule('h1 {text-align:center; }')
styleSheet.addRule('h2 {text-align:center; }')
# Set the JEditorPane background to match the rest of the window
msg_pane.border = BorderFactory.createEmptyBorder(4, 4, 4, 4)
msg_pane.background = Color(238, 238, 238)
# Add the message and the css and to the JEditorPane
doc = kit.createDefaultDocument()
msg_pane.setDocument(doc)
msg_pane.setText(message)
# Set up a hyperlink listener
listener = addEventListener(msg_pane, HyperlinkListener,
'hyperlinkUpdate', self.handleEvent)
# Configure the placement of the JEditorPane
constraints.gridx = 1
constraints.gridy = 1
constraints.fill = GridBagConstraints.BOTH
constraints.anchor = GridBagConstraints.CENTER
panel.add(msg_pane, constraints)
# Build and place the checkbox
self.checkbox = JCheckBox('Don\'t show this message again.',
selected=False)
constraints.gridx = 1
constraints.gridy = 2
panel.add(self.checkbox, constraints)
# Build and place the close button
close_button = JButton('Close', actionPerformed=self.close_action)
constraints.gridx = 2
constraints.gridy = 2
panel.add(close_button, constraints)
return panel
def registerExtenderCallbacks(self, callbacks):
# Initialize the global stdout stream
global stdout
# Keep a reference to our callbacks object
self._callbacks = callbacks
# Obtain an extension helpers object
self._helpers = callbacks.getHelpers()
# set our extension name
callbacks.setExtensionName("Burpsuite Yara Scanner")
# Create the log and a lock on which to synchronize when adding log entries
self._log = ArrayList()
self._lock = Lock()
# main split pane
splitpane = JSplitPane(JSplitPane.VERTICAL_SPLIT)
# table of log entries
logTable = Table(self)
scrollPane = JScrollPane(logTable)
splitpane.setLeftComponent(scrollPane)
# Options panel
optionsPanel = JPanel()
optionsPanel.setLayout(GridBagLayout())
constraints = GridBagConstraints()
yara_exe_label = JLabel("Yara Executable Location:")
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 0
constraints.gridy = 0
optionsPanel.add(yara_exe_label, constraints)
self._yara_exe_txtField = JTextField(25)
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 1
constraints.gridy = 0
optionsPanel.add(self._yara_exe_txtField, constraints)
yara_rules_label = JLabel("Yara Rules File:")
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 0
constraints.gridy = 1
optionsPanel.add(yara_rules_label, constraints)
self._yara_rules_files = Vector()
self._yara_rules_files.add("< None >")
self._yara_rules_fileList = JList(self._yara_rules_files)
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 1
constraints.gridy = 1
optionsPanel.add(self._yara_rules_fileList, constraints)
self._yara_rules_select_files_button = JButton("Select Files")
self._yara_rules_select_files_button.addActionListener(self)
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 1
constraints.gridy = 2
optionsPanel.add(self._yara_rules_select_files_button, constraints)
self._yara_clear_button = JButton("Clear Yara Results Table")
self._yara_clear_button.addActionListener(self)
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.gridx = 1
constraints.gridy = 3
optionsPanel.add(self._yara_clear_button, constraints)
# Tabs with request/response viewers
viewerTabs = JTabbedPane()
self._requestViewer = callbacks.createMessageEditor(self, False)
self._responseViewer = callbacks.createMessageEditor(self, False)
viewerTabs.addTab("Request", self._requestViewer.getComponent())
viewerTabs.addTab("Response", self._responseViewer.getComponent())
splitpane.setRightComponent(viewerTabs)
# Tabs for the Yara output and the Options
self._mainTabs = JTabbedPane()
self._mainTabs.addTab("Yara Output", splitpane)
self._mainTabs.addTab("Options", optionsPanel)
# customize our UI components
callbacks.customizeUiComponent(splitpane)
callbacks.customizeUiComponent(logTable)
callbacks.customizeUiComponent(scrollPane)
callbacks.customizeUiComponent(viewerTabs)
callbacks.customizeUiComponent(self._mainTabs)
# add the custom tab to Burp's UI
callbacks.addSuiteTab(self)
# add ourselves as a context menu factory
callbacks.registerContextMenuFactory(self)
# Custom Menu Item
self.menuItem = JMenuItem("Scan with Yara")
self.menuItem.addActionListener(self)
# obtain our output stream
stdout = PrintWriter(callbacks.getStdout(), True)
# Print a startup notification
stdout.println("Burpsuite Yara scanner initialized.")
def getUiComponent(self):
#
# Button functions
#
# Apply regex and preview
def regexify(event):
withSect = re.sub(regexBox.getText(), lambda m: unichr(167) + m.group(0) + unichr(167), contentBox.getText(), flags = re.M)
resultsBox.setText(withSect)
resultsBox.requestFocusInWindow()
return
# Actually send to Intruder
def sendToIntruder(event):
# TODO Parse host, port, and SSL
offsets = ArrayList()
p = re.compile(regexBox.getText())
for m in p.finditer(contentBox.getText()):
offsets.add(array((m.start(), m.end()), 'i'))
self._callbacks.sendToIntruder("www.example.com", 80, False, contentBox.getText(), offsets)
return
# HTML body box
body = """POST /example?p1=p1val&p2=p2val HTTP/1.0
Cookie: c=cval
Content-Length: 17
p3=p3val&p4=p4val&asdf=1234&qwer=123
<b>test</b>
<xml body:something tag='asdf'>
</xml>
§"""
# HTTP request box
contentBox = JTextArea(body, 10, 80)
contentBoxScroll = JScrollPane(contentBox)
# Regex box
regexBox = JTextField("[0-9]{3}", 40)
# Buttons
btnRegexify = JButton("Regexify", actionPerformed=regexify)
btnSendToIntruder = JButton("Send to Intruder", actionPerformed=sendToIntruder)
# Results box
resultsBox = JTextArea("Results will be shown here", 10, 80)
resultsBoxScroll = JScrollPane(resultsBox)
# Main panel
mainPanel = JPanel(GridBagLayout())
gbc = GridBagConstraints()
gbc.gridx = 0
gbc.gridy = 0
gbc.weightx = 0.8
contentBoxScroll.setPreferredSize(Dimension(1000, 300))
mainPanel.add(contentBoxScroll, gbc)
gbc.gridx = 1
gbc.gridy = 0
gbc.weightx = 0.1
mainPanel.add(regexBox, gbc)
gbc.gridx = 1
gbc.gridy = 1
gbc.weightx = 0.1
mainPanel.add(btnRegexify, gbc)
gbc.gridx = 1
gbc.gridy = 3
gbc.weightx = 0.1
mainPanel.add(btnSendToIntruder, gbc)
gbc.gridx = 0
gbc.gridy = 2
gbc.weightx = 1
gbc.weighty = 1
resultsBoxScroll.setPreferredSize(Dimension(1000, 300))
mainPanel.add(resultsBoxScroll, gbc)
return mainPanel
def registerExtenderCallbacks( self, callbacks):
self._helpers = callbacks.getHelpers()
callbacks.setExtensionName("JWT FuzzHelper")
callbacks.registerIntruderPayloadProcessor(self)
callbacks.registerExtensionStateListener(self)
self._stdout = PrintWriter(callbacks.getStdout(), True)
self._stderr = PrintWriter(callbacks.getStderr(), True)
# Holds values passed by user from Configuration panel
self._fuzzoptions = {
"target" : "Header",
"selector" : None,
"signature" : False,
"algorithm" : "HS256",
"key" : "",
"key_cmd" : ""
}
self._isNone = lambda val: isinstance(val, type(None))
# Configuration panel Layout
self._configurationPanel = JPanel()
gridBagLayout = GridBagLayout()
gridBagLayout.columnWidths = [ 0, 0, 0]
gridBagLayout.rowHeights = [ 10, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
gridBagLayout.columnWeights = [ 0.0, 0.0, 0.0 ]
gridBagLayout.rowWeights = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0]
self._configurationPanel.setLayout(gridBagLayout)
# Setup tabs
self._tabs = JTabbedPane()
self._tabs.addTab('Configuration',self._configurationPanel)
#self._tabs.addTab('Help',self._helpPanel)
# Target Options
targetLabel = JLabel("Target Selection (Required): ")
targetLabel.setFont(Font("Tahoma",Font.BOLD, 12))
c = GridBagConstraints()
c.gridx = 0
c.gridy = 1
c.insets = Insets(0,10,0,0)
c.anchor = GridBagConstraints.LINE_END
self._configurationPanel.add(targetLabel,c)
options = [ 'Header', 'Payload' ]
self._targetComboBox = JComboBox(options)
c = GridBagConstraints()
c.gridx = 1
c.gridy = 1
c.anchor = GridBagConstraints.LINE_START
self._configurationPanel.add(self._targetComboBox,c)
# Help Button
self._helpButton = JButton("Help", actionPerformed=self.helpMenu)
c = GridBagConstraints()
c.gridx = 2
c.gridy = 1
c.anchor = GridBagConstraints.FIRST_LINE_START
self._configurationPanel.add(self._helpButton,c)
# Selector Options
self._selectorLabel = JLabel("JSON Selector [Object Identifier-Index Syntax] (Required): ")
self._selectorLabel.setFont(Font("Tahoma",Font.BOLD, 12))
c = GridBagConstraints()
c.gridx = 0
c.gridy = 2
c.insets = Insets(0,10,0,0)
c.anchor = GridBagConstraints.LINE_END
self._configurationPanel.add(self._selectorLabel, c)
self._selectorTextField = JTextField('',50)
c = GridBagConstraints()
c.gridx = 1
c.gridy = 2
self._configurationPanel.add(self._selectorTextField, c)
# Regex option
self._regexLabel = JLabel("Use regex as JSON Selector? (Optional): ")
self._regexLabel.setFont(Font("Tahoma",Font.BOLD, 12))
c = GridBagConstraints()
c.gridx = 0
c.gridy = 3
c.insets = Insets(0,0,0,0)
c.anchor = GridBagConstraints.LINE_END
self._configurationPanel.add(self._regexLabel,c)
self._regexCheckBox = JCheckBox("", actionPerformed=self.regexSelector)
c = GridBagConstraints()
c.gridx = 1
c.gridy = 3
c.anchor = GridBagConstraints.FIRST_LINE_START
self._configurationPanel.add(self._regexCheckBox,c)
# Signature Options
generateSignatureLabel = JLabel("Generate signature? (Required): ")
generateSignatureLabel.setFont(Font("Tahoma",Font.BOLD, 12))
c = GridBagConstraints()
c.gridx = 0
c.gridy = 4
c.insets = Insets(0,10,0,0)
c.anchor = GridBagConstraints.LINE_END
self._configurationPanel.add(generateSignatureLabel,c)
options = ["False", "True"]
self._generateSignatureComboBox = JComboBox(options)
c = GridBagConstraints()
c.gridx = 1
c.gridy = 4
c.anchor = GridBagConstraints.LINE_START
self._configurationPanel.add(self._generateSignatureComboBox,c)
signatureAlgorithmLabel = JLabel("Signature Algorithm (Optional): ")
signatureAlgorithmLabel.setFont(Font("Tahoma",Font.BOLD, 12))
c = GridBagConstraints()
c.gridx = 0
c.gridy = 5
c.insets = Insets(0,10,0,0)
c.anchor = GridBagConstraints.LINE_END
self._configurationPanel.add(signatureAlgorithmLabel,c)
options = ["None", "HS256","HS384","HS512","ES256","ES384","ES512","RS256","RS384","RS512","PS256","PS256","PS384","PS512"]
self._algorithmSelectionComboBox = JComboBox(options)
c = GridBagConstraints()
c.gridx = 1
c.gridy = 5
c.anchor = GridBagConstraints.LINE_START
self._configurationPanel.add(self._algorithmSelectionComboBox,c)
# Signing key options
self._signingKeyLabel = JLabel("Signing Key (Optional): ")
self._signingKeyLabel.setFont(Font("Tahoma",Font.BOLD, 12))
c = GridBagConstraints()
c.gridx = 0
c.gridy = 6
c.insets = Insets(0,10,0,0)
c.anchor = GridBagConstraints.LINE_END
self._configurationPanel.add(self._signingKeyLabel,c)
self.addSigningKeyTextArea()
self._fromFileTextField = JTextField('',50)
fromFileLabel = JLabel("Signing key from file? (Optional): ")
fromFileLabel.setFont(Font("Tahoma",Font.BOLD, 12))
c = GridBagConstraints()
c.gridx = 0
c.gridy = 7
c.insets = Insets(0,0,0,0)
c.anchor = GridBagConstraints.LINE_END
self._configurationPanel.add(fromFileLabel,c)
self._fromFileCheckBox = JCheckBox("", actionPerformed=self.fromFile)
c = GridBagConstraints()
c.gridx = 1
c.gridy = 7
c.anchor = GridBagConstraints.FIRST_LINE_START
self._configurationPanel.add(self._fromFileCheckBox,c)
self._fromCmdTextField = JTextField('',50)
fromCmdLabel = JLabel("Signing key from command? (Optional): ")
fromCmdLabel.setFont(Font("Tahoma",Font.BOLD, 12))
c = GridBagConstraints()
c.gridx = 0
c.gridy = 8
c.insets = Insets(0,0,0,0)
c.anchor = GridBagConstraints.LINE_END
self._configurationPanel.add(fromCmdLabel,c)
self._fromCmdCheckBox = JCheckBox("", actionPerformed=self.fromCmd)
c = GridBagConstraints()
c.gridx = 1
c.gridy = 8
c.anchor = GridBagConstraints.FIRST_LINE_START
self._configurationPanel.add(self._fromCmdCheckBox,c)
self._saveButton = JButton("Save Configuration", actionPerformed=self.saveOptions)
self._saveButton.setText("Save Configuration")
c = GridBagConstraints()
c.gridx = 1
c.gridy = 9
c.anchor = GridBagConstraints.FIRST_LINE_START
self._configurationPanel.add(self._saveButton,c)
callbacks.customizeUiComponent(self._configurationPanel)
callbacks.customizeUiComponent(self._tabs)
callbacks.addSuiteTab(self)
self._stdout.println("[JWT FuzzHelper] Loaded successfully")
return
def tag_3_1(self, c):
# 输入框-标题
lblParams = JLabel(u'请填写域名:')
self.setFontBold(lblParams)
lblParams.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 0
c.insets = Insets(5, 5, 5, 5)
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.FIRST_LINE_END
self.white_list_domain_settings.add(lblParams, c)
# 输入框
self.white_list_text_field = JTextField()
c.fill = GridBagConstraints.BOTH
c.gridx = 1
c.gridy = 0
self.white_list_domain_settings.add(self.white_list_text_field, c)
lblParamsNote = JLabel(u"白名单域名列表")
self.setFontItalic(lblParamsNote)
c.fill = GridBagConstraints.NONE
c.gridx = 0
c.gridy = 1
self.white_list_domain_settings.add(lblParamsNote, c)
# 添加 文本框
self.white_list_text_area = JTextArea()
self.white_list_text_area.setColumns(20)
self.white_list_text_area.setRows(10)
self.white_list_text_area.setEditable(False)
c.fill = GridBagConstraints.BOTH
self.white_list_mouse_listener = TextAreaMouseListener(
self.white_list_text_area)
self.white_list_text_area.addMouseListener(
self.white_list_mouse_listener)
# 向文本框添加数据
for name in white_list_names:
self.white_list_text_area.append(name + '\n' + os.linesep)
c.gridx = 1
c.gridy = 1
sp = JScrollPane(self.white_list_text_area)
self.white_list_domain_settings.add(sp, c)
# 添加 删除 重置
buttonsPanel = JPanel(GridBagLayout())
_c = GridBagConstraints()
_c.insets = Insets(3, 3, 3, 3)
_c.gridx = 0
_c.fill = GridBagConstraints.BOTH
_c.weightx = 1
_c.gridwidth = 1
handlers = ButtonHandlers(self.white_list_text_field,
self.white_list_text_area,
self.white_list_mouse_listener,
white_list_names)
# 添加按钮
self.white_list_add_button = JButton(
u'添加', actionPerformed=handlers.handler_add)
_c.gridy = 1
buttonsPanel.add(self.white_list_add_button, _c)
# 删除按钮
self.white_list_rm_button = JButton(
u'删除', actionPerformed=handlers.handler_rm)
_c.gridy = 2
buttonsPanel.add(self.white_list_rm_button, _c)
# 重置按钮
self.white_list_restore_button = JButton(
u'重置', actionPerformed=handlers.handler_restore)
_c.gridy = 3
buttonsPanel.add(self.white_list_restore_button, _c)
c.gridx = 2
c.gridy = 1
c.fill = GridBagConstraints.NONE
self.white_list_domain_settings.add(buttonsPanel, c)
