Ejemplo n.º 1
0
    def addInput(self, dataunit, data):
        """
		Adds an input for the color merging filter
		"""
        settings = dataunit.getSettings()
        if not settings.get("PreviewChannel"):
            Logging.info("Not including ",
                         dataunit,
                         "in merging",
                         kw="processing")
            return

        Module.addInput(self, dataunit, data)

        self.n += 1

        ctf = settings.get("ColorTransferFunction")

        #		Logging.info("ctf=",ctf,kw="processing")

        self.ctfs.append(ctf)

        self.alphaTF = settings.get("AlphaTransferFunction")
        self.alphaMode = settings.get("AlphaMode")
        #print "n=",self.n,"self.settings=",self.settings
        #itf=self.settings.getCounted("IntensityTransferFunction",self.n)

        itf = settings.get("IntensityTransferFunction")

        if not itf:
            Logging.info("Didn't get iTF", kw="processing")
        self.intensityTransferFunctions.append(itf)
    def addInput(self, dataunit, data):
        """
		Adds an input for the color merging filter
		"""
        settings = dataunit.getSettings()
        if not settings.get("PreviewChannel"):
            Logging.info("Not including ", dataunit, "in merging", kw="processing")
            return

        Module.addInput(self, dataunit, data)

        self.n += 1

        ctf = settings.get("ColorTransferFunction")

        # 		Logging.info("ctf=",ctf,kw="processing")

        self.ctfs.append(ctf)

        self.alphaTF = settings.get("AlphaTransferFunction")
        self.alphaMode = settings.get("AlphaMode")
        # print "n=",self.n,"self.settings=",self.settings
        # itf=self.settings.getCounted("IntensityTransferFunction",self.n)

        itf = settings.get("IntensityTransferFunction")

        if not itf:
            Logging.info("Didn't get iTF", kw="processing")
        self.intensityTransferFunctions.append(itf)
	def __init__(self, **kws):
		"""
		Initialization
		"""
		Module.__init__(self, **kws)
		self.running = 0
		self.depth = 8
		self.reset()
Ejemplo n.º 4
0
    def __init__(self, **kws):
        """
		Initialization
		"""
        Module.__init__(self, **kws)
        self.running = 0
        self.depth = 8
        self.reset()
Ejemplo n.º 5
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    def addInput(self, dataunit, data):
        """
		Adds an input for the single dataunit processing filter
		"""
        Module.addInput(self, dataunit, data)
        settings = dataunit.getSettings()
        tf = settings.getCounted("IntensityTransferFunctions", self.timepoint)
        if not tf:
            raise ("No Intensity Transfer Function given for Single DataUnit "
                   "to be processed")
        self.intensityTransferFunctions.append(tf)
Ejemplo n.º 6
0
    def reset(self):
        """
		Resets the module to initial state. This method is
					 used mainly when doing previews, when the parameters
					 that control the colocalization are changed and the
					 preview data becomes invalid.
		"""
        Module.reset(self)
        self.preview = None
        self.intensityTransferFunctions = []
        self.extent = None
Ejemplo n.º 7
0
    def addInput(self, dataunit, data):
        """
		Adds an input for the colocalization filter
		"""
        Module.addInput(self, dataunit, data)
        settings = dataunit.getSettings()
        self.settingsLst.append(settings)
        th0 = settings.get("ColocalizationLowerThreshold")
        th1 = settings.get("ColocalizationUpperThreshold")
        self.thresholds.append((th0, th1))
        self.depth = self.settings.get("ColocalizationDepth")
    def __init__(self, **kws):
        """
		Initialization
		"""
        Module.__init__(self, **kws)
        self.doAlpha = 1
        self.extent = []
        self.thresholds = []
        self.merge = None
        self.running = False
        self.reset()
	def addInput(self, dataunit, data):
		"""
		Adds an input for the single dataunit processing filter
		"""
		Module.addInput(self, dataunit, data)
		settings = dataunit.getSettings()
		tf = settings.getCounted("IntensityTransferFunctions", self.timepoint)
		if not tf:            
			raise ("No Intensity Transfer Function given for Single DataUnit "
			"to be processed")
		self.intensityTransferFunctions.append(tf)
	def addInput(self, dataunit, data):
		"""
		Adds an input for the colocalization filter
		"""
		Module.addInput(self, dataunit, data)
		settings = dataunit.getSettings()
		self.settingsLst.append(settings)
		th0 = settings.get("ColocalizationLowerThreshold")
		th1 = settings.get("ColocalizationUpperThreshold")
		self.thresholds.append((th0, th1))
		self.depth = self.settings.get("ColocalizationDepth")
Ejemplo n.º 11
0
    def __init__(self, **kws):
        """
		Initialization
		"""
        Module.__init__(self, **kws)
        self.doAlpha = 1
        self.extent = []
        self.thresholds = []
        self.merge = None
        self.running = False
        self.reset()
	def reset(self):
		"""
		Resets the module to initial state. This method is
					 used mainly when doing previews, when the parameters
					 that control the colocalization are changed and the
					 preview data becomes invalid.
		"""
		Module.reset(self)
		self.preview = None
		self.intensityTransferFunctions = []
		self.extent = None
	def __init__(self, **kws):
		"""
		Initialization
		"""
		Module.__init__(self, **kws)

		# TODO: remove attributes that already exist in base class!
		self.images = []
		self.x, self.y, self.z = 0, 0, 0
		self.extent = None
		self.running = 0
		self.depth = 8

		self.reset()
Ejemplo n.º 14
0
    def __init__(self, **kws):
        """
		Initialization
		"""
        Module.__init__(self, **kws)

        # TODO: remove attributes that already exist in base class!
        self.images = []
        self.x, self.y, self.z = 0, 0, 0
        self.extent = None
        self.running = 0
        self.depth = 8

        self.reset()
Ejemplo n.º 15
0
 def add_module(course_name, module_short_title):
     """
     Link a course and a module
     """
     from lib.CourseModule import CourseModule
     course_ref = Course.get_by_key_name(course_name)
     module_ref = Module.get_by_key_name(module_short_title)
     new_course_module = CourseModule(course=course_ref, module=module_ref)
     new_course_module.put()
Ejemplo n.º 16
0
 def add_module(course_name,
                module_short_title):
     """
     Link a course and a module
     """
     from lib.CourseModule import CourseModule
     course_ref = Course.get_by_key_name(course_name)
     module_ref = Module.get_by_key_name(module_short_title)
     new_course_module = CourseModule(course=course_ref,
                                      module=module_ref)
     new_course_module.put()
	def reset(self):
		"""
		Resets the module to initial state. This method is
					 used mainly when doing previews, when the parameters
					 that control the colocalization are changed and the
					 preview data becomes invalid.
		"""
		Module.reset(self)
		self.colocFilter = vtkbxd.vtkImageColocalizationFilter()
		self.colocFilter.AddObserver('ProgressEvent', lib.messenger.send)
		lib.messenger.connect(self.colocFilter, "ProgressEvent", self.updateProgress)

		self.colocAutoThreshold = vtkbxd.vtkImageAutoThresholdColocalization()
		self.colocAutoThreshold.GetOutput().ReleaseDataFlagOn()
		self.colocAutoThreshold.AddObserver('ProgressEvent', lib.messenger.send)
		lib.messenger.connect(self.colocAutoThreshold, "ProgressEvent", self.updateProgress)
		self.thresholds = []
		self.settingsLst = []
		self.preview = None
		self.n = -1
Ejemplo n.º 18
0
 def remove_module(course_name, module_short_title):
     """
     Remove a module from a course
     """
     course_ref = Course.get_by_key_name(course_name)
     module_ref = Module.get_by_key_name(module_short_title)
     course_module_ref = db.GqlQuery("SELECT * FROM CourseModule WHERE " +\
                                     "course = :1 AND " +\
                                     "module = :2",
                                     course_ref,
                                     module_ref)
     db.delete(course_module_ref)
Ejemplo n.º 19
0
 def remove_module(course_name,
                   module_short_title):  
     """
     Remove a module from a course
     """
     course_ref = Course.get_by_key_name(course_name)
     module_ref = Module.get_by_key_name(module_short_title)
     course_module_ref = db.GqlQuery("SELECT * FROM CourseModule WHERE " +\
                                     "course = :1 AND " +\
                                     "module = :2", 
                                     course_ref, 
                                     module_ref)
     db.delete(course_module_ref)
Ejemplo n.º 20
0
    def reset(self):
        """
		Resets the module to initial state. This method is
					 used mainly when doing previews, when the parameters
					 that control the colocalization are changed and the
					 preview data becomes invalid.
		"""
        Module.reset(self)
        self.colocFilter = vtkbxd.vtkImageColocalizationFilter()
        self.colocFilter.AddObserver('ProgressEvent', lib.messenger.send)
        lib.messenger.connect(self.colocFilter, "ProgressEvent",
                              self.updateProgress)

        self.colocAutoThreshold = vtkbxd.vtkImageAutoThresholdColocalization()
        self.colocAutoThreshold.GetOutput().ReleaseDataFlagOn()
        self.colocAutoThreshold.AddObserver('ProgressEvent',
                                            lib.messenger.send)
        lib.messenger.connect(self.colocAutoThreshold, "ProgressEvent",
                              self.updateProgress)
        self.thresholds = []
        self.settingsLst = []
        self.preview = None
        self.n = -1
Ejemplo n.º 21
0
 def list_modules(course_name):
     """
     List all modules associated with a course
     """
     from lib.CourseModule import CourseModule
     modules = []
     course_ref = Course.get_by_key_name(course_name)
     course_module_ref = db.GqlQuery("SELECT * FROM CourseModule WHERE " +\
                                     "course = :1",                                      
                                     course_ref)
     for module_ref in course_module_ref.run():
         module_key = CourseModule.module.get_value_for_datastore(module_ref)
         module_res = Module.get(module_key)
         modules.append(module_res)
     return modules
Ejemplo n.º 22
0
 def list_modules(course_name):
     """
     List all modules associated with a course
     """
     from lib.CourseModule import CourseModule
     modules = []
     course_ref = Course.get_by_key_name(course_name)
     course_module_ref = db.GqlQuery("SELECT * FROM CourseModule WHERE " +\
                                     "course = :1",
                                     course_ref)
     for module_ref in course_module_ref.run():
         module_key = CourseModule.module.get_value_for_datastore(
             module_ref)
         module_res = Module.get(module_key)
         modules.append(module_res)
     return modules