Example #1
0
	def __init__(self,child,enable_timer=False):
		"""
		@param child: the central GL display widget
		@type child: EMGLWidget
		@param enable_timer: not used... historical purposes???
		"""
		#TODO: figure out why the enable_timer parameter isn't being used
		QtGui.QWidget.__init__(self,None)
		Animator.__init__(self)

		self.child = weakref.ref(child) # Either EMGLWidget.parent_widget or EMParentWin.child must be a weakref for garbage collection purposes.
		self.resize(child.width(),child.height())
		self.setMaximumSize(8000,8000)

		self.hbl = QtGui.QVBoxLayout()
		
		self.hbl.setSpacing(0)
		self.hbl.addWidget(self.child(),100)
		if get_platform() == "Darwin": # because OpenGL widgets in Qt don't leave room in the bottom right hand corner for the resize tool
			self.status = QtGui.QStatusBar()
			self.status.setSizeGripEnabled(True)
			self.hbl.addWidget(self.status,0)
			self.margin = 0
		else:
			self.margin = 5
		self.hbl.setMargin(self.margin)
		self.setLayout(self.hbl)
Example #2
0
    def __init__(self, enable_timer=False):
        """
		@param child: the central GL display widget
		@type child: EMGLWidget
		@param enable_timer: not used... historical purposes???
		"""
        #TODO: figure out why the enable_timer parameter isn't being used
        QtGui.QWidget.__init__(self, None)
        Animator.__init__(self)

        self.setMaximumSize(8000, 8000)
        self.hbl = QtGui.QVBoxLayout(self)

        self.hbl.setSpacing(0)
        if get_platform(
        ) == "Darwin":  # because OpenGL widgets in Qt don't leave room in the bottom right hand corner for the resize tool
            self.status = QtGui.QStatusBar()
            self.status.setSizeGripEnabled(True)
            self.hbl.addWidget(self.status, 0)
            self.margin = 0
        else:
            self.margin = 5
        self.hbl.setMargin(self.margin)
Example #3
0
	def __init__(self,enable_timer=False):
		"""
		@param child: the central GL display widget
		@type child: EMGLWidget
		@param enable_timer: not used... historical purposes???
		"""
		#TODO: figure out why the enable_timer parameter isn't being used
		QtGui.QWidget.__init__(self,None)
		Animator.__init__(self)


		self.setMaximumSize(8000,8000)
		self.hbl = QtGui.QVBoxLayout(self)
		
		self.hbl.setSpacing(0)
		if get_platform() == "Darwin": # because OpenGL widgets in Qt don't leave room in the bottom right hand corner for the resize tool
			self.status = QtGui.QStatusBar()
			self.status.setSizeGripEnabled(True)
			self.hbl.addWidget(self.status,0)
			self.margin = 0
		else:
			self.margin = 5
		self.hbl.setMargin(self.margin)
Example #4
0
	def __init__(self, gl_widget=None, auto=True,sparse_mode=False, file_name = ""):
		self.current_hit = None
		self.events_mode_list = ["navigate", "inspect"]
		self.events_mode = self.events_mode_list[1]


		self.init_lock = True # a lock indicated that we are still in the __init__ function
		self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study
		if auto: # this a flag that tells the eulerxplorer to search for refinement data and automatically add elements to the inspector, if so
			self.gen_refinement_data()

		EM3DSymModel.__init__(self, gl_widget, eulerfilename=file_name)
		Animator.__init__(self)
		self.height_scale = 8.0 # This is a value used in EM3DSymModel which scales the height of the displayed cylinders - I made it 8 because it seemed fine. The user can change it anyhow
		self.projection_file = None  # This is a string - the name of the projection images file
		self.average_file = None # This is a string - the name of the class averages file
		self.proj_class_viewer = None # This will be an EMImageMXWidget that shows the class and/or projection
		self.particle_viewer = None  # This will be an EMImageMXWidget that shows the particles in a class
		self.clsdb = None # I think this will become redundant - it used to be the old database that stores which particles are in a class, but now that's stored in the header
		self.particle_file = None # This will be a string - the name of the file that has the particle files in it. This might be made redundant with the new approach
		self.alignment_file = None # This will be a string - the name of the file containing the alignment parameters - this is essential if you we want to show the aligned particles
		self.refine_dir = None # This will be a string - the name of the current refinement directory that is being studied
		self.dx = None # This is an EMData object storing the x shifts of the alignments for all particles. Generated by e2classaverage
		self.dy = None # This is an EMData object storing the y shifts of the alignments for all particles. Generated by e2classaverage
		self.da = None# This is an EMData object storing the angle of the alignments for all particles. Generated by e2classaverage
		self.dflip = None # This is an EMData object storing whether or not tthe alignment involved a flip, for all particles. Generated by e2classaverage
		self.classes = None # This is an EMData object storing which class(es) a particle belongs to. Generated by e2classaverage
		self.inclusions = None # This is and EMDAta storing a boolean that indicates the particle was actually included in the final average. Generated by e2classaverage

		self.average = None # This the class average itself, an EMData object
		self.projection = None # This is the projection itelse, an EMData object
		self.class_idx = None # This is the idx of the current class being studied in the interface

		self.previous_len = -1 # To keep track of the number of class averages that were previously viewable. This helps to make sure we can switch to the same class average in the context of a different refinement iteration
		self.mirror_eulers = False
		if sparse_mode:
			self.mirror_eulers = True # If True the drawn Eulers are are also rendered on the opposite side of the sphere - see EM3DSymModel.make_sym_dl_lis

		# Grab the symmetry from the workflow database if possible
		sym = "c1"
		if js_check_dict("refine_01/0_refine_parms.json"):
			try: sym = str(js_open_dict("refine_01/0_refine_parms.json")["sym"])
			except: pass

		# Have to tell the EM3DSymModel that there is a new sym
		self.set_symmetry(sym)

		# this object will have
		if self.au_data != None:
			combo_entries = self.au_data.keys()
			combo_entries.sort()
			combo_entries.reverse()

			if len(combo_entries) > 0:
				au = combo_entries[0]
				cls = self.au_data[au][0][0]
				self.au_selected(au,cls)
				self.mirror_eulers = True

		self.init_lock = False
		self.force_update=True # Force a display udpdate in EMImage3DSymModule

		QtCore.QObject.connect(self, QtCore.SIGNAL("point_selected"), self.au_point_selected)
Example #5
0
	def __init__(self, gl_widget=None, auto=True,sparse_mode=False, file_name = "", read_from=None):
		self.current_hit = None
		self.events_mode_list = ["navigate", "inspect"]
		self.events_mode = self.events_mode_list[1]

		self.init_lock = True # a lock indicated that we are still in the __init__ function
		self.au_data = None # This will be a dictionary, keys will be refinement directories, values will be something like available iterations for visual study
		if len(read_from)==0:
			read_from=None
		self.readfrom=read_from
		if self.readfrom:
			
			file_name=""
			auto=False
			datalst=[]
			for rr in self.readfrom:
				datalst.append([rr,None, None, None,rr])
			self.au_data={"data":datalst}

		if auto: # this a flag that tells the eulerxplorer to search for refinement data and automatically add elements to the inspector, if so
			self.gen_refinement_data()
		
		EM3DSymModel.__init__(self, gl_widget, eulerfilename=file_name)
		Animator.__init__(self)
		self.height_scale = 8.0 # This is a value used in EM3DSymModel which scales the height of the displayed cylinders - I made it 8 because it seemed fine. The user can change it anyhow
		self.projection_file = None  # This is a string - the name of the projection images file
		self.average_file = None # This is a string - the name of the class averages file
		self.proj_class_viewer = None # This will be an EMImageMXWidget that shows the class and/or projection
		self.particle_viewer = None  # This will be an EMImageMXWidget that shows the particles in a class
		self.clsdb = None # I think this will become redundant - it used to be the old database that stores which particles are in a class, but now that's stored in the header
		self.particle_file = None # This will be a string - the name of the file that has the particle files in it. This might be made redundant with the new approach
		self.alignment_file = None # This will be a string - the name of the file containing the alignment parameters - this is essential if you we want to show the aligned particles
		self.refine_dir = None # This will be a string - the name of the current refinement directory that is being studied
		self.dx = None # This is an EMData object storing the x shifts of the alignments for all particles. Generated by e2classaverage
		self.dy = None # This is an EMData object storing the y shifts of the alignments for all particles. Generated by e2classaverage
		self.da = None# This is an EMData object storing the angle of the alignments for all particles. Generated by e2classaverage
		self.dflip = None # This is an EMData object storing whether or not tthe alignment involved a flip, for all particles. Generated by e2classaverage
		self.classes = None # This is an EMData object storing which class(es) a particle belongs to. Generated by e2classaverage
		self.inclusions = None # This is and EMDAta storing a boolean that indicates the particle was actually included in the final average. Generated by e2classaverage

		self.average = None # This the class average itself, an EMData object
		self.projection = None # This is the projection itelse, an EMData object
		self.class_idx = None # This is the idx of the current class being studied in the interface

		self.previous_len = -1 # To keep track of the number of class averages that were previously viewable. This helps to make sure we can switch to the same class average in the context of a different refinement iteration
		self.mirror_eulers = False
		if sparse_mode:
			self.mirror_eulers = True # If True the drawn Eulers are are also rendered on the opposite side of the sphere - see EM3DSymModel.make_sym_dl_lis

		# Grab the symmetry from the workflow database if possible
		sym = "c1"
		if js_check_dict("refine_01/0_refine_parms.json"):
			try: sym = str(js_open_dict("refine_01/0_refine_parms.json")["sym"])
			except: pass

		# Have to tell the EM3DSymModel that there is a new sym
		self.set_symmetry(sym)

		# this object will have
		if self.au_data != None:
			combo_entries = self.au_data.keys()
			combo_entries.sort()
			combo_entries.reverse()

			if len(combo_entries) > 0:
				au = combo_entries[0]
				cls = self.au_data[au][0][0]
				self.au_selected(au,cls)
				self.mirror_eulers = True

		self.init_lock = False
		self.force_update=True # Force a display udpdate in EMImage3DSymModule

		QtCore.QObject.connect(self, QtCore.SIGNAL("point_selected"), self.au_point_selected)