poi_manager_logic.PoiManagerLogic Class Reference

This is the Logic class for mapping and tracking bright features in the confocal scan. More...

Inheritance diagram for poi_manager_logic.PoiManagerLogic:

Collaboration diagram for poi_manager_logic.PoiManagerLogic:

Public Member Functions
def	__init__ (self, config, kwargs)
def	on_activate (self)
	Initialisation performed during activation of the module.
def	on_deactivate (self)
def	user_move_deactivates_poi (self, tag)
	Deactivate the active POI if the confocal microscope scanner position is moved by anything other than the optimizer.
def	add_poi (self, position=None, key=None, emit_change=True)
	Creates a new poi and adds it to the list. More...
def	get_confocal_image_data (self)
	Get the current confocal xy scan data to hold as image of ROI.
def	get_all_pois (self, abc_sort=False)
	Returns a list of the names of all existing POIs. More...
def	delete_last_position (self, poikey=None)
	Delete the last position in the history. More...
def	delete_poi (self, poikey=None)
	Completely deletes the whole given poi. More...
def	optimise_poi (self, poikey=None)
	Starts the optimisation procedure for the given poi. More...
def	go_to_poi (self, poikey=None)
	Goes to the given poi and saves it as the current one. More...
def	get_poi_position (self, poikey=None)
	Returns the current position of the given poi, calculated from the POI coords in sample and the current sample position. More...
def	set_new_position (self, poikey=None, newpos=None)
def	move_coords (self, poikey=None, newpos=None)
	Updates the coords of a given POI, and adds a position to the POI history, but DOES NOT update the sample position.
def	rename_poi (self, poikey=None, name=None, emit_change=True)
	Sets the name of the given poi. More...
def	start_periodic_refocus (self, poikey=None)
	Starts the perodic refocussing of the poi. More...
def	set_periodic_optimize_duration (self, duration=None)
	Change the duration of the periodic optimize timer during active periodic refocussing. More...
def	stop_periodic_refocus (self)
	Stops the perodic refocussing of the poi. More...
def	reset_roi (self)
def	set_active_poi (self, poikey=None)
	Set the active POI object.
def	update_poi_tag_in_savelogic (self)
def	save_poi_map_as_roi (self)
	Save a list of POIs with their coordinates to a file.
def	load_roi_from_file (self, filename=None)
def	dict_to_poi_list (self, val)
def	poi_list_to_dict (self, val)
def	active_poi_to_dict (self, val)
def	dict_to_active_poi (self, val)
def	triangulate (self, r, a1, b1, c1, a2, b2, c2)
	Reorients a coordinate r that is known relative to reference points a1, b1, c1 to produce a new vector rnew that has exactly the same relation to rotated/shifted/tilted reference positions a2, b2, c2. More...
def	reorient_roi (self, ref1_coords, ref2_coords, ref3_coords, ref1_newpos, ref2_newpos, ref3_newpos)
	Move and rotate the ROI to a new position specified by the newpos of 3 reference POIs from the saved ROI. More...
def	autofind_pois (self, neighborhood_size=1, min_threshold=10000, max_threshold=1e6)
	Automatically search the xy scan image for POIs. More...

Public Attributes
	go_to_crosshair_after_refocus
	timer
	time_left
	timer_step
	timer_duration
	threadlock
	roi_map_data

Static Public Attributes
	optimizer1 = Connector(interface='OptimizerLogic')
	scannerlogic = Connector(interface='ConfocalLogic')
	savelogic = Connector(interface='SaveLogic')
	poi_list = StatusVar(default=OrderedDict())
	roi_name = StatusVar(default='')
	active_poi = StatusVar(default=None)
	signal_timer_updated = QtCore.Signal()
	signal_poi_updated = QtCore.Signal()
	signal_poi_deleted = QtCore.Signal(str)
	signal_confocal_image_updated = QtCore.Signal()
	signal_periodic_opt_started = QtCore.Signal()
	signal_periodic_opt_duration_changed = QtCore.Signal()
	signal_periodic_opt_stopped = QtCore.Signal()

Detailed Description

This is the Logic class for mapping and tracking bright features in the confocal scan.

Member Function Documentation

add_poi()

def poi_manager_logic.PoiManagerLogic.add_poi	(		self,
			position = None,
			key = None,
			emit_change = True
	)

Creates a new poi and adds it to the list.

Returns

int: key of this new poi

A position can be provided (such as during re-loading a saved ROI). If no position is provided, then the current crosshair position is used.

autofind_pois()

def poi_manager_logic.PoiManagerLogic.autofind_pois	(		self,
			neighborhood_size = 1,
			min_threshold = 10000,
			max_threshold = 1e6
	)

Automatically search the xy scan image for POIs.

Parameters

neighborhood_size	size in microns. Only the brightest POI per neighborhood will be found.
min_threshold	POIs must have c/s above this threshold.
max_threshold	POIs must have c/s below this threshold.

delete_last_position()

def poi_manager_logic.PoiManagerLogic.delete_last_position	(		self,
			poikey = None
	)

Delete the last position in the history.

Parameters

string

poikey: the key of the poi

Returns

int: error code (0:OK, -1:error)

delete_poi()

def poi_manager_logic.PoiManagerLogic.delete_poi	(		self,
			poikey = None
	)

Completely deletes the whole given poi.

Parameters

string

poikey: the key of the poi

Returns

int: error code (0:OK, -1:error)

Does not delete the crosshair and sample.

get_all_pois()

def poi_manager_logic.PoiManagerLogic.get_all_pois	(		self,
			abc_sort = False
	)

Returns a list of the names of all existing POIs.

Returns

string[]: List of names of the POIs

Also crosshair and sample are included.

get_poi_position()

def poi_manager_logic.PoiManagerLogic.get_poi_position	(		self,
			poikey = None
	)

Returns the current position of the given poi, calculated from the POI coords in sample and the current sample position.

Parameters

string

poikey: the key of the poi

Returns

go_to_poi()

def poi_manager_logic.PoiManagerLogic.go_to_poi	(		self,
			poikey = None
	)

Goes to the given poi and saves it as the current one.

Parameters

string

poikey: the key of the poi

Returns

int: error code (0:OK, -1:error)

optimise_poi()

def poi_manager_logic.PoiManagerLogic.optimise_poi	(		self,
			poikey = None
	)

Starts the optimisation procedure for the given poi.

Parameters

string

poikey: the key of the poi

Returns

int: error code (0:OK, -1:error)

This is threaded, so it returns directly. The function _refocus_done handles the data when the optimisation returns.

rename_poi()

def poi_manager_logic.PoiManagerLogic.rename_poi	(		self,
			poikey = None,
			name = None,
			emit_change = True
	)

Sets the name of the given poi.

Parameters

string	poikey: the key of the poi
string	name: name of the poi to be set

Returns

int: error code (0:OK, -1:error)

reorient_roi()

def poi_manager_logic.PoiManagerLogic.reorient_roi	(		self,
			ref1_coords,
			ref2_coords,
			ref3_coords,
			ref1_newpos,
			ref2_newpos,
			ref3_newpos
	)

Move and rotate the ROI to a new position specified by the newpos of 3 reference POIs from the saved ROI.

Parameters

ref1_coords	coordinates (from ROI save file) of reference 1.
ref2_coords	similar, ref2.
ref3_coords	similar, ref3.
ref1_newpos	the new (current) position of POI reference 1.
ref2_newpos	similar, ref2.
ref3_newpos	similar, ref3.

set_periodic_optimize_duration()

def poi_manager_logic.PoiManagerLogic.set_periodic_optimize_duration	(		self,
			duration = None
	)

Change the duration of the periodic optimize timer during active periodic refocussing.

Parameters

float

duration: (optional) the time between periodic optimization.

start_periodic_refocus()

def poi_manager_logic.PoiManagerLogic.start_periodic_refocus	(		self,
			poikey = None
	)

Starts the perodic refocussing of the poi.

Parameters

float	duration: (optional) the time between periodic optimization
string	poikey: (optional) the key of the poi to be set and refocussed on.

Returns

int: error code (0:OK, -1:error)

stop_periodic_refocus()

def poi_manager_logic.PoiManagerLogic.stop_periodic_refocus

(

self

)

Stops the perodic refocussing of the poi.

Returns

int: error code (0:OK, -1:error)

triangulate()

def poi_manager_logic.PoiManagerLogic.triangulate	(		self,
			r,
			a1,
			b1,
			c1,
			a2,
			b2,
			c2
	)

Reorients a coordinate r that is known relative to reference points a1, b1, c1 to produce a new vector rnew that has exactly the same relation to rotated/shifted/tilted reference positions a2, b2, c2.

Parameters

np.array	r: position to be remapped.
np.array	a1: initial location of ref1.
np.array	a2: final location of ref1.
np.array	b1, b2, c1, c2: similar for ref2 and ref3

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The documentation for this class was generated from the following file:

• logic/poi_manager_logic.py