confocal_logic.ConfocalLogic Class Reference

This is the Logic class for confocal scanning. More...

Inheritance diagram for confocal_logic.ConfocalLogic:

Collaboration diagram for confocal_logic.ConfocalLogic:

Public Member Functions
def	__init__ (self, config, kwargs)
def	on_activate (self)
	Initialisation performed during activation of the module.
def	on_deactivate (self)
	Reverse steps of activation. More...
def	switch_hardware (self, to_on=False)
	Switches the Hardware off or on. More...
def	set_clock_frequency (self, clock_frequency)
	Sets the frequency of the clock. More...
def	start_scanning (self, zscan=False, tag='logic')
	Starts scanning. More...
def	continue_scanning (self, zscan, tag='logic')
	Continue scanning. More...
def	stop_scanning (self)
	Stops the scan. More...
def	initialize_image (self)
	Initalization of the image. More...
def	start_scanner (self)
	Setting up the scanner device and starts the scanning procedure. More...
def	continue_scanner (self)
	Continue the scanning procedure. More...
def	kill_scanner (self)
	Closing the scanner device. More...
def	set_position (self, tag, x=None, y=None, z=None, a=None)
	Forwarding the desired new position from the GUI to the scanning device. More...
def	get_position (self)
	Get position from scanning device. More...
def	get_scanner_axes (self)
	Get axes from scanning device. More...
def	get_scanner_count_channels (self)
	Get lis of counting channels from scanning device. More...
def	save_xy_data (self, colorscale_range=None, percentile_range=None)
	Save the current confocal xy data to file. More...
def	save_depth_data (self, colorscale_range=None, percentile_range=None)
	Save the current confocal depth data to file. More...
def	draw_figure (self, data, image_extent, scan_axis=None, cbar_range=None, percentile_range=None, crosshair_pos=None)
	Create a 2-D color map figure of the scan image. More...
def	set_tilt_point1 (self)
	Tilt correction ########################################. More...
def	set_tilt_point2 (self)
	Gets the second reference point for tilt correction. More...
def	set_tilt_point3 (self)
	Gets the third reference point for tilt correction. More...
def	calc_tilt_correction (self)
	Calculates the values for the tilt correction. More...
def	set_tilt_correction (self, enabled)
	Set tilt correction in tilt interfuse. More...
def	history_forward (self)
	Move forward in confocal image history.
def	history_back (self)
	Move backwards in confocal image history.

Public Attributes
	threadlock
	stopRequested
	depth_scan_dir_is_xz
	depth_img_is_xz
	permanent_scan
	x_range
	y_range
	z_range
	history
	history_index
	depth_image
	xy_image
	point1
	point2
	point3

Static Public Attributes
	confocalscanner1 = Connector(interface='ConfocalScannerInterface')
	savelogic = Connector(interface='SaveLogic')
	return_slowness = StatusVar(default=50)
	max_history_length = StatusVar(default=10)
	signal_start_scanning = QtCore.Signal(str)
	signal_continue_scanning = QtCore.Signal(str)
	signal_stop_scanning = QtCore.Signal()
	signal_scan_lines_next = QtCore.Signal()
	signal_xy_image_updated = QtCore.Signal()
	signal_depth_image_updated = QtCore.Signal()
	signal_change_position = QtCore.Signal(str)
	signal_xy_data_saved = QtCore.Signal()
	signal_depth_data_saved = QtCore.Signal()
	signal_tilt_correction_active = QtCore.Signal(bool)
	signal_tilt_correction_update = QtCore.Signal()
	signal_draw_figure_completed = QtCore.Signal()
	signal_position_changed = QtCore.Signal()
	sigImageXYInitialized = QtCore.Signal()
	sigImageDepthInitialized = QtCore.Signal()
	signal_history_event = QtCore.Signal()

Detailed Description

This is the Logic class for confocal scanning.

Member Function Documentation

calc_tilt_correction()

def confocal_logic.ConfocalLogic.calc_tilt_correction

(

self

)

Calculates the values for the tilt correction.

continue_scanner()

def confocal_logic.ConfocalLogic.continue_scanner

(

self

)

Continue the scanning procedure.

Returns

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

continue_scanning()

def confocal_logic.ConfocalLogic.continue_scanning	(		self,
			zscan,
			tag = 'logic'
	)

Continue scanning.

Returns

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

draw_figure()

def confocal_logic.ConfocalLogic.draw_figure	(		self,
			data,
			image_extent,
			scan_axis = None,
			cbar_range = None,
			percentile_range = None,
			crosshair_pos = None
	)

Create a 2-D color map figure of the scan image.

Parameters

get_position()

def confocal_logic.ConfocalLogic.get_position

(

self

)

Get position from scanning device.

Returns

list: with three entries x, y and z denoting the current position in meters

get_scanner_axes()

def confocal_logic.ConfocalLogic.get_scanner_axes

(

self

)

Get axes from scanning device.

Returns

list(str): names of scanner axes

get_scanner_count_channels()

def confocal_logic.ConfocalLogic.get_scanner_count_channels

(

self

)

Get lis of counting channels from scanning device.

Returns

list(str): names of counter channels

initialize_image()

def confocal_logic.ConfocalLogic.initialize_image

(

self

)

Initalization of the image.

Returns

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

kill_scanner()

def confocal_logic.ConfocalLogic.kill_scanner

(

self

)

Closing the scanner device.

Returns

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

on_deactivate()

def confocal_logic.ConfocalLogic.on_deactivate

(

self

)

Reverse steps of activation.

Returns

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

save_depth_data()

def confocal_logic.ConfocalLogic.save_depth_data	(		self,
			colorscale_range = None,
			percentile_range = None
	)

Save the current confocal depth data to file.

Two files are created. The first is the imagedata, which has a text-matrix of count values corresponding to the pixel matrix of the image. Only count-values are saved here.

The second file saves the full raw data with x, y, z, and counts at every pixel.

save_xy_data()

def confocal_logic.ConfocalLogic.save_xy_data	(		self,
			colorscale_range = None,
			percentile_range = None
	)

Save the current confocal xy data to file.

Two files are created. The first is the imagedata, which has a text-matrix of count values corresponding to the pixel matrix of the image. Only count-values are saved here.

The second file saves the full raw data with x, y, z, and counts at every pixel.

A figure is also saved.

Parameters

set_clock_frequency()

def confocal_logic.ConfocalLogic.set_clock_frequency	(		self,
			clock_frequency
	)

Sets the frequency of the clock.

Parameters

int	clock_frequency: desired frequency of the clock

Returns

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

set_position()

def confocal_logic.ConfocalLogic.set_position	(		self,
			tag,
			x = None,
			y = None,
			z = None,
			a = None
	)

Forwarding the desired new position from the GUI to the scanning device.

Parameters

string	tag: TODO
float	x: if defined, changes to postion in x-direction (microns)
float	y: if defined, changes to postion in y-direction (microns)
float	z: if defined, changes to postion in z-direction (microns)
float	a: if defined, changes to postion in a-direction (microns)

Returns

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

set_tilt_correction()

def confocal_logic.ConfocalLogic.set_tilt_correction	(		self,
			enabled
	)

Set tilt correction in tilt interfuse.

Parameters

bool	enabled: whether we want to use tilt correction

set_tilt_point1()

def confocal_logic.ConfocalLogic.set_tilt_point1

(

self

)

Tilt correction ########################################.

Gets the first reference point for tilt correction.

set_tilt_point2()

def confocal_logic.ConfocalLogic.set_tilt_point2

(

self

)

Gets the second reference point for tilt correction.

set_tilt_point3()

def confocal_logic.ConfocalLogic.set_tilt_point3

(

self

)

Gets the third reference point for tilt correction.

start_scanner()

def confocal_logic.ConfocalLogic.start_scanner

(

self

)

Setting up the scanner device and starts the scanning procedure.

Returns

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

start_scanning()

def confocal_logic.ConfocalLogic.start_scanning	(		self,
			zscan = False,
			tag = 'logic'
	)

Starts scanning.

Parameters

bool	zscan: zscan if true, xyscan if false

Returns

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

stop_scanning()

def confocal_logic.ConfocalLogic.stop_scanning

(

self

)

Stops the scan.

Returns

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

switch_hardware()

def confocal_logic.ConfocalLogic.switch_hardware	(		self,
			to_on = False
	)

Switches the Hardware off or on.

Parameters

to_on

True switches on, False switched off

Returns

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

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

• logic/confocal_logic.py