mibView Class Reference

the main view class of MIB More...

Inheritance diagram for mibView:

Collaboration diagram for mibView:

Public Member Functions
function status =	editbox_Callback (hObject, chtype, default_val, variation)
	Check for entered values in an edit box and switch the focus to mib.View.handles.updatefilelistBtn.
function [ xData , yData , zData , xClick , yClick ] =	getClickPoint (nTimes, permuteSw)
	A function that gets ginput function to pick a point within handles.mibImageAxes.
function roiSwitch =	getRoiSwitch ()
	get status of the mibGUI.handles.toolbarShowROISwitch
function volrenModeSwitch =	getVolrenModeSwitch ()
	get status of the mibGUI.handles.volrenToolbarSwitch
function	setVolrenModeSwitch (volrenModeSwitch)
	set status of the mibGUI.handles.volrenToolbarSwitch
function	updateCursor (mode)
	Update brush cursor.
	mibView (controller)
	obj = mibView(controller) mibView class constructor

Static Public Member Functions
static function	Listner_Callback (obj, src, evnt)
	evntobj = evnt.AffectedObject; handles = guidata(obj.gui);

Public Attributes
	gui
	handle to the main gui
	mibModel
	handles to the model
	mibController
	handles to the controller
	handles
	list of handles for the gui
	guiPositions
	structure with default positions of some GUIs to be used for rescaling
	brushPrevXY
	coordinates of the previous pixel for the Brush tool,
	brushSelection
	selection layer during the brush tool movement,
	centerSpotHandle
	a handle to ROI point class that marks the center of the image axes .handle - a handle to the spot roi class .enable - a switch, 1-enable; 0-disable
	altPressed
	set a variable to store slice number where mouse scroll action was triggered obj.altPressed = 0; - indicates that Alt was not preseed obj.altPressed > 0; - indicates slice number when Alt was preseed
	ctrlPressed
	set a variable to deal with the increase of the brush size during the erasing action. Ctrl+left mouse button obj.ctrlPressed: obj.ctrlPressed == 0; - indicates the normal brush mode, i.e. when the control button is not pressed obj.ctrlPressed > 0; - the control button is pressed and handles.ctrlPressed indicates increase of the brush radius obj.ctrlPressed == -1; - a tweak to deal with Ctrl+Mouse wheel action to change size of the brush. -1 indicates that the brush size change mode was triggered see in functions: mibGUI_WindowKeyPressFcn, mibGUI_WindowKeyReleaseFcn, mibGUI_ScrollWheelFcn
	cursor
	a handle to the cursor gui object
	imh
	handle for the currently shown image; should be obj.imh = matlab.graphics.primitive.Image(CData, []); when no image
	Iraw
	a property to keep the currently displayed image in RAW format, used only in the virtual stacking mode to see pixel intensities under the cursor
	Ishown
	a property to keep the currently displayed image in RGB format
	showBrushCursor
	a switch (0, 1) to define whether or not show the brush cursor
	trackerYXZ
	starting point for the Membrane Click-tracer tool
Public Attributes inherited from handle
	addlistener
	Creates a listener for the specified event and assigns a callback function to execute when the event occurs.
	notify
	Broadcast a notice that a specific event is occurring on a specified handle object or array of handle objects.
	delete
	Handle object destructor method that is called when the object's lifecycle ends.
	disp
	Handle object disp method which is called by the display method. See the MATLAB disp function.
	display
	Handle object display method called when MATLAB software interprets an expression returning a handle object that is not terminated by a semicolon. See the MATLAB display function.
	findobj
	Finds objects matching the specified conditions from the input array of handle objects.
	findprop
	Returns a meta.property objects associated with the specified property name.
	fields
	Returns a cell array of string containing the names of public properties.
	fieldnames
	Returns a cell array of string containing the names of public properties. See the MATLAB fieldnames function.
	isvalid
	Returns a logical array in which elements are true if the corresponding elements in the input array are valid handles. This method is Sealed so you cannot override it in a handle subclass.
	eq
	Relational functions example. See details for more information.
	transpose
	Transposes the elements of the handle object array.
	permute
	Rearranges the dimensions of the handle object array. See the MATLAB permute function.
	reshape
	hanges the dimensions of the handle object array to the specified dimensions. See the MATLAB reshape function.
	sort
	ort the handle objects in any array in ascending or descending order.

Detailed Description

the main view class of MIB

Constructor & Destructor Documentation

mibView()

mibView.mibView

(

controller

)

obj = mibView(controller) mibView class constructor

Constructor for the mibView class. Create a new instance of the class with default parameters

Parameters

controller

handle to mibController class

Required fields of controller:

References handle.findobj, mibGUI(), and min.

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Member Function Documentation

editbox_Callback()

function status = mibView.editbox_Callback	(		hObject,
			chtype,
			default_val,
			variation )

Check for entered values in an edit box and switch the focus to mib.View.handles.updatefilelistBtn.

Parameters

hObject	handle to the editbox
chtype	- required type of the input 'int' -> positive and negative integers 'pint' -> positive integers 'float' -> positive and negative floats 'pfloat' -> positive floats and zero 'intrange' -> range of integers without zero 'posintx2' -> two integers separated with comma
default_val	- [optional], default value if the input is wrong. default is 1
variation	[optional] a variation of the input, a vector [minValue, maxValue]

Return values

status

result of the function: - fail - success

Required fields of hObject:

getClickPoint()

function [ xData , yData , zData , xClick , yClick ] = mibView.getClickPoint	(		nTimes,
			permuteSw )

A function that gets ginput function to pick a point within handles.mibImageAxes.

Parameters

nTimes	[optional] number of points to get, default = 1
permuteSw	[optional], can be empty when 0 returns the coordinates for the dataset in the original xy-orientation; when 1 (default) returns coordinates for the dataset so that the currently selected orientation becomes xy

Return values

xData	x - coordinate within the dataset
yData	y - coordinate within the dataset
zData	z - coordinate within the dataset; note! The Z-value is the same for all points
xClick	x - coordinate of the click
yClick	y - coordinate of the dataset

Examples:

[xData,yData,zData, xClick, yClick] = mibView.getClickPoint();  // get 1 point 

[xData,yData,zData, xClick, yClick] = mibView.getClickPoint(5);  // get 5 points 

References ginputc(), and handles.

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getRoiSwitch()

function roiSwitch = mibView.getRoiSwitch

(

)

get status of the mibGUI.handles.toolbarShowROISwitch

Return values

roiSwitch

1 - enabled, return only areas inside ROIs 0 - disabled, return complete dataset

Examples:

roiSwitch = obj.mibView.getRoiSwitch();     // call from mibController: get the toolbarShowROISwitch 

getVolrenModeSwitch()

function volrenModeSwitch = mibView.getVolrenModeSwitch

(

)

get status of the mibGUI.handles.volrenToolbarSwitch

Return values

volrenModeSwitch

1 - enabled, the volume is displayed 0 - disabled, a single 2D slice is displayed

Examples:

volrenModeSwitch = obj.mibView.getVolrenModeSwitch();     // call from mibController: get the blockModeSwitch 

Listner_Callback()

static function mibView.Listner_Callback ( obj, src, evnt )

static

evntobj = evnt.AffectedObject; handles = guidata(obj.gui);

Required fields of src:

setVolrenModeSwitch()

function mibView.setVolrenModeSwitch

(

volrenModeSwitch

)

set status of the mibGUI.handles.volrenToolbarSwitch

Parameters

volrenModeSwitch

1 - or on enabled, show dataset as a volume 0 - or off disabled, show dataset as a 2D slice

Examples:

obj.mibView.setVolrenModeSwitch(0);     // call from mibController: show dataset as a 2D slice 

References handle.notify.

updateCursor()

function mibView.updateCursor

(

mode

)

Update brush cursor.

Parameters

mode	[optional] a string, a mode to use with the brush cursor: dashed (default) - show dashed cursor, solid - show solid cursor when painting.

References handle.isvalid.

Member Data Documentation

altPressed

mibView.altPressed

set a variable to store slice number where mouse scroll action was triggered obj.altPressed = 0; - indicates that Alt was not preseed obj.altPressed > 0; - indicates slice number when Alt was preseed

brushPrevXY

mibView.brushPrevXY

coordinates of the previous pixel for the Brush tool,

Note

dimensions: [x, y] or NaN

brushSelection

mibView.brushSelection

selection layer during the brush tool movement,

{1:2}[1:height,1:width] or NaN 

brushSelection{1} .selection - contains brush selection during drawing .travelPathInPixels - distance of brush travelled during painting brushSelection{2} - contains labels of the supervoxels and some additional information .slic - a label image with superpixels .selectedSlic - a bitmap image of the selected with the Brush tool superpixels .selectedSlicIndices - indices of the selected Slic superpixels .selectedSlicIndicesNew - a list of freshly selected Slic indices when moving the brush, used for the undo with Ctrl+Z .CData - a copy of the shown in the imageAxes image, to be used for the undo brushSelection{3} - a structure that contains information for the adaptive mode: .meanVals - array of mean intensity values for each superpixels .mean - mean intensity value for the initial selection .std - standard deviation of intensities for the initial selection .factor - factor that defines variation of STD variation

Note

the brushSelection is modified with respect to

magFactor 

and crop of the image within the viewing window

centerSpotHandle

mibView.centerSpotHandle

a handle to ROI point class that marks the center of the image axes .handle - a handle to the spot roi class .enable - a switch, 1-enable; 0-disable

ctrlPressed

mibView.ctrlPressed

set a variable to deal with the increase of the brush size during the erasing action. Ctrl+left mouse button obj.ctrlPressed: obj.ctrlPressed == 0; - indicates the normal brush mode, i.e. when the control button is not pressed obj.ctrlPressed > 0; - the control button is pressed and handles.ctrlPressed indicates increase of the brush radius obj.ctrlPressed == -1; - a tweak to deal with Ctrl+Mouse wheel action to change size of the brush. -1 indicates that the brush size change mode was triggered see in functions: mibGUI_WindowKeyPressFcn, mibGUI_WindowKeyReleaseFcn, mibGUI_ScrollWheelFcn

cursor

mibView.cursor

a handle to the cursor gui object

gui

mibView.gui

handle to the main gui

guiPositions

mibView.guiPositions

structure with default positions of some GUIs to be used for rescaling

handles

mibView.handles

list of handles for the gui

Referenced by getClickPoint().

imh

mibView.imh

handle for the currently shown image; should be obj.imh = matlab.graphics.primitive.Image(CData, []); when no image

Iraw

mibView.Iraw

a property to keep the currently displayed image in RAW format, used only in the virtual stacking mode to see pixel intensities under the cursor

Note

Iraw dimensions:

[1:height, 1:width, 1:colors] 

Ishown

mibView.Ishown

a property to keep the currently displayed image in RGB format

Note

Ishown dimensions:

[1:height, 1:width, 1:colors] 

mibController

mibView.mibController

handles to the controller

mibModel

mibView.mibModel

handles to the model

showBrushCursor

mibView.showBrushCursor

a switch (0, 1) to define whether or not show the brush cursor

trackerYXZ

mibView.trackerYXZ

starting point for the Membrane Click-tracer tool

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

• Classes/@mibView/mibView.m
• Classes/@mibView/editbox_Callback.m
• Classes/@mibView/getClickPoint.m
• Classes/@mibView/getRoiSwitch.m
• Classes/@mibView/getVolrenModeSwitch.m
• Classes/@mibView/setVolrenModeSwitch.m
• Classes/@mibView/updateCursor.m