mibBatchController Class Reference

This a template class for making GUI windows for MIB it is the second version that was designed to be compatible with future macro editor. More...

Inheritance diagram for mibBatchController:

Collaboration diagram for mibBatchController:

Public Member Functions
function	updateWidgets ()
	update widgets of mibBatchController class
	mibBatchController (mibModel, varargin)
function	closeWindow ()
	closing mibBatchController window
function	helpBtn_Callback ()
	show help page
function	selectAction_Callback (hObject)
	---------------------------------------------------------------— % Additional functions and callbacks callback for change of the selected actions in popups: sectionPopup and actionPopup defined by hObject
function	updateSelectedActionTable (BatchOpt)
	update selected action table using the BatchOpt structure Parameters: BatchOpt: a structure with parameters .Checkbox - logical, true/false, will be displayed as a checkbox .Popupmenu - a cell array with 2 items for popupmenus. .Popupmenu(1) - {Container 1}, selected item .Popupmenu(2) - [{Container 1},{Container 2},{Container 3'}] .Editbox - a string for edit box
function	displaySelectedActionTableItems ()
	display current options for the highlighted row in the selectedActionTable
function	selectedActionTableItem_Update (hObject)
	update selected action in selectedActionTable
function	selectedActionTable_ContextCallback (parameter)
	callback for context menu over selectedActionTable
function	deleteProtocol ()
	delete current protocol
function	saveProtocol ()
	save protocol to a file
function	loadProtocol ()
	load protocol from a file
function	protocolActions_Callback (options)
	options to modify protocol options: a string with action to perform to the protocol add - add selected action to the protocol duplicate - duplicate selected action insert - insert selected action to the protocol insertstop - insert a stop action update - update selected action of the protocol show - display settings for the selected action delete - delete selected action from the protocol
function	protocolList_SelectionCallback ()
	callback for selection of a row in protocolList
function	updateProtocolList ()
	update protocol list
function	BackupProtocol ()
	backup the current protocol if isempty(obj.Protocol); return; end
function	BackupProtocolRestore (mode)
	restore protocol from the backup Parameters: mode: a string undo - to make an undo redo - to make a redo
function	runProtocolBtn_Callback (parameter)
	run the protocol
function status =	doSeriesLoop (startStep, finishStep)
	do open each series in dataset-container one-by-one and process until end of File loop or end of the protocol Only for Bio-formats!
function status =	doFileLoop (startStep, finishStep, options)
	do the file loop action
function status =	doBatchStep (stepId, stepOptions)
	do a single step of the protocol
function	DirectoryLoopAction_Callback (BatchOptInput)
	callback for selection of Directory Loop action
function	FileOperationsAction_Callback (BatchOptInput)
	do various operations with files
function	DirectoryOperationsAction_Callback (BatchOptInput)
	Directory operations of MIB.
function	FileLoopAction_Callback (BatchOptInput)
	callback for selection of File Loop action
function	gui_WinMouseMotionFcn ()
	get mouse coordinates for the window to change cursor shape when above separatingPanel to rescaling the panels
function	gui_WindowButtonDownFcn ()
	callback for mouse press over the figure, to start rescaling of panels
function	panelShiftBtnUpFcn ()
	get values to change size of the panels
function	sizeChangedFcn ()
	main resizing function for the window
function	listenMIB_Callback ()
	modify listener to actions from MIB

Static Public Member Functions
static function	ViewListner_Callback2 (obj, src, evnt)

Public Attributes
	mibController
	handle to mibController
	mibModel
	handles to the model
	View
	handle to the view
	listener
	a cell array with handles to listeners
	CurrentBatch
	a structure with selected Batch options, returned by returnBatchOpt function of the controller
	jSelectedActionTable
	a handle to java class for the selectedActionTable
	jSelectedActionTableScroll
	a handle to java class for the selectedActionTable scroll
	Protocol
	a structure with picked actions that should be executed
	ProtocolBackups
	a cell array with backuped protocols
	ProtocolBackupsCurrNumber
	current number of the protocol history
	ProtocolBackupsMaxNumber
	maximal number of protocol history for backup
	Sections
	a strutcure with available Sections and corresponding actions Sections(id).Name -> name of available section (i.e. Menu -> File, Menu -> Dataset) Sections(id).Actions(id2).Name -> name of an action available for the selected section (i.e. Tools for Images -> Image Arithmetics, Semi-automatic segmentation --> Global thresholding) Sections(id).Actions(id2).Parameters -> a structure with parameters for the action
	selectedActionTableIndex
	index of a row selected in the selectedActionTable
	protocolListIndex
	index of a row selected in the protocolList
	selectedSection
	index of the selected section, i.e. id for obj.Sections(id) updated by obj.View.handles.sectionPopup
	selectedAction
	index of the selected action for the currect section, i.e. id2 for Sections(id).Actions(id2) updated by obj.View.handles.actionPopup
	stopProtocolSwitch
	stop protocol property
EVENT	closeEvent
	> Description of events event firing when window is closed
EVENT	stopProtocol
	stop batch
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

This a template class for making GUI windows for MIB it is the second version that was designed to be compatible with future macro editor.

obj.startController('mibBatchController'); // as GUI tool

Constructor & Destructor Documentation

mibBatchController()

mibBatchController.mibBatchController	(		mibModel,
			varargin )

References handle.addlistener, findjobj(), mibModel, mibRescaleWidgets(), mibUpdateFontSize(), moveWindowOutside(), and handle.sort.

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Member Function Documentation

BackupProtocol()

function mibBatchController.BackupProtocol

(

)

backup the current protocol if isempty(obj.Protocol); return; end

BackupProtocolRestore()

function mibBatchController.BackupProtocolRestore

(

mode

)

restore protocol from the backup Parameters: mode: a string undo - to make an undo redo - to make a redo

References min.

closeWindow()

function mibBatchController.closeWindow

(

)

closing mibBatchController window

References handle.isvalid, and handle.notify.

deleteProtocol()

function mibBatchController.deleteProtocol

(

)

delete current protocol

DirectoryLoopAction_Callback()

function mibBatchController.DirectoryLoopAction_Callback

(

BatchOptInput

)

callback for selection of Directory Loop action

References handle.notify, and updateBatchOptCombineFields_Shared().

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DirectoryOperationsAction_Callback()

function mibBatchController.DirectoryOperationsAction_Callback

(

BatchOptInput

)

Directory operations of MIB.

References handle.notify, and updateBatchOptCombineFields_Shared().

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displaySelectedActionTableItems()

function mibBatchController.displaySelectedActionTableItems

(

)

display current options for the highlighted row in the selectedActionTable

References handle.fieldnames.

doBatchStep()

function status = mibBatchController.doBatchStep	(		stepId,
			stepOptions )

do a single step of the protocol

Parameters

stepId	index of a step to be done
stepOptions	an optional structure with parameters .DirectoryName -> directory name provided by the File or Directory loop .FilenameFilter -> FilenameFilter == filename provided by the File loop .Filenames -> full path to the filename .FileLoopWaitbar -> when true show waitbar for the file loop only, all waitbars for subfunctions will be disabled

Return values

status

[logical], success or fail of the function

Required fields of stepOptions:

References handle.notify.

doFileLoop()

function status = mibBatchController.doFileLoop	(		startStep,
			finishStep,
			options )

do the file loop action

Parameters

startStep	is index of the first action inside the file loop
finishStep	is index of the last action of the file loop
options	a structure with parameters .DirectoryName - name of the file loop directory .FilenameFilter - filter for filenames .FileLoopWaitbar - when true show waitbar for the file loop only, all waitbars for subfunctions will be disabled

Return values

status

[logical], success or fail of the function

Required fields of options:

doSeriesLoop()

function status = mibBatchController.doSeriesLoop	(		startStep,
			finishStep )

do open each series in dataset-container one-by-one and process until end of File loop or end of the protocol Only for Bio-formats!

Parameters

startStep	is index of the first action inside the file loop
finishStep	is index of the last action of the file loop

Return values

status

[logical], success or fail of the function

FileLoopAction_Callback()

function mibBatchController.FileLoopAction_Callback

(

BatchOptInput

)

callback for selection of File Loop action

References handle.notify, and updateBatchOptCombineFields_Shared().

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FileOperationsAction_Callback()

function mibBatchController.FileOperationsAction_Callback

(

BatchOptInput

)

do various operations with files

References handle.notify, and updateBatchOptCombineFields_Shared().

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gui_WindowButtonDownFcn()

function mibBatchController.gui_WindowButtonDownFcn

(

)

callback for mouse press over the figure, to start rescaling of panels

gui_WinMouseMotionFcn()

function mibBatchController.gui_WinMouseMotionFcn

(

)

get mouse coordinates for the window to change cursor shape when above separatingPanel to rescaling the panels

helpBtn_Callback()

function mibBatchController.helpBtn_Callback

(

)

show help page

listenMIB_Callback()

function mibBatchController.listenMIB_Callback

(

)

modify listener to actions from MIB

loadProtocol()

function mibBatchController.loadProtocol

(

)

load protocol from a file

References mib_uigetfile().

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panelShiftBtnUpFcn()

function mibBatchController.panelShiftBtnUpFcn

(

)

get values to change size of the panels

protocolActions_Callback()

function mibBatchController.protocolActions_Callback

(

options

)

options to modify protocol options: a string with action to perform to the protocol add - add selected action to the protocol duplicate - duplicate selected action insert - insert selected action to the protocol insertstop - insert a stop action update - update selected action of the protocol show - display settings for the selected action delete - delete selected action from the protocol

References max.

protocolList_SelectionCallback()

function mibBatchController.protocolList_SelectionCallback

(

)

callback for selection of a row in protocolList

runProtocolBtn_Callback()

function mibBatchController.runProtocolBtn_Callback

(

parameter

)

run the protocol

Parameters

parameter

a string with details complete - run all steps of the protocol from - run the protocol from the selected step step - run the selected step only stepadvance - run the selected step and advance to next

References min, and handle.notify.

saveProtocol()

function mibBatchController.saveProtocol

(

)

save protocol to a file

References handle.fieldnames, Protocol, and xlswrite2().

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selectAction_Callback()

function mibBatchController.selectAction_Callback

(

hObject

)

---------------------------------------------------------------— % Additional functions and callbacks callback for change of the selected actions in popups: sectionPopup and actionPopup defined by hObject

Required fields of hObject:

selectedActionTable_ContextCallback()

function mibBatchController.selectedActionTable_ContextCallback

(

parameter

)

callback for context menu over selectedActionTable

References handle.fieldnames, mibInputMultiDlg(), and uigetfile_n_dir().

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selectedActionTableItem_Update()

function mibBatchController.selectedActionTableItem_Update

(

hObject

)

update selected action in selectedActionTable

Required fields of hObject:

References handle.fieldnames.

sizeChangedFcn()

function mibBatchController.sizeChangedFcn

(

)

main resizing function for the window

updateProtocolList()

function mibBatchController.updateProtocolList

(

)

update protocol list

updateSelectedActionTable()

function mibBatchController.updateSelectedActionTable

(

BatchOpt

)

update selected action table using the BatchOpt structure Parameters: BatchOpt: a structure with parameters .Checkbox - logical, true/false, will be displayed as a checkbox .Popupmenu - a cell array with 2 items for popupmenus. .Popupmenu(1) - {Container 1}, selected item .Popupmenu(2) - [{Container 1},{Container 2},{Container 3'}] .Editbox - a string for edit box

Required fields of BatchOpt:

References handle.fieldnames.

updateWidgets()

function mibBatchController.updateWidgets

(

)

update widgets of mibBatchController class

ViewListner_Callback2()

static function mibBatchController.ViewListner_Callback2 ( obj, src, evnt )

static

Member Data Documentation

closeEvent

EVENT mibBatchController.closeEvent

> Description of events event firing when window is closed

Events

closeEvent

CurrentBatch

mibBatchController.CurrentBatch

a structure with selected Batch options, returned by returnBatchOpt function of the controller

jSelectedActionTable

mibBatchController.jSelectedActionTable

a handle to java class for the selectedActionTable

jSelectedActionTableScroll

mibBatchController.jSelectedActionTableScroll

a handle to java class for the selectedActionTable scroll

listener

mibBatchController.listener

a cell array with handles to listeners

mibController

mibBatchController.mibController

handle to mibController

mibModel

mibBatchController.mibModel

handles to the model

Referenced by mibBatchController().

Protocol

mibBatchController.Protocol

a structure with picked actions that should be executed

Referenced by saveProtocol().

ProtocolBackups

mibBatchController.ProtocolBackups

a cell array with backuped protocols

ProtocolBackupsCurrNumber

mibBatchController.ProtocolBackupsCurrNumber

current number of the protocol history

ProtocolBackupsMaxNumber

mibBatchController.ProtocolBackupsMaxNumber

maximal number of protocol history for backup

protocolListIndex

mibBatchController.protocolListIndex

index of a row selected in the protocolList

Sections

mibBatchController.Sections

a strutcure with available Sections and corresponding actions Sections(id).Name -> name of available section (i.e. Menu -> File, Menu -> Dataset) Sections(id).Actions(id2).Name -> name of an action available for the selected section (i.e. Tools for Images -> Image Arithmetics, Semi-automatic segmentation --> Global thresholding) Sections(id).Actions(id2).Parameters -> a structure with parameters for the action

selectedAction

mibBatchController.selectedAction

index of the selected action for the currect section, i.e. id2 for Sections(id).Actions(id2) updated by obj.View.handles.actionPopup

selectedActionTableIndex

mibBatchController.selectedActionTableIndex

index of a row selected in the selectedActionTable

selectedSection

mibBatchController.selectedSection

index of the selected section, i.e. id for obj.Sections(id) updated by obj.View.handles.sectionPopup

stopProtocol

EVENT mibBatchController.stopProtocol

stop batch

Events

stopProtocol

stopProtocolSwitch

mibBatchController.stopProtocolSwitch

stop protocol property

Note

This property has the MATLAB attribute SetObservable set to true.

Matlab documentation of property attributes.

View

mibBatchController.View

handle to the view

---

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

• Classes/@mibBatchController/mibBatchController.m
• Classes/@mibBatchController/updateWidgets.m