mibRoiRegion Class Reference

class is responsible to keep regions of interest (ROI) More...

Inheritance diagram for mibRoiRegion:

Collaboration diagram for mibRoiRegion:

Public Member Functions
	mibRoiRegion (mibImage)
	Constructor for the class.
function	clearContents ()
	Set all elements of the class to default values.
function	clearData ()
	Removes all values of the Data structures.
function index =	findIndexByLabel (labelStr)
	Finds index of a ROI that has Data.label == labelStr.
function	addROI (mibController, type, index, coordinates, noPoints)
	Adds ROI.
function	imfreehandFun (mibController, index)
	Adds impoly type of ROI using imfreehand tool.
function	impolyFun (mibController, index, coordinates, noPoints)
	Adds impoly type of ROI.
function	imrectFun (mibController, index, coordinates)
	Adds imrect type of ROI.
function	imellipseFun (mibController, index, coordinates)
	Adds imellipse type of ROI.
function	storeROI (newData, index)
	add or insert ROI information into the obj.Data structure
function	removeROI (index)
	removeROI(obj, index) Remove ROI(s) from the class
function [ number , indices ] =	getNumberOfROI (orientation)
	[number, indices] = getNumberOfROI(obj, orientation) Get number of stored ROI
function	setDefaultOptions ()
	Set all values of the Options structure of the class to default values.
function	updateOptions ()
	Update the Options structure of the class.
function	resample (resampledRatio)
	Recalculation of ROI position during image resampling.
function	crop (cropF)
	Recalculation of ROI position during image crop.
function [ position , screenPosition ] =	drawROI (mibController, type, pos, instant)
	draw a ROI object in the mibGUI.handles.mibImageAxes
function	updateROIposition1 (new_position)
	Update ROI position during movement of imrect and imellipse.
function	updateROIposition2 (new_position)
	Update position during movement of impoly, imline.
function	addROIsToPlot (mibController, mode)
	plot ROIs above the handles.mibImageAxes of mibGUI
function bb =	getBoundingBox (index)
	return the bounding box for the ROI
function mask =	returnMask (index, Height, Width, orient, blockModeSwitch)
	Return a bitmap mask of the specified ROI.
function	updateROIScreenPosition (mode)
	Updates position of ROI when plotting in mibGUI.handles.mibImageAxes.

Public Attributes
	roi
	a structure with ROI data:
	Data
	a new structure for ROI data .Data.label - string with a label .Data.type - type, string: imrect, imellipse, impoly, imfreehand .Data.X - X-coordinates of points .Data.Y - Y-coordinates of points .Data.orientation - orientaion of the ROI: 1-xz, 2-yz, 4-yx .Data.BoundingBox - a structire with bounding box for the current ROI .x - [xmin, xmax]; .y - [ymin, ymax]
	Options
	a structure with show options .Options.marker = s; - style 1 for markers .Options.markersize = 10; - size of markers .Options.linestyle = -; - style 1 for lines .Options.linewidth = 2 ; - width for lines .Options.color = w; - color style .Options.textcolorfg = y; - text color .Options.textcolorbg = none; - color for text background .Options.fontsize = 14; - size of the font .Options.showMarkers = 1; .Options.showLines = 1; .Options.showText = 0;
	mibImage
	handle to mibImage class

Detailed Description

class is responsible to keep regions of interest (ROI)

Constructor & Destructor Documentation

mibRoiRegion()

mibRoiRegion.mibRoiRegion

(

mibImage

)

Constructor for the class.

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

Parameters

mibImage

- handle to imageData class

References mibImage.

Member Function Documentation

addROI()

function mibRoiRegion.addROI	(		mibController,
			type,
			index,
			coordinates,
			noPoints )

Adds ROI.

Parameters

mibController	handle to mibController class, or it can be empty ([]) for imrect, when coordinates are provided
type	type of ROI to add: "imrect", "imellipse", "impoly", "imfreehand"
index	[optional] index of the ROI. If not empty will allow to modify a ROI with the provided index
coordinates	[optional] coordinates for placing the ROI, can be []
noPoints	[@ optional] noPoints for the impoly type, dafault = 5

Examples:

addROIsToPlot()

function mibRoiRegion.addROIsToPlot	(		mibController,
			mode )

plot ROIs above the handles.mibImageAxes of mibGUI

Parameters

mibController	handle to mibController class
mode	a string that defines a mode of the shown image: shown (in most cases), or full (for panning)

Required fields of mibController:

Examples:

obj.mibModel.I{obj.mibModel.Id}.hROI.addROIsToPlot(mibController, 'shown'); // call from mibController class, to show the measurements above the image in mibController.plotImage function 

obj.mibModel.I{obj.mibModel.Id}.hROI.addROIsToPlot(mibController, 'full'); // call from mibController class, to show the measurements above the image in the mibController.WindowButtonDownFcn function 

References mibController.mibModel, and mibController.mibView.

clearContents()

function mibRoiRegion.clearContents

(

)

Set all elements of the class to default values.

Examples:

obj.mibModel.I{obj.mibModel.Id}.hROI.clearContents(); // call from mibController; clear the class contents and reset to default options  

clearData()

function mibRoiRegion.clearData

(

)

Removes all values of the Data structures.

Examples:

obj.mibModel.I{obj.mibModel.Id}.hROI.clearData(); // call from mibController; clear the class contents  

crop()

function mibRoiRegion.crop

(

cropF

)

Recalculation of ROI position during image crop.

Parameters

cropF

a vector [x1, y1, dx, dy, z1, dz] with parameters of the crop. Note! The units are pixels!

Examples:

cropF = [100 512 200 512 5 20];  // define parameters of the crop.  

indices = obj.mibModel.I{obj.mibModel.Id}.hROI.crop(cropF); // call from mibController, crop ROIs 

drawROI()

function [ position , screenPosition ] = mibRoiRegion.drawROI	(		mibController,
			type,
			pos,
			instant )

draw a ROI object in the mibGUI.handles.mibImageAxes

Creates an instanse of Matlab imroi class and store it in mibRoiRegion.roi.imroi

Parameters

mibController	handle to mibController class
type	a type of ROI: 'imline', 'imellipse'
pos	coordinates of the ROI [x1, y1; x2, y2] -> 'imrect' coordinates of two corners [x1, y1, Rwidth, Rheight] -> 'imellipse'
instant	[optional], used only for imellipse to automatically get position of vertices. 1 or 0 (default).

Return values

position	coordinates of the selected area in the Data format
screenPosition	coordinagtes of the selected area in the imageAxes units

Required fields of mibController:

Examples:

position = obj.drawROI(mibController, 'imline', [10, 10; 50, 50]); // draw a line 

References mibController.mibModel, and mibController.mibView.

findIndexByLabel()

function index = mibRoiRegion.findIndexByLabel

(

labelStr

)

Finds index of a ROI that has Data.label == labelStr.

Parameters

labelStr

label string

Return values

index

index of the ROI that has the label

Examples:

obj.mibModel.I{obj.mibModel.I}.hROI.findIndexByLabel('ROI 1'); // Call from mibController; return index of the ROI that has 'ROI 1' label 

getBoundingBox()

function bb = mibRoiRegion.getBoundingBox

(

index

)

return the bounding box for the ROI

Parameters

index

an index of ROI to get mask, use 0 - to get combined mask for all shown ROIs. It is also possible to use obj.Data.label field as string of chars

Return values

bb	a matrix with the bounding box information as [xmin, xmax, ymin, ymax]

References max, and min.

getNumberOfROI()

function [ number , indices ] = mibRoiRegion.getNumberOfROI

(

orientation

)

[number, indices] = getNumberOfROI(obj, orientation) Get number of stored ROI

Parameters

orientation

[optional] defines orienation, 1-xz, 2-yz, 4-yx, 0-get all. When omitted returns number of ROIs for the shown orientation

Return values

number	number of ROIs
indices	indices of ROIs

Examples

number = obj.getNumberOfROI(4); // get the total number of ROIs for the XY orientation 

[number, indices] = obj.mibModel.I{obj.mibModel.Id}.hROI.getNumberOfROI(); // call from mibController, get number of ROIs and thie indices 

imellipseFun()

function mibRoiRegion.imellipseFun	(		mibController,
			index,
			coordinates )

Adds imellipse type of ROI.

Parameters

mibController	handle to mibController class
index	index of the ROI. If not empty will allow to modify a ROI with the provided index
coordinates	[optional] coordinates for placing the ROI manually, [x-center y-center, radiusX, radiusY]

Required fields of mibController:

Examples:

obj.imellipseFun(mibController, 5); // Add a new imellipse ROI to position 5 

obj.imellipseFun(mibController, 5, [100, 150, 250, 350]); // Add a new imellipse ROI to position 5; x1=100, x2=150, radiusX=250; radiusY=350 

References A(), B(), max, mibController.mibModel, mibController.mibView, min, and mibController.plotImage().

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imfreehandFun()

function mibRoiRegion.imfreehandFun	(		mibController,
			index )

Adds impoly type of ROI using imfreehand tool.

Parameters

mibController	handle to mibController class
index	index of the ROI. If not empty will allow to modify a ROI with the provided index

Examples:

obj.imfreehandFun(mibController, 5); // Add a new impoly ROI to position 5 

References mibInputDlg().

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impolyFun()

function mibRoiRegion.impolyFun	(		mibController,
			index,
			coordinates,
			noPoints )

Adds impoly type of ROI.

Parameters

mibController	handle to mibController class
index	index of the ROI. If not empty will allow to modify a ROI with the provided index
coordinates	[optional] coordinates for placing the ROI manually
noPoints	[optional] number of points in the polyline when adding a new ROI

Required fields of mibController:

Examples:

obj.impolyFun(mibController, [], [], 5); // Add a new impoly ROI with 5 vertices 

obj.impolyFun(mibController, 5, [100, 150; 250, 350; 50, 150]); // Add impoly ROI to position 5; with specified vertices 

References max, mibController.mibModel, mibController.mibView, min, and mibController.plotImage().

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imrectFun()

function mibRoiRegion.imrectFun	(		mibController,
			index,
			coordinates )

Adds imrect type of ROI.

Parameters

mibController	a handle to mibController class
index	index of the ROI. If not empty will allow to modify a ROI with the provided index
coordinates	[optional] coordinates for placing the ROI manually

Required fields of mibController:

Examples:

obj.imrectFun(5); // Add a new imrect ROI to position 5 

obj.imrectFunimrectFun(5, [100, 150, 250, 350]); // Add a new imrect ROI to position 5; x1=100, x2=150, width=250; height=350 

References max, mibController.mibModel, mibController.mibView, min, and mibController.plotImage().

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removeROI()

function mibRoiRegion.removeROI

(

index

)

removeROI(obj, index) Remove ROI(s) from the class

Parameters

index

[optional], an index of the measurement point to remove, when empty or zero - removes all ROIs

Examples

Measure.removeROI(); // remove all ROIs 

removeROI(obj, 5); // Call within the class; remove 5th ROI 

resample()

function mibRoiRegion.resample

(

resampledRatio

)

Recalculation of ROI position during image resampling.

Parameters

resampledRatio

a vector [ratioW, ratioH, ratioZ] ratio of new/old dimensions after resampling.

Examples:

resampledRatio = [.5 .5 1];  // bin in 2 times XY dimension.  

indices = obj.mibModel.I{obj.mibModel.Id}.hROI.resample(resampledRatio); // call from mibController, resample ROIs 

returnMask()

function mask = mibRoiRegion.returnMask	(		index,
			Height,
			Width,
			orient,
			blockModeSwitch )

Return a bitmap mask of the specified ROI.

Parameters

index	an index of ROI to get mask, use 0 - to get combined mask for all shown ROIs. It is also possible to use obj.Data.label field as string of chars
Height	[optional] height of the image
Width	[optional] width of the image
orient	[optional] orientation of the dataset: 1-xz, 2-yz, 4-yz, 0-for all orientations. Default, the currently shown orientation.
blockModeSwitch	override the blockModeSwitch

Return values

mask	mask image [1:Height, 1:Width]

Examples:

mask = obj.mibModel.I{obj.mibModel.Id}.hROI.returnMask(new_position, 1); // call from mibController, get mask of ROI number 1 

mask =  obj.mibModel.I{obj.mibModel.Id}.hROI.returnMask(0); // call from mibController, get combined mask of all shown ROIs 

References max, mibConnectPoints(), and min.

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setDefaultOptions()

function mibRoiRegion.setDefaultOptions

(

)

Set all values of the Options structure of the class to default values.

Examples:

mibRoiRegion.setDefaultOptions(); 

setDefaultOptions(obj); // Call within the class 

storeROI()

function mibRoiRegion.storeROI	(		newData,
			index )

add or insert ROI information into the obj.Data structure

Parameters

newData	structure of a new measurement to insert. Fields should match those of obj.Data
index	[optional] position where to add the measurement, default - number of measurements in obj.Data + 1

Examples:

mibRoiRegion.storeROI(newData, 5); insert ROI to position 5 

storeROI(obj, newData); // Call within the class. Add a ROI 

updateOptions()

function mibRoiRegion.updateOptions

(

)

Update the Options structure of the class.

Examples:

obj.mibModel.I{obj.mibModel.Id}.hROI.updateOptions(); // call from mibController class 

References A(), mibInputMultiDlg(), and n.

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updateROIposition1()

function mibRoiRegion.updateROIposition1

(

new_position

)

Update ROI position during movement of imrect and imellipse.

one of two functions resposible for update of Measure.roi. pos. The other one is Measure.updateROIposition2()

Parameters

new_position

a vector with coordinates of a new position [xmin, ymin, width, height]

References max.

updateROIposition2()

function mibRoiRegion.updateROIposition2

(

new_position

)

Update position during movement of impoly, imline.

one of two functions resposible for update of Measure.roi. pos. The other one is Measure.updateROIposition1()

Parameters

new_position

a vector with coordinates of a new position [point_number][x, y]

References max.

updateROIScreenPosition()

function mibRoiRegion.updateROIScreenPosition

(

mode

)

Updates position of ROI when plotting in mibGUI.handles.mibImageAxes.

Parameters

mode	identifier of the updating mode: 'crop' during zooming 'full' during panning of the axes

Examples

Measure.updateROIScreenPosition('crop'); // update positions of all ROIs during zoom in/out 

obj.updateROIScreenPosition('full'); // update positions of all ROIs during panning 

References max.

Member Data Documentation

Data

mibRoiRegion.Data

a new structure for ROI data .Data.label - string with a label .Data.type - type, string: imrect, imellipse, impoly, imfreehand .Data.X - X-coordinates of points .Data.Y - Y-coordinates of points .Data.orientation - orientaion of the ROI: 1-xz, 2-yz, 4-yx .Data.BoundingBox - a structire with bounding box for the current ROI .x - [xmin, xmax]; .y - [ymin, ymax]

mibImage

mibRoiRegion.mibImage

handle to mibImage class

Referenced by mibRoiRegion().

Options

mibRoiRegion.Options

a structure with show options .Options.marker = s; - style 1 for markers .Options.markersize = 10; - size of markers .Options.linestyle = -; - style 1 for lines .Options.linewidth = 2 ; - width for lines .Options.color = w; - color style .Options.textcolorfg = y; - text color .Options.textcolorbg = none; - color for text background .Options.fontsize = 14; - size of the font .Options.showMarkers = 1; .Options.showLines = 1; .Options.showText = 0;

roi

mibRoiRegion.roi

a structure with ROI data:

• roi.pos - coordinates of ROIs, for addNewPositionCallback
• roi.type - ROIs type: imline
• roi.imroi - handle to imroi Matlab class
• roi.cb - array of callbacks to addNewPositionCallback function

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

• Classes/@mibRoiRegion/mibRoiRegion.m